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Sample records for pri ikh obluchenii

  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. Development and validation of a LC-MS assay for the quantification of ikh12 a novel anti-tumor candidate in rat plasma and tissues and its application in a pharmacokinetic study.

    PubMed

    Otaegui, Dorleta; Masdeu, Carme; Aldaba, Eneko; Vara, Yosu; Zubia, Aizpea; San Sebastian, Eider; Alcalá, Maria; Villafruela, Sergio; Cossío, Fernando P; Rodriguez-Gascón, Alicia

    2015-08-01

    IKH12 is a novel histone deacetylase 6 selective inhibitor. A rapid and sensitive liquid chromatography tandem mass spectrometry method was developed and validated for the quantification of IKH12 in rat plasma and tissue with kendine 91 as internal standard (IS). The samples were prepared by liquid-liquid extraction with tert-butyl methyl ether. The chromatographic separation was accomplished by using a Zorbax Extend C18 4.6 × 150 mm, 5 µm column, with a mobile phase consisting of methanol and 0.1% formic acid (75:25 v/v). Multiple reaction monitoring, using electrospray ionization in positive ion mode, was employed to quantitatively detect IKH12 and IS. The monitored transitions were set at m/z 418 → 252 and 444 → 169 for IKH12 and kendine 91, respectively. The calibration curve was linear over the concentration range 2-1000 ng mL(-1) . The intra- and inter-assay precision and accuracy of the quality controls and the limit of quantification were satisfactory in all cases (according to European Medicines Agency guidelines). Stability studies showed that plasma samples were stable in the chromatography rack for 24 h and at -80°C for 2 months and also after three freeze-thaw cycles. This method was successfully applied to a pharmacokinetic study of IKH12 in rat. PMID:25616154

  3. 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, ...

  4. 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…

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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,…

  10. 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

  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

    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. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  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. 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

  2. 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.

  3. 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

  4. 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.

  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. 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...

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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).

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  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. 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

  7. 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

  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. 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

  10. 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

  11. 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.

  12. 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

  13. 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

  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. 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

  17. 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

  18. 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

  19. 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

  20. 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

  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. 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

  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 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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...

  14. 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

  15. 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…

  16. 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...

  17. 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.

  18. 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…

  19. 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

  20. 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…

  1. 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.…

  2. 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...

  3. 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

  4. 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

  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. 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,…

  7. Recognition, assessment and management of hypoglycaemia in childhood.

    PubMed

    Ghosh, Arunabha; Banerjee, Indraneel; Morris, Andrew A M

    2016-06-01

    Hypoglycaemia is frequent in children and prompt management is required to prevent brain injury. In this article we will consider hypoglycaemia in children after the neonatal period. The most common causes are diabetes mellitus and idiopathic ketotic hypoglycaemia (IKH) but a number of endocrine disorders and inborn errors of metabolism (IEMs) need to be excluded. Elucidation of the diagnosis relies primarily on investigations during a hypoglycaemic episode but may also involve biochemical tests between episodes, dynamic endocrine tests and molecular genetics. Specific treatment such as cortisol replacement and pancreatic surgery may be required for endocrine causes of hypoglycaemia, such as adrenal insufficiency and congenital hyperinsulinism. In contrast, in IKH and most IEMs, hypoglycaemia is prevented by limiting the duration of fasting and maintaining a high glucose intake during illnesses. PMID:26718813

  8. 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

  9. 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

  10. 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

  11. 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

  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. 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

  14. 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

  15. 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…

  16. 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.

  17. 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…

  18. 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

  19. 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

  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

    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. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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...

  8. 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...

  9. 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

  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. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. [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

  20. 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

  1. 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

  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. 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

  4. 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

  5. A comprehensive constitutive law for waxy crude oil: a thixotropic yield stress fluid.

    PubMed

    Dimitriou, Christopher J; McKinley, Gareth H

    2014-09-21

    Guided by a series of discriminating rheometric tests, we develop a new constitutive model that can quantitatively predict the key rheological features of waxy crude oils. We first develop a series of model crude oils, which are characterized by a complex thixotropic and yielding behavior that strongly depends on the shear history of the sample. We then outline the development of an appropriate preparation protocol for carrying out rheological measurements, to ensure consistent and reproducible initial conditions. We use RheoPIV measurements of the local kinematics within the fluid under imposed deformations in order to validate the selection of a particular protocol. Velocimetric measurements are also used to document the presence of material instabilities within the model crude oil under conditions of imposed steady shearing. These instabilities are a result of the underlying non-monotonic steady flow curve of the material. Three distinct deformation histories are then used to probe the material's constitutive response. These deformations are steady shear, transient response to startup of steady shear with different aging times, and large amplitude oscillatory shear (LAOS). The material response to these three different flows is used to motivate the development of an appropriate constitutive model. This model (termed the IKH model) is based on a framework adopted from plasticity theory and implements an additive strain decomposition into characteristic reversible (elastic) and irreversible (plastic) contributions, coupled with the physical processes of isotropic and kinematic hardening. Comparisons of experimental to simulated response for all three flows show good quantitative agreement, validating the chosen approach for developing constitutive models for this class of materials. PMID:25008187

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  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. 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.

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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).

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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…

  14. 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...

  15. 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

  16. 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...

  17. 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

  18. 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

  19. 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.

  20. 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...

  1. 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...

  2. 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.

  3. 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...

  4. 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...

  5. 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.

  6. 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…

  7. 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...

  8. 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

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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)...

  15. 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...

  16. 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…

  17. 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...

  18. 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

  19. 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…

  20. 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...

  1. 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...

  2. 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

  3. 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...

  4. 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...

  5. 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...

  6. 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…

  7. 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…

  8. 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…

  9. 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...

  10. 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

  11. 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.

  12. 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...

  13. 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…

  14. 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...

  15. 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.

  16. 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

  17. 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...

  18. 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…

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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…

  6. 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...

  7. 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

  8. 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...

  9. 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...

  10. 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...

  11. 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.

  12. 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...

  13. 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

  14. 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…

  15. 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…

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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...

  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. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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

  9. Monitoring Spring Recovery of Photosynthesis and Spectral Reflectance in Temperate Evergreen and Mixed Deciduous Forests

    NASA Astrophysics Data System (ADS)

    Wong, C. Y.; Arain, M. A.; Ensminger, I.

    2015-12-01

    Evergreen conifers in boreal and temperate regions undergo strong seasonal changes in photoperiod and temperatures, which characterizes their photosynthetic activity with high activity in the growing season and downregulation during the winter season. Monitoring the timing of the transitions in evergreens is difficult since it's a largely invisible process, unlike deciduous trees that have a visible budding and senescence sequence. Spectral reflectance and the photochemical reflectance index (PRI), often used as a proxy for photosynthetic light-use efficiency, provides a promising tool to track the transition of evergreens between inactive and active photosynthetic states. To better understand the relationship between PRI and photosynthetic activity and to contrast this relationship between plant functional types, the spring recovery of an evergreen forest and mixed deciduous forest was monitored using spectral reflectance, chlorophyll fluorescence and gas exchange. All metrics indicate photosynthetic recovery during the spring season. These findings indicate that PRI can be used to observe the spring recovery of photosynthesis in evergreen conifers but may not be best suited for deciduous trees. These findings have implications for remote sensing, which provides a promising long-term monitoring system of whole ecosystems, which is important since their roles in the carbon cycle may shift in response to climate change.

  10. Characterization of function and regulation of miR-24-1 and miR-31

    SciTech Connect

    Sun Fenyong; Wang Jiayi; Pan Qiuhui; Yu Yongchun; Zhang Yue; Wan Yang; Wang Ju; Li Xiaoyan; Hong An

    2009-03-13

    To date, numerous microRNAs (miRNAs) have been discovered. However, the function of these miRNAs is largely unknown. While our knowledge of miRNA post-transcriptional processing has greatly expanded in recent years, we have a limited understanding of the regulation and transcription of miRNA genes. In this study, we characterized two BMP-2 upregulated miRNAs, miR-24-1 and miR-31, in mesenchymal stem cells and showed their opposing function in controlling cellular proliferation, and adipogenesis. Furthermore, we are the first to identify and characterize mouse intronic miR-23b{approx}27b{approx}24-1 and intergenic miR-31 genes. Moreover, we found that pri-miR-23b, pri-miR-27b, and pri-miR-24-1 are transcribed independently and their expression profiles are unique when cells are treated with BMP-2, even though they are located closely together.

  11. 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

  12. 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

  13. 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

  14. Design of a small molecule against an oncogenic noncoding RNA.

    PubMed

    Velagapudi, Sai Pradeep; Cameron, Michael D; Haga, Christopher L; Rosenberg, Laura H; Lafitte, Marie; Duckett, Derek R; Phinney, Donald G; Disney, Matthew D

    2016-05-24

    The design of precision, preclinical therapeutics from sequence is difficult, but advances in this area, particularly those focused on rational design, could quickly transform the sequence of disease-causing gene products into lead modalities. Herein, we describe the use of Inforna, a computational approach that enables the rational design of small molecules targeting RNA to quickly provide a potent modulator of oncogenic microRNA-96 (miR-96). We mined the secondary structure of primary microRNA-96 (pri-miR-96) hairpin precursor against a database of RNA motif-small molecule interactions, which identified modules that bound RNA motifs nearby and in the Drosha processing site. Precise linking of these modules together provided Targaprimir-96 (3), which selectively modulates miR-96 production in cancer cells and triggers apoptosis. Importantly, the compound is ineffective on healthy breast cells, and exogenous overexpression of pri-miR-96 reduced compound potency in breast cancer cells. Chemical Cross-Linking and Isolation by Pull-Down (Chem-CLIP), a small-molecule RNA target validation approach, shows that 3 directly engages pri-miR-96 in breast cancer cells. In vivo, 3 has a favorable pharmacokinetic profile and decreases tumor burden in a mouse model of triple-negative breast cancer. Thus, rational design can quickly produce precision, in vivo bioactive lead small molecules against hard-to-treat cancers by targeting oncogenic noncoding RNAs, advancing a disease-to-gene-to-drug paradigm. PMID:27170187

  15. Prorating WAIS - IV summary scores for patients with relapsing-remitting multiple sclerosis.

    PubMed

    Ryan, Joseph J; Umfleet, Laura Glass; Gontkovsky, Samuel T

    2016-11-01

    We evaluated the utility of prorating appropriate combinations of two, six and eight Wechsler Adult Intelligence Scale - Fourth Edition (WAIS - IV) subtests for estimating the Verbal Comprehension Index (VCI), Perceptual Reasoning Index (PRI), Full Scale IQ (FSIQ) and General Ability Index (GAI) in a sample of individuals diagnosed with multiple sclerosis (MS). Forty-eight outpatients completed the WAIS - IV and Wechsler Memory Scale - Fourth Edition (WMS - IV) as part of a comprehensive neuropsychological battery. Means for age, education and duration of diagnosis were 42.35, 14.21 and 8.30 years, respectively. Paired t-tests showed no significant differences between prorated and standard means for VCI (93.46 vs. 93.73), PRI (90.19 vs. 89.44), FSIQ (88.53 vs. 88.47) or GAI (90.56 vs. 90.65). Correlations between prorated and standard composites were ≥0.89 in every instance. Correlations between the standard and prorated composites and education, disability status and WMS - IV indexes did not reveal a single contrast, where the correlations were significantly different. The present findings support the use of the two-subtest VCI and PRI composites and the eight-subtest FSIQ and four-subtest GAI in the assessment of patients with MS. PMID:26422128

  16. 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.

  17. Modified Omega-k Algorithm for High-Speed Platform Highly-Squint Staggered SAR Based on Azimuth Non-Uniform Interpolation

    PubMed Central

    Zeng, Hong-Cheng; Chen, Jie; Liu, Wei; Yang, Wei

    2015-01-01

    In this work, the staggered SAR technique is employed for high-speed platform highly-squint SAR by varying the pulse repetition interval (PRI) as a linear function of range-walk. To focus the staggered SAR data more efficiently, a low-complexity modified Omega-k algorithm is proposed based on a novel method for optimal azimuth non-uniform interpolation, avoiding zero padding in range direction for recovering range cell migration (RCM) and saving in both data storage and computational load. An approximate model on continuous PRI variation with respect to sliding receive-window is employed in the proposed algorithm, leaving a residual phase error only due to the effect of a time-varying Doppler phase caused by staggered SAR. Then, azimuth non-uniform interpolation (ANI) at baseband is carried out to compensate the azimuth non-uniform sampling (ANS) effect resulting from continuous PRI variation, which is further followed by the modified Omega-k algorithm. The proposed algorithm has a significantly lower computational complexity, but with an equally effective imaging performance, as shown in our simulation results. PMID:25664433

  18. Microprocessor mediates transcriptional termination in long noncoding microRNA genes

    PubMed Central

    Dhir, Ashish; Dhir, Somdutta; Proudfoot, Nick J.; Jopling, Catherine L.

    2015-01-01

    MicroRNA (miRNA) play a major role in the post-transcriptional regulation of gene expression. Mammalian miRNA biogenesis begins with co-transcriptional cleavage of RNA polymerase II (Pol II) transcripts by the Microprocessor complex. While most miRNA are located within introns of protein coding genes, a substantial minority of miRNA originate from long non coding (lnc) RNA where transcript processing is largely uncharacterized. We show, by detailed characterization of liver-specific lnc-pri-miR-122 and genome-wide analysis in human cell lines, that most lnc-pri-miRNA do not use the canonical cleavage and polyadenylation (CPA) pathway, but instead use Microprocessor cleavage to terminate transcription. This Microprocessor inactivation leads to extensive transcriptional readthrough of lnc-pri-miRNA and transcriptional interference with downstream genes. Consequently we define a novel RNase III-mediated, polyadenylation-independent mechanism of Pol II transcription termination in mammalian cells. PMID:25730776

  19. Effects of partial root-zone irrigation on hydraulic conductivity in the soil-root system of maize plants.

    PubMed

    Hu, Tiantian; Kang, Shaozhong; Li, Fusheng; Zhang, Jianhua

    2011-08-01

    Effects of partial root-zone irrigation (PRI) on the hydraulic conductivity in the soil-root system (L(sr)) in different root zones were investigated using a pot experiment. Maize plants were raised in split-root containers and irrigated on both halves of the container (conventional irrigation, CI), on one side only (fixed PRI, FPRI), or alternately on one of two sides (alternate PRI, APRI). Results show that crop water consumption was significantly correlated with L(sr) in both the whole and irrigated root zones for all three irrigation methods but not with L(sr) in the non-irrigated root zone of FPRI. The total L(sr) in the irrigated root zone of two PRIs was increased by 49.0-92.0% compared with that in a half root zone of CI, suggesting that PRI has a significant compensatory effect of root water uptake. For CI, the contribution of L(sr) in a half root zone to L(sr) in the whole root zone was ∼50%. For FPRI, the L(sr) in the irrigated root zone was close to that of the whole root zone. As for APRI, the L(sr) in the irrigated root zone was greater than that of the non-irrigated root zone. In comparison, the L(sr) in the non-irrigated root zone of APRI was much higher than that in the dried zone of FPRI. The L(sr) in both the whole and irrigated root zones was linearly correlated with soil moisture in the irrigated root zone for all three irrigation methods. For the two PRI treatments, total water uptake by plants was largely determined by the soil water in the irrigated root zone. Nevertheless, the non-irrigated root zone under APRI also contributed to part of the total crop water uptake, but the continuously non-irrigated root zone under FPRI gradually ceased to contribute to crop water uptake, suggesting that it is the APRI that can make use of all the root system for water uptake, resulting in higher water use efficiency. PMID:21527627

  20. Effects of partial root-zone irrigation on hydraulic conductivity in the soil–root system of maize plants

    PubMed Central

    Hu, Tiantian; Kang, Shaozhong; Li, Fusheng; Zhang, Jianhua

    2011-01-01

    Effects of partial root-zone irrigation (PRI) on the hydraulic conductivity in the soil–root system (Lsr) in different root zones were investigated using a pot experiment. Maize plants were raised in split-root containers and irrigated on both halves of the container (conventional irrigation, CI), on one side only (fixed PRI, FPRI), or alternately on one of two sides (alternate PRI, APRI). Results show that crop water consumption was significantly correlated with Lsr in both the whole and irrigated root zones for all three irrigation methods but not with Lsr in the non-irrigated root zone of FPRI. The total Lsr in the irrigated root zone of two PRIs was increased by 49.0–92.0% compared with that in a half root zone of CI, suggesting that PRI has a significant compensatory effect of root water uptake. For CI, the contribution of Lsr in a half root zone to Lsr in the whole root zone was ∼50%. For FPRI, the Lsr in the irrigated root zone was close to that of the whole root zone. As for APRI, the Lsr in the irrigated root zone was greater than that of the non-irrigated root zone. In comparison, the Lsr in the non-irrigated root zone of APRI was much higher than that in the dried zone of FPRI. The Lsr in both the whole and irrigated root zones was linearly correlated with soil moisture in the irrigated root zone for all three irrigation methods. For the two PRI treatments, total water uptake by plants was largely determined by the soil water in the irrigated root zone. Nevertheless, the non-irrigated root zone under APRI also contributed to part of the total crop water uptake, but the continuously non-irrigated root zone under FPRI gradually ceased to contribute to crop water uptake, suggesting that it is the APRI that can make use of all the root system for water uptake, resulting in higher water use efficiency. PMID:21527627

  1. TU-F-12A-03: Using 18F-FDG-PET-CT and Deformable Registration During Head-And-Neck Cancer (HNC) Intensity Modulated Radiotherapy (IMRT) to Predict Treatment Response

    SciTech Connect

    Vergalasova, I; Mowery, Y; Yoo, D; Brizel, D; Das, S

    2014-06-15

    Purpose: To evaluate the effect of deformable vs. rigid registration of pre-treatment 18F-FDG-PET-CT to intra-treatment 18F-FDG-PET-CT on different standardized uptake value (SUV) parameters and investigate which parameters correlate best with post-treatment response in patients undergoing IMRT for HNC. Methods: Pre-treatment and intra-treatment PET-CT (after 20Gy) scans were acquired, in addition to a 12 week post-treatment PET-CT to assess treatment response. Primary and lymph node gross tumor volumes (GTV-PRI and GTV-LN) were contoured on the pre-treatment CT. These contours were then mapped to intra-treatment PET images via rigid and deformable registration. Absolute changes from pre- to intra-treatment scans for rigid and deformable registration were extracted for the following parameters: SUV-MAX, SUV-MEAN, SUV-20%, SUV-40%, and SUV-60% (SUV-X% is the minimum SUV to the highest-intensity X% volume). Results: Thirty-eight patients were evaluated, with 27 available for classification as complete or incomplete response (CR/ICR). The pre-treatment average tumor volumes for the patients were 24.05cm{sup 3} for GTV-PRI and 23.4cm{sup 3} for GTV-LN. For GTV-PRI, there was no statistically significant difference between rigid vs. deformable registration across all ΔSUV parameters. For GTV-LN contours, all parameters were significantly different except for ΔSUV-MAX. For deformably-registered GTV-PRI, changes in the following metrics were significantly different for CR vs. ICR: SUV-MEAN(p=0.003), SUV-20%(p=0.02), SUV-40%(p=0.02), and SUV-60%(p=0.008). The following cutoff values separated CR from ICR with high sensitivity and specificity: ΔSUV-MEAN=1.49, ΔSUV-20%=2.39, ΔSUV-40%=1.80 and ΔSUV-60%=1.31. Corresponding areas under the Receiver Operating Characteristics curve were 0.90, 0.81, 0.81, and 0.85, respectively. Conclusion: Rigidly and deformably registered contours yielded statistically similar SUV parameters for GTV-PRI, but not GTV-LN. This implies that

  2. Geomorphological development of Eastern Mongolian plain, Mongolia

    NASA Astrophysics Data System (ADS)

    khukhuudei, Ulambadrakh; otgonbayar, Orolzodmaa

    2016-04-01

    - K-Ar age for Mesozoic volcanic rocks from Eastern Mongolia and Ikh Khyangan dated in range from 160 to 110Ma (Shuvalov, 1987; Makhbadar et al., 1995; Zhou et al., 2006; Bat-Ulzii, 2014). 2. Rift controlling fault - Delgerekh, Modon Ovoo and Matad faults to north-east direction are interpreted and presented in EMP (Khasin, 1973; Tikhonov, 1974; Byamba, 2009). 3. Basin and Range topography - we are interpreting that Nukhet davaa mountain range, Tamsag basin, Matad uplift or range and Choibalsan basin were developed in that time. Hills with 40-150 m height at a present day are interpreted that they developed from the Late Cretaceous period. In post- rift or Late Cretaceous period, lakes disappeared and whole area of Eastern Mongolia became a dry land, dominating by exogenic process. Denudation planation surface at EMP are kept in high and low level. High or old planation surface is proposed by age of the Miocene - Lower Pliocene and low or young planation surface - Late Pliocene. Just a current topography of EMP is formed in Late Neogene - Lower Quaternary period as a peneplain.

  3. Ecosystem based river basin management planning in critical water catchment in Mongolia

    NASA Astrophysics Data System (ADS)

    Tugjamba, Navchaa; Sereeter, Erdenetuul; Gonchigjav, Sarantuya

    2014-05-01

    Developing the ecosystem based adaptation strategies to maintain water security in critical water catchments in Mongolia would be very significant. It will be base by reducing the vulnerability. "Ecosystem Based adaptation" is quite a new term in Mongolia and the ecosystem approach is a strategy for the integrated management of land, water and living resources that promotes conservation and sustainable use in an equitable way. To strengthen equitable economic development, food security, climate resilience and protection of the environment, the implementation of sustainable river basin management in critical water catchments is challenging in Mongolia. The Ulz river basin is considered one of the critical water catchments due to the temperature has increased by in average 1.30Ñ over the period 1976 to 2011. It is more intense than the global warming rate (0.740C/100 years) and a bit higher than the warming rate over whole Mongolia as well. From long-term observations and measurements it is clear that Ulz River has low water in a period of 1970-1980 and since the end of 1980s and middle of 1990s there were dominated years of the flood. However, under the influence of the global warming, climate changes of Mongolia and continuation of drought years with low water since the end of 1990s until today river water was sharply fallen and dried up. For the last ten years rivers are dried up and annual mean run-off is less by 3-5 times from long term mean value. The Ulz is the transboundary river basin and taking its origin from Ikh and Baga Burd springs on territory of Norovlin soum of Khentii province that flows through Khentii and Dornod provinces to the northeast, crossing the state border it flows in Baruun Tari located in Tari Lake concavity in Russia. Based on the integrative baseline study on the 'The Ulz River Basin Environmental and Socioeconomic condition', ecosystem based river basin management was planned. 'Water demand Calculator 3' (WDC) software was used to

  4. ADAR2-Mediated Editing of miR-214 and miR-122 Precursor and Antisense RNA Transcripts in Liver Cancers

    PubMed Central

    Liu, Wan-Hsin; Chen, Chao-Hung; Yeh, Kun-Huei; Li, Chiao-Ling; Wu, Yi-Jinn; Chen, Ding-Shinn; Chen, Pei-Jer; Yeh, Shiou-Hwei

    2013-01-01

    A growing list of microRNAs (miRNAs) show aberrant expression patterns in hepatocellular carcinoma (HCC), but the regulatory mechanisms largely remain unclear. RNA editing catalyzed by members of the adenosine deaminase acting on the RNA (ADAR) family could target the miRNA precursors and affect the biogenesis process. Therefore, we investigate whether RNA editing could be one mechanism contributing to the deregulation of specific miRNAs in HCC. By overexpression of individual ADARs in hepatoma cells, RNA editing on the precursors of 16 miRNAs frequently deregulated in HCC was screened by a sensitive high-resolution melting platform. The results identified RNA precursors of miR-214 and miR-122 as potential targets edited by ADAR2. A subset of HCC showing elevated ADAR2 verified the major editings identified in ARAR2 overexpressed hepatoma cells, either with A-to-I or U-to-C changes. The unusual U-to-C editing at specific residues was demonstrated as being attributed to the A-to-I editing on the RNA transcripts complementary to the pri-miRNAs. The editing event caused a decrease of the RNA transcript complementary to pri-miR-214, which led to the decrease of pri-miR-214 and miR-214 and resulted in the increased protein level of its novel target gene Rab15. In conclusion, the current study discovered ADAR2-mediated editing of the complementary antisense transcripts as a novel mechanism for regulating the biogenesis of specific miRNAs during hepatocarcinogenesis. PMID:24386085

  5. Computationally predicting protein-RNA interactions using only positive and unlabeled examples.

    PubMed

    Cheng, Zhanzhan; Zhou, Shuigeng; Guan, Jihong

    2015-06-01

    Protein-RNA interactions (PRIs) are considerably important in a wide variety of cellular processes, ranging from transcriptional and post-transcriptional regulations of gene expression to the active defense of host against virus. With the development of high throughput technology, large amounts of PRI information is available for computationally predicting unknown PRIs. In recent years, a number of computational methods for predicting PRIs have been developed in the literature, which usually artificially construct negative samples based on verified nonredundant datasets of PRIs to train classifiers. However, such negative samples are not real negative samples, some even may be unknown positive samples. Consequently, the classifiers trained with such training datasets cannot achieve satisfactory prediction performance. In this paper, we propose a novel method PRIPU that employs biased-support vector machine (SVM) for predicting Protein-RNA Interactions using only Positive and Unlabeled examples. To the best of our knowledge, this is the first work that predicts PRIs using only positive and unlabeled samples. We first collect known PRIs as our benchmark datasets and extract sequence-based features to represent each PRI. To reduce the dimension of feature vectors for lowering computational cost, we select a subset of features by a filter-based feature selection method. Then, biased-SVM is employed to train prediction models with different PRI datasets. To evaluate the new method, we also propose a new performance measure called explicit positive recall (EPR), which is specifically suitable for the task of learning positive and unlabeled data. Experimental results over three datasets show that our method not only outperforms four existing methods, but also is able to predict unknown PRIs. Source code, datasets and related documents of PRIPU are available at: http://admis.fudan.edu.cn/projects/pripu.htm . PMID:25790785

  6. Remote estimation of net CO2 emission from boreal ecosystems

    NASA Astrophysics Data System (ADS)

    Rogers, C. A.; Strachan, I. B.

    2010-12-01

    Hydroelectricity is the main source of power in the province of Quebec, Canada. While hydroelectricity is considered to be a relatively green source of energy, reservoir creation is a land use change that involves flooding terrestrial ecosystems and thus a loss of greenhouse gas (GHG) uptake as well as direct GHG emission from decomposing vegetation. Both the lost sink for GHGs and direct emission from the reservoir surface must be included in estimating the net GHG emission attributable to the reservoir’s construction. These emissions can be determined using techniques such as eddy covariance, however, such methods are often costly and time consuming, and require frequent access to remote locations. Remote sensing is able to provide spatially continuous data over large areas, minimizing the need for ground based measurements. We tested the ability of the photochemical reflectance index (PRI) and normalized difference vegetation index (NDVI) to predict fluxes of carbon dioxide in areas representative of boreal forests and peatlands flooded by the Eastmain 1 hydroelectric reservoir in the James Bay region of Quebec, Canada. We collected spectral measurements from hand-held and helicopter-based platforms, as well as continuously monitored the indices PRI and NDVI from tower-mounted sensors at a forest and peatland site. We then compared the vegetation indices to net fluxes of carbon dioxide measured by eddy covariance at each site. PRI was related to fluxes at both the forest and peatland sites, suggesting it is possible to remotely estimate carbon dioxide uptake by vegetation in boreal forests and peatlands and thus greenhouse gas emissions resulting from land use changes in boreal regions, such as reservoir inundation.

  7. Identification of hairy root loci in the T-regions of Agrobacterium rhizogenes Ri plasmids.

    PubMed

    Boulanger, F; Berkaloff, A; Richaud, F

    1986-07-01

    Agrobacterium rhizogenes induces root formation at the wound site of inoculation in plants and inserts a fragment of its plasmid (Ri) into the plant nuclear DNA. Parts of the transferred region (T-region) of the Ri plasmid of A. rhizogenes strain A4 or 8196 are cloned in Escherichia coli. Insertions of the E. coli lacZ coding region into the hybrid plasmids were made in vivo using transduction by miniMu. Twenty insertions localized in the TL-DNA of pRiA4 (or pRi1855) and 2 inserts in the T-DNA of pRi8196 were obtained in E. coli. One of the TL-DNA insertions is saved up because it is linked to an internal T-DNA deletion; the others because they confer a lactose plus phenotype on E. coli; this indicates that the T-DNA harbours sequences that are expressed in E. coli. Fifteen of these T-DNA insertions were transfered to Agrobacterium where they substitute the corresponding wild-type T-DNA of the Ri plasmid by homologous recombination. These strains corresponding to insertion-directed mutagenesis were used to inoculate Daucus carota slices and stems and leaves of Kalanchoe daigremontiana. The two insertions strains obtained in the T-DNA of pRi8196 are avirulent on K. daigremontiana; but their phenotypes differ on D. carota slices, suggesting that insertions affect distinct loci on the T-DNA involved in hairy root formation. Only one insertion out of the twenty obtained in the TL-DNA of pRiA4 (or 1855) induces a loss of virulence on leaves of K. daigremontiana. However the TL-DNA deletion harbouring strain induces a loss of virulence on D. carota and K. daigremontiana (stems and leaves), confirming the importance of the TL-DNA for hairy root induction. re]19850711 rv]19851230 ac]19860114. PMID:24307326

  8. Disaggregation of Remotely Sensed Soil Moisture in Heterogeneous Landscapes Using Holistic Structure-Based Models

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Subit; Judge, Jasmeet; Bongiovanni, Tara; Rangarajan, Anand; Ranka, Sanjay

    2016-08-01

    In this study, a novel machine learning algorithm is presented for disaggregation of satellite soil moisture (SM) based on self-regularized regressive models (SRRM) using high-resolution correlated information from auxiliary sources. It includes regularized clustering that assigns soft memberships to each pixel at fine-scale followed by a kernel regression that computes the value of the desired variable at all pixels. Coarse-scale remotely sensed SM were disaggregated from 10km to 1km using land cover, precipitation, land surface temperature, leaf area index, and in-situ observations of SM. This algorithm was evaluated using multi-scale synthetic observations in NC Florida for heterogeneous agricultural land covers. It was found that the root mean square error (RMSE) for 96% of the pixels was less than 0.02 $m^3/m^3$. The clusters generated represented the data well and reduced the RMSE by upto 40% during periods of high heterogeneity in land-cover and meteorological conditions. The Kullback Leibler divergence (KLD) between the true SM and the disaggregated estimates is close to 0, for both vegetated and baresoil landcovers. The disaggregated estimates were compared to those generated by the Principle of Relevant Information (PRI) method. The RMSE for the PRI disaggregated estimates is higher than the RMSE for the SRRM on each day of the season. The KLD of the disaggregated estimates generated by the SRRM is at least four orders of magnitude lower than those for the PRI disaggregated estimates, while the computational time needed was reduced by three times. The results indicate that the SRRM can be used for disaggregating SM with complex non-linear correlations on a grid with high accuracy.

  9. Hysteretic pinching of human secondary osteons subjected to torsion.

    PubMed

    Ascenzi, Maria-Grazia; Di Comite, Mariasevera; Mitov, Plamen; Kabo, John Michael

    2007-01-01

    The mechanical behavior of bone tissue's ultra- and micro- structure is fundamental to assessment of macroscopic bone mechanics. This paper explores the ultra-structural characteristics of human femoral tissue responsible for energy absorption of secondary osteons under mechanical loading. A novel mathematical interpretation of single osteon mechanics elucidates the behavior of the collagen-apatite interface. Fully calcified single osteon specimens were mechanically tested quasi-statically under cyclic torsional loading about their longitudinal axis. On each hysteretic diagram, all cycles after the initial monotonic cycle appear pinched and share two points. Stiffness degradation and pinching degradation were investigated on the torque versus deflection-angle-per-unit-length diagrams as the number of cycles increases, in relation to the appearance of osteons in cross-section under circularly polarized light microscopy. Material science's Bauschinger effect, originally defined for metals and later extended to structures reinforced with metal bars, is adapted to describe pinching. Material science's prying effect, defined as amplification of eccentric tensile load through lever action, is employed to explain pinching. The presence of the two points shared by all complete cycles is analyzed in terms of the mathematical fixed point theorem. The results allow formulation of the following conjectures: (1) the prying of carbonated apatite crystallites at the interface with the 40 nm long bands of non-calcified collagen fibrils causes pinching; (2) the prying effect increases with the increasing percentage of collagen-apatite elements that form a larger angle with the osteon axis; and (3) micro-cracks increase more in number than in length as the number of cycles increases. PMID:17399724

  10. University woodwind students’ experiences with playing-related injuries and their management: a pilot study

    PubMed Central

    Stanhope, Jessica; Milanese, Steve; Grimmer, Karen

    2014-01-01

    Background This study aimed to determine the experiences of university classical woodwind students with playing-related injuries (PRIs), the impact of these PRIs, the management selected by students with PRIs, and the perceived effectiveness of this management. Materials and methods All classical woodwind students enrolled in vocational education training or undergraduate courses at a university were sent an email with a link to an online survey. Only those aged 18 years and older were eligible. The survey obtained data regarding demographic information, details of PRI experienced (location, if they lasted for more than 3 months, and if they were current), and the impact of these, as well as the types of management strategies tried and their perceived effectiveness. Data were analyzed using descriptive statistics, and comments were reported descriptively. Results Fourteen students returned the survey; however, one of these only completed the questions regarding demographics, and was therefore excluded. A total of 62% of participants reported having experienced a PRI. Common locations for PRI were the wrist/hand/fingers, lower back, and neck. Reducing practice time by half and missing playing commitments were the most commonly reported consequences of PRIs. Playing-related management strategies were most frequently trialed, with these and passive nonplaying-related strategies perceived to be the most effective. Conclusion PRIs are common in this population, with a range of consequences reported. While it is encouraging that students had tried and found effective playing-related management strategies, active nonplaying-related strategies should be encouraged, particularly in preference to passive nonplaying-related strategies. This was a small-scale study, and the results are only applicable to the institution investigated; therefore, similar larger-scale studies are recommended to determine the generalizability of these findings. PMID:24634587

  11. RecG Directs DNA Synthesis during Double-Strand Break Repair

    PubMed Central

    Azeroglu, Benura; Mawer, Julia S. P.; Cockram, Charlotte A.; White, Martin A.; Hasan, A. M. Mahedi; Filatenkova, Milana; Leach, David R. F.

    2016-01-01

    Homologous recombination provides a mechanism of DNA double-strand break repair (DSBR) that requires an intact, homologous template for DNA synthesis. When DNA synthesis associated with DSBR is convergent, the broken DNA strands are replaced and repair is accurate. However, if divergent DNA synthesis is established, over-replication of flanking DNA may occur with deleterious consequences. The RecG protein of Escherichia coli is a helicase and translocase that can re-model 3-way and 4-way DNA structures such as replication forks and Holliday junctions. However, the primary role of RecG in live cells has remained elusive. Here we show that, in the absence of RecG, attempted DSBR is accompanied by divergent DNA replication at the site of an induced chromosomal DNA double-strand break. Furthermore, DNA double-stand ends are generated in a recG mutant at sites known to block replication forks. These double-strand ends, also trigger DSBR and the divergent DNA replication characteristic of this mutant, which can explain over-replication of the terminus region of the chromosome. The loss of DNA associated with unwinding joint molecules previously observed in the absence of RuvAB and RecG, is suppressed by a helicase deficient PriA mutation (priA300), arguing that the action of RecG ensures that PriA is bound correctly on D-loops to direct DNA replication rather than to unwind joint molecules. This has led us to put forward a revised model of homologous recombination in which the re-modelling of branched intermediates by RecG plays a fundamental role in directing DNA synthesis and thus maintaining genomic stability. PMID:26872352

  12. Premagnetization for Enhancing the Reactivity of Multiple Zerovalent Iron Samples toward Various Contaminants.

    PubMed

    Li, Jinxiang; Qin, Hejie; Guan, Xiaohong

    2015-12-15

    Premagnetization was applied to enhance the removal of various oxidative contaminants (including amaranth (AR27), lead ion (Pb(2+)), cupric ion (Cu(2+)), selenite (Se(4+)), silver ion (Ag(+)), and chromate (Cr(6+))) by zerovalent iron (ZVI) from different origins under well-controlled experimental conditions. The rate constants of contaminants by premagnetized ZVI (Mag-ZVI) samples were 1.2-12.2-fold greater than those by pristine ZVI (Pri-ZVI) samples. Generally, there was a linear correlation between the specific reaction rate constants (kSA) of one particular contaminant removal by various Pri-ZVI or Mag-ZVI samples and those of the other contaminant, which could be successfully employed to predict the kSA of one contaminant by one ZVI sample if kSA of the other contaminant by this ZVI sample was available. The specific rate constant of Fe(II) release at pH 4.0 was proposed in this study to stand for the intrinsic reactivity of a ZVI sample. All Mag-ZVI samples had higher intrinsic reactivity than their counterparts without premagnetization. There were strong correlations between the intrinsic reactivity of various Pri-ZVI/Mag-ZVI samples and the removal rate constants of a specific contaminant by these ZVI samples not only at pH 4.0 when the intrinsic reactivity was determined but also at other pH levels. This correlation could be employed to predict the removal rate constant of this contaminant by a ZVI sample that was not included in the original data set once the intrinsic reactivity of the ZVI sample was known. PMID:26575344

  13. Interaction Between Object-Based Attention and Pertinence Values Shapes the Attentional Priority Map of a Multielement Display

    PubMed Central

    2016-01-01

    Previous studies have shown that the perceptual organization of the visual scene constrains the deployment of attention. Here we investigated how the organization of multiple elements into larger configurations alters their attentional weight, depending on the “pertinence” or behavioral importance of the elements’ features. We assessed object-based effects on distinct aspects of the attentional priority map: top-down control, reflecting the tendency to encode targets rather than distracters, and the spatial distribution of attention weights across the visual scene, reflecting the tendency to report elements belonging to the same rather than different objects. In 2 experiments participants had to report the letters in briefly presented displays containing 8 letters and digits, in which pairs of characters could be connected with a line. Quantitative estimates of top-down control were obtained using Bundesen’s Theory of Visual Attention (1990). The spatial distribution of attention weights was assessed using the “paired response index” (PRI), indicating responses for within-object pairs of letters. In Experiment 1, grouping along the task-relevant dimension (targets with targets and distracters with distracters) increased top-down control and enhanced the PRI; in contrast, task-irrelevant grouping (targets with distracters) did not affect performance. In Experiment 2, we disentangled the effect of target-target and distracter-distracter grouping: Pairwise grouping of distracters enhanced top-down control whereas pairwise grouping of targets changed the PRI. We conclude that object-based perceptual representations interact with pertinence values (of the elements’ features and location) in the computation of attention weights, thereby creating a widespread pattern of attentional facilitation across the visual scene. PMID:26752732

  14. Assessing intra-annual vegetation regrowth after fire using the pixel based regeneration index

    NASA Astrophysics Data System (ADS)

    Lhermitte, S.; Verbesselt, J.; Verstraeten, W. W.; Veraverbeke, S.; Coppin, P.

    Several remote sensing studies have discussed the potential of satellite imagery as an alternative for extensive field sampling to quantify fire-vegetation impact over large areas. Most studies depend on Landsat image availability with infrequent image acquisition dates and consequently are limited for assessing intra-annual fire-vegetation dynamics or comparing different fire plots and dates. The control pixel based regeneration index (pRI) derived from SPOT-VEGETATION (VGT) normalized difference vegetation index (NDVI) is used in this study as an alternative to the traditional bi-temporal Landsat approach based on the normalized burn ratio (NBR). The major advantage of the pRI is the use of unburnt control plots which allow the expression of the intra-annual variation due to regeneration processes without external influences. In the comparison of Landsat and VGT data, (i) the inter-annual differences between the bi-temporal and control plot approach were contrasted and (ii) metrics of pRI were derived and compared with the inter-annual dynamics of both VGT and Landsat data. Results of these comparisons, demonstrate the overall similarity between NBR and NDVI data, stress the importance of the elimination of external influences (e.g., phenological variations), and emphasize the failure of including post-fire vegetation responses in bi-temporal Landsat assessments, especially in quickly recovering ecotypes with a strong annual phenological cycle such as savanna. This highlights the importance of using high frequency multi-temporal approaches to estimate fire-vegetation impact in temporally dynamic vegetation types.

  15. Biomass selection for optimal anaerobic treatment of olive mill wastewater.

    PubMed

    Sabbah, I; Yazbak, A; Haj, J; Saliba, A; Basheer, S

    2005-01-01

    This research was conducted to identify the most efficient biomass out of five different types of biomass sources for anaerobic treatment of Olive Mill Wastewater (OMW). This study was first focused on examining the selected biomass in anaerobic batch systems with sodium acetate solutions (control study). Then, the different types of biomass were tested with raw OMW (water-diluted) and with pretreated OMW by coagulation-flocculation using Poly Aluminum Chloride (PACl) combined with hydrated lime (Ca(OH)2). Two types of biomass from wastewater treatment systems of a citrus juice producing company "PriGat" and from a citric acid manufacturing factory "Gadot", were found to be the most efficient sources of microorganisms to anaerobically treat both sodium acetate solution and OMW. Both types of biomass were examined under different concentration ranges (1-40 g l(-1)) of OMW in order to detect the maximal COD tolerance for the microorganisms. The results show that 70-85% of COD removal was reached using Gadot biomass after 8-10 days when the initial concentration of OMW was up to 5 g l(-1), while a similar removal efficiency was achieved using OMW of initial COD concentration of 10 g l(-1) in 2-4 days of contact time with the PriGat biomass. The physico-chemical pretreatment of OMW was found to enhance the anaerobic activity for the treatment of OMW with initial concentration of 20 g l(-1) using PriGat biomass. This finding is attributed to reducing the concentrations of polyphenols and other toxicants originally present in OMW upon the applied pretreatment process. PMID:15747599

  16. P2Y12 receptor inhibition and effect of morphine in patients undergoing primary PCI for ST-segment elevation myocardial infarction. The PRIVATE-ATLANTIC study.

    PubMed

    Silvain, Johanne; Storey, Robert F; Cayla, Guillaume; Esteve, Jean-Baptiste; Dillinger, Jean-Guillaume; Rousseau, Hélène; Tsatsaris, Anne; Baradat, Caroline; Salhi, Néjoua; Hamm, Christian W; Lapostolle, Frédéric; Lassen, Jens Flensted; Collet, Jean-Philippe; Ten Berg, Jurriën M; Van't Hof, Arnoud W; Montalescot, Gilles

    2016-08-01

    PRIVATE-ATLANTIC (P2Y12 Receptor Inhibition with VASP Testing using Elisa kit during the ATLANTIC study) is a pre-specified substudy of the randomised, double-blind ATLANTIC trial in patients with ST-segment elevation myocardial infarction, designed to help interpret the main trial results. The primary objective of ATLANTIC was to assess coronary reperfusion prior to percutaneous coronary intervention (PCI) with pre- vs in-hospital ticagrelor 180 mg loading dose (LD). PRIVATE-ATLANTIC assessed platelet inhibition in 37 patients by measurement of vasodilator-associated stimulated phosphoprotein (VASP) platelet reactivity index (PRI) and VerifyNow platelet reactivity units (PRU) before angiogram (T1), immediately after PCI (T2), 1 (T3), and 6 (T4) hours (h) after PCI, and before next study drug administration (T5). The median time difference between the two ticagrelor LD was 41 minutes. Platelet reactivity was unaffected at T1 when measured by VASP-PRI (89.8 vs 93.9 % for pre- and in-hospital ticagrelor, respectively; p = 0.18) or PRU (239 vs 241; p = 0.82). Numerical differences were apparent at T2 and maximal at T3. Morphine administration significantly delayed onset of platelet inhibition at T3 (VASP-PRI 78.2 vs 23.4 % without morphine; p = 0.0116) and T4 (33.1 vs 11.0 %; p = 0.0057). In conclusion, platelet inhibition in ATLANTIC was unaffected by pre-hospital ticagrelor administration at the time of initial angiogram due to the short transfer delay. The maximum difference in platelet inhibition was detected 1 h after PCI (T3). Morphine administration was associated with delayed onset of action of ticagrelor and appeared more important than timing of ticagrelor administration. PMID:27196998

  17. Interaction between object-based attention and pertinence values shapes the attentional priority map of a multielement display.

    PubMed

    Gillebert, Celine R; Petersen, Anders; Van Meel, Chayenne; Müller, Tanja; McIntyre, Alexandra; Wagemans, Johan; Humphreys, Glyn W

    2016-06-01

    Previous studies have shown that the perceptual organization of the visual scene constrains the deployment of attention. Here we investigated how the organization of multiple elements into larger configurations alters their attentional weight, depending on the "pertinence" or behavioral importance of the elements' features. We assessed object-based effects on distinct aspects of the attentional priority map: top-down control, reflecting the tendency to encode targets rather than distracters, and the spatial distribution of attention weights across the visual scene, reflecting the tendency to report elements belonging to the same rather than different objects. In 2 experiments participants had to report the letters in briefly presented displays containing 8 letters and digits, in which pairs of characters could be connected with a line. Quantitative estimates of top-down control were obtained using Bundesen's Theory of Visual Attention (1990). The spatial distribution of attention weights was assessed using the "paired response index" (PRI), indicating responses for within-object pairs of letters. In Experiment 1, grouping along the task-relevant dimension (targets with targets and distracters with distracters) increased top-down control and enhanced the PRI; in contrast, task-irrelevant grouping (targets with distracters) did not affect performance. In Experiment 2, we disentangled the effect of target-target and distracter-distracter grouping: Pairwise grouping of distracters enhanced top-down control whereas pairwise grouping of targets changed the PRI. We conclude that object-based perceptual representations interact with pertinence values (of the elements' features and location) in the computation of attention weights, thereby creating a widespread pattern of attentional facilitation across the visual scene. (PsycINFO Database Record PMID:26752732

  18. Animal models of ulcerative colitis and their application in drug research

    PubMed Central

    Low, Daren; Nguyen, Deanna D; Mizoguchi, Emiko

    2013-01-01

    The specific pathogenesis underlying inflammatory bowel disease is complex, and it is even more difficult to decipher the pathophysiology to explain for the similarities and differences between two of its major subtypes, Crohn’s disease and ulcerative colitis (UC). Animal models are indispensable to pry into mechanistic details that will facilitate better preclinical drug/therapy design to target specific components involved in the disease pathogenesis. This review focuses on common animal models that are particularly useful for the study of UC and its therapeutic strategy. Recent reports of the latest compounds, therapeutic strategies, and approaches tested on UC animal models are also discussed. PMID:24250223

  19. Drum lid removal tool

    DOEpatents

    Pella, Bernard M.; Smith, Philip D.

    2010-08-24

    A tool for removing the lid of a metal drum wherein the lid is clamped over the drum rim without protruding edges, the tool having an elongated handle with a blade carried by an angularly positioned holder affixed to the midsection of the handle, the blade being of selected width to slice between lid lip and the drum rim and, when the blade is so positioned, upward motion of the blade handle will cause the blade to pry the lip from the rim and allow the lid to be removed.

  20. Neptunium and plutonium complexes with a sterically encumbered triamidoamine (TREN) scaffold

    DOE PAGESBeta

    Brown, Jessie L.; Gaunt, Andrew J.; King, David M.; Liddle, Stephen T.; Reilly, Sean D.; Scott, Brian L.; Wooles, Ashley J.

    2016-03-11

    Here, the syntheses and characterization of isostructural neptunium(IV) and plutonium(IV) complexes [MIV(TRENTIPS)(Cl)] [An = Np, Pu; TRENTIPS = {N(CH2CH2NSiPri3)3}3] are reported, along with the demonstration that they are likely reduced to the corresponding neptunium(III) and plutonium(III) products [MIII(TRENTIPS)]; this chemistry provides new platforms from which to target a plethora of unprecedented molecular functionalities in transuranic chemistry and the neptunium(IV) molecule is the first structurally characterized neptunium(IV)–amide complex.

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

    PubMed Central

    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

  2. Draft Genome Sequence of Agrobacterium rhizogenes Strain NCPPB2659

    PubMed Central

    Valdes Franco, Jose A.; Collier, Ray; Wang, Yi; Huo, Naxin; Gu, Yong

    2016-01-01

    This work reports the draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659 (also known as strain K599). The assembled genome contains 5,277,347 bp, composed of one circular chromosome, the pRi2659 virulence plasmid, and 17 scaffolds pertaining to the linear chromosome. The wild-type strain causes hairy root disease in dicots and has been used to make transgenic hairy root cultures and composite plants (nontransgenic shoots with transgenic roots). Disarmed variants of the strain have been used to produce stable transgenic monocot and dicot plants. PMID:27469966

  3. Abnormal carbene-silicon halide complexes.

    PubMed

    Wang, Yuzhong; Xie, Yaoming; Wei, Pingrong; Schaefer, Henry F; Robinson, Gregory H

    2016-04-14

    Reaction of the anionic N-heterocyclic dicarbene (NHDC), [:C{[N(2,6-Pr(i)2C6H3)]2CHCLi}]n (1), with SiCl4 gives the trichlorosilyl-substituted (at the C4 carbon) N-heterocyclic carbene complex (7). Abnormal carbene-SiCl4 complex (8) may be conveniently synthesized by combining 7 with HCl·NEt3. In addition, 7 may react with CH2Cl2 in warm hexane, giving the abnormal carbene-complexed SiCl3(+) cation (9). The nature of the bonding in 9 was probed with complementary DFT computations. PMID:26605692

  4. Draft Genome Sequence of Agrobacterium rhizogenes Strain NCPPB2659.

    PubMed

    Valdes Franco, Jose A; Collier, Ray; Wang, Yi; Huo, Naxin; Gu, Yong; Thilmony, Roger; Thomson, James G

    2016-01-01

    This work reports the draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659 (also known as strain K599). The assembled genome contains 5,277,347 bp, composed of one circular chromosome, the pRi2659 virulence plasmid, and 17 scaffolds pertaining to the linear chromosome. The wild-type strain causes hairy root disease in dicots and has been used to make transgenic hairy root cultures and composite plants (nontransgenic shoots with transgenic roots). Disarmed variants of the strain have been used to produce stable transgenic monocot and dicot plants. PMID:27469966

  5. JWST Primary Mirror Technology Development

    NASA Technical Reports Server (NTRS)

    Stahl, H. Philip

    2010-01-01

    Mirror Technology was identified as a (if not the) critical capability necessary to achieve the Level 1 science goals. A never before demonstrated space telescope capability was required: 6 to 8 meter class pri mary mirror, diffraction limited at 2 micrometers and operates at temperatures below 50K. Launch vehicle constraints placed significant architectural constraints: deployed/segmented primary mirror (4.5 meter fairing diameter) 20 kg/m2 areal density (PM 1000 kg mass) Such mirror technology had never been demonstrated - and did not exist

  6. Recent development of two new UV Raman standoff explosive detection systems

    NASA Astrophysics Data System (ADS)

    Waterbury, Rob; Babnick, Robert; Cooper, Justin L.; Ford, Alan R.; Herrera, Francisco; Hopkins, Adam J.; Pohl, Ken; Profeta, Luisa T. M.; Sandoval, Juan; Vunck, Darius

    2016-05-01

    Alakai Defense Systems has created two new short range UV Raman standoff explosive detection sensors. These are called the Critical Infrastructure Protection System (CIPS) and Portable Raman Improvised Explosive Detection System (PRIED) and work at standoff ranges of 10cm and 1-10m respectively. Both these systems are designed to detect neartrace quantities of explosives and Homemade Explosives. A short description of the instruments, design trades, and CONOPS of each design is presented. Data includes a wide variety of explosives, precursors, TIC/TIM's, narcotics, and CWA simulants

  7. D-1A nose fairing separation fitting load test

    NASA Technical Reports Server (NTRS)

    Vanvleet, J. O.

    1976-01-01

    Structural testing of the D-1A Centaur nose fairing was completed to determine the loads imposed during flight on the latch bolts of the fairing separation system. This testing was conducted to supplement and/or verify the analytic techniques used in calculating bolt loads for the D-1A, and to gain insight into the general structural behavior of separation latch systems. It was shown that the assumed bolt load magnification due to prying action of the latch fittings on the bolt does occur, but is strongly dependent on fairing shell stiffness.

  8. Linking solar induced fluorescence and the photochemical reflectance index to carbon assimilation in a cornfield

    NASA Astrophysics Data System (ADS)

    Cheng, Y.; Middleton, E.; Zhang, Q.; Corp, L.; Campbell, P. K.; Huemmrich, K. F.; Kustas, W.; Daughtry, C. S.; Dulaney, W. P.; Russ, A.

    2012-12-01

    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. This presentation summarizes a field campaign conducted in a USDA-ARS experimental cornfield site located in Beltsville, MD, USA over a five-year period. The site is equipped with an instrumented tower which makes continuous eddy covariance measurements of CO2 along with incoming PAR. Hyperspectral reflectance observations were acquired over corn canopies with a USB4000 Miniature Fiber Optic Spectrometer (Ocean Optics Inc., Dunedin, Florida, USA) at multiple times a day at various stages through the growing season. On all field days, supporting plant information and leaf level data were acquired (e.g., CO2 gas exchange) as well as biophysical field data, including leaf area index (LAI), mid-day canopy PAR transmission, soil reflectivity, and soil moisture. The canopy optical measurements enabled retrievals of the photochemical reflectance index (PRI) and solar induced fluorescence (SIF) centered at O2-A and -B bands. These two spectrally based bio-indicators have been widely utilized in studies to assess whether vegetation is performing near-optimally or exhibiting symptoms of environmental stress (e.g., drought or nutrient deficiency, non-optimal temperatures, etc.). Both SIF and PRI expressed diurnal dynamics and seasonal changes that followed environmental conditions and physiological status of the cornfield. We further investigated the correlation between these two retrievals and the flux tower based carbon assimilation observations (i.e. gross ecosystem production, GEP). We were able to successfully model the variation of GEP (r2=0.81; RMSE=0.18 mg CO2/m2/s) by utilizing both SIF and PRI. Several cross-validation algorithms were applied to the model to demonstrate the robustness and consistency of the model. Our results suggest great

  9. Platelet inhibition with prasugrel in patients with acute myocardial infarction undergoing therapeutic hypothermia after cardiopulmonary resuscitation.

    PubMed

    Flierl, Ulrike; Röntgen, Philipp; Zauner, Florian; Tongers, Jörn; Berliner, Dominik; Bauersachs, Johann; Schäfer, Andreas

    2016-05-01

    Acute myocardial infarction (AMI) is the leading cause for out-of-hospital cardiac arrest. Therapeutic hypothermia improves neurological outcome in combination with early revascularisation, but seems to affect clopidogrel responsiveness. The more potent thienopyridine prasugrel has not yet been sufficiently evaluated during therapeutic hypothermia. We investigated 23 consecutive AMI patients (61 ± 11 years) following out-of-hospital resuscitation undergoing revascularisation and therapeutic hypothermia. Prasugrel efficacy was assessed by the platelet-reactivity-index (PRI) before and 2, 4, 6, 12, 24, 48, and 72 hours (h) following a loading dose of 60 mg via a gastric tube. Mean PRI (± SD) was 70 ± 12 % prior to loading and 60 ± 16 % (2 h, ns), 52 ± 21 % (4 h, p< 0.01), 42 ± 26 % (6 h, p< 0.01), 37 ± 21 % (12 h, p< 0.01), 27 ± 23 % (24 h, p< 0.01), 18 ± 14 % (48 h, p< 0.01), and 13 ± 10 % (72 h, p< 0.01) after loading. Sufficient platelet inhibition occurred later compared to stable AMI patients (6 h vs 2 h); however, high on-treatment platelet reactivity significantly decreased over time and was non-existent after 72 h (PRI> 50 %: 2 h: 72 %, 4 h: 52 %, 6 h: 43 %, 12 h: 29 %, 24 h: 17 %, 48 h: 5 %, 72 h: 0 %). There was no relation between 30-day mortality rate (26 %) and PRI values. Prasugrel significantly reduced platelet reactivity even during vasopressor use, analgosedation and therapeutic hypothermia. Despite a significant delay compared to stable AMI patients, sufficient platelet inhibition was reached in 83 % of patients within 24 h. Therefore, prasugrel administration via gastric tube might be a useful therapeutic strategy in these patients at high risk, providing potent and effective P2Y12 inhibition. PMID:26790884

  10. Ensenanza de la Astronomia a Traves de Metodos no Tradicionales

    NASA Astrophysics Data System (ADS)

    Tignanelli, H. L.

    1990-11-01

    REUMEN: Se presentan los aspects pri nc ipales de a ense? anza de la astronor:. a para -; s. En esta cc .unicaci #n, 5 ha especial mfasis em Ia descripci':"n de las caracteristicas y las posibi lidades peda gicas de los no tradicionales de aprendiZaje. E' : In the following the principal aspects of teaching of astrono ..y for children) are oresented. In this paper, special emphasis has been given to desc rib the characteristics and pedagogical possibilities of the non traditional methods of learning. : TEACHING

  11. Regeneration of horseradish hairy roots incited by Agrobacterium rhizogenes infection.

    PubMed

    Noda, T; Tanaka, N; Mano, Y; Nabeshima, S; Ohkawa, H; Matsui, C

    1987-07-01

    Surface-sterilized leaf disks of horse-radish (Armoracia lapathifolia) were immersed in a suspension of Agrobacterium rhizogenes harboring the root-inducing plasmid (pRi) and cultured on a solid medium. Within about 10 days after inoculation, adventitious roots (hairy roots) emerged from the leaf disks. No roots emerged from the uninoculated leaf disks. The excised hairy roots grew vigorously in the dark and exhibited extensive lateral branches in the absence of phytohormones. When the hairy roots were moved into the light, numerous adventitious buds thrust out of the roots within about 10 days, and they developed into complete plants (R0 generation). R0 plants revealed leaf wrinkle. Root masses of cultured R0 plants were of two types. One had fibrous roots only and the other had both fibrous and tuberous roots Leaf disks of the R0 plants proliferated adventitious roots (R1 generation) on a solid medium after 1-2 weeks of culture. Phenotypical characters of the R1 roots were the same as those observed with the initial hairy roots. The T-DNA sequences of pRi were detected within DNA isolated from the hairy roots and their regenerants. PMID:24248760

  12. Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity.

    PubMed

    Kourtidis, Antonis; Ngok, Siu P; Pulimeno, Pamela; Feathers, Ryan W; Carpio, Lomeli R; Baker, Tiffany R; Carr, Jennifer M; Yan, Irene K; Borges, Sahra; Perez, Edith A; Storz, Peter; Copland, John A; Patel, Tushar; Thompson, E Aubrey; Citi, Sandra; Anastasiadis, Panos Z

    2015-09-01

    E-cadherin and p120 catenin (p120) are essential for epithelial homeostasis, but can also exert pro-tumorigenic activities. Here, we resolve this apparent paradox by identifying two spatially and functionally distinct junctional complexes in non-transformed polarized epithelial cells: one growth suppressing at the apical zonula adherens (ZA), defined by the p120 partner PLEKHA7 and a non-nuclear subset of the core microprocessor components DROSHA and DGCR8, and one growth promoting at basolateral areas of cell-cell contact containing tyrosine-phosphorylated p120 and active Src. Recruitment of DROSHA and DGCR8 to the ZA is PLEKHA7 dependent. The PLEKHA7-microprocessor complex co-precipitates with primary microRNAs (pri-miRNAs) and possesses pri-miRNA processing activity. PLEKHA7 regulates the levels of select miRNAs, in particular processing of miR-30b, to suppress expression of cell transforming markers promoted by the basolateral complex, including SNAI1, MYC and CCND1. Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor. PMID:26302406

  13. A controlled field trial of the effectiveness of acetone-dried and inactivated and heat-phenol-inactivated typhoid vaccines in Yugoslavia*

    PubMed Central

    1964-01-01

    In 1954-60 a Yugoslav Typhoid Commission showed in the first controlled field trial of typhoid vaccines, carried out in Osijek, Yugoslavia, that heat-phenol-inactivated typhoid vaccine gave a relatively high and long-lasting immunity. However, this liquid vaccine preparation was unstable and laboratory potency tests were inconclusive, and it was therefore decided that stable, dried, heat-killed, phenol-preserved vaccine be tested together with an acetone-inactivated and -dried vaccine in controlled field trials, supported in part by the World Health Organization, in Yugoslavia and British Guiana. This is report on the controlled trials organized in two Yugoslav towns, Bitola and Priština. Three comparable groups were formed by random allocation of vaccines among 45 497 volunteers in the two towns. In each town one group received heat-phenol vaccine, the second group acetone-dried vaccine and the third (control) group tetanus toxoid. Two doses were given four weeks apart in the spring of 1960 and the vaccinated persons were followed up for 2 1/2 years. The effectiveness of the vaccines was measured by comparing typhoid morbidity rates in the three groups. It was found during an outbreak of typhoid fever in Priština two years after primary vaccination that both the acetone-dried and the heat-phenol vaccines were effective, the former being superior. PMID:14196811

  14. Structure of the dimerization domain of DiGeorge critical region 8

    SciTech Connect

    Senturia, R.; Faller, M.; Yin, S.; Loo, J.A.; Cascio, D.; Sawaya, M.R.; Hwang, D.; Clubb, R.T.; Guo, F.

    2010-09-27

    Maturation of microRNAs (miRNAs, {approx}22nt) from long primary transcripts [primary miRNAs (pri-miRNAs)] is regulated during development and is altered in diseases such as cancer. The first processing step is a cleavage mediated by the Microprocessor complex containing the Drosha nuclease and the RNA-binding protein DiGeorge critical region 8 (DGCR8). We previously reported that dimeric DGCR8 binds heme and that the heme-bound DGCR8 is more active than the heme-free form. Here, we identified a conserved dimerization domain in DGCR8. Our crystal structure of this domain (residues 298-352) at 1.7 {angstrom} resolution demonstrates a previously unknown use of a WW motif as a platform for extensive dimerization interactions. The dimerization domain of DGCR8 is embedded in an independently folded heme-binding domain and directly contributes to association with heme. Heme-binding-deficient DGCR8 mutants have reduced pri-miRNA processing activity in vitro. Our study provides structural and biochemical bases for understanding how dimerization and heme binding of DGCR8 may contribute to regulation of miRNA biogenesis.

  15. An Open Source 3-D Printed Modular Micro-Drive System for Acute Neurophysiology

    PubMed Central

    Eskandar, Emad N.

    2014-01-01

    Current, commercial, electrode micro-drives that allow independent positioning of multiple electrodes are expensive. Custom designed solutions developed by individual laboratories require fabrication by experienced machinists working in well equipped machine shops and are therefore difficult to disseminate into widespread use. Here, we present an easy to assemble modular micro-drive system for acute primate neurophysiology (PriED) that utilizes rapid prototyping (3-d printing) and readily available off the shelf-parts. The use of 3-d printed parts drastically reduces the cost of the device, making it available to labs without the resources of sophisticated machine shops. The direct transfer of designs from electronic files to physical parts also gives researchers opportunities to easily modify and implement custom solutions to specific recording needs. We also demonstrate a novel model of data sharing for the scientific community: a publicly available repository of drive designs. Researchers can download the drive part designs from the repository, print, assemble and then use the drives. Importantly, users can upload their modified designs with annotations making them easily available for others to use. PMID:24736691

  16. Effects of auricular transcutaneous electrical nerve stimulation on distal extremity pain: a pilot study.

    PubMed

    Longobardi, A G; Clelland, J A; Knowles, C J; Jackson, J R

    1989-01-01

    The purpose of this pilot study was to determine the effectiveness of auricular acupuncture-like transcutaneous electrical nerve stimulation on pain. Fifteen subjects (6 men, 9 women) experiencing distal extremity pain received either one placebo pill or a 10-minute treatment of acupuncture-like TENS bilaterally to five acupuncture points on the auricle. Pain levels were measured before treatment and at 0, 10, and 30 minutes posttreatment using the visual analogue scale (VAS) and the pain rating index (PRI) of the McGill Pain Questionnaire. The VAS showed no statistically significant differences between Experimental Group (n = 8) and Control Group (n = 7) means at pretreatment or posttreatment; however, both groups showed a reduction in VAS means over time. The Experimental and Control Group means on the PRI were significantly different (p less than .05) at all three posttreatment measurements, but not at pretreatment baseline measurement. These results suggest that auricular acupuncture-like TENS could be an alternative for relief of distal extremity pain. Additional clinical studies are necessary to validate the results of this study. PMID:2783492

  17. Puerto Rico Strong Motion Seismic Network

    NASA Astrophysics Data System (ADS)

    Huerta-Lopez, C. I.; Martínez-Cruzado, J. A.; Martínez-Pagan, J.; Santana-Torres, E. X.; Torres-O, D. M.

    2014-12-01

    The Puerto Rico Strong Motion Seismic Network is currently in charge of the operation of: (i) free-field (ff) strong motion stations, (ii) instrumented structures (STR) (Dams, Bridges, Buildings), and (iii) the data acquisition/monitoring and analysis of earthquakes considered strong from the point of view of their intensity and magnitude. All these instruments are deployed in the Puerto Rico Island (PRI), US-, and British-Virgin Islands (BVI), and Dominican Republic (DR). The Puerto Rico Island and the Caribbean region have high potential to be affected by earthquakes that could be catastrophic for the area. The Puerto Rico Strong Motion Seismic Network (actually Puerto Rico Strong Motion Program, PRSMP) has grown since 1970's from 7 ff strong motion stations and one instrumented building with analog accelerographs to 111 ff strong motion stations and 16 instrumented buildings with digital accelerographs: PRI: 88 ff, 16 STR., DR: 13 ff, BVI: 5 ff, 2 STR collecting data via IP (internet), DU (telephone), and stand alone stations The current stage of the PRSMP seismic network, the analysis of moderate earthquakes that were recorded and/or occurred on the island, results of the intensity distribution of selected earthquakes, as well as results of dynamic parameter identification of some of the instrumented structures are here presented.

  18. Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability.

    PubMed

    Licausi, Francesco; Weits, Daan A; Pant, Bikram Datt; Scheible, Wolf-Rüdiger; Geigenberger, Peter; van Dongen, Joost T

    2011-04-01

    • Reduced oxygen availability is not only associated with flooding, but occurs also during growth and development. It is largely unknown how hypoxia is perceived and what signaling cascade is involved in activating adaptive responses. • We analysed the expression of over 1900 transcription factors (TFs) and 180 microRNA primary transcripts (pri-miRNAs) in Arabidopsis roots exposed to different hypoxic conditions by means of quantitative PCR. We also analysed the promoters of genes induced by hypoxia with respect to over-represented DNA elements that can act as potential TF binding sites and their in vivo interaction was verified. • We identified various subsets of TFs that responded differentially through time and in an oxygen concentration-dependent manner. The regulatory potential of selected TFs and their predicted DNA binding elements was validated. Although the expression of pri-miRNAs was differentially regulated under hypoxia, only one corresponding mature miRNA changed accordingly. Putative target transcripts of the miRNAs were not significantly affected. • Our results show that the regulation of hypoxia-induced genes is controlled via simultaneous interaction of various combinations of TFs. Under anoxic conditions, an additional set of TFs is induced. Regulation of gene expression via miRNAs appears to play a minor role during hypoxia. PMID:20840511

  19. The morphology, proliferation rate, and population doubling time factor of adipose-derived mesenchymal stem cells cultured on to non-aqueous SiO2, TiO2, and hybrid sol-gel-derived oxide coatings.

    PubMed

    Marycz, Krzysztof; Krzak-Roś, Justyna; Donesz-Sikorska, Anna; Śmieszek, Agnieszka

    2014-11-01

    In recent years, much attention has been paid to the development of tissue engineering and regenerative medicine, especially when stem cells of various sources are concerned. In addition to the interest in mesenchymal stem cells isolated from bone marrow, recently more consideration has been given to stem cells isolated from adipose tissue (AdMSCs), due to their less invasive method of collection as well as their ease of isolation and culture. However, the development of regenerative medicine requires both the application of biocompatible material and the stem cells to accelerate the regeneration. In this study, we investigated the morphology, proliferation rate index (PRi), and population doubling time factor of adipose-derived mesenchymal stem cells cultured on non-aqueous sol-gel-derived SiO2, TiO2, and SiO2/TiO2 oxide coatings. The results indicated an increase in PRi of AdMSCs when cultured on to titanium dioxide, suggesting its high attractiveness for AdMSCs. In addition, the proper morphology and the shortest doubling time of AdMSCs were observed when cultured on titanium dioxide coating. PMID:24408867

  20. Field Theory for Multi-Particle System

    NASA Astrophysics Data System (ADS)

    Wang, Shouhong; Ma, Tian

    2016-03-01

    The main objectives of this talk are 1) to introduce some basic postulates for quantum multi-particle systems, and 2) to develop a universal field theory for interacting multi-particle systems coupling both particle fields and interacting fields. By carefully examining the nature of interactions between multi-particles, we conclude that multi-particle systems must obey i) the gauge symmetry, ii) the principle of interaction dynamics (PID), and iii) the principle of representation invariance (PRI). Intuitively, PID takes the variation of the action functional under energy-momentum conservation constraint, offers a different and natural way of introducing Higgs fields, and is also required by the presence of dark matter and dark energy and the quark confinement. PRI requires that the SU(N) gauge theory be independent of representations of SU(N). Based on these principles, a few basic postulates for multi-particle systems are introduced in this talk, leading to a field theory for interacting multi-particle systems. A direct consequence of the field theory is the derivation of general atomic spectrum equations. Supported in Part by the Office of Naval Research, by the US National Science Foundation, and by the Chinese National Science Foundation.

  1. Salt Stress Reveals a New Role for ARGONAUTE1 in miRNA Biogenesis at the Transcriptional and Posttranscriptional Levels.

    PubMed

    Dolata, Jakub; Bajczyk, Mateusz; Bielewicz, Dawid; Niedojadlo, Katarzyna; Niedojadlo, Janusz; Pietrykowska, Halina; Walczak, Weronika; Szweykowska-Kulinska, Zofia; Jarmolowski, Artur

    2016-09-01

    Plants as sessile organisms have developed prompt response mechanisms to react to rapid environmental changes. In addition to the transcriptional regulation of gene expression, microRNAs (miRNAs) are key posttranscriptional regulators of the plant stress response. We show here that the expression levels of many miRNAs were regulated under salt stress conditions. This regulation occurred at the transcriptional and posttranscriptional levels. During salinity stress, the levels of miRNA161 and miRNA173 increased, while the expression of pri-miRNA161 and pri-miRNA173 was down-regulated. Under salt stress conditions, miRNA161 and miRNA173 were stabilized in the cytoplasm, and the expressions of MIR161 and MIR173 were negatively regulated in the nucleus. ARGONAUTE1 (AGO1) participated in both processes. We demonstrated that AGO1 cotranscriptionally controlled the expression of MIR161 and MIR173 in the nucleus. Our results suggests that AGO1 interacts with chromatin at MIR161 and MIR173 loci and causes the disassembly of the transcriptional complex, releasing short and unpolyadenylated transcripts. PMID:27385819

  2. Two-Coordinate Magnesium(I) Dimers Stabilized by Super Bulky Amido Ligands.

    PubMed

    Boutland, Aaron J; Dange, Deepak; Stasch, Andreas; Maron, Laurent; Jones, Cameron

    2016-08-01

    A variety of very bulky amido magnesium iodide complexes, LMgI(solvent)0/1 and [LMg(μ-I)(solvent)0/1 ]2 (L=-N(Ar)(SiR3 ); Ar=C6 H2 {C(H)Ph2 }2 R'-2,6,4; R=Me, Pr(i) , Ph, or OBu(t) ; R'=Pr(i) or Me) have been prepared by three synthetic routes. Structurally characterized examples of these materials include the first unsolvated amido magnesium halide complexes, such as [LMg(μ-I)]2 (R=Me, R'=Pr(i) ). Reductions of several such complexes with KC8 in the absence of coordinating solvents have afforded the first two-coordinate magnesium(I) dimers, LMg-MgL (R=Me, Pr(i) or Ph; R'=Pr(i) , or Me), in low to good yields. Reductions of two of the precursor complexes in the presence of THF have given the related THF adduct complexes, L(THF)Mg-Mg(THF)L (R=Me; R'=Pr(i) ) and LMg-Mg(THF)L (R=Pr(i) ; R'=Me) in trace yields. The X-ray crystal structures of all magnesium(I) complexes were obtained. DFT calculations on the unsolvated examples reveal their Mg-Mg bonds to be covalent and of high s-character, while Ph⋅⋅⋅Mg bonding interactions in the compounds were found to be weak at best. PMID:27303934

  3. Evaluating the prevalence and impact of examiner errors on the Wechsler scales of intelligence: A meta-analysis.

    PubMed

    Styck, Kara M; Walsh, Shana M

    2016-01-01

    The purpose of the present investigation was to conduct a meta-analysis of the literature on examiner errors for the Wechsler scales of intelligence. Results indicate that a mean of 99.7% of protocols contained at least 1 examiner error when studies that included a failure to record examinee responses as an error were combined and a mean of 41.2% of protocols contained at least 1 examiner error when studies that ignored errors of omission were combined. Furthermore, graduate student examiners were significantly more likely to make at least 1 error on Wechsler intelligence test protocols than psychologists. However, psychologists made significantly more errors per protocol than graduate student examiners regardless of the inclusion or exclusion of failure to record examinee responses as errors. On average, 73.1% of Full-Scale IQ (FSIQ) scores changed as a result of examiner errors, whereas 15.8%-77.3% of scores on the Verbal Comprehension Index (VCI), Perceptual Reasoning Index (PRI), Working Memory Index (WMI), and Processing Speed Index changed as a result of examiner errors. In addition, results suggest that examiners tend to overestimate FSIQ scores and underestimate VCI scores. However, no strong pattern emerged for the PRI and WMI. It can be concluded that examiner errors occur frequently and impact index and FSIQ scores. Consequently, current estimates for the standard error of measurement of popular IQ tests may not adequately capture the variance due to the examiner. PMID:26011479

  4. An open source 3-d printed modular micro-drive system for acute neurophysiology.

    PubMed

    Patel, Shaun R; Ghose, Kaushik; Eskandar, Emad N

    2014-01-01

    Current, commercial, electrode micro-drives that allow independent positioning of multiple electrodes are expensive. Custom designed solutions developed by individual laboratories require fabrication by experienced machinists working in well equipped machine shops and are therefore difficult to disseminate into widespread use. Here, we present an easy to assemble modular micro-drive system for acute primate neurophysiology (PriED) that utilizes rapid prototyping (3-d printing) and readily available off the shelf-parts. The use of 3-d printed parts drastically reduces the cost of the device, making it available to labs without the resources of sophisticated machine shops. The direct transfer of designs from electronic files to physical parts also gives researchers opportunities to easily modify and implement custom solutions to specific recording needs. We also demonstrate a novel model of data sharing for the scientific community: a publicly available repository of drive designs. Researchers can download the drive part designs from the repository, print, assemble and then use the drives. Importantly, users can upload their modified designs with annotations making them easily available for others to use. PMID:24736691

  5. Model for detection and assessment of abiotic stress caused by uranium mining in European Black Pine landscapes

    NASA Astrophysics Data System (ADS)

    Filchev, Lachezar; Roumenina, Eugenia

    2013-10-01

    The article presents the results obtained from a study for detection and assessment of abiotic stress through pollution with heavy metals, metalloids, and natural radionuclides in European Black Pine (Pinus nigra L.) forests caused by uranium mining using ground-based biogeochemical, biophysical, and field spectrometry data. The forests are located on a territory subject to underground and open uranium mining. An operational model of the study is proposed. The areas subject to technogeochemical load are outlined based on the aggregate pollution index Zc. Laboratory and field spectrometry data were used to detect the signals of abiotic stress at pixel level. The methods used for determination of stressed and unstressed black pine forests are: four vegetation indices (TCARI, MCARI, MTVI 2, and PRI 1) for stress detection, and the position, depth, asymmetry, and shift of the red-edge. Based on the "blue shift" and the depth and position of the red-edge, registered by the laboratory analysis and field spectral reflectance, it is established that coniferous forests subject to abiotic stress show an increase in total chlorophyll content and carotene. It has been found that the vegetation indices MTVI 2 and PRI 1, as well as the combination of vegetation indices and pigments may be used as a direct indicator of abiotic stress in coniferous forests caused by uranium mining.

  6. Enhanced electrical transport by texture modulation and co-doping for Ca3Co4O9+δ materials

    NASA Astrophysics Data System (ADS)

    Liu, Z. Y.; Zhang, F. P.; Zhang, J. X.; Zhang, X.; Lu, Q. M.; Yang, X. Y.

    The powders as well as the texture modulated Ca2.8BaxPryCo4O9+δ (x, y = 0, 0.05, 0.1, 0.15 and 0.2) bulk materials are prepared via solid state reaction, sol-gel and spark plasma sintering method. The powder and bulk materials are analyzed with regard to their phase composition and microscopic character by X-ray diffraction (XRD) and scanning electron microscope (SEM). The thermoelectric transport properties of the bulk materials are measured and investigated. The results show that the plate-like powders with uniform particle size tend to align regularly rather than the powders with anomaly shape and particle size distribution by spark plasma sintering method. The bulk materials co-doped by elements with lower electronegativity tend to form better texture rather than that of the bulk materials co-doped by elements with higher electronegativity via spark plasma sintering method. The resistivities and Seebeck coefficients are in negative accordance to the bulk material texture as a whole, and the carrier transport mechanism is not influenced. The electrical performance is tuned with optimized power factor 462 μW m-1 K-2 at 973 K for Ca2.8BaxPryCo4O9+δ (x = y = 0.1) bulk materials.

  7. Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley

    PubMed Central

    Kruszka, Katarzyna; Pacak, Andrzej; Swida-Barteczka, Aleksandra; Nuc, Przemyslaw; Alaba, Sylwia; Wroblewska, Zuzanna; Karlowski, Wojciech; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia

    2014-01-01

    Heat stress is one of the major abiotic factors that can induce severe plant damage, leading to a decrease in crop plant productivity. Despite barley being a cereal of great economic importance, few data are available concerning its thermotolerance mechanisms. In this work microRNAs (miRNAs) involved in heat stress response in barley were investigated. The level of selected barley mature miRNAs was examined by hybridization. Quantitative real-time PCR (RT-qPCR) was used to monitor the changes in the expression profiles of primary miRNA (pri-miRNA) precursors, as well as novel and conserved target genes during heat stress. The miRNA-mediated cleavage sites in the target transcripts were confirmed by degradome analysis and the 5’ RACE (rapid amplification of cDNA ends) approach. Four barley miRNAs (miR160a, 166a, 167h, and 5175a) were found which are heat stress up-regulated at the level of both mature miRNAs and precursor pri-miRNAs. Moreover, the splicing of introns hosting miR160a and miR5175a is also heat induced. The results demonstrate transcriptional and post-transcriptional regulation of heat-responsive miRNAs in barley. The observed induction of miRNA expression is correlated with the down-regulation of the expression level of their experimentally identified new and conservative target genes. PMID:25183744

  8. N-Phosphino-amidines and -guanidines: synthesis, structure and P,N-chelate chemistry.

    PubMed

    Baiget, Lise; Batsanov, Andrei S; Dyer, Philip W; Fox, Mark A; Hanton, Martin J; Howard, Judith A K; Lane, Philip K; Solomon, Sophia A

    2008-02-28

    The syntheses of the cyclic N-phosphino-amidines and -guanidines Ph2PN(Pri)C(NPri2)N(Pri) ( 1) and Ph2PN(c-Hex)C(R)N(c-Hex) [R = piperazino ( 2), morpholino ( 3), Me ( 4), and Ph ( 5)] are reported. DFT studies have identified the preferred structures for compounds 1-5 with the E-configuration being the most stable form for the N-phosphino-amidines, while the Z-conformation is preferred for the N-phosphino-guanidines something that highlights the potential of such systems to act as kappa2-P,N-chelates. The differences in donor characteristics of 2-5 have been probed through the study of their corresponding P(V) selenide derivatives ( 6-9) and their complexes with the cis-RhCl(CO) (10-12) and cis-PdCl2 (13-17) fragments. In line with the DFT studies both the amidines and guanidines are found to coordinate as kappa2-P,N-chelates, with the latter being moderately weaker donor ligands. The molecular structures of compounds 3 and 4, together with those of the Rh and Pd complexes 10 and 15, respectively, have been determined in the solid state by X-ray crystallography, the latter confirming bidentate kappa2-P,N-chelation. PMID:18274685

  9. Regulation of Senescence by microRNA Biogenesis Factors

    PubMed Central

    Abdelmohsen, Kotb; Srikantan, Subramanya; Kang, Min-Ju; Gorospe, Myriam

    2012-01-01

    Senescence represents a state of indefinite growth arrest in cells that have reached their replicative life span, have become damaged, or express aberrant levels of cancer-related proteins. While senescence is widely considered to represent tumor-suppressive mechanism, the accumulation of senescent cells in tissues of older organisms is believed to underlie age-associated losses in physiologic function and age-related diseases. With the emergence of microRNAs (miRNAs) as a major class of molecular regulators of senescence, we review the transcriptional and post-transcriptional factors that control senescence-associated microRNA biosynthesis. Focusing on their enhancement or repression of senescence, we describe the transcription factors that govern the synthesis of primary (pri-)miRNAs, the proteins that control the nuclear processing of pri-miRNAs into precursor (pre-)miRNAs, including RNA editing enzymes, RNases, and RNA helicases, and the cytoplasmic proteins that affect the final processing of pre-miRNAs into mature miRNAs. We discuss how miRNA biogenesis proteins enhance or repress senescence, and thus influence the senescent phenotype that affects normal tissue function and pathology. PMID:22306790

  10. Investigation of the influence of mallet and chisel techniques on the lingual fracture line and comparison with the use of splitter and separators during sagittal split osteotomy in cadaveric pig mandibles.

    PubMed

    Verweij, Jop P; Mensink, Gertjan; Houppermans, Pascal N W J; Frank, Michael D; van Merkesteyn, J P Richard

    2015-04-01

    In bilateral sagittal split osteotomy the proximal and distal segments of the mandible are traditionally separated using chisels. Modern modifications include prying and spreading the segments with splitters. This study investigates the lingual fracture patterns and status of the nerve after sagittal split osteotomy (SSO) using the traditional chisel technique and compares these results with earlier studies using the splitter technique. Lingual fractures after SSO in cadaveric pig mandibles were analysed using a lingual split scale and split scoring system. Iatrogenic damage to the inferior alveolar nerve was assessed. Fractures started through the caudal cortex more frequently in the chisel group. This group showed more posterior lingual fractures, although this difference was not statistically significant. Nerve damage was present in three cases in the chisel group, but was not observed in the splitter group. A trend was apparent, that SSO using the chisel technique instead of the splitter technique resulted in more posterior lingual fracture lines, although this difference was not statistically significant. Both techniques resulted in reliable lingual fracture patterns. Splitting without chisels could prevent nerve damage, therefore we propose a spreading and prying technique with splitter and separators. However, caution should be exercised when extrapolating these results to the clinic. PMID:25697050

  11. Mutant p53 induces EZH2 expression and promotes epithelial–mesenchymal transition by disrupting p68-Drosha complex assembly and attenuating miR-26a processing

    PubMed Central

    Wang, Hui-Hui; Zhang, Hui-Lin; Zhang, Jian; Yan, Xiao-Fang; Wang, Xiao-Jun; Che, Qi; Ke, Jie-Qi; Chen, Zheng; Tong, Huan; Zhang, Yong-Li; Wang, Fang-Yuan; Li, Yi-Ran; Wan, Xiao-Ping

    2015-01-01

    The tumor suppressor p53 and the transcriptional repressor Enhancer of Zeste Homolog 2 (EZH2) have both been implicated in the regulation of epithelial-mesenchymal transition (EMT) and tumor metastasis via their impacts on microRNA expression. Here, we report that mutant p53 (mutp53) promotes EMT in endometrial carcinoma (EC) by disrupting p68-Drosha complex assembly. Overexpression of mutp53 has the opposite effect of wild-type p53 (WTp53), repressing miR-26a expression by reducing pri-miR-26a-1 processing in p53-null EC cells. Re-expression of miR-26a in mutp53 EC cells decreases cell invasion and promotes mesenchymal-epithelial transition (MET). Rescuing miR-26a expression also inhibits EZH2, N-cadherin, Vimentin, and Snail expression and induces E-cadherin expression both in vitro and in vivo. Moreover, patients with higher serum miR-26a levels have a better survival rate. These results suggest that p53 gain-of-function mutations accelerate EC tumor progression and metastasis by interfering with Drosha and p68 binding and pri-miR-26a-1 processing, resulting in reduced miR-26a expression and EZH2 overexpression. PMID:26587974

  12. Using Indentation to Characterize Water Transport and Structure in Nafion Thin Films

    NASA Astrophysics Data System (ADS)

    Davis, Eric; Nadermann, Nichole; Page, Kirt; Stafford, Christopher; Chan, Edwin

    Perfluorinated ionomers, specifically Nafion, are the state-of-the-art polymer used in fuel cells. For this application, Nafion is utilized in both a bulk (hundreds of microns) and confined (tens of nanometers) state. For Nafion thin films in a confined state, i.e., Nafion as thin film coatings on catalyst particles, in-plane transport may play a critical role in the movement of water and protons through this catalysis layer. In this study, water transport was measured for a series of Nafion thin film thicknesses using poroelastic relaxation indentation (PRI). Unlike traditional through-thickness diffusion measurement techniques for thin polymer films (e.g., quartz crystal microbalance), PRI can be used to probe the in-plane water transport behavior. Relative to bulk Nafion, reduced in-plane water diffusion was observed in thin film Nafion, and below approximately 1 micron, water diffusivity and Nafion film thickness exhibited a logarithmic relationship. Equilibrium swelling measurements of water saturated Nafion thin films were used in conjunction with pore network theory to develop a picture of how the molecular-scale structure of Nafion changes with confinement to nanoscale film thicknesses. Using Indentation to Characterize Water Transport and Structure in Nafion Thin Films.

  13. [Development of the Coparental Regulation Inventory and cross-sectional analysis of mothers' encouragement and criticism].

    PubMed

    Kato, Michiyo; Kurosawa, Tai; Kamiya, Tetsuji

    2014-02-01

    We developed the Coparental Regulation Inventory to assess the regulatory behavior of the mothers in involving fathers with child rearing. We translated and modified the short form of the Parental Regulation Inventory (PRI) for Japanese couples in different stages of child rearing. An online questionnaire was conducted with mothers (n = 500) and fathers (n = 500) whose youngest child was less than 21-years-old. Exploratory factor analysis identified two factors, which were labeled "encouragement" and "criticism". The resulting Coparental Regulation Inventory (the modified PRI) had high internal consistency and test-retest reliability. The construct validity of the scale was supported by its correlation with parenting alliance, marital satisfaction, and the father's involvement. These findings suggest that the scale is an adequate instrument for identifying the behaviors of mothers related to coparenting. In addition, we examined the frequency of encouragement and criticism used by the mother in relation to the child-rearing stage using cross-sectional analysis. In the mothers' reports, mothers with infants and children encouraged fathers more than mothers with early and late adolescents. Mothers with late adolescents criticized fathers less than mothers with infants. In the fathers' reports, mothers gave more encouragement to fathers who had infants than at any other age, whereas the child's age was not related to mothers' criticism perceived by the fathers. PMID:24669497

  14. Estimation of arsenic in agricultural soils using hyperspectral vegetation indices of rice.

    PubMed

    Shi, Tiezhu; Liu, Huizeng; Chen, Yiyun; Wang, Junjie; Wu, Guofeng

    2016-05-01

    This study systematically analyzed the performance of multivariate hyperspectral vegetation indices of rice (Oryza sativa L.) in estimating the arsenic content in agricultural soils. Field canopy reflectance spectra was obtained in the jointing-booting growth stage of rice. Newly developed and published multivariate vegetation indices were initially calculated to estimate soil arsenic content. The well-performing vegetation indices were then selected using successive projections algorithm (SPA), and the SPA selected vegetation indices were adopted to calibrate a multiple linear regression model for estimating soil arsenic content. Results showed that a three-band vegetation index (R716-R568)/(R552-R568) performed best in the newly developed vegetation indices in estimating soil arsenic content. The photochemical reflectance index (PRI) and red edge position (REP) performed well in the published vegetation indices. Moreover, the linear combination of two vegetation indices ((R716-R568)/(R552-R568) and REP) selected using SPA improved the estimation of soil arsenic content. These results indicated that the newly developed three-band vegetation index (R716-R568)/(R552-R568) might be recommended as an indicator for estimating soil arsenic content in the study area. PRI and REP could be used as universal vegetation indices for monitoring soil arsenic contamination. PMID:26844405

  15. On Estimating Provenances of Lunar Highland Materials

    NASA Technical Reports Server (NTRS)

    Haskin, Larry A.; Jolliff, Brad L.

    1998-01-01

    That even relatively small impacts can spread material across the face of the Moon is evident from the rays of Tycho. Tycho ejecta triggered the landslide that produced the light mantle deposit at Apollo 17 and perhaps excavated the Central Valley craters there. Basin-sized impacts appear to follow the same scaling laws as smaller impacts, as indicated by the satisfaction of a geophysical model. These giant impacts rearranged huge amounts of premare material, complicating the determination of provenance of materials collected from the highlands. We have developed a model to estimate the probability that material at a particular location might derive from a given basin or large crater. This model is based on crater scaling laws, and effects of secondary cratering. Because it accounts for the volume of primary ejecta from the basin-forming transient craters and the excavating and mixing effects of these ejecta with the substrate onto which they fall, it gives much thicker deposits than an early work. Our modeling takes into account the distribution of sizes of primary ejecta fragments (PriFrags) to obtain the probability at a given site for a deposit of a particular thickness and with a fraction of PriFrags.

  16. Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

    PubMed Central

    Barciszewska-Pacak, Maria; Milanowska, Kaja; Knop, Katarzyna; Bielewicz, Dawid; Nuc, Przemyslaw; Plewka, Patrycja; Pacak, Andrzej M.; Vazquez, Franck; Karlowski, Wojciech; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia

    2015-01-01

    Arabidopsis microRNA expression regulation was studied in a wide array of abiotic stresses such as drought, heat, salinity, copper excess/deficiency, cadmium excess, and sulfur deficiency. A home-built RT-qPCR mirEX platform for the amplification of 289 Arabidopsis microRNA transcripts was used to study their response to abiotic stresses. Small RNA sequencing, Northern hybridization, and TaqMan® microRNA assays were performed to study the abundance of mature microRNAs. A broad response on the level of primary miRNAs (pri-miRNAs) was observed. However, stress response at the level of mature microRNAs was rather confined. The data presented show that in most instances, the level of a particular mature miRNA could not be predicted based on the level of its pri-miRNA. This points to an essential role of posttranscriptional regulation of microRNA expression. New Arabidopsis microRNAs responsive to abiotic stresses were discovered. Four microRNAs: miR319a/b, miR319b.2, and miR400 have been found to be responsive to several abiotic stresses and thus can be regarded as general stress-responsive microRNA species. PMID:26089831

  17. The tumor suppressor APC differentially regulates multiple β-catenins through the function of axin and CKIα during C. elegans asymmetric stem cell divisions.

    PubMed

    Baldwin, Austin T; Phillips, Bryan T

    2014-06-15

    The APC tumor suppressor regulates diverse stem cell processes including gene regulation through Wnt-β-catenin signaling and chromosome stability through microtubule interactions, but how the disparate functions of APC are controlled is not well understood. Acting as part of a Wnt-β-catenin pathway that controls asymmetric cell division, Caenorhabditis elegans APC, APR-1, promotes asymmetric nuclear export of the β-catenin WRM-1 by asymmetrically stabilizing microtubules. Wnt function also depends on a second β-catenin, SYS-1, which binds to the C. elegans TCF POP-1 to activate gene expression. Here, we show that APR-1 regulates SYS-1 levels in asymmetric stem cell division, in addition to its known role in lowering nuclear levels of WRM-1. We demonstrate that SYS-1 is also negatively regulated by the C. elegans homolog of casein kinase 1α (CKIα), KIN-19. We show that KIN-19 restricts APR-1 localization, thereby regulating nuclear WRM-1. Finally, the polarity of APR-1 cortical localization is controlled by PRY-1 (C. elegans Axin), such that PRY-1 controls the polarity of both SYS-1 and WRM-1 asymmetries. We propose a model whereby Wnt signaling, through CKIα, regulates the function of two distinct pools of APC - one APC pool negatively regulates SYS-1, whereas the second pool stabilizes microtubules and promotes WRM-1 nuclear export. PMID:24762815

  18. A unique feeding strategy of the extinct marine mammal Kolponomos: convergence on sabretooths and sea otters.

    PubMed

    Tseng, Z Jack; Grohé, Camille; Flynn, John J

    2016-03-16

    Mammalian molluscivores feed mainly by shell-crushing or suction-feeding. The extinct marine arctoid, Kolponomos, has been interpreted as an otter-like shell-crusher based on similar dentitions. However, neither the masticatory biomechanics of the shell-crushing adaptation nor the way Kolponomos may have captured hard-shelled prey have been tested. Based on mandibular symphyseal morphology shared by Kolponomos and sabre-toothed carnivores, we hypothesize a sabretooth-like mechanism for Kolponomos prey-capture, whereby the mandible functioned as an anchor. Torque generated from jaw closure and head flexion was used to dislodge prey by prying, with prey then crushed using cheek teeth. We test this hypothesized feeding sequence using phylogenetically informed biomechanical simulations and shape analyses, and find a strongly supported, shared high mandibular stiffness in simulated prey-capture bites and mandibular shape in Kolponomos and the sabre-toothed cat Smilodon. These two distantly related taxa converged on using mandibles to anchor cranial torqueing forces when prying substrate-bound prey in the former and sabre-driving forces during prey-killing in the latter. Simulated prey-crushing bites indicate that Kolponomos and sea otters exhibit alternative structural stiffness-bite efficiency combinations in mandibular biomechanical adaptation for shell-crushing. This unique feeding system of Kolponomos exemplifies a mosaic of form-function convergence relative to other Carnivora. PMID:26936242

  19. Airborne remote sensing of photosynthetic light use efficiency and carbon uptake along an Arctic transect in Finland

    NASA Astrophysics Data System (ADS)

    Atherton, J.; Hill, T. C.; Prieto-Blanco, A.; Wade, T.; Clement, R.; Moncrieff, J.; Williams, M. D.; Disney, M.; Nichol, C. J.

    2009-12-01

    It is critical to understand the dynamics of ecosystem carbon uptake through seasonal changes and in response to environmental drivers. In this study we utilised aircraft based remote sensing and CO2/H2O flux monitoring systems to quantify changes in photosynthesis along an Arctic transect. The University of Edinburgh's (UK) research aircraft (a Diamond HK 36 TTC-ECO Dimona) was deployed in the Arctic during summer 2008 to carry out a series of transect-flights over a birch-mire mosaic site near Kevo, Finland as part of the Arctic Biosphere Atmosphere Coupling at Multiple Scales (ABACUS) project. The aircraft is equipped with automated dual field-of-view (hyperspectral) radiometers and CO2/H2O flux and meteorological instrumentation. Vegetation indices known to be related to photosynthetic light use efficiency (LUE), including the well established Photochemical Reflectance Index (PRI) and Solar-induced Fluorescence (SiF) as well as the Normalized Difference Vegetation Index (NDVI) were calculated from the spectral data and matched in space to the CO2 flux measurements. We explored spatial relationships between NDVI and CO2 flux, LUE (CO2 flux / Absorbed Photosynthetically Active Radiation) and PRI and finally SiF (calculated using the Fraunhofer infilling method) and relevant environmental drivers. Our results highlight the unique ability of an airborne platform to quantify ecosystem physiology across a landscape and demonstrate how such measurements can bridge the spatial gap between ground and satellite-based observations.

  20. Using molecular tools to decipher the complex world of plant resistance inducers: an apple case study.

    PubMed

    Dugé de Bernonville, Thomas; Marolleau, Brice; Staub, Johan; Gaucher, Matthieu; Brisset, Marie-Noëlle

    2014-11-26

    Exogenous application of plant resistance inducers (PRIs) able to activate plant defenses is an interesting approach for new integrated pest management practices. The full integration of PRIs into agricultural practices requires methods for the fast and objective upstream screening of efficient PRIs and optimization of their application. To select active PRIs, we used a molecular tool as an alternative to methods involving plant protection assays. The expressions of 28 genes involved in complementary plant defense mechanisms were simultaneously determined by quantitative real-time PCR in PRI-treated tissues. Using a set of 10 commercial preparations and considering the pathosystem apple/Erwinia amylovora, this study shows a strong correlation between defense activation and protection efficiency in controlled conditions, thus enabling the easy identification of promising PRIs in fire blight protection. Hence this work clearly highlights the benefits of using a molecular tool to discriminate nonactive PRI preparations and provides useful molecular markers for the optimization of their use in orchard. PMID:25372566

  1. Protecting Data Privacy in Structured P2P Networks

    NASA Astrophysics Data System (ADS)

    Jawad, Mohamed; Serrano-Alvarado, Patricia; Valduriez, Patrick

    P2P systems are increasingly used for efficient, scalable data sharing. Popular applications focus on massive file sharing. However, advanced applications such as online communities (e.g., medical or research communities) need to share private or sensitive data. Currently, in P2P systems, untrusted peers can easily violate data privacy by using data for malicious purposes (e.g., fraudulence, profiling). To prevent such behavior, the well accepted Hippocratic database principle states that data owners should specify the purpose for which their data will be collected. In this paper, we apply such principles as well as reputation techniques to support purpose and trust in structured P2P systems. Hippocratic databases enforce purpose-based privacy while reputation techniques guarantee trust. We propose a P2P data privacy model which combines the Hippocratic principles and the trust notions. We also present the algorithms of PriServ, a DHT-based P2P privacy service which supports this model and prevents data privacy violation. We show, in a performance evaluation, that PriServ introduces a small overhead.

  2. ADAR1 Activation Drives Leukemia Stem Cell Self-Renewal by Impairing Let-7 Biogenesis.

    PubMed

    Zipeto, Maria Anna; Court, Angela C; Sadarangani, Anil; Delos Santos, Nathaniel P; Balaian, Larisa; Chun, Hye-Jung; Pineda, Gabriel; Morris, Sheldon R; Mason, Cayla N; Geron, Ifat; Barrett, Christian; Goff, Daniel J; Wall, Russell; Pellecchia, Maurizio; Minden, Mark; Frazer, Kelly A; Marra, Marco A; Crews, Leslie A; Jiang, Qingfei; Jamieson, Catriona H M

    2016-08-01

    Post-transcriptional adenosine-to-inosine RNA editing mediated by adenosine deaminase acting on RNA1 (ADAR1) promotes cancer progression and therapeutic resistance. However, ADAR1 editase-dependent mechanisms governing leukemia stem cell (LSC) generation have not been elucidated. In blast crisis chronic myeloid leukemia (BC CML), we show that increased JAK2 signaling and BCR-ABL1 amplification activate ADAR1. In a humanized BC CML mouse model, combined JAK2 and BCR-ABL1 inhibition prevents LSC self-renewal commensurate with ADAR1 downregulation. Lentiviral ADAR1 wild-type, but not an editing-defective ADAR1(E912A) mutant, induces self-renewal gene expression and impairs biogenesis of stem cell regulatory let-7 microRNAs. Combined RNA sequencing, qRT-PCR, CLIP-ADAR1, and pri-let-7 mutagenesis data suggest that ADAR1 promotes LSC generation via let-7 pri-microRNA editing and LIN28B upregulation. A small-molecule tool compound antagonizes ADAR1's effect on LSC self-renewal in stromal co-cultures and restores let-7 biogenesis. Thus, ADAR1 activation represents a unique therapeutic vulnerability in LSCs with active JAK2 signaling. PMID:27292188

  3. Isolation of Elusive HAsAsH in a Crystalline Diuranium(IV) Complex

    PubMed Central

    Gardner, Benedict M.; Balázs, Gábor; Wooles, Ashley J.; Tuna, Floriana; McInnes, Eric J. L.; McMaster, Jonathan; Lewis, William; Blake, Alexander J.

    2015-01-01

    Abstract The HAsAsH molecule has hitherto only been proposed tentatively as a short‐lived species generated in electrochemical or microwave‐plasma experiments. After two centuries of inconclusive or disproven claims of HAsAsH formation in the condensed phase, we report the isolation and structural authentication of HAsAsH in the diuranium(IV) complex [{U(TrenTIPS)}2(μ‐η2:η2‐As2H2)] (3, TrenTIPS=N(CH2CH2NSiPri 3)3; Pri=CH(CH3)2). Complex 3 was prepared by deprotonation and oxidative homocoupling of an arsenide precursor. Characterization and computational data are consistent with back‐bonding‐type interactions from uranium to the HAsAsH π*‐orbital. This experimentally confirms the theoretically predicted excellent π‐acceptor character of HAsAsH, and is tantamount to full reduction to the diarsane‐1,2‐diide form. PMID:27478272

  4. Isolation of Elusive HAsAsH in a Crystalline Diuranium(IV) Complex

    PubMed Central

    Gardner, Benedict M; Balázs, Gábor; Scheer, Manfred; Wooles, Ashley J; Tuna, Floriana; McInnes, Eric J L; McMaster, Jonathan; Lewis, William; Blake, Alexander J; Liddle, Stephen T

    2015-01-01

    The HAsAsH molecule has hitherto only been proposed tentatively as a short-lived species generated in electrochemical or microwave-plasma experiments. After two centuries of inconclusive or disproven claims of HAsAsH formation in the condensed phase, we report the isolation and structural authentication of HAsAsH in the diuranium(IV) complex [{U(TrenTIPS)}2(μ-η2:η2-As2H2)] (3, TrenTIPS=N(CH2CH2NSiPri3)3; Pri=CH(CH3)2). Complex 3 was prepared by deprotonation and oxidative homocoupling of an arsenide precursor. Characterization and computational data are consistent with back-bonding-type interactions from uranium to the HAsAsH π*-orbital. This experimentally confirms the theoretically predicted excellent π-acceptor character of HAsAsH, and is tantamount to full reduction to the diarsane-1,2-diide form. PMID:26510123

  5. Unified Field Theory and Force Formulas of Interactions

    NASA Astrophysics Data System (ADS)

    Ma, Tian; Wang, Shouhong

    2013-04-01

    The main objective of this talk is to drive a unified field model coupling four interactions, based on the principle of interaction dynamics (PID) and the principle of representation invariance (PID). Intuitively, PID takes the variation of the action functional under energy-momentum conservation constraint. PRI requires that physical laws be independent of representations of the gauge groups. One important outcome of this unified field model is a natural duality between the interacting fields (g, A, W^a, S^k), corresponding to graviton, photon, intermediate vector bosons W^± and Z and gluons, and the adjoint bosonic fields (φ,, ^aw, ^ks). This duality predicts two Higgs particles of similar mass with one due to weak interaction and the other due to strong interaction. PID and PRI can be applied directly to individual interactions, leading to 1) modified Einstein equations, giving rise to a unified theory for dark matter and dark energy, 2) three levels of strong interaction potentials for quark, nucleon/hadron, and atom respectively, and 3) a weak interaction potential. These potential/force formulas offer a clear mechanism for both quark confinement and asymptotic freedom.

  6. Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

    PubMed Central

    Kourtidis, Antonis; Ngok, Siu P.; Pulimeno, Pamela; Feathers, Ryan W.; Carpio, Lomeli R.; Baker, Tiffany R.; Carr, Jennifer M.; Yan, Irene K.; Borges, Sahra; Perez, Edith A.; Storz, Peter; Copland, John A.; Patel, Tushar; Thompson, E. Aubrey; Citi, Sandra; Anastasiadis, Panos Z.

    2016-01-01

    E-cadherin and p120 catenin (p120) are essential for epithelial homeostasis, but can also exert pro-tumorigenic activities. Here, we resolve this apparent paradox by identifying two spatially and functionally distinct junctional complexes in non-transformed polarized epithelial cells: one growth suppressing at the apical zonula adherens (ZA), defined by the p120 partner PLEKHA7 and a non-nuclear subset of the core microprocessor components DROSHA and DGCR8, and one growth promoting at basolateral areas of cell–cell contact containing tyrosine-phosphorylated p120 and active Src. Recruitment of DROSHA and DGCR8 to the ZA is PLEKHA7 dependent. The PLEKHA7–microprocessor complex co-precipitates with primary microRNAs (pri-miRNAs) and possesses pri-miRNA processing activity. PLEKHA7 regulates the levels of select miRNAs, in particular processing of miR-30b, to suppress expression of cell transforming markers promoted by the basolateral complex, including SNAI1, MYC and CCND1. Our work identifies a mechanism through which adhesion complexes regulate cellular behaviour and reveals their surprising association with the microprocessor. PMID:26302406

  7. Relation of Chlorophyll Fluorescence Sensitive Reflectance Ratios to Carbon Flux Measurements of Montanne Grassland and Norway Spruce Forest Ecosystems in the Temperate Zone

    PubMed Central

    Ač, Alexander; Malenovský, Zbyněk; Urban, Otmar; Hanuš, Jan; Zitová, Martina; Navrátil, Martin; Vráblová, Martina; Olejníčková, Julie; Špunda, Vladimír; Marek, Michal

    2012-01-01

    We explored ability of reflectance vegetation indexes (VIs) related to chlorophyll fluorescence emission (R686/R630, R740/R800) and de-epoxidation state of xanthophyll cycle pigments (PRI, calculated as (R531 − R570)/(R531 − R570)) to track changes in the CO2 assimilation rate and Light Use Efficiency (LUE) in montane grassland and Norway spruce forest ecosystems, both at leaf and also canopy level. VIs were measured at two research plots using a ground-based high spatial/spectral resolution imaging spectroscopy technique. No significant relationship between VIs and leaf light-saturated CO2 assimilation (AMAX) was detected in instantaneous measurements of grassland under steady-state irradiance conditions. Once the temporal dimension and daily irradiance variation were included into the experimental setup, statistically significant changes in VIs related to tested physiological parameters were revealed. ΔPRI and Δ(R686/R630) of grassland plant leaves under dark-to-full sunlight transition in the scale of minutes were significantly related to AMAX (R2 = 0.51). In the daily course, the variation of VIs measured in one-hour intervals correlated well with the variation of Gross Primary Production (GPP), Net Ecosystem Exchange (NEE), and LUE estimated via the eddy-covariance flux tower. Statistical results were weaker in the case of the grassland ecosystem, with the strongest statistical relation of the index R686/R630 with NEE and GPP. PMID:22701368

  8. Absolute calibration of the fast-delivery SAR product processed at Tromso satellite station

    NASA Astrophysics Data System (ADS)

    Weydahl, Dan J.

    1994-12-01

    Tromso Satellite Station (TSS) is the Norwegian national receiving station for ERS-1 SAR data. The TSS Fast Delivery (FD) SAR processor was upgraded during spring 1994 so that the whole processing chain will now be performed in power rather than in voltage. This new FD SAR product from TSS needs absolute calibration, and a calibration constant is therefore estimated. First, a TSS Power-processed ERS-1 SAR image was used. This image covers the ESA transponders in Flevoland. The integration method was used to estimate the backscattered power from the 3 transponders. The Earth ellipsoid, local incidence angle, antenna pattern, range-spread loss, pixel size and RCS were also taken into account in the calculation. The result was a calibration constant of 53.51 dB. An other method is to compare the backscatter from an ESA processed PRI product and a TSS Power-processed FD product acquired at the same place and time. Areas were extracted from two such SAR images, and the pixel values averaged in power. The known calibration constant for the PRI product was used in the comparison of the image products. The calibration constant for the TSS FD product was then found to be 54.20 dB. This is close to the result from using the ESA transponders.

  9. Relating a Spectral Index from MODIS and Tower-based Measurements to Ecosystem Light Use Efficiency for a Fluxnet-Canada Coniferous Forest

    NASA Technical Reports Server (NTRS)

    Middleton, Elizabeth M.; Cheng, Yen-Ben; Hilker, Thomas; Huemmrich, Karl F.; Black, T. Andrew; Krishnan, Praveena; Coops, Nicholas C.

    2008-01-01

    As part of the North American Carbon Program effort to quantify the terrestrial carbon budget of North America, we have been examining the possibility of retrieving ecosystem light use efficiency (LUE, the carbon sequestered per unit photosynthetically active radiation) directly from satellite observations. Our novel approach has been to compare LUE derived from tower fluxes with LUE estimated using spectral indices computed from MODIS satellite observations over forests in the Fluxnet-Canada Research Network, using the MODIS narrow ocean bands acquired over land. We matched carbon flux data collected around the time of the MODIS mid-day overpass for over one hundred relatively clear days in five years (2001-2006) from a mature Douglas fir forest in British Columbia. We also examined hyperspectral reflectance data collected diurnally from the tower in conjunction with the eddy correlation fluxes and meteorological measurements made throughout the 2006 growing season at this site. The tower-based flux data provided an opportunity to examine diurnal and seasonal LUE processes and their relationship to spectral indices at the scale of the forest stand. We evaluated LUE in conjunction with the Photochemical Reflectance Index (PRI), a normalized difference spectral index that uses 531 nm and a reference band to capture responses to high light induced stress afforded by the xanthophyll cycle. Canopy structure information, retrieved from airborne laser scanning radar (LiDAR) observations, was used to partition the forest canopy into sunlit and shaded fractions throughout the day, on numerous days during 2006. At each observation period throughout a day, the PRI was examined for the sunlit, shaded, and intermediate canopy segments defined by their instantaneous position relative to the solar principal plane (SPP). The sunlit sector was associated with the illumination "hotspot" (the reflectance backscatter maximum), the shaded sector with the "cold or dark spot" (the

  10. Microbial Small Talk: Volatiles in Fungal–Bacterial Interactions

    PubMed Central

    Schmidt, Ruth; Etalo, Desalegn W.; de Jager, Victor; Gerards, Saskia; Zweers, Hans; de Boer, Wietse; Garbeva, Paolina

    2016-01-01

    There is increasing evidence that volatile organic compounds (VOCs) play an important role in the interactions between fungi and bacteria, two major groups of soil inhabiting microorganisms. Yet, most of the research has been focused on effects of bacterial volatiles on suppression of plant pathogenic fungi whereas little is known about the responses of bacteria to fungal volatiles. In the current study we performed a metabolomics analysis of volatiles emitted by several fungal and oomycetal soil strains under different nutrient conditions and growth stages. The metabolomics analysis of the tested fungal and oomycetal strains revealed different volatile profiles dependent on the age of the strains and nutrient conditions. Furthermore, we screened the phenotypic responses of soil bacterial strains to volatiles emitted by fungi. Two bacteria, Collimonas pratensis Ter291 and Serratia plymuthica PRI-2C, showed significant changes in their motility, in particular to volatiles emitted by Fusarium culmorum. This fungus produced a unique volatile blend, including several terpenes. Four of these terpenes were selected for further tests to investigate if they influence bacterial motility. Indeed, these terpenes induced or reduced swimming and swarming motility of S. plymuthica PRI-2C and swarming motility of C. pratensis Ter291, partly in a concentration-dependent manner. Overall the results of this work revealed that bacteria are able to sense and respond to fungal volatiles giving further evidence to the suggested importance of volatiles as signaling molecules in fungal–bacterial interactions. PMID:26779150

  11. Analysis of applied forces and electromyography of back and shoulders muscles when performing a simulated hand scaling task.

    PubMed

    Porter, William; Gallagher, Sean; Torma-Krajewski, Janet

    2010-05-01

    Hand scaling is a physically demanding task responsible for numerous overexertion injuries in underground mining. Scaling requires the miner to use a long pry bar to remove loose rock, reducing the likelihood of rock fall injuries. The experiments described in this article simulated "rib" scaling (scaling a mine wall) from an elevated bucket to examine force generation and electromyographic responses using two types of scaling bars (steel and fiberglass-reinforced aluminum) at five target heights ranging from floor level to 176 cm. Ten male and six female subjects were tested in separate experiments. Peak and average force applied at the scaling bar tip and normalized electromyography (EMG) of the left and right pairs of the deltoid and erectores spinae muscles were obtained. Work height significantly affected peak prying force during scaling activities with highest force capacity at the lower levels. Bar type did not affect force generation. However, use of the lighter fiberglass bar required significantly more muscle activity to achieve the same force. Results of these studies suggest that miners scale points on the rock face that are below their knees, and reposition the bucket as often as necessary to do so. PMID:19800050

  12. An Improved Comprehensive Model for the Apparent Viscosity of Blood

    NASA Astrophysics Data System (ADS)

    Jacobitz, Frank; Anderson, Spencer

    2008-11-01

    An improved comprehensive model for the apparent viscosity of blood is developed and used in simulations of the microcirculation in capillary bundles of rat spinotrapezius muscle fascia. In the microcirculation, the apparent viscosity of blood depends on the local vessel diameter, hematocrit, and shear rate. The proposed comprehensive model extends the apparent viscosity model developed by Pries, Secomb, Gaehtgens, and Gross (Circulation Research, 67, 826-834, 1990), which describes the effect of vessel diameter and hematocrit on the apparent viscosity. A shear thinning term is developed using the experimental data of Lipowsky, Usami, and Chien (Microvascular Research, 19, 297-319, 1980). Curve fits of this data can be combined with equations given in the Pries et al. work to create a system of equations that can be used to find the shear thinning factor. The simulations based on the improved apparent viscosity model use realistic vessel topology for the microvasculature, reconstructed from microscope images of tissue samples, and consider passive and active vessel properties. The numerical method is based on a Hagen-Poiseuille balance in the microvessels and a sparse matrix solver is used to obtain the solution. It was found that the inclusion of the shear factor decreases the overall flowrate in the capillary bundle. Many vessel connections in the fascia are characterized by relatively low shear rates and therefore increased apparent viscosity.

  13. A response regulator promotes Francisella tularensis intramacrophage growth by repressing an anti-virulence factor.

    PubMed

    Ramsey, Kathryn M; Dove, Simon L

    2016-08-01

    The orphan response regulator PmrA is essential for the intramacrophage growth and survival of Francisella tularensis. PmrA was thought to promote intramacrophage growth by binding directly to promoters on the Francisella Pathogenicity Island (FPI) and positively regulating the expression of FPI genes, which encode a Type VI secretion system required for intramacrophage growth. Using both ChIP-Seq and RNA-Seq we identify those regions of the F. tularensis chromosome occupied by PmrA and those genes that are regulated by PmrA. We find that PmrA associates with 252 distinct regions of the F. tularensis chromosome, but exerts regulatory effects at only a few of these locations. Rather than by functioning directly as an activator of FPI gene expression we present evidence that PmrA promotes intramacrophage growth by repressing the expression of a single target gene we refer to as priM (PmrA-repressed inhibitor of intramacrophage growth). Our findings thus indicate that the role of PmrA in facilitating intracellular growth is to repress a previously unknown anti-virulence factor. PriM is the first bacterially encoded factor to be described that can interfere with the intramacrophage growth and survival of F. tularensis. PMID:27169554

  14. Expression of miRNA-26a in platelets is associated with clopidogrel resistance following coronary stenting

    PubMed Central

    CHEN, SHUXIA; QI, XIAOYONG; CHEN, HUA; LI, MINGQUAN; GU, JIAN; LIU, CHUNXIA; XUE, HUA; WANG, LILI; GENG, YANPING; QI, PENG; HAN, YUPING

    2016-01-01

    The present study aimed to evaluate the association between platelet microRNA (miRNA)-26a expression and clopidogrel resistance in patients who underwent coronary stenting. Between September 2013 and August 2014, 43 patients with coronary heart disease underwent percutaneous coronary intervention at Heibei General Hospital (Shijiazhuang, China). In the same period, 20 healthy volunteers without any history of cardiovascular disease were enrolled in the present study as the control group. Flow cytometry was used to measure the phosphorylation levels of vasodilator-stimulated phosphoprotein (VASP), and to calculate the platelet reactivity index (PRI). Low response to clopidogrel was defined as PRI ≥50% on day 7 following clopidogrel administration. Western blotting was used to measure protein expression of VASP and reverse transcription-quantitative polymerase chain reaction analysis was performed to determine the expression levels of mRNA and miRNAs. Bioinformatics tools were employed to predict that miR-26a, miR-199 and miR-23a may target VASP mRNA. The results of the present study demonstrated that the activity of platelets in patients with low or high clopidogrel response was increased, as compared with healthy subjects. No differences in platelet VASP protein expression levels were detected between patients with high clopidogrel response and healthy subjects; whereas VASP protein expression was elevated in patients with low clopidogrel response. Furthermore VASP gene transcription was maintained at low levels in healthy subjects and patients with high clopidogrel response, whereas patients with low clopidogrel response exhibited increased VASP mRNA expression levels. Platelet expression of miRNA-26a, but not miRNA-199 or miRNA-23a, was associated with high platelet reactivity. Serum miRNA-26a, miRNA-199 and miRNA-23a were not demonstrated to be involved in clopidogrel resistance. Therefore, the present study demonstrated that platelet miRNA-26a has an

  15. Demonstration of the presence of the "deleted" MIR122 gene in HepG2 cells.

    PubMed

    Hamad, Ibrahim A Y; Fei, Yue; Kalea, Anastasia Z; Yin, Dan; Smith, Andrew J P; Palmen, Jutta; Humphries, Steve E; Talmud, Philippa J; Walker, Ann P

    2015-01-01

    MicroRNA 122 (miR-122) is highly expressed in the liver where it influences diverse biological processes and pathways, including hepatitis C virus replication and metabolism of iron and cholesterol. It is processed from a long non-coding primary transcript (~7.5 kb) and the gene has two evolutionarily-conserved regions containing the pri-mir-122 promoter and pre-mir-122 hairpin region. Several groups reported that the widely-used hepatocytic cell line HepG2 had deficient expression of miR-122, previously ascribed to deletion of the pre-mir-122 stem-loop region. We aimed to characterise this deletion by direct sequencing of 6078 bp containing the pri-mir-122 promoter and pre-mir-122 stem-loop region in HepG2 and Huh-7, a control hepatocytic cell line reported to express miR-122, supported by sequence analysis of cloned genomic DNA. In contrast to previous findings, the entire sequence was present in both cell lines. Ten SNPs were heterozygous in HepG2 indicating that DNA was present in two copies. Three validation isolates of HepG2 were sequenced, showing identical genotype to the original in two, whereas the third was different. Investigation of promoter chromatin status by FAIRE showed that Huh-7 cells had 6.2 ± 0.19- and 2.7 ± 0.01- fold more accessible chromatin at the proximal (HNF4α-binding) and distal DR1 transcription factor sites, compared to HepG2 cells (p=0.03 and 0.001, respectively). This was substantiated by ENCODE genome annotations, which showed a DNAse I hypersensitive site in the pri-mir-122 promoter in Huh-7 that was absent in HepG2 cells. While the origin of the reported deletion is unclear, cell lines should be obtained from a reputable source and used at low passage number to avoid discrepant results. Deficiency of miR-122 expression in HepG2 cells may be related to a relative deficiency of accessible promoter chromatin in HepG2 versus Huh-7 cells. PMID:25811611

  16. Demonstration of the Presence of the “Deleted” MIR122 Gene in HepG2 Cells

    PubMed Central

    Hamad, Ibrahim A. Y.; Fei, Yue; Kalea, Anastasia Z.; Yin, Dan; Smith, Andrew J. P.; Palmen, Jutta; Humphries, Steve E.; Talmud, Philippa J.; Walker, Ann P.

    2015-01-01

    MicroRNA 122 (miR-122) is highly expressed in the liver where it influences diverse biological processes and pathways, including hepatitis C virus replication and metabolism of iron and cholesterol. It is processed from a long non-coding primary transcript (~7.5 kb) and the gene has two evolutionarily-conserved regions containing the pri-mir-122 promoter and pre-mir-122 hairpin region. Several groups reported that the widely-used hepatocytic cell line HepG2 had deficient expression of miR-122, previously ascribed to deletion of the pre-mir-122 stem-loop region. We aimed to characterise this deletion by direct sequencing of 6078 bp containing the pri-mir-122 promoter and pre-mir-122 stem-loop region in HepG2 and Huh-7, a control hepatocytic cell line reported to express miR-122, supported by sequence analysis of cloned genomic DNA. In contrast to previous findings, the entire sequence was present in both cell lines. Ten SNPs were heterozygous in HepG2 indicating that DNA was present in two copies. Three validation isolates of HepG2 were sequenced, showing identical genotype to the original in two, whereas the third was different. Investigation of promoter chromatin status by FAIRE showed that Huh-7 cells had 6.2 ± 0.19- and 2.7 ± 0.01- fold more accessible chromatin at the proximal (HNF4α-binding) and distal DR1 transcription factor sites, compared to HepG2 cells (p=0.03 and 0.001, respectively). This was substantiated by ENCODE genome annotations, which showed a DNAse I hypersensitive site in the pri-mir-122 promoter in Huh-7 that was absent in HepG2 cells. While the origin of the reported deletion is unclear, cell lines should be obtained from a reputable source and used at low passage number to avoid discrepant results. Deficiency of miR-122 expression in HepG2 cells may be related to a relative deficiency of accessible promoter chromatin in HepG2 versus Huh-7 cells. PMID:25811611

  17. Sun-induced chlorophyll fluorescence and photochemical reflectance index improve remote-sensing gross primary production 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.

    2015-11-01

    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 tested whether light-use efficiency (LUE) models driven by remote-sensing quantities (RSMs) 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 a proxy for LUE and NDVI or MTCI as a fraction of absorbed photosynthetically active radiation (fAPAR) - with those of classical MM. Results showed 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 closely related to the mean of plant N content across treatments (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

  18. The magnitude of loss to follow-up of HIV-exposed infants along the prevention of mother-to-child HIV transmission continuum of care: a systematic review and meta-analysis

    PubMed Central

    Sibanda, Euphemia L.; Weller, Ian V.D.; Hakim, James G.; Cowan, Frances M.

    2013-01-01

    Introduction: Although prevention of mother-to-child HIV transmission (PMTCT) programs are widely implemented, many children do not benefit from them because of loss to follow-up (LTFU). We conducted a systematic review to determine the magnitude of infant/baby LTFU along the PMTCT cascade. Methods: Eligible publications reported infant LTFU outcomes from standard care PMTCT programs (not intervention studies) at any stage of the cascade. Literature searches were conducted in Medline, Embase, Web of Knowledge, CINAHL Plus, and Maternity and Infant Care. Extracted data included setting, methods of follow-up, PMTCT regimens, and proportion and timing of LTFU. For programs in sub-Saharan Africa, random-effects meta-analysis was done using Stata v10. Because of heterogeneity, predictive intervals (PrIs; approximate 95% confidence intervals of a future study based on extent of observed heterogeneity) were computed. Results: A total of 826 papers were identified; 25 publications were eligible. Studies were published from 2001 to 2012 and were mostly from sub-Saharan Africa (three were from India, one from UK and one from Ireland). There was extensive heterogeneity in findings. Eight studies reported on LTFU of pregnant HIV-positive women between antenatal care (ANC) registration and delivery, which ranged from 10.9 to 68.1%, pooled proportion 49.08% [95% confidence interval (CI) 39.6–60.9%], and PrI 22.0–100%. Fourteen studies reported LTFU of infants within 3 months of delivery, range 4.8–75%, pooled proportion 33.9% (27.6–41.5), and PrI 15.4–74.2. Children were also lost after HIV testing; this was reported in five studies, pooled estimate 45.5% (35.9–57.6), PrI 18.7–100%. Programs that actively tracked defaulters had better retention outcomes. Conclusion: There is unacceptable infant LTFU from PMTCT programs. Countries should incorporate defaulter-tracking as standard to improve retention. PMID:24056068

  19. Detection and Assessment of Abiotic Stress of Coniferous Landscapes Caused by Uranium Mining (Using Hyperspectral EO-1/Hyperion Data)

    NASA Astrophysics Data System (ADS)

    Filchev, Lachezar

    2013-12-01

    The paper presents the results from a study aiming at detecting and assessing abiotic stress in coniferous landscapes of Black pine monocultures (Pinus nigra L.) by using ground-based geochemical data, models of technogenic pollution, and satellite hyperspectral data from EO-1/Hyperion. Four vegetation indices (VIs), such as, MCARI, TCARI, MTVI 2, and PRI, as well as the shape and area attributes of the red-edge spectral features, have been studied in order to detect changes caused by the geochemical pollution. The analysis was performed on 4 test sites sized each 30m × 30 m, to correspond to EO-1/Hyperion pixel subspace, in homogenous coniferous landscapes in the Teyna River basin - a left tributary to Iskar River. In effect, the red-edge position index for unstressed coniferous landscapes (Black pine) was found to be at about λ=683 nm, whereas the stressed ones' red-edge position is at λ=671 nm. It was found that VIs, such as TCARI/MCARI and Zc has highest correlation (r2 =0.63; F: 5.20 at F: <0.1), followed by MTVI 2 and Zc (r2 =0.42; F: 2.48 at F: <0.21), and PRI and Zc (r2 =0.30; F: 1.34 at F: <0.33). Subsequently, the four test sites chosen were subdivided in two pairs, corresponding to the modeled Zc values after Inverse Multiquadratic Function (IMF) from the set of Radial Basis Function (RBF), into unstressed (test sites No. 2 and No. 5) and stressed coniferous landscapes (test sites No. 10 and No. 11). The hypothesis tested is that the clustering of EO-1/Hyperion VIs corresponds to Zc clustering using hierarchical clustering method (Ward). As a result, the MTVI 2 and TCARI/MCARI values group their first cluster relatively farther than Zc but the PRI does not reflect the Zc clusters. This lead to the conclusion that the satellite hyperspectral narrowband VIs are still not sensitive enough to study the geochemical background and vegetation stress of geochemically stressed coniferous landscapes by uranium mining without a priori ground based data.

  20. Detection and Assessment of Abiotic Stress of Coniferous Landscapes Caused By Uranium Mining (Using Hyperspectral EO-1/Hyperion Data)

    NASA Astrophysics Data System (ADS)

    Filchev, Lachezar

    2013-12-01

    The paper presents the results from a study aiming at detecting and assessing abiotic stress in coniferous landscapes of Black pine monocultures (Pinus nigra L.) by using ground-based geochemical data, models of technogenic pollution, and satellite hyperspectral data from EO-1/Hyperion. Four vegetation indices (VIs), such as, MCARI, TCARI, MTVI 2, and PRI, as well as the shape and area attributes of the red-edge spectral features, have been studied in order to detect changes caused by the geochemical pollution. The analysis was performed on 4 test sites sized each 30m × 30m, to correspond to EO-1/Hyperion pixel subspace, in homogenous coniferous landscapes in the Teyna River basin – a left tributary to Iskar River. In effect, the red-edge position index for unstressed coniferous landscapes (Black pine) was found to be at about λ=683 nm, whereas the stressed ones' red-edge position is at λ=671 nm. It was found that VIs, such as TCARI/MCARI and Zc has highest correlation (r2=0.63; F: 5.20 at F: <0.1), followed by MTVI 2 and Zc (r2=0.42; F: 2.48 at F: <0.21), and PRI and Zc (r2=0.30; F: 1.34 at F: <0.33). Subsequently, the four test sites chosen were subdivided in two pairs, corresponding to the modeled Zc values after Inverse Multiquadratic Function (IMF) from the set of Radial Basis Function (RBF), into unstressed (test sites No. 2 and No. 5) and stressed coniferous landscapes (test sites No. 10 and No. 11). The hypothesis tested is that the clustering of EO-1/Hyperion VIs corresponds to Zc clustering using hierarchical clustering method (Ward). As a result, the MTVI 2 and TCARI/MCARI values group their first cluster relatively farther than Zc but the PRI does not reflect the Zc clusters. This lead to the conclusion that the satellite hyperspectral narrowband VIs are still not sensitive enough to study the geochemical background and vegetation stress of geochemically stressed coniferous landscapes by uranium mining without a priori ground based data.

  1. Control of tyramine and histamine accumulation by lactic acid bacteria using bacteriocin forming lactococci.

    PubMed

    Tabanelli, Giulia; Montanari, Chiara; Bargossi, Eleonora; Lanciotti, Rosalba; Gatto, Veronica; Felis, Giovanna; Torriani, Sandra; Gardini, Fausto

    2014-11-01

    The aim of this study was to evaluate the competitive effects of three bacteriocin producing strains of Lactococcus lactis subsp. lactis against two aminobiogenic lactic acid bacteria, i.e. the tyramine producing strain Enterococcus faecalis EF37 and the histamine producing strain Streptococcus thermophilus PRI60, inoculated at different initial concentrations (from 2 to 6 log cfu/ml). The results showed that the three L. lactis subsp. lactis strains were able to produce bacteriocins: in particular, L. lactis subsp. lactis VR84 and EG46 produced, respectively, nisin Z and lacticin 481, while for the strains CG27 the bacteriocin has not been yet identified, even if its peptidic nature has been demonstrated. The co-culture of E. faecalis EF37 in combination with lactococci significantly reduced the growth potential of this aminobiogenic strain, both in terms of growth rate and maximum cell concentration, depending on the initial inoculum level of E. faecalis. Tyramine accumulation was strongly reduced when E. faecalis EF37 was inoculated at 2 log cfu/ml and, to a lesser extent, at 3 log cfu/ml, as a result of a lower cell load of the aminobiogenic strain. All the lactococci were more efficient in inhibiting streptococci in comparison with E. faecalis EF37; in particular, L. lactis subsp. lactis VR84 induced the death of S. thermophilus PRI60 and allowed the detection of histamine traces only at higher streptococci inoculum levels (5-6 log cfu/ml). The other two lactococcal strains did not show a lethal action against S. thermophilus PRI60, but were able to reduce its growth extent and histamine accumulation, even if L. lactis subsp. lactis EG46 was less effective when the initial streptococci concentration was 5 and 6 log cfu/ml. This preliminary study has clarified some aspects regarding the ratio between bacteriocinogenic strains and aminobiogenic strains with respect to the possibility to accumulate BA and has also showed that different bacteriocins can have

  2. Identification of Novel, Highly Expressed Retroviral MicroRNAs in Cells Infected by Bovine Foamy Virus

    PubMed Central

    Whisnant, Adam W.; Kehl, Timo; Bao, Qiuying; Materniak, Magdalena; Kuzmak, Jacek; Löchelt, Martin

    2014-01-01

    ABSTRACT While numerous viral microRNAs (miRNAs) expressed by DNA viruses, especially herpesvirus family members, have been reported, there have been very few reports of miRNAs derived from RNA viruses. Here we describe three miRNAs expressed by bovine foamy virus (BFV), a member of the spumavirus subfamily of retroviruses, in both BFV-infected cultured cells and BFV-infected cattle. All three viral miRNAs are initially expressed in the form of an ∼122-nucleotide (nt) pri-miRNA, encoded within the BFV long terminal repeat U3 region, that is subsequently cleaved to generate two pre-miRNAs that are then processed to yield three distinct, biologically active miRNAs. The BFV pri-miRNA is transcribed by RNA polymerase III, and the three resultant mature miRNAs were found to contribute a remarkable ∼70% of all miRNAs expressed in BFV-infected cells. These data document the second example of a retrovirus that is able to express viral miRNAs by using embedded proviral RNA polymerase III promoters. IMPORTANCE Foamy viruses are a ubiquitous family of nonpathogenic retroviruses that have potential as gene therapy vectors in humans. Here we demonstrate that bovine foamy virus (BFV) expresses high levels of three viral microRNAs (miRNAs) in BFV-infected cells in culture and also in infected cattle. The BFV miRNAs are unusual in that they are initially transcribed by RNA polymerase III as a single, ∼122-nt pri-miRNA that is subsequently processed to release three fully functional miRNAs. The observation that BFV, a foamy virus, is able to express viral miRNAs in infected cells adds to emerging evidence that miRNA expression is a common, albeit clearly not universal, property of retroviruses and suggests that these miRNAs may exert a significant effect on viral replication in vivo. PMID:24522910

  3. Comparison of radioiodinated TOC, TOCA and Mtr-TOCA: the effect of carbohydration on the pharmacokinetics.

    PubMed

    Wester, Hans-Jürgen; Schottelius, Margret; Scheidhauer, Klemens; Reubi, Jean-Claude; Wolf, Ingo; Schwaiger, Markus

    2002-01-01

    Although somatostatin-based peptide receptor imaging (sst-PRI) and peptide receptor radiotherapy (sst-PRRT) of human endocrine tumours and their metastases has become a valuable method, the experience with radiohalogenated sst-directed peptides has so far been disappointing. To extend the broad spectrum of radiohalogens with suitable radionuclide properties for sst-PRI and PRRT, new strategies in ligand development are required. The major drawbacks to be overcome include fast hepatic uptake, high abdominal background activity and low tumour uptake. Recently we introduced radiolabelled glycated octreotides as a new series of sst-binding radiotracers with excellent physicochemical characteristics. In this study we compared [(125)I]Tyr(3)-octreotide ([(125)I]TOC, ( 1)), [(125)I]Tyr(3)-octreotate ([(125)I]TOCA, ( 2)) and a carbohydrated octreotide derivative, maltotriose-[(125)I]Tyr(3)-octreotate ([(125)I]Mtr-TOCA, ( 3)) to evaluate the effect of single C-terminal oxidation and simultaneous N-terminal carbohydration. The biodistribution was compared in nude mice bearing AR42J tumour xenografts. Compared with ( 1), activity uptake of ( 2) and ( 3) at 1 h was decreased in intestine [36% ( 2), 72% ( 3)], liver [62% ( 2), 79% ( 3)] and kidney [34% ( 2), 41% ( 3)], respectively. Blood clearance was fast for all compounds investigated. Using ( 1) as reference, tumour uptake of ( 2) and ( 3) was 3.8- and 4.3-fold higher at 1 h p.i. At 1 h the tumour-to-blood ratio of ( 3) was 28.2+/-7.3, and the tumour-to-muscle ratio, 147+/-48. Specificity of tumour uptake was demonstrated in AR42J tumour-bearing mice by pretreatment with 0.8 mg TOC/kg 5 min prior to injection of ( 3). In cells transfected with sst1-sst5, the binding profile of I-Mtr-TOCA revealed a very high affinity and selectivity for sst2. In a first scintigraphic [(123)I]Mtr-TOCA study of a patient with a carcinoid of the small intestine with known peritoneal carcinomatosis and a solitary liver metastasis, all tumour

  4. Response of human macrophages to wound matrices in vitro.

    PubMed

    Witherel, Claire E; Graney, Pamela L; Freytes, Donald O; Weingarten, Michael S; Spiller, Kara L

    2016-05-01

    Chronic wounds remain a major burden to the global healthcare system. Myriad wound matrices are commercially available but their mechanisms of action are poorly understood. Recent studies have shown that macrophages are highly influenced by their microenvironment, but it is not known how different biomaterials affect this interaction. Here, it was hypothesized that human macrophages respond differently to changes in biomaterial properties in vitro with respect to phenotype, including pro-inflammatory M1, anti-inflammatory M2a, known for facilitating extracellular matrix deposition and proliferation, and M2c, which has recently been associated with tissue remodeling. Using multiple donors, it was found that collagen scaffolds cross-linked with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysuccinimide (EDC/NHS) promoted the least inflammatory phenotype in primary human macrophages compared with scaffolds cross-linked with formaldehyde or glutaraldehyde. Importantly, gene expression analysis trends were largely conserved between donors, especially TNFa (M1), CCL22 (M2a), and MRC1 (M2a). Then the response of primary and THP1 monocyte-derived macrophages to four commercially available wound matrices were compared-Integra Dermal Regeneration Template (Integra), PriMatrix Dermal Repair Scaffold (PriMatrix), AlloMend Acellular Dermal Matrix (AlloMend), and Oasis Wound Matrix (Oasis). Gene expression trends were different between primary and THP1 monocyte-derived macrophages for all six genes analyzed in this study. Finally, the behavior of primary macrophages cultured onto the wound matrices over time was analyzed. Integra and Oasis caused down-regulation of M2a markers CCL22 and TIMP3. PriMatrix caused up-regulation of TNFa (M1) and CD163 (M2c) and down-regulation of CCL22 and TIMP3 (both M2a). AlloMend caused up-regulation in CD163 (M2c). Lastly, Oasis promoted the largest increase in the combinatorial M1/M2 score, defined as the sum of M1 genes divided by

  5. Estimation of sunlit/shaded light-use efficiency of cropland using tower-based multi-angle remote sensing data and eddy covariance flux measurements

    NASA Astrophysics Data System (ADS)

    Fu, D.; Chen, B.; Zhang, L.

    2014-12-01

    The light-use efficiency (LUE, ɛ) is one of critical parameters in the terrestrial ecosystem production studies. However, it is still a challenge how to up-scale LUE from canopy to the landscape/regional scales. One potential solution is to use automated multi-angle tower-based remote sensing platforms, which observe canopy reflectance with high spatial, temporal, spectral and angle resolution. Although some published paper on the LUE in boreal and temperate forests had used continuous multi-angle measurements of the surface reflectance, lack of study in literature investigated the vegetation physiological parameters of cropland using the surface reflectance with high spatio-temporal and high spectral data with multiple angles. To improve our understanding of physiological status of cropland, the maize within the footprint of the Daman Superstation flux tower site of Heihe Watershed Allied Telemetry Experiment Research (HiWATER) was employed in this study. Based on the observed reflectance and flux data, a Bidirectional Reflectance Distribution Function (BRDF) of vegetation index (Photochemical Reflectance Index, PRI and Vegetation Index using the Universal Pattern Decomposition method, VIUPD) at continuous time series was established by integrating of a semi-empirical kernel-driven BRDF model (RossThick-LiSparse), a footprint model (the Simple Analytical Footprint model on Eulerian coordinates for scalar Flux, SAFE-f) and a LUE model. Besides, based on the sky-condition (direct/diffused radiation) data, the relationships between the vegetation index (PRI and VIUPD) and sunlit/shaded LUE under corresponding sky conditions were established. Taking maize field as an example, the measurements were obtained during June to August, 2012. The relationships between PRI and ɛ for sunlit and shaded leaves were: PRIsu=0.06339×log(ɛsu) + 0.04882,PRIsh= 0.02675×log(ɛsh) + 0.01619, where, the subscript su, sh represent sunlit and shaded leaves respectively; p< 0.0001, R2

  6. Estimation of sunlit/shaded light-use efficiency of cropland using tower-based multi-angle remote sensing data and eddy covariance flux measurements

    NASA Astrophysics Data System (ADS)

    Fu, Dongjie; Chen, Baozhang; Zhang, Lifu

    2015-04-01

    The light-use efficiency (LUE) is one of critical parameters in the terrestrial ecosystem production studies. However, it is still a challenge how to up-scale LUE from canopy to the landscape/regional scales. One potential solution is to use automated multi-angle tower-based remote sensing platforms, which observe canopy reflectance with high spatial, temporal, spectral and angle resolution. Although some published paper on the LUE in boreal and temperate forests had used continuous multi-angle measurements of the surface reflectance, lack of study in literature investigated the vegetation physiological parameters of cropland using the surface reflectance with high spatio-temporal and high spectral data with multiple angles. To improve our understanding of physiological status of cropland, the maize within the footprint of the Daman Superstation flux tower site of Heihe Watershed Allied Telemetry Experiment Research (HiWATER) was employed in this study. Based on the observed reflectance and flux data, a Bidirectional Reflectance Distribution Function (BRDF) of vegetation index (Photochemical Reflectance Index, PRI and Vegetation Index using the Universal Pattern Decomposition method, VIUPD) at continuous time series was established by integrating of a semi-empirical kernel-driven BRDF model (RossThick-LiSparse), a footprint model (the Simple Analytical Footprint model on Eulerian coordinates for scalar Flux, SAFE-f) and a LUE model. Besides, based on the sky-condition (direct/diffused radiation) data, the relationships between the vegetation index (PRI and VIUPD) and sunlit/shaded LUE under corresponding sky conditions were established. Taking maize field as an example, the measurements were obtained during June to August, 2012. The relationships between PRI and LUE for sunlit and shaded leaves were: PRIsu=0.06339×log(LUEsu) + 0.04882, PRIsh= 0.02675×log(LUEsh) + 0.01619, where, the subscript su, sh represent sunlit and shaded leaves respectively; p< 0.0001, R2

  7. Plasma fibrin clot phenotype independently affects intracoronary thrombus ultrastructure in patients with acute myocardial infarction.

    PubMed

    Zalewski, Jaroslaw; Bogaert, Jan; Sadowski, Marcin; Woznicka, Olga; Doulaptsis, Konstantinos; Ntoumpanaki, Maria; Ząbczyk, Michal; Nessler, Jadwiga; Undas, Anetta

    2015-06-01

    Determinants of intracoronary thrombus (ICT) composition in patients with ST-elevation myocardial infarction (STEMI) are largely unknown. We sought to investigate whether plasma fibrin phenotype and platelet reactivity affect ICT ultrastructure. We assessed the content of fibrin, platelets and erythrocytes including polyhedrocytes by scanning electron microscopy on the surface and inside ICT aspirated from 80 STEMI patients within 12 hours since chest pain onset. Plasma fibrin clot permeability (Ks), which indicates the average pore size, lysis time (t50 %), platelet reactivity index (PRI) and ADP-induced platelet aggregation (ADP5, 20µM) were evaluated on admission. All patients received aspirin and 45 (56.3 %) 600 mg of clopidogrel, 80 (60-120) min prior to aspiration. Higher content of fibrin (61.6 vs 34.3 %, P< 0.0001) and platelets (8.2 vs 4.8 %, P=0.018) and lower erythrocyte content (15.8 vs 42.9 %, P< 0.0001) were found on ICT surface compared with its inner part. After adjustment for fibrinogen, in both ICT parts fibrin content was correlated with Ks (r≤-0.55, P< 0.0001) and t50 % (r≥ 0.29, P≤ 0.02) but not with PRI and ADP5,20µM. Polyhedrocytes were observed in 16 (20 %) patients and their large amount expressed as ≥ 50 % fields of view covered by polyhedrocytes was associated with the lower PRI values (40 vs 69 %, P=0.015), but not Ks or t50 %. By multivariate regression, Ks (β=-0.62, P< 0.0001), clopidogrel pretreatment (β=-0.36, P< 0.001), ischemia time (β=0.19, P=0.044) and family history (β=0.18, P=0.049) independently predicted fibrin content in the whole ICT (R²=0.65, P< 0.0001). Formation of denser plasma fibrin clots is independently associated with high fibrin content within the ICT in STEMI. PMID:25739375

  8. The need for an improved risk index for phosphorus losses to water from tile-drained agricultural land

    NASA Astrophysics Data System (ADS)

    Ulén, Barbro; Djodjic, Faruk; Etana, Araso; Johansson, Göran; Lindström, Jan

    2011-03-01

    SummaryA refined version of a conditional phosphorus risk index (PRI) for P losses to waters was developed based on monitoring and analyses of PRI factors from an agricultural catchment in Sweden. The catchment has a hummocky landscape of heavy glacial till overlying moraine and an overall balanced soil P level. Single P source factors and combinations of factors were tested and discussed together with water movement and water management factors important for catchments dominated by drained clay soils. An empirical relationship was established (Pearson correlation coefficient 0.861, p < 0.001) between phosphorus sorption index (PSI-CaCl 2), measured in a weak calcium chloride solution, and iron (Fe-AL) aluminium (Al-AL) and phosphorus (P-AL) in soil extract with acid ammonium lactate. Differing relationships were found for a field that had not received any manure in the last 15 years and a field that had received chicken litter very recently. In addition, a general relationship (Pearson correlation coefficient 0.839, p < 0.001) was found between the ratio of phosphorus extracted from fresh soil in water (Pw) to PSI-CaCl 2 and the degree of phosphorus saturation in lactate extract (DPS-AL). One exception was a single field, representing 7% of agricultural land in the catchment, that had been treated with glyphosate shortly before soil sampling. Saturated hydraulic conductivity (SHC) in heavy clay in contact with the moraine base (at 1 m depth) was on average 0.06 m day -1. In clay not in contact with moraine, SHC was significantly lower (mean 0.007 m day -1). A reduction in the present tile drain spacing (from 14-16 m to 11 m) is theoretically required to maintain satisfactory water discharge and groundwater level. Up to 10% of the arable land was estimated to be a potential source area for P, based on different indices. Parts of a few fields close to farm buildings (1% of total arable land) were identified as essential P source areas, with high DPS-AL values and

  9. Chemical ordering suppresses large-scale electronic phase separation in doped manganites

    NASA Astrophysics Data System (ADS)

    Zhu, Yinyan; Du, Kai; Niu, Jiebin; Lin, Lingfang; Wei, Wengang; Liu, Hao; Lin, Hanxuan; Zhang, Kai; Yang, Tieying; Kou, Yunfang; Shao, Jian; Gao, Xingyu; Xu, Xiaoshan; Wu, Xiaoshan; Dong, Shuai; Yin, Lifeng; Shen, Jian

    2016-04-01

    For strongly correlated oxides, it has been a long-standing issue regarding the role of the chemical ordering of the dopants on the physical properties. Here, using unit cell by unit cell superlattice growth technique, we determine the role of chemical ordering of the Pr dopant in a colossal magnetoresistant (La1-yPry)1-xCaxMnO3 (LPCMO) system, which has been well known for its large length-scale electronic phase separation phenomena. Our experimental results show that the chemical ordering of Pr leads to marked reduction of the length scale of electronic phase separations. Moreover, compared with the conventional Pr-disordered LPCMO system, the Pr-ordered LPCMO system has a metal-insulator transition that is ~100 K higher because the ferromagnetic metallic phase is more dominant at all temperatures below the Curie temperature.

  10. A study of the compatibility of an existing CFD package with a broader class of material constitutions

    NASA Technical Reports Server (NTRS)

    French, K. W., Jr.

    1985-01-01

    The flexibility of the PHOENICS computational fluid dynamics package was assessed along two general avenues; parallel modeling and analog modeling. In parallel modeling the dependent and independent variables retain their identity within some scaling factors, even though the boundary conditions and especially the constitutive relations do not correspond to any realistic fluid dynamic situation. PHOENICS was used to generate a CFD model that should exhibit the physical anomalies of a granular medium and permit reasonable similarity with boundary conditions typical to membrane or porous piston loading. A considerable portion of the study was spent prying into the existing code with a prejudice toward rate type and disarming any inherent fluid behavior. The final stages of the study were directed at the more specific problem of multiaxis loading of cylindrical geometry with a concern for the appearance of bulging, cross slab shear failure modes.

  11. National rural health mission--opportunity for Indian Public Health Association.

    PubMed

    Ray, Sandip Kumar

    2005-01-01

    Indian Public Health Association (IPHA) welcomes the release of National Rural Health Mission (NRHM) documents. It suggests that manpower requirements of the Community Health Centre (CHC) should be rationally determined on the basis of work and patient load of the CHC. Importance should be given on availability of simple & life saving equipment, female staff when male staff is not available. Safe drinking water, an adequate sanitation and excreta disposal facility through Panchayet Raj Institution (PRI) or privatization was proposed. Accredited Social Health Activist (ASHA) has been accepted more streamlining based on the community was suggested. Capacity building or training should be CHC based for grass-root level functionaries with incentive to Medical officer (MO). IPHA proposes to extend support in capacity building, development of manual for ASHA & other categories of health professional as well as Program Implementation Plan (PIP). PMID:16468283

  12. Supreme Court Hears Privacy Case Between NASA and Jet Propulsion Laboratory Scientists

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2010-10-01

    After NASA put into practice the 2004 Homeland Security Presidential Directive-12, known as HSPD-12, Dennis Byrnes talked to then-NASA administrator Michael Griffin. Byrnes recalls that Griffin told him in 2007 that if he didn’t like the agency's implementation of HSPD-12, he should go to court. That's exactly what Byrnes, an employee of the California Institute of Technology (Caltech) working as a senior engineer at NASA's Jet Propulsion Laboratory (JPL) in Pasadena, Calif., did. Concerned about prying and open-ended background investigations of federal contractors through NASA's implementation of HSPD-12, he, along with lead plaintiff Robert Nelson and 26 other Caltech employees working at JPL, sued NASA. Following several lower court decisions, including an injunction issued by a U.S. federal appeals court in response to a plaintiff motion, the case made it all the way to the U.S. Supreme Court, which heard oral arguments on 5 October.

  13. Electrical transport properties of manganite powders under pressure

    NASA Astrophysics Data System (ADS)

    Rodríguez, M. G.; Leyva, A. G.; Acha, C.

    2012-08-01

    We have measured the electrical resistance of micrometric to nanometric powders of the LaPryCaMnO3 (LPCMO with y=0.3) manganite for hydrostatic pressures up to 4 kbar. By applying different final thermal treatments to samples synthesized by a microwave assisted denitration process, we obtained two particular grain characteristic dimensions (40 nm and 1000 nm) which allowed us to analyze the grain size sensitivity of the electrical conduction properties of both the metal electrode interface with manganite (Pt/LPCMO) and the intrinsic intergranular interfaces formed by the LPCMO powder, conglomerate under the only effect of external pressure. We also analyzed the effects of pressure on the phase diagram of these powders. Our results indicate that different magnetic phases coexist at low temperatures and that the electrical transport properties are related to the intrinsic interfaces, as we observe evidences of a granular behavior and an electronic transport dominated by the Space Charge limited Current mechanism.

  14. Linear force device

    NASA Technical Reports Server (NTRS)

    Clancy, John P.

    1988-01-01

    The object of the invention is to provide a mechanical force actuator which is lightweight and manipulatable and utilizes linear motion for push or pull forces while maintaining a constant overall length. The mechanical force producing mechanism comprises a linear actuator mechanism and a linear motion shaft mounted parallel to one another. The linear motion shaft is connected to a stationary or fixed housing and to a movable housing where the movable housing is mechanically actuated through actuator mechanism by either manual means or motor means. The housings are adapted to releasably receive a variety of jaw or pulling elements adapted for clamping or prying action. The stationary housing is adapted to be pivotally mounted to permit an angular position of the housing to allow the tool to adapt to skewed interfaces. The actuator mechanisms is operated by a gear train to obtain linear motion of the actuator mechanism.

  15. Extraction, enumeration and identification methods for monitoring microplastics in the environment

    NASA Astrophysics Data System (ADS)

    Qiu, Qiongxuan; Tan, Zhi; Wang, Jundong; Peng, Jinping; Li, Meimin; Zhan, Zhiwei

    2016-07-01

    There is much research on the occurrence, pollution characteristics and impacts of microplastics in the marine environment but this omits factors which play important roles in the analysis of microplastics. This review summarizes the methods and techniques in the extraction from sediment, seawater and organisms, and assesses their advantages and limitations according to different experimental conditions, such as salt solution and reagents added to remove organic matter. Similarly, this overview includes the enumeration methods of microplastics by many kinds of microscopes (e.g. stereomicroscope, fluorescent microscope, scanning electron microscope). Advantages and challenges of using micro-FTIR, ART-FTIR, FPA-FTIR, Pry-GC/MS, and Raman spectroscopy in the identification methods are also discussed. This review suggests that monitoring microplastics needs standardized protocols for extraction, identification and quantification and that further research on the effects of microplastics to human health is needed.

  16. Non-oxo vanadium(IV) alkoxide chemistry: solid state structures, aggregation equilibria and thermochromic behaviour in solution.

    PubMed

    Westrup, Kátia C M; Gregório, Thaiane; Stinghen, Danilo; Reis, Dayane M; Hitchcock, Peter B; Ribeiro, Ronny R; Barison, Andersson; Back, Davi F; de Sá, Eduardo L; Nunes, Giovana G; Soares, Jaísa F

    2011-04-01

    The reversible thermochromic behaviour of homoleptic [{V(OR)(4)}(n)] complexes in solution [R = Pr(i) (product I), Bu(s) (B(s)), Nep (N) and Cy (C)] is accounted for the existence of an aggregation equilibrium involving dimeric and monomeric species in which vanadium(iv) is respectively five- and four-coordinate. Bulky R groups such as Bu(t) and Pe(t) (tert-pentoxide) prevent aggregation and therefore give rise to exclusively mononuclear compounds (B(t) and P(t), respectively) that are not thermochromic. The complexes and their temperature-dependent interconversion were characterised by single crystal X-ray diffractometry, magnetic susceptibility measurements and electronic, FTIR and EPR spectroscopies in a wide temperature range. Equilibrium constants and enthalpy and entropy changes for the dimerization reactions have been determined and compared with literature data. PMID:21347465

  17. Waveform generation for ultra-wideband radar system

    NASA Astrophysics Data System (ADS)

    Chiang, Hsiao-Feng

    1993-12-01

    In the current literature, ultra-wideband (UWB) waveforms are said to possess several potential advantages such as penetration of foliage, walls and ground, as well as target identification and detection of stealth targets. Due to the potential advantages of UWB waveforms, UWB power sources are currently being developed. This thesis investigates the Fourier synthesis method of waveform generation which is to be used with ultra-wideband radar. The major advantages of this method over traditional methods are that accurate control of pulse shapes and pulse repetition intervals (PRI) can be generated. In this thesis, the Fourier method is extended to generation of binary coded waveforms for UWB systems. The generation of such codes is important as it allows for the use of longer coded pulses. These coded pulses contain more energy and improve signal to noise ratio (SNR) while still retaining the range resolution and other benefits of smaller pulse widths.

  18. Does sun-induced Chlorophyll fluorescence well capture canopy photosynthesis in a rice paddy?

    NASA Astrophysics Data System (ADS)

    Kimm, H.; Ryu, Y.; Kang, M.; Kim, J.

    2015-12-01

    Sun-induced chlorophyll fluorescence (SiF) has emerged as a convincing indicator of carbon assimilation rates under diverse environmental conditions. Here, we present a continuous observation system of SiF at a sporadically irrigated rice paddy site in South Korea. Our site also includes automatic observation systems for eddy covariance, water table depth, and spectral sensors which are composed of LED sensors, and RGB- and NIR cameras. Additionally, we conducted manual observations of photosynthetic parameters (Li-6400), leaf area index (LAI-2200), NDVI and PRI (ASD FieldSpec) once per ten days on average. By analyzing manual- and automatic field observations, we quantify carbon budget of the site. Finally, we investigate how accurately SiF detects canopy photosynthesis, and discuss what factors mainly control canopy photosynthesis.

  19. Studies on the Mechanism of Transduction by Bacteriophage ϕ_entitystart_#947_entit I. Genetic Characterization of the Transducing Segment

    PubMed Central

    Gratia, Jean-Pierre

    1976-01-01

    The bacteriophage Φγ, though related to the lambdoid phage ϕ80, has unusual features in its specialized transduction and is being investigated to determine the mechanism of the transduction process. Genetic analysis of the transducing element gives evidence for a relatively long and uniform linear segment, up to about 1% of the E. coli chromosome, extending in either direction from the prophage attachment site, e.g., on the right side: att80-tonB-trpABCDE-cysB-pryF. The att end includes a variable amount of phage genome, probably very short in most particles. In a small fraction of the transducing particles the phage segment may be more extensive and, conversely, the bacterial segment is shorter, ending around cysB. The transducing segment from modificationless bacteria carries a site susceptible to the K-restriction system which affects the efficiency of transduction. PMID:795713

  20. Cloning and transformation analysis of isoflavone synthase gene into Minshan Trifolium pratense.

    PubMed

    Hu, H H; Jing, C Q; Liu, R; Li, W D; Feng, H G

    2015-01-01

    The aim of this study was to clone the isoflavone synthase (IFS) gene and establish the recombinant Minshan Trifolium pratense. The IFS gene was cloned from the callus of Minshan T. pratense using reverse transcription-polymerase chain reaction. The plant expression vector pRI101-AN-IFS was constructed and introduced into Agrobacterium tumefaciens strain LBA4404, and then screened under cephalosporin. IFS expression was detected by reverse transcription-polymerase chain reaction. The IFS gene was cloned successfully. Sequence analysis indicated that IFS gene had high homology with similar genes from other plants. The IFS-overexpressing callus was obtained by introducing the LBA4404-harboring IFS-pRI101-AN-IFS vector into T. pratense calluses. PMID:26345862

  1. Evolutionary model of stock markets

    NASA Astrophysics Data System (ADS)

    Kaldasch, Joachim

    2014-12-01

    The paper presents an evolutionary economic model for the price evolution of stocks. Treating a stock market as a self-organized system governed by a fast purchase process and slow variations of demand and supply the model suggests that the short term price distribution has the form a logistic (Laplace) distribution. The long term return can be described by Laplace-Gaussian mixture distributions. The long term mean price evolution is governed by a Walrus equation, which can be transformed into a replicator equation. This allows quantifying the evolutionary price competition between stocks. The theory suggests that stock prices scaled by the price over all stocks can be used to investigate long-term trends in a Fisher-Pry plot. The price competition that follows from the model is illustrated by examining the empirical long-term price trends of two stocks.

  2. An examination of the application of space time adaptive processing for the detection of maritime surface targets from high altitude airborne platforms

    NASA Astrophysics Data System (ADS)

    McDonald, Michael; Cerutti-Maori, Delphine

    2013-09-01

    An examination of the application of Space Time Adaptive Processing (STAP) techniques to real, multi-channel, medium grazing angle, radar sea clutter data is undertaken and the detection performance is quantified against simulated moving maritime surface targets. The application of sub-optimal STAP approaches to the maritime radar detection problem is shown to be complicated by non-stationarity of sea clutter and rapid variations of the sea clutter spectrum due to transient wave activity. Observed performance gains from maritime STAP are much more limited than those observed for Ground Moving Target Indication (GMTI) due to the inherent spectral width of sea clutter and the slow Doppler velocities of maritime targets. Three sub-optimal STAP processing architectures are examined and PRI-Staggered Post-Doppler is shown to provide consistently superior detection performance for the data set in question.

  3. Chemical ordering suppresses large-scale electronic phase separation in doped manganites

    PubMed Central

    Zhu, Yinyan; Du, Kai; Niu, Jiebin; Lin, Lingfang; Wei, Wengang; Liu, Hao; Lin, Hanxuan; Zhang, Kai; Yang, Tieying; Kou, Yunfang; Shao, Jian; Gao, Xingyu; Xu, Xiaoshan; Wu, Xiaoshan; Dong, Shuai; Yin, Lifeng; Shen, Jian

    2016-01-01

    For strongly correlated oxides, it has been a long-standing issue regarding the role of the chemical ordering of the dopants on the physical properties. Here, using unit cell by unit cell superlattice growth technique, we determine the role of chemical ordering of the Pr dopant in a colossal magnetoresistant (La1−yPry)1−xCaxMnO3 (LPCMO) system, which has been well known for its large length-scale electronic phase separation phenomena. Our experimental results show that the chemical ordering of Pr leads to marked reduction of the length scale of electronic phase separations. Moreover, compared with the conventional Pr-disordered LPCMO system, the Pr-ordered LPCMO system has a metal–insulator transition that is ∼100 K higher because the ferromagnetic metallic phase is more dominant at all temperatures below the Curie temperature. PMID:27053071

  4. Tracking photosynthetic efficiency with narrow-band spectroradiometry

    NASA Technical Reports Server (NTRS)

    Gamon, John A.; Field, Christopher B.

    1992-01-01

    Narrow-waveband spectroradiometry presents the possibility of detecting subtle signals closely related to the current physiological state of vegetation. One such signal related to the epoxidation state of the xanthophyll cycle pigments, violaxanthin, antheraxanthin, and zeaxanthin is discussed. Recent advances in plant ecophysiology demonstrated a close relationship between these pigments and the regulatory state of photosystem 2 in photosynthesis. Our recent field studies of sunflower (Helianthus annuus) and oak (Quercus agrifolia) demonstrated that a 'xanthophyll signal' can be isolated from the diurnal reflectance spectra of intact canopies. Furthermore, the xanthophyll signal can be used to derive a 'physiological reflectance index' (PRI) that closely correlates with the actual photosynthetic efficiency (defined as the photosynthetic rate divided by the incident PAR) in closed canopies. If these signals were detectable in Airborne Visible/Infrared Imaging Spectrometers (AVIRIS) images, they could lead to improved remote estimates of photosynthetic fluxes.

  5. Suppression of α Smooth Muscle Actin Accumulation by Bovine Fetal Dermal Collagen Matrix in Full Thickness Skin Wounds

    PubMed Central

    Lineaweaver, William; Bush, Katie; James, Kenneth

    2015-01-01

    Abstract The suppression of elements associated with wound contracture and unfavorable scarring is a potentially important strategy in clinical wound management. In this study, the presence of α smooth muscle actin (αSMA), a protein involved in wound contraction, was analyzed in a series of wounds in which bovine fetal collagen (BFC) acellular dermal matrix (PriMatrix) was used in staged split thickness skin graft procedures. The results obtained through histological and quantitative image analyses of incidental biopsies from these wounds demonstrated a suppression of αSMA in the wound regions occupied by assimilated BFC relative to increased levels of αSMA found in other areas of the wound. The αSMA levels found in assimilated BFC were similar to αSMA levels in uninjured human dermis. These findings suggest a mechanism by which application of BFC could decrease contraction of full thickness skin wounds. PMID:25695450

  6. Correction.

    PubMed

    2015-12-01

    In the article by Narayan et al (Narayan O, Davies JE, Hughes AD, Dart AM, Parker KH, Reid C, Cameron JD. Central aortic reservoir-wave analysis improves prediction of cardiovascular events in elderly hypertensives. Hypertension. 2015;65:629–635. doi: 10.1161/HYPERTENSIONAHA.114.04824), which published online ahead of print December 22, 2014, and appeared in the March 2015 issue of the journal, some corrections were needed.On page 632, Figure, panel A, the label PRI has been corrected to read RPI. In panel B, the text by the upward arrow, "10% increase in kd,” has been corrected to read, "10% decrease in kd." The corrected figure is shown below.The authors apologize for these errors. PMID:26558821

  7. Modelling Net Ecosystem Exchange and LUE in Mediterranean Oak Forest by Satellite Remote Sensing

    NASA Astrophysics Data System (ADS)

    Tramontana, Gianluca; Papale, Dario

    2011-01-01

    Net Ecosystem Exchange (NEE) is a key factor defining CO2 fluxes between atmosphere and ecosystems and CO2 flux measurements at individual eddy covariance flux sites provide valuable information on the seasonal dynamics of NEE. In this work, we developed and validated a satellite-based Light Use Efficiency (LUE) model to estimate NEE for a typical oak forest located in Central Italy. Satellite data were acquired by Moderate resolution spectroradiometer (MODIS) sensor installed on board Terra satellite. Oak forest studied is coppice managed; 2 eddy-covariance towers are located inside two forests parcels having different ages. We proposed to estimate LUE like function of mean brightness temperature, Normalized Difference Water Index (NDWI) and Photochemical Reflectance Index (PRI). Empirical multiple regressions models (MR) and Artificial Neural Network (ANN) were parameterized and validated using subset of data acquired by both the stations. Daily, 8-day and monthly temporal resolutions were investigated and accuracy estimation in space and time was performed.

  8. Observations of Saharan dust in the Caribbean and Implications for Regional Climate Variability

    NASA Technical Reports Server (NTRS)

    Remer, L.; Einaudi, Franco

    2001-01-01

    Massive quantities of dust aerosol, originating at source locations in the Saharan desert are frequently transported westward across the Atlantic. Saharan dust has been frequently identified at ground-based stations in South America, on Barbados, in Florida and in Texas. Recently, in July of 2000, the Puerto Rican Dust Experiment (PRiDE), consisting of researchers from the U.S. Navy, NASA, the University of Miami and the University of Puerto Rico joined together to study this important phenomenon. Numerical forecast models tracked each dust event as the dust left the African continent and transversed the Atlantic. Ground-based, ship-based, airborne and satellite sensors were used to characterize the physical and radiative properties of the dust aerosol. The dust plays an important role in terms of radiative forcing of regional climate. Satellite sensors such as NASA's EOS-MODIS aboard the Terra satellite will provide important continuing information on the dust aerosol and its climatic effects.

  9. Influence of bank vegetation on channel morphology in rural and urban watersheds

    NASA Astrophysics Data System (ADS)

    Hession, W. C.; Pizzuto, J. E.; Johnson, T. E.; Horwitz, R. J.

    2003-02-01

    Stream-bank vegetation significantly influences the morphology of streams in the Piedmont region of the United States. We surveyed the morphology of 26 paired stream reaches in southeastern Pennsylvania, northern Maryland, and Delaware. One member of each pair has a forested riparian zone, whereas the other has a riparian zone composed pri marily of grass. The paired reaches are nearly contiguous, so all significant channel-forming variables except riparian vegetation are held constant. The extent of urban development of the watersheds upstream of the paired reaches also varies considerably, allowing us to determine the combined influence of riparian vegetation and urbanization on channel morphology. Statistical analyses indicate that (1) channels with forested riparian zones are wider than channels with nonforested riparian zones, (2) channels in urbanized watersheds are wider than channels in nonurbanized watersheds, and (3) the effect of riparian vegetation is independent of the level of urbanization.

  10. Public/private key certification authority and key distribution. Draft

    SciTech Connect

    Long, J.P.; Christensen, M.J.; Sturtevant, A.P.; Johnston, W.E.

    1995-09-25

    Traditional encryption, which protects messages from prying eyes, has been used for many decades. The present concepts of encryption are built from that heritage. Utilization of modern software-based encryption techniques implies much more than simply converting files to an unreadable form. Ubiquitous use of computers and advances in encryption technology coupled with the use of wide-area networking completely changed the reasons for utilizing encryption technology. The technology demands a new and extensive infrastructure to support these functions. Full understanding of these functions, their utility and value, and the need for an infrastructure, takes extensive exposure to the new paradigm. This paper addresses issues surrounding the establishment and operation of a key management system (i.e., certification authority) that is essential to the successful implementation and wide-spread use of encryption.

  11. Factors that encourage females to pursue physical science careers: Testing five common hypotheses

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

    There are many hypotheses regarding factors that may encourage female students to pursue careers in the physical sciences. Using Propensity Score Matching (PSM) on national data (n=7505) drawn from the Persistence Research in Science and Engineering (PRiSE) project, we test five commonly held beliefs including having a single-sex physics class, having a female physics teacher, having female scientist guest speakers in physics class, discussing the work of women scientists in physics class, and discussing the under-representation of women in physics class. The effect of these experiences is compared for female students who are matched on several factors, including parental education, prior science/math interests, and academic background, thereby controlling for the effect of many confounding variables.

  12. Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome.

    PubMed

    Laubinger, Sascha; Zeller, Georg; Henz, Stefan R; Buechel, Sabine; Sachsenberg, Timo; Wang, Jia-Wei; Rätsch, Gunnar; Weigel, Detlef

    2010-10-12

    In Arabidopsis thaliana, four different dicer-like (DCL) proteins have distinct but partially overlapping functions in the biogenesis of microRNAs (miRNAs) and siRNAs from longer, noncoding precursor RNAs. To analyze the impact of different components of the small RNA biogenesis machinery on the transcriptome, we subjected dcl and other mutants impaired in small RNA biogenesis to whole-genome tiling array analysis. We compared both protein-coding genes and noncoding transcripts, including most pri-miRNAs, in two tissues and several stress conditions. Our analysis revealed a surprising number of common targets in dcl1 and dcl2 dcl3 dcl4 triple mutants. Furthermore, our results suggest that the DCL1 is not only involved in miRNA action but also contributes to silencing of a subset of transposons, apparently through an effect on DNA methylation. PMID:20870966

  13. Theoretical study of stabilities, electronic, and catalytic performance of supported platinum on modified graphene

    NASA Astrophysics Data System (ADS)

    Hongwei, Tian; Wei, Feng; Rui, Wang; Huiling, Liu; Xuri, Huang

    2015-11-01

    The geometry, electronic structure, and catalytic properties for CO oxidation of Pt atom supported on pri-graphene (PG), Haeckelite (H), and Stone-Wales-defect-graphene are investigated by density functional theory (DFT) calculations. In contrast to a Pt atom on PG, defective graphene, especially the Haeckelite, strongly stabilises the Pt atom and makes it more positive and thus the CO poisoning. At the same time the catalytic activities are as high as the pristine one. Langmuir-Hinshelwood mechanisms are favoured as the starting state and are followed by the Eley-Rideal reaction. The results indicate the benefit of Haeckelite as a substrate for the Pt atom and validate the reactivity of catalysts on the atomic scale with low cost and high activity.

  14. Landsat Legacy

    NASA Technical Reports Server (NTRS)

    1991-01-01

    The Landsat resources survey system spawned a number of companies engaged in commercial applications of remote sensing, among them International Imaging Systems (I2S). With initial NASA assistance, I2S has provided remote sensing hardware and software to several foreign countries, developed meteorological analysis systems, medical diagnostic software and scanning equipment for government and commercial use. Latest product is an advanced image-based photogrammetric system employing digital technology - not optical or mechanical systems - to generate terrain elevation data and other processing functions. Called PRI2SM, it compensates automatically for topographic relief displacement, is cheaper, faster, and easier to use and maintain. Company product line includes four major areas: image processing equipment for Earth Resources Management; meteorological analysis systems; satellite ground processing systems; and digital photogrammetric mapping systems.

  15. A comprehensive review of microRNA-related polymorphisms in gastric cancer.

    PubMed

    Han, B W; Li, Z H; Liu, S F; Han, H B; Dong, S J; Zou, H J; Sun, R F; Jia, J

    2016-01-01

    MicroRNAs (miRNAs) are a class of small non-coding RNA molecules of about 22 nucleotides in length. miRNAs are highly conserved in both plants and animals, and function as gene regulators by binding to the 3'-untranslated region of target mRNAs for cleavage and/or translational repression. miRNA biogenesis, stability, and regulation of expression are strongly sequence dependent. Sequence variants, such as single nucleotide polymorphisms (SNPs) in pri-miRNA, pre-miRNA, promoter regions, or miRNA-target sites, can influence miRNA function, thereby contributing to the pathological features of human disease. In this review, we focus on miRNA-related SNPs in gastric cancer and comprehensively analyze some commonly studied SNPs. PMID:27421013

  16. Stress analysis of closure bolts for shipping casks

    SciTech Connect

    Mok, G.C.; Fischer, L.E. ); Hsu, S.T. )

    1993-01-01

    This report specifies the requirements and criteria for stress analysis of closure bolts for shipping casks containing nuclear spent fuels or high level radioactive materials. The specification is based on existing information conceming the structural behavior, analysis, and design of bolted joints. The approach taken was to extend the ASME Boiler and Pressure Vessel Code requirements and criteria for bolting analysis of nuclear piping and pressure vessels to include the appropriate design and load characteristics of the shipping cask. The characteristics considered are large, flat, closure lids with metal-to-metal contact within the bolted joint; significant temperature and impact loads; and possible prying and bending effects. Specific formulas and procedures developed apply to the bolt stress analysis of a circular, flat, bolted closure. The report also includes critical load cases and desirable design practices for the bolted closure, an in-depth review of the structural behavior of bolted joints, and a comprehensive bibliography of current information on bolted joints.

  17. Epigenetic medicine and fetal alcohol spectrum disorders

    PubMed Central

    Resendiz, Marisol; Chen, Yuanyuan; Öztürk, Nail C; Zhou, Feng C

    2013-01-01

    Epigenetic medicine is still in its infancy. To date, only a handful of diseases have documented epigenetic correlates upstream of gene regulation including cancer, developmental syndromes and late-onset diseases. The finding that epigenetic markers are dynamic and heterogeneous at tissue and cellular levels, combined with recent identification of a new form of functionally distinct DNA methylation has opened a wider window for investigators to pry into the epigenetic world. It is anticipated that many diseases will be elucidated through this epigenetic inquiry. In this review, we discuss the normal course of DNA methylation during development, taking alcohol as a demonstrator of the epigenetic impact of environmental factors in disease etiology, particularly the growth retardation and neurodevelopmental deficits of fetal alcohol spectrum disorders. PMID:23414322

  18. Assessing photosynthetic downregulation in sunflower stands with an optically-based model.

    PubMed

    Gamon, J A; Field, C B; Fredeen, A L; Thayer, S

    2001-01-01

    Using a simple light-use efficiency model based on optical measurements, we explored spatial patterns of photosynthetic activity in fertilized and unfertilized sunflower stands. The model had two components: (1) absorbed photosynthetically active radiation (APAR), and (2) radiation-use efficiency. APAR was the product of photosynthetic photon flux density (PPFD) and leaf absorptance, which was derived from leaf reflectance. Radiation-use efficiency was either assumed to be constant or allowed to vary linearly with the photochemical reflectance index (PRI), a measure of xanthophyll cycle pigment activity. When efficiency was assumed to be constant, the model overestimated photosynthetic rates in upper canopy layers exposed to direct PPFD, particularly in the unfertilized canopy due to the greater photosynthetic downregulation associated with higher levels of photoprotective (de-epoxidized) xanthophyll cycle pigments in these conditions. When efficiency was allowed to vary according to the PRI, modeled photosynthetic rates closely matched measured rates for all canopy layers in both treatments. These results illustrate the importance of considering reduced radiation-use efficiency due to photosynthetic downregulation when modeling photosynthesis from reflectance, and illustrate the potential for detecting radiation-use efficiency through leaf optical properties. At least under the conditions of this study, these results also suggest that xanthophyll cycle pigment activity and net carbon uptake are coordinately regulated, allowing assays of Photosystem II activity to reveal changing rates of net assimilation. Because the optical methods in this study are adaptable to multiple spatial scales (leaf to landscape), this approach may provide a scalable model for estimating photosynthetic rates independently from flux measurements. PMID:16228321

  19. The production of fuels and chemicals from food processing wastes using a novel fermenter separator. Annual progress report, January 1991--December 1991

    SciTech Connect

    Dale, M.C.; Venkatesh, K.V.; Choi, Hojoon; Moelhman, M.; Saliceti, L.; Okos, M.R.; Wankat, P.C.

    1991-12-01

    During 1991, considerable progress was made on the waste utilization project. Two small Wisconsin companies have expressed an interest in promoting and developing the ICRS technology. Pilot plant sites at (1) Hopkinton, IA, for a sweet whey plant, and Beaver Dam WI, for an acid whey site have been under development siting ICRS operations. The Hopkinton, IA site is owned and operated by Permeate Refining Inc., who have built a batch ethanol plant across the street from Swiss Valley Farms cheddar cheese operations. Permeate from Swiss Valley is piped across to PRI. PRI has signed a contract to site a 300--500,000 gallon/yr to ICRS pilot plant. They feel that the lower labor, lower energy, continuous process offered by the ICRS will substantially improve their profitability. Catalytics, Inc, is involved with converting whey from a Kraft cream cheese operation to ethanol and yeast. A complete project including whey concentration, sterilization, and yeast growth has been designed for this site. Process design improvements with the ICRS focussed on ethanol recovery techniques during this year`s project. A solvent absorption/extractive distillation (SAED) process has been developed which offers the capability of obtaining an anhydrous ethanol product from vapors off 3 to 9% ethanol solutions using very little energy for distillation. Work on products from waste streams was also performed. a. Diacetyl as a high value flavor compound was very successfully produced in a Stirred Tank Reactor w/Separation. b. Yeast production from secondary carbohydrates in the whey, lactic acid, and glycerol was studied. c. Lactic acid production from cellulose and lactose studies continued. d. Production of anti-fungal reagents by immobilized plant cells; Gossypol has antifungal properties and is produced by G. arboretum.

  20. The production of fuels and chemicals from food processing wastes using a novel fermenter separator

    SciTech Connect

    Dale, M.C.; Venkatesh, K.V.; Choi, Hojoon; Moelhman, M.; Saliceti, L.; Okos, M.R.; Wankat, P.C.

    1991-12-01

    During 1991, considerable progress was made on the waste utilization project. Two small Wisconsin companies have expressed an interest in promoting and developing the ICRS technology. Pilot plant sites at (1) Hopkinton, IA, for a sweet whey plant, and Beaver Dam WI, for an acid whey site have been under development siting ICRS operations. The Hopkinton, IA site is owned and operated by Permeate Refining Inc., who have built a batch ethanol plant across the street from Swiss Valley Farms cheddar cheese operations. Permeate from Swiss Valley is piped across to PRI. PRI has signed a contract to site a 300--500,000 gallon/yr to ICRS pilot plant. They feel that the lower labor, lower energy, continuous process offered by the ICRS will substantially improve their profitability. Catalytics, Inc, is involved with converting whey from a Kraft cream cheese operation to ethanol and yeast. A complete project including whey concentration, sterilization, and yeast growth has been designed for this site. Process design improvements with the ICRS focussed on ethanol recovery techniques during this year's project. A solvent absorption/extractive distillation (SAED) process has been developed which offers the capability of obtaining an anhydrous ethanol product from vapors off 3 to 9% ethanol solutions using very little energy for distillation. Work on products from waste streams was also performed. a. Diacetyl as a high value flavor compound was very successfully produced in a Stirred Tank Reactor w/Separation. b. Yeast production from secondary carbohydrates in the whey, lactic acid, and glycerol was studied. c. Lactic acid production from cellulose and lactose studies continued. d. Production of anti-fungal reagents by immobilized plant cells; Gossypol has antifungal properties and is produced by G. arboretum.

  1. Quantitative investigations on the human entorhinal area: left-right asymmetry and age-related changes.

    PubMed

    Heinsen, H; Henn, R; Eisenmenger, W; Götz, M; Bohl, J; Bethke, B; Lockemann, U; Püschel, K

    1994-08-01

    The total nerve cell numbers in the right and in the left human entorhinal areas have been calculated by volume estimations with the Cavalieri principle and by cell density determinations with the optical disector. Thick gallocyanin-stained serial frozen sections through the parahippocampal gyrus of 22 human subjects (10 female, 12 male) ranging from 18 to 86 years were analysed. The laminar composition of gallocyanin (Nissl)-stained sections could easily be compared with Braak's (1972, 1980) pigmentoarchitectonic study, and Braak's nomenclature of the entorhinal laminas was adopted. Cell-sparse laminae dissecantes can more clearly be distinguished in Nissl than in aldehydefuchsin preparations. These cell-poor dissecantes, lamina dissecans externa (dis-ext), lamina dissecans 1 (dis-1) and lamina dissecans 2 (dis-2), were excluded from nerve cell number determinations. An exact delineation of the entorhinal area is indispensable for any kind of quantitative investigation. We have defined the entorhinal area by the presence of pre-alpha cell clusters and the deeper layers of lamina principalis externa (pre-beta and gamma) separated from lamina principalis interna (pri) by lamina dissecans 1 (dis-1). The human entorhinal area is quantitatively characterized by a left-sided (asymmetric) higher pre-alpha cell number and an age-related nerve cell loss in pre as well as pri layers. At variance with other CNS cortical and subcortical structures, the neuronal number of the entorhinal area appears to decrease continuously from the earliest stages analysed, although a secular trend has to be considered. The asymmetry in pre-alpha cell number is discussed in the context of higher human mental capabilities, especially language. PMID:7818090

  2. Plant Light Stress Tolerance across the New Mexico Elevation Gradient: Scaling from Leaf to Tower

    NASA Astrophysics Data System (ADS)

    Krofcheck, D. J.; Hanson, D.; Fox, A. M.; Litvak, M. E.

    2010-12-01

    Excess light is a major abiotic component of plant stress especially when combined with sustained periods of drought. Arid and semi-arid ecosystems are regularly exposed to sustained high light, low water conditions. A network of nine Eddy Covariance towers oriented along an elevation gradient in central New Mexico has been utilized to assess differences in light use efficiency and light stress response across six distinct biomes, all of which are subjected to a semi-arid climate regulated by a seasonal monsoon. Leaf level measurements of effective quantum yield (ΦPSII ) and non-photochemical quenching (NPQ) parameters were taken at five of these biomes pre and post monsoon using branch mounted and hand held pulse amplitude modulated (PAM) fluorometers. Diurnal samples of leaf tissue were snap frozen to be analyzed for xanthophyll de-epoxidation state via high pressure liquid chromatography. We analyzed these leaf level parameters in the context of tower based and satellite derived measurements of NDVI, PRI and eddy covariance measures of ecosystem function including net ecosystem exchange and light use efficiency. This multi-biome, multi-scale approach aims to investigate not only leaf level photochemical response to excess light, but also how these responses are perceived by remote sensing platforms at flux tower and low earth orbit scales. We hypothesize that plant photochemical status with respect to light use efficiency and excess light mitigation strategies fluctuates as a function of elevation and the seasonal monsoon. We expect to see the highest regulatory capacity at low elevation, low precipitation sites. The NDVI and PRI signal from the tower level will track changes in ecosystem function with respect to NEE and be explained by differences in the ability of biome specific plant functional types to deal with excess light. The tower footprint, parameterized by plant functional type constituents, will be scaled to the landscape level by analysis of MODIS

  3. Prediction of Putative Resistance Islands in a Carbapenem-Resistant Acinetobacter baumannii Global Clone 2 Clinical Isolate

    PubMed Central

    Lee, Yangsoon; D'Souza, Roshan; Lee, Kyungwon

    2016-01-01

    Background We investigated the whole genome sequence (WGS) of a carbapenem-resistant Acinetobacter baumannii isolate belonging to the global clone 2 (GC2) and predicted resistance islands using a software tool. Methods A. baumannii strain YU-R612 was isolated from the sputum of a 61-yr-old man with sepsis. The WGS of the YU-R612 strain was obtained by using the PacBio RS II Sequencing System (Pacific Biosciences Inc., USA). Antimicrobial resistance genes and resistance islands were analyzed by using ResFinder and Genomic Island Prediction software (GIPSy), respectively. Results The YU-R612 genome consisted of a circular chromosome (ca. 4,075 kb) and two plasmids (ca. 74 kb and 5 kb). Its sequence type (ST) under the Oxford scheme was ST191, consistent with assignment to GC2. ResFinder analysis showed that YU-R612 possessed the following resistance genes: four β-lactamase genes blaADC-30, blaOXA-66, blaOXA-23, and blaTEM-1; armA, aadA1, and aacA4 as aminoglycoside resistance-encoding genes; aac(6')Ib-cr for fluoroquinolone resistance; msr(E) for macrolide, lincosamide, and streptogramin B resistance; catB8 for phenicol resistance; and sul1 for sulfonamide resistance. By GIPSy analysis, six putative resistant islands (PRIs) were determined on the YU-R612 chromosome. Among them, PRI1 possessed two copies of Tn2009 carrying blaOXA-23, and PRI5 carried two copies of a class I integron carrying sul1 and armA genes. Conclusions By prediction of resistance islands in the carbapenem-resistant A. baumannii YU-R612 GC2 strain isolated in Korea, PRIs were detected on the chromosome that possessed Tn2009 and class I integrons. The prediction of resistance islands using software tools was useful for analysis of the WGS. PMID:27139604

  4. Transcriptional mechanism for the paired miR-433 and miR-127 genes by nuclear receptors SHP and ERRgamma.

    PubMed

    Song, Guisheng; Wang, Li

    2008-10-01

    MicroRNAs (miRNAs, miRs) are genomically encoded small approximately 22 nt RNA molecules that have been shown to mediate translational repression of target mRNAs involved in cellular proliferation, differentiation and death. Despite intensive studies on their physiological and pathological functions, the molecular mechanism of how miRNA gene transcription is regulated remains largely unknown. Microarray profiling revealed 21 miRNAs clustered on chromosome 12, including miR-433 and miR-127, that were co-upregulated in small heterodimer partner (SHP, NR0B2) SHP knockouts (SHP(-/-)) liver. Gene cloning revealed that the 3'-coding region of pri-miR-433 served as the promoter region of pri-miR-127. Estrogen related receptor (ERRgamma, NR3B3) robustly activated miR-433 and miR-127 promoter reporters through ERRE, which was transrepressed by SHP. The strong elevation of miR-433 and miR-127 in Hepa-1 cells correlated with the down-regulation of SHP and up-regulation of ERRgamma. Ectopic expression of ERRgamma induced miR-433 and miR-127 expression, which was repressed by SHP coexpression. In contrast, knockdown ERRgamma decreased miR-433 and miR-127 expression. In addition, the ERRgamma agonist GSK4716 induced miR-433 and miR-127 expression both in vitro and in vivo, respectively. In summary, the coupled miR-433 and miR-127 genes were transcribed from independent promoters regulated by nuclear receptors ERRgamma/SHP in a compact space by using overlapping genomic regions. PMID:18776219

  5. Determination of trace uranium by resonance fluorescence method coupled with photo-catalytic technology and dual cloud point extraction.

    PubMed

    Li, Jiekang; Li, Guirong; Han, Qian

    2016-12-01

    In this paper, two kinds of salophens (Sal) with different solubilities, Sal1 and Sal2, have been respectively synthesized, and they all can combine with uranyl to form stable complexes: [UO2(2+)-Sal1] and [UO2(2+)-Sal2]. Among them, [UO2(2+)-Sal1] was used as ligand to extract uranium in complex samples by dual cloud point extraction (dCPE), and [UO2(2+)-Sal2] was used as catalyst for the determination of uranium by photocatalytic resonance fluorescence (RF) method. The photocatalytic characteristic of [UO2(2+)-Sal2] on the oxidized pyronine Y (PRY) by potassium bromate which leads to the decrease of RF intensity of PRY were studied. The reduced value of RF intensity of reaction system (ΔF) is in proportional to the concentration of uranium (c), and a novel photo-catalytic RF method was developed for the determination of trace uranium (VI) after dCPE. The combination of photo-catalytic RF techniques and dCPE procedure endows the presented methods with enhanced sensitivity and selectivity. Under optimal conditions, the linear calibration curves range for 0.067 to 6.57ngmL(-1), the linear regression equation was ΔF=438.0 c (ngmL(-1))+175.6 with the correlation coefficient r=0.9981. The limit of detection was 0.066ngmL(-1). The proposed method was successfully applied for the separation and determination of uranium in real samples with the recoveries of 95.0-103.5%. The mechanisms of the indicator reaction and dCPE are discussed. PMID:27380304

  6. Self-organization of coupling optical waveguides by the "pulling water" effect of write beam reflections in photo-induced refractive-index increase media

    NASA Astrophysics Data System (ADS)

    Yoshimura, Tetsuzo; Kaburagi, Hiroshi

    2009-02-01

    To reduce efforts for optical assembly, we developed the reflective self-organized lightwave network (R-SOLNET). In R-SOLNET, optical devices with wavelength filters on their core facets are distributed in photo-induced refractive-index increase (PRI) media such as photo-polymers. Write beams from some devices and reflected write beams from the wavelength filters of the other devices overlap. In the overlap regions, the refractive index increases, pulling the write beams to the wavelength filter locations (the "pulling water" effect). By self-focusing, self-aligned optical waveguide networks are formed between the optical devices. Simulations based on the finite difference time domain method revealed that self-aligned optical waveguides of R-SOLNET are formed between cores with 2-μm and 0.5-μm widths including Y-branching waveguides. Experiments demonstrated that R-SOLNET is formed between an optical fiber and a micro-mirror placed with ~800-μm gap. For angular misalignment of 3o between the optical fiber and the micro-mirror, a bow-shaped R-SOLNET was observed. For lateral misalignment of 30 μm, an S-shaped R-SOLNET was observed. These results suggest that by placing reflective elements in PRI media, optical waveguides can be lead to the elements to form R-SOLNET. This enables self-aligned optical couplings for optoelectronic boards, intra-chip optical circuits, VCSELs/PDs, optical switches, and so on.

  7. [Comparative Research on Estimating the Severity of Yellow Rust in Winter Wheat].

    PubMed

    Wang, Jing; Jing, Yuan-shu; Huang, Wen-jiang; Zhang, Jing-cheng; Zhao, Juan; Zhang, Qing; Wang, Li

    2015-06-01

    In order to improve the accuracy of wheat yellow rust disease severity using remote sensing and to find the optimum inversion model of wheat diseases, the canopy reflectance and disease index (DI) of winter wheat under different severity stripe rust were acquired. The three models of PLS (Partial Least Square), BP neural network using seven hyperspectral vegetation indices which have significant relationship with the occurrence of disease and vegetation index (PRI) were adopted to build a feasible regression model for detecting the disease severity. The results showed that PLS performed much better. The inversion accuracy of PLS method is best than of the VI (PRI, Photochemical Reflectance Index) and BP neural network models. The coefficients of determination (R2) of three methods to estimate disease severity between predicted and measured values are 0.936, 0.918 and 0.767 respectively. Evaluation was made between the estimated DI and the measured DI, indicating that the model based on PLS is suitable for monitoring wheat disease. In addition, to explore the different contributions of diverse types of vegetation index to the models, the paper attempts to use NDVI, GNDVI and MSR which on behalf of vegetation greenness and NDWI and MSI that represents the moisture content to be input variables of PLS model. The results showed that, for the wheat yellow rust disease, changes in chlorophyll content is more sensitive to the disease severity than the changes in water content of the canopy. However, the accuracy of the two models are both lower than predicted when participating in all seven vegetation indices, namely using several species of vegetation indices tends to be more accurate than that using single category. It indicated that it has great potential for evaluating wheat disease severity by using hyper-spectral remote sensing. PMID:26601384

  8. Removal, redistribution, and potential risks of soil Cd, Pb, and Zn after washing with various extractants.

    PubMed

    Chen, Chunle; Chen, Yanhui; Xie, Tuanhui; Wang, Ming Kuang; Wang, Guo

    2015-11-01

    The effectiveness of four different washing extractants--HCl, FeCl3, citric acid, and EDTA--in removing Cd, Pb, and Zn from polluted soil was studied. The removal of these metals, their redistribution between fractions, and the potential risks posed by them, in soils washed with the tested extractants, were examined. Although all the rounds of washing removed Cd, Pb, and Zn from soil, the first round removed more metals than subsequent rounds. Each of the four extractants had different effects on the removal of the metals. At the end of the first round of washing, HCl, EDTA, and FeCl3 were the most effective in removing Zn, Pb, and Cd, respectively. Both the single round and five successive rounds of washing with various extractants resulted in significant increases in Pb in the exchangeable/acid extractable fraction. Washing with HCl, EDTA, and FeCl3 significantly reduced potential risks (calculated as the Potential Risk Index, PRI) posed by Cd in washed soil. The first round of washing, using all extractants, increased the risks posed by Pb and Zn. However, five successive rounds of washing with FeCl3 and EDTA reduced the risk posed by Pb, and washing with citric acid and FeCl3 increased the risks posed by Zn. EDTA and HCl were better for reducing Zn risks, and successive washing with EDTA and FeCl3 were more effective in reducing Pb risks than the other extractants. Finally, five successive rounds of washing, with all the extractants, effectively reduced the potential risks posed by Cd. Among the four reagents, EDTA was advised to be the alternative of the washing reagent by significantly reducing the PRI values of Cd, Pb, and Zn. PMID:26104899

  9. NEUROPSYCHOLOGICAL DEFICITS ASSOCIATED WITH HEAVY PRENATAL ALCOHOL EXPOSURE ARE NOT EXACERBATED BY COMORBID ADHD

    PubMed Central

    Glass, Leila; Ware, Ashley L.; Crocker, Nicole; Deweese, Benjamin N.; Coles, Claire D.; Kable, Julie A.; May, Philip A.; Kalberg, Wendy O.; Sowell, Elizabeth R.; Jones, Kenneth Lyons; Riley, Edward P.; Mattson, Sarah N.

    2013-01-01

    Objective: Neuropsychological functioning of individuals with attention-deficit/hyperactivity disorder (ADHD) or heavy prenatal alcohol exposure has been well documented independently. This study examined the interaction between both factors on cognitive performance in children. Method: As part of a multisite study, 344 children (8-16y, M=12.28, SD=2.52) completed a comprehensive neuropsychological battery. Four subject groups were tested: children with histories of heavy prenatal alcohol exposure (AE) and ADHD (AE+, n=90), alcohol-exposed without ADHD, (AE−, n=38), non-exposed with ADHD (ADHD, n=80), and non-exposed without ADHD (CON, n=136). Results: Separate 2(AE) × 2(ADHD) MANCOVAs revealed significant main and interactive effects of ADHD and AE on overall WISC-IV, D-KEFS, and CANTAB performance. Individual ANOVAs revealed significant interactions on 2 WISC-IV indices [Verbal Comprehension (VCI), Perceptual Reasoning (PRI)], and four D-KEFS and CANTAB subtests [Design Fluency, Verbal Fluency, Trail Making, Spatial Working Memory]. Follow-up analyses demonstrated no difference between AE+ and AE− groups on any measures. The combined AE+/− group demonstrated more severe impairment than the ADHD group on VCI and PRI, but there were no other differences between clinical groups. Conclusions: These results support a combined AE+/− group for neuropsychological research and indicate that, in some cases, the neuropsychological effects seen in ADHD are altered by prenatal alcohol exposure. The effects of alcohol exposure on verbal comprehension and perceptual reasoning were greater than those related to having ADHD without alcohol exposure, although both conditions independently resulted in cognitive impairment compared to controls. Clinically, these findings demonstrate task-dependent patterns of impairment across clinical disorders. PMID:24040921

  10. Mother’s Emotional and Posttraumatic Reactions after a Preterm Birth: The Mother-Infant Interaction Is at Stake 12 Months after Birth

    PubMed Central

    Petit, Anne-Cécile; Eutrope, Julien; Thierry, Aurore; Bednarek, Nathalie; Aupetit, Laurence; Saad, Stéphanie; Vulliez, Lauriane; Sibertin-Blanc, Daniel; Nezelof, Sylvie; Rolland, Anne-Catherine

    2016-01-01

    Objectives Very preterm infants are known to be at risk of developmental disabilities and behavioural disorders. This condition is supposed to alter mother-infant interactions. Here we hypothesize that the parental coping with the very preterm birth may greatly influence mother-infant interactions. Methods 100 dyads were included in 3 university hospitals in France. Preterm babies at higher risk of neurodevelopmental sequelae (PRI>10) were excluded to target the maternal determinants of mother-infant interaction. We report the follow-up of this cohort during 1 year after very preterm birth, with regular assessment of infant somatic state, mother psychological state and the assessment of mother-infant interaction at 12 months by validated scales (mPPQ, HADS, EPDS, PRI, DDST and PIPE). Results We show that the intensity of post-traumatic reaction of the mother 6 months after birth is negatively correlated with the quality of mother-infant interaction at 12 months. Moreover, the anxious and depressive symptoms of the mother 6 and 12 months after birth are also correlated with the quality of mother-infant interaction at 12 months. By contrast, this interaction is not influenced by the initial affective state of the mother in the 2 weeks following birth. In this particular population of infants at low risk of sequelae, we also show that the quality of mother-infant interaction is not correlated with the assessment of the infant in the neonatal period but is correlated with the fine motor skills of the baby 12 months after birth. Conclusions This study suggests that mothers’ psychological condition has to be monitored during the first year of very preterm infants’ follow-up. It also suggests that parental interventions have to be proposed when a post-traumatic, anxious or depressive reaction is suspected. PMID:27022953

  11. Influence of differential expression of acetylcholinesterase in brain and muscle on respiration

    PubMed Central

    Boudinot, Eliane; Bernard, Véronique; Camp, Shelley; Taylor, Palmer; Champagnat, Jean; Krejci, Eric; Foutz, Arthur S.

    2009-01-01

    A mouse strain with a deleted acetylcholinesterase (AChE) gene (AChE knockout) shows a decreased inspiration time and increased tidal volume and ventilation. To investigate the respective roles of AChE in brain and muscle, we recorded respiration by means of whole-body plethysmography in knockout mice with tissue selective deletions in AChE expression. A mouse strain with the anchoring domains of AChE deleted (del E5+6 knockout mice) has very low activity in the brain and neuromuscular junction, but increased monomeric AChE in serum. A mouse strain with deletion of the muscle specific region of AChE (del i1RR knockout mice) exhibits no expression in muscle, but unaltered expression in the central nervous system. Neither strain exhibits the pronounced phenotypic traits observed in the complete AChE knockout strain. A third strain lacking the anchor molecule PRiMA, has no functional AChE and butyrylcholinesterase (BChE) in brain and an unaltered respiratory function. BChE inhibition by bambuterol decreases tidal volume and body temperature in del E5+6 and i1RR knockout strains, but not in PRiMA deletion or wild-type controls. We find that: (1) deletion of the full AChE gene is required for a pronounced alteration in respiratory phenotype, (2) BChE is involved in respiratory muscles contraction and temperature control in del E5+6 and i1RR knockout mice, and (3) AChE expression requiring a gene product splice to either exons 5 and 6 or regulated by intron1 influences temperature control. PMID:18977317

  12. Optical Sensing of Ecosystem Carbon Fluxes Combining Spectral Reflectance Indices with Solar Induced Fluorescence

    NASA Astrophysics Data System (ADS)

    Huemmrich, K. F.; Middleton, E.; Corp, L. A.; Campbell, P. K.; Kustas, W. P.

    2014-12-01

    Optical sampling of spectral reflectance and solar induced fluorescence provide information on the physiological status of vegetation that can be used to infer stress responses and estimates of production. Multiple repeated observations are required to observe the effects of changing environmental conditions on vegetation. This study examines the use of optical signals to determine inputs to a light use efficiency (LUE) model describing productivity of a cornfield where repeated observations of carbon flux, spectral reflectance and fluorescence were collected. Data were collected at the Optimizing Production Inputs for Economic and Environmental Enhancement (OPE3) fields (39.03°N, 76.85°W) at USDA Beltsville Agricultural Research Center. Agricultural Research Service researchers measured CO2 fluxes using eddy covariance methods throughout the growing season. Optical measurements were made from the nearby tower supporting the NASA FUSION sensors. The sensor system consists of two dual channel, upward and downward looking, spectrometers used to simultaneously collect high spectral resolution measurements of reflected and fluoresced light from vegetation canopies. Estimates of chlorophyll fluorescence, combined with measures of vegetation pigment content and the Photosynthetic Reflectance Index (PRI) derived from the spectral reflectance are compared with CO2 fluxes over diurnal periods for multiple days. PRI detects changes in Xanthophyll cycle pigments using reflectance at 531 nm compared to a reference band at 570 nm. The relationships among the different optical measurements indicate that they are providing different types of information on the vegetation and that combinations of these measurements provide improved retrievals of CO2 fluxes than any index alone.

  13. Effect of prenatal and postnatal malnutrition on intellectual functioning in early school-aged children in rural western China.

    PubMed

    Li, Chao; Zhu, Ni; Zeng, Lingxia; Dang, Shaonong; Zhou, Jing; Yan, Hong

    2016-08-01

    The aim of this study was to evaluate the effect of prenatal and postnatal malnutrition on the intellectual functioning of early school-aged children. We followed the offspring of women who had participated in a trial of prenatal supplementation with different combinations of micronutrients and who remained resident in the study field. We measured their intellectual functioning using the Wechsler intelligence scale for children (WISC-IV). Height-for-age, weight-for-age, and body mass index (BMI)-for-age were used as anthropometric nutritional status indices. Four of the 5 composite scores derived from the WISC-IV, except for working memory index (WMI), were significantly lower in low birth weight children after adjusting for confounds. All 5 composite scores, including full-scale intelligence quotient (FSIQ), verbal comprehension index (VCI), WMI, perceptual reasoning index (PRI), and processing speed index (PSI) were significant lower in stunted and underweight children. The differences in the means of WISC-IV test scores were greatest between stunted and nonstunted children. The means for FSIQ, VCI, WMI, PRI, and PSI were as follows: 5.88 (95% confidence interval [CI]: 2.84-8.92), 5.08 (95% CI: 1.12-8.41), 4.71 (95% CI: 1.78-7.66), 6.13 (95% CI: 2.83-9.44), and 5.81 (95% CI: 2.61-9.00). These means were lower in stunted children after adjusting for confounds. Our results suggest the important influences of low birth weight and postnatal malnutrition (stunting, low body weight) on intellectual functioning in early school-aged children. PMID:27495020

  14. Efficacy of compression of different capacitance beds in the amelioration of orthostatic hypotension

    NASA Technical Reports Server (NTRS)

    Denq, J. C.; Opfer-Gehrking, T. L.; Giuliani, M.; Felten, J.; Convertino, V. A.; Low, P. A.

    1997-01-01

    Orthostatic hypotension (OH) is the most disabling and serious manifestation of adrenergic failure, occurring in the autonomic neuropathies, pure autonomic failure (PAF) and multiple system atrophy (MSA). No specific treatment is currently available for most etiologies of OH. A reduction in venous capacity, secondary to some physical counter maneuvers (e.g., squatting or leg crossing), or the use of compressive garments, can ameliorate OH. However, there is little information on the differential efficacy, or the mechanisms of improvement, engendered by compression of specific capacitance beds. We therefore evaluated the efficacy of compression of specific compartments (calves, thighs, low abdomen, calves and thighs, and all compartments combined), using a modified antigravity suit, on the end-points of orthostatic blood pressure, and symptoms of orthostatic intolerance. Fourteen patients (PAF, n = 9; MSA, n = 3; diabetic autonomic neuropathy, n = 2; five males and nine females) with clinical OH were studied. The mean age was 62 years (range 31-78). The mean +/- SEM orthostatic systolic blood pressure when all compartments were compressed was 115.9 +/- 7.4 mmHg, significantly improved (p < 0.001) over the head-up tilt value without compression of 89.6 +/- 7.0 mmHg. The abdomen was the only single compartment whose compression significantly reduced OH (p < 0.005). There was a significant increase of peripheral resistance index (PRI) with compression of abdomen (p < 0.001) or all compartments (p < 0.001); end-diastolic index and cardiac index did not change. We conclude that denervation increases vascular capacity, and that venous compression improves OH by reducing this capacity and increasing PRI. Compression of all compartments is the most efficacious, followed by abdominal compression, whereas leg compression alone was less effective, presumably reflecting the large capacity of the abdomen relative to the legs.

  15. A single nucleotide polymorphism in primary-microRNA-146a reduces the expression of mature microRNA-146a in patients with Alzheimer's disease and is associated with the pathogenesis of Alzheimer's disease

    PubMed Central

    ZHANG, BIN; WANG, AIHONG; XIA, CUIPING; LIN, QUNFENG; CHEN, CHUNFU

    2015-01-01

    Alzheimer's disease (AD) is a progressive neurodegenerative disorder and is the most common form of dementia among the aging population. Although the incidence of the disease continues to increase, no cure has been developed. Effective treatment is restricted not only due to the lack of curative medicine, but also due to limited understanding of the underlying mechanisms and the diffculties in accurately diagnosing AD in its earliest stages prior to clinical symptoms. Micro (mi) RNAs (miR) have gained increasing attention in the investigation of neurodegenerative diseases. Previous reports have demonstrated that deregulation of miR-146a-5p is associated with the pathogenesis of human AD. In the present study, the coding region of primary (pri)-miR-146a in patients with AD was scanned and the rare C allele of rs2910164 was found to be associated with AD. Using reverse transcription quantitative polymerase chain reaction, it was demonstrated that site variation reduced the expression of mature miR-146a-5p. Notably, a reduction in the expression of miR-146a-5p led to less effcient inhibition of target genes, including Toll-like receptor (TLR)2, which is important in the pathogenesis of AD. Biological function investigations in RAW264.7 cells indicated that, compared with the G allele, the rare C allele upregulated the expression of tumor necrosis factor-α following stimulation with β-amyloid. These findings suggested that one common polymorphism in pri-miR-146a may contribute to the genetic predisposition to AD by disrupting the production of miR-146a-5p and affecting the expression and function of TLR2. PMID:26095531

  16. Phenotypic and Genotypic Description of Sedimenticola selenatireducens Strain CUZ, a Marine (Per)Chlorate-Respiring Gammaproteobacterium, and Its Close Relative the Chlorate-Respiring Sedimenticola Strain NSS

    PubMed Central

    Carlström, Charlotte I.; Loutey, Dana E.; Wang, Ouwei; Engelbrektson, Anna; Clark, Iain; Lucas, Lauren N.; Somasekhar, Pranav Y.

    2015-01-01

    Two (per)chlorate-reducing bacteria, strains CUZ and NSS, were isolated from marine sediments in Berkeley and San Diego, CA, respectively. Strain CUZ respired both perchlorate and chlorate [collectively designated (per)chlorate], while strain NSS respired only chlorate. Phylogenetic analysis classified both strains as close relatives of the gammaproteobacterium Sedimenticola selenatireducens. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) preparations showed the presence of rod-shaped, motile cells containing one polar flagellum. Optimum growth for strain CUZ was observed at 25 to 30°C, pH 7, and 4% NaCl, while strain NSS grew optimally at 37 to 42°C, pH 7.5 to 8, and 1.5 to 2.5% NaCl. Both strains oxidized hydrogen, sulfide, various organic acids, and aromatics, such as benzoate and phenylacetate, as electron donors coupled to oxygen, nitrate, and (per)chlorate or chlorate as electron acceptors. The draft genome of strain CUZ carried the requisite (per)chlorate reduction island (PRI) for (per)chlorate respiration, while that of strain NSS carried the composite chlorate reduction transposon responsible for chlorate metabolism. The PRI of strain CUZ encoded a perchlorate reductase (Pcr), which reduced both perchlorate and chlorate, while the genome of strain NSS included a gene for a distinct chlorate reductase (Clr) that reduced only chlorate. When both (per)chlorate and nitrate were present, (per)chlorate was preferentially utilized if the inoculum was pregrown on (per)chlorate. Historically, (per)chlorate-reducing bacteria (PRB) and chlorate-reducing bacteria (CRB) have been isolated primarily from freshwater, mesophilic environments. This study describes the isolation and characterization of two highly related marine halophiles, one a PRB and the other a CRB, and thus broadens the known phylogenetic and physiological diversity of these unusual metabolisms. PMID:25662971

  17. E2F1-miR-20a-5p/20b-5p auto-regulatory feedback loop involved in myoblast proliferation and differentiation

    PubMed Central

    Luo, Wen; Li, Guihuan; Yi, Zhenhua; Nie, Qinghua; Zhang, Xiquan

    2016-01-01

    miR-17 family microRNAs (miRNAs) are crucial for embryo development, however, their role in muscle development is still unclear. miR-20a-5p and miR-20b-5p belong to the miR-17 family and are transcribed from the miR-17~92 and miR-106a~363 clusters respectively. In this study, we found that miR-20a-5p and miR-20b-5p promoted myoblast differentiation and repressed myoblast proliferation by directly binding the 3′ UTR of E2F transcription factor 1 (E2F1) mRNA. E2F1 is an important transcriptional factor for organism’s normal development. Overexpression of E2F1 in myoblasts promoted myoblast proliferation and inhibited myoblast differentiation. Conversely, E2F1 inhibition induced myoblast differentiation and repressed myoblast proliferation. Moreover, E2F1 can bind directly to promoters of the miR-17~92 and miR-106a~363 clusters and activate their transcription, and E2F1 protein expression is correlated with the expression of pri-miR-17~92 and pri-miR-106a~363 during myoblast differentiation. These results suggested an auto-regulatory feedback loop between E2F1 and miR-20a-5p/20b-5p, and indicated that miR-20a-5p, miR-20b-5p and E2F1 are involved in myoblast proliferation and differentiation through the auto-regulation between E2F1 and miR-20a-5p/20b-5p. These findings provide new insight into the mechanism of muscle differentiation, and further shed light on the understanding of muscle development and muscle diseases. PMID:27282946

  18. Impact of aspirin dose on adenosine diphosphate-mediated platelet activities. Results of an in vitro pilot investigation.

    PubMed

    Tello-Montoliu, Antonio; Thano, Estela; Rollini, Fabiana; Patel, Ronakkumar; Wilson, Ryan E; Muñiz-Lozano, Ana; Franchi, Francesco; Darlington, Andrew; Desai, Bhaloo; Guzman, Luis A; Bass, Theodore A; Angiolillo, Dominick J

    2013-10-01

    Different aspirin dosing regimens have been suggested to impact outcomes when used in combination with adenosine diphosphate (ADP) P2Y12 receptor antagonists. Prior investigations have shown that not only aspirin, but also potent ADP P2Y12 receptor blockade can inhibit thromboxane A2-mediated platelet activation. The impact of aspirin dosing on ADP mediated platelet activities is unknown and represents the aim of this in vitro pilot pharmacodynamic (PD) investigation. Twenty-six patients with stable coronary artery disease on aspirin 81 mg/day and P2Y12 naïve were enrolled. PD assessments were performed at baseline, while patients were on 81 mg/day aspirin and after switching to 325 mg/day for 7 ± 2 days with and without escalating concentrations (vehicle, 1, 3, and 10 μM) of prasugrel's active metabolite (P-AM). PD assays included flow cytometric assessment of VASP to define the platelet reactivity index (PRI) and the Multiplate Analyzer (MEA) using multiple agonists [ADP, ADP + prostaglandin (PGE1), arachidonic acid (AA), and collagen]. Escalating P-AM concentrations showed incremental platelet P2Y12 inhibition measured by VASP-PRI (p<0.001). However, there were no differences according to aspirin dosing regimen at any P-AM concentration (vehicle: p=0.899; 1 μM: p=0.888; 3 μM: p=0.524; 10 μM: p=0.548). Similar findings were observed in purinergic markers assessed by MEA (ADP and ADP+PGE1). P-AM addition significantly reduced AA and collagen induced platelet aggregation (p<0.001 for all measures), irrespective of aspirin dose. In conclusion, aspirin dosing does not appear to affect PD measures of ADP-mediated platelet reactivity irrespective of the degree of P2Y12 receptor blockade. P2Y12 receptor blockade modulates platelet reactivity mediated by alternative activators. PMID:23884248

  19. Effects of music therapy on pain among female breast cancer patients after radical mastectomy: results from a randomized controlled trial.

    PubMed

    Li, Xiao-Mei; Yan, Hong; Zhou, Kai-Na; Dang, Shao-Nong; Wang, Duo-Lao; Zhang, Yin-Ping

    2011-07-01

    Music therapy has been used in multiple health care settings to reduce patient pain, anxiety, and stress. However, few available studies have investigated its effect on pain among breast cancer patients after radical mastectomy. The aim of this study was to explore the effects of music therapy on pain reduction in patients with breast cancer after radical mastectomy. This randomized controlled trial was conducted at the Surgical Department of Oncology Center, First Affiliated Hospital of Xi'an Jiaotong University from March to November 2009. A total of 120 breast cancer patients who received Personal Controlled Analgesia (PCA) following surgery (mastectomy) were randomly allocated to two groups, an intervention group and a control group (60 patients in each group). The intervention group accepted music therapy from the first day after radical mastectomy to the third admission to hospital for chemotherapy in addition to the routine nursing care, while the control group received only routine nursing care. Pain scores were measured at baseline and three post-tests using the General Questionnaire and Chinese version of Short-Form of McGill Pain Questionnaire. The primary endpoint was the change in the Pain Rating Index (PRI-total) score from baseline. Music therapy was found to reduce the PRI-total score in the intervention group significantly compared with the control group with a mean difference (95% CI) of -2.38 (-2.80, -1.95), -2.41 (-2.85, -1.96), and -1.87 (-2.33, -1.42) for the 1st, 2nd, and 3rd post-tests, respectively. Similar results were found for Visual Analogue Scale (VAS) and Present Pain Intensity (PPI) scores. The findings of the study provide some evidence that music therapy has both short- and long-term positive effects on alleviating pain in breast cancer patients following radical mastectomy. PMID:21537935

  20. Effect of prenatal and postnatal malnutrition on intellectual functioning in early school-aged children in rural western China

    PubMed Central

    Li, Chao; Zhu, Ni; Zeng, Lingxia; Dang, Shaonong; Zhou, Jing; Yan, Hong

    2016-01-01

    Abstract The aim of this study was to evaluate the effect of prenatal and postnatal malnutrition on the intellectual functioning of early school-aged children. We followed the offspring of women who had participated in a trial of prenatal supplementation with different combinations of micronutrients and who remained resident in the study field. We measured their intellectual functioning using the Wechsler intelligence scale for children (WISC-IV). Height-for-age, weight-for-age, and body mass index (BMI)-for-age were used as anthropometric nutritional status indices. Four of the 5 composite scores derived from the WISC-IV, except for working memory index (WMI), were significantly lower in low birth weight children after adjusting for confounds. All 5 composite scores, including full-scale intelligence quotient (FSIQ), verbal comprehension index (VCI), WMI, perceptual reasoning index (PRI), and processing speed index (PSI) were significant lower in stunted and underweight children. The differences in the means of WISC-IV test scores were greatest between stunted and nonstunted children. The means for FSIQ, VCI, WMI, PRI, and PSI were as follows: 5.88 (95% confidence interval [CI]: 2.84–8.92), 5.08 (95% CI: 1.12–8.41), 4.71 (95% CI: 1.78–7.66), 6.13 (95% CI: 2.83–9.44), and 5.81 (95% CI: 2.61–9.00). These means were lower in stunted children after adjusting for confounds. Our results suggest the important influences of low birth weight and postnatal malnutrition (stunting, low body weight) on intellectual functioning in early school-aged children. PMID:27495020

  1. Identification of new loci involved in adhesion of Listeria monocytogenes to eukaryotic cells. European Listeria Genome Consortium.

    PubMed

    Milohanic, E; Pron, B; Berche, P; Gaillard, J L

    2000-03-01

    Insertional mutagenesis was performed with Tn1545 in the genetic background of an inIAB deletion mutant to identify new adhesion determinants in Listeria monocytogenes. Four insertion mutants defective in adhesion to eukaryotic cells were identified. Insertion sites were cloned by inverse-PCR and sequenced. The genetic organization of insertion regions was further analysed by screening and sequencing DNA fragments from a HindIII library and by searching databases. Three adhesion-defective mutants each had one copy of Tn1545 inserted into their chromosome. The insertion sites were different in the three mutants: (i) upstream from two ORFs in tandem, similar to dfp and priA of Bacillus subtilis, respectively; (ii) within an ORF encoding a putative 126 amino-acid-polypeptide with no significant similarity to any known protein; (iii) within an ORF similar to a B. subtilis ORF with no known function, just upstream from an operon similar to an ABC (ATP-binding cassette) transporter operon from B. subtilis. The excisants obtained from these mutants using the excision reporter plasmid pTCR9 recovered full adhesion capacity. A fourth mutant was the most severely defective in adhesion. It had five Tn1545 insertions, one of which was upstream from dfp and priA, and another of which was upstream from ami, a gene encoding a surface-exposed autolysin with a C terminus similar to that of InIB. Ami was clearly involved because an ami null mutant constructed in an EGDdeltainIA-F background was adhesion-defective. Thus new regions involved in the adhesion of L. monocytogenes to eukaryotic cells were identified. Further study is required to define more accurately the roles of these regions in the adhesion process itself. PMID:10746777

  2. A novel mobile dual-wavelength laser altimetry system for improved site-specific Nitrogen fertilizer applications

    NASA Astrophysics Data System (ADS)

    Eitel, J.; Magney, T. S.; Vierling, L. A.; Brown, T. T.; Huggins, D. R.

    2012-12-01

    Reducing fertilizer inputs while maintaining yield would increase farmer's profits and similarly lessen the adverse environmental effects of production agriculture. The development of technologies that allow precise, site-specific application of Nitrogen (N) fertilizer has thus been an important research goal over the past decades. Remote sensing of foliar crop properties and function with tractor-mountable optical sensors has thought to be useful to optimize N fertilizer applications. However, on-the-go sensing of foliar crop properties and function has proven difficult, particularly during early crop growth stages when fertilizer decisions are often made. This difficulty arises from the fact that the spectral signal measured by on-the-go sensors is dominated by soil reflectance during early crop growth stages. Here, we present the basic principles behind a novel, dual-wavelength, tractor mountable laser altimetry system that measures the laser return intensity of the reflected green and red laser light. The green (532 nm) and the red (660 nm) wavelength combination allows calculation of a modified Photochemical Reflectance Index (mPRI) that have shown to be sensitive to both crop function and foliar chemistry. The small field of view of the laser points (diameter: 4 mm) combined with its high sampling rate (1000 points sec-1) allows vegetation returns to be isolated from ground returns by using simple thresholds. First tests relating foliar N of winter wheat (Triticum aestivum L.) with laser derived mPRI are promising (r2 = 0.72). Further research is needed to test the relationship between laser derived spectral indices and crop function.

  3. Early Viral Suppression Improves Neurocognitive Outcomes in HIV-infected Children

    PubMed Central

    CROWELL, Claudia S.; HUO, Yanling; TASSIOPOULOS, Katherine; MALEE, Kathleen M.; YOGEV, Ram; HAZRA, Rohan; RUTSTEIN, Richard M.; NICHOLS, Sharon L.; SMITH, Renee A.; WILLIAMS, Paige L.; OLESKE, James; MULLER, William J.

    2014-01-01

    Objective To estimate the association of age of viral suppression and central nervous system penetration effectiveness (CPE) score with neurocognitive functioning among school-age children with perinatally-acquired HIV infection (PHIV+). Design We analyzed data from two U.S.-based multisite prospective cohort studies. Methods Multivariable general linear regression models were used to evaluate associations of age at viral suppression and CPE scores [of initial ART regimen and weighted average] with WISC-III or WISC-IV neurocognitive assessments [full scale IQ (FSIQ); performance IQ/ perceptual reasoning index (PIQ/PRI); and verbal IQ/ verbal comprehension index (VIQ/VCI)], adjusted for demographic and clinical covariates. Sensitivity analyses were stratified by birth cohort (before vs after 1996). Results 396 PHIV+ children were included. Estimated differences in mean FSIQ (comparing virally suppressed vs. unsuppressed children) by each age cutoff were 3.7, 2.2, 3.2, 4.4, and 3.9 points at ages 1, 2, 3, 4, and 5, respectively. For PIQ/PRI, estimated mean differences were 3.7, 2.4, 2.2, 4.6, and 4.5 at ages 1 through 5 respectively. In both cases, these differences were significant only at the age 4 and 5 thresholds. After stratifying by birth cohort the association between age at suppression and cognitive function persisted only among those born after 1996. Age at viral suppression was not associated with VIQ/VCI; CPE score was not associated with FSIQ, verbal comprehension or perceptual reasoning indices. Conclusions Virologic suppression during infancy or early childhood is associated with improved neurocognitive outcomes in school-aged PHIV+ children. In contrast, CPE scores showed no association with neurocognitive outcomes. PMID:25686678

  4. Gene flow on ice: the role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus).

    PubMed

    Elizabeth Alter, S; Rosenbaum, Howard C; Postma, Lianne D; Whitridge, Peter; Gaines, Cork; Weber, Diana; Egan, Mary G; Lindsay, Melissa; Amato, George; Dueck, Larry; Brownell, Robert L; Heide-Jørgensen, Mads-Peter; Laidre, Kristin L; Caccone, Gisella; Hancock, Brittany L

    2012-11-01

    Sea ice is believed to be a major factor shaping gene flow for polar marine organisms, but it remains unclear to what extent it represents a true barrier to dispersal for arctic cetaceans. Bowhead whales are highly adapted to polar sea ice and were targeted by commercial whalers throughout Arctic and subarctic seas for at least four centuries, resulting in severe reductions in most areas. Both changing ice conditions and reductions due to whaling may have affected geographic distribution and genetic diversity throughout their range, but little is known about range-wide genetic structure or whether it differed in the past. This study represents the first examination of genetic diversity and differentiation across all five putative stocks, including Baffin Bay-Davis Strait, Hudson Bay-Foxe Basin, Bering-Beaufort-Chukchi, Okhotsk, and Spitsbergen. We also utilized ancient specimens from Prince Regent Inlet (PRI) in the Canadian Arctic and compared them with modern stocks. Results from analysis of molecular variance and demographic simulations are consistent with recent and high gene flow between Atlantic and Pacific stocks in the recent past. Significant genetic differences between ancient and modern populations suggest PRI harbored unique maternal lineages in the past that have been recently lost, possibly due to loss of habitat during the Little Ice Age and/or whaling. Unexpectedly, samples from this location show a closer genetic relationship with modern Pacific stocks than Atlantic, supporting high gene flow between the central Canadian Arctic and Beaufort Sea over the past millennium despite extremely heavy ice cover over much of this period. PMID:23170222

  5. Gene flow on ice: the role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus)

    PubMed Central

    Elizabeth Alter, S; Rosenbaum, Howard C; Postma, Lianne D; Whitridge, Peter; Gaines, Cork; Weber, Diana; Egan, Mary G; Lindsay, Melissa; Amato, George; Dueck, Larry; Brownell, Robert L; Heide-Jørgensen, Mads-Peter; Laidre, Kristin L; Caccone, Gisella; Hancock, Brittany L

    2012-01-01

    Sea ice is believed to be a major factor shaping gene flow for polar marine organisms, but it remains unclear to what extent it represents a true barrier to dispersal for arctic cetaceans. Bowhead whales are highly adapted to polar sea ice and were targeted by commercial whalers throughout Arctic and subarctic seas for at least four centuries, resulting in severe reductions in most areas. Both changing ice conditions and reductions due to whaling may have affected geographic distribution and genetic diversity throughout their range, but little is known about range-wide genetic structure or whether it differed in the past. This study represents the first examination of genetic diversity and differentiation across all five putative stocks, including Baffin Bay-Davis Strait, Hudson Bay-Foxe Basin, Bering-Beaufort-Chukchi, Okhotsk, and Spitsbergen. We also utilized ancient specimens from Prince Regent Inlet (PRI) in the Canadian Arctic and compared them with modern stocks. Results from analysis of molecular variance and demographic simulations are consistent with recent and high gene flow between Atlantic and Pacific stocks in the recent past. Significant genetic differences between ancient and modern populations suggest PRI harbored unique maternal lineages in the past that have been recently lost, possibly due to loss of habitat during the Little Ice Age and/or whaling. Unexpectedly, samples from this location show a closer genetic relationship with modern Pacific stocks than Atlantic, supporting high gene flow between the central Canadian Arctic and Beaufort Sea over the past millennium despite extremely heavy ice cover over much of this period. PMID:23170222

  6. [The Study Based on Rectification of Vegetation Indices with Dust Impact].

    PubMed

    Chen, Fan-tao; Zhao, Wen-ji; Yan, Xing

    2015-10-01

    Vegetation indices are the simplest and most effective metric parameters representing the features of vegetation cover and growth condition. This paper used Euonymus japonicas Thunb as a study case and collected 200 leaf samples in 20 locations. Using electronic analytical balance and ASD hyperspectral radiometer with Win FOLIA leaf area meter obtained the data of the amount of dust, spectral information and leaf area. Through comparative analysis between dust and clean leaves, differences of spectral curve and vegetation indices were apparent. Then, combined with dust weight and spectral data, dust correction models-for vegetation indices were built. The analysis results showed that the spectral curve between clean and dust leaves have typical characteristics: blue edge and red edge were at 520 and 705 nm; however, dust influenced leaf reflectance significantly in range of 350-700, 750-1 350, 1 500-1 850, 1 900-2 100 nm wavelength, and had a greater impact on vegetation indices. With dust weight increasing, the linear correlation of dust with NDVI AND PRI was non-significant, but that with NDWI, NDII and CAI was still significant. The verification of correction models showed that coefficient of determination (R2) of NDVI, NDII, CAI and PRI were 0.547, 0.430, 0.653 and 0.96 and their root mean square error (RMSE) was 0.035, 0.020, 0.112 and 0.009 respectively. Furthermore, it showed that applying dust correction models can improve the accuracy of vegetation indices calculation. PMID:26904827

  7. Evaluation of leaf energy dissipation by the Photochemical Reflectance

    NASA Astrophysics Data System (ADS)

    Raddi, S.; Magnani, F.

    Starting from the early paper by Heber (1969), several studies have demonstrated a subtle shift in leaf spectroscopic characteristics (both absorbance and reflectance) in response to rapid changes in environmental conditions. More recent work, briefly reviewed here, has also demonstrated the existence of two components in the maked peak centered at 505-540 nm: an irreversible component, attributed to the interconversion of leaf xanthophylls, and a reversible component at slightly longer wavelengths, resulting from conformational changes induced by the buildup of a pH gradient across the thylakoid membrane associated with photosynthetic electron transport. Both processes (xanthophyll de-epoxidation and conformational changes) are known to contribute to the dissipation of excess energy in Photosystem II (PSII). Leaf spectroscopy could therefore provide a powerful non-invasive tool for the determination of leaf photosynthetic processes. This led to the development of the normalized spectral index PRI (Photochemical Reflectance Index; Gamon, Penuelas &Field 1992; Gamon, Serrano &Surfus 1997), which relates the functional signal at 531 nm to a reference signal at 570 nm. The index has been found to track diurnal changes in xanthophyll de-epoxidation state, radiation use efficiency and fluorescence in response to light, both at the leaf and more recently at the canopy level. A common relationship has also beenreported across species and functional types, although such a generality has not always been confirmed. Recent reports (Stylinski et al. 2000) have also hinted of a possible link between PRI and leaf photosynthetic potential, possibly through the correlation between xanthophyll content and electron transport machinery in the chloroplast. Such a link, if confirmed, could prove very useful for the remote sensing and modelling ofvegetation. Some of these open questions were addressed in the present study. The correlation between leaf function and reflectance was

  8. Passive fluorescence measurements during SIFLEX

    NASA Astrophysics Data System (ADS)

    Moya, I.; Ounis, A.; Louis, J.; Evain, S.; Ducruet, J.-M.

    The goal of the participation of the LURE team to the SIFLEX campaign was %to provide clear evidence of quantitative absolute measurements of natural fluorescence andfluorescence flux evaluation by passive methods in the Fraunhofer lines. More specifically, to quantify the fluorescence flux in A and B absorption bands of atmospheric oxygen. The measurements have been focus on: Testing specific passive fluorescence instrumentation recently developed at LURE for assessing the sun induced fluorescence radiance from vegetation. Investigating diurnal and seasonal change of fluorescence and its behaviour with respect to plant condition, pigment content, global radiation amount and its correlation against accumulated biomass during growing period, Cross-correlate the fluorescence signal with hyperspectral reflectance and thermal IR radiance. A special attention has been paid to diurnal cycle and seasonal variations. Comparing fluorescence fluxes with CO2 fluxes measured by the already existing gas exchange equipment of the site. Instrumentation PMFD (Passive Multiwavelength Fluorescence Detector) was the main instrument used to asses fluorescence fluxes. The instrument was based on the Fraunhofer line principle, applied in the atmospheric oxygen A and B bands (760nm and 687nm, respectively). The output parameters were two stationary fluorescence flux at 687nm and 760nm and the NDVI (NDVI = (R760-R687) / (R760+R687)) index. Two additional channels of the instrument are devoted to measure reflectance variations at 531nm and 570 nm in order to calculate the PRI (PRI = (R531-R570) / (R531+R570)) index. This instrument was installed on the main tower, 10 m above the crown of the trees and maintained in the same viewing direction during the campaign (towards the north direction). The zenith angle was set to about 50-65 degrees. The footprint of the instrument contained the crowns of several trees. BD was a second passive detector operating solely in the atmospheric oxygen A

  9. Estimating photosynthesis with high resolution field spectroscopy in a Mediterranean grassland under different nutrient availability

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Recent studies have shown how human induced N:P imbalances are affecting essential processes (e.g. photosynthesis, plant growth rate) that lead to important changes in ecosystem structure and function. In this regard, the accuracy of the approaches based on remotely-sensed data for monitoring and modeling gross primary production (GPP) relies on the ability of vegetation indices (VIs) to track the dynamics of vegetation physiological and biophysical properties/variables. Promising results have been recently obtained when Chlorophyll-sensitive VIs and Chlorophyll fluorescence are combined with structural indices in the framework of the Monteith's light use efficiency (LUE) model. However, further ground-based experiments are required to validate LUE model performances, and their capability to be generalized under different nutrient availability conditions. In this study, the overall objective was to investigate the sensitivity of VIs to track short- and long-term GPP variations in a Mediterranean grassland under different N and P fertilization treatments. Spectral VIs were acquired manually using high resolution spectrometers (HR4000, OceanOptics, USA) along a phenological cycle. The VIs examined included photochemical reflectance index (PRI), MERIS terrestrial-chlorophyll index (MTCI) and normalized difference vegetation index (NDVI). Solar-induced chlorophyll fluorescence calculated at the oxygen absorption band O2-A (F760) using spectral fitting methods was also used. Simultaneously, measurements of GPP and environmental variables were conducted using a transient-state canopy chamber. Overall, GPP, F760 and VIs showed a clear seasonal time-trend in all treatments, which was driven by the phenological development of the grassland. Results showed significant differences (p<0.05) in midday GPP values between N and without N addition plots, in particular at the peak of the growing season during the flowering stage and at the end of the season during senescence. While

  10. Bmo-miR-2758 Targets BmFMBP-1 (Lepidoptera: Bombycidae) and Suppresses Its Expression in BmN Cells.

    PubMed

    Wang, Xin; Tang, Shunming; Song, Fei; Chen, Chen; Guo, Xijie; Shen, Xingjia

    2016-01-01

    MicroRNAs (miRNAs) are an abundant family of endogenous noncoding small RNA molecules. They play crucial roles on regulation of life processes both in plants and animals. Fibroin modulator binding protein-1 (FMBP-1) is a silk gland transcription factor of Bombyx mori, which is considered as a trans-activator of fibroin genes. And bioinformatics prediction showed that at the 3' untranslated region (3' UTR) of BmFMBP-1 there were binding sites for three bmo-miRNAs, bmo-miR-2b*, bmo-miR-305, and bmo-miR-2758, separately. In order to validate whether these bmo-miRNAs involved in the regulation of BmFMBP-1 expression, the expression levels of three bmo-miRNAs and BmFMBP-1 in the middle silk gland (MSG) and posterior silk gland (PSG) during the fourth- and fifth-larval stages of B. mori were measured by semi-quantitative reverse transcription polymerase chain reaction. The results revealed that the expression level of bmo-miR-2758 was the highest in the three, and it expressed higher in the PSG than in the MSG with a similar expression pattern as BmFMBP-1, implying that bmo-miR-2758 may involved in regulation of BmFMBP-1. To validate the regulation function of bmo-miR-2758 on BmFMBP-1, recombinant plasmids pcDNA3 [ie1-egfp-pri-bmo-miR-2758-SV40] and pGL3 [A3-luc-FMBP-1 3' UTR-SV40] were constructed and co-transfected in BmN cells. The dual-luciferase reporter assay system was used for assay of transient expression. The results showed that the expression of the luciferase reporter was significantly decreased when pGL3 [A3-luc-FMBP-1 3' UTR-SV40] co-transfected with pcDNA3 [ie1-egfp-pri-bmo-miR-2758-SV40] (P <  .01). Furthermore, when the artificial antisense RNA of bmo-miR-2758 (inhibitor) was added to the above co-transfection, the expression of the luciferase reporter was recovered significantly (P < 0.01). These results suggest that bmo-miR-2758 represses the expression of BmFMBP-1 in vitro. PMID:27001963

  11. Amount and Percentage of Current Societal Assets in Areas on Kaua'i, Hawai'i, within the 1992 Hurricane 'Iniki Storm-Surge Inundation Zone

    USGS Publications Warehouse

    Wood, Nathan

    2008-01-01

    The Pacific Risk Management 'Ohana (PRiMO) is a network of partners and stakeholders involved in the development, delivery, and communication of risk management-related information, products, and services across the Pacific Ocean (National Oceanic and Atmospheric Administration Pacific Services Center, 2008). One PRiMO-related project is the NOAA National Climatic Data Center's Integrated Data and Environmental Applications (IDEA) Center's Pacific Region Integrated Climatology Information Products (PRICIP) initiative, which seeks to improve the understanding of patterns and trends of storm frequency and intensity ('storminess') within the Pacific region and to develop a suite of integrated information products that can be used by emergency managers, mitigation planners, government agencies, and other decision-makers (National Oceanic and Atmospheric Administration Integrated Data and Environmental Applications Center, 2008a). One of the PRICIP information products is a historical storm 'event anatomy', which includes a summary of sector-specific socioeconomic impacts associated with a particular event, as well as information about the event and its climatological context. The intent of an event anatomy is to convey the causes of an extreme storm event and the associated impacts in a format that users can understand. The event anatomies also are intended to familiarize users with the in-place and remotely sensed products typically employed to track and forecast weather and climate. The first event anatomy developed as a prototype and hosted on the PRICIP portal is for Hurricane 'Iniki (National Oceanic and Atmospheric Administration Integrated Data and Environmental Applications Center, 2008b), a Category 3-4 hurricane that made landfall on the south coast of Kaua'i Island on September 11, 1992, with estimated maximum sustained winds of more than 140 mph and gusts as high as 175 mph. Storm-surge inundation occurred on the southern and northeastern coast of Kaua

  12. Effectiveness of massage therapy for subacute low-back pain: a randomized controlled trial

    PubMed Central

    Preyde, M

    2000-01-01

    BACKGROUND: The effectiveness of massage therapy for low-back pain has not been documented. This randomized controlled trial compared comprehensive massage therapy (soft-tissue manipulation, remedial exercise and posture education), 2 components of massage therapy and placebo in the treatment of subacute (between 1 week and 8 months) low-back pain. METHODS: Subjects with subacute low-back pain were randomly assigned to 1 of 4 groups: comprehensive massage therapy (n = 25), soft-tissue manipulation only (n = 25), remedial exercise with posture education only (n = 22) or a placebo of sham laser therapy (n = 26). Each subject received 6 treatments within approximately 1 month. Outcome measures obtained at baseline, after treatment and at 1-month follow-up consisted of the Roland Disability Questionnaire (RDQ), the McGill Pain Questionnaire (PPI and PRI), the State Anxiety Index and the Modified Schober test (lumbar range of motion). RESULTS: Of the 107 subjects who passed screening, 98 (92%) completed post-treatment tests and 91 (85%) completed follow-up tests. Statistically significant differences were noted after treatment and at follow-up. The comprehensive massage therapy group had improved function (mean RDQ score 1.54 v. 2.86-6.5, p < 0.001), less intense pain (mean PPI score 0.42 v. 1.18-1.75, p < 0.001) and a decrease in the quality of pain (mean PRI score 2.29 v. 4.55-7.71, p = 0.006) compared with the other 3 groups. Clinical significance was evident for the comprehensive massage therapy group and the soft-tissue manipulation group on the measure of function. At 1-month follow-up 63% of subjects in the comprehensive massage therapy group reported no pain as compared with 27% of the soft-tissue manipulation group, 14% of the remedial exercise group and 0% of the sham laser therapy group. INTERPRETATION: Patients with subacute low-back pain were shown to benefit from massage therapy, as regulated by the College of Massage Therapists of Ontario and delivered by

  13. Seasonal patterns of photosynthetic gas-exchange and leaf reflectance characteristics in male and female riparian cottonwoods of southern Alberta

    NASA Astrophysics Data System (ADS)

    Letts, M. G.; Phelan, C. A.; Johnson, D. R.; Pearce, D. W.; Rood, S. B.

    2007-12-01

    Riparian, or streamside, cottonwood trees ( Populus spp.) are dioecious phreatophytes of hydrological and ecological importance in arid and semi-arid ecosystems throughout the northern hemisphere. In southern Alberta, groundwater and soil moisture levels typically decline during the May to September growth season. To understand how narrowleaf cottonwoods ( Populus angustifolia James) respond to this seasonal decrease in moisture availability, we repeatedly measured photosynthetic gas exchange, leaf reflectance, chlorophyll fluorescence and stable carbon isotope composition (δ13C) in four male and four female trees of the Oldman River valley, throughout the 2006 growth season. Maximum light-saturated net photosynthesis rates (Amax), near 16 μmol m-2 s-1, occurred on day of year (DOY) 205, one month after peak soil moisture, but coincident with the maximum quantum efficiency of Photosystem II (Fv/Fm), chlorophyll index (CI) and scaled photochemical reflectance index (sPRI). CI data suggest that the early-season rise in Amax and Fv/Fm was partly due to growth in the chlorophyll pool. Thereafter, Amax fell to near 10 μmol m-2 s-1, largely due to its positive logarithmic relationship with stomatal conductance (gs; r2=0.89), which decreased from 559 to 246 mmol m-2 s-1 from DOY 205 to 237. The normalized difference vegetation index (NDVI), CI, sPRI and quantum yield of electron transfer at Photosystem II (ΦPSII) also declined in response to lower volumetric soil moisture content (θv) and increasing groundwater depth (Zgw). Little change in transpiration rate (E) was observed in response to changing environmental conditions, except on DOY 237, when a combination of unseasonably low vapour pressure deficit (D) and low θv above the deepening capillary fringe caused E to decrease. No significant difference was observed between the mean WUE (Amax/E) of males (2.1 ± 0.2 mmol mol-1) and females (2.5 ± 0.2 mmol mol-1; repeated measures ANOVA, df=6, F=2.39, p=0

  14. Leaf gas exchange, chlorophyll fluorescence and pigment indexes of Eugenia uniflora L. in response to changes in light intensity and soil flooding.

    PubMed

    Mielke, Marcelo S; Schaffer, Bruce

    2010-01-01

    The interactive effects of changing light intensity and soil flooding on the photosynthetic performance of Eugenia uniflora L. (Myrtaceae) seedlings in containers were examined. Two hypotheses were tested: (i) the photosynthetic apparatus of shade-adapted leaves can be rapidly acclimated to high light after transfer from shade to full sun, and (ii) photosynthetic acclimation to changing light intensity may be influenced by soil flooding. Seedlings cultivated in a shade house (40% of full sun, approximately 12 mol m(-)(2) day(-)(1)) for 6 months were transferred to full sun (20-40 mol m(-2) day(-1)) or shade (30% of full sun, approximately 8 mol m(-2) day(-1)) and subjected to soil flooding for 23 days or not flooded. Chlorophyll content index (CCI), chlorophyll fluorescence, leaf weight per area (LWA), photosynthetic light-response curves and leaf reflectance indexes were measured during soil flooding and after plants were unflooded. The CCI values increased throughout the experiment in leaves of shaded plants and decreased in leaves of plants transferred to full sun. There were no significant interactions between light intensity and flooding treatments for most of the variables analyzed, with the exception of Fv/Fm 22 days after plants were flooded and 5 days after flooded plants were unflooded. The light environment significantly affected LWA, and light environment and soil flooding significantly affected the light-saturated gross CO(2) assimilation rate expressed on area and dry weight bases (A(max-area) and A(max-wt), respectively), stomatal conductance of water vapor (g(ssat)) and intrinsic water use efficiency (A/g(s)). Five days after flooded plants were unflooded, the normalized difference vegetation index (NDVI) and the scaled photochemical reflectance index (sPRI) were significantly higher in shade than in sun leaves. Thirty days after transferring plants from the shade house to the light treatment, LWA was 30% higher in sun than in shade leaves, and A

  15. Evaluation of optical remote sensing parameters to improve modeling of gross primary productivity in a heterogeneous agricultural area

    NASA Astrophysics Data System (ADS)

    Schickling, A.; Damm, A.; Schween, J.; Rascher, U.; Crewell, S.; Wahner, A.

    2011-12-01

    Terrestrial photosynthesis greatly determines plant mediated exchange processes in the vegetation atmosphere system and substantially influences patterns in atmospheric carbon dioxide (CO2) concentrations and water vapor. Therefore, an accurate quantification of photosynthetic CO2 uptake, commonly referred to as gross primary productivity (GPP), is a key parameter to distinguish those atmospheric patterns on various spatio-temporal scales. Remote sensing (RS) offers the unique possibility to determine GPP at different spatial scales ranging from the local to the global scale. Attempts to estimate GPP from RS data focus on the light use efficiency (LUE) concept of Monteith which relates GPP to the absorbed photosynthetically active radiation and the efficiency of plant canopies to utilize the absorbed radiation for photosynthesis. To reliably predict GPP on different spatio-temporal scales LUE has to be linked to optical RS parameters which detect changes in photosynthetic efficiency due to environmental conditions. In this study we evaluated two optical RS parameters, namely the sun-induced fluorescence (Fs) and the photochemical reflectance index (PRI), for their potential to serve as a proxy for LUE. The parameters were derived from two ASD FieldSpec spectrometers which were operated in parallel. During several days one instrument was installed on the ground above the vegetation canopy of either a winter wheat or a sugar beet field. The second instrument was operated from a small research aircraft continuously crossing the observation sites at low altitude (< 300 m). GPP was calculated on a diurnal basis including optical parameters in Monteith's LUE concept. The calculated GPP was compared to simultaneously acquired GPP data from eddy covariance measurements. The diurnal behavior of calculated and measured GPP corresponded well indicating that optical RS parameters are able to track the diurnal response of physiological regulation of photosynthesis to changing

  16. Characterization of Herpes Simplex Virus 2 Primary MicroRNA Transcript Regulation

    PubMed Central

    Bosch-Marce, Marta; Patel, Amita; Margolis, Todd P.

    2015-01-01

    ABSTRACT In order to understand factors that may influence latency-associated transcription and latency-associated transcript (LAT) phenotypes, we studied the expression of the herpes simplex virus 2 (HSV-2) LAT-associated microRNAs (miRNAs). We mapped the transcription initiation sites of all three primary miRNA transcripts and identified the ICP4-binding sequences at the transcription initiation sites of both HSV-2 LAT (pri-miRNA for miR-I and miR-II, which target ICP34.5, and miR-III, which targets ICP0) and L/ST (a pri-miRNA for miR-I and miR-II) but not at that of the primary miR-H6 (for which the target is unknown). We confirmed activity of the putative HSV-2 L/ST promoter and found that ICP4 trans-activates the L/ST promoter when the ICP4-binding site at its transcription initiation site is mutated, suggesting that ICP4 may play a dual role in regulating transcription of L/ST and, consequently, of miR-I and miR-II. LAT exon 1 (containing LAT enhancer sequences), together with the LAT promoter region, comprises a bidirectional promoter required for the expression of both LAT-encoded miRNAs and miR-H6 in latently infected mouse ganglia. The ability of ICP4 to suppress ICP34.5-targeting miRNAs and to activate lytic viral genes suggests that ICP4 could play a key role in the switch between latency and reactivation. IMPORTANCE The HSV-2 LAT and viral miRNAs expressed in the LAT region are the most abundant viral transcripts during HSV latency. The balance between the expression of LAT and LAT-associated miRNAs and the expression of lytic viral transcripts from the opposite strand appears to influence whether individual HSV-infected neurons will be latently or productively infected. The outcome of neuronal infection may thus depend on regulation of gene expression of the corresponding primary miRNAs. In the present study, we characterize promoter sequences responsible for miRNA expression, including identification of the primary miRNA 5′ ends and evaluation of

  17. Bmo-miR-2758 Targets BmFMBP-1 (Lepidoptera: Bombycidae) and Suppresses Its Expression in BmN Cells

    PubMed Central

    Wang, Xin; Tang, Shunming; Song, Fei; Chen, Chen; Guo, Xijie; Shen, Xingjia

    2016-01-01

    MicroRNAs (miRNAs) are an abundant family of endogenous noncoding small RNA molecules. They play crucial roles on regulation of life processes both in plants and animals. Fibroin modulator binding protein-1 (FMBP-1) is a silk gland transcription factor of Bombyx mori, which is considered as a trans-activator of fibroin genes. And bioinformatics prediction showed that at the 3′ untranslated region (3′ UTR) of BmFMBP-1 there were binding sites for three bmo-miRNAs, bmo-miR-2b*, bmo-miR-305, and bmo-miR-2758, separately. In order to validate whether these bmo-miRNAs involved in the regulation of BmFMBP-1 expression, the expression levels of three bmo-miRNAs and BmFMBP-1 in the middle silk gland (MSG) and posterior silk gland (PSG) during the fourth- and fifth-larval stages of B. mori were measured by semi-quantitative reverse transcription polymerase chain reaction. The results revealed that the expression level of bmo-miR-2758 was the highest in the three, and it expressed higher in the PSG than in the MSG with a similar expression pattern as BmFMBP-1, implying that bmo-miR-2758 may involved in regulation of BmFMBP-1. To validate the regulation function of bmo-miR-2758 on BmFMBP-1, recombinant plasmids pcDNA3 [ie1-egfp-pri-bmo-miR-2758-SV40] and pGL3 [A3-luc-FMBP-1 3′ UTR-SV40] were constructed and co-transfected in BmN cells. The dual-luciferase reporter assay system was used for assay of transient expression. The results showed that the expression of the luciferase reporter was significantly decreased when pGL3 [A3-luc-FMBP-1 3′ UTR-SV40] co-transfected with pcDNA3 [ie1-egfp-pri-bmo-miR-2758-SV40] (P < 0.01). Furthermore, when the artificial antisense RNA of bmo-miR-2758 (inhibitor) was added to the above co-transfection, the expression of the luciferase reporter was recovered significantly (P < 0.01). These results suggest that bmo-miR-2758 represses the expression of BmFMBP-1 in vitro. PMID:27001963

  18. Reviews and Syntheses: optical sampling of the flux tower footprint

    NASA Astrophysics Data System (ADS)

    Gamon, J. A.

    2015-07-01

    The purpose of this review is to address the reasons and methods for conducting optical remote sensing within the flux tower footprint. Fundamental principles and conclusions gleaned from over 2 decades of proximal remote sensing at flux tower sites are reviewed. The organizing framework used here is the light-use efficiency (LUE) model, both because it is widely used, and because it provides a useful theoretical construct for integrating optical remote sensing with flux measurements. Multiple ways of driving this model, ranging from meteorological measurements to remote sensing, have emerged in recent years, making it a convenient conceptual framework for comparative experimental studies. New interpretations of established optical sampling methods, including the photochemical reflectance index (PRI) and solar-induced chlorophyll fluorescence (SIF), are discussed within the context of the LUE model. Multi-scale analysis across temporal and spatial axes is a central theme because such scaling can provide links between ecophysiological mechanisms detectable at the level of individual organisms and broad patterns emerging at larger scales, enabling evaluation of emergent properties and extrapolation to the flux footprint and beyond. Proper analysis of the sampling scale requires an awareness of sampling context that is often essential to the proper interpretation of optical signals. Additionally, the concept of optical types, vegetation exhibiting contrasting optical behavior in time and space, is explored as a way to frame our understanding of the controls on surface-atmosphere fluxes. Complementary normalized difference vegetation index (NDVI) and PRI patterns across ecosystems are offered as an example of this hypothesis, with the LUE model and light-response curve providing an integrating framework. I conclude that experimental approaches allowing systematic exploration of plant optical behavior in the context of the flux tower network provides a unique way to

  19. Optical sampling of the flux tower footprint

    NASA Astrophysics Data System (ADS)

    Gamon, J. A.

    2015-03-01

    The purpose of this review is to address the reasons and methods for conducting optical remote sensing within the flux tower footprint. Fundamental principles and conclusions gleaned from over two decades of proximal remote sensing at flux tower sites are reviewed. An organizing framework is the light-use efficiency (LUE) model, both because it is widely used, and because it provides a useful theoretical construct for integrating optical remote sensing with flux measurements. Multiple ways of driving this model, ranging from meteorological measurements to remote sensing, have emerged in recent years, making it a convenient conceptual framework for comparative experimental studies. New interpretations of established optical sampling methods, including the Photochemical Reflectance Index (PRI) and Solar-Induced Fluorescence (SIF), are discussed within the context of the LUE model. Multi-scale analysis across temporal and spatial axes is a central theme, because such scaling can provide links between ecophysiological mechanisms detectable at the level of individual organisms and broad patterns emerging at larger scales, enabling evaluation of emergent properties and extrapolation to the flux footprint and beyond. Proper analysis of sampling scale requires an awareness of sampling context that is often essential to the proper interpretation of optical signals. Additionally, the concept of optical types, vegetation exhibiting contrasting optical behavior in time and space, is explored as a way to frame our understanding of the controls on surface-atmosphere fluxes. Complementary NDVI and PRI patterns across ecosystems are offered as an example of this hypothesis, with the LUE model and light-response curve providing an integrating framework. We conclude that experimental approaches allowing systematic exploration of plant optical behavior in the context of the flux tower network provides a unique way to improve our understanding of environmental constraints and

  20. Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions

    PubMed Central

    Menigatti, M; Staiano, T; Manser, C N; Bauerfeind, P; Komljenovic, A; Robinson, M; Jiricny, J; Buffoli, F; Marra, G

    2013-01-01

    Epigenetic silencing of protein-encoding genes is common in early-stage colorectal tumorigenesis. Less is known about the methylation-mediated silencing of genes encoding microRNAs (miRNAs), which are also important epigenetic modulators of gene expression. Using quantitative PCR, we identified 56 miRNAs that were expressed in normal colorectal mucosa and in HT29 colorectal cancer cells treated with demethylating agents but not in untreated HT29 cells, suggesting that they probably undergo methylation-induced silencing during colorectal tumorigenesis. One of these, miR-195, had recently been reported to be underexpressed in colorectal cancers and to exert tumor-suppressor effects in colorectal cancer cells. We identified the transcription start site (TSS) for primary miRNA (pri-miR)-497/195, the primary precursor that yields miR-195 and another candidate on our list, miR-497, and a single CpG island upstream to the TSS, which controls expression of both miRNAs. Combined bisulfite restriction analysis and bisulfite genomic sequencing studies revealed monoallelic methylation of this island in normal colorectal mucosa (50/50 samples) and full methylation in most colorectal adenomas (38/50; 76%). The hypermethylated precancerous lesions displayed significantly downregulated expression of both miRNAs. Similar methylation patterns were observed at two known imprinted genes, MEG3 and GNAS-AS1, which encode several of the 56 miRNAs on our list. Imprinting at these loci was lost in over half the adenomas (62% at MEG3 and 52% at GNAS-AS1). Copy-number alterations at MEG3, GNAS-AS1 and pri-miR-497/195, which are frequent in colorectal cancers, were less common in adenomas and confined to tumors displaying differential methylation at the involved locus. Our data show that somatically acquired, epigenetic changes at monoallelically methylated regions encoding miRNAs are relatively frequent in sporadic colorectal adenomas and might contribute to the onset and progression of

  1. Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions.

    PubMed

    Menigatti, M; Staiano, T; Manser, C N; Bauerfeind, P; Komljenovic, A; Robinson, M; Jiricny, J; Buffoli, F; Marra, G

    2013-01-01

    Epigenetic silencing of protein-encoding genes is common in early-stage colorectal tumorigenesis. Less is known about the methylation-mediated silencing of genes encoding microRNAs (miRNAs), which are also important epigenetic modulators of gene expression. Using quantitative PCR, we identified 56 miRNAs that were expressed in normal colorectal mucosa and in HT29 colorectal cancer cells treated with demethylating agents but not in untreated HT29 cells, suggesting that they probably undergo methylation-induced silencing during colorectal tumorigenesis. One of these, miR-195, had recently been reported to be underexpressed in colorectal cancers and to exert tumor-suppressor effects in colorectal cancer cells. We identified the transcription start site (TSS) for primary miRNA (pri-miR)-497/195, the primary precursor that yields miR-195 and another candidate on our list, miR-497, and a single CpG island upstream to the TSS, which controls expression of both miRNAs. Combined bisulfite restriction analysis and bisulfite genomic sequencing studies revealed monoallelic methylation of this island in normal colorectal mucosa (50/50 samples) and full methylation in most colorectal adenomas (38/50; 76%). The hypermethylated precancerous lesions displayed significantly downregulated expression of both miRNAs. Similar methylation patterns were observed at two known imprinted genes, MEG3 and GNAS-AS1, which encode several of the 56 miRNAs on our list. Imprinting at these loci was lost in over half the adenomas (62% at MEG3 and 52% at GNAS-AS1). Copy-number alterations at MEG3, GNAS-AS1 and pri-miR-497/195, which are frequent in colorectal cancers, were less common in adenomas and confined to tumors displaying differential methylation at the involved locus. Our data show that somatically acquired, epigenetic changes at monoallelically methylated regions encoding miRNAs are relatively frequent in sporadic colorectal adenomas and might contribute to the onset and progression of

  2. Combined mixed approach algorithm for in-line phase-contrast x-ray imaging

    SciTech Connect

    De Caro, Liberato; Scattarella, Francesco; Giannini, Cinzia; Tangaro, Sabina; Rigon, Luigi; Longo, Renata; Bellotti, Roberto

    2010-07-15

    Purpose: In the past decade, phase-contrast imaging (PCI) has been applied to study different kinds of tissues and human body parts, with an increased improvement of the image quality with respect to simple absorption radiography. A technique closely related to PCI is phase-retrieval imaging (PRI). Indeed, PCI is an imaging modality thought to enhance the total contrast of the images through the phase shift introduced by the object (human body part); PRI is a mathematical technique to extract the quantitative phase-shift map from PCI. A new phase-retrieval algorithm for the in-line phase-contrast x-ray imaging is here proposed. Methods: The proposed algorithm is based on a mixed transfer-function and transport-of-intensity approach (MA) and it requires, at most, an initial approximate estimate of the average phase shift introduced by the object as prior knowledge. The accuracy in the initial estimate determines the convergence speed of the algorithm. The proposed algorithm retrieves both the object phase and its complex conjugate in a combined MA (CMA). Results: Although slightly less computationally effective with respect to other mixed-approach algorithms, as two phases have to be retrieved, the results obtained by the CMA on simulated data have shown that the obtained reconstructed phase maps are characterized by particularly low normalized mean square errors. The authors have also tested the CMA on noisy experimental phase-contrast data obtained by a suitable weakly absorbing sample consisting of a grid of submillimetric nylon fibers as well as on a strongly absorbing object made of a 0.03 mm thick lead x-ray resolution star pattern. The CMA has shown a good efficiency in recovering phase information, also in presence of noisy data, characterized by peak-to-peak signal-to-noise ratios down to a few dBs, showing the possibility to enhance with phase radiography the signal-to-noise ratio for features in the submillimetric scale with respect to the attenuation

  3. Ruthenium chalcogenonitrosyl and bridged nitrido complexes containing chelating sulfur and oxygen ligands.

    PubMed

    Ng, Ho-Yuen; Cheung, Wai-Man; Kwan Huang, Enrique; Wong, Kang-Long; Sung, Herman H-Y; Williams, Ian D; Leung, Wa-Hung

    2015-11-14

    Ruthenium thio- and seleno-nitrosyl complexes containing chelating sulfur and oxygen ligands have been synthesised and their de-chalcogenation reactions have been studied. The reaction of mer-[Ru(N)Cl3(AsPh3)2] with elemental sulfur and selenium in tetrahydrofuran at reflux afforded the chalcogenonitrosyl complexes mer-[Ru(NX)Cl3(AsPh3)2] [X = S (1), Se (2)]. Treatment of 1 with KN(R2PS)2 afforded trans-[Ru(NS)Cl{N(R2PS)2}2] [R = Ph (3), Pr(i) (4), Bu(t) (5)]. Alternatively, the thionitrosyl complex 5 was obtained from [Bu(n)4N][Ru(N)Cl4] and KN(Bu(t)2PS)2, presumably via sulfur atom transfer from [N(Bu(t)2PS)2](-) to the nitride. Reactions of 1 and 2 with NaLOEt (LOEt(-) = [Co(η(5)-C5H5){P(O)(LOEt)2}3](-)) gave [Ru(NX)LOEtCl2] (X = S (8), Se (9)). Treatment of [Bu(n)4N][Ru(N)Cl4] with KN(R2PS)2 produced Ru(IV)-Ru(IV)μ-nitrido complexes [Ru2(μ-N){N(R2PS)2}4Cl] [R = Ph (6), Pr(i) (7)]. Reactions of 3 and 9 with PPh3 afforded 6 and [Ru(NPPh3)LOEtCl2], respectively. The desulfurisation of 5 with [Ni(cod)2] (cod = 1,5-cyclooctadiene) gave the mixed valance Ru(III)-Ru(IV)μ-nitrido complex [Ru2(μ-N){N(Bu(t)2PS)2}4] (10) that was oxidised by [Cp2Fe](PF6) to give the Ru(IV)-Ru(IV) complex [Ru2(μ-N){N(Bu(t)2PS)2}4](PF6) ([10]PF6). The crystal structures of 1, 2, 3, 7, 9 and 10 have been determined. PMID:26442594

  4. Fine Pathogen Discrimination within the APL1 Gene Family Protects Anopheles gambiae against Human and Rodent Malaria Species

    PubMed Central

    Mitri, Christian; Jacques, Jean-Claude; Thiery, Isabelle; Riehle, Michelle M.; Xu, Jiannong; Bischoff, Emmanuel; Morlais, Isabelle; Nsango, Sandrine E.; Vernick, Kenneth D.; Bourgouin, Catherine

    2009-01-01

    Genetically controlled resistance of Anopheles gambiae mosquitoes to Plasmodium falciparum is a common trait in the natural population, and a cluster of natural resistance loci were mapped to the Plasmodium-Resistance Island (PRI) of the A. gambiae genome. The APL1 family of leucine-rich repeat (LRR) proteins was highlighted by candidate gene studies in the PRI, and is comprised of paralogs APL1A, APL1B and APL1C that share ≥50% amino acid identity. Here, we present a functional analysis of the joint response of APL1 family members during mosquito infection with human and rodent Plasmodium species. Only paralog APL1A protected A. gambiae against infection with the human malaria parasite P. falciparum from both the field population and in vitro culture. In contrast, only paralog APL1C protected against the rodent malaria parasites P. berghei and P. yoelii. We show that anti-P. falciparum protection is mediated by the Imd/Rel2 pathway, while protection against P. berghei infection was shown to require Toll/Rel1 signaling. Further, only the short Rel2-S isoform and not the long Rel2-F isoform of Rel2 confers protection against P. falciparum. Protection correlates with the transcriptional regulation of APL1A by Rel2-S but not Rel2-F, suggesting that the Rel2-S anti-parasite phenotype results at least in part from its transcriptional control over APL1A. These results indicate that distinct members of the APL1 gene family display a mutually exclusive protective effect against different classes of Plasmodium parasites. It appears that a gene-for-pathogen-class system orients the appropriate host defenses against distinct categories of similar pathogens. It is known that insect innate immune pathways can distinguish between grossly different microbes such as Gram-positive bacteria, Gram-negative bacteria, or fungi, but the function of the APL1 paralogs reveals that mosquito innate immunity possesses a more fine-grained capacity to distinguish between classes of closely

  5. Large and Small Scale Nitrogen and Phosporous Manipulation Experiment in a Tree-Grass Ecosystem: first year of results

    NASA Astrophysics Data System (ADS)

    Migliavacca, Mirco; Perez Priego, Oscar; El-Madany, Tarek; Guan, JinHong; Carrara, Arnaud; Fava, Francesco; Moreno, Gerardo; Kolle, Olaf; Rossini, Micol; Schrumpf, Marion; Julitta, Tommaso; Reichstein, Markus

    2015-04-01

    Recent studies have shown how human induced N/P imbalances affect essential ecosystem processes (e.g. photosynthesis, plant growth rate, respiration), and might be particularly important in water-limited ecosystems. In this contribution we will present the experimental design and the results of the first year of two nutrient manipulation experiments conducted at different spatial scale. In the first experiment a cluster of 2 eddy covariance (EC) flux towers has been set up beside a long-term EC site (Las Majadas del Tietar, Spain). Sites are selected in a way to have similar nutrient conditions, canopy structure, and stoichiometry of the different vegetation and soil pools. Two of the three footprints will be manipulated with addition of N and NP fertilizer at the beginning of 2015. The comparison of the three EC flux towers installed during the first year of the experiment (without fertilization) will be shown. We characterized the differences of the responses of carbon and water fluxes measured by the EC systems to environmental drivers, and structural and biophysical properties of the canopy. The second experiment was conducted over a Mediterranean grassland, where 16 plots of 10x10 meters that were manipulated by adding nutrient (N, P, and NP). The overall objective was to investigate the response of the gross primary productivity (GPP), assessed by using transparent transient-state canopy chambers, to different nutrient availability. The second objective was to evaluate the capability of hyperspectral data and Solar induced fluorescence to track short- and long-term GPP and light use efficiency variation under different N and P fertilization treatments. Spectral vegetation indices (VIs) were acquired manually using high resolution spectrometers (HR4000, OceanOptics, USA) along a phenological cycle. The VIs used included photochemical reflectance index (PRI), MERIS terrestrial-chlorophyll index (MTCI) and normalized difference vegetation index (NDVI). Solar

  6. Endogenous target mimics down-regulate miR160 mediation of ARF10, -16, and -17 cleavage during somatic embryogenesis in Dimocarpus longan Lour

    PubMed Central

    Lin, Yuling; Lai, Zhongxiong; Tian, Qilin; Lin, Lixia; Lai, Ruilian; Yang, Manman; Zhang, Dongmin; Chen, Yukun; Zhang, Zihao

    2015-01-01

    MicroRNA160 plays a critical role in plant development by negatively regulating the auxin response factors ARF10, -16, and -17. However, the ways in which miR160 expression is regulated at the transcriptional level, and how miR160 interacts with its targets during plant embryo development, remain unknown. Here, we studied the regulatory relationships among endogenous target mimics (eTMs), and miR160 and its targets, and their involvement in hormone signaling and somatic embryogenesis (SE) in Dimocarpus longan. We identified miR160 family members and isolated the miR160 precursor, primary transcript, and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, abscisic acid, salicylic acid (SA) and heat stress. The pri-miR160 was down-regulated in response to SA but up-regulated by gibberellic acid, ethylene, and methyl jasmonate treatment, suggesting that pri-miR160 was associated with hormone transduction. Dlo-miR160a, -a∗ and -d∗ reached expression peaks in torpedo-shaped embryos, globular embryos and cotyledonary embryos, respectively, but were barely detectable in friable-embryogenic callus. This suggests that they have expression-related and functional diversity, especially during the middle and later developmental stages of SE. Four potential eTMs for miR160 were identified. Two of them, glucan endo-1,3-beta- glucosidase-like protein 2-like and calpain-type cysteine protease DEK1, were confirmed to control the corresponding dlo-miR160a∗ expression level. This suggests that they may function to abolish the binding between dlo-miR160a∗ and its targets. These two eTMs also participated in 2,4-D and ABA signal transduction. DlARF10, -16, and -17 targeting by dlo-miR160a was confirmed; their expression levels were higher in friable-embryogenic callus and incomplete compact pro-embryogenic cultures and responded to 2,4-D, suggesting they may play a major role in the early stages of longan SE dependent on 2,4-D. The eTMs, mi

  7. Molecular characterization of a CpTRIM35-like protein and its splice variants from whitespotted bamboo shark (Chiloscyllium plagiosum)

    SciTech Connect

    Zhang, Xinshang Zhao, Heng Chen, Yeyu Luo, Huiying Yao, Bin

    2014-10-24

    Highlights: • A TRIM gene and three splice variants were firstly cloned from elasmobranch fish. • The genes were constitutively expressed with high levels in spleen and kidney. • The gene products were distributed in cytoplasm alone or cytoplasm and nucleus. • As E3 ubiquitin ligases, the proteins differed in immune responses to challenges. - Abstract: The tripartite motif (TRIM) proteins play important roles in a broad range of biological processes, including apoptosis, cell proliferation and innate immunity response. In this study, a TRIM gene and its three splice variants were cloned from an elasmobranch fish—whitespotted bamboo shark (Chiloscyllium plagiosum Bennett). Phylogenetic analysis indicated that the gene was closely related to TRIM35 homologs, thus termed CpTRIM35-like. Deduced CpTRIM35 has a RBCC-PRY/SPRY structure typical of TRIM proteins, and its splice variants (CpTRIM35-1–3) have different truncations at the C-terminus. The gene products were constitutively expressed in adult sharks with the highest levels in spleen and kidney. The different subcellular locations, upregulation upon LPS and poly I:C stimulation, and significant E3 ubiquitin ligase activities suggested their different roles in immune responses as an E3 ubiquitin ligase. This is the first TRIM protein ever characterized in elasmobranch fish.

  8. Image spectroscopy and stable isotopes elucidate functional dissimilarity between native and nonnative plant species in the aquatic environment.

    PubMed

    Santos, Maria J; Hestir, Erin L; Khanna, Shruti; Ustin, Susan L

    2012-02-01

    • Nonnative species may change ecosystem functionality at the expense of native species. Here, we examine the similarity of functional traits of native and nonnative submersed aquatic plants (SAP) in an aquatic ecosystem. • We used field and airborne imaging spectroscopy and isotope ratios of SAP species in the Sacramento-San Joaquin Delta, California (USA) to assess species identification, chlorophyll (Chl) concentration, and differences in photosynthetic efficiency. • Spectral separability between species occurs primarily in the visible and near-infrared spectral regions, which is associated with morphological and physiological differences. Nonnatives had significantly higher Chl, carotene, and anthocyanin concentrations than natives and had significantly higher photochemical reflectance index (PRI) and δ(13) C values. • Results show nonnative SAPs are functionally dissimilar to native SAPs, having wider leaf blades and greater leaf area, dense and evenly distributed vertical canopies, and higher pigment concentrations. Results suggest that nonnatives also use a facultative C(4) -like photosynthetic pathway, allowing efficient photosynthesis in high-light and low-light environments. Differences in plant functionality indicate that nonnative SAPs have a competitive advantage over native SAPs as a result of growth form and greater light-use efficiency that promotes growth under different light conditions, traits affecting system-wide species distributions and community composition. PMID:22126662

  9. Effects of a student pharmacist consultation on patient knowledge and attitudes about vaccines.

    PubMed

    Chou, Tony I-Fan; Lash, David Benjamin; Malcolm, Benjamin; Yousify, Layla; Quach, Julie Yennhi; Dong, Sandy; Yu, Junhua

    2014-01-01

    OBJECTIVE To measure the impact of student pharmacists' consultation on participant knowledge and attitudes about influenza and tetanus-diphtheria-acellular pertussis (Tdap) vaccines. DESIGN Pre- and post-consultation surveys. SETTING Free health care service and immunization clinics in Vallejo and Martinez, CA. PARTICIPANTS Children and adults 13 years of age or older. INTERVENTION A convenience sample of participants completed a preintervention survey (PrIs) on basic vaccine knowledge and attitudes. Student pharmacists then delivered the intervention, which consisted of a 5-minute consultation on vaccines. A postintervention (PoIs) survey was administered immediately after the intervention. MAIN OUTCOME MEASURES Cumulative scores for eight knowledge-based questions and four attitude-based questions. RESULTS 198 participants completed both PrIs and PoIs. Compared with the PrI scores, the PoI scores showed significant improvement in basic vaccine knowledge and attitudes toward receiving vaccinations. Participants also were more likely to view pharmacists as a source of information about vaccines after the intervention. Student pharmacists administered 109 total vaccinations during the study, including 68 influenza vaccinations and 41 Tdap vaccinations. CONCLUSION A short, 5-minute consultation by a student pharmacist may increase vaccination rates and help serve as a vehicle to change the public's view of vaccines as well as pharmacists and their role in primary and preventive care. PMID:24632928

  10. Mannotriose regulates learning and memory signal transduction in the hippocampus

    PubMed Central

    Zhang, Lina; Dai, Weiwei; Zhang, Xueli; Gong, Zhangbin; Jin, Guoqin

    2013-01-01

    Rehmannia is a commonly used Chinese herb, which improves learning and memory. However, the crucial components of the signal transduction pathway associated with this effect remain elusive. Pri-mary hippocampal neurons were cultured in vitro, insulted with high-concentration (1 × 10−4 mol/L) cor-ticosterone, and treated with 1 × 10−4 mol/L mannotriose. Thiazolyl blue tetrazolium bromide assay and western blot analysis showed that hippocampal neuron survival rates and protein levels of glucocorti-coid receptor, serum and glucocorticoid-regulated protein kinase, and brain-derived neurotrophic factor were all dramatically decreased after high-concentration corticosterone-induced injury. This effect was reversed by mannotriose, to a similar level as RU38486 and donepezil. Our findings indicate that mannotriose could protect hippocampal neurons from high-concentration corticosterone-induced injury. The mechanism by which this occurred was associated with levels of glucocorticoid receptor protein, serum and glucocorticoid-regulated protein kinase, and brain-derived neurotrophic factor. PMID:25206622

  11. Identification of metastasis-associated genes in colorectal cancer through an integrated genomic and transcriptomic analysis

    PubMed Central

    Peng, Sihua

    2013-01-01

    Objective Identification of colorectal cancer (CRC) metastasis genes is one of the most important issues in CRC research. For the purpose of mining CRC metastasis-associated genes, an integrated analysis of microarray data was presented, by combined with evidence acquired from comparative genomic hybridization (CGH) data. Methods Gene expression profile data of CRC samples were obtained at Gene Expression Omnibus (GEO) website. The 15 important chromosomal aberration sites detected by using CGH technology were used for integrated genomic and transcriptomic analysis. Significant Analysis of Microarray (SAM) was used to detect significantly differentially expressed genes across the whole genome. The overlapping genes were selected in their corresponding chromosomal aberration regions, and analyzed by using the Database for Annotation, Visualization and Integrated Discovery (DAVID). Finally, SVM-T-RFE gene selection algorithm was applied to identify metastasis-associated genes in CRC. Results A minimum gene set was obtained with the minimum number [14] of genes, and the highest classification accuracy (100%) in both PRI and META datasets. A fraction of selected genes are associated with CRC or its metastasis. Conclusions Our results demonstrated that integration analysis is an effective strategy for mining cancer-associated genes. PMID:24385689

  12. The Escherichia coli UvrD helicase is essential for Tus removal during recombination-dependent replication restart from Ter sites.

    PubMed

    Bidnenko, Vladimir; Lestini, Roxane; Michel, Bénédicte

    2006-10-01

    Blocking replication forks in the Escherichia coli chromosome by ectopic Ter sites renders the RecBCD pathway of homologous recombination and SOS induction essential for viability. In this work, we show that the E. coli helicase II (UvrD) is also essential for the growth of cells where replication forks are arrested at ectopic Ter sites. We propose that UvrD is required for Tus removal from Ter sites. The viability of a SOS non-inducible Ter-blocked strain is fully restored by the expression of the two SOS-induced proteins UvrD and RecA at high level, indicating that these are the only two SOS-induced proteins required for replication across Ter/Tus complexes. Several observations suggest that UvrD acts in concert with homologous recombination and we propose that UvrD is associated with recombination-initiated replication forks and that it removes Tus when a PriA-dependent, restarted replication fork goes across the Ter/Tus complex. Finally, expression of the UvrD homologue from Bacilus subtilis PcrA restores the growth of uvrD-deficient Ter-blocked cells, indicating that the capacity to dislodge Tus is conserved in this distant bacterial species. PMID:17020578

  13. Unwinding of forked DNA structures by UvrD.

    PubMed

    Cadman, Chris J; Matson, Steven W; McGlynn, Peter

    2006-09-01

    Many studies have demonstrated the need for processing of blocked replication forks to underpin genome duplication. UvrD helicase in Escherichia coli has been implicated in the processing of damaged replication forks, or the recombination intermediates formed from damaged forks. Here we show that UvrD can unwind forked DNA structures, in part due to the ability of UvrD to initiate unwinding from discontinuities within the phosphodiester backbone of DNA. UvrD does therefore have the capacity to target DNA intermediates of replication and recombination. Such an activity resulted in unwinding of what would be the parental duplex DNA ahead of either a stalled replication fork or a D-loop formed by recombination. However, UvrD had a substrate preference for fork structures having a nascent lagging strand at the branch point but no leading strand. Furthermore, at such structures the polarity of UvrD altered so that unwinding of the lagging strand predominated. This reaction is reminiscent of the PriC-Rep pathway of replication restart, suggesting that UvrD and Rep may have at least partially redundant functions. PMID:16890954

  14. Measurement of SOS expression in individual Escherichia coli K-12 cells using fluorescence microscopy.

    PubMed

    McCool, Jesse D; Long, Edward; Petrosino, Joseph F; Sandler, Hilary A; Rosenberg, Susan M; Sandler, Steven J

    2004-09-01

    Many recombination, DNA repair and DNA replication mutants have high basal levels of SOS expression as determined by a sulAp-lacZ reporter gene system on a population of cells. Two opposing models to explain how the SOS expression is distributed in these cells are: (i) the 'Uniform Expression Model (UEM)' where expression is evenly distributed in all cells or (ii) the 'Two Population Model (TPM)' where some cells are highly induced while others are not at all. To distinguish between these two models, a method to quantify SOS expression in individual bacterial cells was developed by fusing an SOS promoter (sulAp) to the green fluorescent protein (gfp) reporter gene and inserting it at attlambda on the Escherichia coli chromosome. It is shown that the fluorescence in sulAp-gfp cells is regulated by RecA and LexA. This system was then used to distinguish between the two models for several mutants. The patterns displayed by priA, dnaT, recG, uvrD, dam, ftsK, rnhA, polA and xerC mutants were explained best by the TPM while only lexA (def), lexA3 (ind-) and recA defective mutants were explained best by the UEM. These results are discussed in a context of how the processes of DNA replication and recombination may affect cells in a population differentially. PMID:15387814

  15. Genetic analysis of Escherichia coli RadA: functional motifs and genetic interactions.

    PubMed

    Cooper, Deani L; Boyle, Daniel C; Lovett, Susan T

    2015-03-01

    The RadA/Sms protein is a RecA-related protein found universally in eubacteria and plants, implicated in processing of recombination intermediates. Here we show that the putative Zn finger, Walker A motif, KNRXG motif and Lon protease homology domain of the Escherichia coli RadA protein are required for DNA damage survival. RadA is unlikely to possess protease activity as the putative active site serine is not required. Mutants in RadA have strong synergistic phenotypes with those in the branch migration protein RecG. Sensitivity of radA recG mutants to azidothymidine (AZT) can be rescued by blocking recombination with recA or recF mutations or by overexpression of RuvAB, suggesting that lethal recombination intermediates accumulate in the absence of RadA and RecG. Synthetic genetic interactions for survival to AZT or ciprofloxacin exposure were observed between RadA and known or putative helicases including DinG, Lhr, PriA, Rep, RuvAB, UvrD, YejH and YoaA. These represent the first affected phenotypes reported for Lhr, YejH and YoaA. The specificity of these effects sheds new light on the role of these proteins in DNA damage avoidance and repair and implicates a role in replication gap processing for DinG and YoaA and a role in double-strand break repair for YejH. PMID:25484163

  16. Quantification of mature microRNAs using pincer probes and real-time PCR amplification.

    PubMed

    Huang, Tinghua; Yang, Jun; Liu, Guopin; Jin, Wei; Liu, Zhi; Zhao, Shuhong; Yao, Min

    2015-01-01

    The robust and reliable detection of small microRNAs (miRNAs) is important to understand the functional significance of miRNAs. Several methods can be used to quantify miRNAs. Selectively quantifying mature miRNAs among miRNA precursors, pri-miRNAs, and other miRNA-like sequences is challenging because of the short length of miRNAs. In this study, we developed a two-step miRNA quantification system based on pincer probe capture and real-time PCR amplification. The performance of the method was tested using synthetic mature miRNAs and clinical RNA samples. Results showed that the method demonstrated dynamic range of seven orders of magnitude and sensitivity of detection of hundreds of copies of miRNA molecules. The use of pincer probes allowed excellent discrimination of mature miRNAs from their precursors with five Cq (quantification cycle) values difference. The developed method also showed good discrimination of highly homologous family members with cross reaction less than 5%. The pincer probe-based approach is a potential alternative to currently used methods for mature miRNA quantification. PMID:25768430

  17. Cesium Toxicity Alters MicroRNA Processing and AGO1 Expressions in Arabidopsis thaliana.

    PubMed

    Jung, Il Lae; Ryu, Moonyoung; Cho, Seok Keun; Shah, Pratik; Lee, Ju Hye; Bae, Hansol; Kim, In Gyu; Yang, Seong Wook

    2015-01-01

    MicroRNAs (miRNAs) are short RNA fragments that play important roles in controlled gene silencing, thus regulating many biological processes in plants. Recent studies have indicated that plants modulate miRNAs to sustain their survival in response to a variety of environmental stimuli, such as biotic stresses, cold, drought, nutritional starvation, and toxic heavy metals. Cesium and radio-cesium contaminations have arisen as serious problems that both impede plant growth and enter the food chain through contaminated plants. Many studies have been performed to define plant responses against cesium intoxication. However, the complete profile of miRNAs in plants during cesium intoxication has not been established. Here we show the differential expression of the miRNAs that are mostly down-regulated during cesium intoxication. Furthermore, we found that cesium toxicity disrupts both the processing of pri-miRNAs and AGONOUTE 1 (AGO1)-mediated gene silencing. AGO 1 seems to be especially destabilized by cesium toxicity, possibly through a proteolytic regulatory pathway. Our study presents a comprehensive profile of cesium-responsive miRNAs, which is distinct from that of potassium, and suggests two possible mechanisms underlying the cesium toxicity on miRNA metabolism. PMID:25946015

  18. Stonefish toxin defines an ancient branch of the perforin-like superfamily

    PubMed Central

    Ellisdon, Andrew M.; Reboul, Cyril F.; Huynh, Kitmun; Oellig, Christine A.; Winter, Kelly L.; Hodgson, Wayne C.; Seymour, Jamie; Dearden, Peter K.; Tweten, Rodney K.; Whisstock, James C.; McGowan, Sheena

    2015-01-01

    The lethal factor in stonefish venom is stonustoxin (SNTX), a heterodimeric cytolytic protein that induces cardiovascular collapse in humans and native predators. Here, using X-ray crystallography, we make the unexpected finding that SNTX is a pore-forming member of an ancient branch of the Membrane Attack Complex-Perforin/Cholesterol-Dependent Cytolysin (MACPF/CDC) superfamily. SNTX comprises two homologous subunits (α and β), each of which comprises an N-terminal pore-forming MACPF/CDC domain, a central focal adhesion-targeting domain, a thioredoxin domain, and a C-terminal tripartite motif family-like PRY SPla and the RYanodine Receptor immune recognition domain. Crucially, the structure reveals that the two MACPF domains are in complex with one another and arranged into a stable early prepore-like assembly. These data provide long sought after near-atomic resolution insights into how MACPF/CDC proteins assemble into prepores on the surface of membranes. Furthermore, our analyses reveal that SNTX-like MACPF/CDCs are distributed throughout eukaryotic life and play a broader, possibly immune-related function outside venom. PMID:26627714

  19. Cesium Toxicity Alters MicroRNA Processing and AGO1 Expressions in Arabidopsis thaliana

    PubMed Central

    Cho, Seok Keun; Shah, Pratik; Lee, Ju Hye; Bae, Hansol; Kim, In Gyu; Yang, Seong Wook

    2015-01-01

    MicroRNAs (miRNAs) are short RNA fragments that play important roles in controlled gene silencing, thus regulating many biological processes in plants. Recent studies have indicated that plants modulate miRNAs to sustain their survival in response to a variety of environmental stimuli, such as biotic stresses, cold, drought, nutritional starvation, and toxic heavy metals. Cesium and radio-cesium contaminations have arisen as serious problems that both impede plant growth and enter the food chain through contaminated plants. Many studies have been performed to define plant responses against cesium intoxication. However, the complete profile of miRNAs in plants during cesium intoxication has not been established. Here we show the differential expression of the miRNAs that are mostly down-regulated during cesium intoxication. Furthermore, we found that cesium toxicity disrupts both the processing of pri-miRNAs and AGONOUTE 1 (AGO1)-mediated gene silencing. AGO 1 seems to be especially destabilized by cesium toxicity, possibly through a proteolytic regulatory pathway. Our study presents a comprehensive profile of cesium-responsive miRNAs, which is distinct from that of potassium, and suggests two possible mechanisms underlying the cesium toxicity on miRNA metabolism. PMID:25946015

  20. Fetal Bovine Collagen Matrix in the Treatment of a Full Thickness Burn Wound: A Case Report With Long-Term Follow-Up

    PubMed Central

    Strong, Amy L.; Bennett, Danielle K.; Spreen, Elizabeth B.; Adhvaryu, Dhaval V.; Littleton, Jeffrey C.

    2016-01-01

    The treatment of full thickness skin wounds commonly associated with large burns continues to represent a challenging clinical entity. The current treatment for large TBSA burns is split thickness autologous skin grafting; however, this treatment often results in poor textural durability, hypertrophic scarring, and fibrotic contractures. In this case report, we describe our experience and long-term follow-up results after the application of fetal bovine collagen (FBC) matrix (PriMatrix, TEI Biosciences, Boston, MA) to burn wounds clinically assessed as full thickness that healed without the need for subsequent skin grafting. The patient presented with 25% TBSA burns and was debrided and covered with FBC on postburn day 7. By postoperative day 12, the patient had large areas of reepithelialization distributed throughout the wound bed. By postoperative day 26, the patient had significantly more areas of wound closure and was discharged. Reepithelialization and repigmentation continued, and long-term follow-up after 26 months demonstrated complete reepithelialization and nearly complete repigmentation, without the appearance of contractures or hypertrophic scarring. This case report highlights the use of FBC as a scaffold capable of dermal regeneration and spontaneous reepithelialization with an excellent long-term functional and cosmetic outcome. PMID:25494213

  1. Fetal Bovine Collagen Matrix in the Treatment of a Full Thickness Burn Wound: A Case Report With Long-Term Follow-Up.

    PubMed

    Strong, Amy L; Bennett, Danielle K; Spreen, Elizabeth B; Adhvaryu, Dhaval V; Littleton, Jeffrey C; Mencer, Ernest J

    2016-01-01

    The treatment of full thickness skin wounds commonly associated with large burns continues to represent a challenging clinical entity. The current treatment for large TBSA burns is split thickness autologous skin grafting; however, this treatment often results in poor textural durability, hypertrophic scarring, and fibrotic contractures. In this case report, we describe our experience and long-term follow-up results after the application of fetal bovine collagen (FBC) matrix (PriMatrix, TEI Biosciences, Boston, MA) to burn wounds clinically assessed as full thickness that healed without the need for subsequent skin grafting. The patient presented with 25% TBSA burns and was debrided and covered with FBC on postburn day 7. By postoperative day 12, the patient had large areas of reepithelialization distributed throughout the wound bed. By postoperative day 26, the patient had significantly more areas of wound closure and was discharged. Reepithelialization and repigmentation continued, and long-term follow-up after 26 months demonstrated complete reepithelialization and nearly complete repigmentation, without the appearance of contractures or hypertrophic scarring. This case report highlights the use of FBC as a scaffold capable of dermal regeneration and spontaneous reepithelialization with an excellent long-term functional and cosmetic outcome. PMID:25494213

  2. Spaceflight-induced variation on biological traits and effective components of Cassia obtusifolia.

    PubMed

    Mao, Ren-jun; Qi, Zhi-hong; Han, Rui-lian; Liu, Feng-hua; Liu, Yan; Liang, Zong-suo

    2015-07-01

    The dry seeds of Cassia obtusifolia were carried by the "ShenZhou 8" satellite and sowed after landing. Based on our pri- or study on SP1, the characteristics of plants growth, physiological index and content of effective components were examined. The results showed that the QC10, QC29 strains matured 5 d earlier compared with control. The plant height, across diameter and ground diameter of QC10, QC29, QC46 strains was superior to the control at whole growth period. The branch number increased ranging from 4 to 11 and the number of pods reached 321, 313,281, respectively, which was dramatically higher than the control (246). The yield of QC10, QC29, QC46 strains increased noticeably from 31.4 to 63.2 g. The 1000-seed-weight of QC10, QC29, QC46 strains was 25.86, 25.88, 24.06 g, while the control was 23.69 g. Compared to the control, the mass fraction of chlorophyll was enhanced 1.098, 1.016, 0.297 mg. There was no significant difference in aurantio-obtusin and chrysophanol content of seeds. Through two years research, three high-yield mutant strains were obtained. This study indicates that spaceflight-induced mutants could provide new germplasm for C. obtusifolia breeding and offers the theoretical basis for further utilization of spaceflight-induced mutation to breed high-quality C. obtusifolia strains. PMID:26697680

  3. HNRNPA2B1 Is a Mediator of m(6)A-Dependent Nuclear RNA Processing Events.

    PubMed

    Alarcón, Claudio R; Goodarzi, Hani; Lee, Hyeseung; Liu, Xuhang; Tavazoie, Saeed; Tavazoie, Sohail F

    2015-09-10

    N(6)-methyladenosine (m(6)A) is the most abundant internal modification of messenger RNA. While the presence of m(6)A on transcripts can impact nuclear RNA fates, a reader of this mark that mediates processing of nuclear transcripts has not been identified. We find that the RNA-binding protein HNRNPA2B1 binds m(6)A-bearing RNAs in vivo and in vitro and its biochemical footprint matches the m(6)A consensus motif. HNRNPA2B1 directly binds a set of nuclear transcripts and elicits similar alternative splicing effects as the m(6)A writer METTL3. Moreover, HNRNPA2B1 binds to m(6)A marks in a subset of primary miRNA transcripts, interacts with the microRNA Microprocessor complex protein DGCR8, and promotes primary miRNA processing. Also, HNRNPA2B1 loss and METTL3 depletion cause similar processing defects for these pri-miRNA precursors. We propose HNRNPA2B1 to be a nuclear reader of the m(6)A mark and to mediate, in part, this mark's effects on primary microRNA processing and alternative splicing. PAPERCLIP. PMID:26321680

  4. Composition dependence of charge and magnetic length scales in mixed valence manganite thin films

    NASA Astrophysics Data System (ADS)

    Singh, Surendra; Freeland, J. W.; Fitzsimmons, M. R.; Jeen, H.; Biswas, A.

    2016-07-01

    Mixed-valence manganese oxides present striking properties like the colossal magnetoresistance, metal-insulator transition (MIT) that may result from coexistence of ferromagnetic, metallic and insulating phases. Percolation of such phase coexistence in the vicinity of MIT leads to first-order transition in these manganites. However the length scales over which the electronic and magnetic phases are separated across MIT which appears compelling for bulk systems has been elusive in (La1‑yPry)1‑xCaxMnO3 films. Here we show the in-plane length scale over which charge and magnetism are correlated in (La0.4Pr0.6)1‑xCaxMnO3 films with x = 0.33 and 0.375, across the MIT temperature. We combine electrical transport (resistance) measurements, x-ray absorption spectroscopy (XAS), x-ray magnetic circular dichroism (XMCD), and specular/off-specular x-ray resonant magnetic scattering (XRMS) measurements as a function of temperature to elucidate relationships between electronic, magnetic and morphological structure of the thin films. Using off-specular XRMS we obtained the charge-charge and charge-magnetic correlation length of these LPCMO films across the MIT. We observed different charge-magnetic correlation length for two films which increases below the MIT. The different correlation length shown by two films may be responsible for different macroscopic (transport and magnetic) properties.

  5. Colossal piezoresistance in manganites.

    NASA Astrophysics Data System (ADS)

    Tosado, Jacob; Lopez, Josymir; Dhakal, Tara; Biswas, Amlan

    2007-03-01

    We have studied the effect of the application of direct mechanical stress on thin films of the hole-doped manganese oxide (manganite) (La1-yPry)1-xCaxMnO3 (LPCMO). The two competing phases in manganites are the pseudocubic ferromagnetic metallic (FMM) phase and the orthorhombic charge-ordered insulating (COI) phase. Due to the different structures of the FMM and COI phases, manganites are susceptible to mechanical stresses. The traditional methods of applying stress on oxide thin films result in different growth modes which makes it difficult to quantify the strain in the thin film. Using a calibrated screw we applied direct mechanical stress on the substrate and measured the change in the phase diagram of the manganite as a function of strain. Our results show that the effect of strain is the largest in the fluid phase separated region of the phase diagram^2, where we observe a strain-induced change in resistance of about 5 orders of magnitude. [2] Tara Dhakal, et. al, Cond-mat/0607502.

  6. Genome-wide analysis of YB-1-RNA interactions reveals a novel role of YB-1 in miRNA processing in glioblastoma multiforme

    PubMed Central

    Wu, Shuai-Lai; Fu, Xing; Huang, Jinyan; Jia, Ting-Ting; Zong, Feng-Yang; Mu, Shi-Rong; Zhu, Hong; Yan, Yong; Qiu, Shuwei; Wu, Qun; Yan, Wei; Peng, Ying; Chen, Juxiang; Hui, Jingyi

    2015-01-01

    Altered miRNA expression is believed to play a crucial role in a variety of human cancers; however, the mechanisms leading to the dysregulation of miRNA expression remain elusive. In this study, we report that the human Y box-binding protein (YB-1), a major mRNA packaging protein, is a novel modulator of miRNA processing in glioblastoma multiforme (GBM). Using individual nucleotide-resolution crosslinking immunoprecipitation coupled to deep sequencing (iCLIP-seq), we performed the first genome-wide analysis of the in vivo YB-1-RNA interactions and found that YB-1 preferentially recognizes a UYAUC consensus motif and binds to the majority of coding gene transcripts including pre-mRNAs and mature mRNAs. Remarkably, our data show that YB-1 also binds extensively to the terminal loop region of pri-/pre-miR-29b-2 and regulates the biogenesis of miR-29b-2 by blocking the recruitment of microprocessor and Dicer to its precursors. Furthermore, we show that down-regulation of miR-29b by YB-1, which is up-regulated in GBM, is important for cell proliferation. Together, our findings reveal a novel function of YB-1 in regulating non-coding RNA expression, which has important implications in tumorigenesis. PMID:26240386

  7. Spectrum Handoffs Based on Preemptive Repeat Priority Queue in Cognitive Radio Networks.

    PubMed

    Yang, Xiaolong; Tan, Xuezhi; Ye, Liang; Ma, Lin

    2016-01-01

    Cognitive radio can significantly improve the spectrum efficiency, and spectrum handoff is considered as an important functionality to guarantee the quality of service (QoS) of primary users (PUs) and the continuity of data transmission of secondary users (SUs). In this paper, we propose an analytical framework based on a preemptive repeat identical (PRI) M/G/1 queuing network model to characterize spectrum handoff behaviors with general service time distribution of both primary and secondary connections, multiple interruptions and transmission delay resulting from the appearance of primary connections. Then, we derive the close-expression of the extended data delivery and the system sojourn time in both staying and changing scenarios. In addition, based on analysis of spectrum handoff behaviors resulting from multiple interruptions caused by the appearance of the primary connections, we investigate the traffic-adaptive policy, by which the considered SU will optimally adjust its handoff spectrum policy. Moreover, we investigate the admissible region and provide the reference for designing the admission control rule for the arriving secondary connection requests. Finally, simulation results verify that our proposed analytical framework is reasonable and can provide the reference for executing the optimal spectrum handoff strategy and designing the admission control rule for the SU in cognitive radio networks. PMID:27447644

  8. Composition dependence of charge and magnetic length scales in mixed valence manganite thin films.

    PubMed

    Singh, Surendra; Freeland, J W; Fitzsimmons, M R; Jeen, H; Biswas, A

    2016-01-01

    Mixed-valence manganese oxides present striking properties like the colossal magnetoresistance, metal-insulator transition (MIT) that may result from coexistence of ferromagnetic, metallic and insulating phases. Percolation of such phase coexistence in the vicinity of MIT leads to first-order transition in these manganites. However the length scales over which the electronic and magnetic phases are separated across MIT which appears compelling for bulk systems has been elusive in (La1-yPry)1-xCaxMnO3 films. Here we show the in-plane length scale over which charge and magnetism are correlated in (La0.4Pr0.6)1-xCaxMnO3 films with x = 0.33 and 0.375, across the MIT temperature. We combine electrical transport (resistance) measurements, x-ray absorption spectroscopy (XAS), x-ray magnetic circular dichroism (XMCD), and specular/off-specular x-ray resonant magnetic scattering (XRMS) measurements as a function of temperature to elucidate relationships between electronic, magnetic and morphological structure of the thin films. Using off-specular XRMS we obtained the charge-charge and charge-magnetic correlation length of these LPCMO films across the MIT. We observed different charge-magnetic correlation length for two films which increases below the MIT. The different correlation length shown by two films may be responsible for different macroscopic (transport and magnetic) properties. PMID:27461993

  9. Comparative Proteomics and Expression Analysis of Five Genes in Epicauta chinensis Larvae from the First to Fifth Instar

    PubMed Central

    Li, Qiurong; Wang, Dun; Lv, Shumin; Zhang, Yalin

    2014-01-01

    Blister beetle is an important insect model for both medicinal and pure research. Previous research has mainly focused on its biology and biochemistry, but very little data is yet available in the molecular biology. This study uses differential proteomics technology to analyze the soluble proteins extracted from each of the 5 instars larvae of Epicauta chinensis. 42 of the differentially-expressed proteins were identified successfully by MALDI-TOF/TOF-MS. Some of these proteins’ function and their expression profiles are analyzed. Our analysis revealed dynamics regulation of the following proteins: Axin-like protein pry-1 (APR-1), dihydrolipoyl dehydrogenase (DLD), vitellogenin (Vg) and lysozyme C (Lmz-S). APR-1 negatively regulates the Wnt signaling pathway. Its overexpression could result in embryo, leg, eye and ovary ectopica or malformation. DLD catalyzes the pyruvate into acetyl-CoA, the latter is the starting material of juvenile hormone (JH) and ipsdienol biosynthesis through the MVA pathway in insects. While Vg synthesis can be regulated by JH and stimulated by food factors. So DLD may affect the synthesis of JH, ipsdienol and Vg indirectly. The activity of lysozyme is an indicator of the immunity. Nutrition/food should be taken into account for its potential role during the development of larva in the future. Among the five genes and their corresponding proteins’ expression, only hsc70 gene showed a good correspondence with the protein level. This reflects the fluctuating relationship between mRNA and protein levels. PMID:24586908

  10. Long-Term Persistence of Bi-functionality Contributes to the Robustness of Microbial Life through Exaptation

    PubMed Central

    Sterner, Reinhard; Merkl, Rainer

    2016-01-01

    Modern enzymes are highly optimized biocatalysts that process their substrates with extreme efficiency. Many enzymes catalyze more than one reaction; however, the persistence of such ambiguities, their consequences and evolutionary causes are largely unknown. As a paradigmatic case, we study the history of bi-functionality for a time span of approximately two billion years for the sugar isomerase HisA from histidine biosynthesis. To look back in time, we computationally reconstructed and experimentally characterized three HisA predecessors. We show that these ancient enzymes catalyze not only the HisA reaction but also the isomerization of a similar substrate, which is commonly processed by the isomerase TrpF in tryptophan biosynthesis. Moreover, we found that three modern-day HisA enzymes from Proteobacteria and Thermotogae also possess low TrpF activity. We conclude that this bi-functionality was conserved for at least two billion years, most likely without any evolutionary pressure. Although not actively selected for, this trait can become advantageous in the case of a gene loss. Such exaptation is exemplified by the Actinobacteria that have lost the trpF gene but possess the bi-functional HisA homolog PriA, which adopts the roles of both HisA and TrpF. Our findings demonstrate that bi-functionality can perpetuate in the absence of selection for very long time-spans. PMID:26824644

  11. LMTK3 escapes tumour suppressor miRNAs via sequestration of DDX5.

    PubMed

    Jacob, Jimmy; Favicchio, Rosy; Karimian, Negin; Mehrabi, Maryam; Harding, Victoria; Castellano, Leandro; Stebbing, Justin; Giamas, Georgios

    2016-03-01

    Lemur tyrosine kinase-3 (LMTK3) plays an important role in cancer progression and is associated with breast, lung, gastric and colorectal cancer. MicroRNAs (miRNAs) are small endogenous non-coding RNAs that typically repress target genes at post-transcriptional level and have an important role in tumorigenesis. By performing a miRNA expression profile, we identified a subset of miRNAs modulated by LMTK3. We show that LMTK3 induces miR-34a, miR-196-a2 and miR-182 levels by interacting with DEAD-box RNA helicase p68 (DDX5). LMTK3 binds via DDX5 to the pri-miRNA of these three mature miRNAs, thereby sequestrating them from further processing. Ectopic expression of miR-34a and miR-182 in LMTK3-overexpressing cell lines (MCF7-LMTK3 and MDA-MB-231-LMTK3) inhibits breast cancer proliferation, invasion and migration. Interestingly, miR-34a and miR-182 directly bind to the 3'UTR of LMTK3 mRNA and consequently inhibit both its stability and translation, acting as tumour suppressor-like miRNAs. In aggregate, we show that LMTK3 is involved in miRNA biogenesis through modulation of the Microprocessor complex, inducing miRNAs that target LMTK3 itself. PMID:26739063

  12. Crystal structure of bis­[μ-(4-meth­oxy­phen­yl)methane­thiol­ato-κ2 S:S]bis­[chlorido­(η6-1-isopropyl-4-methyl­benzene)­ruthenium(II)] chloro­form disolvate

    PubMed Central

    Stíbal, David; Süss-Fink, Georg; Therrien, Bruno

    2015-01-01

    The mol­ecular structure of the title complex, [Ru2(C8H9OS)2Cl2(C10H14)2]·2CHCl3 or (p-MeC6H4Pri)2Ru2(SCH2-p-C6H5-OCH3)2Cl2·2CHCl3, shows inversion symmetry. The two symmetry-related RuII atoms are bridged by two 4-meth­oxy-α-toluene­thiol­ato [(4-meth­oxy­phen­yl)methane­thiol­ato] units. One chlorido ligand and the p-cymene ligand complete the typical piano-stool coordination environment of the RuII atom. In the crystal, the CH moiety of the chloro­form mol­ecule inter­acts with the chlorido ligand of the dinuclear complex, while one Cl atom of the solvent inter­acts more weakly with the methyl group of the bridging 4-meth­oxy-α-toluene­thiol­ato unit. This assembly leads to the formation of supra­molecular chains extending parallel to [021]. PMID:26594410

  13. Interchain electron states in polyethylene

    NASA Astrophysics Data System (ADS)

    Serra, S.; Tosatti, E.; Iarlori, S.; Scandolo, S.; Santoro, G.

    2000-08-01

    We present a theoretical study of the nature of the lowest empty conduction-band states in crystalline polyethylene (PE), conducted through density-functional electronic structure calculations. Results reveal that the wave function of the conduction-band edge is of interchain character, as opposed to the intrachain character of all the filled valence-band states. Thus, while a hole added to neutral PE will mainly belong to the PE chain backbone bonds, an added electron in PE will mostly reside between the chains, and far from the existing bonds. Moreover, the added electron state charge centroid is predicted to move further out from the chain backbone towards the low-density interstitial region, if and when the chains are pried apart. This suggests that injected electrons will naturally flow to low-density regions inside real PE, and that the experimentally established propensity of PE to expel electrons out of the bulk, should be directly related to the interchain nature of the conduction states.

  14. Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes

    DOE PAGESBeta

    Gardner, Shea N.; Jaing, Crystal J.; Elsheikh, Maher M.; Peña, José; Hysom, David A.; Borucki, Monica K.

    2014-01-01

    Background . Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. Degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. Results . A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. The new script, run_tiled_primers, is part of the PriMux software. Primers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses, Arenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus.more » Each group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross reactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to specifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo. Conclusions . This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family.« less

  15. A Graphical User Interface for Parameterizing Biochemical Models of Photosynthesis and Chlorophyll Fluorescence

    NASA Astrophysics Data System (ADS)

    Kornfeld, A.; Van der Tol, C.; Berry, J. A.

    2015-12-01

    Recent advances in optical remote sensing of photosynthesis offer great promise for estimating gross primary productivity (GPP) at leaf, canopy and even global scale. These methods -including solar-induced chlorophyll fluorescence (SIF) emission, fluorescence spectra, and hyperspectral features such as the red edge and the photochemical reflectance index (PRI) - can be used to greatly enhance the predictive power of global circulation models (GCMs) by providing better constraints on GPP. The way to use measured optical data to parameterize existing models such as SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes) is not trivial, however. We have therefore extended a biochemical model to include fluorescence and other parameters in a coupled treatment. To help parameterize the model, we then use nonlinear curve-fitting routines to determine the parameter set that enables model results to best fit leaf-level gas exchange and optical data measurements. To make the tool more accessible to all practitioners, we have further designed a graphical user interface (GUI) based front-end to allow researchers to analyze data with a minimum of effort while, at the same time, allowing them to change parameters interactively to visualize how variation in model parameters affect predicted outcomes such as photosynthetic rates, electron transport, and chlorophyll fluorescence. Here we discuss the tool and its effectiveness, using recently-gathered leaf-level data.

  16. mTORC2 promotes cell survival through c-Myc–dependent up-regulation of E2F1

    PubMed Central

    Zou, Zhipeng; Chen, Juan; Liu, Anling; Zhou, Xuan; Song, Qiancheng; Jia, Chunhong; Chen, Zhenguo; Lin, Jun; Yang, Cuilan; Li, Ming; Jiang, Yu

    2015-01-01

    Previous studies have reported that mTORC2 promotes cell survival through phosphorylating AKT and enhancing its activity. We reveal another mechanism by which mTORC2 controls apoptosis. Inactivation of mTORC2 promotes binding of CIP2A to PP2A, leading to reduced PP2A activity toward c-Myc serine 62 and, consequently, enhancement of c-Myc phosphorylation and expression. Increased c-Myc activity induces transcription of pri-miR-9-2/miR-9-3p, in turn inhibiting expression of E2F1, a transcriptional factor critical for cancer cell survival and tumor progression, resulting in enhanced apoptosis. In vivo experiments using B cell–specific mTORC2 (rapamycin-insensitive companion of mTOR) deletion mice and a xenograft tumor model confirmed that inactivation of mTORC2 causes up-regulation of c-Myc and miR-9-3p, down-regulation of E2F1, and consequent reduction in cell survival. Conversely, Antagomir-9-3p reversed mTORC1/2 inhibitor–potentiated E2F1 suppression and resultant apoptosis in xenograft tumors. Our in vitro and in vivo findings collectively demonstrate that mTORC2 promotes cell survival by stimulating E2F1 expression through a c-Myc– and miR-9-3p–dependent mechanism. PMID:26459601

  17. The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3′ ends

    PubMed Central

    Xie, Mingyi; Zhang, Wei; Shu, Mei-Di; Xu, Acer; Lenis, Diana A.; DiMaio, Daniel; Steitz, Joan A.

    2015-01-01

    Herpesvirus saimiri (HVS) is an oncogenic γ-herpesvirus that produces microRNAs (miRNAs) by cotranscription of precursor miRNA (pre-miRNA) hairpins immediately downstream from viral small nuclear RNAs (snRNA). The host cell Integrator complex, which recognizes the snRNA 3′ end processing signal (3′ box), generates the 5′ ends of HVS pre-miRNA hairpins. Here, we identify a novel 3′ box-like sequence (miRNA 3′ box) downstream from HVS pre-miRNAs that is essential for miRNA biogenesis. In vivo knockdown and rescue experiments confirmed that the 3′ end processing of HVS pre-miRNAs also depends on Integrator activity. Interaction between Integrator and HVS primary miRNA (pri-miRNA) substrates that contain only the miRNA 3′ box was confirmed by coimmunoprecipitation and an in situ proximity ligation assay (PLA) that we developed to localize specific transient RNA–protein interactions inside cells. Surprisingly, in contrast to snRNA 3′ end processing, HVS pre-miRNA 3′ end processing by Integrator can be uncoupled from transcription, enabling new approaches to study Integrator enzymology. PMID:26220997

  18. Early detection of plant disease using close range sensing system for input into digital earth environment

    NASA Astrophysics Data System (ADS)

    Chew, W. C.; Hashim, M.; Lau, A. M. S.; Battay, A. E.; Kang, C. S.

    2014-02-01

    A case study on pre-symptom stage of plant disease infection using ground based hyperspectral remote sensing was conducted. The objectives of the study are: (1) to validate the existence of pre-symptom stage of Ralstonia Solanacearum infection in Solanum Melongena L. (eggplant), and (2) to determine the induced electromagnetic spectral response for infected eggplant. From the experiment, the pre-symptom duration of Ralstonia Solanacearum infection in the case of eggplant was estimated (with the artificial photosynthetic stress conditions were adopted in the experiment to induce measurable changes in daily hyperspectral measurement of disease infected eggplant samples during the pre-symptom stage) as four days which is the critical period for practicing effective treatments. Vegetation indices namely, (1) Chlorophyll Absorption Integral (CAI), (2) Photochemical Radiation Index (PRI), and (3) Normalized Difference Vegetation Index (NDVI) have successfully shown noticeable progress of index value from the infected sample plant (with 100% light stress condition) throughout the study. Yet, other infected sample plants with moderate light stress conditions (50% or 75%) did not result any similar progress of index value from the daily leaf scale hyperspectral measurements. Apparently, extreme light stress can induce significant changes at visible portion in hyperspectral measurements for a disease infected eggplant during the pre-symptom stage.

  19. Structural Determinants of Arabidopsis thaliana Hyponastic Leaves 1 Function In Vivo

    PubMed Central

    Burdisso, Paula; Milia, Fernando; Schapire, Arnaldo L.; Bologna, Nicolás G.; Palatnik, Javier F.; Rasia, Rodolfo M.

    2014-01-01

    MicroRNAs have turned out to be important regulators of gene expression. These molecules originate from longer transcripts that are processed by ribonuclease III (RNAse III) enzymes. Dicer proteins are essential RNAse III enzymes that are involved in the generation of microRNAs (miRNAs) and other small RNAs. The correct function of Dicer relies on the participation of accessory dsRNA binding proteins, the exact function of which is not well-understood so far. In plants, the double stranded RNA binding protein Hyponastic Leaves 1 (HYL1) helps Dicer Like protein (DCL1) to achieve an efficient and precise excision of the miRNAs from their primary precursors. Here we dissected the regions of HYL1 that are essential for its function in Arabidopsis thaliana plant model. We generated mutant forms of the protein that retain their structure but affect its RNA-binding properties. The mutant versions of HYL1 were studied both in vitro and in vivo, and we were able to identify essential aminoacids/residues for its activity. Remarkably, mutation and even ablation of one of the purportedly main RNA binding determinants does not give rise to any major disturbances in the function of the protein. We studied the function of the mutant forms in vivo, establishing a direct correlation between affinity for the pri-miRNA precursors and protein activity. PMID:25409478

  20. Results on three predictions for July 2012 federal elections in Mexico based on past regularities.

    PubMed

    Hernández-Saldaña, H

    2013-01-01

    The Presidential Election in Mexico of July 2012 has been the third time that PREP, Previous Electoral Results Program works. PREP gives voting outcomes based in electoral certificates of each polling station that arrive to capture centers. In previous ones, some statistical regularities had been observed, three of them were selected to make predictions and were published in arXiv:1207.0078 [physics.soc-ph]. Using the database made public in July 2012, two of the predictions were completely fulfilled, while, the third one was measured and confirmed using the database obtained upon request to the electoral authorities. The first two predictions confirmed by actual measures are: (ii) The Partido Revolucionario Institucional, PRI, is a sprinter and has a better performance in polling stations arriving late to capture centers during the process. (iii) Distribution of vote of this party is well described by a smooth function named a Daisy model. A Gamma distribution, but compatible with a Daisy model, fits the distribution as well. The third prediction confirms that errare humanum est, since the error distributions of all the self-consistency variables appeared as a central power law with lateral lobes as in 2000 and 2006 electoral processes. The three measured regularities appeared no matter the political environment. PMID:24386103

  1. Testing genotoxicity and cytotoxicity strategies for the evaluation of commercial radiosterilized fetal calf sera.

    PubMed

    Pilili, Juan Pablo; González, Norma V; Molinari, Gabriela; Reigosa, Miguel A; Soloneski, Sonia; Larramendy, Marcelo L

    2010-01-01

    Effects of 18 commercial lots of fetal calf serum (FCS) after gamma-irradiation and their non-irradiated counterparts were comparatively analyzed on CHO-K1 and MDBK MDL1 cells for genotoxicity [sister chromatid exchange (SCE), micronuclei (MNi), and single cell gel electrophoresis (SCGE)], cytotoxicity [cell-cycle progression (CCP), proliferative replication index (PRI), mitotic index (MI), growth promotion (GP), and plating efficiency (PE)], and microbiological properties (mycoplasma and bovine viral diarrhea virus contamination). SCE and SCGE were the most informative end-points for genotoxicity since significant differences were found in 44.4% (P<0.05-0.001, Student's t-test) and 61.1% (P<0.05-0.001, chi(2) test) samples, respectively. MI was the cytotoxicity assay revealing the greatest variation, showing differences in 66.7% (P<0.05-0.001, chi(2) test) samples. Thus, these three end-points for screening bioproducts such as FCS were found most suitable for detecting potential geno-cytotoxicants in biological samples; their simultaneous use could be strongly recommended. PMID:19716317

  2. Infanticide by a solitary koinobiont ichneumonid ectoparasitoid of spiders

    NASA Astrophysics Data System (ADS)

    Takasuka, Keizo; Matsumoto, Rikio

    2011-06-01

    When encountering an already parasitized host, a parasitoid's optimal choices (superparasitism, host rejection, host feeding or infanticide) seem to depend on the individual species' life history, because the same choice may have different fitness consequences. We demonstrate infanticide under laboratory conditions by a polysphinctine, Zatypota albicoxa, which is a solitary koinobiont ectoparasitoid of spiders. The female always removed any previously attached egg or larva from the body of the host spider, Parasteatoda tepidariorum, with a rubbing behaviour. She rubbed her ovipositor back and forth toward the undersurface of the attached egg or of the saddle under the attached larva to pry it off and laid an egg after removal. When removing a larva, the infanticidal female engaged exclusively in unfastening the `saddle' which fastens the larva to the body of the spider. All larvae were removed with the `saddle' attached to the ventral surface of the body. The female invested more time to remove the medium second and the large penultimate instar larvae than to remove eggs and first instar larvae because of the labour involved in unfastening the saddle. Oviposition with infanticide of the medium second and the penultimate instar larvae imposed more time upon the female than that on an unparasitized host. Removal of any previous occupant in spite of the associated labour costs suggests that infanticide will always be adaptive, no matter the time costs to Z. albicoxa, because so much is invested in attacking the host and because the parasitoid cannot detect whether the spider is already parasitized until she achieves subjugation.

  3. Activation of CO by Hydrogenated Magnesium(I) Dimers: Sterically Controlled Formation of Ethenediolate and Cyclopropanetriolate Complexes.

    PubMed

    Lalrempuia, Ralte; Kefalidis, Christos E; Bonyhady, Simon J; Schwarze, Benedikt; Maron, Laurent; Stasch, Andreas; Jones, Cameron

    2015-07-22

    This study details the formal hydrogenation of two magnesium(I) dimers {(Nacnac)Mg}2 (Nacnac = [{(C6H3R2-2,6)NCMe}2CH](-); R = Pr(i) ((Dip)Nacnac), Et ((Dep)Nacnac)) using 1,3-cyclohexadiene. These reactions afford the magnesium(II) hydride complexes, {(Nacnac)Mg(μ-H)}2. Their reactions with excess CO are sterically controlled and lead cleanly to different C-C coupled products, viz. the ethenediolate complex, ((Dip)Nacnac)Mg{κ(1)-O-[((Dip)Nacnac)Mg(κ(2)-O,O-O2C2H2)]}, and the first cyclopropanetriolate complex of any metal, cis-{((Dep)Nacnac)Mg}3{μ-C3(H3)O3}. Computational studies imply the CO activation processes proceed via very similar mechanisms to those previously reported for related reactions involving f-block metal hydride compounds. This work highlights the potential magnesium compounds hold for use in the "Fischer-Tropsch-like" transformation of CO/H2 mixtures to value added oxygenate products. PMID:26135846

  4. Isolation of Elusive HAsAsH in a Crystalline Diuranium(IV) Complex.

    PubMed

    Gardner, Benedict M; Balázs, Gábor; Scheer, Manfred; Wooles, Ashley J; Tuna, Floriana; McInnes, Eric J L; McMaster, Jonathan; Lewis, William; Blake, Alexander J; Liddle, Stephen T

    2015-12-01

    The HAsAsH molecule has hitherto only been proposed tentatively as a short-lived species generated in electrochemical or microwave-plasma experiments. After two centuries of inconclusive or disproven claims of HAsAsH formation in the condensed phase, we report the isolation and structural authentication of HAsAsH in the diuranium(IV) complex [{U(Tren(TIPS) )}2 (μ-η(2) :η(2) -As2 H2 )] (3, Tren(TIPS) =N(CH2 CH2 NSiPr(i) 3 )3 ; Pr(i) =CH(CH3 )2 ). Complex 3 was prepared by deprotonation and oxidative homocoupling of an arsenide precursor. Characterization and computational data are consistent with back-bonding-type interactions from uranium to the HAsAsH π*-orbital. This experimentally confirms the theoretically predicted excellent π-acceptor character of HAsAsH, and is tantamount to full reduction to the diarsane-1,2-diide form. PMID:26510123

  5. Photosynthetic limitation of several representative subalpine species in the Catalan Pyrenees in summer.

    PubMed

    Fernàndez-Martínez, J; Fleck, I

    2016-07-01

    Information on the photosynthetic process and its limitations is essential in order to predict both the capacity of species to adapt to conditions associated with climate change and the likely changes in plant communities. Considering that high-mountain species are especially sensitive, three species representative of subalpine forests of the Central Catalan Pyrenees: mountain pine (Pinus uncinata Mill.), birch (Betula pendula Roth) and rhododendron (Rhododendron ferrugineum L.) were studied under conditions associated with climate change, such as low precipitation, elevated atmospheric [CO2 ] and high solar irradiation incident at Earth's surface, in order to detect any photosynthetic limitations. Short-term high [CO2 ] increased photosynthesis rates (A) and water use efficiency (WUE), especially in birch and mountain pine, whereas stomatal conductance (gs ) was not altered in either species. Birch showed photosynthesis limitation through stomatal closure related to low rainfall, which induced photoinhibition and early foliar senescence. Rhododendron was especially affected by high irradiance, showing early photosynthetic saturation in low light, highest chlorophyll content, lowest gas exchange rates and least photoprotection. Mountain pine had the highest A, photosynthetic capacity (Amax ) and light-saturated rates of net CO2 assimilation (Asat ), which were maintained under reduced precipitation. Furthermore, maximum quantum yield (Fv /Fm ), thermal energy dissipation, PRI and SIPI radiometric index, and ascorbate content indicated improved photoprotection with respect to the other two species. However, maximum velocity of carboxylation of RuBisco (Vcmax ) indicated that N availability would be the main photosynthetic limitation in this species. PMID:26833754

  6. Light-Inducible MiR163 Targets PXMT1 Transcripts to Promote Seed Germination and Primary Root Elongation in Arabidopsis1[OPEN

    PubMed Central

    Chung, Pil Joong; Park, Bong Soo; Wang, Huan

    2016-01-01

    Expression of many plant microRNAs is responsive to hormones and environmental stimuli, but none has yet been associated with light. Arabidopsis (Arabidopsis thaliana) miR163 is 24 nucleotides in length and targets mRNAs encoding several S-adenosyl-Met-dependent carboxyl methyltransferase family members. Here, we found that miR163 is highly induced by light during seedling de-etiolation as well as seed germination. Under the same condition, its target PXMT1, encoding a methyltransferase that methylates 1,7-paraxanthine, is down-regulated. Light repression of PXMT1 is abolished in a mir163 null mutant, but the repression can be restored to wild-type levels in complementation lines expressing pri-miR163 gene in the mir163 mutant background. During seed germination, miR163 and its target PXMT1 are predominantly expressed in the radicle, and the expression patterns of the two genes are inversely correlated. Moreover, compared with the wild type, mir163 mutant or PXMT1 overexpression line shows delayed seed germination under continuous light, and seedlings develop shorter primary roots with an increased number of lateral roots under long-day condition. Together, our results indicate that miR163 targets PXMT1 mRNA to promote seed germination and modulate root architecture during early development of Arabidopsis seedlings. PMID:26768601

  7. Comparative proteomics and expression analysis of five genes in Epicauta chinensis larvae from the first to fifth instar.

    PubMed

    Li, Qiurong; Wang, Dun; Lv, Shumin; Zhang, Yalin

    2014-01-01

    Blister beetle is an important insect model for both medicinal and pure research. Previous research has mainly focused on its biology and biochemistry, but very little data is yet available in the molecular biology. This study uses differential proteomics technology to analyze the soluble proteins extracted from each of the 5 instars larvae of Epicauta chinensis. 42 of the differentially-expressed proteins were identified successfully by MALDI-TOF/TOF-MS. Some of these proteins' function and their expression profiles are analyzed. Our analysis revealed dynamics regulation of the following proteins: Axin-like protein pry-1 (APR-1), dihydrolipoyl dehydrogenase (DLD), vitellogenin (Vg) and lysozyme C (Lmz-S). APR-1 negatively regulates the Wnt signaling pathway. Its overexpression could result in embryo, leg, eye and ovary ectopica or malformation. DLD catalyzes the pyruvate into acetyl-CoA, the latter is the starting material of juvenile hormone (JH) and ipsdienol biosynthesis through the MVA pathway in insects. While Vg synthesis can be regulated by JH and stimulated by food factors. So DLD may affect the synthesis of JH, ipsdienol and Vg indirectly. The activity of lysozyme is an indicator of the immunity. Nutrition/food should be taken into account for its potential role during the development of larva in the future. Among the five genes and their corresponding proteins' expression, only hsc70 gene showed a good correspondence with the protein level. This reflects the fluctuating relationship between mRNA and protein levels. PMID:24586908

  8. Utilizing a Tower Based System for Optical Sensing of Ecosystem Carbon Fluxes

    NASA Astrophysics Data System (ADS)

    Huemmrich, K. F.; Corp, L. A.; Middleton, E.; Campbell, P. K. E.; Landis, D.; Kustas, W. P.

    2015-12-01

    Optical sampling of spectral reflectance and solar induced fluorescence provide information on the physiological status of vegetation that can be used to infer stress responses and estimates of production. Multiple repeated observations are required to observe the effects of changing environmental conditions on vegetation. This study examines the use of optical signals to determine inputs to a light use efficiency (LUE) model describing productivity of a cornfield where repeated observations of carbon flux, spectral reflectance and fluorescence were collected. Data were collected at the Optimizing Production Inputs for Economic and Environmental Enhancement (OPE3) fields (39.03°N, 76.85°W) at USDA Beltsville Agricultural Research Center. Agricultural Research Service researchers measured CO2 fluxes using eddy covariance methods throughout the growing season. Optical measurements were made from the nearby tower supporting the NASA FUSION sensors. The sensor system consists of two dual channel, upward and downward looking, spectrometers used to simultaneously collect high spectral resolution measurements of reflected and fluoresced light from vegetation canopies at multiple view angles. Estimates of chlorophyll fluorescence, combined with measures of vegetation pigment content and the Photosynthetic Reflectance Index (PRI) derived from the spectral reflectance are compared with CO2 fluxes over diurnal periods for multiple days. The relationships among the different optical measurements indicate that they are providing different types of information on the vegetation and that combinations of these measurements provide improved retrievals of CO2 fluxes than any index alone

  9. Similarity is not enough: Tipping points of Ebola Zaire mortalities

    NASA Astrophysics Data System (ADS)

    Phillips, J. C.

    2015-06-01

    In early 2014 an outbreak of a slightly mutated Zaire Ebola subtype appeared in West Africa which is less virulent than 1976 and 1994 strains. The numbers of cases per year appear to be ∼1000 times larger than the earlier strains, suggesting a greatly enhanced transmissibility. Although the fraction of the 2014 spike glycoprotein mutations is very small (∼3%), the mortality is significantly reduced, while the transmission appears to have increased strongly. Bioinformatic scaling had previously shown similar inversely correlated trends in virulence and transmission in N1 (H1N1) and N2 (H3N2) influenza spike glycoprotein mutations. These trends appear to be related to various external factors (migration, availability of pure water, and vaccination programs). The molecular mechanisms for Ebola's mutational response involve mainly changes in the disordered mucin-like domain (MLD) of its spike glycoprotein amino acids. The MLD has been observed to form the tip of an oligomeric amphiphilic wedge that selectively pries apart cell-cell interfaces via an oxidative mechanism.

  10. EUROSPEC: at the interface between remote sensing and ecosystem CO2 flux measurements in Europe

    NASA Astrophysics Data System (ADS)

    Porcar-Castell, A.; Mac Arthur, A.; Rossini, M.; Eklundh, L.; Pacheco-Labrador, J.; Anderson, K.; Balzarolo, M.; Martín, M. P.; Jin, H.; Tomelleri, E.; Cerasoli, S.; Sakowska, K.; Hueni, A.; Julitta, T.; Nichol, C. J.; Vescovo, L.

    2015-08-01

    Resolving the spatial and temporal dynamics of gross primary productivity (GPP) of terrestrial ecosystems across different scales remains a challenge. Remote sensing is regarded as the solution to upscale point observations conducted at the ecosystem level, using the eddy covariance (EC) technique, to the landscape and global levels. In addition to traditional vegetation indices, the photochemical reflectance index (PRI) and the emission of solar-induced chlorophyll fluorescence (SIF), now measurable from space, provide a new range of opportunities to monitor the global carbon cycle using remote sensing. However, the scale mismatch between EC observations and the much coarser satellite-derived data complicates the integration of the two sources of data. The solution is to establish a network of in situ spectral measurements that can act as bridge between EC measurements and remote sensing data. In situ spectral measurements have been already conducted for many years at EC sites, but using variable instrumentation, setups, and measurement standards. In Europe in particular, in situ spectral measurements remain highly heterogeneous. The goal of EUROSPEC Cost Action ES0930 was to promote the development of common measuring protocols and new instruments towards establishing best practices and standardization of in situ spectral measurements. In this review we describe the background and main tradeoffs of in situ spectral measurements, review the main results of EUROSPEC Cost Action, and discuss the future challenges and opportunities of in situ spectral measurements for improved estimation of local and global carbon cycle.

  11. EUROSPEC: at the interface between remote-sensing and ecosystem CO2 flux measurements in Europe

    NASA Astrophysics Data System (ADS)

    Porcar-Castell, A.; Mac Arthur, A.; Rossini, M.; Eklundh, L.; Pacheco-Labrador, J.; Anderson, K.; Balzarolo, M.; Martín, M. P.; Jin, H.; Tomelleri, E.; Cerasoli, S.; Sakowska, K.; Hueni, A.; Julitta, T.; Nichol, C. J.; Vescovo, L.

    2015-10-01

    Resolving the spatial and temporal dynamics of gross primary productivity (GPP) of terrestrial ecosystems across different scales remains a challenge. Remote sensing is regarded as the solution to upscale point observations conducted at the ecosystem level, using the eddy covariance (EC) technique, to the landscape and global levels. In addition to traditional vegetation indices, the photochemical reflectance index (PRI) and the emission of solar-induced chlorophyll fluorescence (SIF), now measurable from space, provide a new range of opportunities to monitor the global carbon cycle using remote sensing. However, the scale mismatch between EC observations and the much coarser satellite-derived data complicate the integration of the two sources of data. The solution is to establish a network of in situ spectral measurements that can act as a bridge between EC measurements and remote-sensing data. In situ spectral measurements have already been conducted for many years at EC sites, but using variable instrumentation, setups, and measurement standards. In Europe in particular, in situ spectral measurements remain highly heterogeneous. The goal of EUROSPEC Cost Action ES0930 was to promote the development of common measuring protocols and new instruments towards establishing best practices and standardization of these measurements. In this review we describe the background and main tradeoffs of in situ spectral measurements, review the main results of EUROSPEC Cost Action, and discuss the future challenges and opportunities of in situ spectral measurements for improved estimation of local and global estimates of GPP over terrestrial ecosystems.

  12. [The Barbie-Matrix: effectiveness of a school-based German program for the primary prevention of anorexia nervosa developed for girls up to the age of 12].

    PubMed

    Berger, Uwe; Joseph, Andrea; Sowa, Melanie; Strauss, Bernhard

    2007-06-01

    More than 25 % of the 12-year-old girls in Thuringia (Germany) show problematic eating behaviour as measured with the Eating-Attitudes-Test (EAT-26D), which corresponds to an increased risk for the development of anorexia nervosa or bulimia nervosa. This was the starting position of a controlled study using a pre-post-design to check the effectiveness of a newly developed German program for the prevention of anorexia nervosa in girls ("PriMa"). 42 Thuringian schools (20 as treatment group) with 1006 girls participated in the pilot study, which lasted from September 2004 to July 2005. Program effectiveness was analysed with mostly standardized questionnaires at three times of measurement (before, after the intervention and at 3 months follow-up) referring to body related self esteem (FBeK), satisfaction with body shape (KEDS), eating behaviour (EAT-26D) and body related attitudes. The program was established in 9 x 90-minute lessons including interactive exercises and discussing especially developed posters that show scenes of a Barbie-doll's life including the reports of a patient suffering from anorexia. Significant improvements on all variables could be reached for the higher risk group (EAT-26D >/= 10 points; = 26,7 %). Mean values in the EAT-26D decreased 5 points at the average which is equivalent with 6.6 % of the EAT-26D range, reflecting a practically significant change effect. PMID:17357902

  13. Enhancement of hydrocarbon waste biodegradation by addition of a biosurfactant from Bacillus subtilis O9.

    PubMed

    Morán, A C; Olivera, N; Commendatore, M; Esteves, J L; Siñeriz, F

    2000-01-01

    A non-sterile biosurfactant preparation (surfactin) was obtained from a 24-h culture of Bacillus subtilis O9 grown on sucrose and used to study its effect on the biodegradation of hydrocarbon wastes by an indigenous microbial community at the Erlenmeyer-flask scale. Crude biosurfactant was added to the cultures to obtain concentrations above and below the critical micelle concentration (CMC). Lower concentration affected neither biodegradation nor microbial growth. Higher concentration gave higher cell concentrations. Biodegradation of aliphatic hydrocarbons increased from 20.9 to 35.5% and in the case of aromatic hydrocarbons from nil to 41%, compared to the culture without biosurfactant. The enhancement effect of biosurfactant addition was more noticeable in the case of long chain alkanes. Pristane and phytane isoprenoids were degraded to the same extent as n-C17 and n-C18 alkanes and, consequently, no decrease in the ratios n-C17/pri and n-C18/phy was observed. Rapid production of surfactin crude preparation could make it practical for bioremediation of ship bilge wastes. PMID:11194975

  14. Development and validation of a liquid chromatography method for simultaneous determination of three process-related impurities: yeastolates, triton X-100 and methotrexate.

    PubMed

    Fang, Shiping; Lollo, Charles P; Derunes, Celine; LaBarre, Michael J

    2011-11-15

    Yeastolates, triton X-100 (TX-100) and methotrexate (MTX) are common process-related impurities (PRI) in cell-based bioproduction of many active biopharmaceuticals. In this study, a reverse phase high performance liquid chromatography (RP-HPLC) method coupled with ultraviolet (UV) detection was developed for simultaneous determination and quantitation of these impurities. The chromatographic separation was achieved using a Jupiter C4 column and analyses of yeastolates, TX-100 and MTX were monitored at 257, 280 and 302 nm, respectively. The method was further validated with respect to selectivity, linearity, limit of detection (LOD), limit of quantitation (LOQ), precision and accuracy. The limits of quantitation for yeastolates, TX-100 and MTX were determined to be 27 ppm, 10 ppm and 41 ppb, respectively. Finally, the suitability of the method for analyses of recombinant human hyaluronidase (rHuPH20) in-process (viral inactivation, QFF, PS, APB and CHT filtered, final viral filtrate) and final manufacturing materials was demonstrated, and trace levels of yeastolates, TX-100 and MTX were reliably measured except for three matrices early in the purification process in which TX-100 was not accurately determined due to interfering effects. PMID:22030454

  15. Growth and characterization of Bi, Pr- and Bi, Sc-substituted lutetium iron garnet films with planar magnetization for magneto-optic visualization

    NASA Astrophysics Data System (ADS)

    Syvorotka, Igor M.; Ubizskii, Sergii B.; Kucera, Miroslav; Kuhn, Marcus; Vértesy, Zofia

    2001-04-01

    The series of epitaxial garnet films of general composition Lu3-x-yBixPryFe5- zAlzO12 and Lu3-xBixFe5-y- zScyAlzO12 were grown on (111) oriented GGG (gadolinium gallium garnet) substrates by the liquid phase epitaxy. Their magnetic and magneto-optical properties were studied using both experimental techniques and modelling. All obtained films demonstrated generally a magnetic anisotropy close to the easy-plane type. The Pr-containing films exhibited large negative uniaxial anisotropy and significant cubic anisotropy. The latter causes a distortion of magnetization curves in samples magnetized in a direction normal to the film plane, especially at low temperatures. The large negative uniaxial anisotropy of Pr-substituted iron garnets allows us to increase the saturation field up to 0.5 T at liquid nitrogen temperature. The Sc-doped films displayed small positive uniaxial anisotropy that did not exceed the shape anisotropy. The magnetization curves of these films did not show any distortion due to the cubic anisotropy. The suitability of Pr- and Sc-doped garnets that meet the requirements for indicator layers for magneto-optic visualization at liquid nitrogen temperature is discussed.

  16. Cobalt(II) amido complexes derived from a monodentate arylamido ligand featuring a highly electron-withdrawing C6F5 substituent.

    PubMed

    Yao, Shuang; Tam, Dennis Yiu Sun; Cheung, Pak Shing; Lam, Chi-Keung; Guo, Pei; Lam, Sik Lok; Lee, Hung Kay

    2015-11-01

    A series of cobalt(ii) complexes of a highly electron-withdrawing amido ligand, [N(C6F5)(C6H3Pr(i)2-2,6)](-) (L), were synthesized and structurally characterized. Mononuclear [CoL(Cl)(TMEDA)] (3) and heterobimetallic [CoL2(μ-Cl)Li(THF)3] (4) were obtained by direct metathetical reactions of anhydrous CoCl2 with one molar equivalent of [LiL(TMEDA)] (1) (TMEDA = Me2NCH2CH2NMe2) and [LiL(THF)3] (2), respectively. Complex 3 underwent facile ligand substitution reactions with LiMe and NaN3, yielding the corresponding mixed-ligand complexes [CoL(X)(TMEDA)] (X = Me 5, N36). Treatment of 3 with NaOMe led to the heterobimetallic complex [CoL2(μ-OMe)Na(TMEDA)] (7). The solid-state structures of complexes 1-7 were established by X-ray diffraction analysis. PMID:26418474

  17. Seismic behavior of outrigger truss-wall shear connections using multiple steel angles

    NASA Astrophysics Data System (ADS)

    Li, Xian; Wang, Wei; Lü, Henglin; Zhang, Guangchang

    2016-06-01

    An experimental investigation on the seismic behavior of a type of outrigger truss-reinforced concrete wall shear connection using multiple steel angles is presented. Six large-scale shear connection models, which involved a portion of reinforced concrete wall and a shear tab welded onto a steel endplate with three steel angles, were constructed and tested under combined actions of cyclic axial load and eccentric shear. The effects of embedment lengths of steel angles, wall boundary elements, types of anchor plates, and thicknesses of endplates were investigated. The test results indicate that properly detailed connections exhibit desirable seismic behavior and fail due to the ductile fracture of steel angles. Wall boundary elements provide beneficial confinement to the concrete surrounding steel angles and thus increase the strength and stiffness of connections. Connections using whole anchor plates are prone to suffer concrete pry-out failure while connections with thin endplates have a relatively low strength and fail due to large inelastic deformations of the endplates. The current design equations proposed by Chinese Standard 04G362 and Code GB50011 significantly underestimate the capacities of the connection models. A revised design method to account for the influence of previously mentioned test parameters was developed.

  18. Interpretation of the Stephan Quintet Galaxy Cluster using Hydro-Gravitational-Dynamics: Viscosity and Fragmentation

    NASA Astrophysics Data System (ADS)

    Gibson, Carl H.; Schild, Rudolph E.

    2011-10-01

    Stephan's Quintet (SQ) is a compact group of galaxies that has been well studied since its discovery in 1877 but is mysterious using cold dark mat- ter hierarchical clustering cosmology (CDMHCC). Anomalous red shifts z = (0.0027, 0.019, 0.022, 0.022, 0.022) among galaxies in SQ either reduce it to a Trio with two highly improbable intruders from CDMHCC or support the Arp (1973) hypothesis that its red shifts are intrinsic. An alternative is provided by the Gib- son 1996-2006 hydro-gravitational-dynamics (HGD) theory where superclusters, clusters and galaxies all originate by gravitational fragmentation in the super- viscous plasma epoch and at planetary and star cluster mass scales in the pri- mordial gas of the expanding universe. By this fluid-mechanical cosmology, the SQ galaxies gently separate and remain precisely along a line of sight because of perspective and the small transverse velocities permitted by their sticky viscous- gravitational beginnings. Star and gas bridges and young-globular-star-cluster (YGC) trails observed by the Hubble Space Telescope are triggered as SQ galax- ies separate through viscous baryonic-dark-matter halos of dark proto-globular- cluster (PGC) clumps of frozen Earth-mass primordial-fog-particles (PFPs).

  19. Coordination of N-donor ligands to a uranyl(V) beta-diketiminate complex.

    PubMed

    Schettini, Michael F; Wu, Guang; Hayton, Trevor W

    2009-12-21

    Addition of 2 equiv of AgOTf to [UO(2)(Ar(2)nacnac)Cl](2) (Ar(2)nacnac = {(2,6-Pr(i)(2)C(6)H(3))NC(Me)}(2)CH) in the presence of excess pyridine, followed by addition of Cp(2)Co, generates the uranyl(V) complex UO(2)(Ar(2)nacnac)(py)(2) (2), in moderate yield. Complex 2 has proven to be an excellent precursor for the synthesis of other U(V) complexes. Thus, addition of 2,2'-bipyridine (bipy), 1,10-phenanthroline (phen), TMEDA, or 1-methylimidazole (MeIm) to 2 provides UO(2)(Ar(2)nacnac)(bipy) (3), UO(2)(Ar(2)nacnac)(phen) (4), UO(2)(Ar(2)nacnac)(TMEDA) (5), and UO(2)(Ar(2)nacnac)(MeIm)(2) (6), respectively. Complexes 2-6 have been fully characterized and their structures confirmed by X-ray crystallography. Attempts to form the analogous hexavalent uranyl complexes of bipy, phen, and TMEDA have not been successful. However, reaction of [UO(2)(Ar(2)nacnac)Cl](2) with AgOTf and 2 equiv of MeIm leads to the isolation of [UO(2)(Ar(2)nacnac)(MeIm)(2)][OTf] (7), which has been fully characterized. Attempts to ligate sulfur donor ligands to either the UO(2)(Ar(2)nacnac) or the [UO(2)(Ar(2)nacnac)](+) fragments were unsuccessful. PMID:19947577

  20. Elevation of Il6 is associated with disturbed let-7 biogenesis in a genetic model of depression.

    PubMed

    Wei, Y B; Liu, J J; Villaescusa, J C; Åberg, E; Brené, S; Wegener, G; Mathé, A A; Lavebratt, C

    2016-01-01

    Elevation of the proinflammatory cytokine IL-6 has been implicated in depression; however, the mechanisms remain elusive. MicroRNAs (miRNAs) are small non-coding RNAs that inhibit gene expression post-transcriptionally. The lethal-7 (let-7) miRNA family was suggested to be involved in the inflammation process and IL-6 was shown to be one of its targets. In the present study, we report elevation of Il6 in the prefrontal cortex (PFC) of a genetic rat model of depression, the Flinders Sensitive Line (FSL) compared to the control Flinders Resistant Line. This elevation was associated with an overexpression of LIN28B and downregulation of let-7 miRNAs, the former an RNA-binding protein that selectively represses let-7 synthesis. Also DROSHA, a key enzyme in miRNA biogenesis was downregulated in FSL. Running was previously shown to have an antidepressant-like effect in the FSL rat. We found that running reduced Il6 levels and selectively increased let-7i and miR-98 expression in the PFC of FSL, although there were no differences in LIN28B and DROSHA expression. Pri-let-7i was upregulated in the running FSL group, which associated with increased histone H4 acetylation. In conclusion, the disturbance of let-7 family biogenesis may underlie increased proinflammatory markers in the depressed FSL rats while physical activity could reduce their expression, possibly through regulating primary miRNA expression via epigenetic mechanisms. PMID:27529677

  1. The role of Ets2 transcription factor in the induction of microRNA-155 (miR-155) by lipopolysaccharide and its targeting by interleukin-10.

    PubMed

    Quinn, Susan R; Mangan, Niamh E; Caffrey, Brian E; Gantier, Michael P; Williams, Bryan R G; Hertzog, Paul J; McCoy, Claire E; O'Neill, Luke A J

    2014-02-14

    MicroRNA-155 (miR-155) is highly expressed in many cancers such as B cell lymphomas and myeloid leukemia and inflammatory disorders such as rheumatoid arthritis, atopic dermatitis, and multiple sclerosis. The role of miR-155 as both a promoter of inflammation and an oncogenic agent provides a clear need for miR-155 itself to be stringently regulated. We therefore investigated the transcriptional regulation of miR-155 in response to the respective pro- and anti-inflammatory mediators LPS and IL-10. Bioinformatic analysis revealed Ets binding sites on the miR-155 promoter, and we found that Ets2 is critical for miR-155 induction by LPS. Truncation and mutational analysis of the miR-155 promoter confirmed the role of the Ets2 binding site proximal to the transcription start site for LPS responsiveness. We observed increased binding of Ets2 to the miR-155 promoter and Ets2 deficient mice displayed decreased induction of miR-155 in response to LPS. IL-10 inhibited the induction of Ets2 mRNA and protein by LPS, thereby decreasing Ets2 function on the pri-155 promoter. We have thus identified Ets2 as a key novel regulator in both the positive and negative control of miR-155 in the inflammatory response. PMID:24362029

  2. Features of follicular dendritic cells in ovine pharyngeal tonsil: an in vivo and in vitro study in the context of scrapie pathogenesis.

    PubMed

    Toppets, Vinciane; Defaweux, Valerie; Piret, Joelle; Kirschvink, Nathalie; Grobet, Luc; Antoine, Nadine

    2011-05-15

    Although the alimentary tract has been suggested as the most likely portal of entry in natural scrapie, a growing amount of data indicates that the respiratory system and more specifically the pharyngeal tonsils serve as a natural portal of entry for scrapie. This study describes for the first time the broad cell populations in the lymphoid compartment of pharyngeal tonsils and more specifically inside the lymphoid follicles where the scrapie agent accumulates during the period of latency. Follicular dendritic cells (FDCs), stromal cells located in the light zone of the germinal centre of lymphoid follicles, seem to be the principal causal factor in the accumulation of the infectious agent in transmissible spongiform encephalopathy (TSE) diseases. Knowing that efficient lymphoreticular prion propagation requires PrPc expression, we analysed the expression of PrPc with the mouse monoclonal antibody Pri 909 both in situ and on FDC-cluster-enriched cell suspensions. In situ, a positive staining was observed in the germinal centre of pharyngeal lymph follicles. The germinal centre labelling was due to the presence of a follicular dendritic network as revealed after immunogold staining of isolated FDC clusters. Our results suggest that the pharyngeal lymphoreticular system and more specifically PrPc expressing follicular dendritic cells could serve as a prion "reservoir" during the latency phase, thus playing a key role during the scrapie lymphoinvasion. PMID:21353313

  3. Synthesis and Characterization of an f-Block Terminal Parent Imido [U=NH] Complex: A Masked Uranium(IV) Nitride

    PubMed Central

    2014-01-01

    Deprotonation of [U(TrenTIPS)(NH2)] (1) [TrenTIPS = N(CH2CH2NSiPri3)3] with organoalkali metal reagents MR (M = Li, R = But; M = Na–Cs, R = CH2C6H5) afforded the imido-bridged dimers [{U(TrenTIPS)(μ-N[H]M)}2] [M = Li–Cs (2a–e)]. Treatment of 2c (M = K) with 2 equiv of 15-crown-5 ether (15C5) afforded the uranium terminal parent imido complex [U(TrenTIPS)(NH)][K(15C5)2] (3c), which can also be viewed as a masked uranium(IV) nitride. The uranium–imido linkage was found to be essentially linear, and theoretical calculations suggested σ2π4 polarized U–N multiple bonding. Attempts to oxidize 3c to afford the neutral uranium terminal parent imido complex [U(TrenTIPS)(NH)] (4) resulted in spontaneous disproportionation to give 1 and the uranium–nitride complex [U(TrenTIPS)(N)] (5); this reaction is a new way to prepare the terminal uranium–nitride linkage and was calculated to be exothermic by −3.25 kcal mol–1. PMID:24697157

  4. Guidelines for the optimal design of miRNA-based shRNAs.

    PubMed

    Bofill-De Ros, Xavier; Gu, Shuo

    2016-07-01

    RNA interference (RNAi) is an extremely useful tool for inhibiting gene expression. It can be triggered by transfected synthetic small interfering RNA (siRNA) or by expressed small hairpin RNA (shRNA). The cellular machinery processes the latter into siRNA in vivo. shRNA is preferred or required in genetic screens and specific RNAi approaches in gene therapy settings. Despite its many successes, the field of shRNAs faces many challenges. Insufficient knockdowns and off-target effects become obstacles for shRNA usage in many applications. Numerous failures are triggered by pitfalls in shRNA design that is often associated with impoverished biogenesis. Here, based on current understanding of the miRNA maturation pathway, we discuss the principles of different shRNA design (pre-miRNA-like, pri-miRNA-like and Ago-shRNA) with an emphasis on the RNA structure. We also provide detailed instructions for an optimal design of pre-miRNA-like shRNA. PMID:27083402

  5. Analysis of Agrobacterium tumefaciens plasmid pTiC58 replication region with a novel high-copy-number derivative.

    PubMed Central

    Gallie, D R; Hagiya, M; Kado, C I

    1985-01-01

    The origin of replication, ori, of the nopaline tumor-inducing plasmid, pTiC58, mapped in a region that shares sequence homology with octopine plasmids pTiAch5 and pTiB6. Within this region, the minimum amount of DNA necessary for maintaining autonomous replication was a 2.6-kilobase region, which also comprised the incompatibility function inc. pTiC58 derivatives containing inc were incompatible with Agrobacterium tumefaciens plasmids pTiC58, pTiD1439, pTiAch5, pTi15955, and pTiA5 and were compatible with A. rhizogenes plasmid pRi12. Situated adjacent to the origin region was a 1.5-kilobase par segment involved in stable inheritance of pTiC58 under nonselective growth conditions. When par was present, plasmid maintenance approached that of the wild-type pTiC58. Rapid loss from the cell population was observed for plasmids not containing this locus. Another 1.5-kilobase region, cop, positively regulated pTiC58 copy number, enabling certain pTiC58 derivatives to exist at a copy number up to 80 times higher than that of wild-type pTiC58. Deletions within the cop locus resulted in reduced copy number. The ori/inc regions were flanked on either side by the par and cop loci. Images PMID:3972769

  6. Colossal Piezoresistance in strained La0.67Sr0.33MnO3 thin films

    NASA Astrophysics Data System (ADS)

    Viitaniemi, Maria; Kwak, In Hae; Biswas, Amlan

    2015-03-01

    Piezoresistance is the change in electrical resistance as a function of strain. A known mechanism leading to piezoresistance is thermodynamic phase separation. It has been shown that the compound (La1-yPry)1-xCaxMnO3 (LPCMO) exhibits colossal piezoresistance (CPR) at low temperatures due to electronic phase separation. For use in many applications, such as sensors, materials must exhibit CPR near room temperature. A possible candidate compound is La0.67Sr0.33MnO3 (LSMO) which has a Curie temperature of approximately 350 K. However, bulk LSMO single crystals do not show CPR since such samples are uniformly ferromagnetic and metallic with no phase separation. In this study, we examine the piezoresistance of ultrathin LSMO films grown on SrTiO3 (STO) substrates using a three-point beam bending method to control the compressive and tensile strain. It has been suggested that the lattice mismatch strain due to the substrate induces phase separation in these thin films. We have observed CPR in such strained LSMO thin films even at room temperature. NSF DMR-1410237.

  7. Spectrum Handoffs Based on Preemptive Repeat Priority Queue in Cognitive Radio Networks

    PubMed Central

    Yang, Xiaolong; Tan, Xuezhi; Ye, Liang; Ma, Lin

    2016-01-01

    Cognitive radio can significantly improve the spectrum efficiency, and spectrum handoff is considered as an important functionality to guarantee the quality of service (QoS) of primary users (PUs) and the continuity of data transmission of secondary users (SUs). In this paper, we propose an analytical framework based on a preemptive repeat identical (PRI) M/G/1 queuing network model to characterize spectrum handoff behaviors with general service time distribution of both primary and secondary connections, multiple interruptions and transmission delay resulting from the appearance of primary connections. Then, we derive the close-expression of the extended data delivery and the system sojourn time in both staying and changing scenarios. In addition, based on analysis of spectrum handoff behaviors resulting from multiple interruptions caused by the appearance of the primary connections, we investigate the traffic-adaptive policy, by which the considered SU will optimally adjust its handoff spectrum policy. Moreover, we investigate the admissible region and provide the reference for designing the admission control rule for the arriving secondary connection requests. Finally, simulation results verify that our proposed analytical framework is reasonable and can provide the reference for executing the optimal spectrum handoff strategy and designing the admission control rule for the SU in cognitive radio networks. PMID:27447644

  8. Mechanism of the AAA+ ATPases pontin and reptin in the biogenesis of H/ACA RNPs

    PubMed Central

    Machado-Pinilla, Rosario; Liger, Dominique; Leulliot, Nicolas; Meier, U. Thomas

    2012-01-01

    The AAA+ ATPases pontin and reptin function in a staggering array of cellular processes including chromatin remodeling, transcriptional regulation, DNA damage repair, and assembly of macromolecular complexes, such as RNA polymerase II and small nucleolar (sno) RNPs. However, the molecular mechanism for all of these AAA+ ATPase associated activities is unknown. Here we document that, during the biogenesis of H/ACA RNPs (including telomerase), the assembly factor SHQ1 holds the pseudouridine synthase NAP57/dyskerin in a viselike grip, and that pontin and reptin (as components of the R2TP complex) are required to pry NAP57 from SHQ1. Significantly, the NAP57 domain captured by SHQ1 harbors most mutations underlying X-linked dyskeratosis congenita (X-DC) implicating the interface between the two proteins as a target of this bone marrow failure syndrome. Homing in on the essential first steps of H/ACA RNP biogenesis, our findings provide the first insight into the mechanism of action of pontin and reptin in the assembly of macromolecular complexes. PMID:22923768

  9. Complementation of Agrobacterium tumefaciens tumor-inducing aux mutants by genes from the TR-region of the Ri plasmid of Agrobacterium rhizogenes

    PubMed Central

    Offringa, I. A.; Melchers, L. S.; Regensburg-Tuink, A. J. G.; Costantino, P.; Schilperoort, R. A.; Hooykaas, P. J. J.

    1986-01-01

    In this paper we provide information indicating that the agropine-type root-inducing (Ri) plasmid pRi1855 of Agrobacterium rhizogenes contains functional genes for auxin production (aux) in the right transferred DNA (T-DNA) region (TR-region). These genes were cloned and introduced into the T-region of the tumor-inducing (Ti) plasmids of mutants of Agrobacterium tumefaciens carrying an aux mutation. Depending on the Ri aux gene present, the oncogenicity of the Ti aux-1 and/or aux-2 mutations was restored, showing that the Ri aux genes are able to complement the Ti aux genes. Agrobacterium strains with an agropine-type Ri plasmid not only cause hairy root on certain plant species, but they also induce tumors on other plant species. In this paper it is shown that a mutation in either of the aux genes in the Ri plasmid leads to a total loss of tumorigenicity and a strongly diminished rhizogenicity of the host bacterium, revealing that the aux genes are important for tumor and root induction. Agrobacterium strains containing the TR-region but not the TL (left)-region of the Ri plasmid are still tumorigenic on certain plant species but are no longer capable of hairy-root induction. Images PMID:16593762

  10. Evidence of a double peak in muscle activation to enhance strike speed and force: an example with elite mixed martial arts fighters.

    PubMed

    McGill, Stuart M; Chaimberg, Jon D; Frost, David M; Fenwick, Chad M J

    2010-02-01

    The main issue addressed here is the paradox of muscle contraction to optimize speed and strike force. When muscle contracts, it increases in both force and stiffness. Force creates faster movement, but the corresponding stiffness slows the change of muscle shape and joint velocity. The purpose of this study was to investigate how this speed strength is accomplished. Five elite mixed martial arts athletes were recruited given that they must create high strike force very quickly. Muscle activation using electromyography and 3-dimensional spine motion was measured. A variety of strikes were performed. Many of the strikes intend to create fast motion and finish with a very large striking force, demonstrating a "double peak" of muscle activity. An initial peak was timed with the initiation of motion presumably to enhance stiffness and stability through the body before motion. This appeared to create an inertial mass in the large "core" for limb muscles to "pry" against to initiate limb motion. Then, some muscles underwent a relaxation phase as speed of limb motion increased. A second peak was observed upon contact with the opponent (heavy bag). It was postulated that this would increase stiffness through the body linkage, resulting in a higher effective mass behind the strike and likely a higher strike force. Observation of the contract-relax-contract pulsing cycle during forceful and quick strikes suggests that it may be fruitful to consider pulse training that involves not only the rate of muscle contraction but also the rate of muscle relaxation. PMID:20072065

  11. Ohanin, a novel protein from king cobra venom, induces hypolocomotion and hyperalgesia in mice.

    PubMed

    Pung, Yuh Fen; Wong, Peter T H; Kumar, Prakash P; Hodgson, Wayne C; Kini, R Manjunatha

    2005-04-01

    We have identified, purified, and determined the complete amino acid sequence of a novel protein, ohanin from Ophiophagus hannah (king cobra) venom. It is a small protein containing 107 amino acid residues with a molecular mass of 11951.47 +/- 0.67 Da as assessed by electrospray ionization-mass spectrometry. It does not show similarity to any known families of snake venom proteins and hence is the first member of a new family of snake venom proteins. It shows similarity to PRY and SPRY domain proteins. It is nontoxic up to 10 mg/kg when injected intraperitoneally in mice. Ohanin produced statistically significant and dose-dependent hypolocomotion in mice. In a pain threshold assay, it showed dose-dependent hyperalgesic effect. The ability of the protein to elicit a response at greatly reduced doses when injected intracerebroventricularly as compared with intraperitoneal administration in both the locomotion and hot plate experiments strongly suggests that ohanin acts on the central nervous system. Since the natural abundance of the protein in the venom is low (approximately 1 mg/g), a synthetic gene was constructed and expressed. The recombinant protein, which was obtained in the insoluble fraction in Escherichia coli, was purified under denaturing condition and was refolded. Recombinant ohanin is structurally and functionally similar to native protein as determined by circular dichroism and hot plate assay, suggesting that it will be useful in future structure-function relationship studies. PMID:15668253

  12. Ohanin, a novel protein from king cobra venom: its cDNA and genomic organization.

    PubMed

    Pung, Yuh Fen; Kumar, Sanjeed Vijaya; Rajagopalan, Nandhakishore; Fry, Bryan G; Kumar, Prakash P; Kini, R Manjunatha

    2006-04-26

    Ohanin, from king cobra venom, is a novel protein which induces hypolocomotion and hyperalgesia in mice [Pung, Y.F., Wong, P.T.H., Kumar, P.P., Hodgson W.C., Kini, R.M., 2005. Ohanin, a novel protein from king cobra venom induces hypolocomotion and hyperalgesia in mice. J. Biol. Chem. 280, 13137-13147.]. It is weakly similar to PRY-SPRY domains (B30.2-like domain). Here we report the complete cDNA and genomic organization of ohanin. Interestingly, cDNA sequence does not show significant sequence similarity to any known sequences, including those of B30.2-like domain-containing proteins. Its full-length cDNA sequence of 1558 bp encodes for prepro-ohanin with a propeptide segment at the C-terminal. Ohanin is the first member of a new subfamily of proteins containing B30.2-like domain with short N-terminal segment. We named this subfamily as vespryns. There are two mRNA subtypes differing in their 5'-untranslated regions. Southern hybridization study shows that ohanin is encoded by a single gene. Its genomic sequence is 7086 bp with five exons and four introns, and the two types of mRNAs are generated by alternative splicing of exon 2. Our results indicate that ohanin and vespryns may have evolved from the same ancestral gene as B30.2 domain. PMID:16472942

  13. A Multi-Stage Reverse Logistics Network Problem by Using Hybrid Priority-Based Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Lee, Jeong-Eun; Gen, Mitsuo; Rhee, Kyong-Gu

    Today remanufacturing problem is one of the most important problems regarding to the environmental aspects of the recovery of used products and materials. Therefore, the reverse logistics is gaining become power and great potential for winning consumers in a more competitive context in the future. This paper considers the multi-stage reverse Logistics Network Problem (m-rLNP) while minimizing the total cost, which involves reverse logistics shipping cost and fixed cost of opening the disassembly centers and processing centers. In this study, we first formulate the m-rLNP model as a three-stage logistics network model. Following for solving this problem, we propose a Genetic Algorithm pri (GA) with priority-based encoding method consisting of two stages, and introduce a new crossover operator called Weight Mapping Crossover (WMX). Additionally also a heuristic approach is applied in the 3rd stage to ship of materials from processing center to manufacturer. Finally numerical experiments with various scales of the m-rLNP models demonstrate the effectiveness and efficiency of our approach by comparing with the recent researches.

  14. Inhibition by Ethylene of Auxin-Promotion of Flower Bud Formation in Tobacco Explants Is Absent in Plants Transformed by Agrobacterium rhizogenes

    PubMed Central

    Smulders, Marinus J. M.; Croes, Anton F.; Kemp, Anke; Hese, Karin M.; Harren, Frans; Wullems, George J.

    1991-01-01

    The in vitro regeneration of flower buds was studied in pedicel explants from tobacco (Nicotiana tabacum L., cv Petit Havana) transformed with Agrobacterium rhizogenes, pRi 1855 (agropine type). At a low concentration (0.1 micromolar) of 1-naphthalene-acetic acid, pedicel strips from phenotypically aberrant plants regenerated two to three times more flower buds than explants from untransformed tobacco. Intermediate bud numbers were observed in transformants with a less extreme phenotype. The results can be explained by an increased sensitivity of the transformed explants to auxin with respect to flower bud regeneration. The effect of transformation on the auxin response is fully accounted for by the absence of a negative interaction of endogenous ethylene with 1-naphthaleneacetic acid, a phenomenon normally encountered in untransformed tissues. Three observations led to this conclusion. Application of 1 micromolar AgNO3 to untransformed explants increased the number of flower buds to the level observed in transformed tissues but had no effect on transformed pedicel strips; exposure to 10 microliters per liter ethylene strongly reduced the response to auxin at all concentrations in untransformed explants but was almost ineffective in the transformed tissues; and endogenous ethylene synthesis occurred at the same rate in both types of explants. PMID:16668309

  15. [Subcellular localization and resistance to Botrytis cinerea of a new type lipid transfer protein AtDhyPRP1 from Arabidopsis thaliana].

    PubMed

    Zhang, Chen; Li, Lan; Xu, Ziqin

    2012-05-01

    Genetic transformation was adopted to analyze the subcellular localization and the resistance to fungal pathogens of Arabidopsis lipid transfer protein AtDHyPRP1. The coding sequence of AtDHyPRP1 amplified by PCR from Ws ecotype was used to construct the plant binary expression vector pRI101-AN-AtDHyPRP1 and the fusion expression vector pCAMBIA1302-AtDHyPRP1-GFP. Transgenic tobacco and Arabidopsis plants were produced by leaf disc and floral dip protocols, respectively. AtDHyPRP1 could improve the resistance of tobacco to Botrytis cinerea remarkably and the infection sites on transgenic tobacco leaves accumulated large amounts of H2O2. Observation under laser scanning confocal microscope showed that AtDHyPRP1 was localized to cell surface. It suggested that AtDHyPRP1 might play special function after secretion to outside of the cell and was involved in plant defense system against pathogens. PMID:22916498

  16. Mining Tacitus: secrets of empire, nature and art in the reason of state.

    PubMed

    Keller, Vera

    2012-06-01

    A new political practice, the 'reason of state', informed the ends and practices of natural study in the late sixteenth century. Informed by the study of the Roman historian Tacitus, political writers gathered 'secrets of empire' from both history and travel. Following the economic reorientation of 'reason of state' by Giovanni Botero (1544-1617), such secrets came to include bodies of useful particulars concerning nature and art collected by an expanding personnel of intelligencers. A comparison between various writers describing wide-scale collections, such as Botero, Francis Bacon (1561-1626), Jakob Bornitz (1560-1625) and Matthias Bernegger (1582-1640), reveals that seventeenth-century natural intelligencers across Europe not only were analogous to political intelligencers, but also were sometimes one and the same. Those seeking political prudence cast themselves as miners, prying precious particulars from the recesses of history, experience and disparate disciplines, including mathematics, alchemy and natural philosophy. The seventeenth-century practice of combining searches for secrets of empire, nature and art contests a frequent historiographical divide between empirical science and Tacitism or reason of state. It also points to the ways political cunning shaped the management of information for both politics and the study of nature and art. PMID:23050367

  17. [Transformation of sainfoin by Agrobacterium rhizogenes LBA9402 Bin19 and regeneration of transgenic plants].

    PubMed

    Xu, Z Q; Ma, H J; Hao, J G; Jia, J F

    2000-03-01

    Hypocotyl segments of Onobrychis viciaefolia were transformed by Agrobacterium rhizogenes LBA9402 which harboured pBin19 and pRi1855. Seedling age and preculture time of hypocotyl segments influenced the transformation frequency. Paper electrophoresis revealed that 70% of single hairy root cultures could synthesize agropine. Calli were induced from hairy root segments on MS medium containing 0-9.05 mumol/L 2,4-D and 0-2.22 mumol/L 6-BA at first, then they were transferred onto MS0 medium without kanamycin for regeneration. Constitution and concentration of phytohormones in callus induction media affected subsequent regeneration of calluses on MS0 medium remarkably. Regeneration frequency and shoot number per callus declined when 2,4-D concentration in callus induction media increased from 4.52 to 9.05 mumol/L, while they ascended when 6-BA in callus induction media increased from 0 to 2.22 mumol/L. On MS medium supplemented with 4.52 mumol/L 2,4-D and 2.22 mumol/L 6-BA, only 14.2% hairy root segments could produce calluses, but the regeneration frequency reached 58.1% and the shoot number per callus was 37.2. In 32 analysed plants regenerated from 8 kanamycin resistant hairy root lines, 25 were nptII positive and showed different copy numbers. PMID:12548853

  18. Enhancing the Apoptotic Effect of a Low Dose of Paclitaxel on Tumor Cells in Mice by Arabinoxylan Rice Bran (MGN-3/Biobran).

    PubMed

    Badr El-Din, Nariman K; Ali, Doaa A; Alaa El-Dein, Mai; Ghoneum, Mamdooh

    2016-01-01

    In this study, we examine the ability of arabinoxylan rice bran (MGN-3/Biobran) to enhance the apoptotic effect of paclitaxel (Taxol) at low concentration [2 mg/kg body weight (BW)] in animals bearing Ehrlich ascites carcinoma (EAC) cells and elucidate its mechanisms of action. On Day 8 following tumor cells inoculation, mice bearing tumors were administered MGN-3 alone (40 mg/kg BW), paclitaxel alone, or MGN-3 plus paclitaxel. On Day 30 post-tumor inoculation, we observed significant suppression of tumor volume (TV) with paclitaxel alone (59%), MGN-3 alone (77%), and MGN-3 plus paclitaxel (88%). Inhibition of tumor growth post-treatment with both agents, as compared with either treatment alone, was associated with a decrease in cell proliferation, a marked increase in the sub-G0/G1 population, an increase in DNA damage and apoptosis of tumor cells, and a significant maximization of the apoptosis index (AI)/proliferation index (PrI) ratio. Histopathological and electron microscopy examination of the combined treatment group showed an increase in the degenerative regions of the solid tumor tissue and abundant apoptotic cells. These data suggest that MGN-3 supplementation enhances tumor cell demise in the presence of a low dose of chemotherapeutic agent via apoptotic mechanism. PMID:27367621

  19. Development of in-situ imaging tools to quantify vegetation stress, plant mortality, and species composition

    NASA Astrophysics Data System (ADS)

    Goulden, M.

    2014-12-01

    We have developed and deployed an imaging system at an eddy covariance site in a Southern California Pinyon-Juniper woodland; our goals are to quantify the species-level patterns of stress and mortality over time, and also to learn how to better interpret the Landsat record. Our imaging system combines a four channel spectrometer with cameras that are sensitive to Visible, Near Infrared (NIR), Shortwave Infrared (SWIR), and Thermal radiation; these cameras include filters that mimic the spectral sensitivity of several Landsat bands. The cameras and spectrometer foreoptic are positioned on a pan-tilt mount on the tower that scans a 300o x 90o area every hour and allows us to collect images of hundreds of distinct plants. The imaging system is being used to test several approaches that have been proposed to detect vegetation stress, mortality, and species composition. We are exploring the potential to detect stomatal closure and stress by: a) increased canopy temperature with decreased evaporative cooling, b) Photochemical Reflectance Index (PRI), c) Fraunhofer line fluorescence, and d) water band indices. Similarly, we are exploring the potential to detect plant mortality by: a) NIR reflectance, b) SWIR reflectance, and c) radiance temperature with soil exposure, and to identify plant species by: a) differential phenological and interannual patterns, b) spectral reflectance, and c) BRDF and the effect of solar angle.

  20. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain.

    PubMed

    Vesely, Cornelia; Tauber, Stefanie; Sedlazeck, Fritz J; Tajaddod, Mansoureh; von Haeseler, Arndt; Jantsch, Michael F

    2014-10-29

    Adenosine deaminases that act on RNA (ADARs) deaminate adenosines to inosines in double-stranded RNAs including miRNA precursors. A to I editing is widespread and required for normal life. By comparing deep sequencing data of brain miRNAs from wild-type and ADAR2 deficient mouse strains, we detect editing sites and altered miRNA processing at high sensitivity. We detect 48 novel editing events in miRNAs. Some editing events reach frequencies of up to 80%. About half of all editing events depend on ADAR2 while some miRNAs are preferentially edited by ADAR1. Sixty-four percent of all editing events are located within the seed region of mature miRNAs. For the highly edited miR-3099, we experimentally prove retargeting of the edited miRNA to novel 3' UTRs. We show further that an abundant editing event in miR-497 promotes processing by Drosha of the corresponding pri-miRNA. We also detect reproducible changes in the abundance of specific miRNAs in ADAR2-deficient mice that occur independent of adjacent A to I editing events. This indicates that ADAR2 binding but not editing of miRNA precursors may influence their processing. Correlating with changes in miRNA abundance we find misregulation of putative targets of these miRNAs in the presence or absence of ADAR2. PMID:25260591