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Sample records for oskolkov pri fotodelenii

  1. PriMux

    Energy Science and Technology Software Center (ESTSC)

    2010-08-31

    PriMux is used to compute sets of compatible Polymerase Chain Reaction (PCR)signatures that can be used for detecting the presence of biological species in a small sample of material. Before use, the computed signatures must be empirically tested in a wet lab.

  2. MISR Browse Images: Puerto Rico Dust Experiment (PRiDE)

    Atmospheric Science Data Center

    2013-04-02

    MISR Browse Images: Puerto Rico Dust Experiment (PRiDE) These MISR Browse images provide ... overview of the region observed during the Puerto Rico Dust Experiment (PRiDE) field campaign. PRiDE was a study of the radiative, ...

  3. Linking Knowledge and Action: PRI's Community Consultant.

    ERIC Educational Resources Information Center

    Spencer, Gregory P.

    Within the Partnership for Rural Improvement (PRI), community consultants operate within three complex sets of relationships: client groups, the organizational structure of PRI, and the local operational base. Community consultants are responsible for developing and facilitating rural development and for providing assistance in community and…

  4. DnaT is a PriC-binding protein.

    PubMed

    Huang, Chien-Chih; Huang, Cheng-Yang

    2016-09-01

    DnaT and PriC are replication restart primosomal proteins required for re-initiating chromosomal DNA replication. DnaT is a component of the PriA-dependent primosome, while PriC belongs to the PriC-dependent primosome. Whether DnaT can interact with PriC is still unknown. In this study, we define a direct interaction between PriC, a key initiator protein in PriC-mediated DNA replication restart, and DnaT, a DnaB/C complex loader protein, from Klebsiella pneumoniae. In fluorescence titrations, PriC bound to single-stranded DNA with a binding-site size of approximately 9 nt. Gold nanoparticle assay showed that the solution of DnaT-PriC changed from red to purple, which indicated the protein-protein interactions due to gold nanoparticle aggregate. In addition, this DnaT-PriC complex could be co-purified by the heparin HP column. Surface plasmon resonance analysis showed that the Kd value of DnaT bound to PriC was 2.9 × 10(-8) M. These results constitute a pioneering study of the DnaT-PriC interaction and present a putative link between the two independent replication restart pathways, namely, PriA- and PriC-dependent primosome assemblies. Further research can directly focus on determining how DnaT binds to the PriC-SSB-DNA tricomplex and regulates the PriC-dependent replication restart. PMID:27387236

  5. Deinococcus radiodurans PriA is a Pseudohelicase

    PubMed Central

    Lopper, Matthew E.; Boone, Jacob; Morrow, Christopher

    2015-01-01

    Reactivation of repaired DNA replication forks in bacteria is catalyzed by PriA helicase. This broadly-conserved bacterial enzyme can remodel the structure of DNA at a repaired DNA replication fork by unwinding small portions of duplex DNA to prepare the fork for replisome reloading. While PriA’s helicase activity is not strictly required for cell viability in E. coli, the sequence motifs that confer helicase activity upon PriA are well-conserved among sequenced bacterial priA genes, suggesting that PriA’s duplex DNA unwinding activity confers a selective advantage upon cells. However, these helicase sequence motifs are not well-conserved among priA genes from the Deinococcus-Thermus phylum. Here, we show that PriA from a highly radiation-resistant member of that phylum, Deinococcus radiodurans, lacks the ability to hydrolyze ATP and unwind duplex DNA, thus qualifying D. radiodurans PriA as a pseudohelicase. Despite the lack of helicase activity, D. radiodurans PriA has retained the DNA binding activity expected of a typical PriA helicase, and we present evidence for a physical interaction between D. radiodurans PriA and its cognate replicative helicase, DnaB. This suggests that PriA has retained a role in replisome reloading onto repaired DNA replication forks in D. radiodurans despite its lack of helicase activity. PMID:26182205

  6. Remotely Sensing the Photochemical Reflectance Index (PRI)

    NASA Technical Reports Server (NTRS)

    Vanderbilt, Vern

    2015-01-01

    In remote sensing, the Photochemical Reflectance Index (PRI) provides insight into physiological processes occurring inside the leaves in a stand of plants. Developed by Gamon et al., (1990 and 1992), PRI evolved from laboratory measurements of the reflectance of individual leaves (Bilger et al.,1989). Yet in a remotely sensed image, a pixel measurement may include light from both reflecting and transmitting leaves. We conducted laboratory experiments comparing values of PRI based upon polarized reflectance and transmittance measurements of water and nutrient stressed leaves. We illuminated single detached leaves using a current controlled light source (Oriel model 66881) and measured the leaf weight using an analytical balance (Mettler model AE 260) and the light reflected and transmitted by the leaf during dry down using two Analytical Spectral Devices spectroradiometers. Polarizers on the incident and reflected light beams allowed us to divide the leaf reflectance into two parts: a polarized surface reflectance and a non-polarized 'leaf interior' reflectance. Our results underscore the importance when calculating PRI of removing the leaf surface reflection, which contains no information about physiological processes ongoing in the leaf interior. The results show that the leaf physiology information is in the leaf interior reflectance, not the leaf transmittance. Applied to a plant stand, these results suggest use of polarization measurements in sun-view directions that minimize the number of sunlit transmitting leaves in the sensor field of view.

  7. Differential interference of vitamin D analogs PRI-1906, PRI-2191, and PRI-2205 with the renewal of human colon cancer cells refractory to treatment with 5-fluorouracil.

    PubMed

    Kotlarz, Agnieszka; Przybyszewska, Małgorzata; Swoboda, Paweł; Miłoszewska, Joanna; Grygorowicz, Monika Anna; Kutner, Andrzej; Markowicz, Sergiusz

    2016-04-01

    This study was aimed to determine whether hypocalcemic analogs of active forms of vitamins D modulate expression of genes related to stem-like phenotype in colon cancer cell lines HT-29 and HCT-116 undergoing renewal after the treatment with 5-fluorouracil (5-FU). Both lines express vitamin D receptor, but differ in differentiation stage and vitamin D sensitivity. Cells that resisted the 5-FU exposure were treated with synthetic analog of 1,25-dihydroxyvitamin D2 (PRI-1906) and analogs of 1,25-dihydroxyvitamin D3 (PRI-2191 and PRI-2205). Proliferative activity was more profoundly affected by vitamin D analogs in HT-29/5-FU than in HCT-116/5-FU cells. In HT-29/5-FU cells, analogs PRI-1906 and PRI-2191 downregulated the expression of genes related to survival, re-growth, and invasiveness during renewal, while PRI-2205 increased expression of genes related to differentiation only. In HCT-116/5-FU cells, PRI-2191 decreased the expression of stemness- and angiogenesis-related genes, whereas PRI-1906 augmented their expression. The effects in HCT-116/5-FU cells were observed at higher concentrations of the analogs than those used for HT-29/5-FU cells. Out of the series of analogs studied, PRI-2191 might be used to counteract the renewal of both moderately and poorly differentiated cancer cells following conventional treatment. PMID:26511971

  8. Finding the SurPriSe: A Case Study of a Faculty Learning Community

    ERIC Educational Resources Information Center

    Michel, Roberta M.

    2014-01-01

    This article details a faculty learning community (FLC) that started in 2009 on the campus of a Midwestern University and has evolved into an interdisciplinary research, teaching and social community of practice and learning called SurPriSe. SurPriSe is an acronym that reflects the interest area of the FLC; Sur for surveillance, Pri for privacy,…

  9. Canopy Level Chlorophyll Fluorescence and the PRI in a Cornfield

    NASA Technical Reports Server (NTRS)

    Middleton, Elizabeth M.; Cheng, Yen-Ben; Corp, Lawrence A.; Campbell, Petya K. E.; Huemmrich, K. Fred; Zhang, Qingyuan; Kustas, William P.

    2012-01-01

    Two bio-indicators, the Photochemical Reflectance Index (PRI) and solar-induced red and far-red Chlorophyll Fluorescence (SIF), were derived from directional hyperspectral observations and studied in a cornfield on two contrasting days in the growing season. Both red and far-red SIF exhibited higher values on the day when the canopy in the early senescent stage, but only the far-red SIF showed sensitivity to viewing geometry. Consequently, the red/far-red SIF ratio varied greatly among azimuth positions while the largest values were obtained for the "hotspot" at both growth stages. This ratio was lower (approx.0.88 +/- 0.4) in early July than in August when the ratio approached equivalence (near approx.1). In concert, the PRI exhibited stronger responses to both zenith and azimuth angles and different values on the two growth stages. The potential of using these indices to monitor photosynthetic activities needs further investigation

  10. Prodifferentiation Activity of Novel Vitamin D₂ Analogs PRI-1916 and PRI-1917 and Their Combinations with a Plant Polyphenol in Acute Myeloid Leukemia Cells.

    PubMed

    Nachliely, Matan; Sharony, Ehud; Bolla, Narasimha Rao; Kutner, Andrzej; Danilenko, Michael

    2016-01-01

    1α,25-dihydroxyvitamin D₃ (1,25D3) is a powerful differentiation inducer for acute myeloid leukemia (AML) cells. However, 1,25D3 doses required for differentiation of AML cells may cause lethal hypercalcemia in vivo. There is evidence that vitamin D₂ is less toxic than vitamin D₃ in animals. Here, we determined the differentiation effects of novel analogs of 1α,25-dihydroxyvitamin D₂ (1,25D2), PRI-1916 and PRI-1917, in which the extended side chains of their previously reported precursors (PRI-1906 and PRI-1907, respectively) underwent further 24Z (24-cis) modification. Using four human AML cell lines representing different stages of myeloid maturation (KG-1a, HL60, U937, and MOLM-13), we found that the potency of PRI-1916 was slightly higher or equal to that of PRI-1906 while PRI-1917 was significantly less potent than PRI-1907. We also demonstrated that 1,25D2 was a less effective differentiation agent than 1,25D3 in these cell lines. Irrespective of their differentiation potency, all the vitamin D₂ derivatives tested were less potent than 1,25D3 in transactivating the DR3-type vitamin D response elements. However, similar to 1,25D3, both 1,25D2 and its analogs could strongly cooperate with the plant polyphenol carnosic acid in inducing cell differentiation and inhibition of G1-S cell cycle transition. These results indicate that the 24Z modification has contrasting effects on the differentiation ability of PRI-1906 and PRI-1907 and that the addition of a plant polyphenol could result in a similar extent of cell differentiation induced by different vitamin D compounds. The enhanced antileukemic effects of the tested combinations may constitute the basis for the development of novel approaches for differentiation therapy of AML. PMID:27399677

  11. Prodifferentiation Activity of Novel Vitamin D2 Analogs PRI-1916 and PRI-1917 and Their Combinations with a Plant Polyphenol in Acute Myeloid Leukemia Cells

    PubMed Central

    Nachliely, Matan; Sharony, Ehud; Bolla, Narasimha Rao; Kutner, Andrzej; Danilenko, Michael

    2016-01-01

    1α,25-dihydroxyvitamin D3 (1,25D3) is a powerful differentiation inducer for acute myeloid leukemia (AML) cells. However, 1,25D3 doses required for differentiation of AML cells may cause lethal hypercalcemia in vivo. There is evidence that vitamin D2 is less toxic than vitamin D3 in animals. Here, we determined the differentiation effects of novel analogs of 1α,25-dihydroxyvitamin D2 (1,25D2), PRI-1916 and PRI-1917, in which the extended side chains of their previously reported precursors (PRI-1906 and PRI-1907, respectively) underwent further 24Z (24-cis) modification. Using four human AML cell lines representing different stages of myeloid maturation (KG-1a, HL60, U937, and MOLM-13), we found that the potency of PRI-1916 was slightly higher or equal to that of PRI-1906 while PRI-1917 was significantly less potent than PRI-1907. We also demonstrated that 1,25D2 was a less effective differentiation agent than 1,25D3 in these cell lines. Irrespective of their differentiation potency, all the vitamin D2 derivatives tested were less potent than 1,25D3 in transactivating the DR3-type vitamin D response elements. However, similar to 1,25D3, both 1,25D2 and its analogs could strongly cooperate with the plant polyphenol carnosic acid in inducing cell differentiation and inhibition of G1–S cell cycle transition. These results indicate that the 24Z modification has contrasting effects on the differentiation ability of PRI-1906 and PRI-1907 and that the addition of a plant polyphenol could result in a similar extent of cell differentiation induced by different vitamin D compounds. The enhanced antileukemic effects of the tested combinations may constitute the basis for the development of novel approaches for differentiation therapy of AML. PMID:27399677

  12. Presenilin-1 influences processing of the acetylcholinesterase membrane anchor PRiMA.

    PubMed

    García-Ayllón, María-Salud; Campanari, María-Letizia; Montenegro, María-Fernanda; Cuchillo-Ibáñez, Inmaculada; Belbin, Olivia; Lleó, Alberto; Tsim, Karl; Vidal, Cecilio J; Sáez-Valero, Javier

    2014-07-01

    Presenilin-1 (PS1) is the catalytic component of the γ-secretase complex. In this study, we explore if PS1 participates in the processing of the cholinergic acetylcholinesterase (AChE). The major AChE variant expressed in the brain is a tetramer (G(4)) bound to a proline-rich membrane anchor (PRiMA). Overexpression of the transmembrane PRiMA protein in Chinese hamster ovary cells expressing AChE and treated with the γ-secretase inhibitor N-[N-(3,5-difluorophenacetyl)-l-alanyl]-S-phenylglycine t-butyl ester have enabled us to study whether, through its γ-secretase activity, PS1 participates in the processing of PRiMA-linked AChE. γ-Secretase inhibition led to a notable increase in the level of PRiMA-linked AChE, suggesting that γ-secretase is involved in the cleavage of PRiMA. We demonstrate that cleavage of PRiMA by γ-secretase results in a C-terminal PRiMA fragment. Immunofluorescence labeling allowed us to identify this PRiMA fragment in the nucleus. Moreover, we have determined changes in the proportion of the raft-residing AChE-PRiMA in a PS1 conditional knockout mouse. Our results are of interest as both enzymes have therapeutic relevance for Alzheimer's disease. PMID:24612677

  13. Diffuse sky radiation influences the relationship between canopy PRI and shadow fraction

    NASA Astrophysics Data System (ADS)

    Mõttus, Matti; Takala, Tuure L. H.; Stenberg, Pauline; Knyazikhin, Yuri; Yang, Bin; Nilson, Tiit

    2015-07-01

    The Photochemical Reflectance Index (PRI) of green leaves is an indicator of photosynthetic downregulation: when the photosynthetic apparatus is close to the saturation limit, PRI becomes dependent on light conditions. Therefore, by measuring the PRI of leaves under different local irradiance conditions, it should be possible to determine the saturation level of the leaves and obtain information on the light use efficiency (LUE) of a vegetation canopy. The dependence of PRI on the ratio of sunlit to shaded foliage (quantified by the canopy shadow fraction) in the field of view of an instrument has been used to remotely measure canopy LUE on clear days. However, besides photosynthetic downregulation, the dependence of canopy PRI on shadow fraction is affected by the blue sky radiation caused by scattering in the atmosphere. To quantify this effect on remotely sensed PRI, we present the underlying definitions relating leaf and canopy PRI and perform the required calculations for typical midsummer conditions in Central Finland. We demonstrate that the effect of blue sky radiation on the variation of PRI with canopy shadow fraction is similar in shape and magnitude to that of LUE variations reported in literature.

  14. Correcting the relationship between PRI and shadow fraction for the blue sky effect

    NASA Astrophysics Data System (ADS)

    Mõttus, Matti

    2016-04-01

    The Photochemical Reflectance Index (PRI) is defined as the normalized difference ratio of leaf reflectance at two specific wavelengths in the green spectral region. Its value depends on the status of leaf carotenoid content, and especially that of the xanthophyll cycle pigments. Due to the dependence on the xanthophyll cycle, when the photosynthetic apparatus of green leaves is close to the saturation limit, their PRI becomes dependent on light conditions. Therefore, by measuring the PRI of leaves in the same canopy under different local irradiance conditions on a sunny day, it should be possible to determine the saturation level of the leaves. In turn, this gives information on the light use efficiency (LUE) of the vegetation canopy. The average light conditions of visible foliage elements are often quantified with the shadow fraction -- the fraction of visible foliage not lit by direct sunlight. The dependence of PRI on the shadow fraction has been used to remotely measure canopy LUE on clear days. Variations in shadow fraction have been achieved with multiangular measurement. However, besides photosynthetic downregulation, the dependence of canopy PRI on shadow fraction is affected by the blue sky radiation caused by scattering in the atmosphere. To quantify this effect on remotely sensed PRI, we present the underlying definitions relating leaf and canopy PRI and perform the required calculations for typical midsummer conditions in Central Finland. We demonstrate that the effect of blue sky radiation on the variation of PRI with canopy shadow fraction is similar in shape and magnitude to that of LUE variations reported in literature. Next, we propose a new method to assess these PRI variations in structured vegetation. We investiagate this blue sky effect on the PRI -- shadow fraction relationship with high spatial (60 cm) and spectral (9.8 nm) resolution airborne imaging spectroscopy data from Hyytiälä, Finland. We evaluate the spectral irradiance in

  15. Monitoring seasonal and diurnal changes in photosynthetic pigments with automated PRI and NDVI sensors

    NASA Astrophysics Data System (ADS)

    Gamon, J. A.; Kovalchuck, O.; Wong, C. Y. S.; Harris, A.; Garrity, S. R.

    2015-07-01

    The vegetation indices normalized difference vegetation index (NDVI) and photochemical reflectance index (PRI) provide indicators of pigmentation and photosynthetic activity that can be used to model photosynthesis from remote sensing with the light-use-efficiency model. To help develop and validate this approach, reliable proximal NDVI and PRI sensors have been needed. We tested new NDVI and PRI sensors, "spectral reflectance sensors" (SRS sensors; recently developed by Decagon Devices, during spring activation of photosynthetic activity in evergreen and deciduous stands. We also evaluated two methods of sensor cross-calibration - one that considered sky conditions (cloud cover) at midday only, and another that also considered diurnal sun angle effects. Cross-calibration clearly affected sensor agreement with independent measurements, with the best method dependent upon the study aim and time frame (seasonal vs. diurnal). The seasonal patterns of NDVI and PRI differed for evergreen and deciduous species, demonstrating the complementary nature of these two indices. Over the spring season, PRI was most strongly influenced by changing chlorophyll : carotenoid pool sizes, while over the diurnal timescale, PRI was most affected by the xanthophyll cycle epoxidation state. This finding demonstrates that the SRS PRI sensors can resolve different processes affecting PRI over different timescales. The advent of small, inexpensive, automated PRI and NDVI sensors offers new ways to explore environmental and physiological constraints on photosynthesis, and may be particularly well suited for use at flux tower sites. Wider application of automated sensors could lead to improved integration of flux and remote sensing approaches for studying photosynthetic carbon uptake, and could help define the concept of contrasting vegetation optical types.

  16. Monitoring seasonal and diurnal changes in photosynthetic pigments with automated PRI and NDVI sensors

    NASA Astrophysics Data System (ADS)

    Gamon, J. A.; Kovalchuk, O.; Wong, C. Y. S.; Harris, A.; Garrity, S. R.

    2015-02-01

    The vegetation indices normalized difference vegetation index (NDVI) and photochemical reflectance index (PRI) provide indicators of pigmentation and photosynthetic activity that can be used to model photosynthesis from remote sensing with the light-use efficiency model. To help develop and validate this approach, reliable proximal NDVI and PRI sensors have been needed. We tested new NDVI and PRI sensors, "SRS" sensors recently developed by Decagon Devices, during spring activation of photosynthetic activity in evergreen and deciduous stands. We also evaluated two methods of sensor cross-calibration, one that considered sky conditions (cloud cover) at midday only, and the other that also considered diurnal sun angle effects. Cross-calibration clearly affected sensor agreement with independent measurements, with the best method dependent upon the study aim and time frame (seasonal vs. diurnal). The seasonal patterns of NDVI and PRI differed for evergreen and deciduous species, demonstrating the complementary nature of these two indices. Over the spring season, PRI was most strongly influenced by changing chlorophyll : carotenoid pool sizes, while over the diurnal time scale PRI was most affected by the xanthophyll cycle epoxidation state. This finding demonstrates that the SRS PRI sensors can resolve different processes affecting PRI over different time scales. The advent of small, inexpensive, automated PRI and NDVI sensors offers new ways to explore environmental and physiological constraints on photosynthesis, and may be particularly well-suited for use at flux tower sites. Wider application of automated sensors could lead to improved integration of flux and remote sensing approaches to studying photosynthetic carbon uptake, and could help define the concept of contrasting vegetation optical types.

  17. Structure and Function of the PriC DNA Replication Restart Protein.

    PubMed

    Wessel, Sarah R; Cornilescu, Claudia C; Cornilescu, Gabriel; Metz, Alice; Leroux, Maxime; Hu, Kaifeng; Sandler, Steven J; Markley, John L; Keck, James L

    2016-08-26

    Collisions between DNA replication complexes (replisomes) and barriers such as damaged DNA or tightly bound protein complexes can dissociate replisomes from chromosomes prematurely. Replisomes must be reloaded under these circumstances to avoid incomplete replication and cell death. Bacteria have evolved multiple pathways that initiate DNA replication restart by recognizing and remodeling abandoned replication forks and reloading the replicative helicase. In vitro, the simplest of these pathways is mediated by the single-domain PriC protein, which, along with the DnaC helicase loader, can load the DnaB replicative helicase onto DNA bound by the single-stranded DNA (ssDNA)-binding protein (SSB). Previous biochemical studies have identified PriC residues that mediate interactions with ssDNA and SSB. However, the mechanisms by which PriC drives DNA replication restart have remained poorly defined due to the limited structural information available for PriC. Here, we report the NMR structure of full-length PriC from Cronobacter sakazakii PriC forms a compact bundle of α-helices that brings together residues involved in ssDNA and SSB binding at adjacent sites on the protein surface. Disruption of these interaction sites and of other conserved residues leads to decreased DnaB helicase loading onto SSB-bound DNA. We also demonstrate that PriC can directly interact with DnaB and the DnaB·DnaC complex. These data lead to a model in which PriC acts as a scaffold for recruiting DnaB·DnaC to SSB/ssDNA sites present at stalled replication forks. PMID:27382050

  18. Structural and functional characterization of the CAP domain of pathogen-related yeast 1 (Pry1) protein

    NASA Astrophysics Data System (ADS)

    Darwiche, Rabih; Kelleher, Alan; Hudspeth, Elissa M.; Schneiter, Roger; Asojo, Oluwatoyin A.

    2016-06-01

    The production, crystal structure, and functional characterization of the C-terminal cysteine-rich secretory protein/antigen 5/pathogenesis related-1 (CAP) domain of pathogen-related yeast protein-1 (Pry1) from Saccharomyces cerevisiae is presented. The CAP domain of Pry1 (Pry1CAP) is functional in vivo as its expression restores cholesterol export to yeast mutants lacking endogenous Pry1 and Pry2. Recombinant Pry1CAP forms dimers in solution, is sufficient for in vitro cholesterol binding, and has comparable binding properties as full-length Pry1. Two crystal structures of Pry1CAP are reported, one with Mg2+ coordinated to the conserved CAP tetrad (His208, Glu215, Glu233 and His250) in spacegroup I41 and the other without divalent cations in spacegroup P6122. The latter structure contains four 1,4-dioxane molecules from the crystallization solution, one of which sits in the cholesterol binding site. Both structures reveal that the divalent cation and cholesterol binding sites are connected upon dimerization, providing a structural basis for the observed Mg2+-dependent sterol binding by Pry1.

  19. Structural and functional characterization of the CAP domain of pathogen-related yeast 1 (Pry1) protein

    PubMed Central

    Darwiche, Rabih; Kelleher, Alan; Hudspeth, Elissa M.; Schneiter, Roger; Asojo, Oluwatoyin A.

    2016-01-01

    The production, crystal structure, and functional characterization of the C-terminal cysteine-rich secretory protein/antigen 5/pathogenesis related-1 (CAP) domain of pathogen-related yeast protein-1 (Pry1) from Saccharomyces cerevisiae is presented. The CAP domain of Pry1 (Pry1CAP) is functional in vivo as its expression restores cholesterol export to yeast mutants lacking endogenous Pry1 and Pry2. Recombinant Pry1CAP forms dimers in solution, is sufficient for in vitro cholesterol binding, and has comparable binding properties as full-length Pry1. Two crystal structures of Pry1CAP are reported, one with Mg2+ coordinated to the conserved CAP tetrad (His208, Glu215, Glu233 and His250) in spacegroup I41 and the other without divalent cations in spacegroup P6122. The latter structure contains four 1,4-dioxane molecules from the crystallization solution, one of which sits in the cholesterol binding site. Both structures reveal that the divalent cation and cholesterol binding sites are connected upon dimerization, providing a structural basis for the observed Mg2+-dependent sterol binding by Pry1. PMID:27344972

  20. Structural and functional characterization of the CAP domain of pathogen-related yeast 1 (Pry1) protein.

    PubMed

    Darwiche, Rabih; Kelleher, Alan; Hudspeth, Elissa M; Schneiter, Roger; Asojo, Oluwatoyin A

    2016-01-01

    The production, crystal structure, and functional characterization of the C-terminal cysteine-rich secretory protein/antigen 5/pathogenesis related-1 (CAP) domain of pathogen-related yeast protein-1 (Pry1) from Saccharomyces cerevisiae is presented. The CAP domain of Pry1 (Pry1CAP) is functional in vivo as its expression restores cholesterol export to yeast mutants lacking endogenous Pry1 and Pry2. Recombinant Pry1CAP forms dimers in solution, is sufficient for in vitro cholesterol binding, and has comparable binding properties as full-length Pry1. Two crystal structures of Pry1CAP are reported, one with Mg(2+) coordinated to the conserved CAP tetrad (His208, Glu215, Glu233 and His250) in spacegroup I41 and the other without divalent cations in spacegroup P6122. The latter structure contains four 1,4-dioxane molecules from the crystallization solution, one of which sits in the cholesterol binding site. Both structures reveal that the divalent cation and cholesterol binding sites are connected upon dimerization, providing a structural basis for the observed Mg(2+)-dependent sterol binding by Pry1. PMID:27344972

  1. Bi-directional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1

    PubMed Central

    Zhu, Hongliang; Zhou, Yuyi; Castillo-González, Claudia; Lu, Amber; Ge, Chunxiao; Zhao, Ying-Tao; Duan, Liusheng; Li, Zhaohu; Axtell, Michael J.; Wang, Xiu-Jie; Zhang, Xiuren

    2013-01-01

    miRNAs originate from primary transcripts (pri-miRNAs) with characteristic stem-loop structures. Accurate processing of pri-miRNAs is required for functional miRNAs. Here, using pri-miR166 family as a paradigm, we report the decisive role of pri-miRNA terminal loops in miRNA biogenesis. We found that multi-branched terminal loops in pri-miR166s substantially suppressed miR166 expression in vivo. Unlike canonical processing of pri-miRNAs, terminal-loop-branched (TLBed) pri-miRNAs can be processed by Dicer-like1 (DCL1) complexes bi-directionally: from base to loop and from loop to base, resulting in productive and abortive processing of miRNAs, respectively. In either case, DCL1 complexes canonically cut pri-miRNAs at a distance of 16-17 base pairs (bp) from a reference single-stranded loop region. DCL1 also adjusts processing sites toward an internal loop through its helicase domain. Thus, these results provide new insight into the poorly understood processing mechanism of pri-miRNAs with complicated secondary structures. PMID:23934148

  2. Diurnal and Directional Responses of Chlorophyll Fluorescence and the PRI in a Cornfield

    NASA Technical Reports Server (NTRS)

    Middleton, Elizabeth; Cheng, Y. B.; Corp, L.; Campbell, P.; Kustas, W.

    2010-01-01

    Determining the health and vigor of vegetation using high spectral resolution remote sensing is an important goal which has application to monitoring agriculture and ecosystem productivity and carbon exchange. Two spectral indices used to assess whether vegetation is performing near-optimally or exhibiting symptoms of environmental stress (e.g., drought or nutrient deficiency, non-optimal temperatures, etc.) are the Photochemical Reflectance Index (PRI) and solar-induced red and far-red Chlorophyll Fluorescence (Fs). Both the PRI and Fs capture the dynamics of photoprotection mechanisms within green foliage: the PRI is based on the association of the reflected radiation in the green spectrum with the xanthophyll cycle, whereas Fs measures the emitted radiation in the red and far-red spectrum. Fs was determined from retrievals in the atmospheric oxygen absorption features centered at 688 and 760 nm using a modified Fraunhofer Line Depth (FLD) method. We previously demonstrated diurnal and seasonal PRI differences for sunlit vs. shaded foliage in a conifer forest canopy, as expressed in the hotspot and darkspot of the Bidirectional Reflectance Function (BRF). In a USDA-ARS experimental field site located in Beltsville, MD, USA, measurements were acquired over a corn crop from a nadir view in 2008 with an ASD FieldSpec Pro (Analytical Spectral Devices, Inc., Boulder, CO, USA) to study the behavior of the PRI for sunlit and shaded foliage as captured in reflectance variations associated with the BRF, in a I m tall canopy in the vegetative growth stage. Those observations were compared to simulations obtained from two radiative transfer models. Measurements were then acquired to examine whether the PRI and Fs were influenced by view zenith and azimuth geometries at different times of day. Those measurements were made in 2010 with the Ocean Optics USB4000 Miniature Fiber Optic Spectrometer (Ocean Optics Inc., Dunedin, Florida, USA) at several times during the day on

  3. Fluorescence, PRI and canopy temperature for water stress detection in cereal crops

    NASA Astrophysics Data System (ADS)

    Panigada, C.; Rossini, M.; Meroni, M.; Cilia, C.; Busetto, L.; Amaducci, S.; Boschetti, M.; Cogliati, S.; Picchi, V.; Pinto, F.; Marchesi, A.; Colombo, R.

    2014-08-01

    Narrow-band multispectral remote sensing techniques and thermal imagery were investigated for water stress detection in cereal crops. Visible and near infrared AISA Eagle (Specim, Finland) and thermal AHS-160 (Sensytech Inc., USA) imageries were acquired with an airborne survey on a farm-level experimental site where maize (Zea mays L.) and sorghum (Sorghum bicolor L.) were grown with three different irrigation treatments. Vegetation biophysical and eco-physiological measurements were collected concurrently with the airborne campaign. Leaf fluorescence yield (ΔF/Fm‧) resulted to be a good indirect measure of water stress. Therefore, ΔF/Fm‧ measurements were compared against remotely sensed indicators: (i) the Photochemical Reflectance Index (PRI), (ii) the sun-induced chlorophyll fluorescence at 760 nm (F760), retrieved by the Fraunhofer line depth method and (iii) the canopy temperature (TC) calculated decoupling soil and vegetation contributions. TC was related to ΔF/Fm‧ with the highest determination coefficient (R2 = 0.65), followed by PRI586 (reference band at 586 nm) (R2 = 0.51). The relationship with F760 was significant but weaker (R2 = 0.36). The coefficient of determination increased up to 0.54 when pigment concentration was considered by multiplying ΔF/Fm‧ and chlorophyll content, confirming the close relationship between passive fluorescence signal, pigment content and light photosystem efficiency. PRI586, F760 and TC maps were produced in maize and sorghum plots. The differences in the average values of PRI586, F760 and TC extracted from the plots with different water treatments showed that water treatments were well discriminated in maize plots by the three remotely sensed indicators. This was confirmed by the visual observation of the PRI586, F760 and TC maps, while in sorghum plots, F760 and TC appeared more sensitive to water stress compared to PRI586.

  4. Diurnal and directional responses of chlorophyll fluorescence and pri in a cornfield

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two high spectral resolution reflectance-based indices were used to assess whether vegetation in a cornfield was performing near-optimally or exhibiting symptoms of environmental stress. These were the Photochemical Reflectance Index (PRI) and solar-induced Chlorophyll Fluorescence (SIF). This study...

  5. Distinct localization of Collagen Q and PRiMA forms of Acetylcholinesterase at the neuromuscular junction

    PubMed Central

    Bernard, Véronique; Girard, Emmanuelle; Hrabovska, Anna; Camp, Shelley; Taylor, Palmer; Plaud, Benoit; Krejci, Eric

    2015-01-01

    Acetylcholinesterase (AChE) terminates the action of acetylcholine at cholinergic synapses thereby preventing rebinding of acetylcholine to nicotinic post-synaptic receptors at the neuromuscular junction. Here we show that AChE is not localized close to these receptors on the post-synaptic surface, but is instead clustered along the presynaptic membrane and deep in the post-synaptic folds. Because AChE is anchored by ColQ in the basal lamina and is linked to the plasma membrane by a transmembrane subunit (PRiMA), we used a genetic approach to evaluate the respective contribution of each anchoring oligomer. By visualization and quantification of AChE in mouse strains devoid of ColQ, PRiMA or AChE, specifically in the muscle, we found that along the nerve terminus, the vast majority of AChE is anchored by ColQ that is only produced by the muscle, whereas very minor amounts of AChE are anchored by PRiMA that is produced by motoneurons. In its synaptic location, AChE is therefore positioned to scavenge ACh that effluxes from the nerve by non-quantal release. AChE-PRiMA, produced by the muscle, is diffusely distributed along the muscle in extra-junctional regions. PMID:20883790

  6. Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio

    SciTech Connect

    Liebschner, Dorothee; Brzezinski, Krzysztof; Dauter, Miroslawa; Dauter, Zbigniew; Nowak, Marta; Kur, Józef; Olszewski, Marcin

    2012-12-01

    The N-terminal domain of the PriB protein from the thermophilic bacterium T. tengcongensis (TtePriB) was expressed and its crystal structure has been solved at the atomic resolution of 1.09 Å by direct methods. PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the full 220-residue protein, adopts the characteristic oligonucleotide/oligosaccharide-binding (OB) structure consisting of a five-stranded β-barrel filled with hydrophobic residues and equipped with four loops extending from the barrel. In the crystal two protomers dimerize, forming a six-stranded antiparallel β-sheet. The structure of the N-terminal OB domain of T. tengcongensis shows significant differences compared with mesophile PriBs. While in all other known structures of PriB a dimer is formed by two identical OB domains in separate chains, TtePriB contains two consecutive OB domains in one chain. However, sequence comparison of both the N-terminal and the C-terminal domains of TtePriB suggests that they have analogous structures and that the natural protein possesses a structure similar to a dimer of two N-terminal domains.

  7. Functional interactions between polypyrimidine tract binding protein and PRI peptide ligand containing proteins.

    PubMed

    Coelho, Miguel B; Ascher, David B; Gooding, Clare; Lang, Emma; Maude, Hannah; Turner, David; Llorian, Miriam; Pires, Douglas E V; Attig, Jan; Smith, Christopher W J

    2016-08-15

    Polypyrimidine tract binding protein (PTBP1) is a heterogeneous nuclear ribonucleoprotein (hnRNP) that plays roles in most stages of the life-cycle of pre-mRNA and mRNAs in the nucleus and cytoplasm. PTBP1 has four RNA binding domains of the RNA recognition motif (RRM) family, each of which can bind to pyrimidine motifs. In addition, RRM2 can interact via its dorsal surface with proteins containing short peptide ligands known as PTB RRM2 interacting (PRI) motifs, originally found in the protein Raver1. Here we review our recent progress in understanding the interactions of PTB with RNA and with various proteins containing PRI ligands. PMID:27528752

  8. Remote detection of water stress conditions via a diurnal photochemical reflectance index (PRI) improves yield prediction in rainfed wheat

    NASA Astrophysics Data System (ADS)

    Magney, T. S.; Vierling, L. A.; Eitel, J.

    2014-12-01

    Employing remotely sensed techniques to quantify the existence and magnitude of midday photosynthetic downregulation using the photochemical reflectance index (PRI) may reveal new information about plant responses to abiotic stressors in space and time. However, the interpretation and application of the PRI can be confounded because of its sensitivity to several variables changing at the diurnal (e.g., irradiation, shadow fraction) and seasonal (e.g., leaf area, chlorophyll and carotene pigment concentrations, irradiation) time scales. We explored different techniques to correct the PRI for variations in canopy structure and relative chlorophyll content (ChlR) using highly temporally resolved (frequency = five minutes) in-situ radiometric measurements of PRI and the Normalized Difference Vegetation Index (NDVI) over eight soft white spring wheat (Triticum aestivum L.)field plots under varying nitrogen and soil water conditions over two seasons. Our results suggest that the influence of seasonal variation in canopy ChlR and LAI on the diurnally measured PRI (PRIdiurnal) can be minimized using simple correction techniques, therefore improving the strength of PRI as a tool to quantify abiotic stressors such as daily changes in soil volumetric water content (SVWC), and vapor pressure deficit (VPD). PRIdiurnal responded strongly to available nitrogen, and linearly tracked seasonal changes in SVWC, VPD, and stomatal conductance (gc). Utilizing the PRI as an indicator of stress, yield predictions significantly over greenness indices such as the NDVI. This study provides insight towards the future interpretation and scaling of PRI to quantify rapid changes in photosynthesis, and as an indicator of plant stress.

  9. Blocking the maturation of OncomiRNAs using pri-miRNA-17∼92 aptamer in retinoblastoma.

    PubMed

    Subramanian, Nithya; Kanwar, Jagat R; Kanwar, Rupinder K; Krishnakumar, Subramanian

    2015-02-01

    The miR-17∼92. or oncomiR-1, cluster encodes oncogenic microRNAs (miRNAs), and it also promotes retinoblastoma (RB) tumor formation. Antagomir and miRNA mimics based approaches are widely tried against oncogenic and tumor suppressive miRNAs. Other methods for targeting cancer related miRNAs are still under development. In the current study, we focused on the pri-miRNA-17∼92 aptamer (pri-apt), which can potentially replace the mix of five antagomirs by one aptamer that function to abrogate the maturation of miR-17, miR-18a, and miR-19b (P<0.05) for targeting RB. We used RB cell lines WERI-Rb1 and Y79 as an in vitro model. Cellular changes upon transfecting the pri-apt led to S-phase arrest in WERI-Rb1 cells and onset of apoptosis in both Y79 and WERI-Rb1 cell lines. There was increased cytotoxicity as measured by lactate dehydrogenase activity in pri-apt treated Y79 cells (P<0.05), and significant inhibition of cell proliferation was observed in both of the cell lines. Thus we showed the antiproliferative property of pri-apt in RB cell lines, which can be readily modified by developing appropriate vectors for the delivery of the aptamer specifically to cancer cells. PMID:25513843

  10. Blocking the Maturation of OncomiRNAs Using pri-miRNA-17∼92 Aptamer in Retinoblastoma

    PubMed Central

    Subramanian, Nithya; Kanwar, Jagat R.; Kanwar, Rupinder K.

    2015-01-01

    The miR-17∼92. or oncomiR-1, cluster encodes oncogenic microRNAs (miRNAs), and it also promotes retinoblastoma (RB) tumor formation. Antagomir and miRNA mimics based approaches are widely tried against oncogenic and tumor suppressive miRNAs. Other methods for targeting cancer related miRNAs are still under development. In the current study, we focused on the pri-miRNA-17∼92 aptamer (pri-apt), which can potentially replace the mix of five antagomirs by one aptamer that function to abrogate the maturation of miR-17, miR-18a, and miR-19b (P<0.05) for targeting RB. We used RB cell lines WERI-Rb1 and Y79 as an in vitro model. Cellular changes upon transfecting the pri-apt led to S-phase arrest in WERI-Rb1 cells and onset of apoptosis in both Y79 and WERI-Rb1 cell lines. There was increased cytotoxicity as measured by lactate dehydrogenase activity in pri-apt treated Y79 cells (P<0.05), and significant inhibition of cell proliferation was observed in both of the cell lines. Thus we showed the antiproliferative property of pri-apt in RB cell lines, which can be readily modified by developing appropriate vectors for the delivery of the aptamer specifically to cancer cells. PMID:25513843

  11. The crystal structure of Neisseria gonorrhoeae PriB reveals mechanistic differences among bacterial DNA replication restart pathways

    SciTech Connect

    Dong, Jinlan; George, Nicholas P.; Duckett, Katrina L.; DeBeer, Madeleine A.P.; Lopper, Matthew E.

    2010-05-25

    Reactivation of repaired DNA replication forks is essential for complete duplication of bacterial genomes. However, not all bacteria encode homologs of the well-studied Escherichia coli DNA replication restart primosome proteins, suggesting that there might be distinct mechanistic differences among DNA replication restart pathways in diverse bacteria. Since reactivation of repaired DNA replication forks requires coordinated DNA and protein binding by DNA replication restart primosome proteins, we determined the crystal structure of Neisseria gonorrhoeae PriB at 2.7 {angstrom} resolution and investigated its ability to physically interact with DNA and PriA helicase. Comparison of the crystal structures of PriB from N. gonorrhoeae and E. coli reveals a well-conserved homodimeric structure consisting of two oligosaccharide/oligonucleotide-binding (OB) folds. In spite of their overall structural similarity, there is significant species variation in the type and distribution of surface amino acid residues. This correlates with striking differences in the affinity with which each PriB homolog binds single-stranded DNA and PriA helicase. These results provide evidence that mechanisms of DNA replication restart are not identical across diverse species and that these pathways have likely become specialized to meet the needs of individual organisms.

  12. Use of ERS SAR interferometric coherence and PRI images to evaluate crop height and soil moisture and to identify crops

    NASA Astrophysics Data System (ADS)

    Moeremans, Benoit; Dautrebande, Sylvia

    1998-12-01

    The aim of the present project was to identify the capabilities of multitemporal ERS SAR interferometric coherence and PRI images to evaluate soil moisture, to estimate crop height and to identify crops for four crop types (winter wheat, potato, sugar beet and maize) and for different pilot fields. The coherence images acquired during the winter and spring seasons can be used to identify bare or nearly bare fields with a threshold value, and then PRI images were used to quantify soil moisture value for each bare field. The coherence images acquired during the growing season were used to evaluate crop height for each studied crop type. Moreover, the coherence image provided some additional information to PRI images for the crop type identification. This study was carried out in the framework of the PRODEX program financed by the Belgian Federal Office for Scientific, Technical and Cultural affairs (OSTC) and the European Space Agency (ESA).

  13. Explaining the variability of Photochemical Reflectance Index (PRI): deconvolution of variability related to Light Use Efficiency and Canopy attributes.

    NASA Astrophysics Data System (ADS)

    Merlier, Elodie; Hmimina, Gabriel; Dufrêne, Eric; Soudani, Kamel

    2014-05-01

    The Photochemical Reflectance Index (PRI) was designed as a proxy of the state of xanthophyll cycle which is used as a response of plants to excess of light (Gamon et al., 1990; 1992). Strong relationships between PRI and LUE were shown at leaf and canopy scales and over a wide range of species (Garbulsky et al., 2011). However, its use at canopy scale was shown to be significantly hampered by effects of confounding factors such as the PRI sensitivity to leaf pigment content (Gamon et al. 2001; Nakaji et al. 2006) and to canopy structure (Hilker et al. 2008). Several approaches aimed at correcting such effects and recent works focused on the deconvolution of LUE related and LUE unrelated PRI variability (Rahimzadeh-Bajgiran et al. 2012).In this study, the PRI variability at canopy scale is investigated over two years on three species (Fagus sylvatica, Quercus robur and Pinus sylvestris) growing under two water regimes. At daily scale, PRI variability is mainly explained by radiation conditions. As already reported at leaf scale in Hmimina et al. (2014), analysis of PRI responses to incoming photosynthetically active radiation over seasonal scale allowed to separate two sources of variability : a constitutive variability mainly related to canopy structure and leaf chlorophyll content and a facultative variability mainly related to LUE and soil moisture content. These results highlight the composite nature of PRI signal measured at canopy scale and the importance of disentangling its sources of variability in order to accurately assess ecosystem light use efficiency. Gamon JA, Field CB, Bilger W, Björkman O, Fredeen AL, Peñuelas J. 1990. Remote sensing of the xanthophyll cycle and chlorophyll fluorescence in sunflower leaves and canopies. Oecologia 85, 1-7. Gamon JA, Field CB, Fredeen A AL, Thayer S. 2001. Assessing photosynthetic downregulation in sunflower stands with an optically-based model. Photosynthesis Research 67, 113-125. Gamon JA, Peñuelas J, Field CB

  14. SDZ PRI 053, an orally bioavailable human immunodeficiency virus type 1 proteinase inhibitor containing the 2-aminobenzylstatine moiety.

    PubMed Central

    Billich, A; Fricker, G; Müller, I; Donatsch, P; Ettmayer, P; Gstach, H; Lehr, P; Peichl, P; Scholz, D; Rosenwirth, B

    1995-01-01

    A series of inhibitors of human immunodeficiency virus type 1 (HIV-1) proteinase containing the 2-aralkyl-amino-substituted statine moiety as a novel transition-state analog was synthesized, with the aim to obtain compounds which combine anti-HIV potency with oral bioavailability. The reduced-size 2-aminobenzylstatine derivative SDZ PRI 053, which contains 2-(S)-amino-3-(R)-hydroxyindane in place of an amino acid amide, is a potent and orally bioavailable inhibitor of HIV-1 replication. The antiviral activity of SDZ PRI 053 was demonstrated in various cell lines, in primary lymphocytes, and in primary monocytes, against laboratory strains as well as clinical HIV-1 isolates (50% effective dose = 0.028 to 0.15 microM). Cell proliferation was impaired only at 100- to 300-fold-higher concentrations. The mechanism of antiviral action of the proteinase inhibitor SDZ PRI 0.53 was demonstrated to be inhibition of gag precursor protein processing. The finding that the inhibitory potency of SDZ PRI 053 in chronic virus infection, determined by p24 release, was considerably lower than that in de novo infection may be explained by the fact that the virus particles produced in the presence of SDZ PRI 053 are about 50-fold less infectious than those from untreated cultures. Upon intravenous administration, half-lives in blood of 100 and 32 min in mice and rats, respectively, were measured. Oral bioavailability of SDZ PRI 053 in rodents was 20 to 60%, depending on the dose. In mice, rats, and dogs, the inhibitor levels after oral administration remained far above the concentrations needed to efficiently block HIV replication in vitro for a prolonged period. This compound is thus a promising candidate for clinical use in HIV disease. PMID:7492076

  15. Assessing canopy PRI from airborne imagery to map water stress in maize

    NASA Astrophysics Data System (ADS)

    Rossini, M.; Fava, F.; Cogliati, S.; Meroni, M.; Marchesi, A.; Panigada, C.; Giardino, C.; Busetto, L.; Migliavacca, M.; Amaducci, S.; Colombo, R.

    2013-12-01

    This paper presents a method for mapping water stress in a maize field using hyperspectral remote sensing imagery. An airborne survey using AISA (Specim, Finland) was performed in July 2008 over an experimental farm in Italy. Hyperspectral data were acquired over a maize field with three different irrigation regimes. An intensive field campaign was also conducted concurrently with imagery acquisition to measure relative leaf water content (RWC), active chlorophyll fluorescence (ΔF/Fm‧), leaf temperature (Tl) and Leaf Area Index (LAI). The analysis of the field data showed that at the time of the airborne overpass the maize plots with irrigation deficits were experiencing a moderate water stress, affecting the plant physiological status (ΔF/Fm‧, difference between Tl and air temperature (Tair), and RWC) but not the canopy structure (LAI). Among the different Vegetation Indices (VIs) computed from the airborne imagery the Photochemical Reflectance Index computed using the reflectance at 570 nm as the reference band (PRI570) showed the strongest relationships with ΔF/Fm‧ (r2 = 0.76), Tl - Tair (r2 = 0.82) and RWC (r2 = 0.64) and the red-edge Chlorophyll Index (CIred-edge) with LAI (r2 = 0.64). Thus PRI has been proven to be related to water stress at early stages, before structural changes occurred.

  16. Remote sensing of plant emissions of volatile isoprenoids with PRI. Prospects for upscaling (Invited)

    NASA Astrophysics Data System (ADS)

    Penuelas, J.

    2013-12-01

    Josep Peñuelas*1,2, Giovanni Marino1,2,3,4, Joan LLusia1,2, Catherine Morfopoulos1,2,5, Gerard Farre-Armengol1,2, Shawn Kefauver, Alex Guenther6 , Francesca Rapparini7 , Roger Seco1,2,6, Marc Estiarte1,2, Mónica Mejia-Chang1,2, Romà Ogaya1,2, Jordi Sardans1,2 , Andrew Turnipseed6, Peter Harley6, Osvaldo Facini7, Rita Baraldi7, Jim Greenberg6 , Iolanda Filella1,2 1 CSIC, Global Ecology Unit CREAF-CEAB-UAB, Cerdanyola del Vallés 08193, Catalonia, Spain 2 CREAF, Cerdanyola del Vallés 08193, Catalonia, Spain 3 Dipartimento di Bioscienze e Territorio, Università degli Studi del Molise, Contrada Fonte Lappone, 86090 Pesche (IS), Italy 4 Institute for Plant Protection, National Research Council, Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy 5 Division of Ecology and Evolution, Imperial College, Silwood Park, Ascot, SL5 7PY, UK 6 Atmospheric Chemistry Division, National Center for Atmospheric Research, P.O. Box 3000, Boulder, CO 80307-3000, USA 7 Biometeorology Institute, IBIMET-CNR, Via P. Gobetti 101, Bologna, Italy Abstract Terrestrial plants re-emit around 1-2% of the carbon they fix as isoprene and monoterpenes. These emissions play major roles in the ecological relationships among living organisms and in atmospheric chemistry and climate, and yet their actual quantification at the ecosystem level in different regions is far from being resolved. Phenomenological models are used to estimate the emission rates, but the limited understanding of the function and regulation of these emissions leads to large uncertainties in such estimations. Many measurements have been made at the foliar but few at the ecosystem level, and those that do exist are limited in space and time. We here provide evidence that a simple remote sensing index, the photochemical reflectance index (PRI), which is indicative of light use efficiency (LUE), is a good indirect estimator of foliar isoprenoid emissions and therefore can be used to sense them remotely. These results open

  17. Developmentally regulated expression and complex processing of barley pri-microRNAs

    PubMed Central

    2013-01-01

    Background MicroRNAs (miRNAs) regulate gene expression via mRNA cleavage or translation inhibition. In spite of barley being a cereal of great economic importance, very little data is available concerning its miRNA biogenesis. There are 69 barley miRNA and 67 pre-miRNA sequences available in the miRBase (release 19). However, no barley pri-miRNA and MIR gene structures have been shown experimentally. In the present paper, we examine the biogenesis of selected barley miRNAs and the developmental regulation of their pri-miRNA processing to learn more about miRNA maturation in barely. Results To investigate the organization of barley microRNA genes, nine microRNAs - 156g, 159b, 166n, 168a-5p/168a-3p, 171e, 397b-3p, 1120, and 1126 - were selected. Two of the studied miRNAs originate from one MIR168a-5p/168a-3p gene. The presence of all miRNAs was confirmed using a Northern blot approach. The miRNAs are encoded by genes with diverse organizations, representing mostly independent transcription units with or without introns. The intron-containing miRNA transcripts undergo complex splicing events to generate various spliced isoforms. We identified miRNAs that were encoded within introns of the noncoding genes MIR156g and MIR1126. Interestingly, the intron that encodes miR156g is spliced less efficiently than the intron encoding miR1126 from their specific precursors. miR397b-3p was detected in barley as a most probable functional miRNA, in contrast to rice where it has been identified as a complementary partner miRNA*. In the case of miR168a-5p/168a-3p, we found the generation of stable, mature molecules from both pre-miRNA arms, confirming evolutionary conservation of the stability of both species, as shown in rice and maize. We suggest that miR1120, located within the 3′ UTR of a protein-coding gene and described as a functional miRNA in wheat, may represent a siRNA generated from a mariner-like transposable element. Conclusions Seven of the eight barley miRNA genes

  18. The PriA Replication Restart Protein Blocks Replicase Access Prior to Helicase Assembly and Directs Template Specificity through Its ATPase Activity*

    PubMed Central

    Manhart, Carol M.; McHenry, Charles S.

    2013-01-01

    The PriA protein serves as an initiator for the restart of DNA replication on stalled replication forks and as a checkpoint protein that prevents the replicase from advancing in a strand displacement reaction on forks that do not contain a functional replicative helicase. We have developed a primosomal protein-dependent fluorescence resonance energy transfer (FRET) assay using a minimal fork substrate composed of synthetic oligonucleotides. We demonstrate that a self-loading reaction, which proceeds at high helicase concentrations, occurs by threading of a preassembled helicase over free 5′-ends, an event that can be blocked by attaching a steric block to the 5′-end or coating DNA with single-stranded DNA binding protein. The specificity of PriA for replication forks is regulated by its intrinsic ATPase. ATPase-defective PriA K230R shows a strong preference for substrates that contain no gap between the leading strand and the duplex portion of the fork, as demonstrated previously. Wild-type PriA prefers substrates with larger gaps, showing maximal activity on substrates on which PriA K230R is inactive. We demonstrate that PriA blocks replicase function on forks by blocking its binding. PMID:23264623

  19. siRNA release from pri-miRNA scaffolds is controlled by the sequence and structure of RNA.

    PubMed

    Galka-Marciniak, Paulina; Olejniczak, Marta; Starega-Roslan, Julia; Szczesniak, Michal W; Makalowska, Izabela; Krzyzosiak, Wlodzimierz J

    2016-04-01

    shmiRs are pri-miRNA-based RNA interference triggers from which exogenous siRNAs are expressed in cells to silence target genes. These reagents are very promising tools in RNAi in vivo applications due to their good activity profile and lower toxicity than observed for other vector-based reagents such as shRNAs. In this study, using high-resolution northern blotting and small RNA sequencing, we investigated the precision with which RNases Drosha and Dicer process shmiRs. The fidelity of siRNA release from the commonly used pri-miRNA shuttles was found to depend on both the siRNA insert and the pri-miR scaffold. Then, we searched for specific factors that may affect the precision of siRNA release and found that both the structural features of shmiR hairpins and the nucleotide sequence at Drosha and Dicer processing sites contribute to cleavage site selection and cleavage precision. An analysis of multiple shRNA intermediates generated from several reagents revealed the complexity of shmiR processing by Drosha and demonstrated that Dicer selects substrates for further processing. Aside from providing new basic knowledge regarding the specificity of nucleases involved in miRNA biogenesis, our results facilitate the rational design of more efficient genetic reagents for RNAi technology. PMID:26921501

  20. mirEX: a platform for comparative exploration of plant pri-miRNA expression data.

    PubMed

    Bielewicz, Dawid; Dolata, Jakub; Zielezinski, Andrzej; Alaba, Sylwia; Szarzynska, Bogna; Szczesniak, Michal W; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia; Karlowski, Wojciech M

    2012-01-01

    mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex. PMID:22013167

  1. Binding Specificity of E. coli SSB protein for the χ subunit of DNA pol III Holoenzyme and PriA helicase.†

    PubMed Central

    Kozlov, Alexander G.; Jezewska, Maria J.; Bujalowski, Wlodzimierz; Lohman, Timothy M.

    2010-01-01

    The E. coli single stranded DNA binding (SSB) protein plays a central role in DNA metabolism through its high affinity interactions with ssDNA, as well as its interactions with numerous other proteins via its unstructured C-termini. Although SSB interacts with at least 14 other proteins, it is not understood how SSB might recruit one protein over another for a particular metabolic role. To probe the specificity of these interactions we have used isothermal titration calorimetry to examine the thermodynamics of binding of SSB to two E. coli proteins important for DNA replication, the χ subunit of DNA polymerase III holoenzyme and the PriA helicase. We find that an SSB tetramer can bind up to four molecules of either protein primarily via interactions with the last ~ 9 amino acids in the conserved SSB C-terminal tails (SSB-Ct). We observe intrinsic specificity for the binding of an isolated SSB-Ct peptide to PriA over χ due primarily to a more favorable enthalpic component. PriA and χ also bind with weaker affinity to SSB (in the absence of ssDNA) than to isolated SSB-Ct peptides, indicating an inhibitory effect of the SSB protein core. Although the binding affinity of SSB for both χ and PriA is enhanced if SSB is prebound to ssDNA, this effect is larger with PriA indicating a further enhancement of SSB specificity for PriA. These results also suggest that DNA binding proteins such as PriA, which also interact with SSB, could use this interaction to gain access to ssDNA by first interacting with the SSB C-termini. PMID:20329707

  2. Linking chlorophyll fluorescence, hyperspectral reflectance and plant physiological responses to detect stress using the photochemical reflectance index (PRI) (Invited)

    NASA Astrophysics Data System (ADS)

    Naumann, J. C.; Young, D.; Anderson, J.

    2009-12-01

    The concept of using vegetation as sentinels to indicate natural or anthropogenic stress is not new and could potentially provide an ideal mechanism for large-scale detection. Advances in fluorescence spectroscopy and reflectance-derived fluorescence have made possible earlier detection of stress in plants, especially before changes in chlorophyll content are visible. Our studies have been used to fuse leaf fluorescence and reflectance characteristics to remotely sense and rapidly detect vegetation stress and terrain characteristics. Laboratory studies have indicated that light-adapted fluorescence (ΔF/F‧m) measurements have been successful in all experiments at detecting stress from flooding, salinity, drought, herbicide and TNT contamination prior to visible signs of damage. ΔF/F‧m was related to plant physiological status in natural stress conditions, as seen in the relationships with stomatal conductance and photosynthesis The photochemical reflectance index (PRI) and other reflectance ratios were effective at tracking changes in ΔF/F‧m at the leaf and canopy-level scales. At the landscape-level, chlorophyll fluorescence and airborne reflectance imagery were used to evaluate spatial variations in stress in the dominant shrub on a barrier island, Myrica cerifera, during a severe drought and compared to an extremely wet year. Measurements of relative water content and the water band index (WBI970) indicated that water stress did not vary across the island. In contrast, there were significant differences in tissue chlorides across sites. Using PRI we were able to detect salinity stress across the landscape. PRI did not differ between wet and dry years. There was a positive relationship between PRI and ΔF/F‧m for M. cerifera (r2 = 0.79). The normalized difference vegetation index (NDVI), the chlorophyll index (CI) and WBI970 were higher during the wet summer but varied little across the island. PRI was not significantly related to NDVI, suggesting that

  3. Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.

    PubMed

    Nepal, Chirag; Coolen, Marion; Hadzhiev, Yavor; Cussigh, Delphine; Mydel, Piotr; Steen, Vidar M; Carninci, Piero; Andersen, Jesper B; Bally-Cuif, Laure; Müller, Ferenc; Lenhard, Boris

    2016-04-20

    MicroRNAs (miRNAs) play a major role in the post-transcriptional regulation of target genes, especially in development and differentiation. Our understanding about the transcriptional regulation of miRNA genes is limited by inadequate annotation of primary miRNA (pri-miRNA) transcripts. Here, we used CAGE-seq and RNA-seq to provide genome-wide identification of the pri-miRNA core promoter repertoire and its dynamic usage during zebrafish embryogenesis. We assigned pri-miRNA promoters to 152 precursor-miRNAs (pre-miRNAs), the majority of which were supported by promoter associated post-translational histone modifications (H3K4me3, H2A.Z) and RNA polymerase II (RNAPII) occupancy. We validated seven miR-9 pri-miRNAs byin situhybridization and showed similar expression patterns as mature miR-9. In addition, processing of an alternative intronic promoter ofmiR-9-5was validated by 5' RACE PCR. Developmental profiling revealed a subset of pri-miRNAs that are maternally inherited. Moreover, we show that promoter-associated H3K4me3, H2A.Z and RNAPII marks are not only present at pri-miRNA promoters but are also specifically enriched at pre-miRNAs, suggesting chromatin level regulation of pre-miRNAs. Furthermore, we demonstrated that CAGE-seq also detects 3'-end processing of pre-miRNAs on Drosha cleavage site that correlates with miRNA-offset RNAs (moRNAs) production and provides a new tool for detecting Drosha processing events and predicting pre-miRNA processing by a genome-wide assay. PMID:26673698

  4. Dysfunctional Presynaptic M2 Receptors in the Presence of Chronically High Acetylcholine Levels: Data from the PRiMA Knockout Mouse

    PubMed Central

    Mohr, Franziska; Krejci, Eric; Zimmermann, Martina; Klein, Jochen

    2015-01-01

    The muscarinic M2 receptor (M2R) acts as a negative feedback regulator in central cholinergic systems. Activation of the M2 receptor limits acetylcholine (ACh) release, especially when ACh levels are increased because acetylcholinesterase (AChE) activity is acutely inhibited. Chronically high ACh levels in the extracellular space, however, were reported to down-regulate M2R to various degrees. In the present study, we used the PRiMA knockout mouse which develops severely reduced AChE activity postnatally to investigate ACh release, and we used microdialysis to investigate whether the function of M2R to reduce ACh release in vivo was impaired in adult PRiMA knockout mice. We first show that striatal and hippocampal ACh levels, while strongly increased, still respond to AChE inhibitors. Infusion or injection of oxotremorine, a muscarinic M2 agonist, reduced ACh levels in wild-type mice but did not significantly affect ACh levels in PRiMA knockout mice or in wild-type mice in which ACh levels were artificially increased by infusion of neostigmine. Scopolamine, a muscarinic antagonist, increased ACh levels in wild-type mice receiving neostigmine, but not in wild-type mice or in PRiMA knockout mice. These results demonstrate that M2R are dysfunctional and do not affect ACh levels in PRiMA knockout mice, likely because of down-regulation and/or loss of receptor-effector coupling. Remarkably, this loss of function does not affect cognitive functions in PRiMA knockout mice. Our results are discussed in the context of AChE inhibitor therapy as used in dementia. PMID:26506622

  5. Evaluation of the pri-miR-34b/c rs4938723 polymorphism and its association with breast cancer risk

    PubMed Central

    SANAEI, SARA; HASHEMI, MOHAMMAD; REZAEI, MARYAM; HASHEMI, SEYED MEHDI; BAHARI, GHOLAMREZA; GHAVAMI, SAEID

    2016-01-01

    MicroRNAs (miRNAs or miRs) are a family of small non-coding RNAs that function as oncogenes or tumor suppressor genes. Recent evidence suggests that the pri-miR-34b/c rs4938723 variant is associated with the development of cancer. At present, there is an inconsistent association between the single-nucleotide polymorphism in pri-miR-34b/c and cancer in the limited studies. The present study is a case-control investigation, with 263 breast cancer (BC) patients and 221 control women, which examined the potential association of the pri-miR-34b/c rs4938723 polymorphisms with BC susceptibility. The polymorphisms were genotyped by the polymerase chain reaction restriction fragment length polymorphism method. No significant association between the pri-miR-34b/c rs4938723 variant and BC was identified [TC vs. TT: Odds ratio (OR), 0.87; 95% confidence interval (CI), 0.60–1.26; P=0.506; CC vs. TT: OR, 1.22; 95% CI, 0.61–2.47; P=0.600; TC+CC vs. TT: OR, 0.91; 95% CI, 0.64–1.31; P=0.648; CC vs. TT+TC: OR, 1.32; 95% CI, 0.67–2.59; P=0.498; C vs. T: OR, 0.99; 95% CI, 0.75–1.31; P=0.986]. However, a significant association was observed between the pri-miR-34b/c rs4938723 genotypes and clinicopathological characteristics, such a grade, progesterone receptor and human epidermal growth factor receptor 2 status were observed (P<0.05). These findings suggest that the pri-miR-34b/c rs4938723 variant may not be a risk factor for the development of BC. PMID:27347415

  6. Pri-let-7a-1 rs10739971 polymorphism is associated with gastric cancer prognosis and might affect mature let-7a expression

    PubMed Central

    Li, Ying; Xu, Qian; Liu, Jingwei; He, Caiyun; Yuan, Quan; Xing, Chengzhong; Yuan, Yuan

    2016-01-01

    The relationship between the pri-let-7a-1 rs10739971 polymorphism and gastric cancer (GC) risk has been reported. However, the role of this polymorphism in the prognosis of GC remains largely elusive. Sequenom MassARRAY platform method and the polymerase chain reaction (PCR)-restriction fragment length polymorphism were used to investigate pri-let-7a-1 rs10739971 G→A in 334 GC patients. Real-time PCR detected expression of mature let-7a in serum and tissue. Patients with AA or GA+AA genotypes of the pri-let-7a-1 rs10739971 polymorphism demonstrated significantly longer survival time than those with the wild GG genotype. Stratified analysis indicated that survival time was significantly longer in women with AA or GA+AA genotypes and in Borrmann type I/II patients with GA heterozygote or GA+AA genotypes. AA genotype was more frequent in the lymphatic-metastasis-negative subgroup. Serum mature let-7a expression in healthy people with the GA heterozygote and the GA+AA genotype was higher than in those with the GG genotype, and the difference remained significant in the female healthy subgroup. Pri-let-7a-1 rs10739971 polymorphism might be a biomarker for GC prognosis, especially for female and Borrmann type I/II patients. The pri-let-7a-1 rs10739971 polymorphism might affect serum mature let-7a expression, and partly explain the mechanism of the relationship between the pri-let-7a-1 rs10739971 polymorphism and GC survival. PMID:27445488

  7. Identification and Analysis of Genetic Variations in Pri-MiRNAs Expressed Specifically or at a High Level in Sheep Skeletal Muscle

    PubMed Central

    Zhang, Wei; Wang, Limin; Zhou, Ping; Song, Guangchao; Shen, Min; Gan, Shangquan; Shi, Guoqing

    2015-01-01

    MicroRNAs (miRNAs) are key regulators in miRNA-mediated gene regulatory networks and play important roles in many biological processes, such as growth and development of mammals. In this study, we used microarrays to detect 261 miRNAs that are expressed in sheep skeletal muscle. We found 22 miRNAs that showed high levels of expression and equated to 89% of the total miRNA. Genetic variations in these 22 pri-miRNAs were further investigated using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and sequencing. A total of 49 genetic variations, which included 41 single nucleotide polymorphisms (SNPs) and 8 deletions/insertions, were identified in four sheep breeds. Three variations were further researched in a larger sample set, including five sheep breeds with different meat production performances. We found that the genotype and allele frequencies of the CCC deletion/insertion in pri-miR-133a were significantly related to the sheep meat production trait. Finally, cell assays and quantitative reverse transcription PCR (qRT-PCR) were employed to investigate the effect of pri-miRNA genetic variation on the miRNA biogenesis process. The results confirmed that genetic variations can influence miRNA biogenesis and increase or decrease the levels of mature miRNAs, in accordance with the energy and stability change of hair-pin secondary structures. Our findings will help to further the understanding of the functions of genetic variations in sheep pri-miRNAs in skeletal muscle growth and development. PMID:25699993

  8. RecG protein and single-strand DNA exonucleases avoid cell lethality associated with PriA helicase activity in Escherichia coli.

    PubMed

    Rudolph, Christian J; Mahdi, Akeel A; Upton, Amy L; Lloyd, Robert G

    2010-10-01

    Replication of the Escherichia coli chromosome usually initiates at a single origin (oriC) under control of DnaA. Two forks are established and move away in opposite directions. Replication is completed when these meet in a broadly defined terminus area half way around the circular chromosome. RecG appears to consolidate this arrangement by unwinding D-loops and R-loops that PriA might otherwise exploit to initiate replication at other sites. It has been suggested that without RecG such replication generates 3' flaps as the additional forks collide and displace nascent leading strands, providing yet more potential targets for PriA. Here we show that, to stay alive, cells must have either RecG or a 3' single-stranded DNA (ssDNA) exonuclease, which can be exonuclease I, exonuclease VII, or SbcCD. Cells lacking all three nucleases are inviable without RecG. They also need RecA recombinase and a Holliday junction resolvase to survive rapid growth, but SOS induction, although elevated, is not required. Additional requirements for Rep and UvrD are identified and linked with defects in DNA mismatch repair and with the ability to cope with conflicts between replication and transcription, respectively. Eliminating PriA helicase activity removes the requirement for RecG. The data are consistent with RecG and ssDNA exonucleases acting to limit PriA-mediated re-replication of the chromosome and the consequent generation of linear DNA branches that provoke recombination and delay chromosome segregation. PMID:20647503

  9. Zeaxanthin-independent energy quenching and alternative electron sinks cause a decoupling of the relationship between the photochemical reflectance index (PRI) and photosynthesis in an evergreen conifer during spring.

    PubMed

    Fréchette, Emmanuelle; Wong, Christopher Y S; Junker, Laura Verena; Chang, Christine Yao-Yun; Ensminger, Ingo

    2015-12-01

    In evergreen conifers, the winter down-regulation of photosynthesis and its recovery during spring are the result of a reorganization of the chloroplast and adjustments of energy-quenching mechanisms. These phenological changes may remain undetected by remote sensing, as conifers retain green foliage during periods of photosynthetic down-regulation. The aim was to assess if the timing of the spring recovery of photosynthesis and energy-quenching characteristics are accurately monitored by the photochemical reflectance index (PRI) in the evergreen conifer Pinus strobus. The recovery of photosynthesis was studied using chlorophyll fluorescence, leaf gas exchange, leaf spectral reflectance, and photosynthetic pigment measurements. To assess if climate change might affect the recovery of photosynthesis, seedlings were exposed to cold spring conditions or warm spring conditions with elevated temperature. An early spring decoupling of the relationship between photosynthesis and PRI in both treatments was observed. This was caused by differences between the timing of the recovery of photosynthesis and the timing of carotenoid and chlorophyll pool size adjustments which are the main factors controlling PRI during spring. It was also demonstrated that zeaxanthin-independent NPQ mechanisms undetected by PRI further contributed to the early spring decoupling of the PRI-LUE relationship. An important mechanism undetected by PRI seems to involve increased electron transport around photosystem I, which was a significant energy sink during the entire spring transition, particularly in needles exposed to a combination of high light and cold temperatures. PMID:26386258

  10. Assessing Steady-state Fluorescence and PRI from Hyperspectral Proximal Sensing as Early Indicators of Plant Stress: The Case of Ozone Exposure

    PubMed Central

    Meroni, Michele; Rossini, Micol; Picchi, Valentina; Panigada, Cinzia; Cogliati, Sergio; Nali, Cristina; Colombo, Roberto

    2008-01-01

    High spectral resolution spectrometers were used to detect optical signals of ongoing plant stress in potted white clover canopies subjected to ozone fumigation. The case of ozone stress is used in this manuscript as a paradigm of oxidative stress. Steady-state fluorescence (Fs) and the Photochemical Reflectance Index (PRI) were investigated as advanced hyperspectral remote sensing techniques able to sense variations in the excess energy dissipation pathways occurring when photosynthesis declines in plants exposed to a stress agent. Fs and PRI were monitored in control and ozone fumigated canopies during a 21-day experiment together with the traditional Normalized Difference Vegetation Index (NDVI) and physiological measurements commonly employed by physiologists to describe stress development (i.e. net CO2 assimilation, active fluorimetry, chlorophyll concentration and visible injuries). It is shown that remote detection of an ongoing stress through Fs and PRI can be achieved in an early phase, characterized by the decline of photosynthesis. On the contrary, NDVI was able to detect the stress only when damage occurred. These results open up new possibilities for assessment of plant stress by means of hyperspectral remote sensing.

  11. Characterization of Staphylococcus aureus Primosomal DnaD Protein: Highly Conserved C-Terminal Region Is Crucial for ssDNA and PriA Helicase Binding but Not for DnaA Protein-Binding and Self-Tetramerization

    PubMed Central

    Huang, Chien-Chih; Huang, Cheng-Yang

    2016-01-01

    The role of DnaD in the recruitment of replicative helicase has been identified. However, knowledge of the DNA, PriA, and DnaA binding mechanism of this protein for the DnaA- and PriA-directed replication primosome assemblies is limited. We characterized the DNA-binding properties of DnaD from Staphylococcus aureus (SaDnaD) and analyzed its interactions with SaPriA and SaDnaA. The gel filtration chromatography analysis of purified SaDnaD and its deletion mutant proteins (SaDnaD1-195, SaDnaD1-200 and SaDnaD1-204) showed a stable tetramer in solution. This finding indicates that the C-terminal region aa 196–228 is not crucial for SaDnaD oligomerization. SaDnaD forms distinct complexes with ssDNA of different lengths. In fluorescence titrations, SaDnaD bound to ssDNA with a binding-site size of approximately 32 nt. A stable complex of SaDnaD1-195, SaDnaD1-200, and SaDnaD1-204 with ssDNA dT40 was undetectable, indicating that the C-terminal region of SaDnaD (particularly aa 205–228) is crucial for ssDNA binding. The SPR results revealed that SaDnaD1-195 can interact with SaDnaA but not with SaPriA, which may indicate that DnaD has different binding sites for PriA and DnaA. Both SaDnaD and SaDnaDY176A mutant proteins, but not SaDnaD1-195, can significantly stimulate the ATPase activity of SaPriA. Hence, the stimulation effect mainly resulted from direct contact within the protein—protein interaction, not via the DNA—protein interaction. Kinetic studies revealed that the SaDnaD-SaPriA interaction increases the Vmax of the SaPriA ATPase fivefold without significantly affecting the Km. These results indicate that the conserved C-terminal region is crucial for ssDNA and PriA helicase binding, but not for DnaA protein-binding and self-tetramerization. PMID:27304067

  12. Zeaxanthin-independent energy quenching and alternative electron sinks cause a decoupling of the relationship between the photochemical reflectance index (PRI) and photosynthesis in an evergreen conifer during spring

    PubMed Central

    Fréchette, Emmanuelle; Wong, Christopher Y. S.; Junker, Laura Verena; Chang, Christine Yao-Yun; Ensminger, Ingo

    2015-01-01

    In evergreen conifers, the winter down-regulation of photosynthesis and its recovery during spring are the result of a reorganization of the chloroplast and adjustments of energy-quenching mechanisms. These phenological changes may remain undetected by remote sensing, as conifers retain green foliage during periods of photosynthetic down-regulation. The aim was to assess if the timing of the spring recovery of photosynthesis and energy-quenching characteristics are accurately monitored by the photochemical reflectance index (PRI) in the evergreen conifer Pinus strobus. The recovery of photosynthesis was studied using chlorophyll fluorescence, leaf gas exchange, leaf spectral reflectance, and photosynthetic pigment measurements. To assess if climate change might affect the recovery of photosynthesis, seedlings were exposed to cold spring conditions or warm spring conditions with elevated temperature. An early spring decoupling of the relationship between photosynthesis and PRI in both treatments was observed. This was caused by differences between the timing of the recovery of photosynthesis and the timing of carotenoid and chlorophyll pool size adjustments which are the main factors controlling PRI during spring. It was also demonstrated that zeaxanthin-independent NPQ mechanisms undetected by PRI further contributed to the early spring decoupling of the PRI–LUE relationship. An important mechanism undetected by PRI seems to involve increased electron transport around photosystem I, which was a significant energy sink during the entire spring transition, particularly in needles exposed to a combination of high light and cold temperatures. PMID:26386258

  13. Quantitative Analysis of Histidine Decarboxylase Gene (hdcA) Transcription and Histamine Production by Streptococcus thermophilus PRI60 under Conditions Relevant to Cheese Making▿†

    PubMed Central

    Rossi, Franca; Gardini, Fausto; Rizzotti, Lucia; La Gioia, Federica; Tabanelli, Giulia; Torriani, Sandra

    2011-01-01

    This study evaluated the influence of parameters relevant for cheese making on histamine formation by Streptococcus thermophilus. Strains possessing a histidine decarboxylase (hdcA) gene represented 6% of the dairy isolates screened. The most histaminogenic, S. thermophilus PRI60, exhibited in skim milk a high basal level of expression of hdcA, upregulation in the presence of free histidine and salt, and repression after thermization. HdcA activity persisted in cell extracts, indicating that histamine might accumulate after cell lysis in cheese. PMID:21378060

  14. Experimental oxygen potentials of U1-yPryO2± x and thermodynamic assessment of the U-Pr-O system

    DOE PAGESBeta

    McMurray, Jake W.; Silva, Chinthaka M.

    2015-12-09

    Thermogravimetric analysis (TGA) was used to determine the oxygen potentials of fluorite urania-praseodymia (U1-yPryO2± x) solid solutions for y = 0.10 and 0.20 between 1000 and 1500 °C. A thermodynamic assessment of U-Pr-O system was performed using the CALPHAD (CALculation of PHAse Diagrams) method. Furthermore, the models well reproduce the TGA measurements and the computed phase relations are in good agreement with those proposed from an X-ray diffraction investigation.

  15. Experimental oxygen potentials for U1-yPryO2±x and thermodynamic assessment of the U-Pr-O system

    NASA Astrophysics Data System (ADS)

    McMurray, J. W.; Silva, C. M.

    2016-03-01

    Thermogravimetric analysis (TGA) was used to determine the oxygen potentials of fluorite urania-praseodymia (U1-yPryO2±x) solid solutions for y = 0.10 and 0.20 between 1000 and 1500 °C. A thermodynamic assessment of U-Pr-O system was performed using the CALPHAD (CALculation of PHAse Diagrams) method. The models well reproduce the TGA measurements and the computed phase relations are in good agreement with those proposed from an X-ray diffraction investigation.

  16. Agrobacterium rhizogenes pRi8196 T-DNA: mapping and DNA sequence of functions involved in mannopine synthesis and hairy root differentiation.

    PubMed Central

    Hansen, G; Larribe, M; Vaubert, D; Tempé, J; Biermann, B J; Montoya, A L; Chilton, M D; Brevet, J

    1991-01-01

    This paper presents the map and DNA sequence analysis of pRi8196 transferred DNA (T-DNA) genes encoding root-inducing and mannopine synthesis functions. A canonical 24-base-pair border repeat as well as two "pseudoborders" are present at the functional right T-DNA border. To the left of this border are homologs of the mas1' and mas2' genes of TR pRiA4. Next to these are five open reading frames (ORFs) homologous to ORFs 10-14 of TL of pRiA4. ORFs 10-12 (rolA, rolB, and rolC) are less related to their pRiA4 homologs than are the other large ORFs analyzed here. In contrast to T-DNA genes of pRiA4, pRi8196 T-DNA ORFs 11 and 12 (rolB and rolC) are sufficient to induce hairy roots on carrot disks. Images PMID:1909028

  17. Sun-induced Chlorophyll fluorescence and PRI improve remote sensing GPP estimates under varying nutrient availability in a typical Mediterranean savanna ecosystem

    NASA Astrophysics Data System (ADS)

    Perez-Priego, O.; Guan, J.; Rossini, M.; Fava, F.; Wutzler, T.; Moreno, G.; Carvalhais, N.; Carrara, A.; Kolle, O.; Julitta, T.; Schrumpf, M.; Reichstein, M.; Migliavacca, M.

    2015-07-01

    This study investigates the performances of different optical indices to estimate gross primary production (GPP) of herbaceous stratum in a Mediterranean savanna with different Nitrogen (N) and Phosphorous (P) availability. Sun-induced chlorophyll Fluorescence yield computed at 760 nm (Fy760), scaled-photochemical reflectance index (sPRI), MERIS terrestrial-chlorophyll index (MTCI) and Normalized difference vegetation index (NDVI) were computed from near-surface field spectroscopy measurements collected using high spectral resolution spectrometers covering the visible near-infrared regions. GPP was measured using canopy-chambers on the same locations sampled by the spectrometers. We hypothesized that light-use efficiency (LUE) models driven by remote sensing quantities (RSM) can better track changes in GPP caused by nutrient supplies compared to those driven exclusively by meteorological data (MM). Particularly, we compared the performances of different RSM formulations - relying on the use of Fy760 or sPRI as proxy for LUE and NDVI or MTCI as fraction of absorbed photosynthetically active radiation (fAPAR) - with those of classical MM. Results showed significantly higher GPP in the N fertilized experimental plots during the growing period. These differences in GPP disappeared in the drying period when senescence effects masked out potential differences due to plant N content. Consequently, although MTCI was tightly related to plant N content (r2 = 0.86, p < 0.01), it was poorly related to GPP (r2 = 0.45, p < 0.05). On the contrary sPRI and Fy760 correlated well with GPP during the whole measurement period. Results revealed that the relationship between GPP and Fy760 is not unique across treatments but it is affected by N availability. Results from a cross validation analysis showed that MM (AICcv = 127, MEcv = 0.879) outperformed RSM (AICcv = 140, MEcv = 0.8737) when soil moisture was used to constrain the seasonal dynamic of LUE. However, residual analyses

  18. The RdgC protein of Escherichia coli binds DNA and counters a toxic effect of RecFOR in strains lacking the replication restart protein PriA

    PubMed Central

    Moore, Timothy; McGlynn, Peter; Ngo, Hien-Ping; Sharples, Gary J.; Lloyd, Robert G.

    2003-01-01

    PriA protein provides a means to load the DnaB replicative helicase at DNA replication fork and D loop structures, and is therefore a key factor in the rescue of stalled or broken forks and subsequent replication restart. We show that the nucleoid-associated RdgC protein binds non-specifically to single-stranded (ss) DNA and double-stranded DNA. It is also essential for growth of a strain lacking PriA, indicating that it might affect replication fork progression or fork rescue. dnaC suppressors of priA overcome this inviability, especially when RecF, RecO or RecR is inactivated, indicating that RdgC avoids or counters a toxic effect of these proteins. Mutations modifying ssDNA-binding (SSB) protein also negate this toxic effect, suggesting that the toxicity reflects inappropriate loading of RecA on SSB-coated ssDNA, leading to excessive or untimely RecA activity. We suggest that binding of RdgC to DNA limits RecA loading, avoiding problems at replication forks that would otherwise require PriA to promote replication restart. Mutations in RNA polymerase also reduce the toxic effect of RecFOR, providing a further link between DNA replication, transcription and repair. PMID:12554673

  19. The PRY/SPRY/B30.2 Domain of Butyrophilin 1A1 (BTN1A1) Binds to Xanthine Oxidoreductase

    PubMed Central

    Jeong, Jaekwang; Rao, Anita U.; Xu, Jinling; Ogg, Sherry L.; Hathout, Yetrib; Fenselau, Catherine; Mather, Ian H.

    2009-01-01

    Butyrophilin 1A1 (BTN1A1) and xanthine oxidoreductase (XOR) are highly expressed in the lactating mammary gland and are secreted into milk associated with the milk fat globule membrane (MFGM). Ablation of the genes encoding either protein causes severe defects in the secretion of milk lipid droplets, suggesting that the two proteins may function in the same pathway. Therefore, we determined whether BTN1A1 and XOR directly interact using protein binding assays, surface plasmon resonance analysis, and gel filtration. Bovine XOR bound with high affinity in a pH- and salt-sensitive manner (KD = 101 ± 31 nm in 10 mm HEPES, 150 mm NaCl, pH 7.4) to the PRY/SPRY/B30.2 domain in the cytoplasmic region of bovine BTN1A1. Binding was stoichiometric, with one XOR dimer binding to either two BTN1A1 monomers or one dimer. XOR bound to BTN1A1 orthologs from mice, humans, or cows but not to the cytoplasmic domains of the closely related human paralogs, BTN2A1 or BTN3A1, or to the B30.2 domain of human RoRet (TRIM 38), a protein in the TRIM family. Analysis of the protein composition of the MFGM of wild type and BTN1A1 null mice showed that most of the XOR in mice lacking BTN1A1 was released from the MFGM in a soluble form when the milk lipid droplets were disrupted to prepare membrane, compared with wild-type mice, in which most of the XOR remained membrane-bound. Thus BTN1A1 functions in vivo to stabilize the association of XOR with the MFGM by direct interactions through the PRY/SPRY/B30.2 domain. The potential significance of BTN1A1/XOR interactions in the mammary gland and other tissues is discussed. PMID:19531472

  20. Optimization of growth conditions for (La1-yPry)1-x CaxMnO3 thin films on annealed oxide substrates

    NASA Astrophysics Data System (ADS)

    Schaefer, Brian; Grant, Daniel; Biswas, Amlan

    2014-03-01

    Consistent growth of flat, epitaxial thin films is essential for uncovering the unique transport characteristics of rare-earth manganite systems. We have developed pulsed laser deposition growth conditions for (La1-yPry)1-x CaxMnO3 (LPCMO, y = 0.4, 0.5, 0.6) thin films on annealed NdGaO3 (NGO) and SrTiO3 (STO) substrates. The extra annealing step for NGO and STO produces atomically flat substrates with well-defined terraces of unit cell step height. Films grown on these annealed substrates demonstrate better lattice matching compared to films grown on as-received substrates. Consequently, annealing substrates before film growth leads to higher quality thin films with a more controllable thickness. We demonstrate that these optimized growth parameters yield LPCMO thin films that are also atomically flat, as confirmed by atomic force microscopy. We are using these thin films to restrict phase growth to reduced dimensions and to study the origin of thermodynamic phase competition due to first order transitions in manganites. NSF DMR-0804452

  1. A SNP in pri-miR-10a is associated with recurrent spontaneous abortion in a Han-Chinese population

    PubMed Central

    Zhang, Lu; Lv, Xiao-Dan; Su, Xing; Tian, Shi; Liu, Chun-Mei; Ma, Xu; Xia, Hong-Fei

    2016-01-01

    MicroRNA-10a (miR-10a) has a wide range of functions in nearly all mammalian tissues and is involved in the occurrence of many diseases. However, it remains unknown whether miR-10a is associated with human recurrent spontaneous abortion (RSA). In this study, we found that rs3809783 A > T in miR-10a coding region was significantly associated with the increase of the risk of human unexplained RSA (URSA) acquisition in a Han-Chinese population. The T allele of rs3809783 hindered the production of mature miR-10a. A to T substitution in miR-10a rs3809783 repressed cell proliferation and migratory capacity. Further investigation discovered that Bcl-2-interacting mediator (Bim) was the functional target of miR-10a and inversely regulated Bim expression. Dual-luciferase assay indicated that A allele in miR-10a rs3809783 could more effectively suppress Bim expression than T allele. In addition, A to T substitution in miR-10a rs3809783 attenuated the sensibility of cells to progesterone and its antagonist mifepristone. Collectively, our data suggest that rs3809783 A > T in pri-miR-10a may be conductive to the genetic predisposition to RSA by disrupting the production of mature miR-10a and reinforcing the expression of Bim. PMID:26824181

  2. A SNP in pri-miR-10a is associated with recurrent spontaneous abortion in a Han-Chinese population.

    PubMed

    Li, Ying; Wang, Xue-Qin; Zhang, Lu; Lv, Xiao-Dan; Su, Xing; Tian, Shi; Liu, Chun-Mei; Ma, Xu; Xia, Hong-Fei

    2016-02-16

    MicroRNA-10a (miR-10a) has a wide range of functions in nearly all mammalian tissues and is involved in the occurrence of many diseases. However, it remains unknown whether miR-10a is associated with human recurrent spontaneous abortion (RSA). In this study, we found that rs3809783 A > T in miR-10a coding region was significantly associated with the increase of the risk of human unexplained RSA (URSA) acquisition in a Han-Chinese population. The T allele of rs3809783 hindered the production of mature miR-10a. A to T substitution in miR-10a rs3809783 repressed cell proliferation and migratory capacity. Further investigation discovered that Bcl-2-interacting mediator (Bim) was the functional target of miR-10a and inversely regulated Bim expression. Dual-luciferase assay indicated that A allele in miR-10a rs3809783 could more effectively suppress Bim expression than T allele. In addition, A to T substitution in miR-10a rs3809783 attenuated the sensibility of cells to progesterone and its antagonist mifepristone. Collectively, our data suggest that rs3809783 A > T in pri-miR-10a may be conductive to the genetic predisposition to RSA by disrupting the production of mature miR-10a and reinforcing the expression of Bim. PMID:26824181

  3. A Simple and High-Throughput Analysis of Amatoxins and Phallotoxins in Human Plasma, Serum and Urine Using UPLC-MS/MS Combined with PRiME HLB μElution Platform

    PubMed Central

    Zhang, Shuo; Zhao, Yunfeng; Li, Haijiao; Zhou, Shuang; Chen, Dawei; Zhang, Yizhe; Yao, Qunmei; Sun, Chengye

    2016-01-01

    Amatoxins and phallotoxins are toxic cyclopeptides found in the genus Amanita and are among the predominant causes of fatal food poisoning in China. In the treatment of Amanita mushroom poisoning, an early and definite diagnosis is necessary for a successful outcome, which has prompted the development of protocols for the fast and confirmatory determination of amatoxins and phallotoxins in human biological fluids. For this purpose, a simple, rapid and sensitive multiresidue UPLC-MS/MS method for the simultaneous determination of α-amanitin, β-amanitin, γ-amanitin, phalloidin (PHD) and phallacidin (PCD) in human plasma, serum and urine was developed and validated. The diluted plasma, serum and urine samples were directly purified with a novel PRiME technique on a 96-well μElution plate platform, which allowed high-throughput sample processing and low reagent consumption. After purification, a UPLC-MS/MS analysis was performed using positive electrospray ionization (ESI+) in multiple reaction monitoring (MRM) mode. This method fulfilled the requirements of a validation test, with good results for the limit of detection (LOD), lower limit of quantification (LLOQ), accuracy, intra- and inter-assay precision, recovery and matrix effects. All of the analytes were confirmed and quantified in authentic plasma, serum and urine samples obtained from cases of poisoning using this method. Using the PRiME μElution technique for quantification reduces labor and time costs and represents a suitable method for routine toxicological and clinical emergency analysis. PMID:27153089

  4. A Simple and High-Throughput Analysis of Amatoxins and Phallotoxins in Human Plasma, Serum and Urine Using UPLC-MS/MS Combined with PRiME HLB μElution Platform.

    PubMed

    Zhang, Shuo; Zhao, Yunfeng; Li, Haijiao; Zhou, Shuang; Chen, Dawei; Zhang, Yizhe; Yao, Qunmei; Sun, Chengye

    2016-01-01

    Amatoxins and phallotoxins are toxic cyclopeptides found in the genus Amanita and are among the predominant causes of fatal food poisoning in China. In the treatment of Amanita mushroom poisoning, an early and definite diagnosis is necessary for a successful outcome, which has prompted the development of protocols for the fast and confirmatory determination of amatoxins and phallotoxins in human biological fluids. For this purpose, a simple, rapid and sensitive multiresidue UPLC-MS/MS method for the simultaneous determination of α-amanitin, β-amanitin, γ-amanitin, phalloidin (PHD) and phallacidin (PCD) in human plasma, serum and urine was developed and validated. The diluted plasma, serum and urine samples were directly purified with a novel PRiME technique on a 96-well μElution plate platform, which allowed high-throughput sample processing and low reagent consumption. After purification, a UPLC-MS/MS analysis was performed using positive electrospray ionization (ESI+) in multiple reaction monitoring (MRM) mode. This method fulfilled the requirements of a validation test, with good results for the limit of detection (LOD), lower limit of quantification (LLOQ), accuracy, intra- and inter-assay precision, recovery and matrix effects. All of the analytes were confirmed and quantified in authentic plasma, serum and urine samples obtained from cases of poisoning using this method. Using the PRiME μElution technique for quantification reduces labor and time costs and represents a suitable method for routine toxicological and clinical emergency analysis. PMID:27153089

  5. An autoregulatory network between menin and pri-miR-24-1 is required for the processing of its specific modulator miR-24-1 in BON1 cells.

    PubMed

    Luzi, Ettore; Marini, Francesca; Ciuffi, Simone; Galli, Gianna; Brandi, Maria Luisa

    2016-05-24

    Multiple endocrine neoplasia type 1 (MEN1) is a rare hereditary cancer complex syndrome manifesting a variety of endocrine and non-endocrine neoplasms and lesions. MEN1 is characterized by tumours of the parathyroids, of the neuroendocrine cells of the gastroenteropancreatic tract, and of the anterior pituitary. The MEN1 gene, a tumour suppressor gene, encodes the menin protein. Loss of heterozygosity (LOH) at 11q13 is typical of MEN1 tumours in agreement with Knudson's two-hit hypothesis. We previously showed that the MEN1 parathyroid tumorigenesis is under the control of an "incoherent feedback loop" between miR-24-1 and the menin protein that generates a "Gene Regulatory Network" (GRN) that mimics the second hit of Knudson's hypothesis and that could buffer the effect of the stochastic factors that contribute to the onset and progression of this disease. Here we show, in the BON1 cell line derived from lymphnode metastasis of a human carcinoid tumour of the pancreas, that menin binds specifically to the primary RNA sequence pri-miR-24-1 by promoting the miR-24-1 biogenesis. Network simulation showed a new feed-forward loop between menin, microRNA-24-1 and Musashi-1 proteins. This result shows a novel mechanism whereby menin, a RNA-binding protein, facilitates the processing of its specific miRNA by regulating the dynamics of the menin-miR-24 Gene Regulatory Network at the level of pri-miRNA processing. PMID:27098433

  6. Preliminary evidence for association of genetic variants in pri-miR-34b/c and abnormal miR-34c expression with attention deficit and hyperactivity disorder.

    PubMed

    Garcia-Martínez, I; Sánchez-Mora, C; Pagerols, M; Richarte, V; Corrales, M; Fadeuilhe, C; Cormand, B; Casas, M; Ramos-Quiroga, J A; Ribasés, M

    2016-01-01

    Attention deficit and hyperactivity disorder (ADHD) is a prevalent neurodevelopmental disorder characterized by impairment to sustain attention and inability to control impulses and activity level. The etiology of ADHD is complex, with an estimated heritability of 70-80%. Under the hypothesis that alterations in the processing or target binding of microRNAs (miRNAs) may result in functional alterations predisposing to ADHD, we explored whether common polymorphisms potentially affecting miRNA-mediated regulation are involved in this psychiatric disorder. We performed a comprehensive association study focused on 134 miRNAs in 754 ADHD subjects and 766 controls and found association between the miR-34b/c locus and ADHD. Subsequently, we provided preliminary evidence for overexpression of the miR-34c-3p mature form in peripheral blood mononuclear cells of ADHD subjects. Next, we tested the effect on gene expression of single-nucleotide polymorphisms within the ADHD-associated region and found that rs4938923 in the promoter of the pri-miR-34b/c tags cis expression quantitative trait loci for both miR-34b and miR-34c and has an impact on the expression levels of 681 transcripts in trans, including genes previously associated with ADHD. This gene set was enriched for miR-34b/c binding sites, functional categories related to the central nervous system, such as axon guidance or neuron differentiation, and serotonin biosynthesis and signaling canonical pathways. Our results provide preliminary evidence for the contribution to ADHD of a functional variant in the pri-miR-34b/c promoter, possibly through dysregulation of the expression of mature forms of miR-34b and miR-34c and some target genes. These data highlight the importance of abnormal miRNA function as a potential epigenetic mechanism contributing to ADHD. PMID:27576168

  7. Substrate-dependent post-annealing effects on the strain state and electrical transport of epitaxial La5/8-yPryCa3/8MnO3 films

    NASA Astrophysics Data System (ADS)

    Hu, Sixia; Huang, Haoliang; Yang, Yuanjun; Luo, Zhenlin; Yang, Mengmeng; Wang, Haibo; Dong, Yongqi; Hong, Bing; He, Hao; Bao, Jun; Gao, Chen

    2014-06-01

    Large scale electronic phase separation (EPS) between ferromagnetic metallic and charge-ordered insulating phases in La5/8-yPryCa3/8MnO3 (y = 0.3) (LPCMO) is very sensitive to the structural changes. This work investigates the effects of post-annealing on the strain states and electrical transport properties of LPCMO films epitaxially grown on (001)pc SrTiO3 (tensile strain), LaAlO3 (compressive strain) and NdGaO3 (near-zero strain) substrates. Before annealing, all the films are coherent-epitaxial and insulating through the measured temperature range. Obvious change of film lattice is observed during the post-annealing: the in-plane strain in LPCMO/LAO varies from -1.5% to -0.1% while that in LPCMO/STO changes from 1.6% to 1.3%, and the lattice of LPCMO/NGO keeps constant because of the good lattice-match between LPCMO and NGO. Consequently, the varied film strain leads to the emergence of metal-insulator transitions (MIT) and shift of the critical transition temperature in the electrical transport. These results demonstrate that lattice-mismatch combined with post-annealing is an effective approach to tune strain in epitaxial LPCMO films, and thus to control the EPS and MIT in the films.

  8. Are the SSB-Interacting Proteins RecO, RecG, PriA and the DnaB-Interacting Protein Rep Bound to Progressing Replication Forks in Escherichia coli?

    PubMed

    Bentchikou, Esma; Chagneau, Carine; Long, Emilie; Matelot, Mélody; Allemand, Jean-François; Michel, Bénédicte

    2015-01-01

    In all organisms several enzymes that are needed upon replication impediment are targeted to replication forks by interaction with a replication protein. In most cases these proteins interact with the polymerase clamp or with single-stranded DNA binding proteins (SSB). In Escherichia coli an accessory replicative helicase was also shown to interact with the DnaB replicative helicase. Here we have used cytological observation of Venus fluorescent fusion proteins expressed from their endogenous loci in live E. coli cells to determine whether DNA repair and replication restart proteins that interact with a replication protein travel with replication forks. A custom-made microscope that detects active replisome molecules provided that they are present in at least three copies was used. Neither the recombination proteins RecO and RecG, nor the replication accessory helicase Rep are detected specifically in replicating cells in our assay, indicating that either they are not present at progressing replication forks or they are present in less than three copies. The Venus-PriA fusion protein formed foci even in the absence of replication forks, which prevented us from reaching a conclusion. PMID:26244508

  9. Multiple magnetic transitions, dynamical magnetic liquid and magnetic glass in La1-x-yPryCaxMnO3 (x≈0.42, y≈0.40) thin films: A thickness dependent study

    NASA Astrophysics Data System (ADS)

    Agarwal, Vasudha; Kandpal, Lalit M.; Siwach, P. K.; Awana, V. P. S.; Singh, H. K.

    2015-11-01

    The influence of substrate induced strain and its relaxation on the evolution of the multiple magnetic transitions and ensuing modifications in the degree of phase separation, the nature of the dynamical magnetic liquid, the randomly frozen glass and insulator-metal transitions have been investigated in single crystalline La1-x-yPryCaxMnO3 (x≈0.42, y≈0.40) in t~20-140 nm thick films deposited on LaAlO3 (001) substrates. The ferromagnetic (FM) transition temperature (TC) first decreases as the film thickness is increased from t~20 nm to t~60 nm and then increases with increasing film thickness. In contrast the charge ordering (CO), antiferromagnetic (AFM) and glass transition temperatures shift towards higher values with increasing film thickness. The field cooled cooling (FCC) and field cooled warming (FCW) magnetization (M-T) of films having t≥60 nm shows pronounced hysteresis and ΔTC=TCFCW-TCFCC decreases concomitantly from 46 K to 35 K as the thickness increases from ~60 to ~140 nm. The thinnest film shows insulator to metal transitions (IMT) only at magnetic field H>40 kOe. Films with t≥TC show sharp hysteretic IMT, with ΔTIM=TIMW-TIMC decreasing from ~70 K to ~50 K as the thickness increases from ~60 nm to ~140 nm. Such strong hysteresis is a characteristic of first order phase transition and also a signature of magnetic liquid like phase created by the magnetic frustration created by the delicate balance between FM and AFM/CO phases. The H induced AFM/CO to FM transition reduces ΔTIM and at higher fields the phase transition appears akin to the second order. The observed difference in the magnetic and transport properties have been explained in terms of the substrate induced strain at lower film thickness and its relaxation at higher thickness.

  10. Impact of nanostructuring on the magnetic and magnetocaloric properties of microscale phase-separated La5/8–yPryCa3/8MnO₃ manganites

    DOE PAGESBeta

    Bingham, N. S.; Lampen, P.; Phan, M. H.; Hoang, T. D.; Chinh, H. D.; Zhang, C. L.; Cheong, S. W.; Srikanth, H.

    2012-08-16

    Bulk manganites of the form La5/8–yPryCa3/8MnO₃ (LPCMO) exhibit a complex phase diagram due to coexisting charge-ordered antiferromagnetic (CO/AFM), charge-disordered paramagnetic (PM), and ferromagnetic (FM) phases. Because phase separation in LPCMO occurs on the microscale, reducing particle size to below this characteristic length is expected to have a strong impact on the magnetic properties of the system. Through a comparative study of the magnetic and magnetocaloric properties of single-crystalline (bulk) and nanocrystalline LPCMO (y=3/8) we show that the AFM, CO, and FM transitions seen in the single crystal can also be observed in the large particle sizes (400 and 150 nm),more » while only a single PM to FM transition is found for the small particles (55 nm). Magnetic and magnetocaloric measurements reveal that decreasing particle size affects the balance of competing phases in LPCMO and narrows the range of fields over which PM, FM, and CO phases coexist. The FM volume fraction increases with size reduction, until CO is suppressed below some critical size, ~100 nm. With size reduction, the saturation magnetization and field sensitivity first increase as long-range CO is inhibited, then decrease as surface effects become increasingly important. The trend that the FM phase is stabilized on the nanoscale is contrasted with the stabilization of the charge-disordered PM phase occurring on the microscale, demonstrating that in terms of the characteristic phase separation length, a few microns and several hundred nanometers represent very different regimes in LPCMO.« less

  11. Modeling of colossal magnetoresistance in La0.67Ca0.33MnO3/Pr0.67Ca0.33MnO3 superlattices: Comparison with individual (La1-yPry)0.67Ca0.33MnO3 films

    NASA Astrophysics Data System (ADS)

    Hühn, S.; Jungbauer, M.; Michelmann, M.; Massel, F.; Koeth, F.; Ballani, C.; Moshnyaga, V.

    2013-05-01

    Colossal magnetoresistance (CMR) and nm-scale electronic inhomogeneity close to the first order phase transition in perovskite manganites, e.g., (La1-yPry)0.67Ca0.33MnO3 still remain a puzzling phenomenon. We experimentally model a metal-insulator phase coexistence by growing a short period (LCMOn/PCMOn)m superlattices (SLs) with the same thickness for both components. CMR effect was studied as a function of the individual layer thickness n = 2-8 and then compared with chemically homogeneous (La1-yPry)0.67Ca0.33MnO3 LPCMO films. We show that SLs can be superimposed in the phase diagram of LPCMO. The results also point out the importance of the nm-scale electronic rather than chemical separation for realization of the CMR effect as well as limits the lowest boundary for the thickness of an individual manganite material to n ˜4u.c.

  12. Canopy level chlorophyll flouresence and PRI in a cornfield

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determining the health and vigor of vegetation using high spectral resolution remote sensing techniques is a critical component in monitoring productivity from both natural and managed ecosystems and their feedbacks to climate. Two spectrally based indices now used in field studies to assess whether...

  13. Prying the Gates Wide Open: Academic Freedom and Gender Equality at Brown University, 1974-1977

    ERIC Educational Resources Information Center

    Porwancher, Andrew

    2013-01-01

    In 1974, Brown University's Department of Anthropology denied tenure to assistant professor Louise Lamphere. Convinced that her dismissal was the product of sex discrimination, Lamphere filed suit against Brown. Lamphere and three other female scholars who joined her suit successfully pressed Brown into an out-of-court settlement in 1977.…

  14. Ca-Pri a Cellular Automata Phenomenological Research Investigation: Simulation Results

    NASA Astrophysics Data System (ADS)

    Iannone, G.; Troisi, A.

    2013-05-01

    Following the introduction of a phenomenological cellular automata (CA) model capable to reproduce city growth and urban sprawl, we develop a toy model simulation considering a realistic framework. The main characteristic of our approach is an evolution algorithm based on inhabitants preferences. The control of grown cells is obtained by means of suitable functions which depend on the initial condition of the simulation. New born urban settlements are achieved by means of a logistic evolution of the urban pattern while urban sprawl is controlled by means of the population evolution function. In order to compare model results with a realistic urban framework we have considered, as the area of study, the island of Capri (Italy) in the Mediterranean Sea. Two different phases of the urban evolution on the island have been taken into account: a new born initial growth as induced by geographic suitability and the simulation of urban spread after 1943 induced by the population evolution after this date.

  15. Pushing, Pulling, and Prying: Renewing Senior Faculty Performance through College Dean Efforts

    ERIC Educational Resources Information Center

    Miller, Michael T.; Newman, Richard E.

    2011-01-01

    The quality of college faculty members is directly linked to the institutional experience that students encounter, and as such, administrators and leaders are deeply concerned about the productivity, professionalism, and ability of their faculty. One result has been an extreme investment in faculty development and renewal activities, including…

  16. Introns of plant pri-miRNAs enhance miRNA biogenesis

    PubMed Central

    Bielewicz, Dawid; Kalak, Malgorzata; Kalyna, Maria; Windels, David; Barta, Andrea; Vazquez, Franck; Szweykowska-Kulinska, Zofia; Jarmolowski, Artur

    2013-01-01

    Plant MIR genes are independent transcription units that encode long primary miRNA precursors, which usually contain introns. For two miRNA genes, MIR163 and MIR161, we show that introns are crucial for the accumulation of proper levels of mature miRNA. Removal of the intron in both cases led to a drop-off in the level of mature miRNAs. We demonstrate that the stimulating effects of the intron mostly reside in the 5′ss rather than on a genuine splicing event. Our findings are biologically significant as the presence of functional splice sites in the MIR163 gene appears mandatory for pathogen-triggered accumulation of miR163 and proper regulation of at least one of its targets. PMID:23681439

  17. The Politics of Parental Involvement: How Opportunity Hoarding and Prying Shape Educational Opportunity

    ERIC Educational Resources Information Center

    Lyken-Segosebe, Dawn; Hinz, Serena E.

    2015-01-01

    As more state legislatures join the debate on school-choice and parent-trigger legislation, their discussions draw attention to an evolving landscape outside school walls where parental action shapes educational opportunity. Parents wield their political, social, economic, and cultural capital to secure the best educational outcomes for their…

  18. Directional hyperspectral observations to detect plant stress with the PRI and SIF in a cornfield

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We examined the impact of drought stress and temperature on plant hyperspectral, fluorescence, and photosynthetic responses during the 2012 growing season at an experimental USDA (United States Department of Agriculture) cornfield in Beltsville, MD USA. The manipulations included 4 nitrogen (N) appl...

  19. Fearing Prying U.S. Eyes, Canada's Colleges Crack Down On Computing

    ERIC Educational Resources Information Center

    Carnevale, Dan

    2007-01-01

    The USA Patriot Act is having far-reaching effects on the kinds of data that wind up on some academics' computers in Canada. Canadian colleges, responding to provincial laws passed in reaction to the Patriot Act, are preventing professors from entering the United States with students' private data on their laptops and limiting the locations of…

  20. Sensor4PRI: A Sensor Platform for the Protection of Railway Infrastructures

    PubMed Central

    Cañete, Eduardo; Chen, Jaime; Díaz, Manuel; Llopis, Luis; Rubio, Bartolomé

    2015-01-01

    Wireless Sensor Networks constitute pervasive and distributed computing systems and are potentially one of the most important technologies of this century. They have been specifically identified as a good candidate to become an integral part of the protection of critical infrastructures. In this paper we focus on railway infrastructure protection and we present the details of a sensor platform designed to be integrated into a slab track system in order to carry out both installation and maintenance monitoring activities. In the installation phase, the platform helps operators to install the slab tracks in the right position. In the maintenance phase, the platform collects information about the structural health and behavior of the infrastructure when a train travels along it and relays the readings to a base station. The base station uses trains as data mules to upload the information to the internet. The use of a train as a data mule is especially suitable for collecting information from remote or inaccessible places which do not have a direct connection to the internet and require less network infrastructure. The overall aim of the system is to deploy a permanent economically viable monitoring system to improve the safety of railway infrastructures. PMID:25734648

  1. 7 CFR 14.6 - Criteria for determining the pri- mary purpose of payments with respect to potential exclusion...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... income. (a) Soil conservation. (1) Payments shall be considered to be made primarily for the purpose of soil conservation if they are intended to finance activities, measures, or practices to reduce soil deterioration. (2) Soil deterioration refers to impairments of the physical or chemical properties of soil...

  2. A Multimethod Assessment of Juvenile Psychopathy: Comparing the Predictive Utility of the PCL:YV, YPI, and NEO PRI

    PubMed Central

    Cauffman, Elizabeth; Kimonis, Eva R.; Dmitrieva, Julia; Monahan, Kathryn C.

    2009-01-01

    The current study compares 3 distinct approaches for measuring juvenile psychopathy and their utility for predicting short- and long-term recidivism among a sample of 1,170 serious male juvenile offenders. The assessment approaches compared a clinical interview method (the Psychopathy Checklist: Youth Version [PCL:YV]; Forth, Kosson, & Hare, 2003), a new self-report measure (the Youth Psychopathic Traits Inventory; Andershed, Kerr, Stattin, & Levander, 2002), and a personality-based approach (the NEO Psychopathy Resemblance Index; Lynam & Widiger, 2007). Results indicate a modest overlap between the 3 measures (rs = .26–.36); however, youths were often identified as psychopathic by 1 measure but not by others. Measures were weakly correlated with reoffending during subsequent 6- and 12-month periods. Findings suggest that although such scores may be useful indicators of the need for heightened monitoring in the short term, care should be taken when making predictions about long-term recidivism among adolescents. Moreover, the lack of long-term predictive power for the PCL:YV and the inconsistent psychopathy designations obtained with different measures raise serious questions about the use of such measures as the basis for legal or clinical treatment decisions. PMID:19947787

  3. Limited access to HIV prevention in French prisons (ANRS PRI2DE): implications for public health and drug policy

    PubMed Central

    2011-01-01

    Background Overpopulation, poor hygiene and disease prevention conditions in prisons are major structural determinants of increased infectious risk within prison settings but evidence-based national and WHO guidelines provide clear indications on how to reduce this risk. We sought to estimate the level of infectious risk by measuring how French prisons adhere to national and WHO guidelines. Methods A nationwide survey targeting the heads of medical (all French prisons) and psychiatric (26 French prisons) units was conducted using a postal questionnaire and a phone interview mainly focusing on access to prevention interventions, i.e. bleach, opioid substitution treatment (OST), HBV vaccination and post-exposure prophylaxis (PEP) for French prisoners. Two scores were built reflecting adherence to national and WHO international guidelines, ranging from 0 (no adherence) to 10 (maximum adherence) and 0 to 9 respectively. Results A majority (N = 113 (66%)) of the 171 prisons answered the questionnaires, representing 74% coverage (46,786 prisoners) of the French prison population: 108 were medical units and 12 were psychiatric units. Inmate access to prevention was poor. The median[IQR] score measuring adherence to national guidelines was quite low (4.5[2.5; 5.5]) but adherence to WHO guidelines was even lower 2.5[1.5; 3.5]; PEP was absent despite reported risky practices. Unsuitable OST delivery practices were frequently observed. Conclusions A wide gap exists between HIV prevention policies and their application in prisons. Similar assessments in other countries may be needed to guide a global policy reform in prison settings. Adequate funding together with innovative interventions able to remove structural and ideological barriers to HIV prevention are now needed to motivate those in charge of prison health, to improve their working environment and to relieve French prisoners from their currently debilitating conditions. PMID:21619573

  4. A Multimethod Assessment of Juvenile Psychopathy: Comparing the Predictive Utility of the PCL:YV, YPI, and NEO PRI

    ERIC Educational Resources Information Center

    Cauffman, Elizabeth; Kimonis, Eva R.; Dmitrieva, Julia; Monahan, Kathryn C.

    2009-01-01

    The current study compares 3 distinct approaches for measuring juvenile psychopathy and their utility for predicting short- and long-term recidivism among a sample of 1,170 serious male juvenile offenders. The assessment approaches compared a clinical interview method (the Psychopathy Checklist: Youth Version [PCL:YV]; Forth, Kosson, & Hare,…

  5. 7 CFR 14.6 - Criteria for determining the pri- mary purpose of payments with respect to potential exclusion...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... the productive capacity of the soil are forms of soil deterioration. (b) Water conservation. (1) Water conservation includes actions that, for a given level of water supply, reduce the demand for or use of water by... be made primarily for the purpose of water conservation if they are intended to finance...

  6. The Long, the Short, and the Unstructured: A Unifying Model of miRNA Biogenesis.

    PubMed

    Denzler, Rémy; Stoffel, Markus

    2015-10-01

    In this issue, Fang and Bartel (2015) report the identification of novel sequence and structural features of human pri-miRNAs, which--together with previously identified sequence motifs--define a unifying model of mammalian pri-miRNAs and advances the de novo design of artificial pri-miRNAs. PMID:26431024

  7. On function classes related pertaining to strong approximation of double Fourier series

    NASA Astrophysics Data System (ADS)

    Baituyakova, Zhuldyz

    2015-09-01

    The investigation of embedding of function classes began a long time ago. After Alexits [1], Leindler [2], and Gogoladze[3] investigated estimates of strong approximation by Fourier series in 1965, G. Freud[4] raised the corresponding saturation problem in 1969. The list of the authors dealing with embedding problems partly is also very long. It suffices to mention some names: V. G. Krotov, W. Lenski, S. M. Mazhar, J. Nemeth, E. M. Nikisin, K. I. Oskolkov, G. Sunouchi, J. Szabados, R. Taberski and V. Totik. Study on this topic has since been carried on over a decade, but it seems that most of the results obtained are limited to the case of one dimension. In this paper, embedding results are considered which arise in the strong approximation by double Fourier series. We prove theorem on the interrelation between the classes Wr1,r2HS,M ω and H(λ, p, r1, r2, ω(δ1, δ2)), in the one-dimensional case proved by L. Leindler.

  8. Antiproliferative Activity and in Vivo Toxicity of Double-Point Modified Analogs of 1,25-Dihydroxyergocalciferol

    PubMed Central

    Trynda, Justyna; Turlej, Eliza; Milczarek, Magdalena; Pietraszek, Anita; Chodyński, Michał; Kutner, Andrzej; Wietrzyk, Joanna

    2015-01-01

    Analogs of 1,25-dihydroxyergocalciferol, modified in the side-chain and in the A-ring, were tested for their antiproliferative activity against a series of human cancer cell lines in vitro and in vivo toxicity. The proliferation inhibition caused by the analogs was higher than that of the parent compounds, while the toxicity, measured as the serum calcium level, was lower. All analogs were able to induce, in HL-60 and MV4-11 leukemic cells, G0/G1 cell cycle arrest and differentiation expressed as morphological signs typical for monocytes. The analogs also induced the expression of CD11b and/or CD14 cell-differentiation markers. The most potent analogs, PRI-5105, PRI-5106, PRI-5201 and PRI-5202, were also able to induce vitamin D receptor (VDR) protein expression, mainly in the cytoplasmic fraction of HL-60 or MV4-11 cells. The most active analogs were the 19-nor ones with an extended and rigidified side-chain (PRI-5201 and PRI-5202), as in the former analogs PRI-1906 and PRI-1907. Epimerization at C-24 (PRI-5101) or introduction of an additional hydroxyl at C-23 (PRI-5104) reduced the toxicity of the analog with retained antiproliferative activity. PMID:26492238

  9. DGCR8 recognizes primary transcripts of microRNAs through highly cooperative binding and formation of higher-order structures

    PubMed Central

    Faller, Michael; Toso, Daniel; Matsunaga, Michio; Atanasov, Ivo; Senturia, Rachel; Chen, Yanqiu; Zhou, Z. Hong; Guo, Feng

    2010-01-01

    DiGeorge critical region 8 (DGCR8) is essential for maturation of microRNAs (miRNAs) in animals. In the cleavage of primary transcripts of miRNAs (pri-miRNAs) by the Drosha nuclease, the DGCR8 protein directly binds and recognizes pri-miRNAs through a mechanism currently controversial. Our previous data suggest that DGCR8 trimerizes upon cooperative binding to pri-mir-30a. However, a separate study proposed a model in which a DGCR8 molecule contacts one or two pri-miRNA molecules using its two double-stranded RNA binding domains. Here, we extensively characterized the interaction between DGCR8 and pri-miRNAs using biochemical and structural methods. First, a strong correlation was observed between the association of DGCR8 with pri-mir-30a and the rate of pri-miRNA processing in vitro. Second, we show that the high binding cooperativity allows DGCR8 to distinguish pri-miRNAs from a nonspecific competitor with subtle differences in dissociation constants. The highly cooperative binding of DGCR8 to a pri-miRNA is mediated by the formation of higher-order structures, most likely a trimer of DGCR8 dimers, on the pri-miRNA. These properties are not limited to its interaction with pri-mir-30a. Furthermore, the amphipathic C-terminal helix of DGCR8 is important both for trimerization of DGCR8 on pri-miRNAs and for the cleavage of pri-miRNAs by Drosha. Finally, our three-dimensional model from electron tomography analysis of the negatively stained DGCR8–pri-mir-30a complex directly supports the trimerization model. Our study provides a molecular basis for recognition of pri-miRNAs by DGCR8. We further propose that the higher-order structures of the DGCR8–pri-miRNA complexes trigger the cleavage of pri-miRNAs by Drosha. PMID:20558544

  10. Targeting Acetylcholinesterase to Membrane Rafts

    PubMed Central

    Xie, Heidi Q.; Liang, Dong; Leung, K. Wing; Chen, Vicky P.; Zhu, Kevin Y.; Chan, Wallace K. B.; Choi, Roy C. Y.; Massoulié, Jean; Tsim, Karl W. K.

    2010-01-01

    In the mammalian brain, acetylcholinesterase (AChE) is anchored in cell membranes by a transmembrane protein PRiMA (proline-rich membrane anchor). We present evidence that at least part of the PRiMA-linked AChE is integrated in membrane microdomains called rafts. A significant proportion of PRiMA-linked AChE tetramers from rat brain was recovered in raft fractions; this proportion was markedly higher at low rather than at high concentrations of cold Triton X-100. The detergent-resistant fraction increased during brain development. In NG108-15 neuroblastoma cells transfected with cDNAs encoding AChET and PRiMA, PRiMA-linked G4 AChE was found in membrane rafts and showed the same sensitivity to cold Triton X-100 extraction as in the brain. The association of PRiMA-linked AChE with rafts was weaker than that of glycosylphosphatidylinositol-anchored G2 AChE or G4 QN-HC-linked AChE. It was found to depend on the presence of a cholesterol-binding motif, called CRAC (cholesterol recognition/interaction amino acid consensus), located at the junction of transmembrane and cytoplasmic domains of both PRiMA I and II isoforms. The cytoplasmic domain of PRiMA, which differs between PRiMA I and PRiMA II, appeared to play some role in stabilizing the raft localization of G4 AChE, because the Triton X-100-resistant fraction was smaller with the shorter PRiMA II isoform than that with the longer PRiMA I isoform. PMID:20147288

  11. Frequency and fate of microRNA editing in human brain

    PubMed Central

    Kawahara, Yukio; Megraw, Molly; Kreider, Edward; Iizasa, Hisashi; Valente, Louis; Hatzigeorgiou, Artemis G.; Nishikura, Kazuko

    2008-01-01

    Primary transcripts of certain microRNA (miRNA) genes (pri-miRNAs) are subject to RNA editing that converts adenosine to inosine (A→I RNA editing). However, the frequency of the pri-miRNA editing and the fate of edited pri-miRNAs remain largely to be determined. Examination of already known pri-miRNA editing sites indicated that adenosine residues of the UAG triplet sequence might be edited more frequently. In the present study, therefore, we conducted a large-scale survey of human pri-miRNAs containing the UAG triplet sequence. By direct sequencing of RT–PCR products corresponding to pri-miRNAs, we examined 209 pri-miRNAs and identified 43 UAG and also 43 non-UAG editing sites in 47 pri-miRNAs, which were highly edited in human brain. In vitro miRNA processing assay using recombinant Drosha-DGCR8 and Dicer-TRBP (the human immuno deficiency virus transactivating response RNA-binding protein) complexes revealed that a majority of pri-miRNA editing is likely to interfere with the miRNA processing steps. In addition, four new edited miRNAs with altered seed sequences were identified by targeted cloning and sequencing of the miRNAs that would be processed from edited pri-miRNAs. Our studies predict that ∼16% of human pri-miRNAs are subject to A→I editing and, thus, miRNA editing could have a large impact on the miRNA-mediated gene silencing. PMID:18684997

  12. The NF90-NF45 Complex Functions as a Negative Regulator in the MicroRNA Processing Pathway▿ †

    PubMed Central

    Sakamoto, Shuji; Aoki, Kazuma; Higuchi, Takuma; Todaka, Hiroshi; Morisawa, Keiko; Tamaki, Nobuyuki; Hatano, Etsuro; Fukushima, Atsuki; Taniguchi, Taketoshi; Agata, Yasutoshi

    2009-01-01

    The positive regulatory machinery in the microRNA (miRNA) processing pathway is relatively well characterized, but negative regulation of the pathway is largely unknown. Here we show that a complex of nuclear factor 90 (NF90) and NF45 proteins functions as a negative regulator in miRNA biogenesis. Primary miRNA (pri-miRNA) processing into precursor miRNA (pre-miRNA) was inhibited by overexpression of the NF90 and NF45 proteins, and considerable amounts of pri-miRNAs accumulated in cells coexpressing NF90 and NF45. Treatment of cells overexpressing NF90 and NF45 with an RNA polymerase II inhibitor, α-amanitin, did not reduce the amounts of pri-miRNAs, suggesting that the accumulation of pri-miRNAs is not due to transcriptional activation. In addition, the NF90 and NF45 complex was not found to interact with the Microprocessor complex, which is a processing factor of pri-miRNAs, but was found to bind endogenous pri-miRNAs. NF90-NF45 exhibited higher binding activity for pri-let-7a than pri-miR-21. Of note, depletion of NF90 caused a reduction of pri-let-7a and an increase of mature let-7a miRNA, which has a potent antiproliferative activity, and caused growth suppression of transformed cells. These findings suggest that the association of the NF90-NF45 complex with pri-miRNAs impairs access of the Microprocessor complex to the pri-miRNAs, resulting in a reduction of mature miRNA production. PMID:19398578

  13. In-vitro and in-vivo evaluation of the anticancer activity of diruthenium-2, a new trithiolato arene ruthenium complex [(η6-p-MeC6H4Pri)2Ru2(μ-S-p-C6H4OH)3]Cl.

    PubMed

    Muthná, Darina; Tomšík, Pavel; Havelek, Radim; Köhlerová, Renata; Kasilingam, Vidhya; Čermáková, Eva; Stíbal, David; Řezáčová, Martina; Süss-Fink, Georg

    2016-08-01

    In the present study, we investigated the anticancer action of the trithiolato arene ruthenium complex, [(η-p-MeC6H4Pr)2Ru2(μ-S-p-C6H4OH)3]Cl, named diruthenium-2, both in vitro and in vivo. The mechanism of antiproliferative, cytotoxic, and DNA-damaging activity, and the effect on expressions of cell cycle regulatory proteins were investigated using a WST-1-based proliferation assay, lactate dehydrogenase leakage assay, comet assay, flow cytometry, and western blot analysis. In-vivo anticancer activity was evaluated using Ehrlich tumor-bearing NMRI mice. Diruthenium-2 inhibited the growth of all cancer cell lines used, the most sensitive being gastric (AGS), breast cancer (BT-549, MCF-7, MDA-MB-231), and leukemic (HL-60, MOLT-4) cells. In MCF-7 cells, it caused a G1/S cell cycle arrest, along with an increase in the expression of protein p21 and cyclin B1. We also observed increased levels of MRN complex proteins, which, together with the results from the comet assay, indicate the formation of DNA double-strand breaks. In tumor-bearing mice, diruthenium-2 at doses of 3 and 5 mg/kg inhibits the growth of solid Ehrlich tumor, although weaker than cisplatin. However, it did not prolong the post-therapeutic survival. Our results suggest the in-vitro potential of diruthenium-2 should be further evaluated in studies using other in-vivo models. PMID:27187018

  14. A Hand-Off Mechanism for Primosome Assembly in Replication Restart

    SciTech Connect

    Lopper, Matthew; Boonsombat, Ruethairat; Sandler, Steven J.; Keck, James L.

    2008-11-12

    Collapsed DNA replication forks must be reactivated through origin-independent reloading of the replication machinery (replisome) to ensure complete duplication of cellular genomes. In E. coli, the PriA-dependent pathway is the major replication restart mechanism and requires primosome proteins PriA, PriB, and DnaT for replisome reloading. However, the molecular mechanisms that regulate origin-independent replisome loading are not fully understood. Here, we demonstrate that assembly of primosome protein complexes represents a key regulatory mechanism, as inherently weak PriA-PriB and PriB-DnaT interactions are strongly stimulated by single-stranded DNA. Furthermore, the binding site on PriB for single-stranded DNA partially overlaps the binding sites for PriA and DnaT, suggesting a dynamic primosome assembly process in which single-stranded DNA is handed off from one primosome protein to another as a repaired replication fork is reactivated. This model helps explain how origin-independent initiation of DNA replication is restricted to repaired replication forks, preventing overreplication of the genome.

  15. Meta-Analysis of the Effect of Practical Reasoning Instruction on Student Outcome in Home Economics Education in Korea

    ERIC Educational Resources Information Center

    Yu, Nan Sook

    2012-01-01

    This meta-analysis reviewed the effect of practical reasoning instruction (PRI) on student outcome in Home Economics education in Korea. In this meta-analysis, 25 studies with 35 effect sizes were analyzed. The results of this review indicated that PRI is more effective than traditional instruction on student outcomes. A medium and significant…

  16. Peeking inside the "Black Box" of the Flynn Effect: Evidence from Three Wechsler Instruments

    ERIC Educational Resources Information Center

    Zhou, Xiaobin; Zhu, Jianjun; Weiss, Lawrence G.

    2010-01-01

    This study investigated the Wechsler Performance IQ (PIQ) or Perceptual Reasoning Index (PRI)/ Perceptual Organization Index (POI) change over time and its relation to ability levels. PIQ or PRI/ POI was analyzed because of the known sensitivity of nonverbal scales to the Flynn effect. Scores were analyzed using two methods. First, analysis of…

  17. Biological Evaluation of Double Point Modified Analogues of 1,25-Dihydroxyvitamin D₂ as Potential Anti-Leukemic Agents.

    PubMed

    Corcoran, Aoife; Nadkarni, Sharmin; Yasuda, Kaori; Sakaki, Toshiyuki; Brown, Geoffrey; Kutner, Andrzej; Marcinkowska, Ewa

    2016-01-01

    Structurally similar double-point modified analogues of 1,25-dihydroxyvitamin D₂ (1,25D₂) were screened in vitro for their pro-differentiating activity against the promyeloid cell line HL60. Their affinities towards human full length vitamin D receptor (VDR) and metabolic stability against human vitamin D 24-hydroxylase (CYP24A1) were also tested. The analogues (PRI-1730, PRI-1731, PRI-1732, PRI-1733 and PRI-1734) contained 5,6-trans modification of the A-ring and of the triene system, additional hydroxyl or unsaturation at C-22 in the side chain and reversed absolute configuration (24-epi) at C-24 of 1,25D₂. As presented in this paper, introduction of selected structural modifications simultaneously in two distinct parts of the vitamin D molecule resulted in a divergent group of analogues. Analogues showed lower VDR affinity in comparison to that of the parent hormones, 1,25D₂ and 1,25D₃, and they caused effective HL60 cell differentiation only at high concentrations of 100 nM and above. Unexpectedly, introducing of a 5,6-trans modification combined with C-22 hydroxyl and 24-epi configuration switched off entirely the cell differentiation activity of the analogue (PRI-1734). However, this analogue remained a moderate substrate for CYP24A1, as it was metabolized at 22%, compared to 35% for 1,25D₂. Other analogues from this series were either less (12% for PRI-1731 and PRI-1733) or more (52% for PRI-1732) resistant to the enzymatic deactivation. Although the inactive analogue PRI-1734 failed to show VDR antagonism, when tested in HL60 cells, its structure might be a good starting point for our design of a vitamin D antagonist. PMID:26840307

  18. Biological Evaluation of Double Point Modified Analogues of 1,25-Dihydroxyvitamin D2 as Potential Anti-Leukemic Agents

    PubMed Central

    Corcoran, Aoife; Nadkarni, Sharmin; Yasuda, Kaori; Sakaki, Toshiyuki; Brown, Geoffrey; Kutner, Andrzej; Marcinkowska, Ewa

    2016-01-01

    Structurally similar double-point modified analogues of 1,25-dihydroxyvitamin D2 (1,25D2) were screened in vitro for their pro-differentiating activity against the promyeloid cell line HL60. Their affinities towards human full length vitamin D receptor (VDR) and metabolic stability against human vitamin D 24-hydroxylase (CYP24A1) were also tested. The analogues (PRI-1730, PRI-1731, PRI-1732, PRI-1733 and PRI-1734) contained 5,6-trans modification of the A-ring and of the triene system, additional hydroxyl or unsaturation at C-22 in the side chain and reversed absolute configuration (24-epi) at C-24 of 1,25D2. As presented in this paper, introduction of selected structural modifications simultaneously in two distinct parts of the vitamin D molecule resulted in a divergent group of analogues. Analogues showed lower VDR affinity in comparison to that of the parent hormones, 1,25D2 and 1,25D3, and they caused effective HL60 cell differentiation only at high concentrations of 100 nM and above. Unexpectedly, introducing of a 5,6-trans modification combined with C-22 hydroxyl and 24-epi configuration switched off entirely the cell differentiation activity of the analogue (PRI-1734). However, this analogue remained a moderate substrate for CYP24A1, as it was metabolized at 22%, compared to 35% for 1,25D2. Other analogues from this series were either less (12% for PRI-1731 and PRI-1733) or more (52% for PRI-1732) resistant to the enzymatic deactivation. Although the inactive analogue PRI-1734 failed to show VDR antagonism, when tested in HL60 cells, its structure might be a good starting point for our design of a vitamin D antagonist. PMID:26840307

  19. The Effect of Analogues of 1α,25-Dihydroxyvitamin D₂ on the Regrowth and Gene Expression of Human Colon Cancer Cells Refractory to 5-Fluorouracil.

    PubMed

    Neska, Jacek; Swoboda, Paweł; Przybyszewska, Małgorzata; Kotlarz, Agnieszka; Bolla, Narasimha Rao; Miłoszewska, Joanna; Grygorowicz, Monika Anna; Kutner, Andrzej; Markowicz, Sergiusz

    2016-01-01

    This study aimed to evaluate the capacity of hypocalcemic analogues of 1α,25-dihydroxyvitamin D₂ (1,25D2) and 1α,25-dihydroxyvitamin D₃ (1,25D3) to inhibit regrowth and regulate the stemness-related gene expression in colon cancer cells undergoing renewal after exposure to 5-fluorouracil (5-FU). All of the tested analogues of 1,25D2 equally potently decreased the clonogenicity and the proliferative activity of HT-29 cells which survived the exposure to 5-FU, but differently regulated gene expression of these cells during their renewal. 1,25D2 and analogues (PRI-1907 and PRI-1917), as well as 1,25D3 and analogue PRI-2191, decreased the relative expression level of several stemness-related genes, such as NANOG, OCT3/4, PROM1, SOX2, ALDHA1, CXCR4, in HT-29/5-FU cells during their renewal, in comparison to untreated HT-29/5-FU cells. The other 1,25D2 analogues (PRI-1906 and PRI-1916) were not capable of downregulating the expression of these stemness-related genes as the analogues PRI-1907 and PRI-1917 did. All of the tested vitamin D analogues upregulated CDH1, the gene encoding E-cadherin associated with epithelial phenotype. Out of the series of analogues studied, side-chain branched analogues of 1,25D2 (PRI-1907, PRI-1917) and the analogue of 1,25D3 (PRI-2191) might be used to target cancer cells with stem-like phenotypes that survive conventional chemotherapy. PMID:27314328

  20. The Effect of Analogues of 1α,25-Dihydroxyvitamin D2 on the Regrowth and Gene Expression of Human Colon Cancer Cells Refractory to 5-Fluorouracil

    PubMed Central

    Neska, Jacek; Swoboda, Paweł; Przybyszewska, Małgorzata; Kotlarz, Agnieszka; Bolla, Narasimha Rao; Miłoszewska, Joanna; Grygorowicz, Monika Anna; Kutner, Andrzej; Markowicz, Sergiusz

    2016-01-01

    This study aimed to evaluate the capacity of hypocalcemic analogues of 1α,25-dihydroxyvitamin D2 (1,25D2) and 1α,25-dihydroxyvitamin D3 (1,25D3) to inhibit regrowth and regulate the stemness-related gene expression in colon cancer cells undergoing renewal after exposure to 5-fluorouracil (5-FU). All of the tested analogues of 1,25D2 equally potently decreased the clonogenicity and the proliferative activity of HT-29 cells which survived the exposure to 5-FU, but differently regulated gene expression of these cells during their renewal. 1,25D2 and analogues (PRI-1907 and PRI-1917), as well as 1,25D3 and analogue PRI-2191, decreased the relative expression level of several stemness-related genes, such as NANOG, OCT3/4, PROM1, SOX2, ALDHA1, CXCR4, in HT-29/5-FU cells during their renewal, in comparison to untreated HT-29/5-FU cells. The other 1,25D2 analogues (PRI-1906 and PRI-1916) were not capable of downregulating the expression of these stemness-related genes as the analogues PRI-1907 and PRI-1917 did. All of the tested vitamin D analogues upregulated CDH1, the gene encoding E-cadherin associated with epithelial phenotype. Out of the series of analogues studied, side-chain branched analogues of 1,25D2 (PRI-1907, PRI-1917) and the analogue of 1,25D3 (PRI-2191) might be used to target cancer cells with stem-like phenotypes that survive conventional chemotherapy. PMID:27314328

  1. Homodimerization of HYL1 ensures the correct selection of cleavage sites in primary miRNA

    PubMed Central

    Yang, Xi; Ren, Wenqing; Zhao, Qiuxia; Zhang, Peng; Wu, Feijie; He, Yuke

    2014-01-01

    MicroRNA (miRNA) plays an important role in the control of gene expression. HYPONASTIC LEAVES1 (HYL1) is a double-stranded RNA-binding protein that forms a complex with DICER-LIKE1 (DCL1) and SERRATE (SE) to process primary miRNA (pri-miRNA) into mature miRNA. Although HYL1 has been shown to partner with DCL1 to enhance miRNA accuracy, the mechanism by which HYL1 selects the DCL1-targeted cleavage sites in pri-miRNA has remained unknown. By mutagenesis of HYL1 and analysis of in vivo pri-miRNA processing, we investigated the role of HYL1 in pri-miRNA cleavage. HYL1 forms homodimers in which the residues Gly147 and Leu165 in the dsRBD2 domain are shown to be critical. Disruption of HYL1 homodimerization causes incorrect cleavage at sites in pri-miRNA without interrupting the interaction of HYL1 with DCL1 and accumulation of pri-miRNAs in HYL1/pri-miRNA complexes, leading to a reduction in the efficiency and accuracy of miRNAs that results in strong mutant phenotypes of the plants. HYL1 homodimers may function as a molecular anchor for DCL1 to cleave at a distance from the ssRNA–dsRNA junction in pri-miRNA. These results suggest that HYL1 ensures the correct selection of pri-miRNA cleavage sites through homodimerization and thus contributes to gene silencing and plant development. PMID:25294831

  2. Structural determinants of miR156a precursor processing in temperature-responsive flowering in Arabidopsis

    PubMed Central

    Kim, Wanhui; Kim, Hee-Eun; Jun, A Rim; Jung, Myeong Gyo; Jin, Suhyun; Lee, Joon-Hwa; Ahn, Ji Hoon

    2016-01-01

    MicroRNAs originate from primary transcripts (pri-miRNAs) containing hairpin structures. Plant pri-miRNAs have highly variable structures and little is known about the information encoded in their secondary structures. Arabidopsis miR156 is an ambient temperature-responsive miRNA and plays an important role in regulating flowering time. To identify the structural determinants for miR156 processing, we analyzed the effects of mutations introduced in the upper stem of pri-miR156a on its temperature-dependent processing and flowering time. The levels of pri-miR156a and mature miR156 were opposite at different temperatures. Mutations in the upper stem, especially the region closer to the miR156a/miR156a* duplex, reduced miR156 processing at 23 °C and 16 °C and caused a less severe phenotype compared with the un-mutated construct. Mutation in the second stem near the first cleavage site of pri-miR156a affected miR156 processing at 23 °C, but not at 16 °C. This was also seen in pri-miR172a, another ambient temperature-responsive miRNA. Replacement of the upper stem of pri-miR156a with that of pri-miR172a severely affected miR156 processing and flowering time. These results suggested that the upper stem of pri-miR156a is important for miR156 processing at different temperatures. In particular, the second stem adjacent to the first cleavage site plays a role in the regulation of ambient temperature-responsive flowering. PMID:27335452

  3. Identification and analysis of residues contained on β → α loops of the dual-substrate (βα)8 phosphoribosyl isomerase A specific for its phosphoribosyl anthranilate isomerase activity

    PubMed Central

    Noda-García, Lianet; Camacho-Zarco, Aldo R; Verdel-Aranda, Karina; Wright, Helena; Soberón, Xavier; Fülöp, Vilmos; Barona-Gómez, Francisco

    2010-01-01

    A good model to experimentally explore evolutionary hypothesis related to enzyme function is the ancient-like dual-substrate (βα)8 phosphoribosyl isomerase A (PriA), which takes part in both histidine and tryptophan biosynthesis in Streptomyces coelicolor and related organisms. In this study, we determined the Michaelis–Menten enzyme kinetics for both isomerase activities in wild-type PriA from S. coelicolor and in selected single-residue monofunctional mutants, identified after Escherichia coli in vivo complementation experiments. Structural and functional analyses of a hitherto unnoticed residue contained on the functionally important β → α loop 5, namely, Arg139, which was postulated on structural grounds to be important for the dual-substrate specificity of PriA, is presented for the first time. Indeed, enzyme kinetics analyses done on the mutant variants PriA_Ser81Thr and PriA_Arg139Asn showed that these residues, which are contained on β → α loops and in close proximity to the N-terminal phosphate-binding site, are essential solely for the phosphoribosyl anthranilate isomerase activity of PriA. Moreover, analysis of the X-ray crystallographic structure of PriA_Arg139Asn elucidated at 1.95 Å herein strongly implicates the occurrence of conformational changes in this β → α loop as a major structural feature related to the evolution of the dual-substrate specificity of PriA. It is suggested that PriA has evolved by tuning a fine energetic balance that allows the sufficient degree of structural flexibility needed for accommodating two topologically dissimilar substrates—within a bifunctional and thus highly constrained active site—without compromising its structural stability. PMID:20066665

  4. ASSESSMENT OF BEST AVAILABLE TECHNOLOGY ECONOMICALLY ACHIEVABLE FOR SYNTHETIC RUBBER MANUFACTURING WASTEWATER

    EPA Science Inventory

    An assessment of The Best Available Technology Economically Achievable (BATEA) for treatment of synthetic rubber manufacturing wastewaters has been conducted. This assessment was based on feasibility tests with actual wastewater samples, both end-of-pipe (untreated) and after pri...

  5. Developing a Roadmap for Integrating Computational and In Vitro Approaches in Risk-Based Chemical Safety Decisions (SSCT-SweTox)

    EPA Science Inventory

    Multiple drivers shape the types of chemical assessments performed within many regulatory agencies including economic considerations, data availability, and the ultimate application of the assessment. The result is that chemical assessments are “fit-for-purpose” ranging from pri...

  6. Two-coordinate terminal zinc hydride complexes: synthesis, structure and preliminary reactivity studies.

    PubMed

    Dawkins, Michael J C; Middleton, Ewart; Kefalidis, Christos E; Dange, Deepak; Juckel, Martin M; Maron, Laurent; Jones, Cameron

    2016-08-18

    The first examples of essentially two-coordinate, monomeric zinc hydride complexes, LZnH (L = -N(Ar)(SiR3)) (Ar = C6H2{C(H)Ph2}2R'-2,6,4; R = Me, R' = Pr(i) (L'); R = Pr(i), R' = Me (L*); R = Pr(i), R' = Pr(i) (L(†))) have been prepared and shown by crystallographic studies to have near linear N-Zn-H fragments. The results of computational studies imply that any PhZn interactions in the compounds are weak at best. Preliminary reactivity studies reveal the compounds to be effective for the stoichiometric hydrozincation and catalytic hydrosilylation of carbonyl compounds. PMID:27499232

  7. Lock and key to transcription: σ-DNA interaction.

    PubMed

    Liu, Xin; Bushnell, David A; Kornberg, Roger D

    2011-12-01

    How does RNA polymerase recognize a promoter in duplex DNA? How are the DNA strands pried apart to enable RNA synthesis? A crystal structure by Feklistov and Darst unexpectedly reveals that these two processes are interconnected. PMID:22153066

  8. Solution Method of Multi-Product Two-Stage Logistics Problem with Constraints of Delivery Course

    NASA Astrophysics Data System (ADS)

    Ataka, Shinichiro; Gen, Mitsuo

    The logistics network design is one of the important phase of Supply Chain Management (SCM) and it is the problem that should be optimized for long-term promotion of efficiency of the whole supply chain. Usually a plant produces different type of products. Even if it is a factory of the same company, delivery is different by a kind of a produced product. The restrictions which this model has are deeply concerned with TP in the real world. In this paper, we consider the logistics network design problems with multi-products and constraints for delivery course. To solve the problem, we used a hybrid priority-based Genetic Algorithm (h-priGA), and we tried the comparison experiment with priority-based Genetic Algorithm (priGA)and h-priGA, we show it about the effectiveness of h-priGA.

  9. N6-methyl-adenosine (m6A) marks primary microRNAs for processing

    PubMed Central

    Alarcón, Claudio R.; Lee, Hyeseung; Goodarzi, Hani; Halberg, Nils

    2015-01-01

    The first step in the biogenesis of microRNAs is the processing of primary microRNAs (pri-miRNAs) by the microprocessor complex, composed of the RNA binding protein DGCR8 and the ribonuclease type III DROSHA1–4. This initial event requires the recognition of the junction between the stem and the flanking single-stranded RNA of the pri-miRNA hairpin by DGCR8 followed by recruitment of DROSHA, which cleaves the RNA duplex to yield the pre-miRNA product5. While the mechanisms underlying pri-miRNA processing have been elucidated, the mechanism by which DGCR8 recognizes and binds pri-miRNAs as opposed to other secondary structures present in transcripts is not understood. We find that methyltransferase like 3 (METTL3) methylates pri-miRNAs, marking them for recognition and processing by DGCR8. Consistent with this, METTL3 depletion reduced the binding of DGCR8 to pri-miRNAs and resulted in the global reduction of mature miRNAs and concomitant accumulation of unprocessed pri-miRNAs. In vitro processing reactions confirmed the sufficiency of the m6A mark in promoting pri-miRNA processing. Finally, gain-of-function experiments revealed that METTL3 is sufficient to enhance miRNA maturation in a global and non-cell-type specific manner. Our findings reveal that the m6A mark acts as a key post-transcriptional modification that promotes the initiation of miRNA biogenesis. PMID:25799998

  10. Binding of NF-kappaB p65 subunit to the promoter elements is involved in LPS-induced transactivation of miRNA genes in human biliary epithelial cells

    PubMed Central

    Zhou, Rui; Hu, Guoku; Gong, Ai-Yu; Chen, Xian-Ming

    2010-01-01

    The majority of human miRNA genes is transcribed by polymerase II and can be classified as class II genes similar to protein-coding genes. Whereas current research on miRNAs has focused on the physiological and pathological functions, the molecular mechanisms underlying their transcriptional regulation are largely unknown. We recently reported that lipopolysaccharide (LPS) alters mature miRNA expression profile in human biliary epithelial cells. In this study, we tested the role of transcription factor NF-κB in LPS-induced transcription of select miRNA genes. Of the majority of LPS-up-regulated mature miRNAs in cultured human biliary epithelial cells, potential NF-κB binding sites were identified in the putative promoter elements of their corresponding genes. Inhibition of NF-κB activation by SC-514, an IKK2 inhibitor, blocked LPS-induced up-regulation of a subset of pri-miRNAs, including pri-miR-17-92, pri-miR-125b-1, pri-miR-21, pri-miR-23b-27b-24-1, pri-miR-30b, pri-miR-130a and pri-miR-29a. Moreover, direct binding of NF-κB p65 subunit to the promoter elements of mir-17-92, mir-125b-1, mir-21, mir-23b-27b-24-1, mir-30b and mir-130a genes was identified by chromatin immunoprecipitation analysis and confirmed by the luciferase reporter assay. Thus, a subset of miRNA genes is regulated in human biliary epithelial cells through NF-κB activation induced by LPS, suggesting a role of the NF-κB pathway in the transcriptional regulation of miRNA genes. PMID:20144951

  11. [Estimation of light-use efficiency of China' s mid-subtropical planted coniferous forest based on flux measurements and spectral observations].

    PubMed

    Chen, Die-cong; Wang, Shao-qiang; Huang, Kun; Zhou, Lei; Yu, Quan-zhou; Wang, Hui-min; Sun, Lei-gang

    2015-11-01

    The photochemical reflectance index (PRI) calculated from spectral reflectance has universally become a proxy for the light-use efficiency (LUE), which significantly improves the LUE-based estimation of ecosystem gross primary productivity on a large scale through upscaling. In this study, we observed the vegetation spectral reflectance of a planted subtropical coniferous forest from the top of a flux tower at Qianyanzhou Station, one of the ChinaFLUX sites, in September and December 2013, and simultaneously measured CO2 flux and meteorological variables for correlation and regression analysis. Results showed that PRI had a better correlation with LUE (R2 = 0.20, P< 0.001) than that of normalized difference vegetation index (NDVI), i.e., PRI was preferred in LUE retrieval. During the whole observation period, PRI and soil water content (SWC)-based bivariate regression model correlated well with LUE (R2 = 0.29, P < 0.001 and R2 = 0.30, P < 0.01 for daytime and midday observation, respectively), but in autumn the bivariate regression model of PRI and vapor pressure deficit (VPD) had a higher correlation with LUE (R2 = 0.448, P < 0.001) for midday observation, which showed that environmental factors, i.e., SWC and VPD, had a potential in improving the LUE retrieval from PRI, but the choice of appropriate environmental factors depended on season. PMID:26915199

  12. Pose Estimation using 1D Fourier Transform and Euclidean Distance Matching of CAD Model and Inspected Model Part

    NASA Astrophysics Data System (ADS)

    Zulkoffli, Zuliani; Abu Bakar, Elmi

    2016-02-01

    This paper present pose estimation relation of CAD model object and Projection Real Object (PRI). Image sequence of PRI and CAD model rotate on z axis at 10 degree interval in simulation and real scene used in this experiment. All this image is go through preprocessing stage to rescale object size and image size and transform all the image into silhouette. Correlation of CAD and PRI image is going through in this stage. Magnitude spectrum shows a reliable value in range 0.99 to 1.00 and Phase spectrum correlation shows a fluctuate graph in range 0.56 - 0.97. Euclidean distance correlation graph for CAD and PRI shows 2 zone of similar value due to almost symmetrical object shape. Processing stage of retrieval inspected PRI image in CAD database was carried out using range phase spectrum and maximum magnitude spectrum value within ±10% tolerance. Additional processing stage of retrieval inspected PRI image using Euclidean distance within ±5% tolerance also carried out. Euclidean matching shows a reliable result compared to range phase spectrum and maximum magnitude spectrum value by sacrificing more than 5 times processing time.

  13. Global Prioritization of Disease Candidate Metabolites Based on a Multi-omics Composite Network

    PubMed Central

    Yao, Qianlan; Xu, Yanjun; Yang, Haixiu; Shang, Desi; Zhang, Chunlong; Zhang, Yunpeng; Sun, Zeguo; Shi, Xinrui; Feng, Li; Han, Junwei; Su, Fei; Li, Chunquan; Li, Xia

    2015-01-01

    The identification of disease-related metabolites is important for a better understanding of metabolite pathological processes in order to improve human medicine. Metabolites, which are the terminal products of cellular regulatory process, can be affected by multi-omic processes. In this work, we propose a powerful method, MetPriCNet, to predict and prioritize disease candidate metabolites based on integrated multi-omics information. MetPriCNet prioritized candidate metabolites based on their global distance similarity with seed nodes in a composite network, which integrated multi-omics information from the genome, phenome, metabolome and interactome. After performing cross-validation on 87 phenotypes with a total of 602 metabolites, MetPriCNet achieved a high AUC value of up to 0.918. We also assessed the performance of MetPriCNet on 18 disease classes and found that 4 disease classes achieved an AUC value over 0.95. Notably, MetPriCNet can also predict disease metabolites without known disease metabolite knowledge. Some new high-risk metabolites of breast cancer were predicted, although there is a lack of known disease metabolite information. A predicted disease metabolic landscape was constructed and analyzed based on the results of MetPriCNet for 87 phenotypes to help us understand the genetic and metabolic mechanism of disease from a global view. PMID:26598063

  14. Crystal structure of DnaT84–153-dT10 ssDNA complex reveals a novel single-stranded DNA binding mode

    PubMed Central

    Liu, Zheng; Chen, Peng; Wang, Xuejuan; Cai, Gang; Niu, Liwen; Teng, Maikun; Li, Xu

    2014-01-01

    DnaT is a primosomal protein that is required for the stalled replication fork restart in Escherichia coli. As an adapter, DnaT mediates the PriA-PriB-ssDNA ternary complex and the DnaB/C complex. However, the fundamental function of DnaT during PriA-dependent primosome assembly is still a black box. Here, we report the 2.83 Å DnaT84–153-dT10 ssDNA complex structure, which reveals a novel three-helix bundle single-stranded DNA binding mode. Based on binding assays and negative-staining electron microscopy results, we found that DnaT can bind to phiX 174 ssDNA to form nucleoprotein filaments for the first time, which indicates that DnaT might function as a scaffold protein during the PriA-dependent primosome assembly. In combination with biochemical analysis, we propose a cooperative mechanism for the binding of DnaT to ssDNA and a possible model for the assembly of PriA-PriB-ssDNA-DnaT complex that sheds light on the function of DnaT during the primosome assembly and stalled replication fork restart. This report presents the first structure of the DnaT C-terminal complex with ssDNA and a novel model that explains the interactions between the three-helix bundle and ssDNA. PMID:25053836

  15. Cellular Response to a Novel Fetal Acellular Collagen Matrix: Implications for Tissue Regeneration

    PubMed Central

    Rennert, Robert C.; Garg, Ravi K.; Gurtner, Geoffrey C.

    2013-01-01

    Introduction. PriMatrix (TEI Biosciences Inc., Boston, MA, USA) is a novel acellular collagen matrix derived from fetal bovine dermis that is designed for use in partial- and full-thickness wounds. This study analyzes the cellular response to PriMatrix in vivo, as well as the ability of this matrix to facilitate normal tissue regeneration. Methods. Five by five mm squares of rehydrated PriMatrix were implanted in a subcutaneous fashion on the dorsum of wild-type mice. Implant site tissue was harvested for histology, immunohistochemistry (IHC), and flow cytometric analyses at multiple time points until day 28. Results. PriMatrix implants were found to go through a biological progression initiated by a transient infiltrate of inflammatory cells, followed by mesenchymal cell recruitment and vascular development. IHC analysis revealed that the majority of the implanted fetal dermal collagen fibers persisted through day 28 but underwent remodeling and cellular repopulation to form tissue with a density and morphology consistent with healthy dermis. Conclusions. PriMatrix implants undergo progressive in vivo remodeling, facilitating the regeneration of histologically normal tissue through a mild inflammatory and progenitor cell response. Regeneration of normal tissue is especially important in a wound environment, and these findings warrant further investigation of PriMatrix in this setting. PMID:23970899

  16. Integrating Solar Induced Fluorescence and the Photochemical Reflectance Index for Estimating Gross Primary Production in a Cornfield

    NASA Technical Reports Server (NTRS)

    Cheng, Yen-Ben; Middleton, Elizabeth M.; Zhang, Qingyuan; Huemmrich, Karl F.; Campbell, Petya K. E.; Corp, Lawrence A.; Cook, Bruce D.; Kustas, William P.; Daughtry, Criag S.

    2013-01-01

    The utilization of remotely sensed observations for light use efficiency (LUE) and tower-based gross primary production (GPP) estimates was studied in a USDA cornfield. Nadir hyperspectral reflectance measurements were acquired at canopy level during a collaborative field campaign conducted in four growing seasons. The Photochemical Reflectance Index (PRI) and solar induced chlorophyll fluorescence (SIF), were derived. SIF retrievals were accomplished in the two telluric atmospheric oxygen absorption features centered at 688 nm (O2-B) and 760 nm (O2-A). The PRI and SIF were examined in conjunction with GPP and LUE determined by flux tower-based measurements. All of these fluxes, environmental variables, and the PRI and SIF exhibited diurnal as well as day-to-day dynamics across the four growing seasons. Consistent with previous studies, the PRI was shown to be related to LUE (r2 = 0.54 with a logarithm fit), but the relationship varied each year. By combining the PRI and SIF in a linear regression model, stronger performances for GPP estimation were obtained. The strongest relationship (r2 = 0.80, RMSE = 0.186 mg CO2/m2/s) was achieved when using the PRI and SIF retrievals at 688 nm. Cross-validation approaches were utilized to demonstrate the robustness and consistency of the performance. This study highlights a GPP retrieval method based entirely on hyperspectral remote sensing observations.

  17. Vitamin D Analogs Potentiate the Antitumor Effect of Imatinib Mesylate in a Human A549 Lung Tumor Model

    PubMed Central

    Maj, Ewa; Filip-Psurska, Beata; Świtalska, Marta; Kutner, Andrzej; Wietrzyk, Joanna

    2015-01-01

    In previous papers, we presented data on studies on the anticancer activity of the vitamin D3 analogs, named PRI-2191 and PRI-2205, in different cancer models. In this study, we showed the improved antiproliferative activity of a combination of imatinib mesylate (Gleevec, GV) and cytostatic agents in in vitro studies, when used with a third compound, namely PRI-2191, in an A549 human lung cancer model. Furthermore, we analyzed the influence of both PRI-2191, as well as PRI-2205 on the anticancer activity of GV in mice bearing A549 tumors. The route of PRI-2191 analog administration showed a significant impact on the outcome of GV treatment: subcutaneous injection was more efficient and less toxic than oral gavage. Moreover, both vitamin D compounds increased the anticancer activity of GV; however, they might also potentiate some adverse effects. We also evaluated in tumor tissue the expression of VEGF, PDGF-BB, vitamin D receptor, CYP27B1, CYP24, p53 and Bcl-2, as well as PDGF receptors: α and β. We observed the upregulation of p53 expression and the downregulation of Bcl-2, as well as VEGF in A549 tumors as a result of the tested treatment. However, vitamin D analogs did not significantly influence the expression of these proteins. PMID:26580599

  18. Vitamin D Analogs Potentiate the Antitumor Effect of Imatinib Mesylate in a Human A549 Lung Tumor Model.

    PubMed

    Maj, Ewa; Filip-Psurska, Beata; Świtalska, Marta; Kutner, Andrzej; Wietrzyk, Joanna

    2015-01-01

    In previous papers, we presented data on studies on the anticancer activity of the vitamin D₃ analogs, named PRI-2191 and PRI-2205, in different cancer models. In this study, we showed the improved antiproliferative activity of a combination of imatinib mesylate (Gleevec, GV) and cytostatic agents in in vitro studies, when used with a third compound, namely PRI-2191, in an A549 human lung cancer model. Furthermore, we analyzed the influence of both PRI-2191, as well as PRI-2205 on the anticancer activity of GV in mice bearing A549 tumors. The route of PRI-2191 analog administration showed a significant impact on the outcome of GV treatment: subcutaneous injection was more efficient and less toxic than oral gavage. Moreover, both vitamin D compounds increased the anticancer activity of GV; however, they might also potentiate some adverse effects. We also evaluated in tumor tissue the expression of VEGF, PDGF-BB, vitamin D receptor, CYP27B1, CYP24, p53 and Bcl-2, as well as PDGF receptors: α and β. We observed the upregulation of p53 expression and the downregulation of Bcl-2, as well as VEGF in A549 tumors as a result of the tested treatment. However, vitamin D analogs did not significantly influence the expression of these proteins. PMID:26580599

  19. Monitoring water stress and fruit quality in an orange orchard under regulated deficit irrigation using narrow-band structural and physiological remote sensing indices

    NASA Astrophysics Data System (ADS)

    Stagakis, S.; González-Dugo, V.; Cid, P.; Guillén-Climent, M. L.; Zarco-Tejada, P. J.

    2012-07-01

    This paper deals with the monitoring of water status and the assessment of the effect of stress on citrus fruit quality using structural and physiological remote sensing indices. Four flights were conducted over a citrus orchard in 2009 using an unmanned aerial vehicle (UAV) carrying a multispectral camera with six narrow spectral bands in the visible and near infrared. Physiological indices such as the Photochemical Reflectance Index (PRI570), a new structurally robust PRI formulation that uses the 515 nm as the reference band (PRI515), and a chlorophyll ratio (R700/R670) were compared against the Normalized Difference Vegetation Index (NDVI), Renormalized Difference Vegetation Index (RDVI) and Modified Triangular Vegetation Index (MTVI) canopy structural indices for their performance in tracking water status and the effects of sustained water stress on fruit quality at harvest. The irrigation setup in the commercial orchard was compared against a treatment scheduled to satisfy full requirements (based on estimated crop evapotranspiration) using two regulated deficit irrigation (RDI) strategies. The water status of the trees throughout the experiment was monitored with frequent field measurements of stem water potential (Ψx), while titratable acidity (TA) and total soluble solids (TSS) were measured at harvest on selected trees from each irrigation treatment. The high spatial resolution of the multispectral imagery (30 cm pixel size) enabled identification of pure tree crown components, extracting the tree reflectance from shaded, sunlit and aggregated pixels. The physiological and structural indices were then calculated from each tree at the following levels: (i) pure sunlit tree crown, (ii) entire crown, aggregating the within-crown shadows, and (iii) simulating a lower resolution pixel, including tree crown, sunlit and shaded soil pixels. The resulting analysis demonstrated that both PRI formulations were able to track water status, except when water stress

  20. Retrieval of the photochemical reflectance index for assessing xanthophyll cycle activity: a comparison of near-surface optical sensors

    NASA Astrophysics Data System (ADS)

    Harris, A.; Gamon, J. A.; Pastorello, G. Z.; Wong, C. Y. S.

    2014-11-01

    Unattended optical sensors are increasingly being deployed on eddy covariance flux towers and are often used to complement existing vegetation and micrometeorological measurements to enable assessment of biophysical states and biogeochemical processes over a range of spatial scales. Of particular interest are sensors that can measure the photochemical reflectance index (PRI), which can provide information pertaining to leaf pigments and photosynthetic activity. This interest has facilitated the production of a new range of lower-cost multispectral sensors specifically designed to measure temporal changes in the PRI signal. However, little is known about the characteristics (spectral, radiometric and temporal) of many of these PRI sensors, making it difficult to compare data obtained from these sensors across time, geographical locations and instruments. Furthermore, direct testing of the capability of these sensors to actually detect the conversion of the xanthophyll cycle, which is the original biological basis of the PRI diurnal signal, is largely absent, often resulting in an unclear interpretation of the signal, particularly given the wide range of factors now known to influence PRI. Through a series of experiments, we assess the sensitivity of one of the leading brands of PRI sensor (Skye SKR 1800) to changes in vegetation photosynthetic activity in response to changing irradiance. We compare the results with those obtained using a more expensive industry-standard visible to near-infrared hyperspectral spectrometer (PP Systems UniSpec) and determine the radiometric compatibility of measurements made by the different instruments. Results suggest that the SKR 1800 instrument is able to track rapid (seconds to minutes) and more gradual diurnal changes in photosynthetic activity associated with xanthophyll cycle pigment conversion. Measurements obtained from both the high and lower cost instrument were significantly linearly correlated but were subject to a large

  1. Alternate partial root-zone irrigation reduces bundle-sheath cell leakage to CO2 and enhances photosynthetic capacity in maize leaves

    PubMed Central

    Wang, Zhenchang; Kang, Shaozhong; Jensen, Christian R.; Liu, Fulai

    2012-01-01

    The physiological basis for the advantage of alternate partial root-zone irrigation (PRI) over common deficit irrigation (DI) in improving crop water use efficiency (WUE) remains largely elusive. Here leaf gas exchange characteristics and photosynthetic CO2–response and light–response curves for maize (Zea mays L.) leaves exposed to PRI and DI were analysed under three N-fertilization rates, namely 75, 150, and 300 mg N kg−1 soil. Measurements of net photosynthetic rate (An) and stomatal conductance (gs) showed that, across the three N-fertilization rates, the intrinsic WUE was significantly higher in PRI than in DI leaves. Analysis of the CO2–response curve revealed that both carboxylation efficiency (CE) and the CO2-saturated photosynthetic rate (Asat) were significantly higher in PRI than in DI leaves across the three N-fertilization rates; whereas the N-fertilization rates did not influence the shape of the curves. The enhanced CE and Asat in the PRI leaves was accompanied by significant decreases in carbon isotope discrimination (Δ13C) and bundle-sheath cell leakiness to CO2 (Φ). Analysis of the light–response curve indicated that, across the three N-fertilization rates, the quantum yield (α) and light-saturated gross photosynthetic rate (Amax) were identical for the two irrigation treatments; whilst the convexity (κ) of the curve was significantly greater in PRI than in DI leaves, which coincided with the greater CE and Asat derived from the CO2–response curve at a photosynthetic photon flux density of 1500 μmol m−2 s−1. Collectively, the results suggest that, in comparison with the DI treatment, PRI improves photosynthetic capacity parameters CE, Asat, and κ of maize leaves and that contributes to the greater intrinsic WUE in those plants. PMID:22121199

  2. Estimating Light Use Efficiency Of A Pine And Beech Forest From Leaf To Ecosystem Scale Using The Photochemical Reflectance Index

    NASA Astrophysics Data System (ADS)

    Vanikiotis, Theofilos; Markos, Nikos; Stagakis, Stavros; Tzotsos, Angelos; Sykioti, Olga; Kyparissis, Aris

    2013-12-01

    The prospect of accurately tracking photosynthetic processes using satellite observations is very important for understanding and monitoring global carbon cycle and climate change. The present study investigates the efficiency of the Photochemical Reflectance Index (PRI) in detecting light use efficiency (ɛ) in different spatial scales. The study sites concern two dense and homogenous forests in the region of Epirus (Greece), one evergreen coniferous forest dominated by Pinus nigra species and one deciduous forest dominated by Fagus sylvatica. Field and laboratory measurements of canopy structure (Leaf Area Index - LAI, needle and shoot structure characteristics), leaf pigment concentrations, leaf photosynthesis and water potential were performed throughout the growth period. These measurements were used for an accurate description of the ecophysiological characteristics of the two species and thus the parameterization of a Canopy Photosynthesis Model in order to estimate canopy photosynthesis. During the same period, leaf and canopy reflectance measurements were performed in the field to test and evaluate PRI regarding it's efficiency to track ɛ in leaf and canopy scale. In order to investigate the potential application of PRI for estimating ɛ in a broader spatial scale, satellite hyperspectral or superspectral sensors can be used. Compact High Resolution Imaging Spectrometer (CHRIS) and Moderate Resolution Imaging Spectroradiometer (MODIS) are currently available for this purpose and their performances were tested within the present study. An agreement between the fluctuations of CHRIS PRI and the field measured canopy PRI has been found, with both of them appearing to track the ɛ fluctuation efficiently. However, MODIS PRI shows no intense fluctuation and no relationship with ɛ and field measured PRI, probably due to lack of atmospheric correction and the effects of viewing and illumination geometry.

  3. The Association between the PR Interval and Left Ventricular Measurements in the Multiethnic Study of Atherosclerosis

    PubMed Central

    Husby, Michael P.; Soliman, Elsayed Z.; Goldberger, Jeffrey J.; Liu, Kiang; Lloyd-Jones, Don; Durazo-Arvizu, Ramon; Kramer, Holly

    2015-01-01

    Introduction. Few studies have examined the association between the PR interval (PRi) and subclinical cardiovascular disease measures. Methods and Results. The Multiethnic Study of Atherosclerosis (MESA) is a population-based study of 6814 men and women aged 45–84 years without clinical cardiovascular disease and 4962 had complete baseline data on cardiac magnetic resonance imaging measures of LV dimension and ejection fraction and surface electrocardiogram. Linear regression models were constructed to determine the adjusted association between the PRi and measures of LV stroke volume, LV mass, LV end-systolic and end-diastolic volumes, and ejection fraction. Overall, mean age was 61.5 years, and 47.6% were male and race/ethnicity was white in 39.1%, Chinese in 13.1%, African-American in 25.7%, and Hispanic in 22.2%. The PRi ranged from 88 to 308 ms with a median value of 162 ms. As a continuous variable, every standard deviation unit (25 ms) increment in PRi was associated with a 2.00 mL (95% CI 1.52, 2.48) higher stroke volume, a 3.08 g (95% CI 2.30, 3.86) higher LV mass, a 1.36 g/m2 (95% CI 0.96, 1.76) higher LV mass index, and 1.31 mL (95% CI 0.88, 1.73) higher end-systolic and 3.31 mL (95% CI 2.58, 4.03) higher end-diastolic volumes after adjustment for all covariates. No significant association was noted between the PRi and LV ejection fraction. Conclusions. A prolonged PRi is associated with LV measures and may in part explain the link between a prolonged PRi and cardiovascular outcomes. PMID:26558133

  4. Determination of primary combustion source organic carbon-to-elemental carbon (OC / EC) ratio using ambient OC and EC measurements: secondary OC-EC correlation minimization method

    NASA Astrophysics Data System (ADS)

    Wu, Cheng; Zhen Yu, Jian

    2016-05-01

    Elemental carbon (EC) has been widely used as a tracer to track the portion of co-emitted primary organic carbon (OC) and, by extension, to estimate secondary OC (SOC) from ambient observations of EC and OC. Key to this EC tracer method is to determine an appropriate OC / EC ratio that represents primary combustion emission sources (i.e., (OC / EC)pri) at the observation site. The conventional approaches include regressing OC against EC within a fixed percentile of the lowest (OC / EC) ratio data (usually 5-20 %) or relying on a subset of sampling days with low photochemical activity and dominated by local emissions. The drawback of these approaches is rooted in its empirical nature, i.e., a lack of clear quantitative criteria in the selection of data subsets for the (OC / EC)pri determination. We examine here a method that derives (OC / EC)pri through calculating a hypothetical set of (OC / EC)pri and SOC followed by seeking the minimum of the coefficient of correlation (R2) between SOC and EC. The hypothetical (OC / EC)pri that generates the minimum R2(SOC,EC) then represents the actual (OC / EC)pri ratio if variations of EC and SOC are independent and (OC / EC)pri is relatively constant in the study period. This Minimum R Squared (MRS) method has a clear quantitative criterion for the (OC / EC)pri calculation. This work uses numerically simulated data to evaluate the accuracy of SOC estimation by the MRS method and to compare with two commonly used methods: minimum OC / EC (OC / ECmin) and OC / EC percentile (OC / EC10 %). Log-normally distributed EC and OC concentrations with known proportion of SOC are numerically produced through a pseudorandom number generator. Three scenarios are considered, including a single primary source, two independent primary sources, and two correlated primary sources. The MRS method consistently yields the most accurate SOC estimation. Unbiased SOC estimation by OC / ECmin and OC / EC10 % only occurs when the left tail of

  5. Light Use Efficiency and Photochemical Reflectance Index: do we have a common basis defining them? Implications for productivity estimation (Invited)

    NASA Astrophysics Data System (ADS)

    Gitelson, A. A.; Gamon, J. A.

    2013-12-01

    There are at least three commonly used definitions of photosynthetic Light Use Efficiency (LUE) based on: (a) incident radiation (LUEinc); (b) total absorbed light (LUEtotal); and (c) radiation absorbed by photosynthetically active vegetation (LUEps). Consequently, LUE values reported do not have a common basis, bringing confusion and limiting the utility of reported LUE values for comparative analyses. Not surprisingly, the value of LUE reported in literature varies by a factor of three. Similarly, the Photochemical Reflectance Index (PRI) has different operational definitions, resulting in a wide range of reported values for comparable conditions. The objectives of this paper are to investigate (a) temporal behavior of each definition of LUE; and (b) factors affecting PRI, often used as a surrogate of LUE at leaf and canopy levels. We focused on annual and winter-deciduous vegetation where total chlorophyll content is closely tied to the seasonal dynamics of GPP. In these conditions, LUEinc is closely related to total plant chlorophyll (Chl) content. LUEtotal oscillates around a constant value during the vegetative stage, depending mainly on plant physiological status, PAR composition and magnitude, while in reproductive and senescence stages it relates closely to Chl content. LUEps may vary 2- to 3-fold during the growing season with no clear seasonal pattern, and does not seem to be related to any biophysical characteristic studied; rather, it depends on the physiological status of vegetation, PAR composition and magnitude as well as air temperature and soil moisture. At the leaf level, PRI depends greatly on pigment content and composition and relates closely to the ratio of Chl to carotenoid content. At the canopy and stand levels, both total plant Chl content and green LAI are responsible for more than 95% of PRI variation, demonstrating that PRI is confounded by pigment pool sizes and canopy structure in these conditions. Importantly, the close relationship

  6. Structural insight into HIV-1 capsid recognition by rhesus TRIM5α

    PubMed Central

    Yang, Haitao; Ji, Xiaoyun; Zhao, Gongpu; Ning, Jiying; Zhao, Qi; Aiken, Christopher; Gronenborn, Angela M.; Zhang, Peijun; Xiong, Yong

    2012-01-01

    Tripartite motif protein isoform 5 alpha (TRIM5α) is a potent antiviral protein that restricts infection by HIV-1 and other retroviruses. TRIM5α recognizes the lattice of the retrovirus capsid through its B30.2 (PRY/SPRY) domain in a species-specific manner. Upon binding, TRIM5α induces premature disassembly of the viral capsid and activates the downstream innate immune response. We have determined the crystal structure of the rhesus TRIM5α PRY/SPRY domain that reveals essential features for capsid binding. Combined cryo-electron microscopy and biochemical data show that the monomeric rhesus TRIM5α PRY/SPRY, but not the human TRIM5α PRY/SPRY, can bind to HIV-1 capsid protein assemblies without causing disruption of the capsid. This suggests that the PRY/SPRY domain alone constitutes an important pattern-sensing component of TRIM5α that is capable of interacting with viral capsids of different curvatures. Our results provide molecular insights into the mechanisms of TRIM5α-mediated retroviral restriction. PMID:23091002

  7. Tracking diurnal variation in photosynthetic down-regulation using low cost spectroscopic instrumentation.

    PubMed

    van Leeuwen, Martin; Kremens, Robert L; van Aardt, Jan

    2015-01-01

    Photosynthetic light-use efficiency (LUE) has gained wide interest as an input to modeling forest gross primary productivity (GPP). The photochemical reflectance index (PRI) has been identified as a principle means to inform LUE-based models, using airborne and satellite-based observations of canopy reflectance. More recently, low-cost electronics have become available with the potential to provide for dense in situ time-series measurements of PRI. A recent design makes use of interference filters to record light transmission within narrow wavebands. Uncertainty remains as to the dynamic range of these sensors and performance under low light conditions, the placement of the reference band, and methodology for reflectance calibration. This paper presents a low-cost sensor design and is tested in a laboratory set-up, as well in the field. The results demonstrate an excellent performance against a calibration standard (R2 = 0.9999) and at low light conditions. Radiance measurements over vegetation demonstrate a reversible reduction in green reflectance that was, however, seen in both the reference and signal wavebands. Time-series field measurements of PRI in a Douglas-fir canopy showed a weak correlation with eddy-covariance-derived LUE and a significant decline in PRI over the season. Effects of light quality, bidirectional scattering effects, and possible sensor artifacts on PRI are discussed. PMID:25951342

  8. Risk Management in Magnetic Resonance: Failure Mode, Effects, and Criticality Analysis

    PubMed Central

    Granata, Vincenza; Filice, Salvatore; Raiano, Nicola; Amato, Daniela Maria; Zirpoli, Maria; di Finizio, Alessandro; Sansone, Mario; Russo, Anna; Covelli, Eugenio Maria; Pedicini, Tonino; Triassi, Maria

    2013-01-01

    The aim of the study was to perform a risk management procedure in “Magnetic Resonance Examination” process in order to identify the critical phases and sources of radiological errors and to identify potential improvement projects including procedures, tests, and checks to reduce the error occurrence risk. In this study we used the proactive analysis “Failure Mode Effects Criticality Analysis,” a qualitative and quantitative risk management procedure; has calculated Priority Risk Index (PRI) for each activity of the process; have identified, on the PRI basis, the most critical activities and, for them, have defined improvement projects; and have recalculated the PRI after implementation of improvement projects for each activity. Time stop and audits are performed in order to control the new procedures. The results showed that the most critical tasks of “Magnetic Resonance Examination” process were the reception of the patient, the patient schedule drafting, the closing examination, and the organization of activities. Four improvement projects have been defined and executed. PRI evaluation after improvement projects implementation has shown that the risk decreased significantly following the implementation of procedures and controls defined in improvement projects, resulting in a reduction of the PRI between 43% and 100%. PMID:24171173

  9. Remotely-sensed detection of effects of extreme droughts on gross primary production

    PubMed Central

    Vicca, Sara; Balzarolo, Manuela; Filella, Iolanda; Granier, André; Herbst, Mathias; Knohl, Alexander; Longdoz, Bernard; Mund, Martina; Nagy, Zoltan; Pintér, Krisztina; Rambal, Serge; Verbesselt, Jan; Verger, Aleixandre; Zeileis, Achim; Zhang, Chao; Peñuelas, Josep

    2016-01-01

    Severe droughts strongly impact photosynthesis (GPP), and satellite imagery has yet to demonstrate its ability to detect drought effects. Especially changes in vegetation functioning when vegetation state remains unaltered (no browning or defoliation) pose a challenge to satellite-derived indicators. We evaluated the performance of different satellite indicators to detect strong drought effects on GPP in a beech forest in France (Hesse), where vegetation state remained largely unaffected while GPP decreased substantially. We compared the results with three additional sites: a Mediterranean holm oak forest (Puéchabon), a temperate beech forest (Hainich), and a semi-arid grassland (Bugacpuszta). In Hesse, a three-year reduction in GPP following drought was detected only by the Enhanced Vegetation Index (EVI). The Photochemical Reflectance Index (PRI) also detected this drought effect, but only after normalization for absorbed light. In Puéchabon normalized PRI outperformed the other indicators, while the short-term drought effect in Hainich was not detected by any tested indicator. In contrast, most indicators, but not PRI, captured the drought effects in Bugacpuszta. Hence, PRI improved detection of drought effects on GPP in forests and we propose that PRI normalized for absorbed light is considered in future algorithms to estimate GPP from space. PMID:27301671

  10. Tracking Diurnal Variation in Photosynthetic Down-Regulation Using Low Cost Spectroscopic Instrumentation

    PubMed Central

    van Leeuwen, Martin; Kremens, Robert L.; van Aardt, Jan

    2015-01-01

    Photosynthetic light-use efficiency (LUE) has gained wide interest as an input to modeling forest gross primary productivity (GPP). The photochemical reflectance index (PRI) has been identified as a principle means to inform LUE-based models, using airborne and satellite-based observations of canopy reflectance. More recently, low-cost electronics have become available with the potential to provide for dense in situ time-series measurements of PRI. A recent design makes use of interference filters to record light transmission within narrow wavebands. Uncertainty remains as to the dynamic range of these sensors and performance under low light conditions, the placement of the reference band, and methodology for reflectance calibration. This paper presents a low-cost sensor design and is tested in a laboratory set-up, as well in the field. The results demonstrate an excellent performance against a calibration standard (R2 = 0.9999) and at low light conditions. Radiance measurements over vegetation demonstrate a reversible reduction in green reflectance that was, however, seen in both the reference and signal wavebands. Time-series field measurements of PRI in a Douglas-fir canopy showed a weak correlation with eddy-covariance-derived LUE and a significant decline in PRI over the season. Effects of light quality, bidirectional scattering effects, and possible sensor artifacts on PRI are discussed. PMID:25951342

  11. Bronchodilator response following methacholine-induced bronchoconstriction predicts acute asthma exacerbations.

    PubMed

    Park, Heung-Woo; Song, Woo-Jung; Chang, Yoon-Suk; Cho, Sang-Heon; Datta, Soma; Weiss, Scott T; Tantisira, Kelan G

    2016-07-01

    Methacholine bronchial provocation test provides the concentration of methacholine causing a 20% decrease in forced expiratory volume in 1 s (FEV1) from baseline (PC20). The dose-response slope (DRS), and other continuous indices of responsiveness (CIR; the percentage decline from the post-diluent baseline FEV1 after the last dose of methacholine), and per cent recovery index (PRI; the percentage increase from the maximally reduced FEV1 after bronchodilator inhalation) are alternative measures. The clinical relevance of these indices in predicting acute asthma exacerbations has not been fully evaluated.In two prospective cohorts of childhood and elderly asthmatics, baseline PC20, DRS, CIR and PRI were measured and evaluated as predictors of acute asthma exacerbations.We found that PRI was significantly related to the presence of asthma exacerbations during the first year of follow-up in both cohorts of childhood (p=0.025) and elderly asthmatics (p=0.003). In addition, PRI showed a significant association with the total number of steroid bursts during 4.3 years of follow-up in the cohort of childhood asthmatics (p=0.04).We demonstrated that PRI, an index of reversibility following methacholine-induced bronchoconstriction, was a good clinical predictor of acute exacerbations of asthma in both childhood and elderly asthmatics. PMID:27076579

  12. Risk management in magnetic resonance: failure mode, effects, and criticality analysis.

    PubMed

    Petrillo, Antonella; Fusco, Roberta; Granata, Vincenza; Filice, Salvatore; Raiano, Nicola; Amato, Daniela Maria; Zirpoli, Maria; di Finizio, Alessandro; Sansone, Mario; Russo, Anna; Covelli, Eugenio Maria; Pedicini, Tonino; Triassi, Maria

    2013-01-01

    The aim of the study was to perform a risk management procedure in "Magnetic Resonance Examination" process in order to identify the critical phases and sources of radiological errors and to identify potential improvement projects including procedures, tests, and checks to reduce the error occurrence risk. In this study we used the proactive analysis "Failure Mode Effects Criticality Analysis," a qualitative and quantitative risk management procedure; has calculated Priority Risk Index (PRI) for each activity of the process; have identified, on the PRI basis, the most critical activities and, for them, have defined improvement projects; and have recalculated the PRI after implementation of improvement projects for each activity. Time stop and audits are performed in order to control the new procedures. The results showed that the most critical tasks of "Magnetic Resonance Examination" process were the reception of the patient, the patient schedule drafting, the closing examination, and the organization of activities. Four improvement projects have been defined and executed. PRI evaluation after improvement projects implementation has shown that the risk decreased significantly following the implementation of procedures and controls defined in improvement projects, resulting in a reduction of the PRI between 43% and 100%. PMID:24171173

  13. Remotely-sensed detection of effects of extreme droughts on gross primary production

    NASA Astrophysics Data System (ADS)

    Vicca, Sara; Balzarolo, Manuela; Filella, Iolanda; Granier, André; Herbst, Mathias; Knohl, Alexander; Longdoz, Bernard; Mund, Martina; Nagy, Zoltan; Pintér, Krisztina; Rambal, Serge; Verbesselt, Jan; Verger, Aleixandre; Zeileis, Achim; Zhang, Chao; Peñuelas, Josep

    2016-06-01

    Severe droughts strongly impact photosynthesis (GPP), and satellite imagery has yet to demonstrate its ability to detect drought effects. Especially changes in vegetation functioning when vegetation state remains unaltered (no browning or defoliation) pose a challenge to satellite-derived indicators. We evaluated the performance of different satellite indicators to detect strong drought effects on GPP in a beech forest in France (Hesse), where vegetation state remained largely unaffected while GPP decreased substantially. We compared the results with three additional sites: a Mediterranean holm oak forest (Puéchabon), a temperate beech forest (Hainich), and a semi-arid grassland (Bugacpuszta). In Hesse, a three-year reduction in GPP following drought was detected only by the Enhanced Vegetation Index (EVI). The Photochemical Reflectance Index (PRI) also detected this drought effect, but only after normalization for absorbed light. In Puéchabon normalized PRI outperformed the other indicators, while the short-term drought effect in Hainich was not detected by any tested indicator. In contrast, most indicators, but not PRI, captured the drought effects in Bugacpuszta. Hence, PRI improved detection of drought effects on GPP in forests and we propose that PRI normalized for absorbed light is considered in future algorithms to estimate GPP from space.

  14. The photochemical reflectance index provides an optical indicator of spring photosynthetic activation in evergreen conifers.

    PubMed

    Wong, Christopher Y S; Gamon, John A

    2015-04-01

    In evergreens, the seasonal down-regulation and reactivation of photosynthesis is largely invisible and difficult to assess with remote sensing. This invisible phenology may be changing as a result of climate change. To better understand the mechanism and timing of these hidden physiological transitions, we explored several assays and optical indicators of spring photosynthetic activation in conifers exposed to a boreal climate. The photochemical reflectance index (PRI), chlorophyll fluorescence, and leaf pigments for evergreen conifer seedlings were monitored over 1 yr of a boreal climate with the addition of gas exchange during the spring. PRI, electron transport rate, pigment levels, light-use efficiency and photosynthesis all exhibited striking seasonal changes, with varying kinetics and strengths of correlation, which were used to evaluate the mechanisms and timing of spring activation. PRI and pigment pools were closely timed with photosynthetic reactivation measured by gas exchange. The PRI provided a clear optical indicator of spring photosynthetic activation that was detectable at leaf and stand scales in conifers. We propose that PRI might provide a useful metric of effective growing season length amenable to remote sensing and could improve remote-sensing-driven models of carbon uptake in evergreen ecosystems. PMID:25641209

  15. Remotely-sensed detection of effects of extreme droughts on gross primary production.

    PubMed

    Vicca, Sara; Balzarolo, Manuela; Filella, Iolanda; Granier, André; Herbst, Mathias; Knohl, Alexander; Longdoz, Bernard; Mund, Martina; Nagy, Zoltan; Pintér, Krisztina; Rambal, Serge; Verbesselt, Jan; Verger, Aleixandre; Zeileis, Achim; Zhang, Chao; Peñuelas, Josep

    2016-01-01

    Severe droughts strongly impact photosynthesis (GPP), and satellite imagery has yet to demonstrate its ability to detect drought effects. Especially changes in vegetation functioning when vegetation state remains unaltered (no browning or defoliation) pose a challenge to satellite-derived indicators. We evaluated the performance of different satellite indicators to detect strong drought effects on GPP in a beech forest in France (Hesse), where vegetation state remained largely unaffected while GPP decreased substantially. We compared the results with three additional sites: a Mediterranean holm oak forest (Puéchabon), a temperate beech forest (Hainich), and a semi-arid grassland (Bugacpuszta). In Hesse, a three-year reduction in GPP following drought was detected only by the Enhanced Vegetation Index (EVI). The Photochemical Reflectance Index (PRI) also detected this drought effect, but only after normalization for absorbed light. In Puéchabon normalized PRI outperformed the other indicators, while the short-term drought effect in Hainich was not detected by any tested indicator. In contrast, most indicators, but not PRI, captured the drought effects in Bugacpuszta. Hence, PRI improved detection of drought effects on GPP in forests and we propose that PRI normalized for absorbed light is considered in future algorithms to estimate GPP from space. PMID:27301671

  16. Remote sensing of assimilating branch light use efficiency using the photochemical reflectance index in Haloxylon ammodendron forest

    NASA Astrophysics Data System (ADS)

    Nyongesah, Maina John; Quan, Wang; Lu, Xu

    2016-04-01

    Five healthy Haloxylon ammodendron trees were randomly selected to monitor the photochemical reflectance index (PRI) and its relation to light use efficiency (LUE) in shaded and sunlit assimilating branches. Linear regression was performed where the results revealed that LUE decreased with seasonal courses with vivid midday depression regardless of light variation within canopies. PRI and LUE decoupled in early spring when the foliage was deeply downregulated, with high correlation (R2=0.8, p<0.001) during most parts of the year. Measured and estimated LUE were highly correlated for the July to September dataset (R2=0.73, p<0.001) compared to May to June datasets (R2=0.35, p<0.001). The estimated LUE for young assimilating branches could be obtained with a high RMSE of 0.01, compared to mature branches with an RMSE of 0.003. The measured LUE values were ˜20% higher than estimated LUE during the period from May to June, and values were slightly lower at the end of the growing season. This was attributed to differences in the physiological and biochemical mechanisms controlling the seasonal dynamics of PRI. Therefore, PRI is the best estimator of LUE when age-related changes and canopy light partitioning are considered in assimilating organs. Combined use of PRI with pigments could improve the remote evaluation of LUE.

  17. The viability of the Parenting Representations Interview for assessing and measuring change in parents of adolescents.

    PubMed

    Scharf, Miri; Mayseless, Ofra; Kivenson-Baron, Inbal

    2015-01-01

    Parents' representations include parents' views of their adolescent, of their own parenting and of the parent-adolescent relationship. Two longitudinal studies of parents and their adolescent sons and daughters support the validity of scales coding mothers in the Parenting Representations Interview-Adolescence (PRI-A). The studies, conducted in Israel during the transition from home to military service, demonstrated that three dimensions derived from the PRI-A: positive representations of adolescents, negative emotionality and inadequate boundaries were associated with adolescents' AAI variables, relatedness-autonomy behaviors with mothers, and with other indicators, such as adolescents' wellbeing, romantic intimacy and individuation. Examining parenting representations could help practitioners pinpoint targets for intervention and evaluate the changes that families go through during psychotherapy, as well as the therapeutic process and its outcomes. The findings support the viability of the PRI for use in attachment based interventions for adolescents. PMID:25703357

  18. Impulsive sounds change European seabass swimming patterns: Influence of pulse repetition interval.

    PubMed

    Neo, Y Y; Ufkes, E; Kastelein, R A; Winter, H V; Ten Cate, C; Slabbekoorn, H

    2015-08-15

    Seismic shootings and offshore pile-driving are regularly performed, emitting significant amounts of noise that may negatively affect fish behaviour. The pulse repetition interval (PRI) of these impulsive sounds may vary considerably and influence the behavioural impact and recovery. Here, we tested the effect of four PRIs (0.5-4.0s) on European seabass swimming patterns in an outdoor basin. At the onset of the sound exposures, the fish swam faster and dived deeper in tighter shoals. PRI affected the immediate and delayed behavioural changes but not the recovery time. Our study highlights that (1) the behavioural changes of captive European seabass were consistent with previous indoor and outdoor studies; (2) PRI could influence behavioural impact differentially, which may have management implications; (3) some acoustic metrics, e.g. SELcum, may have limited predictive power to assess the strength of behavioural impacts of noise. Noise impact assessments need to consider the contribution of sound temporal structure. PMID:26088542

  19. Primary MicroRNA Processing Assay Reconstituted Using Recombinant Drosha and DGCR8

    PubMed Central

    Barr, Ian; Guo, Feng

    2016-01-01

    In animals, the Microprocessor complex cleaves primary transcripts of microRNAs (pri-miRNAs) to produce precursor microRNAs in the nucleus. The core components of Microprocessor include the Drosha ribonuclease and its RNA-binding partner protein DiGeorge critical region 8 (DGCR8). DGCR8 has been shown to tightly bind an Fe(III) heme cofactor, which activates its pri-miRNA processing activity. Here we describe how to reconstitute pri-miRNA processing using recombinant human Drosha and DGCR8 proteins. In particular, we present the procedures for expressing and purifying DGCR8 as an Fe(III) heme-bound dimer, the most active form of this protein, and for estimating its heme content. PMID:24166303

  20. A Short Open Reading Frame Encompassing the MicroRNA173 Target Site Plays a Role in trans-Acting Small Interfering RNA Biogenesis.

    PubMed

    Yoshikawa, Manabu; Iki, Taichiro; Numa, Hisataka; Miyashita, Kyoko; Meshi, Tetsuo; Ishikawa, Masayuki

    2016-05-01

    trans-Acting small interfering RNAs (tasiRNAs) participate in the regulation of organ morphogenesis and determination of developmental timing in plants by down-regulating target genes through mRNA cleavage. The production of tasiRNAs is triggered by microRNA173 (miR173) and other specific microRNA-mediated cleavage of 5'-capped and 3'-polyadenylated primary TAS transcripts (pri-TASs). Although pri-TASs are not thought to encode functional proteins, they contain multiple short open reading frames (ORFs). For example, the primary TAS2 transcript (pri-TAS2) contains 11 short ORFs, and the third ORF from the 5' terminus (ORF3) encompasses the miR173 target site. Here, we show that nonsense mutations in ORF3 of pri-TAS2 upstream of the miR173 recognition site suppress tasiRNA accumulation and that ORF3 is translated in vitro. Glycerol gradient centrifugation analysis of Arabidopsis (Arabidopsis thaliana) plant extracts revealed that pri-TAS2 and its miR173-cleaved 5' and 3' fragments are fractionated together in the polysome fractions. These and previous results suggest that the 3' fragment of pri-TAS2, which is a source of tasiRNAs, forms a huge complex containing SGS3, miR173-programmed AGO1 RNA-induced silencing complex, the 5' fragment, and ribosomes. This complex overaccumulated, moderately accumulated, and did not accumulate in rdr6, sde5, and sgs3 mutants, respectively. The sgs3 sde5 and rdr6 sde5 double mutants showed phenotypes similar to those of sgs3 and sde5 single mutants, respectively, with regard to the TAS2-related RNA accumulation, suggesting that the complex is formed in an SGS3-dependent manner, somehow modified and stabilized by SDE5, and becomes competent for RDR6 action. Ribosomes in this complex likely play an important role in this process. PMID:26966170

  1. Comparative effects of deficit irrigation and alternate partial root-zone irrigation on xylem pH, ABA and ionic concentrations in tomatoes

    PubMed Central

    Wang, Yaosheng; Liu, Fulai; Jensen, Christian Richardt

    2012-01-01

    Comparative effects of partial root-zone irrigation (PRI) and deficit irrigation (DI) on xylem pH, ABA, and ionic concentrations of tomato (Lycopersicon esculentum L.) plants were investigated in two split-root pot experiments. Results showed that PRI plants had similar or significantly higher xylem pH, which was increased by 0.2 units relative to DI plants. Nitrate and total ionic concentrations (cations+anions), and the proportion of cations influenced xylem pH such that xylem pH increases as nitrate and total ionic concentrations decrease, and the proportion of cations increases. In most cases, the xylem ABA concentration was similar for PRI and DI plants, and a clear association between increases in xylem pH with increasing xylem ABA concentration was only found when the soil water content was relatively low. The concentrations of anions, cations, and the sum of anions and cations in PRI were higher than in the DI treatment when soil water content was relatively high in the wetted soil compartment. However, when water content in both soil compartments of the PRI pots were very low before the next irrigation, the acquisition of nutrients by roots was reduced, resulting in lower concentrations of anions and cations in the PRI than in the DI treatment. It is therefore essential that the soil water content in the wet zone should be maintained relatively high while that in the drying soil zone should not be very low, both conditions are crucial to maintain high soil and plant water status while sustaining ABA signalling of the plants. PMID:22162869

  2. miR-34a expression, epigenetic regulation, and function in human placental diseases

    PubMed Central

    Doridot, Ludivine; Houry, Dorothée; Gaillard, Harald; Chelbi, Sonia T; Barbaux, Sandrine; Vaiman, Daniel

    2014-01-01

    Preeclampsia (PE) is the major pregnancy-induced hypertensive disorder responsible for maternal and fetal morbidity and mortality that can be associated with intrauterine growth restriction (IUGR). PE and IUGR are thought to be due to a placental defect, occurring early during pregnancy. Several placental microRNAs (miRNAs) have been shown to be deregulated in the context of placental diseases and could thus play a role in the pathophysiology of PE. Here, we show that pri-miR-34a is overexpressed in preeclamptic placentas and that its placental expression is much higher during the first trimester of pregnancy than at term, suggesting a possible developmental role. We explored pri-miR-34a regulation and showed that P53, a known activator of miR-34a, is reduced in all pathological placentas and that hypoxia can induce pri-miR-34a expression in JEG-3 cells. We also studied the methylation status of the miR-34a promoter and revealed hypomethylation in all preeclamptic placentas (associated or not with IUGR), whereas hypoxia induced a hypermethylation in JEG-3 cells at 72 h. Despite the overexpression of pri-miR-34a in preeclampsia, there was a striking decrease of the mature miR-34a in this condition, suggesting preeclampsia-driven alteration of pri-miR-34a maturation. SERPINA3, a protease inhibitor involved in placental diseases, is elevated in IUGR and PE. We show here that miR-34a overexpression in JEG-3 downregulates SERPINA3. The low level of mature miR-34a could thus be an important mechanism contributing to SERPINA3 upregulation in placental diseases. Overall, our results support a role for miR-34a in the pathophysiology of preeclampsia, through deregulation of the pri-miRNA expression and its altered maturation. PMID:24081307

  3. bmo-miR-0001 and bmo-miR-0015 down-regulate expression of Bombyx mori fibroin light chain gene in vitro*

    PubMed Central

    Chen, Chen; Fan, Yang-yang; Wang, Xin; Song, Fei; Jiang, Tao; Qian, Ping; Tang, Shun-ming; Shen, Xing-jia

    2016-01-01

    Based on bioinformatic analysis, we selected two novel microRNAs (miRNAs), bmo-miR-0001 and bmo-miR-0015, from high-throughput sequencing of the Bombyx mori larval posterior silk gland (PSG). Firstly, we examined the expression of bmo-miR-0001 and bmo-miR-0015 in 12 different tissues of the 5th instar Day-3 larvae of the silkworm. The results showed that the expression levels of both bmo-miR-0001 and bmo-miR-0015 were obviously higher in the PSG than in other tissues, implying there is a spatio-temporal condition for bmo-miR-0001 and bmo-miR-0015 to regulate the expression of BmFib-L. To test this hypothesis, we constructed pri-bmo-miR-0001 expressing the plasmid pcDNA3.0 [ie1-egfp-pri-bmo-miR-0001-SV40] and pri-bmo-miR-0015 expressing the plasmid pcDNA3.0 [ie1-egfp-pri-bmo-miR-0015-SV40]. Finally, the BmN cells were harvested and luciferase activity was detected. The results showed that luciferase activity was reduced significantly (P<0.05) in BmN cells co-transfected by pcDNA3.0 [ie1-egfp-pri-bmo-miR-0001-SV40] or pcDNA3.0 [ie1-egfp-pri-bmo-miR-0015-SV40] with pGL3.0 [A3-luc-Fib-L-3'UTR-SV40], suggesting that both bmo-miR-0001 and bmo-miR-0015 can down-regulate the expression of BmFib-L in vitro. PMID:26834013

  4. Relation between clopidogrel active metabolite levels and different platelet aggregation methods in patients receiving clopidogrel and aspirin.

    PubMed

    Liang, Yan; Johnston, Marilyn; Hirsh, Jack; Pare, Guillaume; Li, Chunjian; Mehta, Shamir; Teo, Koon K; Sloane, Debi; Yi, Qilong; Zhu, Jun; Eikelboom, John W

    2012-11-01

    Clopidogrel is a prodrug that undergoes bioconversion via cytochrome P450 system to form an active metabolite (AM) that binds to the platelet ADP receptor. The antiplatelet effect of clopidogrel is commonly assessed by measuring the aggregatory response to 5 μM ADP by light transmission aggregation (LTA) or multiple electrode aggregometry (MEA) or by the vasodilator-stimulated phosphoprotein platelet reactivity index (VASP-PRI). To determine which of these three tests of platelet ADP receptor pathway inhibition most closely correlates with clopidogrel AM levels. We analyzed blood samples from 82 patients with coronary artery disease who were randomized to receive double-dose or standard dose clopidogrel for 2 weeks. We measured peak clopidogrel AM levels, platelet aggregation in response to ADP and VASP-PRI on days 1, and repeated all the measures on days 7 and 14. Linear regression analysis was used to examine the correlation between clopidogrel AM and LTA, MEA and VASP-PRI. Bland-Altman plots were used to explore the agreement between tests of the antiplatelet effects of clopidogrel. Clopidogrel AM on day 1 correlated most closely with VASP-PRI (r = -0.5767) and demonstrated weaker correlations with LTA (r = -0.4656) and MEA (r = -0.3384) (all p < 0.01). Intra-class correlation (ICC) between VASP-PRI and LTA was 0.6446; VASP-PRI and MEA was 0.4720; and LTA and MEA was 0.4693. Similar results were obtained on days 7 and 14. Commonly used pharmacodynamic measures of clopidogrel response are only moderately correlated with clopidogrel AM levels and may not be suitable to measure the adequacy of clopidogrel therapy. PMID:22797934

  5. Evaluation of the photochemical reflectance index in AVIRIS imagery

    NASA Technical Reports Server (NTRS)

    Gamon, John A.; Roberts, Dar A.; Green, Robert O.

    1995-01-01

    In this paper, we evaluate the potential for extracting the 'photochemical reflectance index' (PRI; previously called the 'physiological reflectance index') from AVIRIS data. This index, which is derived from narrow-band reflectance at 531 and 570 nm, has proven to be a useful indicator of photosynthetic function at the leaf and canopy scales. At the leaf level, PRI varies with photosynthetic capacity, radiation-use efficiency, and vegetation type (unpublished data). This finding is consistent with the hypothesis that vegetation types exhibiting chronically reduced photosynthesis during periods of stress (e.g. drought-tolerant evergreens) invest proportionally more in photoprotective processes than vegetation with high photosynthetic capacity (e.g. crops or deciduous perennials). Vertical transects in tropical and boreal forest canopies have indicated declines in PRI associated with downregulation of photosynthesis at the canopy tops under sunny, dry midday conditions (unpublished data). This reduced PRI in upper canopy levels provides a further basis for examining this signal with the 'view from above' afforded by aircraft overflights. Although many factors could confound interpretation of a subtle physiological signal at the landscape scale, we conducted a preliminary examination of PRI extracted from existing, AVIRIS imagery of Stanford University's Jasper Ridge Biological Preserve obtained on the June 2nd, 1992, overflight. The goal was to use the hyperspectral capabilities of AVIRIS to evaluate the potential of this index for obtaining useful physiological data at the landscape scale. The expectation based on leaf- and canopy-level studies was that regions containing vegetation of reduced photosynthetic capacity (e.g. chaparral or evergreen woodland) would exhibit lower PRI values than regions of high capacity (e.g. deciduous woodland).

  6. Mechanical Model of Steel-concrete Composite Joint under Sagging Bending Moment

    NASA Astrophysics Data System (ADS)

    Pisarek, Zdzisław

    2012-06-01

    In buildings with steel-concrete composite floors, joints are designed to transmit mainly hogging bending moment. In case of the large horizontal loads due to wind, earthquake or accidental events, sagging bending moments in a joint can also occur. Additionally, large deformations of the structure cause tying and prying effects. In the paper, a mechanical model based on "component method" for evaluation of characteristics of the composite joint is presented. The influence of tying and prying actions on distribution of the internal forces in a joint is also analyzed. The procedure for calculation of the characteristics of the composite joint with bolted endplate connection is elaborated too.

  7. Co-occurrence of analogous enzymes determines evolution of a novel (βα)8-isomerase sub-family after non-conserved mutations in flexible loop.

    PubMed

    Verduzco-Castro, Ernesto A; Michalska, Karolina; Endres, Michael; Juárez-Vazquez, Ana L; Noda-García, Lianet; Chang, Changsoo; Henry, Christopher S; Babnigg, Gyorgy; Joachimiak, Andrzej; Barona-Gómez, Francisco

    2016-05-01

    We investigate the evolution of co-occurring analogous enzymes involved in L-tryptophan and L-histidine biosynthesis in Actinobacteria Phylogenetic analysis of trpF homologues, a missing gene in certain clades of this lineage whose absence is complemented by a dual-substrate HisA homologue, termed PriA, found that they fall into three categories: (i) trpF-1, an L-tryptophan biosynthetic gene horizontally acquired by certain Corynebacterium species; (ii) trpF-2, a paralogue known to be involved in synthesizing a pyrrolopyrrole moiety and (iii) trpF-3, a variable non-conserved orthologue of trpF-1 We previously investigated the effect of trpF-1 upon the evolution of PriA substrate specificity, but nothing is known about the relationship between trpF-3 and priA After in vitro steady-state enzyme kinetics we found that trpF-3 encodes a phosphoribosyl anthranilate isomerase. However, mutation of this gene in Streptomyces sviceus did not lead to auxothrophy, as expected from the biosynthetic role of trpF-1 Biochemical characterization of a dozen co-occurring TrpF-2 or TrpF-3, with PriA homologues, explained the prototrophic phenotype, and unveiled an enzyme activity trade-off between TrpF and PriA. X-ray structural analysis suggests that the function of these PriA homologues is mediated by non-conserved mutations in the flexible L5 loop, which may be responsible for different substrate affinities. Thus, the PriA homologues that co-occur with TrpF-3 represent a novel enzyme family, termed PriB, which evolved in response to PRA isomerase activity. The characterization of co-occurring enzymes provides insights into the influence of functional redundancy on the evolution of enzyme function, which could be useful for enzyme functional annotation. PMID:26929404

  8. Coherent radar observations of a storm sudden commencement having a preliminary reverse impulse

    SciTech Connect

    McDiarmid, D.R.; Nielsen, E. )

    1987-01-01

    Observations of the February 4, 1983, storm sudden commencement (ssc) by the STARE and SABRE radar systems are presented. The observing stations were in the dusk sector, where the ssc was accompanied by a preliminary reverse impulse (PRI). The radar data show the PRI to be a consequence of the ssc compression wave producing an initial antisunward flow. The polarization of the ssc electric field in the ionosphere is seen to have both longitudinal and latitudinal structure. The observations are discussed in terms of the propagation of the ssc disturbance throughout the magnetosphere.

  9. Utilizing In Situ Directional Hyperspectral Measurements to Validate Bio-Indicator Simulations for a Corn Crop Canopy

    NASA Technical Reports Server (NTRS)

    Cheng, Yen-Ben; Middleton, Elizabeth M.; Huemmrich, Karl F.; Zhang, Qingyuan; Campbell, Petya K. E.; Corp, Lawrence A.; Russ, Andrew L.; Kustas, William P.

    2010-01-01

    Two radiative transfer canopy models, SAIL and the two-layer Markov-Chain Canopy Reflectance Model (MCRM), were coupled with in situ leaf optical properties to simulate canopy-level spectral band ratio vegetation indices with the focus on the photochemical reflectance index in a cornfield. In situ hyperspectral measurements were made at both leaf and canopy levels. Leaf optical properties were obtained from both sunlit and shaded leaves. Canopy reflectance was acquired for eight different relative azimuth angles (psi) at three different view zenith angles (Theta (sub v)), and later used to validate model outputs. Field observations of photochemical reflectance index (PRI) for sunlit leaves exhibited lower values than shaded leaves, indicating higher light stress. Canopy PRI expressed obvious sensitivity to viewing geometry, as a function of both Theta (sub v) and psi . Overall, simulations from MCRM exhibited better agreements with in situ values than SAIL. When using only sunlit leaves as input, the MCRM-simulated PRI values showed satisfactory correlation and RMSE, as compared to in situ values. However, the performance of the MCRM model was significantly improved after defining a lower canopy layer comprised of shaded leaves beneath the upper sunlit leaf layer. Four other widely used band ratio vegetation indices were also studied and compared with the PRI results. MCRM simulations were able to generate satisfactory simulations for these other four indices when using only sunlit leaves as input; but unlike PRI, adding shaded leaves did not improve the performance of MCRM. These results support the hypothesis that the PRI is sensitive to physiological dynamics while the others detect static factors related to canopy structure. Sensitivity analysis was performed on MCRM in order to better understand the effects of structure related parameters on the PRI simulations. Leaf area index (LAI) showed the most significant impact on MCRM-simulated PRI among the parameters

  10. The Photochemical Reflectance Index from Directional Cornfield Reflectances: Observations and Simulations

    NASA Technical Reports Server (NTRS)

    Cheng, Yen-Ben; Middleton, Elizabeth M.; Zhang, Qingyuan; Corp, Lawrence A.; Dandois, Jonathan; Kustas, William P.

    2012-01-01

    The two-layer Markov chain Analytical Canopy Reflectance Model (ACRM) was linked with in situ hyperspectral leaf optical properties to simulate the Photochemical Reflectance Index (PRI) for a corn crop canopy at three different growth stages. This is an extended study after a successful demonstration of PRI simulations for a cornfield previously conducted at an early vegetative growth stage. Consistent with previous in situ studies, sunlit leaves exhibited lower PRI values than shaded leaves. Since sunlit (shaded) foliage dominates the canopy in the reflectance hotspot (coldspot), the canopy PRI derived from field hyperspectral observations displayed sensitivity to both view zenith angle and relative azimuth angle at all growth stages. Consequently, sunlit and shaded canopy sectors were most differentiated when viewed along the azimuth matching the solar principal plane. These directional PRI responses associated with sunlit/shaded foliage were successfully reproduced by the ACRM. As before, the simulated PRI values from the current study were closer to in situ values when both sunlit and shaded leaves were utilized as model input data in a two-layer mode, instead of a one-layer mode with sunlit leaves only. Model performance as judged by correlation between in situ and simulated values was strongest for the mature corn crop (r = 0.87, RMSE = 0.0048), followed by the early vegetative stage (r = 0.78; RMSE = 0.0051) and the early senescent stage (r = 0.65; RMSE = 0.0104). Since the benefit of including shaded leaves in the scheme varied across different growth stages, a further analysis was conducted to investigate how variable fractions of sunlit/shaded leaves affect the canopy PRI values expected for a cornfield, with implications for 20 remote sensing monitoring options. Simulations of the sunlit to shaded canopy ratio near 50/50 +/- 10 (e.g., 60/40) matching field observations at all growth stages were examined. Our results suggest in the importance of the

  11. Collaboration and Integration in Rural Development.

    ERIC Educational Resources Information Center

    Lassey, William R.; Hagood, Richard A.

    Reporting on a rural planning and development program that proposes to develop, install, and evaluate alternative models for more effective collaboration and integration of the complex bureaucracies with responsibility for rural regions, this paper describes "Partnership for Rural Improvement" (PRI). Focusing on 11 counties in northcentral and…

  12. Production of bermudagrass for bio-fuels: effect of two genotypes on pyrolysis product yield

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bermudagrass is the perennial grass used as forage for livestock and harvested as hay on 10 to 15 million acres in Southern United States. It has potential as an energy crop for the production of biofuels through the lignocellulosic conversion program. Coastal was released in 1943 and was the pri...

  13. Research and Teaching. The Science Identity of College Students: Exploring the Intersection of Gender, Race, and Ethnicity

    ERIC Educational Resources Information Center

    Hazari, Zahra; Sadler, Philip M.; Sonnert, Gerhard

    2013-01-01

    This study explores students' self-perceptions across science subjects (biology, chemistry, and physics) by gender and underrepresented minority group membership. The data are drawn from the Persistence Research in Science and Engineering (PRiSE) project, which surveyed 7,505 students (enrolled in college English courses required for all…

  14. IMPACT OF URBAN AND INDUSTRIAL EMISSIONS ON MESOSCALE PRECIPITATION QUALITY

    EPA Science Inventory

    Results from an 'acid rain' field study around the city of Philadelphia are presented. The study involved the sampling of wet deposition at a network of 40 sites within a distance of 60 km from the Delaware River. Emphasis was placed on event-type rain sampling of frontal and pri...

  15. The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary MicroRNAs

    PubMed Central

    Sun, Zhenfei; Guo, Tongtong; Liu, Yin; Liu, Qi; Fang, Yuda

    2015-01-01

    The precise regulation of microRNA (miRNA) transcription and processing is important for eukaryotic development. Plant miRNAs are first transcribed as stem-loop primary miRNAs (pri-miRNAs) by RNA polymerase II,then cleaved in the nucleus into mature miRNAs by Dicer-like 1 (DCL1). We identified a cycling DOF transcription factor, CDF2, which interacts with DCL1 and regulates the accumulation of a population of miRNAs. CDF2 binds directly to the promoters of some miRNAs and works as a transcription activator or repressor for these miRNA genes. CDF2 binds preferentially to the pri-miRNAs regulated by itself and affects DCL1-mediated processing of these pri-miRNAs. Genetically, CDF2 works in the same pathway as miR156 or miR172 to control flowering. We conclude that CDF2 regulates a group of pri-miRNAs at both the transcriptional and posttranscriptional levels to maintain proper levels of their mature miRNAs to control plant development. PMID:26473486

  16. 77 FR 4858 - 60-Day Notice of Proposed Information Collection: DS 5507, Affidavit of Physical Presence or...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-31

    ... . Mail (paper, disk, or CD-ROM submissions): U.S. Department of State, CA/OCS/PRI, SA-29, 4th Floor...- 29, 4th Floor, Washington, DC 20520 or at ASKPRI@state.gov . SUPPLEMENTARY INFORMATION: We are... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF STATE...

  17. MIDDLE REACH OF THE SNAKE RIVER: WATER QUALITY AND BENTHIC BIOMONITORING

    EPA Science Inventory

    This study examined spatial and temporal trends in water quality, sestonic and benthic algal concentrations, and benthic macroinvertebrate taxa richness, population density, and biomass at nine stations along the Middle Snake River from Pillar Falls to Upper Salmon Falls Dam. Pri...

  18. Relationship of antral follicle counts to fertility and ovarian AMH mRNA levels in beef cows

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In mammalian females, reproductive senescence is associated with decreased numbers of follicles in the ovary. Anti-Mullerian Hormone (AMH) of ovarian origin has been proposed to be a biomarker of the number of follicles in the ovary and of fertility in women, as well as to control activation of pri...

  19. REGIONAL PARTICULATE MODEL - 1. MODEL DESCRIPTION AND PRELIMINARY RESULTS

    EPA Science Inventory

    The gas-phase chemistry and transport mechanisms of the Regional Acid Deposition Model have been modified to create the Regional Particulate Model, a three-dimensional Eulerian model that simulates the chemistry, transport, and dynamics of sulfuric acid aerosol resulting from pri...

  20. STRUCTURE-ACTIVITY APPROACHES IN THE SCREENING OF ENVIRONMENTAL AGENTS FOR DEVELOPMENTAL TOXICITY

    EPA Science Inventory

    In drug development, SARs are an integral part of the process of finding efficacious and non-toxic analogues, and in vitro test systems which detect the biological activity of a particular chemical class have found an important role in SAR research. n contrast, SARs are not a pri...

  1. 49 CFR 239.101 - Emergency preparedness plan.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... operations on elevated structures, including drawbridges, and in electrified territory. (iii) Parallel... action to coordinate emergency efforts where adjacent rail modes of transportation run parallel to either... minimum: (A) One fire extinguisher per passenger car; (B) One pry bar per passenger car; and (C)...

  2. Evaluation of Ethanol Extracted Surface Antigens of Mycobacterium bovis for Diagnosis of Bovine Tuberculosis in Livestock Cattle and Wild Deer

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Bovine tuberculosis (TB), caused by Mycobacterium bovis, is a zoonotic disease resulting in chronic granulomatous lymphadenitis, particularly in the lungs and lung-associated lymph nodes. Although bovine TB has been nearly eradicated in many developed countries, the disease persists pri...

  3. ADHD and College Students: Exploratory and Confirmatory Factor Structures With Student and Parent Data

    ERIC Educational Resources Information Center

    Glutting, Joseph J.; Youngstrom, Eric A.; Watkins, Marley W.

    2005-01-01

    Exploratory factor analyses (EFAs) and confirmatory factor analyses (CFAs) were used to investigate the structure of the Student Report Inventory (SRI) and Parent Report Inventory (PRI) of the College Attention-Deficit/Hyperactivity Disorder (ADHD) Response Evaluation. The sample was composed of 1,080 college students and their parents and was…

  4. Dual purpose use of preterm piglets as a model of pediatric GI disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Necrotizing enterocolitis (NEC) is the most common gastrointestinal complication in human neonates, yet the pathogenesis of this disease remains poorly understood. A fundamental approach to understanding the etiology and underlying biology of NEC is the use of in vivo experimental animal models, pri...

  5. Genome Sequence of the Emerging Plant Pathogen Dickeya solani Strain RNS 08.23.3.1A

    PubMed Central

    Khayi, Slimane; Mondy, Samuel; Beury-Cirou, Amélie; Moumni, Mohieddine; Hélias, Valérie

    2014-01-01

    Here we present the genome sequence of Dickeya solani strain RNS 08.23.3.1A (PRI3337), isolated from Solanum tuberosum. Dickeya solani, recently described on potato cultures in Europe, is a proposed new taxon closely related to the Dickeya dianthicola and Dickeya dadantii species. PMID:24482527

  6. Gone but Not Forgotten

    ERIC Educational Resources Information Center

    Monastersky, Richard

    2006-01-01

    Neanderthals, those long-lost cousins of modern humans, will not remain lost for long, at least from the prying eyes of geneticists. Two teams of scientists announced that for the first time they had analyzed DNA from the nuclei of cells preserved in 37,000-year-old Neanderthal fossils. That, they say, lays the groundwork for determining the…

  7. ENVIRONMENTAL QUALITY INFORMATION SYSTEM - EQULS® - ITER

    EPA Science Inventory

    This project consisted of an evaluation of the Environmental Quality Information System (EQuIS) software designed by Earthsoft, Inc. as an environmental data management and analysis platform for monitoring and remediation projects. In consultation with the EQuIS vendor, six pri...

  8. Improved high-throughput bioassay for Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As we gain more information through functional genomic studies of Rhyzopertha dominica (F.), we need a high throughput bioassay system to screen potential biopesticides. R. dominica is an internal feeder during immature stages and presents unique challenges with traditional bioassay methods. Our pri...

  9. Rbfox3 Controls the Biogenesis of a Subset of MicroRNAs

    PubMed Central

    Kim, Kee K.; Yang, Yanqin; Zhu, Jun; Adelstein, Robert S.; Kawamoto, Sachiyo

    2014-01-01

    RNA-binding proteins (RBPs) regulate numerous aspects of gene expression, thus identification of endogenous targets of RBPs is important for understanding their functions in cells. Here we identified transcriptome-wide targets of Rbfox3 in neuronally differentiated P19 cells and mouse brain using Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP). Although Rbfox3 is known to regulate pre-mRNA splicing through binding to the UGCAUG motif, PAR-CLIP analysis revealed diverse Rbfox3 targets including primary-microRNAs (pri-miRNAs) which lack the UGCAUG motif. Induced expression and depletion of Rbfox3 led to changes in the expression levels of a subset of PAR-CLIP-detected miRNAs. In vitro analyses revealed that Rbfox3 functions as a positive and a negative regulator at the stage of pri-miRNA processing to precursor-miRNA. Rbfox3 binds directly to pri-miRNAs and regulates the recruitment of the microprocessor complex to pri-miRNAs. Our study proposes a novel function for Rbfox3 in miRNA biogenesis. PMID:25240799

  10. Integrative analysis of 111 reference human epigenomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for pri...

  11. Development and Validation of Rapid Assessment Indices of Condition for Coastal for Coastal Wetlands in Southern New England, USA

    EPA Science Inventory

    Vegetation, soils, on-site disturbances, and watershed land use and land cover were assessed at 81 coastal wetland sites using the New England Rapid Asssessment Method (NERAM). Condition indices (CIs) were derived from various combinations of the multi-dimensional data using pri...

  12. EPA'S STUDY OF THE GENERATION AND CONTROL OF AIR POLLUTANTS FROM THE COMBUSTION OF ORIMULSION

    EPA Science Inventory

    The paper discusses an EPA study of the grneration and control of air pollutants from the combustion of Orimulsion, a high-sulfur liquid petroleum fuel composed of approximately 70% Venezuelan bitumen, 30% water, and trace amounts of surfactant. (NOTE: It is being used as the pri...

  13. Characteristics of Criterion-Referenced Instruments: Implications for Materials Selection for the Learning Disabled.

    ERIC Educational Resources Information Center

    Blasi, Joyce F.

    Discussed are characteristics of criterion referenced reading tests for use with learning disabled (LD) children, and analyzed are the Basic Educational Skills Inventory (BESI), the Prescriptive Reading Inventory (PRI), and the Cooper-McGuire Diagnostic Work-Analysis Test (CooperMcGuire). Criterion referenced tests are defined; and problems in…

  14. Beyond the Narrative Mode in the Composition Classroom: Embracing a Return to the Personal Essay

    ERIC Educational Resources Information Center

    Haugen, Hayley Mitchell

    2013-01-01

    Knoblauch and Brannon might suggest I pry loose the grip that ancient rhetorical tradition has on my modern classroom, but I'm not convinced I can so easily abandon the ancient rhetoricians. Learning to embrace the different, more creative, and less frequently acknowledged elements of this tradition may be the way for me to go instead. The ancient…

  15. WISC-IV and WISC-III Profiles in Children with ADHD

    ERIC Educational Resources Information Center

    Mayes, Susan Dickerson; Calhoun, Susan L.

    2006-01-01

    Wechsler Intelligence Scale for Children, 3rd and 4th editions (WISC-III n = 586 and WISC-IV n = 118), profiles were compared for children with ADHD and normal intelligence. Mean Verbal Comprehension Index (VCI) and Perceptual Organization/Perceptual Reasoning Index (POI/PRI) scores were significantly higher than Freedom From…

  16. SEASONAL AND REGIONAL VARIATIONS OF PRIMARY AND SECONDARY ORGANIC AEROSOLS OVER THE CONTINENTAL UNITED STATES: SEMI-EMPIRICAL ESTIMATES AND MODEL EVALUATION

    EPA Science Inventory

    Seasonal and regional variations of primary (OCpri) and secondary (OCsec) organic carbon aerosols across the continental U.S. for the year 2001 were examined by a semi-empirical technique using observed OC and elemental carbon (EC) data from 142 routine moni...

  17. Interactive effects of deficit irrigation, elevated temperature, and elevated [CO2] on peanut growth in low irrigation production settings

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Improving crop water use (both agronomic and biological) is critical to most cropping areas around the world. The persistance of adverse climate conditions and predicted decreased availability of fresh water for crop production are the largest challenges to agriculture in the coming decades. Our pri...

  18. Cobalt(III) Protoporphyrin Activates the DGCR8 Protein and Can Compensate microRNA Processing Deficiency.

    PubMed

    Barr, Ian; Weitz, Sara H; Atkin, Talia; Hsu, PeiKen; Karayiorgou, Maria; Gogos, Joseph A; Weiss, Shimon; Guo, Feng

    2015-06-18

    Processing of microRNA primary transcripts (pri-miRNAs) is highly regulated and defects in the processing machinery play a key role in many human diseases. In 22q11.2 deletion syndrome (22q11.2DS), heterozygous deletion of DiGeorge critical region gene 8 (DGCR8) causes a processing deficiency, which contributes to abnormal brain development. The DGCR8 protein is the RNA-binding partner of Drosha RNase, both essential for processing canonical pri-miRNAs. To identify an agent that can compensate reduced DGCR8 expression, we screened for metalloporphyrins that can mimic the natural DGCR8 heme cofactor. We found that Co(III) protoporphyrin IX (PPIX) stably binds DGCR8 and activates it for pri-miRNA processing in vitro and in HeLa cells. Importantly, treating cultured Dgcr8(+/-) mouse neurons with Co(III)PPIX can compensate the pri-miRNA processing defects. Co(III)PPIX is effective at concentrations as low as 0.2 μM and is not degraded by heme degradation enzymes, making it useful as a research tool and a potential therapeutic. PMID:26091172

  19. DETECTION OF POLYMORPHISM USING CAPS AND DCAPS MARKERS IN TWO CHICKPEA GENOTYPES.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cleaved amplified polymorphic sequence (CAPS) and derived cleaved amplified polymorphic sequence markers (dCAPS) are sequence based and co-dominant markers. Primers were designed from the ends of bacterial artificial chromosome clones 4m10 and 15o9 as well as a partial sequence of aldolase using Pri...

  20. Diurnal and seasonal dynamics of canopy-level solar-induced chlorophyll fluorescence and spectral reflectance indices in a cornfield

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A collaborative field campaign was undertaken to examine the temporal dynamics of canopy-level solar-induced fluorescence (SIF) and the Photochemical Reflectance Index (PRI) in conjunction with photosynthetic light use efficiency (LUE) obtained from fluxes measured at an instrumented tower. We condu...

  1. Unlocking Student Data Could Lead to "App Economy" for Colleges: Colleges Are Pressured to Open Up Student Data

    ERIC Educational Resources Information Center

    DeSantis, Nick

    2012-01-01

    College campuses are hothouses of data, including course schedules, degree requirements, and grades. But much of the information remains spread out across software systems or locked on university servers. Start-up companies want to pry the information loose from campus servers in order to offer personalized services that could transform the…

  2. Utilizing in situ Directional Hyperpectral Measurements to Validate Bio-Indicator Simulations for a Corn Crop Canaopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two radiative transfer canopy models, SAIL and the Markov-Chain Canopy Reflectance Model (MRCM), were coupled with in situ leaf optical properties to simulate canopy-level spectral band ratio vegetation indices with the focus on the Photochemical Reflectance Index (PRI) in a cornfield. In situ hyper...

  3. Alternative splicing affects the subcellular localization of Drosha

    PubMed Central

    Link, Steffen; Grund, Stefanie E.; Diederichs, Sven

    2016-01-01

    The RNase III enzyme Drosha is a key factor in microRNA (miRNA) biogenesis and as such indispensable for cellular homeostasis and developmental processes. Together with its co-factor DGCR8, it converts the primary transcript (pri-miRNA) into the precursor hairpin (pre-miRNA) in the nucleus. While the middle and the C-terminal domain are crucial for pri-miRNA processing and DGCR8 binding, the function of the N-terminus remains cryptic. Different studies have linked this region to the subcellular localization of Drosha, stabilization and response to stress. In this study, we identify alternatively spliced Drosha transcripts that are devoid of a part of the arginine/serine-rich (RS-rich) domain and expressed in a large set of human cells. In contrast to their expected habitation, we find two isoforms also present in the cytoplasm, while the other two isoforms reside exclusively in the nucleus. Their processing activity for pri-miRNAs and the binding to co-factors remains unaltered. In multiple cell lines, the endogenous mRNA expression of the Drosha isoforms correlates with the localization of endogenous Drosha proteins. The pri-miRNA processing efficiency is not significantly different between groups of cells with or without cytoplasmic Drosha expression. In summary, we discovered novel isoforms of Drosha with differential subcellular localization pointing toward additional layers of complexity in the regulation of its activity. PMID:27185895

  4. The conservation-production interface in rangelands: Acknowledging tradeoffs and moving towards win-win solutions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Provision of wildlife habitat in rangelands, particularly for birds of conservation concern, is increasingly recognized as an important ecosystem service. Accommodating human use is also a key component of ecosystem management. Most remaining grassland bird habitat in the western Great Plains is pri...

  5. STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis

    PubMed Central

    Ben Chaabane, Samir; Liu, Renyi; Chinnusamy, Viswanathan; Kwon, Yerim; Park, Joo-hyuk; Kim, Seo Yeon; Zhu, Jian-Kang; Yang, Seong Wook; Lee, Byeong-ha

    2013-01-01

    MicroRNAs (miRNAs) are small regulatory RNAs that have important regulatory roles in numerous developmental and metabolic processes in most eukaryotes. In Arabidopsis, DICER-LIKE1 (DCL1), HYPONASTIC LEAVES 1, SERRATE, HUA ENHANCER1 and HASTY are involved in processing of primary miRNAs (pri-miRNAs) to yield precursor miRNAs (pre-miRNAs) and eventually miRNAs. In addition to these components, mRNA cap-binding proteins, CBP80/ABA HYPERSENSITIVE1 and CBP20, also participate in miRNA biogenesis. Here, we show that STABILIZED1 (STA1), an Arabidopsis pre-mRNA processing factor 6 homolog, is also involved in the biogenesis of miRNAs. Similar to other miRNA biogenesis-defective mutants, sta1-1 accumulated significantly lower levels of mature miRNAs and concurrently higher levels of pri-miRNAs than wild type. The dramatic reductions of mature miRNAs were associated with the accumulation of their target gene transcripts and developmental defects. Furthermore, sta1-1 impaired splicing of intron containing pri-miRNAs and decreased transcript levels of DCL1. These results suggest that STA1 is involved in miRNA biogenesis directly by functioning in pri-miRNA splicing and indirectly by modulating the DCL1 transcript level. PMID:23268445

  6. Inhibition of Cyclic Adenosine Monophosphate (cAMP)-response Element-binding Protein (CREB)-binding Protein (CBP)/β-Catenin Reduces Liver Fibrosis in Mice

    PubMed Central

    Osawa, Yosuke; Oboki, Keisuke; Imamura, Jun; Kojika, Ekumi; Hayashi, Yukiko; Hishima, Tsunekazu; Saibara, Toshiji; Shibasaki, Futoshi; Kohara, Michinori; Kimura, Kiminori

    2015-01-01

    Wnt/β-catenin is involved in every aspect of embryonic development and in the pathogenesis of many human diseases, and is also implicated in organ fibrosis. However, the role of β-catenin-mediated signaling on liver fibrosis remains unclear. To explore this issue, the effects of PRI-724, a selective inhibitor of the cAMP-response element-binding protein-binding protein (CBP)/β-catenin interaction, on liver fibrosis were examined using carbon tetrachloride (CCl4)- or bile duct ligation (BDL)-induced mouse liver fibrosis models. Following repetitive CCl4 administrations, the nuclear translocation of β-catenin was observed only in the non-parenchymal cells in the liver. PRI-724 treatment reduced the fibrosis induced by CCl4 or BDL. C-82, an active form of PRI-724, inhibited the activation of isolated primary mouse quiescent hepatic stellate cells (HSCs) and promoted cell death in culture-activated HSCs. During the fibrosis resolution period, an increase in F4/80+ CD11b+ and Ly6Clow CD11b+ macrophages was induced by CCl4 and was sustained for two weeks thereafter, even after having stopped CCl4 treatment. PRI-724 accelerated the resolution of CCl4-induced liver fibrosis, and this was accompanied by increased matrix metalloproteinase (MMP)-9, MMP-2, and MMP-8 expression in intrahepatic leukocytes. In conclusion, targeting the CBP/β-catenin interaction may become a new therapeutic strategy in treating liver fibrosis. PMID:26870800

  7. Tool Removes Coil-Spring Thread Inserts

    NASA Technical Reports Server (NTRS)

    Collins, Gerald J., Jr.; Swenson, Gary J.; Mcclellan, J. Scott

    1991-01-01

    Tool removes coil-spring thread inserts from threaded holes. Threads into hole, pries insert loose, grips insert, then pulls insert to thread it out of hole. Effects essentially reverse of insertion process to ease removal and avoid further damage to threaded inner surface of hole.

  8. Atmospheric Modeling

    EPA Science Inventory

    Although air quality models have been applied historically to address issues specific to ambient air quality standards (i.e., one criteria pollutant at a time) or welfare (e.g.. acid deposition or visibility impairment). they are inherently multipollutant based. Therefore. in pri...

  9. Free Amino Acid Profiles from 'Pinot Noir' Grapes are Influenced by Vine N-status and Sample Preparation Method

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study examined the impact of extraction method on ammonia, free amino acids, and YAN (yeast assimilable nitrogen) concentrations in 'Pinot noir' berries obtained from a vine nutrition study (altered supply of N, P, or K). Berries were either juiced or exhaustively extracted as whole berries pri...

  10. In vitro Reconstitution Assay of miRNA Biogenesis by Arabidopsis DCL1

    PubMed Central

    Wang, Tian; Castillo-González, Claudia; You, Lan; Li, Rui; Wen, Liwei; Zhu, Hongliang; Zhang, Xiuren

    2016-01-01

    microRNAs (miRNAs) are small non-coding RNAs, regulating most if not all, biological processes in eukaryotic organisms. miRNAs are initially processed from primary transcripts (pri-miRNAs) to produce miRNA precursors (pre-miRNAs), that are further processed into miRNA and its complementary strands (miRNA/*). In Arabidopsis, and possibly other plants, the processing from pri-miRNAs to pre-miRNAs and from pre-miRNAs to miRNA/* are both implemented through Dicer-like 1 (DCL1) complexes. Recently, we demonstrated isolation of DCL1 complexes of unprecedented quality from in planta. We further successfully reconstituted DCL1 cleavage assays in vitro that were able to fully recapitulate in vivo miRNA biogenesis. Here we provide a detailed protocol of DCL1 reconstitution assays. The protocol comprises three major parts (Figure 1): 1) Preparation of pri- and pre-miRNA transcripts (Procedures A-C); 2) Purification of the recombinant Arabidopsis DCL1 machinery from Nicotiana benthamiana (N. benthamiana) through immunoprecipitation (IP) (Procedures D and E); and 3) in vitro processing of radioisotope-labeled pri- or pre-miRNAs using the isolated DCL1 complexes (Procedure F). It is our desire that the protocol be a powerful tool for the RNAi community to study mechanistic issues or to develop RNA silencing technologies.

  11. CONTINUOUS STIRRED TANK REACTOR INVESTIGATION OF THE GAS-PHASE REACTION OF HYDROXYL RADICALS AND TOLUENE

    EPA Science Inventory

    A continuous stirred tank reactor (CSTR) was used to study the gas phase reaction between HO and toluene. HO was generated by the in situ photolysis of nitrous acid. Flow reactor operation at steady state conditions with a residence time of 20 minutes allowed investigation of pri...

  12. The photochemical reflectance index from directional cornfield reflectances: Observations and simulations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The two-layer Markov chain Analytical Canopy Reflectance Model (ACRM) was linked with in situ hyperspectral leaf optical properties to simulate the Photochemical Reflectance Index (PRI) for a corn crop canopy at three different growth stages. This is an extended study after a successful demonstratio...

  13. Predicting Photosynthetic Fluxes from Spectral Reflectance of Leaves and Canopies

    NASA Technical Reports Server (NTRS)

    Gamon, John A.

    1997-01-01

    The central hypothesis of this study has been that photosynthetic efficiency and capacity can be predicted from 'physiological reflectance indices' derived from spectral reflectance of leaves and canopies. I have approached this topic with a combination of laboratory and field experiments, and have also explored the potential of deriving a meaningful physiological index from imaging spectrometry (e.g. AVIRIS). A few highlights are presented below. The main emphasis has been on the 'Photochemical Reflectance Index' (PRI), derived from reflectance at 531 nm and 570 nm. Unlike most 'conventional' vegetation indices (e.g. NDVI), PRI changes rapidly both with illumination and physiological state, because it detects the interconversion of xanthophyll cycle pigments, which serve as photoregulatory pigments and control energy distribution for the photosynthetic system. This approach has differed dramatically from most remote sensing in that it has emphasized temporal variation in narrow-band spectral signatures, instead of spatial patterns of broadband indices. Our primary conclusion has been that PRI works well as an index of photosynthetic light-use efficiency at the leaf scale, much in the same way as the fluorescence index DeltaF/Fm. However, unlike DeltaF/Fm which must be measured at close scales, PRI can be sampled at a range of spatial scales, presenting the possibility of monitoring photosynthetic fluxes remotely.

  14. CORN FLAVOR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Corn is a large part of the modern diet through sweeteners, oil, processed foods, and animal-derived foods. In addition, corn is eaten directly in bread and cereal-type foods, snack foods, and foods made from masa flour. Corn gluten meal is a byproduct of grain processed by wet milling. Although pri...

  15. Vegetation index differencing for broad-scale assessment of productivity under prolonged drought and sequential high rainfall conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ability to evaluate large tracts of land with in a consistent manner using readily available moderate resolution satellite data is a highly valuable tool for land resource managers. Herein we present a multi-scale approach using remotely sensed imagery that holds the potential to effectively pri...

  16. Alternative splicing affects the subcellular localization of Drosha.

    PubMed

    Link, Steffen; Grund, Stefanie E; Diederichs, Sven

    2016-06-20

    The RNase III enzyme Drosha is a key factor in microRNA (miRNA) biogenesis and as such indispensable for cellular homeostasis and developmental processes. Together with its co-factor DGCR8, it converts the primary transcript (pri-miRNA) into the precursor hairpin (pre-miRNA) in the nucleus. While the middle and the C-terminal domain are crucial for pri-miRNA processing and DGCR8 binding, the function of the N-terminus remains cryptic. Different studies have linked this region to the subcellular localization of Drosha, stabilization and response to stress. In this study, we identify alternatively spliced Drosha transcripts that are devoid of a part of the arginine/serine-rich (RS-rich) domain and expressed in a large set of human cells. In contrast to their expected habitation, we find two isoforms also present in the cytoplasm, while the other two isoforms reside exclusively in the nucleus. Their processing activity for pri-miRNAs and the binding to co-factors remains unaltered. In multiple cell lines, the endogenous mRNA expression of the Drosha isoforms correlates with the localization of endogenous Drosha proteins. The pri-miRNA processing efficiency is not significantly different between groups of cells with or without cytoplasmic Drosha expression. In summary, we discovered novel isoforms of Drosha with differential subcellular localization pointing toward additional layers of complexity in the regulation of its activity. PMID:27185895

  17. Molecular Technique to Fingerprint Aspergillus flavus Causing Aflatoxin Contamination in Food

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A retrotransposon, AFLAV (A. flavus retrotransposon), has been recently characterized in A. flavus. Complete DNA sequence of 7784 bp containing the AFLAV has been submitted to GenBank (accession number AY485785). Multicopies of this transposon are dispersed in the chromosomes of A. flavus. PCR pri...

  18. Separation Of Metals Bonded With Two-Sided Tape

    NASA Technical Reports Server (NTRS)

    Kelly, Michael L.

    1993-01-01

    Procedure developed to separate, without pulling, bending, or prying, objects temporarily bonded together with two-sided tape. Ultrasonic cleaning in hot kerosene enables separation without damage. Procedure applicable in removal of protective backing from metals as received, or in removing temporary bonding tape from metal specimens.

  19. Exposure to ozone modulates human airway protease/antiprotease balance contributing to increased influenza A infection

    EPA Science Inventory

    Exposure to oxidant air pollution is associated with Increased respiratory morbiditses and susceptibility to Infections Ozone is a commonly encountered oxidant air pollutant, yet Its effects on influenza infections in humans are not known ‘the greater Mexico City area was the pri...

  20. Bioassessment Tools for Stony Corals: Field Testing of Monitoring Protocols in the US Virgin Islands (St. Croix)

    EPA Science Inventory

    Survey protocols for assessing coral reef condition were field tested at 61 reef stations in St. Croix, US Virgin Islands (USVI) during 2006. Three observations for stony corals were recorded: species, size, and percent live tissue. Stony corals were selected because they are pri...

  1. 12 CFR 19.170 - Discovery depositions.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... before the scheduled hearing date, except with permission of the administrative law judge for good cause... electronic sound recording device; (ii) Upon agreement of the parties, by any other method; or (iii) For good...) Involves unwarranted attempts to pry into a party's preparation for trial; or (4) Is being conducted in...

  2. Trends in experimental high-energy physics

    SciTech Connect

    Sanford, T.W.L.

    1982-06-01

    Data from a scan of papers in Physical Review Letters and Physical Review are used to demonstrate that American high-energy physicists show a pattern of accelerator and instrumentation usage characteristic of that expected from the logistic-substitution model of Marchetti and of Fischer and Pry.

  3. Development and comparison of a Primer-Probe Energy Transfer based assay and a 5' conjugated Minor Groove Binder assay for sensitive real-time PCR detection of infectious laryngotracheitis virus.

    PubMed

    McMenamy, M J; McKillen, J; Hjertner, B; Kiss, I; Yacoub, A; Leijon, M; Duffy, C; Belák, S; Welsh, M; Allan, G

    2011-08-01

    In this study the design and development of two real-time PCR assays for the rapid, sensitive and specific detection of infectious laryngotracheitis virus (ILTV) DNA is described. A Primer-Probe Energy Transfer (PriProET) assay and 5' conjugated Minor Groove Binder (MGB) method are compared and contrasted. Both have been designed to target the thymidine kinase gene of the ILTV genome. Both PriProET and MGB assays are capable of detecting 20 copies of a DNA standard per reaction and are linear from 2×10(8) to 2×10(2)copies/μl. Neither PriProET, nor MGB reacted with heterologous herpesviruses, indicating a high specificity of the two methods as novel tools for virus detection and identification. This study demonstrates the suitability of PriProET and 5' conjugated MGB probes as real-time PCR chemistries for the diagnosis of respiratory diseases caused by ILTV. PMID:21539859

  4. Spectral Bio-indicator Simulations for Tracking Photosynthetic Activities in a Corn Field

    NASA Technical Reports Server (NTRS)

    Cheng, Yen-Ben; Middleton, Elizabeth M.; Huemmrich, K. Fred; Zhang, Qingyuan; Corp, Lawrence; Campbell, Petya; Kustas, William

    2011-01-01

    Accurate assessment of vegetation canopy optical properties plays a critical role in monitoring natural and managed ecosystems under environmental changes. In this context, radiative transfer (RT) models simulating vegetation canopy reflectance have been demonstrated to be a powerful tool for understanding and estimating spectral bio-indicators. In this study, two narrow band spectroradiometers were utilized to acquire observations over corn canopies for two summers. These in situ spectral data were then used to validate a two-layer Markov chain-based canopy reflectance model for simulating the Photochemical Reflectance Index (PRI), which has been widely used in recent vegetation photosynthetic light use efficiency (LUE) studies. The in situ PRI derived from narrow band hyperspectral reflectance exhibited clear responses to: 1) viewing geometry which affects the asset of light environment; and 2) seasonal variation corresponding to the growth stage. The RT model (ACRM) successfully simulated the responses to the variable viewing geometry. The best simulations were obtained when the model was set to run in the two layer mode using the sunlit leaves as the upper layer and shaded leaves as the lower layer. Simulated PRI values yielded much better correlations to in situ observations when the cornfield was dominated by green foliage during the early growth, vegetative and reproductive stages (r = 0.78 to 0.86) than in the later senescent stage (r = 0.65). Further sensitivity analyses were conducted to show the important influences of leaf area index (LAI) and the sunlit/shaded ratio on PRI observations.

  5. Superinfection exclusion of the ruminant pathogen anaplasma marginale in the tick vector is dependent on time between exposures to the strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The remarkable genetic diversity of vector-borne pathogens allows for the establishment of superinfection in the mammalian host. To have a long-term impact on population strain structure, the introduced strains must also be transmitted by a vector population that has been exposed to the existing pri...

  6. Factors that Affect the Physical Science Career Interest of Female Students: Testing Five Common Hypotheses

    ERIC Educational Resources Information Center

    Hazari, Zahra; Potvin, Geoff; Lock, Robynne M.; Lung, Florin; Sonnert, Gerhard; Sadler, Philip M.

    2013-01-01

    There are many hypotheses regarding factors that may encourage female students to pursue careers in the physical sciences. Using multivariate matching methods on national data drawn from the Persistence Research in Science and Engineering (PRiSE) project ("n" = 7505), we test the following five commonly held beliefs regarding what…

  7. PEPTIC ULCER DISEASE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peptic ulcer disease (PUD) is an ulcerative condition of the stomach or duodenum that may be accompanied by mucosal inflammation. PUD is classified as primary when it occurs in healthy children and as secondary when underlying disorders associated with injury, illness, or drug therapy co-exists. Pri...

  8. Inhibition of Cyclic Adenosine Monophosphate (cAMP)-response Element-binding Protein (CREB)-binding Protein (CBP)/β-Catenin Reduces Liver Fibrosis in Mice.

    PubMed

    Osawa, Yosuke; Oboki, Keisuke; Imamura, Jun; Kojika, Ekumi; Hayashi, Yukiko; Hishima, Tsunekazu; Saibara, Toshiji; Shibasaki, Futoshi; Kohara, Michinori; Kimura, Kiminori

    2015-11-01

    Wnt/β-catenin is involved in every aspect of embryonic development and in the pathogenesis of many human diseases, and is also implicated in organ fibrosis. However, the role of β-catenin-mediated signaling on liver fibrosis remains unclear. To explore this issue, the effects of PRI-724, a selective inhibitor of the cAMP-response element-binding protein-binding protein (CBP)/β-catenin interaction, on liver fibrosis were examined using carbon tetrachloride (CCl4)- or bile duct ligation (BDL)-induced mouse liver fibrosis models. Following repetitive CCl4 administrations, the nuclear translocation of β-catenin was observed only in the non-parenchymal cells in the liver. PRI-724 treatment reduced the fibrosis induced by CCl4 or BDL. C-82, an active form of PRI-724, inhibited the activation of isolated primary mouse quiescent hepatic stellate cells (HSCs) and promoted cell death in culture-activated HSCs. During the fibrosis resolution period, an increase in F4/80(+) CD11b(+) and Ly6C(low) CD11b(+) macrophages was induced by CCl4 and was sustained for two weeks thereafter, even after having stopped CCl4 treatment. PRI-724 accelerated the resolution of CCl4-induced liver fibrosis, and this was accompanied by increased matrix metalloproteinase (MMP)-9, MMP-2, and MMP-8 expression in intrahepatic leukocytes. In conclusion, targeting the CBP/β-catenin interaction may become a new therapeutic strategy in treating liver fibrosis. PMID:26870800

  9. Predicting the establishment and spread of plant disease from regulatory sampling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Invasive plant diseases can have devastating consequences on the local plant populations, in both agricultural and natural landscapes. Knowledge of the spatial patterns of pathogen spread can be used to guide more time- and cost-effective disease management strategies. Based on disease dispersal pri...

  10. Adaptation of a Visual Readability Instrument to Multimedia Format.

    ERIC Educational Resources Information Center

    Vrasidas, Charalambos; Lantz, Chris

    This paper describes a study in which a Picture Readability Index (PRI) was used to investigate initial and extended perceptions of photographs. Readability criteria for evaluating instructional text seems to have been in place for a long time, yet instructional visuals like photographs and illustrations have typically been subject to no such…

  11. SEASONAL AND REGIONAL VARIATIONS OF PRIMARY AND SECONDARY ORGANIC AEROSOLS OVER THE CONTINENTAL UNITED STATES: OBSERVATION-BASED ESTIMATES AND MODEL EVALUATION

    EPA Science Inventory

    Due to the lack of an analytical technique for directly quantifying the atmospheric concentrations of primary (OCpri) and secondary (OCsec) organic carbon aerosols, different indirect methods have been developed to estimate their concentrations. In this stu...

  12. Health Instruction Packages: Consumer--Birth Control.

    ERIC Educational Resources Information Center

    Pries, Rose Mary; And Others

    Designed for the general public, these three learning modules utilize text, illustrations, and exercises to describe various methods of birth control. The first module, "All about Contraception for the Teenage New Mother" by Rose Mary Pries, discusses the desirability of planned pregnancy and reviews the effectiveness and side effects of birth…

  13. Extraction of pulse repetition intervals from sperm whale click trains for ocean acoustic data mining.

    PubMed

    Zaugg, Serge; van der Schaar, Mike; Houégnigan, Ludwig; André, Michel

    2013-02-01

    The analysis of acoustic data from the ocean is a valuable tool to study free ranging cetaceans and anthropogenic noise. Due to the typically large volume of acquired data, there is a demand for automated analysis techniques. Many cetaceans produce acoustic pulses (echolocation clicks) with a pulse repetition interval (PRI) remaining nearly constant over several pulses. Analyzing these pulse trains is challenging because they are often interleaved. This article presents an algorithm that estimates a pulse's PRI with respect to neighboring pulses. It includes a deinterleaving step that operates via a spectral dissimilarity metric. The sperm whale (SW) produces trains with PRIs between 0.5 and 2 s. As a validation, the algorithm was used for the PRI-based identification of SW click trains with data from the NEMO-ONDE observatory that contained other pulsed sounds, mainly from ship propellers. Separation of files containing SW clicks with a medium and high signal to noise ratio from files containing other pulsed sounds gave an area under the receiver operating characteristic curve value of 0.96. This study demonstrates that PRI can be used for the automated identification of SW clicks and that deinterleaving via spectral dissimilarity contributes to algorithm performance. PMID:23363108

  14. Mexico: Democracy and the Future

    ERIC Educational Resources Information Center

    Bruhn, Kathleen

    2009-01-01

    During most of the twentieth century, Mexico was governed by one of the longest-ruling authoritarian parties in the contemporary world. Even as most Latin American countries democratized in the 1980s, Mexico remained under the control of the Institutional Revolutionary Party (PRI). It was not until the 2000 presidential election that a two-party…

  15. Spectral determination of concentrations of functionally diverse pigments in increasingly complex arctic tundra canopies.

    PubMed

    Boelman, Natalie T; Magney, Troy S; Logan, Barry A; Griffin, Kevin L; Eitel, Jan U H; Greaves, Heather; Prager, Case M; Vierling, Lee A

    2016-09-01

    As the Arctic warms, tundra vegetation is becoming taller and more structurally complex, as tall deciduous shrubs become increasingly dominant. Emerging studies reveal that shrubs exhibit photosynthetic resource partitioning, akin to forests, that may need accounting for in the "big leaf" net ecosystem exchange models. We conducted a lab experiment on sun and shade leaves from S. pulchra shrubs to determine the influence of both constitutive (slowly changing bulk carotenoid and chlorophyll pools) and facultative (rapidly changing xanthophyll cycle) pigment pools on a suite of spectral vegetation indices, to devise a rapid means of estimating within canopy resource partitioning. We found that: (1) the PRI of dark-adapted shade leaves (PRIo) was double that of sun leaves, and that PRIo was sensitive to variation among sun and shade leaves in both xanthophyll cycle pool size (V + A + Z) (r (2) = 0.59) and Chla/b (r (2) = 0.64); (2) A corrected PRI (difference between dark and illuminated leaves, ΔPRI) was more sensitive to variation among sun and shade leaves in changes to the epoxidation state of their xanthophyll cycle pigments (dEPS) (r (2) = 0.78, RMSE = 0.007) compared to the uncorrected PRI of illuminated leaves (PRI) (r (2) = 0.34, RMSE = 0.02); and (3) the SR680 index was correlated with each of (V + A + Z), lutein, bulk carotenoids, (V + A + Z)/(Chla + b), and Chla/b (r (2) range = 0.52-0.69). We suggest that ΔPRI be employed as a proxy for facultative pigment dynamics, and the SR680 for the estimation of constitutive pigment pools. We contribute the first Arctic-specific information on disentangling PRI-pigment relationships, and offer insight into how spectral indices can assess resource partitioning within shrub tundra canopies. PMID:27193900

  16. MicroRNA Expression during Bovine Oocyte Maturation and Fertilization.

    PubMed

    Gilchrist, Graham C; Tscherner, Allison; Nalpathamkalam, Thomas; Merico, Daniele; LaMarre, Jonathan

    2016-01-01

    Successful fertilization and subsequent embryo development rely on complex molecular processes starting with the development of oocyte competence through maturation. MicroRNAs (miRNAs) are small non-coding RNA molecules that function as gene regulators in many biological systems, including the oocyte and embryo. In order to further explore the roles of miRNAs in oocyte maturation, we employed small RNA sequencing as a screening tool to identify and characterize miRNA populations present in pools of bovine germinal vesicle (GV) oocytes, metaphase II (MII) oocytes, and presumptive zygotes (PZ). Each stage contained a defined miRNA population, some of which showed stable expression while others showed progressive changes between stages that were subsequently confirmed by quantitative reverse transcription polymerase chain reaction (RT-PCR). Bta-miR-155, bta-miR-222, bta-miR-21, bta-let-7d, bta-let-7i, and bta-miR-190a were among the statistically significant differentially expressed miRNAs (p < 0.05). To determine whether changes in specific primary miRNA (pri-miRNA) transcripts were responsible for the observed miRNA changes, we evaluated pri-miR-155, -222 and let-7d expression. Pri-miR-155 and -222 were not detected in GV oocytes but pri-miR-155 was present in MII oocytes, indicating transcription during maturation. In contrast, levels of pri-let-7d decreased during maturation, suggesting that the observed increase in let-7d expression was likely due to processing of the primary transcript. This study demonstrates that both dynamic and stable populations of miRNAs are present in bovine oocytes and zygotes and extend previous studies supporting the importance of the small RNA landscape in the maturing bovine oocyte and early embryo. PMID:26999121

  17. MicroRNA Expression during Bovine Oocyte Maturation and Fertilization

    PubMed Central

    Gilchrist, Graham C.; Tscherner, Allison; Nalpathamkalam, Thomas; Merico, Daniele; LaMarre, Jonathan

    2016-01-01

    Successful fertilization and subsequent embryo development rely on complex molecular processes starting with the development of oocyte competence through maturation. MicroRNAs (miRNAs) are small non-coding RNA molecules that function as gene regulators in many biological systems, including the oocyte and embryo. In order to further explore the roles of miRNAs in oocyte maturation, we employed small RNA sequencing as a screening tool to identify and characterize miRNA populations present in pools of bovine germinal vesicle (GV) oocytes, metaphase II (MII) oocytes, and presumptive zygotes (PZ). Each stage contained a defined miRNA population, some of which showed stable expression while others showed progressive changes between stages that were subsequently confirmed by quantitative reverse transcription polymerase chain reaction (RT-PCR). Bta-miR-155, bta-miR-222, bta-miR-21, bta-let-7d, bta-let-7i, and bta-miR-190a were among the statistically significant differentially expressed miRNAs (p < 0.05). To determine whether changes in specific primary miRNA (pri-miRNA) transcripts were responsible for the observed miRNA changes, we evaluated pri-miR-155, -222 and let-7d expression. Pri-miR-155 and -222 were not detected in GV oocytes but pri-miR-155 was present in MII oocytes, indicating transcription during maturation. In contrast, levels of pri-let-7d decreased during maturation, suggesting that the observed increase in let-7d expression was likely due to processing of the primary transcript. This study demonstrates that both dynamic and stable populations of miRNAs are present in bovine oocytes and zygotes and extend previous studies supporting the importance of the small RNA landscape in the maturing bovine oocyte and early embryo. PMID:26999121

  18. Seasonal Changes in Remote Vegetation Indices and Net Photosynthesis of Japanese Larch Needles

    NASA Astrophysics Data System (ADS)

    Nishida, K.; Nakaji, T.; Oguma, H.; Fujinuma, Y.

    2004-12-01

    We investigated the seasonal pattern of four kinds of remote vegetation indices (NDVI, PRI, [(1/rRedEdge)-(1/rNIR)] and [(1/rGreen)-(1/rNIR)]) and their correlation to photosynthetic activity in the needle leaves of Japanese larch. In the 42-year-old larch forest (Tomakomai, Japan), the diurnal courses of spectral reflectance and gas exchange rates of larch needles were periodically investigated during early June to late October in 2003. In the Tomakomai larch forest, expansion of short-shoot needles was started from mid-May, and yellow color change of the needle leaves was observed in late October. The seasonal pattern of index value differed among the vegetation indices. For example, daytime mean NDVI showed constant value from late June to early October. The [(1/rRedEdge)-(1/rNIR)] and PRI were increased during summer, and their peak were observed in July and August, respectively. Although the values of NDVI, PRI and [(1/rRedEdge)-(1/rNIR)] were depressed in late October with autumn senescence of the needles, the [(1/rGreen)-(1/rNIR)] in larch needles was not changed even in yellow colored needles. Consequently, correlation of these vegetation indices and seasonal changed photosynthetic parameters such as net photosynthetic rate (Pn) and photosynthetic light use efficiency (LUE) also differed among the indices. Although the PRI, NDVI and [(1/rRedEdge)-(1/rNIR)] positively correlated with daily maximum Pn and daily means of Pn and LUE, no correlation was found between [(1/rGreen)-(1/rNIR)] and the measured photosynthetic parameters. Based on the results of Pearson_fs correlation test, PRI and [(1/rRedEdge)-(1/rNIR)] were considered to be most useful index for the estimations of seasonal changes in Pn and LUE, respectively.

  19. Seasonal photosynthetic activity in evergreen conifer leaves monitored with spectral reflectance

    NASA Astrophysics Data System (ADS)

    Wong, C. Y.; Gamon, J. A.

    2013-12-01

    Boreal evergreen conifers must maintain photosynthetic systems in environments where temperatures vary greatly across seasons from high temperatures in the summer to freezing levels in the winter. This involves seasonal downregulation and photoprotection during periods of extreme temperatures. To better understand this downregulation, seasonal dynamics of photosynthesis of lodgepole (Pinus contorta D.) and ponderosa pine (Pinus ponderosa D.) were monitored in Edmonton, Canada over two years. Spectral reflectance at the leaf and stand scales was measured weekly and the Photochemical Reflectance Index (PRI), often used as a proxy for chlorophyll and carotenoid pigment levels and photosynthetic light-use efficiency (LUE), was used to track the seasonal dynamics of photosynthetic activity. Additional physiological measurements included leaf pigment content, chlorophyll fluorescence, and gas exchange. All the metrics indicate large seasonal changes in photosynthetic activity, with a sharp transition from winter downregulation to active photosynthesis in the spring and a more gradual fall transition into winter. The PRI was a good indicator of several other variables including seasonally changing photosynthetic activity, chlorophyll fluorescence, photosynthetic LUE, and pigment pool sizes. Over the two-year cycle, PRI was primarily driven by changes in constitutive (chlorophyll:carotenoid) pigment levels correlated with seasonal photosynthetic activity, with a much smaller variation caused by diurnal changes in xanthophyll cycle activity (conversion between violaxanthin & zeaxanthin). Leaf and canopy scale PRI measurements exhibited parallel responses during the winter-spring transition. Together, our findings indicate that evergreen conifers photosynthetic system possesses a remarkable degree of resilience in response to large temperature changes across seasons, and that optical remote sensing can be used to observe the seasonal effects on photosynthesis and

  20. On the Use of Leaf Spectral Indices to Assess Water Status and Photosynthetic Limitations in Olea europaea L. during Water-Stress and Recovery

    PubMed Central

    Sun, Pengsen; Wahbi, Said; Tsonev, Tsonko; Haworth, Matthew; Liu, Shirong; Centritto, Mauro

    2014-01-01

    Diffusional limitations to photosynthesis, relative water content (RWC), pigment concentrations and their association with reflectance indices were studied in olive (Olea europaea) saplings subjected to water-stress and re-watering. RWC decreased sharply as drought progressed. Following rewatering, RWC gradually increased to pre-stress values. Photosynthesis (A), stomatal conductance (gs), mesophyll conductance (gm), total conductance (gt), photochemical reflectance index (PRI), water index (WI) and relative depth index (RDI) closely followed RWC. In contrast, carotenoid concentration, the carotenoid to chlorophyll ratio, water content reflectance index (WCRI) and structural independent pigment index (SIPI) showed an opposite trend to that of RWC. Photosynthesis scaled linearly with leaf conductance to CO2; however, A measured under non-photorespiratory conditions (A1%O2) was approximately two times greater than A measured at 21% [O2], indicating that photorespiration likely increased in response to drought. A1%O2 also significantly correlated with leaf conductance parameters. These relationships were apparent in saturation type curves, indicating that under non-photorespiratory conditions, CO2 conductance was not the major limitations to A. PRI was significant correlated with RWC. PRI was also very sensitive to pigment concentrations and photosynthesis, and significantly tracked all CO2 conductance parameters. WI, RDI and WCRI were all significantly correlated with RWC, and most notably to leaf transpiration. Overall, PRI correlated more closely with carotenoid concentration than SIPI; whereas WI tracked leaf transpiration more effectively than RDI and WCRI. This study clearly demonstrates that PRI and WI can be used for the fast detection of physiological traits of olive trees subjected to water-stress. PMID:25136798

  1. The estrogen receptor-α-induced microRNA signature regulates itself and its transcriptional response

    PubMed Central

    Castellano, Leandro; Giamas, Georgios; Jacob, Jimmy; Coombes, R. Charles; Lucchesi, Walter; Thiruchelvam, Paul; Barton, Geraint; Jiao, Long R.; Wait, Robin; Waxman, Jonathan; Hannon, Gregory J.; Stebbing, Justin

    2009-01-01

    Following estrogenic activation, the estrogen receptor-α (ERα) directly regulates the transcription of target genes via DNA binding. MicroRNAs (miRNAs) modulated by ERα have the potential to fine tune these regulatory systems and also provide an alternate mechanism that could impact on estrogen-dependent developmental and pathological systems. Through a microarray approach, we identify the subset of microRNAs (miRNAs) modulated by ERα, which include upregulation of miRNAs derived from the processing of the paralogous primary transcripts (pri-) mir-17–92 and mir-106a-363. Characterization of the mir-17–92 locus confirms that the ERα target protein c-MYC binds its promoter in an estrogen-dependent manner. We observe that levels of pri-mir-17–92 increase earlier than the mature miRNAs derived from it, implicating precursor cleavage modulation after transcription. Pri-mir-17–92 is immediately cleaved by DROSHA to pre-miR-18a, indicating that its regulation occurs during the formation of the mature molecule from the precursor. The clinical implications of this novel regulatory system were confirmed by demonstrating that pre-miR-18a was significantly upregulated in ERα-positive compared to ERα-negative breast cancers. Mechanistically, miRNAs derived from these paralogous pri-miRNAs (miR-18a, miR-19b, and miR-20b) target and downregulate ERα, while a subset of pri-miRNA-derived miRNAs inhibit protein translation of the ERα transcriptional p160 coactivator, AIB1. Therefore, different subsets of miRNAs identified act as part of a negative autoregulatory feedback loop. We propose that ERα, c-MYC, and miRNA transcriptional programs invoke a sophisticated network of interactions able to provide the wide range of coordinated cellular responses to estrogen. PMID:19706389

  2. Overexpression of NF90-NF45 Represses Myogenic MicroRNA Biogenesis, Resulting in Development of Skeletal Muscle Atrophy and Centronuclear Muscle Fibers

    PubMed Central

    Todaka, Hiroshi; Higuchi, Takuma; Yagyu, Ken-ichi; Sugiyama, Yasunori; Yamaguchi, Fumika; Morisawa, Keiko; Ono, Masafumi; Fukushima, Atsuki; Tsuda, Masayuki; Taniguchi, Taketoshi

    2015-01-01

    MicroRNAs (miRNAs) are involved in the progression and suppression of various diseases through translational inhibition of target mRNAs. Therefore, the alteration of miRNA biogenesis induces several diseases. The nuclear factor 90 (NF90)-NF45 complex is known as a negative regulator in miRNA biogenesis. Here, we showed that NF90-NF45 double-transgenic (dbTg) mice develop skeletal muscle atrophy and centronuclear muscle fibers in adulthood. Subsequently, we found that the levels of myogenic miRNAs, including miRNA 133a (miR-133a), which promote muscle maturation, were significantly decreased in the skeletal muscle of NF90-NF45 dbTg mice compared with those in wild-type mice. However, levels of primary transcripts of the miRNAs (pri-miRNAs) were clearly elevated in NF90-NF45 dbTg mice. This result indicated that the NF90-NF45 complex suppressed miRNA production through inhibition of pri-miRNA processing. This finding was supported by the fact that processing of pri-miRNA 133a-1 (pri-miR-133a-1) was inhibited via binding of NF90-NF45 to the pri-miRNA. Finally, the level of dynamin 2, a causative gene of centronuclear myopathy and concomitantly a target of miR-133a, was elevated in the skeletal muscle of NF90-NF45 dbTg mice. Taken together, we conclude that the NF90-NF45 complex induces centronuclear myopathy through increased dynamin 2 expression by an NF90-NF45-induced reduction of miR-133a expression in vivo. PMID:25918244

  3. Multi-parameter assessment of platelet inhibition and its stability during aspirin and clopidogrel therapy

    PubMed Central

    Timur, A. Anil; Murugesan, Gurunathan; Zhang, Li; Barnard, John; Bhatt, Deepak L.; Kottke-Marchant, Kandice

    2014-01-01

    Introduction Poor response to antiplatelet drugs is associated with adverse outcomes. We assessed platelet inhibition and its stability and tested correlation and agreement between platelet function assays. Methods Peripheral blood from 58 patients on both aspirin and clopidogrel who underwent percutaneous coronary intervention (PCI) was collected at hospital discharge (visit-1) and at 30–90 days (visit-2). Platelet function was measured using light transmission aggregometry (LTA-AA and LTA-ADP), VerifyNow (Aspirin; ARU and P2Y12; PRU), ex vivo TxB2, urinary 11dhTxB2, and VASP (PRI) assays. Data were analyzed as continuous, quartiles and binary. Patients were defined as aspirin poor responder (PR) with ARU ≥550, LTA-AA maximum ≥20%, TxB2 ≥1 ng/mL or 11dhTxB2 ≥1,500 pg/mg of creatinine and as clopidogrel PR with PRU ≥240, PRU ≥208, LTA-ADP maximum ≥40%, PRI ≥50%, or PRI ≥66%. Results Aspirin PR was 3–33% and clopidogrel PR was 10–35% in visit-1. LTA-AA, 11dhTxB2, and all clopidogrel-response measures showed correlation and agreement between visit-1 and visit-2. The highest agreement between two visits was revealed by PRU ≥240 and PRI ≥66% (PRU-κ=0.7, 95% CI=0.47, 0.93; PRI-κ=0.69, 95% CI=0.42, 0.95, p-values<0.001). Comparison of platelet function assays in a single visit (Visit-1) revealed a poor correlation between LTA-AA and 11dhTxB2 assays and no agreement among aspirin-response assays. The highest correlation and agreement were obtained between VerifyNow P2Y12 and VASP assays (rho=0.7, p-value<0.001 and PRU ≥208-PRI-κ=0.41–0.42, 95% CI=0.13, 0.69, p-values<0.001). Conclusions Platelet inhibition is stable during aspirin and clopidogrel treatment. Clopidogrel-response assays correlate and agree with each other better than aspirin-response assays. PMID:24852729

  4. Effects of resource availability on plant reflectance and physiology

    NASA Astrophysics Data System (ADS)

    Stylinski, Cathlyn Davis

    Remote sensing is an important means of examining net CO2 exchange between terrestrial ecosystems and the atmosphere and the effects of elevated [CO2] on plant productivity at multiple spatial and temporal scales. In particular, indices derived from narrow-waveband reflectance that are sensitive to dynamic physiological attributes may reveal periods of photosynthetic downregulation and may improve plant productivity models. Here we examined the relationship between photosynthesis, photoprotective xanthophyll cycle pigments, and the Photochemical Reflectance Index (PRI) for mature woody Mediterranean plants under two conditions: natural drought and exposure to atmospheric CO2 enrichment. We also examined plants under severe water stress to test and compare the effects of physiology and structure on PRI, the Normalized Difference Vegetation Index (NDVI), and the Water Band Index (WBI). PRI varied primarily with leaf physiology, and NDVI primarily with stand structure. WBI was affected by both attributes and, unlike PRI, did not scale well from leaves to whole stands. PRI was well linked to photoprotective xanthophyll cycle pigments and electron transport. Both PRI and these pigments varied with seasonal changes in midday photosynthesis, demonstrating that the xanthophyll cycle is an important form of photoprotection for evergreen Mediterranean species undergoing photosynthetic downregulation. By contrast, NDVI was not sensitive to physiological changes but was well correlated with green canopy cover. These results suggest that the "big-leaf hypothesis" (which states that canopies can be characterized by a single reference leaf) cannot be applied to all physiological indices. Furthermore, in agreement with the "functional convergence hypothesis" (which states that plant physiology and structure change to match CO2 fixation capacity), our results indicate a coordinated regulation of photosystem two activity and carbon uptake. However, they also demonstrate that this

  5. Methylation by NSun2 Represses the Levels and Function of MicroRNA 125b

    PubMed Central

    Yuan, Shuai; Tang, Hao; Xing, Junyue; Fan, Xiuqin; Cai, Xiaoyu; Li, Qiu; Han, Pei; Luo, Yuhong; Zhang, Zhuojun; Jiang, Bin; Dou, Yali; Gorospe, Myriam

    2014-01-01

    Methylation is a prevalent posttranscriptional modification of RNAs. However, whether mammalian microRNAs are methylated is unknown. Here, we show that the tRNA methyltransferase NSun2 methylates primary (pri-miR-125b), precursor (pre-miR-125b), and mature microRNA 125b (miR-125b) in vitro and in vivo. Methylation by NSun2 inhibits the processing of pri-miR-125b2 into pre-miR-125b2, decreases the cleavage of pre-miR-125b2 into miR-125, and attenuates the recruitment of RISC by miR-125, thereby repressing the function of miR-125b in silencing gene expression. Our results highlight the impact of miR-125b function via methylation by NSun2. PMID:25047833

  6. small ORFs: A new class of essential genes for development.

    PubMed

    Albuquerque, João Paulo; Tobias-Santos, Vitória; Rodrigues, Aline Cáceres; Mury, Flávia Borges; da Fonseca, Rodrigo Nunes

    2015-01-01

    Genes that contain small open reading frames (smORFs) constitute a new group of eukaryotic genes and are expected to represent 5% of the Drosophila melanogaster transcribed genes. In this review we provide a historical perspective of their recent discovery, describe their general mechanism and discuss the importance of smORFs for future genomic and transcriptomic studies. Finally, we discuss the biological role of the most studied smORF so far, the Mlpt/Pri/Tal gene in arthropods. The pleiotropic action of Mlpt/Pri/Tal in D. melanogaster suggests a complex evolutionary scenario that can be used to understand the origins, evolution and integration of smORFs into complex gene regulatory networks. PMID:26500431

  7. small ORFs: A new class of essential genes for development

    PubMed Central

    Albuquerque, João Paulo; Tobias-Santos, Vitória; Rodrigues, Aline Cáceres; Mury, Flávia Borges; da Fonseca, Rodrigo Nunes

    2015-01-01

    Genes that contain small open reading frames (smORFs) constitute a new group of eukaryotic genes and are expected to represent 5% of the Drosophila melanogaster transcribed genes. In this review we provide a historical perspective of their recent discovery, describe their general mechanism and discuss the importance of smORFs for future genomic and transcriptomic studies. Finally, we discuss the biological role of the most studied smORF so far, the Mlpt/Pri/Tal gene in arthropods. The pleiotropic action of Mlpt/Pri/Tal in D. melanogaster suggests a complex evolutionary scenario that can be used to understand the origins, evolution and integration of smORFs into complex gene regulatory networks. PMID:26500431

  8. Two Fundamental Principles of Nature's Interactions

    NASA Astrophysics Data System (ADS)

    Ma, Tian; Wang, Shouhong

    2014-03-01

    In this talk, we present two fundamental principles of nature's interactions, the principle of interaction dynamics (PID) and the principle of representation invariance (PRI). Intuitively, PID takes the variation of the action functional under energy-momentum conservation constraint. PID offers a completely different and natural way of introducing Higgs fields. PRI requires that physical laws be independent of representations of the gauge groups. These two principles give rise to a unified field model for four interactions, which can be naturally decoupled to study individual interactions. With these two principles, we are able to derive 1) a unified theory for dark matter and dark energy, 2) layered strong and weak interaction potentials, and 3) the energy levels of subatomic particles. Supported in part by NSF, ONR and Chinese NSF.

  9. A typology of pain coping strategies in pediatric patients with chronic abdominal pain.

    PubMed

    Walker, Lynn S; Baber, Kari Freeman; Garber, Judy; Smith, Craig A

    2008-07-15

    This study aimed to identify clinically meaningful profiles of pain coping strategies used by youth with chronic abdominal pain (CAP). Participants (n=699) were pediatric patients (ages 8-18 years) and their parents. Patients completed the Pain Response Inventory (PRI) and measures of somatic and depressive symptoms, disability, pain severity and pain efficacy, and perceived competence. Parents rated their children's pain severity and coping efficacy. Hierarchical cluster analysis based on the 13 PRI subscales identified pain coping profiles in Sample 1 (n=311) that replicated in Sample 2 (n=388). Evidence was found of external validity and distinctiveness of the profiles. The findings support a typology of pain coping that reflects the quality of patients' pain mastery efforts and interpersonal relationships associated with pain coping. Results are discussed in relation to developmental processes, attachment styles, and treatment implications. PMID:17928144

  10. Symmetry relations in the generalized Lorenz-Mie theory for lossless negative refractive index media

    NASA Astrophysics Data System (ADS)

    André Ambrosio, Leonardo

    2016-09-01

    In this paper we present a theoretical analysis of the generalized Lorenz-Mie theory for negative refractive index (NRI) media and spherical scatterers, extending the well-known concepts and definitions found in the literature involving dielectric or positive refractive index (PRI) particles. The consequences of a negative phase velocity and an anti-parallelism of the wave vector with respect to the Poynting vector are investigated and interpreted in this framework and, together with the symmetries found for the beam-shape coefficients when compared to the conventional PRI case, it is shown that the description of plane waves, Gaussian beams and, more generally, on-axis azimuthally symmetric waves along a NRI medium, their fields and all physical properties can be conveniently correlated with that of dielectric media once the electromagnetic response functions are replaced by their corresponding dielectric counterparts.

  11. Magneto-optic imaging inspection of selected corrosion specimens

    NASA Astrophysics Data System (ADS)

    Bobo, Stephen N.

    1992-07-01

    A feasibility demonstration was conducted at the facilities of Physical Research Instrumentation Company (PRI) in Redmond, Washington. The purpose of the demonstration was to compare the effectiveness of the PRI Model 301-1 magneto-optic imaging (MOI) system with conventional eddy current methods of detecting corrosion in aircraft test panels, previously identified by eddy current scanning. The study indicated that MOI may not be able to detect gradual differences in thinning that are less than 10 percent of base metal thickness. Also, with MOI, it appears to be more difficult to provide quantitative estimates of residual thickness than is the case with eddy current scanning. On the other hand, MOI visualization of the extent of corrosion is simple and free of the labor intensive point-by-point mapping, which is required by eddy current scanning.

  12. Morin, Jean-Baptiste (1583-1656)

    NASA Astrophysics Data System (ADS)

    Murdin, P.

    2000-11-01

    Doctor, alchemist and astrologer, born in Villefranche, Beaujolais, France, became professor of mathematics at the Collège Royal, published a defense of ARISTOTLE, attacked GALILEO, being convinced that the Earth was fixed in space. Morin proposed an impractical method to solve the longitude problem, based on measuring absolute time by the position of the Moon. He put the method in for a pri...

  13. bmo-miR-0001 and bmo-miR-0015 down-regulate expression of Bombyx mori fibroin light chain gene in vitro.

    PubMed

    Chen, Chen; Fan, Yang-yang; Wang, Xin; Song, Fei; Jiang, Tao; Qian, Ping; Tang, Shun-ming; Shen, Xing-jia

    2016-02-01

    Based on bioinformatic analysis, we selected two novel microRNAs (miRNAs), bmo-miR-0001 and bmo-miR-0015, from high-throughput sequencing of the Bombyx mori larval posterior silk gland (PSG). Firstly, we examined the expression of bmo-miR-0001 and bmo-miR 12 different tissues of the 5th instar Day-3 larvae of the silkworm. The results showed that the expression levels of both bmo-miR-0001 and bmo-miR-0015 were obviously higher in the PSG than in other tissues, implying there is a spatio-temporal condition for bmo-miR-0001 and bmo-miR-0015 to regulate the expression of BmFib-L. To test this hypothesis, we constructed pri-bmo-miR-0001 expressing the plasmid pcDNA3.0 and pri-bmo-miR-0015 expressing the plasmid pcDNA3.0 [ie1-egfp-pri-bmo-miR-0015-SV40]. Finally, the BmN cells were harvested and luciferase activity was detected. The results showed that luciferase activity was reduced significantly (P<0.05) in BmN cells co-transfected by pcDNA3.0 [ie1-egfp-pri-bmo-miR-0001-SV40] or pcDNA3.0 with pGL3.0 [A3-luc-Fib-L-3'UTR-SV40], suggesting that both bmo-miR-0001 and bmo-miR-0015 can down-regulate the expression of BmFib-L in vitro. PMID:26834013

  14. Dehydroepiandrosterone Activation of G-protein-coupled Estrogen Receptor Rapidly Stimulates MicroRNA-21 Transcription in Human Hepatocellular Carcinoma Cells.

    PubMed

    Teng, Yun; Radde, Brandie N; Litchfield, Lacey M; Ivanova, Margarita M; Prough, Russell A; Clark, Barbara J; Doll, Mark A; Hein, David W; Klinge, Carolyn M

    2015-06-19

    Little is known about the regulation of the oncomiR miR-21 in liver. Dehydroepiandrosterone (DHEA) regulates gene expression as a ligand for a G-protein-coupled receptor and as a precursor for steroids that activate nuclear receptor signaling. We report that 10 nm DHEA increases primary miR-21 (pri-miR-21) transcription and mature miR-21 expression in HepG2 cells in a biphasic manner with an initial peak at 1 h followed by a second, sustained response from 3-12 h. DHEA also increased miR-21 in primary human hepatocytes and Hep3B cells. siRNA, antibody, and inhibitor studies suggest that the rapid DHEA-mediated increase in miR-21 involves a G-protein-coupled estrogen receptor (GPER/GPR30), estrogen receptor α-36 (ERα36), epidermal growth factor receptor-dependent, pertussis toxin-sensitive pathway requiring activation of c-Src, ERK1/2, and PI3K. GPER antagonist G-15 attenuated DHEA- and BSA-conjugated DHEA-stimulated pri-miR-21 transcription. Like DHEA, GPER agonists G-1 and fulvestrant increased pri-miR-21 in a GPER- and ERα36-dependent manner. DHEA, like G-1, increased GPER and ERα36 mRNA and protein levels. DHEA increased ERK1/2 and c-Src phosphorylation in a GPER-responsive manner. DHEA increased c-Jun, but not c-Fos, protein expression after 2 h. DHEA increased androgen receptor, c-Fos, and c-Jun recruitment to the miR-21 promoter. These results suggest that physiological concentrations of DHEA activate a GPER intracellular signaling cascade that increases pri-miR-21 transcription mediated at least in part by AP-1 and androgen receptor miR-21 promoter interaction. PMID:25969534

  15. Language Impairment in Children Perinatally Infected with HIV Compared to Children Who Were HIV-Exposed and Uninfected

    PubMed Central

    Rice, Mabel L.; Buchanan, Ashley L.; Siberry, George K; Malee, Kathleen M.; Zeldow, Bret; Frederick, Toni; Purswani, Murli U.; Hoffman, Howard J.; Sirois, Patricia A.; Smith, Renee; Torre, Peter; Allison, Susannah M; Williams, Paige L.

    2011-01-01

    Objective To investigate risk for language impairment in children perinatally infected or exposed to HIV. Methods We evaluated the prevalence of language impairment (LI) in 7–16 year old children with perinatal HIV infection (HIV+) compared to children HIV-exposed and uninfected (HEU), using a comprehensive standardized language test (CELF-4). LI was classified as primary LI (Pri-LI) (monolingual English exposure and no cognitive or hearing impairment), concurrent LI (Con-LI) (cognitive or hearing impairment), or no LI. Associations of demographic, caregiver, HIV disease and antiretroviral treatment (ART) factors with LI category were evaluated using univariate and multivariable logistic regression models. Results Of 468 children with language assessments, 184 (39%) had LI. No difference was observed by HIV infection status for overall LI or for Pri-LI or Con-LI; mean (SD) CELF-4 scores were 88.5 (18.4) for HIV+ vs 87.5 (17.9) for HEU. After adjustment, Black children had higher odds of Pri-LI vs no LI (aOR=2.43, p=0.03). Children who were Black, Hispanic, had a caregiver with low education or low IQ, or a non-biological parent as caregiver had higher odds of Con-LI vs no LI. Among HIV+ children, viral load >400 copies/ml (aOR=3.04, p<0.001), CDC Class C (aOR=2.19, p=0.02) and ART initiation <6 months of age (aOR=2.12, p=0.02) were associated with higher odds of Con-LI vs. no LI. Conclusions Children perinatally exposed to HIV are at high risk for LI, but such risk was not increased for youth with HIV. Risk factors differed for Pri-LI and Con-LI. PMID:22179050

  16. NUCLEAR ESPIONAGE: Report Details Spying on Touring Scientists.

    PubMed

    Malakoff, D

    2000-06-30

    A congressional report released this week details dozens of sometimes clumsy attempts by foreign agents to obtain nuclear secrets from U.S. nuclear scientists traveling abroad, ranging from offering scientists prostitutes to prying off the backs of their laptop computers. The report highlights the need to better prepare traveling researchers to safeguard secrets and resist such temptations, say the two lawmakers who requested the report and officials at the Department of Energy, which employs the scientists. PMID:17769833

  17. Evolution of substrate specificity in a recipient's enzyme following horizontal gene transfer.

    PubMed

    Noda-García, Lianet; Camacho-Zarco, Aldo R; Medina-Ruíz, Sofía; Gaytán, Paul; Carrillo-Tripp, Mauricio; Fülöp, Vilmos; Barona-Gómez, Francisco

    2013-09-01

    Despite the prominent role of horizontal gene transfer (HGT) in shaping bacterial metabolism, little is known about the impact of HGT on the evolution of enzyme function. Specifically, what is the influence of a recently acquired gene on the function of an existing gene? For example, certain members of the genus Corynebacterium have horizontally acquired a whole l-tryptophan biosynthetic operon, whereas in certain closely related actinobacteria, for example, Mycobacterium, the trpF gene is missing. In Mycobacterium, the function of the trpF gene is performed by a dual-substrate (βα)8 phosphoribosyl isomerase (priA gene) also involved in l-histidine (hisA gene) biosynthesis. We investigated the effect of a HGT-acquired TrpF enzyme upon PriA's substrate specificity in Corynebacterium through comparative genomics and phylogenetic reconstructions. After comprehensive in vivo and enzyme kinetic analyses of selected PriA homologs, a novel (βα)8 isomerase subfamily with a specialized function in l-histidine biosynthesis, termed subHisA, was confirmed. X-ray crystallography was used to reveal active-site mutations in subHisA important for narrowing of substrate specificity, which when mutated to the naturally occurring amino acid in PriA led to gain of function. Moreover, in silico molecular dynamic analyses demonstrated that the narrowing of substrate specificity of subHisA is concomitant with loss of ancestral protein conformational states. Our results show the importance of HGT in shaping enzyme evolution and metabolism. PMID:23800623

  18. Business-led efforts to control costs.

    PubMed

    Kenkel, P J

    1991-07-29

    Business-led initiatives to compare medical quality and prices are becoming commonplace as employers seek ways to cap medical expenses. But employers are meeting with varying degrees of cooperation from hospitals. The tale of two cities' efforts to pry open the secrets of controlling costs provides a vivid contrast in the way purchasers have tried to solve the cost-containment puzzle. PMID:10111874

  19. Subacute Changes in Cleavage Processing of Amyloid Precursor Protein and Tau following Penetrating Traumatic Brain Injury.

    PubMed

    Cartagena, Casandra M; Mountney, Andrea; Hwang, Hye; Swiercz, Adam; Rammelkamp, Zoe; Boutte, Angela M; Shear, Deborah A; Tortella, Frank C; Schmid, Kara E

    2016-01-01

    Traumatic brain injury (TBI) is an established risk factor for the development of Alzheimer's disease (AD). Here the effects of severe penetrating TBI on APP and tau cleavage processing were investigated in a rodent model of penetrating ballistic-like brain injury (PBBI). PBBI was induced by stereotactically inserting a perforated steel probe through the right frontal cortex of the anesthetized rat and rapidly inflating/deflating the probe's elastic tubing into an elliptical shaped balloon to 10% of total rat brain volume causing temporary cavitation injury. Separate animals underwent probe injury (PrI) alone without balloon inflation. Shams underwent craniectomy. Brain tissue was collected acutely (4h, 24h, 3d) and subacutely (7d) post-injury and analyzed by immunoblot for full length APP (APP-FL) and APP beta c-terminal fragments (βCTFs), full length tau (tau-FL) and tau truncation fragments and at 7d for cytotoxic Beta amyloid (Aβ) peptides Aβ40 and Aβ42 analysis. APP-FL was significantly decreased at 3d and 7d following PBBI whereas APP βCTFs were significantly elevated by 4h post-injury and remained elevated through 7d post-injury. Effects on βCTFs were mirrored with PrI, albeit to a lesser extent. Aβ40 and Aβ42 were significantly elevated at 7d following PBBI and PrI. Tau-FL decreased substantially 3d and 7d post-PBBI and PrI. Importantly, a 22 kDa tau fragment (tau22), similar to that found in AD, was significantly elevated by 4h and remained elevated through 7d post-injury. Thus both APP and tau cleavage was dramatically altered in the acute and subacute periods post-injury. As cleavage of these proteins has also been implicated in AD, TBI pathology shown here may set the stage for the later development of AD or other tauopathies. PMID:27428544

  20. Higher body weight patients on clopidogrel maintenance therapy have lower active metabolite concentrations, lower levels of platelet inhibition, and higher rates of poor responders than low body weight patients.

    PubMed

    Wagner, Henrik; Angiolillo, Dominick J; Ten Berg, Jurrien M; Bergmeijer, Thomas O; Jakubowski, Joseph A; Small, David S; Moser, Brian A; Zhou, Chunmei; Brown, Patricia; James, Stefan; Winters, Kenneth J; Erlinge, David

    2014-01-01

    Body weight is a predictor of clopidogrel response. However, no prospective studies have compared pharmacodynamic (PD) and pharmacokinetic (PK) data based on body weight. We compared PD and PK effects of clopidogrel 75 mg in low body weight (LBW, <60 kg) and higher body weight (HBW, ≥60 kg) patients with stable coronary artery disease. LBW (n = 34, 56.4 ± 3.7 kg) and HBW (n = 38, 84.7 ± 14.9 kg) aspirin-treated patients received clopidogrel 75 mg for 10-14 days. The area under the concentration-time curve of active metabolite (Clop-AM) calculated through the last quantifiable concentration up to 4 h postdose, AUC(0-tlast), was calculated by noncompartmental methods. Light transmission aggregometry (LTA) (maximum platelet aggregation and inhibition of platelet aggregation to 20 μM adenosine diphosphate (ADP), and residual platelet aggregation to 5 μM ADP), VerifyNow(®) P2Y12 reaction units (PRU), and vasodilator-associated stimulated phosphoprotein phosphorylation platelet reactivity index (VASP-PRI) were performed. Mean AUC(0-tlast) was lower in HBW than LBW patients: 12.8 versus 17.9 ng h/mL. HBW patients had higher platelet reactivity as measured by LTA (all p ≤ 0.01), PRU (207 ± 68 vs. 152 ± 57, p < 0.001), and VASP-PRI (56 ± 18 vs. 39 ± 17, p < 0.001). More HBW patients exhibited high on-treatment platelet reactivity (HPR) using PRU (35 vs. 9%) and VASP-PRI (65 vs. 27%). Body weight correlated with PRU and VASP-PRI (both p < 0.001), and inversely with log transformed AUC(0-tlast) (p < 0.001). In conclusion, HBW patients had lower levels of Clop-AM, and higher platelet reactivity and rates of HPR than LBW subjects, contributing to their suboptimal response to clopidogrel. PMID:24043374

  1. Synthesis and coordination chemistry of tridentate (PNN) amine enamido phosphine ligands with ruthenium.

    PubMed

    Wambach, T C; Lenczyk, C; Patrick, B O; Fryzuk, M D

    2016-04-01

    Tridentate amine-imine-phosphine ligands, R2PC5H7NC2H4NEt2 [(R)PNN(H)], where R = Pr(i) or Bu(t) are synthesized using a straightforward protocol of condensation, deprotonation, and addition of a chlorodialkylphosphine. Multinuclear NMR spectroscopy shows the ligands exist exclusively in the enamine tautomeric form in solution. Treating these ligands with RuHCl(PPr(i)3)2(CO) forms the desired coordination compounds, RuHCl[(R)PNN(H)](CO), where the imine tautomeric form of the ligands coordinates to ruthenium. Deuterium labelling experiments show Ru-H/N-D scrambling occurs during ligand coordination. Treating the RuHCl[(R)PNN(H)](CO) precursors with potassium tert-butoxide allows for the synthesis of two new ruthenium enamido-phosphine complexes, RuH[(R)PNN](CO), which were fully characterized. The structure of one of the derivatives was confirmed by X-ray crystallography (R = Pr(i)). The reactivity of the enamido-phosphine complexes with H2 and benzyl alcohol is also reported. For the enamido phosphine complex where R = Pr(i), the reaction with H2 is reversible and forms (RuH(CO)[(Pri)PNN(H)])2(μ-H)2, a hydride-bridged dimer that results from cooperative activation of H2. The reactivity of both amine-enamido-phosphine ruthenium compounds with benzyl alcohol establishes that the complexes are catalyst precursors for acceptorless dehydrogenation (AD), although the turnover frequencies measured using both catalyst precursors are modest. PMID:26916542

  2. Miravirsen (SPC3649) can inhibit the biogenesis of miR-122

    PubMed Central

    Gebert, Luca F. R.; Rebhan, Mario A. E.; Crivelli, Silvia E. M.; Denzler, Rémy; Stoffel, Markus; Hall, Jonathan

    2014-01-01

    MicroRNAs (miRNAs) are short noncoding RNAs, which bind to messenger RNAs and regulate protein expression. The biosynthesis of miRNAs includes two precursors, a primary miRNA transcript (pri-miRNA) and a shorter pre-miRNA, both of which carry a common stem-loop bearing the mature miRNA. MiR-122 is a liver-specific miRNA with an important role in the life cycle of hepatitis C virus (HCV). It is the target of miravirsen (SPC3649), an antimiR drug candidate currently in clinical testing for treatment of HCV infections. Miravirsen is composed of locked nucleic acid (LNAs) ribonucleotides interspaced throughout a DNA phosphorothioate sequence complementary to mature miR-122. The LNA modifications endow the drug with high affinity for its target and provide resistance to nuclease degradation. While miravirsen is thought to work mainly by hybridizing to mature miR-122 and blocking its interaction with HCV RNA, its target sequence is also present in pri- and pre-miR-122. Using new in vitro and cellular assays specifically developed to discover ligands that suppress biogenesis of miR-122, we show that miravirsen binds to the stem-loop structure of pri- and pre-miR-122 with nanomolar affinity, and inhibits both Dicer- and Drosha-mediated processing of miR-122 precursors. This inhibition may contribute to the pharmacological activity of the drug in man. PMID:24068553

  3. Self-Management, Amitriptyline, and Amitripyline plus Triamcinolone in the Management of Vulvodynia

    PubMed Central

    Wan, Jim; Bachmann, Gloria; Rosen, Ray

    2009-01-01

    Abstract Objective To conduct a prospective study to determine the efficacy of self-management interventions, amitriptyline, and amitriptyline plus topical triamcinolone in reducing vulvar pain in women with vulvodynia. Methods This was a randomized, prospective study of 53 women between the ages of 18 and 72 with vulvodynia. Participants undertook one of three treatment interventions for a period of 12 weeks: self-management, oral amitriptyline (10–20 mg/day), or topical triamcinolone plus oral amitriptyline (10–20 mg/day). The McGill Pain Questionnaire (MPQ) was used to measure changes in qualitative pain using the pain rating index (PRI) and in quantitative pain using the present pain intensity (PPI) scale. Results Of the 53 randomized subjects, 43 completed the trial. There were no statistically significant differences in PRI or PPI scores among the three treatment groups. Significant within-group differences were observed in the self-management group on the PRI and in the amitriptyline group on the PPI. Conclusions This first randomized, prospective trial suggests that self-management has a modest effect and that low-dose amitriptyline (with and without topical triamcinolone) is not effective in reducing pain in women with vulvodynia. PMID:19183087

  4. Association analysis of photoperiodic flowering time genes in west and central African sorghum [Sorghum bicolor (L.) Moench

    PubMed Central

    2012-01-01

    Background Photoperiod-sensitive flowering is a key adaptive trait for sorghum (Sorghum bicolor) in West and Central Africa. In this study we performed an association analysis to investigate the effect of polymorphisms within the genes putatively related to variation in flowering time on photoperiod-sensitive flowering in sorghum. For this purpose a genetically characterized panel of 219 sorghum accessions from West and Central Africa was evaluated for their photoperiod response index (PRI) based on two sowing dates under field conditions. Results Sorghum accessions used in our study were genotyped for single nucleotide polymorphisms (SNPs) in six genes putatively involved in the photoperiodic control of flowering time. Applying a mixed model approach and previously-determined population structure parameters to these candidate genes, we found significant associations between several SNPs with PRI for the genes CRYPTOCHROME 1 (CRY1-b1) and GIGANTEA (GI). Conclusions The negative values of Tajima's D, found for the genes of our study, suggested that purifying selection has acted on genes involved in photoperiodic control of flowering time in sorghum. The SNP markers of our study that showed significant associations with PRI can be used to create functional markers to serve as important tools for marker-assisted selection of photoperiod-sensitive cultivars in sorghum. PMID:22394582

  5. In-vivo quantification of primary microRNA processing by Drosha with a luciferase based system

    SciTech Connect

    Allegra, Danilo; Mertens, Daniel

    2011-03-25

    Research highlights: {yields} Posttranscriptional regulation of miRNA processing is difficult to quantify. {yields} Our in-vivo processing assay can quantify Drosha cleavage in live cells. {yields} It is based on luciferase reporters fused with pri-miRNAs. {yields} The assay validates the processing defect caused by a mutation in pri-16-1. {yields} It is a sensitive method to quantify pri-miRNA cleavage by Drosha in live cells. -- Abstract: The RNAse III Drosha is responsible for the first step of microRNA maturation, the cleavage of primary miRNA to produce the precursor miRNA. Processing by Drosha is finely regulated and influences the amount of mature microRNA in a cell. We describe in the present work a method to quantify Drosha processing activity in-vivo, which is applicable to any microRNA. With respect to other methods for measuring Drosha activity, our system is faster and scalable, can be used with any cellular system and does not require cell sorting or use of radioactive isotopes. This system is useful to study regulation of Drosha activity in physiological and pathological conditions.

  6. Genotoxicity of the anticonvulsant drug phenytoin (PHT): a follow-up study of PHT-untreated epileptic patients. II. Mitotic index (MI) and proliferation kinetics.

    PubMed

    Kaul, A; Goyle, S

    1999-01-01

    The mitotic index and proliferation rate index were investigated to determine the effect of phenytoin (PHT) in cultured blood lymphocytes of epileptics prior to and following administration of PHT over a period of 9 months (grouped in multiples of 3 months) and 40 control subjects (age range 10-30 years). Treatment with PHT brought inhibition of the mitotic index (MI) and proliferation rate index (PRI), which were significantly higher in treated subjects or which were more expressive in treated lymphocytes (P < 0.001) for all the three durations of treatment. In addition, statistically significant heterogeneity of first, second, and third metaphases between the treated, untreated, and control subjects was found. Mean PRI values were used to estimate cell cycle delays, showing the highest effect in treated lymphocytes (P < 0.001). There was no considerable variation between the control and untreated (P > 0.05). The study demonstrates that PHT may be potentially genotoxic and hence the usefulness of MI and PRI in monitoring epileptics on anticonvulsant treatment. PMID:10321412

  7. Non-replicative helicases at the replication fork.

    PubMed

    Heller, Ryan C; Marians, Kenneth J

    2007-07-01

    Reactivation of stalled or collapsed replication forks is an essential process in bacteria. Restart systems operate to restore the 5'-->3' replicative helicase, DnaB, to the lagging-strand template. However, other non-replicative 3'-->5' helicases play an important role in the restart process as well. Here we examine the DNA-binding specificity of three of the latter group, PriA, Rep, and UvrD. Only PriA and Rep display structure-specific fork binding. Interestingly, their specificity is opposite: PriA binds a leading-strand fork, presumably reflecting its restart activity in directing loading of DnaB to the lagging-strand template. Rep binds a lagging-strand fork, presumably reflecting its role in partially displacing Okazaki fragments that originate near the fork junction. This activity is necessary for generating a single-stranded landing pad for DnaB. While UvrD shows little structure-specificity, there is a slight preference for lagging-strand forks, suggesting that there might be some redundancy between Rep and UvrD and possibly explaining the observed synthetic lethality that occurs when mutations in the genes encoding these two proteins are combined. PMID:17382604

  8. Analysis of Seismic Activity of the last 15 Years Nearby Puerto Rico and Caribbean Region.

    NASA Astrophysics Data System (ADS)

    Huerta-Lopez, C. I.; Torres-Ortíz, D. M.; Fernández-Heredia, A. I.; Martínez-Cruzado, J. A.

    2015-12-01

    An earthquake catalog of the seismicity occurred during the last 15 years in the Caribbean region, nearby the vicinity of Puerto Rico Island (PRI) was compiled in order to capture the big picture of the regional seismic activity ratio and in particular at the epicentral regions of several historical and instrumentally recorded (during 2008-20015) large to moderate magnitude earthquakes occurred nearby PRI in onshore and offshore, which include the M6.4 earthquake of 01/13/2014, the largest earthquake recorded instrumentally nearby PRI. From the point of view of joint temporal-spatial distribution of epicenters, episodic temporal-spatial seismic activity is clearly seen as temporal-spatial concentrations during certain time intervals in different regions. These localized concentrations of epicenters that occur during certain time intervals in well localized/concentrated regions may suggest "seismic gaps" that shows no regular time interval, neither spatial pattern. In the epicentral region of the M6.4 01/13/2014 earthquake and the historical Mona Passage M7.5 earthquake of 10/11/1918, episodic concentrations in time and space of small magnitude earthquakes epicenters is evident, however do not show temporal pattern. Preliminary results of statistical analysis of an ongoing research in terms of the parameter b (Gutenberg-Richter relationship), and the Omori's law with the aim to relate the tectonic framework of the region (or sub-regions) such as structural heterogeneity stress are here presented/discussed.

  9. Life cycle of a data warehousing project in healthcare.

    PubMed

    Verma, R; Harper, J

    2001-01-01

    Hill Physicians Medical Group (and its medical management firm, PriMed Management) early on recognized the need for a data warehouse. Management demanded that data from many sources be integrated, cleansed, and formatted. As a first step, an operational data store (ODS) was built and populated with data from the main transactional system; encounter data were added. The ODS has served its purpose well and has whetted management's appetite for more information and faster, more reliable access, all in one location. PriMed hired Annams Systems Consulting (Annams) for this effort. A team was formed, made up of consultants from Annams and members of PriMed's information services (IS) team. The "classical" approach is being taken: enhancing the ODS, which is largely normalized in structure, and integrating data from various sources, along with enforcing business rules. The team is designing and implementing data marts and a "star schema" style of data modeling--a useful tool for management to evaluate results before investing further. PMID:11452573

  10. The use of artificial microRNA technology to control gene expression in Arabidopsis thaliana.

    PubMed

    Eamens, Andrew L; McHale, Marcus; Waterhouse, Peter M

    2014-01-01

    In plants, double-stranded RNA (dsRNA) is an effective trigger of RNA silencing, and several classes of endogenous small RNA (sRNA), processed from dsRNA substrates by DICER-like (DCL) endonucleases, are essential in controlling gene expression. One such sRNA class, the microRNAs (miRNAs) control the expression of closely related genes to regulate all aspects of plant development, including the determination of leaf shape, leaf polarity, flowering time, and floral identity. A single miRNA sRNA silencing signal is processed from a long precursor transcript of nonprotein-coding RNA, termed the primary miRNA (pri-miRNA). A region of the pri-miRNA is partially self-complementary allowing the transcript to fold back onto itself to form a stem-loop structure of imperfectly dsRNA. Artificial miRNA (amiRNA) technology uses endogenous pri-miRNAs, in which the miRNA and miRNA* (passenger strand of the miRNA duplex) sequences have been replaced with corresponding amiRNA/amiRNA* sequences that direct highly efficient RNA silencing of the targeted gene. Here, we describe the rules for amiRNA design, as well as outline the PCR and bacterial cloning procedures involved in the construction of an amiRNA plant expression vector to control target gene expression in Arabidopsis thaliana. PMID:24057368