Science.gov

Sample records for 3-digit zip code

  1. Changing Postal ZIP Code Boundaries

    DTIC Science & Technology

    2006-06-23

    for distribution to a specific delivery post office, identified by the fourth and fifth digits. For example, the ZIP Code for Alturas , the county seat...distribution point for some California post offices such as Alturas , Cedarville (96104), Fort Bidwell (96112), and Likely (96116), distinguished by the

  2. 77 FR 18716 - Transportation Security Administration Postal Zip Code Change; Technical Amendment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-28

    ... Postal Zip Code Change; Technical Amendment AGENCY: Transportation Security Administration, DHS. ACTION... zip code. This rule revises existing regulations to reflect organizational changes and it has no.... Background Beginning December 17, 2008, the postal zip codes for TSA headquarters facilities in Virginia...

  3. Application Of Mathematical Morphology To Handwritten ZIP Code Recognition

    NASA Astrophysics Data System (ADS)

    Gillies, Andrew M.; Gader, Paul D.; Whalen, Michael P.; Mitchell, Brian T.

    1989-11-01

    This paper describes applications of mathematical morphology to a system for recognizing handwritten ZIP Codes. It discusses morphological techniques used for preprocessing address block images, locating address block lines, splitting touching characters, and identifying handwritten numerals. These techniques combine mathematical morphology, hierarchical matching of object models to symbolic image representations, and a strategy of propagating multiple hypotheses. The various submodules of the system have been trained on over two thousand real address block images and tested on one thousand representative images. On the one thousand test images, the system correctly located 82.5 percent, correctly identified 45.6 percent, and incorrectly classified only 0.8% of the ZIP Codes. This system performance level could lead to a significant cost savings in mail piece sorting.

  4. Using ZIP code business patterns data to measure alcohol outlet density.

    PubMed

    Matthews, Stephen A; McCarthy, John D; Rafail, Patrick S

    2011-07-01

    Some states maintain high-quality alcohol outlet databases but quality varies by state, making comprehensive comparative analysis across US communities difficult. This study assesses the adequacy of using ZIP Code Business Patterns (ZIP-BP) data on establishments as estimates of the number of alcohol outlets by ZIP code. Specifically we compare ZIP-BP alcohol outlet counts with high-quality data from state and local records surrounding 44 college campus communities across 10 states plus the District of Columbia. Results show that a composite measure is strongly correlated (R=0.89) with counts of alcohol outlets generated from official state records. Analyses based on Generalized Estimation Equation models show that community and contextual factors have little impact on the concordance between the two data sources. There are also minimal inter-state differences in the level of agreement. To validate the use of a convenient secondary data set (ZIP-BP) it is important to have a high correlation with the more complex, high quality and more costly data product (i.e., datasets based on the acquisition and geocoding of state and local records) and then to clearly demonstrate that the discrepancy between the two to be unrelated to relevant explanatory variables. Thus our overall findings support the adequacy of using a conveniently available data set (ZIP-BP data) to estimate alcohol outlet densities in ZIP code areas in future research.

  5. Why Your ZIP Code Matters More Than Your Genetic Code: Promoting Healthy Outcomes from Mother to Child.

    PubMed

    Graham, Garth N

    2016-10-01

    Health equity has long been the dominant theme in the work of the Aetna Foundation. Recent data have focused on disparities through another lens, particularly the correlation between where people live (i.e., ZIP code) and their quality-and length-of life. In various cities across America, average life expectancies in certain communities are 20-30 years shorter than those mere miles away. In general, health disparities are founded on a complex interplay of racial, economic, educational, and other social factors. For example, breastfeeding rates in the United States differ significantly depending upon the race and income of the mother. Government policy makers are acutely aware of these disparities, but recent health system reforms have focused predominately on the processes used to administer, finance, and deliver care. What is needed is an approach that considers the health and wellness of all people in a geographic area, beyond established patients, and that measures more than clinical factors-such as genetics, environmental health, social circumstances, and individual behaviors. Solutions also must extend beyond the traditional healthcare arena. In particular, novel technological innovations show promise to bridge gaps between our healthcare capabilities and the needs of underserved populations. Digital tools are poised to revolutionize measurement, diagnostics, treatment, and global aspect of our healthcare system. The Aetna Foundation views technology as a core strategy in reducing health inequities through an approach that addresses both clinical and social factors in populations to dismantle the persistent paradigm of ZIP code as personal health destiny.

  6. Diagnosis of HNF-1alpha mutations on a PNA zip-code microarray by single base extension.

    PubMed

    Song, Jae Yang; Park, Hyun Gyu; Jung, Sung-Ouk; Park, JaeChan

    2005-02-01

    In the present study, we exploited the superior features of peptide nucleic acids (PNAs) to develop an efficient PNA zip-code microarray for the detection of hepatocyte nuclear factor-1alpha (HNF-1alpha) mutations that cause type 3 maturity onset diabetes of the young (MODY). A multi-epoxy linker compound was synthesized and used to achieve an efficient covalent linking of amine-modified PNA to an aminated glass surface. PCR was performed to amplify the genomic regions containing the mutation sites. The PCR products were then employed as templates in a subsequent multiplex single base extension reaction using chimeric primers with 3' complementarity to the specific mutation site and 5' complementarity to the respective PNA zip-code sequence on the microarray. The primers were extended by a single base at each corresponding mutation site in the presence of biotin-labeled ddNTPs, and the products were hybridized to the PNA microarray. Compared to the corresponding DNA, the PNA zip-code sequence showed a much higher duplex specificity for the complementary DNA sequence. The PNA zip-code microarray was finally stained with streptavidin-R-phycoerythrin to generate a fluorescent signal. Using this strategy, we were able to correctly diagnose several mutation sites in exon 2 of HNF-1alpha with a wild-type and mutant samples including a MODY3 patient. This work represents one of the few successful applications of PNA in DNA chip technology.

  7. Bias with respect to socioeconomic status: A closer look at zip code matching in a pneumococcal vaccine effectiveness study.

    PubMed

    Link-Gelles, Ruth; Westreich, Daniel; Aiello, Allison E; Shang, Nong; Weber, David J; Holtzman, Corinne; Scherzinger, Karen; Reingold, Arthur; Schaffner, William; Harrison, Lee H; Rosen, Jennifer B; Petit, Susan; Farley, Monica; Thomas, Ann; Eason, Jeffrey; Wigen, Christine; Barnes, Meghan; Thomas, Ola; Zansky, Shelley; Beall, Bernard; Whitney, Cynthia G; Moore, Matthew R

    2016-12-01

    In 2010, 13-valent pneumococcal conjugate vaccine (PCV13) was introduced in the US for prevention of invasive pneumococcal disease in children. Individual-level socioeconomic status (SES) is a potential confounder of the estimated effectiveness of PCV13 and is often controlled for in observational studies using zip code as a proxy. We assessed the utility of zip code matching for control of SES in a post-licensure evaluation of the effectiveness of PCV13 (calculated as [1-matched odds ratio]*100). We used a directed acyclic graph to identify subsets of confounders and collected SES variables from birth certificates, geo-coding, a parent interview, and follow-up with medical providers. Cases tended to be more affluent than eligible controls (for example, 48.3% of cases had private insurance vs. 44.6% of eligible controls), but less affluent than enrolled controls (52.9% of whom had private insurance). Control of confounding subsets, however, did not result in a meaningful change in estimated vaccine effectiveness (original estimate: 85.1%, 95% CI 74.8-91.9%; adjusted estimate: 82.5%, 95% CI 65.6-91.1%). In the context of a post-licensure vaccine effectiveness study, zip code appears to be an adequate, though not perfect, proxy for individual SES.

  8. The role of complement in age-related macular degeneration: heparan sulphate, a ZIP code for complement factor H?

    PubMed

    Langford-Smith, Alex; Keenan, Tiarnan D L; Clark, Simon J; Bishop, Paul N; Day, Anthony J

    2014-01-01

    Age-related macular degeneration (AMD) is the leading cause of blindness in developed nations and has been associated with complement dysregulation in the central retina. The Y402H polymorphism in the complement regulatory protein factor H (CFH) can confer a >5-fold increased risk of developing AMD and is present in approximately 30% of people of European descent. CFH, in conjunction with other factors, regulates complement activation in host tissues, and the Y402H polymorphism has been found to alter the protein's specificity for heparan sulphate (HS) - a complex polysaccharide found ubiquitously in mammals. HS, which is present on the cell surface and also in the extracellular matrix, exhibits huge structural diversity due to variations in the level/pattern of sulphation, where particular structures may act as 'ZIP codes' for different tissue/cellular locations. Recent work has demonstrated that CFH contains two HS-binding domains that each recognize specific HS ZIP codes, allowing differential recognition of Bruch's membrane (in the eye) or the glomerular basement membrane (in the kidney). Importantly, the Y402H polymorphism impairs the binding of CFH to the HS in Bruch's membrane, which could result in increased complement activation and chronic local inflammation (in 402H individuals) and thereby contribute to AMD pathology.

  9. Enhanced Gene Expression Rather than Natural Polymorphism in Coding Sequence of the OsbZIP23 Determines Drought Tolerance and Yield Improvement in Rice Genotypes

    PubMed Central

    Dey, Avishek; Samanta, Milan Kumar; Gayen, Srimonta; Sen, Soumitra K.; Maiti, Mrinal K.

    2016-01-01

    Drought is one of the major limiting factors for productivity of crops including rice (Oryza sativa L.). Understanding the role of allelic variations of key regulatory genes involved in stress-tolerance is essential for developing an effective strategy to combat drought. The bZIP transcription factors play a crucial role in abiotic-stress adaptation in plants via abscisic acid (ABA) signaling pathway. The present study aimed to search for allelic polymorphism in the OsbZIP23 gene across selected drought-tolerant and drought-sensitive rice genotypes, and to characterize the new allele through overexpression (OE) and gene-silencing (RNAi). Analyses of the coding DNA sequence (CDS) of the cloned OsbZIP23 gene revealed single nucleotide polymorphism at four places and a 15-nucleotide deletion at one place. The single-copy OsbZIP23 gene is expressed at relatively higher level in leaf tissues of drought-tolerant genotypes, and its abundance is more in reproductive stage. Cloning and sequence analyses of the OsbZIP23-promoter from drought-tolerant O. rufipogon and drought-sensitive IR20 cultivar showed variation in the number of stress-responsive cis-elements and a 35-nucleotide deletion at 5’-UTR in IR20. Analysis of the GFP reporter gene function revealed that the promoter activity of O. rufipogon is comparatively higher than that of IR20. The overexpression of any of the two polymorphic forms (1083 bp and 1068 bp CDS) of OsbZIP23 improved drought tolerance and yield-related traits significantly by retaining higher content of cellular water, soluble sugar and proline; and exhibited decrease in membrane lipid peroxidation in comparison to RNAi lines and non-transgenic plants. The OE lines showed higher expression of target genes-OsRab16B, OsRab21 and OsLEA3-1 and increased ABA sensitivity; indicating that OsbZIP23 is a positive transcriptional-regulator of the ABA-signaling pathway. Taken together, the present study concludes that the enhanced gene expression rather

  10. Enhanced Gene Expression Rather than Natural Polymorphism in Coding Sequence of the OsbZIP23 Determines Drought Tolerance and Yield Improvement in Rice Genotypes.

    PubMed

    Dey, Avishek; Samanta, Milan Kumar; Gayen, Srimonta; Sen, Soumitra K; Maiti, Mrinal K

    2016-01-01

    Drought is one of the major limiting factors for productivity of crops including rice (Oryza sativa L.). Understanding the role of allelic variations of key regulatory genes involved in stress-tolerance is essential for developing an effective strategy to combat drought. The bZIP transcription factors play a crucial role in abiotic-stress adaptation in plants via abscisic acid (ABA) signaling pathway. The present study aimed to search for allelic polymorphism in the OsbZIP23 gene across selected drought-tolerant and drought-sensitive rice genotypes, and to characterize the new allele through overexpression (OE) and gene-silencing (RNAi). Analyses of the coding DNA sequence (CDS) of the cloned OsbZIP23 gene revealed single nucleotide polymorphism at four places and a 15-nucleotide deletion at one place. The single-copy OsbZIP23 gene is expressed at relatively higher level in leaf tissues of drought-tolerant genotypes, and its abundance is more in reproductive stage. Cloning and sequence analyses of the OsbZIP23-promoter from drought-tolerant O. rufipogon and drought-sensitive IR20 cultivar showed variation in the number of stress-responsive cis-elements and a 35-nucleotide deletion at 5'-UTR in IR20. Analysis of the GFP reporter gene function revealed that the promoter activity of O. rufipogon is comparatively higher than that of IR20. The overexpression of any of the two polymorphic forms (1083 bp and 1068 bp CDS) of OsbZIP23 improved drought tolerance and yield-related traits significantly by retaining higher content of cellular water, soluble sugar and proline; and exhibited decrease in membrane lipid peroxidation in comparison to RNAi lines and non-transgenic plants. The OE lines showed higher expression of target genes-OsRab16B, OsRab21 and OsLEA3-1 and increased ABA sensitivity; indicating that OsbZIP23 is a positive transcriptional-regulator of the ABA-signaling pathway. Taken together, the present study concludes that the enhanced gene expression rather than

  11. A Comparison of the Nutritional Quality of Food Products Advertised in Grocery Store Circulars of High- versus Low-Income New York City Zip Codes

    PubMed Central

    Ethan, Danna; Basch, Corey H.; Rajan, Sonali; Samuel, Lalitha; Hammond, Rodney N.

    2013-01-01

    Grocery stores can be an important resource for health and nutrition with the variety and economic value of foods offered. Weekly circulars are a means of promoting foods at a sale price. To date, little is known about the extent that nutritious foods are advertised and prominently placed in circulars. This study’s aim was to compare the nutritional quality of products advertised on the front page of online circulars from grocery stores in high- versus low-income neighborhoods in New York City (NYC). Circulars from grocery stores in the five highest and five lowest median household income NYC zip codes were analyzed. Nutrition information for food products was collected over a two-month period with a total of 805 products coded. The study found no significant difference between the nutritional quality of products advertised on the front page of online circulars from grocery stores in high- versus low-income neighborhoods in New York City (NYC). In both groups, almost two-thirds of the products advertised were processed, one-quarter were high in carbohydrates, and few to no products were low-sodium, high-fiber, or reduced-, low- or zero fat. Through innovative partnerships with health professionals, grocery stores are increasingly implementing in-store and online health promotion strategies. Weekly circulars can be used as a means to regularly advertise and prominently place more healthful and seasonal foods at an affordable price, particularly for populations at higher risk for nutrition-related chronic disease. PMID:24384775

  12. A comparison of the nutritional quality of food products advertised in grocery store circulars of high- versus low-income New York City zip codes.

    PubMed

    Ethan, Danna; Basch, Corey H; Rajan, Sonali; Samuel, Lalitha; Hammond, Rodney N

    2013-12-31

    Grocery stores can be an important resource for health and nutrition with the variety and economic value of foods offered. Weekly circulars are a means of promoting foods at a sale price. To date, little is known about the extent that nutritious foods are advertised and prominently placed in circulars. This study's aim was to compare the nutritional quality of products advertised on the front page of online circulars from grocery stores in high- versus low-income neighborhoods in New York City (NYC). Circulars from grocery stores in the five highest and five lowest median household income NYC zip codes were analyzed. Nutrition information for food products was collected over a two-month period with a total of 805 products coded. The study found no significant difference between the nutritional quality of products advertised on the front page of online circulars from grocery stores in high- versus low-income neighborhoods in New York City (NYC). In both groups, almost two-thirds of the products advertised were processed, one-quarter were high in carbohydrates, and few to no products were low-sodium, high-fiber, or reduced-, low- or zero fat. Through innovative partnerships with health professionals, grocery stores are increasingly implementing in-store and online health promotion strategies. Weekly circulars can be used as a means to regularly advertise and prominently place more healthful and seasonal foods at an affordable price, particularly for populations at higher risk for nutrition-related chronic disease.

  13. Moderate zinc deficiency reduces testicular Zip6 and Zip10 abundance and impairs spermatogenesis in mice.

    PubMed

    Croxford, Thomas P; McCormick, Nicholas H; Kelleher, Shannon L

    2011-03-01

    Male infertility accounts for ~40% of cases of failure to conceive. Testes have a strict zinc (Zn) requirement and severe Zn deficiency compromises spermatogenesis, sperm viability, and motility, compromising fertility in men. Despite the high prevalence of marginal Zn deficiency in humans, less emphasis has been placed on understanding the consequences on male reproduction. Swiss Webster mice were used to visualize Zip protein expression during spermatogenesis using immunohistochemistry. Data suggest Zip5 imports Zn into Sertoli cells and spermatocytes, augmented by Zip10 (primary spermatocytes) and Zip8 (secondary spermatocytes). Zip6, 8, and 10 expression was retained in round spermatids, although Zip8 and Zip10 expression disappears during spermatid maturation. Zip1 and Zip6 expression was detected in mature, elongated spermatids. Zip14 was detected in undifferentiated spermatogonia and Leydig cells. Mice fed diets (n = 10/group) reduced in Zn concentration [marginal-Zn diet (MZD), 10 mg Zn/kg; low-Zn diet (ZD), 7 mg Zn/kg] for 30 d had >35% lower liver Zn concentrations than mice fed the control diet (C; 30 mg Zn/kg) (P < 0.05). Plasma Zn and testosterone concentrations and the testes Zn concentration and weight were not significantly lower than in controls. Plasma Zn was greater in the ZD group than in the C and MZD groups. Mice fed ZD had a reduced number of terminal deoxynucleotidyl transferase dUTP nick end labeling-positive cells (~50%; P < 0.05), compromised seminiferous tubule structure, and reduced Zip10 and Zip6 abundance (>50%; P < 0.5) compared with mice fed C. Our data provide compelling evidence that reduced Zn intake may be associated with infertility in men, perhaps independent of decreased levels of circulating Zn or testosterone, which warrants further investigation in human populations.

  14. Effect of ZIP2 Gln/Arg/Leu (rs2234632) polymorphism on zinc homeostasis and inflammatory response following zinc supplementation.

    PubMed

    Giacconi, Robertina; Costarelli, Laura; Malavolta, Marco; Cardelli, Maurizio; Galeazzi, Roberta; Piacenza, Francesco; Gasparini, Nazzarena; Basso, Andrea; Mariani, Erminia; Fulop, Tamas; Rink, Lothar; Dedoussis, George; Herbein, Georges; Jajte, Jolanta; Provinciali, Mauro; Busco, Franco; Mocchegiani, Eugenio

    2015-01-01

    Zinc dyshomeostasis may lead to an augmented production of proinflammatory cytokines promoting chronic inflammation and increasing the susceptibility to age-related diseases. Several studies suggest that the zinc transporter protein ZIP2 may play a relevant role in the immune system especially during zinc deficiency, while a polymorphism on the coding region of ZIP2 gene (Gln/Arg/Leu) has been associated with severe carotid artery disease. The aim of this study is to investigate the role of ZIP2 SNP on zinc and inflammatory status in 1090 elderly healthy free-living subjects enrolled in the ZincAge project and to assess the effect of zinc supplementation on zinc status, inflammatory mediators, and zinc transporter expression depending on ZIP2 genotype. ZIP2 Leu- (Arg43Arg) carriers showed enhanced IL-6, TNF-α, and RANTES plasma levels associated with decreased free cytosolic zinc in PBMCs and an upregulation of zinc transporters ZIP2, ZIP8, and Znt1. Moreover, Leu- subjects displayed significant decrement of inflammatory mediators such as MCP-1, TNF-α, and RANTES following zinc supplementation. In summary, this investigation provides new evidence on the effect of ZIP2 Gln/Arg/Leu polymorphism on proinflammatory mediators and zinc homeostasis in elderly population with a more pronounced anti-inflammatory effect of zinc supplementation in subjects carrying ZIP2 Leu- (Arg43Arg) genotype. These novel findings could be useful in identifying elderly subjects who may benefit of zinc intervention to decrease the inflammatory status and to prevent or delay the development of age-related diseases.

  15. Zip1, Zip2, and Zip8 mRNA expressions were associated with growth hormone level during the growth hormone provocation test in children with short stature.

    PubMed

    Sun, Ping; Wang, Shifu; Jiang, Yali; Tao, Yanting; Tian, Yuanyuan; Zhu, Kai; Wan, Haiyan; Zhang, Lehai; Zhang, Lianying

    2013-10-01

    Short stature of children is affected by multiple factors. One of them is growth hormone (GH) deficiency. Growth hormone therapy can increase the final height of children with growth hormone deficiency. Zinc is found to induce dimerization and to enhance the bioactivity of human GH. Two gene families have been identified involved in zinc homeostasis. Previous studies in our laboratory have shown that Zip1, Zip2, Zip6, and ZnT1 mRNA were associated with zinc level in established human breast cancer in nude mice model; Zip8 was significantly lower in zinc-deficient Wistar rats in kidney. In this study, five zinc transporters: Zip1, Zip2, Zip6, Zip8, and ZnT1 were chosen. We aimed to investigate the mRNA expression of zinc transporters and to explore the relationship between zinc transporters and growth hormone in short stature children. Growth hormone provocation test is used to confirm the diagnosis of growth hormone deficiency. Six short children for the test were enrolled. At the same time, 15 sex- and age-matched normal children were enrolled as control. The expression levels of zinc transporters in peripheral blood mononuclear cells were determined by quantitative real-time PCR. Zip1 and Zip2 mRNA expression positively correlated with growth hormone level (r = 0.5133, P = 0.0371; r = 0.6719, P = 0.0032); Zip8 mRNA expression negatively correlated with growth hormone level (r = -0.5264, P = 0.0285) during the test in short stature children. The average expression level of Zip2 was significantly higher and Zip6, Zip8 mRNA levels were significantly lower in short stature children than in health controls at 0 min (P < 0.05, P < 0.05).

  16. Zinc transporter ZIP10 forms a heteromer with ZIP6 which regulates embryonic development and cell migration

    PubMed Central

    Taylor, Kathryn M.; Muraina, Issa A.; Brethour, Dylan; Schmitt-Ulms, Gerold; Nimmanon, Thirayost; Ziliotto, Silvia; Kille, Peter; Hogstrand, Christer

    2016-01-01

    There is growing evidence that zinc and its transporters are involved in cell migration during development and in cancer. In the present study, we show that zinc transporter ZIP10 (SLC39A10) stimulates cell motility and proliferation, both in mammalian cells and in the zebrafish embryo. This is associated with inactivation of GSK (glycogen synthase kinase)-3α and -3β and down-regulation of E-cadherin (CDH1). Morpholino-mediated knockdown of zip10 causes delayed epiboly and deformities of the head, eye, heart and tail. Furthermore, zip10 deficiency results in overexpression of cdh1, zip6 and stat3, the latter gene product driving transcription of both zip6 and zip10. The non-redundant requirement of Zip6 and Zip10 for epithelial to mesenchymal transition (EMT) is consistent with our finding that they exist as a heteromer. We postulate that a subset of ZIPs carrying prion protein (PrP)-like ectodomains, including ZIP6 and ZIP10, are integral to cellular pathways and plasticity programmes, such as EMT. PMID:27274087

  17. Zinc transporter ZIP10 forms a heteromer with ZIP6 which regulates embryonic development and cell migration.

    PubMed

    Taylor, Kathryn M; Muraina, Issa A; Brethour, Dylan; Schmitt-Ulms, Gerold; Nimmanon, Thirayost; Ziliotto, Silvia; Kille, Peter; Hogstrand, Christer

    2016-08-15

    There is growing evidence that zinc and its transporters are involved in cell migration during development and in cancer. In the present study, we show that zinc transporter ZIP10 (SLC39A10) stimulates cell motility and proliferation, both in mammalian cells and in the zebrafish embryo. This is associated with inactivation of GSK (glycogen synthase kinase)-3α and -3β and down-regulation of E-cadherin (CDH1). Morpholino-mediated knockdown of zip10 causes delayed epiboly and deformities of the head, eye, heart and tail. Furthermore, zip10 deficiency results in overexpression of cdh1, zip6 and stat3, the latter gene product driving transcription of both zip6 and zip10 The non-redundant requirement of Zip6 and Zip10 for epithelial to mesenchymal transition (EMT) is consistent with our finding that they exist as a heteromer. We postulate that a subset of ZIPs carrying prion protein (PrP)-like ectodomains, including ZIP6 and ZIP10, are integral to cellular pathways and plasticity programmes, such as EMT.

  18. 39 CFR Appendix A to Part 121 - Tables Depicting Service Standard Day Ranges

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... & USVI Periodicals 1 1-3 1 1-3 1-4 (AK) 11 (JNU) 11 (KTN) 1 (HI) 2 (GU) 1-4 10-11 10 8-10 Standard Mail 2... = Juneau AK 3-digit ZIP Code 998; KTN = Ketchikan AK 3-digit ZIP Code 999; HI = Hawaii 3-digit ZIP...

  19. 39 CFR Appendix A to Part 121 - Tables Depicting Service Standard Day Ranges

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... & USVI Periodicals 1 1-3 1 1-3 1-4 (AK) 11 (JNU) 11 (KTN) 1 (HI) 2 (GU) 1-4 10-11 10 8-10 Standard Mail 2... = Juneau AK 3-digit ZIP Code 998; KTN = Ketchikan AK 3-digit ZIP Code 999; HI = Hawaii 3-digit ZIP...

  20. A novel wheat bZIP transcription factor, TabZIP60, confers multiple abiotic stress tolerances in transgenic Arabidopsis.

    PubMed

    Zhang, Lina; Zhang, Lichao; Xia, Chuan; Zhao, Guangyao; Liu, Ji; Jia, Jizeng; Kong, Xiuying

    2015-04-01

    The basic region/leucine zipper (bZIP) transcription factors (TFs) play vital roles in the response to abiotic stress. However, little is known about the function of bZIP genes in wheat abiotic stress. In this study, we report the isolation and functional characterization of the TabZIP60 gene. Three homologous genome sequences of TabZIP60 were isolated from hexaploid wheat and mapped to the wheat homoeologous group 6. A subcellular localization analysis indicated that TabZIP60 is a nuclear-localized protein that activates transcription. Furthermore, TabZIP60 gene transcripts were strongly induced by polyethylene glycol, salt, cold and exogenous abscisic acid (ABA) treatments. Further analysis showed that the overexpression of TabZIP60 in Arabidopsis resulted in significantly improved tolerances to drought, salt, freezing stresses and increased plant sensitivity to ABA in seedling growth. Meanwhile, the TabZIP60 was capable of binding ABA-responsive cis-elements that are present in promoters of many known ABA-responsive genes. A subsequent analysis showed that the overexpression of TabZIP60 led to enhanced expression levels of some stress-responsive genes and changes in several physiological parameters. Taken together, these results suggest that TabZIP60 enhances multiple abiotic stresses through the ABA signaling pathway and that modifications of its expression may improve multiple stress tolerances in crop plants.

  1. A ZIP6-ZIP10 heteromer controls NCAM1 phosphorylation and integration into focal adhesion complexes during epithelial-to-mesenchymal transition

    PubMed Central

    Brethour, Dylan; Mehrabian, Mohadeseh; Williams, Declan; Wang, Xinzhu; Ghodrati, Farinaz; Ehsani, Sepehr; Rubie, Elizabeth A.; Woodgett, James R.; Sevalle, Jean; Xi, Zhengrui; Rogaeva, Ekaterina; Schmitt-Ulms, Gerold

    2017-01-01

    The prion protein (PrP) evolved from the subbranch of ZIP metal ion transporters comprising ZIPs 5, 6 and 10, raising the prospect that the study of these ZIPs may reveal insights relevant for understanding the function of PrP. Building on data which suggested PrP and ZIP6 are critical during epithelial-to-mesenchymal transition (EMT), we investigated ZIP6 in an EMT paradigm using ZIP6 knockout cells, mass spectrometry and bioinformatic methods. Reminiscent of PrP, ZIP6 levels are five-fold upregulated during EMT and the protein forms a complex with NCAM1. ZIP6 also interacts with ZIP10 and the two ZIP transporters exhibit interdependency during their expression. ZIP6 contributes to the integration of NCAM1 in focal adhesion complexes but, unlike cells lacking PrP, ZIP6 deficiency does not abolish polysialylation of NCAM1. Instead, ZIP6 mediates phosphorylation of NCAM1 on a cluster of cytosolic acceptor sites. Substrate consensus motif features and in vitro phosphorylation data point toward GSK3 as the kinase responsible, and interface mapping experiments identified histidine-rich cytoplasmic loops within the ZIP6/ZIP10 heteromer as a novel scaffold for GSK3 binding. Our data suggests that PrP and ZIP6 inherited the ability to interact with NCAM1 from their common ZIP ancestors but have since diverged to control distinct posttranslational modifications of NCAM1. PMID:28098160

  2. Investigation of Super*Zip separation joint

    NASA Technical Reports Server (NTRS)

    Bement, Laurence J.; Schimmel, Morry L.

    1988-01-01

    An investigation to determine the most likely cause of two failures of five tests on 79 inch diameter Lockheed Super*Zip spacecraft separation joints being used for the development of a Shuttle/Centaur propulsion system. This joint utilizes an explosively expanded tube to fracture surrounding prenotched aluminum plates to achieve planar separation. A test method was developed and more than 300 tests firings were made to provide an understanding of severance mechanisms and the functional performance effects of system variables. An approach for defining functional margin was developed, and specific recommendations were made for improving existing and future systems.

  3. Characterization of poplar ZIP family members ZIP1 and ZNT1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A plant must regulate heavy metals to maintain adequate resources for plant processes while protecting against excess metal damage. Regulation of heavy metals such as zinc (Zn) has been attributed to the Zn transporter ZNT1 gene and other members of its larger ZIP transporter family. However, these ...

  4. 39 CFR Appendix A to Part 121 - Tables Depicting Service Standard Day Ranges

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Hawaii, Guam, & American Samoa Puerto Rico & USVI Periodicals 1 1-3 1 1-3 1-4 (AK)11 (JNU) 11 (KTN) 1 (HI...-digit ZIP Code 999; HI = Hawaii 3-digit ZIP Codes 967 and 968; GU = Guam 3-digit ZIP Code 969....

  5. A conserved proline residue in the leucine zipper region of AtbZIP34 and AtbZIP61 in Arabidopsis thaliana interferes with the formation of homodimer

    SciTech Connect

    Shen Huaishun; Cao Kaiming; Wang Xiping

    2007-10-19

    Two putative Arabidopsis E group bZIP transcript factors, AtbZIP34 and AtbZIP61, are nuclear-localized and their transcriptional activation domain is in their N-terminal region. By searching GenBank, we found other eight plant homologues of AtbZIP34 and AtbZIP61. All of them have a proline residue in the third heptad of zipper region. Yeast two-hybrid assay and EMSA showed that AtbZIP34 and AtbZIP61 could not form homodimer while their mutant forms, AtbZIP34m and AtbZIP61m, which the proline residue was replaced by an alanine residue in the zipper region, could form homodimer and bind G-box element. These results suggest that the conserved proline residue interferes with the homodimer formation. However, both AtbZIP34 and AtbZIP61 could form heterodimers with members of I group and S group transcription factors in which some members involved in vascular development. So we speculate that AtbZIP34 and AtbZIP61 may participate in plant development via interacting with other group bZIP transcription factors.

  6. Family reunion--the ZIP/prion gene family.

    PubMed

    Ehsani, Sepehr; Huo, Hairu; Salehzadeh, Ashkan; Pocanschi, Cosmin L; Watts, Joel C; Wille, Holger; Westaway, David; Rogaeva, Ekaterina; St George-Hyslop, Peter H; Schmitt-Ulms, Gerold

    2011-03-01

    Prion diseases are fatal neurodegenerative diseases of humans and animals which, in addition to sporadic and familial modes of manifestation, can be acquired via an infectious route of propagation. In disease, the prion protein (PrP(C)) undergoes a structural transition to its disease-causing form (PrP(Sc)) with profoundly different physicochemical properties. Surprisingly, despite intense interest in the prion protein, its function in the context of other cellular activities has largely remained elusive. We recently employed quantitative mass spectrometry to characterize the interactome of the prion protein in a murine neuroblastoma cell line (N2a), an established cell model for prion replication. Extensive bioinformatic analyses subsequently established an evolutionary link between the prion gene family and the family of ZIP (Zrt-, Irt-like protein) metal ion transporters. More specifically, sequence alignments, structural threading data and multiple additional pieces of evidence placed a ZIP5/ZIP6/ZIP10-like ancestor gene at the root of the PrP gene family. In this review we examine the biology of prion proteins and ZIP transporters from the viewpoint of a shared phylogenetic origin. We summarize and compare available data that shed light on genetics, function, expression, signaling, post-translational modifications and metal binding preferences of PrP and ZIP family members. Finally, we explore data indicative of retropositional origins of the prion gene founder and discuss a possible function for the prion-like (PL) domain within ZIP transporters. While throughout the article emphasis is placed on ZIP proteins, the intent is to highlight connections between PrP and ZIP transporters and uncover promising directions for future research.

  7. A Ramie bZIP Transcription Factor BnbZIP2 Is Involved in Drought, Salt, and Heavy Metal Stress Response.

    PubMed

    Huang, Chengjian; Zhou, Jinghua; Jie, Yucheng; Xing, Hucheng; Zhong, Yingli; Yu, Weilin; She, Wei; Ma, Yushen; Liu, Zehang; Zhang, Ying

    2016-12-01

    bZIP transcription factors play key roles in plant growth, development, and stress signaling. A bZIP gene BnbZIP2 (GenBank accession number: KP642148) was cloned from ramie. BnbZIP2 has a 1416 base pair open reading frame, encoding a 471 amino acid protein containing a characteristic bZIP domain and a leucine zipper. BnbZIP2 shares high sequence similarity with bZIP factors from other plants. The BnbZIP2 protein is localized to both nuclei and cytoplasm. Transcripts of BnbZIP2 were found in various tissues in ramie, with significantly higher levels in female and male flowers. Its expression was induced by drought, high salinity, and abscisic acid treatments. Analysis of the cis-elements in promoters of BnbZIP2 identified cis-acting elements involved in growth, developmental processes, and a variety of stress responses. Transgenic Arabidopsis plants' overexpression of BnbZIP2 exhibited more sensitivity to drought and heavy metal Cd stress during seed germination, whereas more tolerance to high-salinity stress than the wild type during both seed germination and plant development. Thus, BnbZIP2 may act as a positive regulator in plants' response to high-salinity stress and be an important candidate gene for molecular breeding of salt-tolerant plants.

  8. Characterization of pollen-expressed bZIP protein interactions and the role of ATbZIP18 in the male gametophyte.

    PubMed

    Gibalová, Antónia; Steinbachová, Lenka; Hafidh, Said; Bláhová, Veronika; Gadiou, Zuzana; Michailidis, Christos; Műller, Karel; Pleskot, Roman; Dupľáková, Nikoleta; Honys, David

    2017-03-01

    KEY MESSAGE : bZIP TF network in pollen. Transcriptional control of gene expression represents an important mechanism guiding organisms through developmental processes and providing plasticity towards environmental stimuli. Because of their sessile nature, plants require effective gene regulation for rapid response to variation in environmental and developmental conditions. Transcription factors (TFs) provide such control ensuring correct gene expression in spatial and temporal manner. Our work reports the interaction network of six bZIP TFs expressed in Arabidopsis thaliana pollen and highlights the potential functional role for AtbZIP18 in pollen. AtbZIP18 was shown to interact with three other pollen-expressed bZIP TFs-AtbZIP34, AtbZIP52, and AtbZIP61 in yeast two-hybrid assays. AtbZIP18 transcripts are highly expressed in pollen, and at the subcellular level, an AtbZIP18-GFP fusion protein was located in the nucleus and cytoplasm/ER. To address the role of AtbZIP18 in the male gametophyte, we performed phenotypic analysis of a T-DNA knockout allele, which showed slightly reduced transmission through the male gametophyte. Some of the phenotype defects in atbzip18 pollen, although observed at low penetrance, were similar to those seen at higher frequency in the T-DNA knockout of the interacting partner, AtbZIP34. To gain deeper insight into the regulatory role of AtbZIP18, we analysed atbzip18/- pollen microarray data. Our results point towards a potential repressive role for AtbZIP18 and its functional redundancy with AtbZIP34 in pollen.

  9. Zipping dielectric elastomer actuators: characterization, design and modeling

    NASA Astrophysics Data System (ADS)

    Maffli, L.; Rosset, S.; Shea, H. R.

    2013-10-01

    We report on miniature dielectric elastomer actuators (DEAs) operating in zipping mode with an analytical model that predicts their behavior. Electrostatic zipping is a well-known mechanism in silicon MEMS to obtain large deformations and forces at lower voltages than for parallel plate electrostatic actuation. We extend this concept to DEAs, which allows us to obtain much larger out-of-plane displacements compared to silicon thanks to the softness of the elastomer membrane. We study experimentally the effect of sidewall angles and elastomer prestretch on 2.3 mm diameter actuators with PDMS membranes. With 15° and 22.5° sidewall angles, the devices zip in a bistable manner down 300 μm to the bottom of the chambers. The highly tunable bistable behavior is controllable by both chamber geometry and membrane parameters. Other specific characteristics of zipping DEAs include well-controlled deflected shape, tunable displacement versus voltage characteristics to virtually any shape, including multi-stable modes, sealing of embedded holes or channels for valving action and the reduction of the operating voltage. These properties make zipping DEAs an excellent candidate for applications such as integrated microfluidics actuators or Braille displays.

  10. The Phaseolus vulgaris ZIP gene family: identification, characterization, mapping, and gene expression

    PubMed Central

    Astudillo, Carolina; Fernandez, Andrea C.; Blair, Matthew W.; Cichy, Karen A.

    2013-01-01

    Zinc is an essential mineral for humans and plants and is involved in many physiological and biochemical processes. In humans, Zn deficiency has been associated with retarded growth and reduction of immune response. In plants, Zn is an essential component of more than 300 enzymes including RNA polymerase, alkaline phosphatase, alcohol dehydrogenase, Cu/Zn superoxidase dismutase, and carbonic anhydrase. The accumulation of Zn in plants involves many genes and characterization of the role of these genes will be useful in biofortification. Here we report the identification and phlyogenetic and sequence characterization of the 23 members of the ZIP (ZRT, IRT like protein) family of metal transporters and three transcription factors of the bZIP family in Phaseolus vulgaris L. Expression patterns of seven of these genes were characterized in two bean genotypes (G19833 and DOR364) under two Zn treatments. Tissue analyzed included roots and leaves at vegetative and flowering stages, and pods at 20 days after flowering. Four of the genes, PvZIP12, PvZIP13, PvZIP16, and Pv bZIP1, showed differential expression based on tissue, Zn treatment, and/or genotype. PvZIP12 and PvZIP13 were both more highly expressed in G19833 than DOR364. PvZIP12 was most highly expressed in vegetative leaves under the Zn (−) treatment. PvZIP16 was highly expressed in leaf tissue, especially leaf tissue at flowering stage grown in the Zn (−) treatment. Pv bZIP1 was most highly expressed in leaf and pod tissue. The 23 PvZIP genes and three bZIP genes were mapped on the DOR364 × G19833 linkage map. PvZIP12, PvZIP13, and PvZIP18, Pv bZIP2, and Pv bZIP3 were located near QTLs for Zn accumulation in the seed. Based on the expression and mapping results, PvZIP12 is a good candidate gene for increasing seed Zn concentration and increase understanding of the role of ZIP genes in metal uptake, distribution, and accumulation of zinc in P. vulgaris. PMID:23908661

  11. HvZIP7 mediates zinc accumulation in barley (Hordeum vulgare) at moderately high zinc supply.

    PubMed

    Tiong, Jingwen; McDonald, Glenn K; Genc, Yusuf; Pedas, Pai; Hayes, Julie E; Toubia, John; Langridge, Peter; Huang, Chun Y

    2014-01-01

    High expression of zinc (Zn)-regulated, iron-regulated transporter-like protein (ZIP) genes increases root Zn uptake in dicots, leading to high accumulation of Zn in shoots. However, none of the ZIP genes tested previously in monocots could enhance shoot Zn accumulation. In this report, barley (Hordeum vulgare) HvZIP7 was investigated for its functions in Zn transport. The functions of HvZIP7 in planta were studied using in situ hybridization and transient analysis of subcellular localization with a green fluorescent protein (GFP) reporter. Transgenic barley lines overexpressing HvZIP7 were also generated to further understand the functions of HvZIP7 in metal transport. HvZIP7 is strongly induced by Zn deficiency, primarily in vascular tissues of roots and leaves, and its protein was localized in the plasma membrane. These properties are similar to its closely related homologs in dicots. Overexpression of HvZIP7 in barley plants increased Zn uptake when moderately high concentrations of Zn were supplied. Significantly, there was a specific enhancement of shoot Zn accumulation, with no measurable increase in iron (Fe), manganese (Mn), copper (Cu) or cadmium (Cd). HvZIP7 displays characteristics of low-affinity Zn transport. The unique function of HvZIP7 provides new insights into the role of ZIP genes in Zn homeostasis in monocots, and offers opportunities to develop Zn biofortification strategies in cereals.

  12. The ZIP family zinc transporters support the virulence of Cryptococcus neoformans.

    PubMed

    Do, Eunsoo; Hu, Guanggan; Caza, Mélissa; Kronstad, James W; Jung, Won Hee

    2016-08-01

    Zinc is an essential element in living organisms and a cofactor for various metalloproteins. To disseminate and survive, a pathogenic microbe must obtain zinc from the host, which is an environment with extremely limited zinc availability. In this study, we investigated the roles of the ZIP family zinc transporters Zip1 and Zip2 in the human pathogenic fungus Cryptococcus neoformans Zip1 and Zip2 are homologous to Zrt1 and Zrt2 of the model fungus, Saccharomyces cerevisiae, respectively. We found that the expression of ZIP1 was regulated by the zinc concentration in the environment. Furthermore, the mutant lacking ZIP1 displayed a severe growth defect under zinc-limited conditions, while the mutant lacking ZIP2 displayed normal growth. Inductively coupled plasma-atomic emission spectroscopy analysis showed that the absence of Zip1 expression significantly reduced total cellular zinc levels relative to that in the wild type, while overexpression of Zip1 was associated with increased cellular zinc levels. These findings suggested that Zip1 plays roles in zinc uptake in C. neoformans We also constructed a Zip1-FLAG fusion protein and found, by immunofluorescence, not only that the protein was localized to the periphery implying it is a membrane transporter, but also that the protein was N-glycosylated. Furthermore, the mutant lacking ZIP1 showed attenuated virulence in a murine inhalation model of cryptococcosis and reduced survival within murine macrophages. Overall, our data suggest that Zip1 plays essential roles in zinc transport and the virulence of C. neoformans.

  13. Zip14 (Slc39a14) mediates non-transferrin-bound iron uptake into cells.

    PubMed

    Liuzzi, Juan P; Aydemir, Fikret; Nam, Hyeyoung; Knutson, Mitchell D; Cousins, Robert J

    2006-09-12

    Zip14 is a member of the SLC39A zinc transporter family, which is involved in zinc uptake by cells. Up-regulation of Zip14 by IL-6 appears to contribute to the hepatic zinc accumulation and hypozincemia of inflammation. At least three members of the SLC39A family transport other trace elements, such as iron and manganese, in addition to zinc. We analyzed the capability of Zip14 to mediate non-transferrin-bound iron (NTBI) uptake by overexpressing mouse Zip14 in HEK 293H cells and Sf9 insect cells. Zip14 was found to localize to the plasma membrane, and its overexpression increased the uptake of both (65)Zn and (59)Fe. Addition of bathophenanthroline sulfonate, a cell-impermeant ferrous iron chelator, inhibited Zip14-mediated iron uptake from ferric citrate, suggesting that iron is taken up by HEK cells as Fe(2+). Iron uptake by HEK and Sf9 cells expressing Zip14 was inhibited by zinc. Suppression of endogenous Zip14 expression by using Zip14 siRNA reduced the uptake of both iron and zinc by AML12 mouse hepatocytes. Zip14 siRNA treatment also decreased metallothionein mRNA levels, suggesting that compensatory mechanisms were not sufficient to restore intracellular zinc. Collectively, these results indicate that Zip14 can mediate the uptake of zinc and NTBI into cells and that it may play a role in zinc and iron metabolism in hepatocytes, where this transporter is abundantly expressed. Because NTBI is commonly found in plasma of patients with hemochromatosis and transfusional iron overload, Zip14-mediated NTBI uptake may contribute to the hepatic iron loading that characterizes these diseases.

  14. In vivo binding of hot pepper bZIP transcription factor CabZIP1 to the G-box region of pathogenesis-related protein 1 promoter

    SciTech Connect

    Lee, Boo-Ja; Park, Chang-Jin; Kim, Sung-Kyu; Kim, Ki-Jeong; Paek, Kyung-Hee . E-mail: khpaek95@korea.ac.kr

    2006-05-26

    We find that salicylic acid and ethephon treatment in hot pepper increases the expression of a putative basic/leucine zipper (bZIP) transcription factor gene, CabZIP1. CabZIP1 mRNA is expressed ubiquitously in various organs. The green fluorescent protein-fused transcription factor, CabZIP1::GFP, can be specifically localized to the nucleus, an action that is consistent with the presence of a nuclear localization signal in its protein sequence. Transient overexpression of the CabZIP1 transcription factor results in an increase in PR-1 transcripts level in Nicotiana benthamiana leaves. Using chromatin immunoprecipitation, we demonstrate that CabZIP1 binds to the G-box elements in native promoter of the hot pepper pathogenesis-related protein 1 (CaPR-1) gene in vivo. Taken together, our results suggest that CabZIP1 plays a role as a transcriptional regulator of the CaPR-1 gene.

  15. The soybean GmbZIP1 transcription factor enhances multiple abiotic stress tolerances in transgenic plants.

    PubMed

    Gao, Shi-Qing; Chen, Ming; Xu, Zhao-Shi; Zhao, Chang-Ping; Li, Liancheng; Xu, Hui-jun; Tang, Yi-miao; Zhao, Xin; Ma, You-Zhi

    2011-04-01

    Abscisic acid (ABA)-responsive element binding proteins (AREBs) are basic domain/leucine zipper transcription factors that bind to the ABA-responsive element (ABRE) in the promoter regions of ABA-inducible genes in plants. A novel bZIP transcription factor gene, GmbZIP1, encoding 438 amino acids with a conserved bZIP domain composed of 60 amino acids was isolated from salt-tolerant soybean cv. Tiefeng 8. Southern blotting showed that only one copy was present in the soybean genome. Phylogenetic analyses showed that GmbZIP1 belonged to the AREB subfamily of the bZIP family and was most closely related to AtABF2 and OsTRAB1. The expression of GmbZIP1 was highly induced by ABA, drought, high salt and low temperature; and GmbZIP1 was expressed in soybean roots, stems and leaves under different stress conditions. GmbZIP1 was localized inside the nuclei of transformed onion epidermal cells. Overexpression of GmbZIP1 enhanced the responses of transgenic plants to ABA and triggered stomatal closure under stresses, potentially leading to improved tolerances to several abiotic stresses such as high salt, low temperature and drought in transgenic plants. Furthermore, overexpression of GmbZIP1 affected the expression of some ABA or stress-related genes involved in regulating stomatal closure in Arabidopsis under ABA, drought and high salt stress conditions. A few AREB elements were detected in the promoter region of those ABA or stress-related genes, suggesting that GmbZIP1 regulates the ABA response or stomatal closure mediated by those downstream genes in transgenic Arabidopsis. Moreover, GmbZIP1 was used to improve the drought tolerance trait of Chinese wheat varieties BS93. Functional analysis showed that overexpression of GmbZIP1 enhanced the drought tolerance of transgenic wheat, and transcripts of GmbZIP1 were detected in transgenic wheat using RT-PCR. In addition, GmbZIP1 overexpression did not result in growth retardation in all transgenic plants, suggesting that GmbZIP

  16. 39 CFR 121.4 - Package Services.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Time is 2 days when the origin Processing & Distribution Center/Facility and the SCF are the same... before the day-zero Critical Entry Time is 3 days, for each remaining (non-intra-SCF) 3-digit ZIP Code... Critical Entry Time is 4 days for each remaining 3-digit ZIP Code origin-destination pair within a...

  17. An unusual zip gun suicide--medicolegal and ballistic examination.

    PubMed

    Hejna, Petr; Safr, Miroslav

    2010-01-01

    Home-made guns are imitations of typical firearms and usually have handgun characteristics. This article presents an unusual case of a suicide carried out by means of a fatal gunshot wound to the head using a home-made zip gun. A 49-year-old male, with a history of paranoid psychosis was found dead in the dwelling place of a family house. The investigation at the crime scene did not lead to suspicion of a gunshot wound because of the unusual nature of the firearm used. A medical examiner diagnosed an opened head injury as the primary cause of the victim's death. The autopsy findings provided immediate grounds for further inspection of the crime scene. Subsequently, a simple zip gun, which had been overlooked during the scene investigation, was discovered. An undeformed projectile recovered from the victim's head was consistent with the use of the home-made firearm. Following the completion of the investigations and autopsy, the death was classified as a suicide.

  18. Decryption-decompression of AES protected ZIP files on GPUs

    NASA Astrophysics Data System (ADS)

    Duong, Tan Nhat; Pham, Phong Hong; Nguyen, Duc Huu; Nguyen, Thuy Thanh; Le, Hung Duc

    2011-10-01

    AES is a strong encryption system, so decryption-decompression of AES encrypted ZIP files requires very large computing power and techniques of reducing the password space. This makes implementations of techniques on common computing system not practical. In [1], we reduced the original very large password search space to a much smaller one which surely containing the correct password. Based on reduced set of passwords, in this paper, we parallel decryption, decompression and plain text recognition for encrypted ZIP files by using CUDA computing technology on graphics cards GeForce GTX295 of NVIDIA, to find out the correct password. The experimental results have shown that the speed of decrypting, decompressing, recognizing plain text and finding out the original password increases about from 45 to 180 times (depends on the number of GPUs) compared to sequential execution on the Intel Core 2 Quad Q8400 2.66 GHz. These results have demonstrated the potential applicability of GPUs in this cryptanalysis field.

  19. Defect Dynamics and Zipping of 2D Colloidal Crystallites

    NASA Astrophysics Data System (ADS)

    Bowley, Chris; Smullin, Sylvia; Ling, Xinsheng

    1998-03-01

    We use video microscopy to study defect dynamics in 2D colloidal (charged polystyrene microspheres) crystallites formed at the water-air interface. For small 2D crystallites, one might expect to see free edge dislocations in such small systems since the cost of forming such defects scales logarithmically with the size of the crystallite. But we found that as soon as an edge dislocation forms, it quickly moves to the edge of the crystallite and disappears. This is due to an attraction with an image dislocation outside the edge. As a result, most crystallites are defect-free during most of the time. Interesting things happen when two crystallites try to bind to each other, or zip together. A sharp transition occurs at the shared edge of the two crystallites during the zipping process. This is clearly manifested by a sudden change in the relative velocity between two drifting crystallites or a sudden re-orientation of one of the crystallites relative to the other. This work was supported by the startup funds and a Richard Salomon Faculty Research Award from Brown University.

  20. Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development

    PubMed Central

    Van Leene, Jelle; Blomme, Jonas; Kulkarni, Shubhada R; Cannoot, Bernard; De Winne, Nancy; Eeckhout, Dominique; Persiau, Geert; Van De Slijke, Eveline; Vercruysse, Leen; Vanden Bossche, Robin; Heyndrickx, Ken S; Vanneste, Steffen; Goossens, Alain; Gevaert, Kris; Vandepoele, Klaas; Gonzalez, Nathalie; Inzé, Dirk; De Jaeger, Geert

    2016-01-01

    Plant bZIP group I transcription factors have been reported mainly for their role during vascular development and osmosensory responses. Interestingly, bZIP29 has been identified in a cell cycle interactome, indicating additional functions of bZIP29 in plant development. Here, bZIP29 was functionally characterized to study its role during plant development. It is not present in vascular tissue but is specifically expressed in proliferative tissues. Genome-wide mapping of bZIP29 target genes confirmed its role in stress and osmosensory responses, but also identified specific binding to several core cell cycle genes and to genes involved in cell wall organization. bZIP29 protein complex analyses validated interaction with other bZIP group I members and provided insight into regulatory mechanisms acting on bZIP dimers. In agreement with bZIP29 expression in proliferative tissues and with its binding to promoters of cell cycle regulators, dominant-negative repression of bZIP29 altered the cell number in leaves and in the root meristem. A transcriptome analysis on the root meristem, however, indicated that bZIP29 might regulate cell number through control of cell wall organization. Finally, ectopic dominant-negative repression of bZIP29 and redundant factors led to a seedling-lethal phenotype, pointing to essential roles for bZIP group I factors early in plant development. PMID:27660483

  1. Poplar PtabZIP1-like enhances lateral root formation and biomass growth under drought stress.

    PubMed

    Dash, Madhumita; Yordanov, Yordan S; Georgieva, Tatyana; Tschaplinski, Timothy J; Yordanova, Elena; Busov, Victor

    2017-02-01

    Developing drought-resistance varieties is a major goal for bioenergy crops, such as poplar (Populus), which will be grown on marginal lands with little or no water input. Root architecture can affect drought resistance, but few genes that affect root architecture in relation to water availability have been identified. Here, using activation tagging in the prime bioenergy crop poplar, we have identified a mutant that overcomes the block of lateral root (LR) formation under osmotic stress. Positioning of the tag, validation of the activation and recapitulation showed that the phenotype is caused by the poplar PtabZIP1-like (PtabZIP1L) gene with highest homology to bZIP1 from Arabidopsis. PtabZIP1L is predominantly expressed in roots, particularly in zones where lateral root primordia (LRP) initiate and LR differentiate and emerge. Transgenics overexpressing PtabZIP1L showed precocious LRP and LR development, while PtabZIP1L suppression significantly delayed both LRP and LR formation. Transgenic overexpression and suppression of PtabZIP1L also resulted in modulation of key metabolites like proline, asparagine, valine and several flavonoids. Consistently, expression of both of the poplar Proline Dehydrogenase orthologs and two of the Flavonol Synthases genes was also increased and decreased in overexpressed and suppressed transgenics, respectively. These findings suggest that PtabZIP1L mediates LR development and drought resistance through modulation of multiple metabolic pathways.

  2. Differential expression of four soybean bZIP genes during Phakopsora pachyrhizi infection.

    PubMed

    Alves, Murilo S; Soares, Zamira G; Vidigal, Pedro M P; Barros, Everaldo G; Poddanosqui, Adriana M P; Aoyagi, Luciano N; Abdelnoor, Ricardo V; Marcelino-Guimarães, Francismar C; Fietto, Luciano G

    2015-11-01

    Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is one of most important diseases in the soybean (Glycine max (L.) Merr.) agribusiness. The identification and characterization of genes related to plant defense responses to fungal infection are essential to develop ASR-resistant plants. In this work, we describe four soybean genes, GmbZIP62, GmbZIP105, GmbZIPE1, and GmbZIPE2, which encode transcription factors containing a basic leucine zipper (bZIP) domain from two divergent classes, and that are responsive to P. pachyrhizi infection. Molecular phylogenetic analyses demonstrated that these genes encode proteins similar to bZIP factors responsive to pathogens. Yeast transactivation assays showed that only GmbZIP62 has strong transactivation activity in yeast. In addition, three of the bZIP transcription factors analyzed were also differentially expressed by plant defense hormones, and all were differentially expressed by fungal attack, indicating that these proteins might participate in response to ASR infection. The results suggested that these bZIP proteins are part of the plant defense response to P. pachyrhizi infection, by regulating the gene expression related to ASR infection responses. These bZIP genes are potential targets to obtain new soybean genotypes resistant to ASR.

  3. Poplar PtabZIP1-like enhances lateral root formation and biomass growth under drought stress

    DOE PAGES

    Dash, Madhumita; Yordanov, Yordan S.; Georgieva, Tatyana; ...

    2017-02-10

    Developing drought-resistance varieties is a major goal for bioenergy crops, such as poplar (Populus), which will be grown on marginal lands with little or no water input. Root architecture can affect drought resistance, but few genes that affect root architecture in relation to water availability have been identified. Here in this study, using activation tagging in the prime bioenergy crop poplar, we have identified a mutant that overcomes the block of lateral root (LR) formation under osmotic stress. Positioning of the tag, validation of the activation and recapitulation showed that the phenotype is caused by the poplar PtabZIP1-like (PtabZIP1L) genemore » with highest homology to bZIP1 from Arabidopsis. PtabZIP1L is predominantly expressed in roots, particularly in zones where lateral root primordia (LRP) initiate and LR differentiate and emerge. Transgenics overexpressing PtabZIP1L showed precocious LRP and LR development, while PtabZIP1L suppression significantly delayed both LRP and LR formation. Transgenic overexpression and suppression of PtabZIP1L also resulted in modulation of key metabolites like proline, asparagine, valine and several flavonoids. Consistently, expression of both of the poplar Proline Dehydrogenase orthologs and two of the Flavonol Synthases genes was also increased and decreased in overexpressed and suppressed transgenics, respectively. These findings suggest that PtabZIP1L mediates LR development and drought resistance through modulation of multiple metabolic pathways.« less

  4. HTLV-1 Tax Protein Stimulation of DNA Binding of bZIP Proteins by Enhancing Dimerization

    NASA Astrophysics Data System (ADS)

    Wagner, Susanne; Green, Michael R.

    1993-10-01

    The Tax protein of human T cell leukemia virus type-1 (HTLV-I) transcriptionally activates the HTLV-I promoter. This activation requires binding sites for activating transcription factor (ATF) proteins, a family of cellular proteins that contain basic region-leucine zipper (bZIP) DNA binding domains. Data are presented showing that Tax increases the in vitro DNA binding activity of multiple ATF proteins. Tax also stimulated DNA binding by other bZIP proteins, but did not affect DNA binding proteins that lack a bZIP domain. The increase in DNA binding occurred because Tax promotes dimerization of the bZIP domain in the absence of DNA, and the elevated concentration of the bZIP homodimer then facilitates the DNA binding reaction. These results help explain how Tax activates viral transcription and transforms cells.

  5. Zip nucleic acids are potent hydrolysis probes for quantitative PCR

    PubMed Central

    Paris, Clément; Moreau, Valérie; Deglane, Gaëlle; Voirin, Emilie; Erbacher, Patrick; Lenne-Samuel, Nathalie

    2010-01-01

    Zip nucleic acids (ZNAs) are oligonucleotides conjugated with cationic spermine units that increase affinity for their target. ZNAs were recently shown to enable specific and sensitive reactions when used as primers for polymerase chain reaction (PCR) and reverse-transcription. Here, we report their use as quantitative PCR hydrolysis probes. Ultraviolet duplex melting data demonstrate that attachment of cationic residues to the 3′ end of an oligonucleotide does not alter its ability to discriminate nucleotides nor the destabilization pattern relative to mismatch location in the oligonucleotide sequence. The stability increase provided by the cationic charges allows the use of short dual-labeled probes that significantly improve single-nucleotide polymorphism genotyping. Longer ZNA probes were shown to display reduced background fluorescence, therefore, generating greater sensitivity and signal level as compared to standard probes. ZNA probes thus provide broad flexibility in assay design and also represent an effective alternative to minor groove binder- and locked nucleic-acid-containing probes. PMID:20071749

  6. The bZIP transcription factor PfZipA regulates secondary metabolism and oxidative stress response in the plant endophytic fungus Pestalotiopsis fici.

    PubMed

    Wang, Xiuna; Wu, Fan; Liu, Ling; Liu, Xingzhong; Che, Yongsheng; Keller, Nancy P; Guo, Liyun; Yin, Wen-Bing

    2015-08-01

    The bZIP transcription factors are conserved in all eukaryotes and play critical roles in organismal responses to environmental challenges. In filamentous fungi, several lines of evidence indicate that secondary metabolism (SM) is associated with oxidative stress mediated by bZIP proteins. Here we uncover a connection with a bZIP protein and oxidative stress induction of SM in the plant endophytic fungus Pestalotiopsis fici. A homology search of the P. fici genome with the bZIP protein RsmA, involved in SM and the oxidative stress response in Aspergillus nidulans, identified PfZipA. Deletion of PfzipA resulted in a strain that displayed resistant to the oxidative reagents tert-butylhydroperoxide (tBOOH), diamide, and menadione sodium bisulfite (MSB), but increased sensitivity to H2O2 as compared to wild type (WT). Secondary metabolite production presented a complex pattern dependent on PfzipA and oxidative reagents. Without oxidative treatment, the ΔPfzipA strain produced less isosulochrin and ficipyroneA than WT; addition of tBOOH further decreased production of iso-A82775C and pestaloficiol M in ΔPfzipA; diamide treatment resulted in equivalent production of isosulochrin and ficipyroneA in the two strains; MSB treatment further decreased production of RES1214-1 and iso-A82775C but increased pestaloficiol M production in the mutant; and H2O2 treatment resulted in enhanced production of isosulochrin, RES1214-1 and pestheic acid but decreased ficipyroneA and pestaloficiol M in ΔPfzipA compared to WT. Our results suggest that PfZipA regulation of SM is modified by oxidative stress pathways and provide insights into a possible role of PfZipA in mediating SM synthesis in the endophytic lifestyle of P. fici.

  7. Characterization of Zinc Influx Transporters (ZIPs) in Pancreatic β Cells: ROLES IN REGULATING CYTOSOLIC ZINC HOMEOSTASIS AND INSULIN SECRETION.

    PubMed

    Liu, Ying; Batchuluun, Battsetseg; Ho, Louisa; Zhu, Dan; Prentice, Kacey J; Bhattacharjee, Alpana; Zhang, Ming; Pourasgari, Farzaneh; Hardy, Alexandre B; Taylor, Kathryn M; Gaisano, Herbert; Dai, Feihan F; Wheeler, Michael B

    2015-07-24

    Zinc plays an essential role in the regulation of pancreatic β cell function, affecting important processes including insulin biosynthesis, glucose-stimulated insulin secretion, and cell viability. Mutations in the zinc efflux transport protein ZnT8 have been linked with both type 1 and type 2 diabetes, further supporting an important role for zinc in glucose homeostasis. However, very little is known about how cytosolic zinc is controlled by zinc influx transporters (ZIPs). In this study, we examined the β cell and islet ZIP transcriptome and show consistent high expression of ZIP6 (Slc39a6) and ZIP7 (Slc39a7) genes across human and mouse islets and MIN6 β cells. Modulation of ZIP6 and ZIP7 expression significantly altered cytosolic zinc influx in pancreatic β cells, indicating an important role for ZIP6 and ZIP7 in regulating cellular zinc homeostasis. Functionally, this dysregulated cytosolic zinc homeostasis led to impaired insulin secretion. In parallel studies, we identified both ZIP6 and ZIP7 as potential interacting proteins with GLP-1R by a membrane yeast two-hybrid assay. Knock-down of ZIP6 but not ZIP7 in MIN6 β cells impaired the protective effects of GLP-1 on fatty acid-induced cell apoptosis, possibly via reduced activation of the p-ERK pathway. Therefore, our data suggest that ZIP6 and ZIP7 function as two important zinc influx transporters to regulate cytosolic zinc concentrations and insulin secretion in β cells. In particular, ZIP6 is also capable of directly interacting with GLP-1R to facilitate the protective effect of GLP-1 on β cell survival.

  8. Zip-DNA: A Novel DNA Structure Formed Under Mechanical Stress

    NASA Astrophysics Data System (ADS)

    Balaeff, Alexander; Mikhailov, Ivan; Turabekova, Malakhat; Craig, Stephen; Beratan, David

    2014-03-01

    Zip-DNA is a novel DNA structure predicted by molecular dynamics simulations of forced DNA extension. In the zip-DNA form, the Watson-Crick hydrogen bonds are broken and nucleobases from the opposite DNA strands interdigitate with each other, forming a continuous single-base aromatic stack. The B-Zip DNA structural transition is proposed to be responsible for the famous overstretching plateau on the force-extension curve of DNA. The simulations show that zip-DNA may either self-assemble from force-melted DNA strands or evolve from B-DNA through an earlier recognized S-DNA. Zip-DNA is shown to be consistent with multiple experimental observations; notably, the S-DNA transition state is shown to be a highly disordered state consistent with experimentally measured thermodynamic characteristics of DNA extension. We predict that zip-DNA possesses increased molecular conductivity compared to the B-DNA form and, therefore, may find applications in molecular electronics. A conductive state of a stretched non-complementary double-stranded DNA would, if detected, become a ``smoking gun'' experiment validating the existence of zip-DNA.

  9. Structural insights of ZIP4 extracellular domain critical for optimal zinc transport

    PubMed Central

    Zhang, Tuo; Sui, Dexin; Hu, Jian

    2016-01-01

    The ZIP zinc transporter family is responsible for zinc uptake from the extracellular milieu or intracellular vesicles. The LIV-1 subfamily, containing nine out of the 14 human ZIP proteins, is featured with a large extracellular domain (ECD). The critical role of the ECD is manifested by disease-causing mutations on ZIP4, a representative LIV-1 protein. Here we report the first crystal structure of a mammalian ZIP4-ECD, which reveals two structurally independent subdomains and an unprecedented dimer centred at the signature PAL motif. Structure-guided mutagenesis, cell-based zinc uptake assays and mapping of the disease-causing mutations indicate that the two subdomains play pivotal but distinct roles and that the bridging region connecting them is particularly important for ZIP4 function. These findings lead to working hypotheses on how ZIP4-ECD exerts critical functions in zinc transport. The conserved dimeric architecture in ZIP4-ECD is also demonstrated to be a common structural feature among the LIV-1 proteins. PMID:27321477

  10. Structural insights of ZIP4 extracellular domain critical for optimal zinc transport

    NASA Astrophysics Data System (ADS)

    Zhang, Tuo; Sui, Dexin; Hu, Jian

    2016-06-01

    The ZIP zinc transporter family is responsible for zinc uptake from the extracellular milieu or intracellular vesicles. The LIV-1 subfamily, containing nine out of the 14 human ZIP proteins, is featured with a large extracellular domain (ECD). The critical role of the ECD is manifested by disease-causing mutations on ZIP4, a representative LIV-1 protein. Here we report the first crystal structure of a mammalian ZIP4-ECD, which reveals two structurally independent subdomains and an unprecedented dimer centred at the signature PAL motif. Structure-guided mutagenesis, cell-based zinc uptake assays and mapping of the disease-causing mutations indicate that the two subdomains play pivotal but distinct roles and that the bridging region connecting them is particularly important for ZIP4 function. These findings lead to working hypotheses on how ZIP4-ECD exerts critical functions in zinc transport. The conserved dimeric architecture in ZIP4-ECD is also demonstrated to be a common structural feature among the LIV-1 proteins.

  11. Molecular pathogenesis of Spondylocheirodysplastic Ehlers-Danlos syndrome caused by mutant ZIP13 proteins

    PubMed Central

    Bin, Bum-Ho; Hojyo, Shintaro; Hosaka, Toshiaki; Bhin, Jinhyuk; Kano, Hiroki; Miyai, Tomohiro; Ikeda, Mariko; Kimura-Someya, Tomomi; Shirouzu, Mikako; Cho, Eun-Gyung; Fukue, Kazuhisa; Kambe, Taiho; Ohashi, Wakana; Kim, Kyu-Han; Seo, Juyeon; Choi, Dong-Hwa; Nam, Yeon-Ju; Hwang, Daehee; Fukunaka, Ayako; Fujitani, Yoshio; Yokoyama, Shigeyuki; Superti-Furga, Andrea; Ikegawa, Shiro; Lee, Tae Ryong; Fukada, Toshiyuki

    2014-01-01

    The zinc transporter protein ZIP13 plays critical roles in bone, tooth, and connective tissue development, and its dysfunction is responsible for the spondylocheirodysplastic form of Ehlers-Danlos syndrome (SCD-EDS, OMIM 612350). Here, we report the molecular pathogenic mechanism of SCD-EDS caused by two different mutant ZIP13 proteins found in human patients: ZIP13G64D, in which Gly at amino acid position 64 is replaced by Asp, and ZIP13ΔFLA, which contains a deletion of Phe-Leu-Ala. We demonstrated that both the ZIP13G64D and ZIP13ΔFLA protein levels are decreased by degradation via the valosin-containing protein (VCP)-linked ubiquitin proteasome pathway. The inhibition of degradation pathways rescued the protein expression levels, resulting in improved intracellular Zn homeostasis. Our findings uncover the pathogenic mechanisms elicited by mutant ZIP13 proteins. Further elucidation of these degradation processes may lead to novel therapeutic targets for SCD-EDS. PMID:25007800

  12. Neurulation and neurite extension require the zinc transporter ZIP12 (slc39a12)

    PubMed Central

    Chowanadisai, Winyoo; Graham, David M.; Keen, Carl L.; Rucker, Robert B.; Messerli, Mark A.

    2013-01-01

    Zn2+ is required for many aspects of neuronal structure and function. However, the regulation of Zn2+ in the nervous system remains poorly understood. Systematic analysis of tissue-profiling microarray data showed that the zinc transporter ZIP12 (slc39a12) is highly expressed in the human brain. In the work reported here, we confirmed that ZIP12 is a Zn2+ uptake transporter with a conserved pattern of high expression in the mouse and Xenopus nervous system. Mouse neurons and Neuro-2a cells produce fewer and shorter neurites after ZIP12 knockdown without affecting cell viability. Zn2+ chelation or loading in cells to alter Zn2+ availability respectively mimicked or reduced the effects of ZIP12 knockdown on neurite outgrowth. ZIP12 knockdown reduces cAMP response element-binding protein activation and phosphorylation at serine 133, which is a critical pathway for neuronal differentiation. Constitutive cAMP response element-binding protein activation restores impairments in neurite outgrowth caused by Zn2+ chelation or ZIP12 knockdown. ZIP12 knockdown also reduces tubulin polymerization and increases sensitivity to nocodazole following neurite outgrowth. We find that ZIP12 is expressed during neurulation and early nervous system development in Xenopus tropicalis, where ZIP12 antisense morpholino knockdown impairs neural tube closure and arrests development during neurulation with concomitant reduction in tubulin polymerization in the neural plate. This study identifies a Zn2+ transporter that is specifically required for nervous system development and provides tangible links between Zn2+, neurulation, and neuronal differentiation. PMID:23716681

  13. Genome-wide characterization and analysis of bZIP transcription factor gene family related to abiotic stress in cassava

    PubMed Central

    Hu, Wei; Yang, Hubiao; Yan, Yan; Wei, Yunxie; Tie, Weiwei; Ding, Zehong; Zuo, Jiao; Peng, Ming; Li, Kaimian

    2016-01-01

    The basic leucine zipper (bZIP) transcription factor family plays crucial roles in various aspects of biological processes. Currently, no information is available regarding the bZIP family in the important tropical crop cassava. Herein, 77 bZIP genes were identified from cassava. Evolutionary analysis indicated that MebZIPs could be divided into 10 subfamilies, which was further supported by conserved motif and gene structure analyses. Global expression analysis suggested that MebZIPs showed similar or distinct expression patterns in different tissues between cultivated variety and wild subspecies. Transcriptome analysis of three cassava genotypes revealed that many MebZIP genes were activated by drought in the root of W14 subspecies, indicating the involvement of these genes in the strong resistance of cassava to drought. Expression analysis of selected MebZIP genes in response to osmotic, salt, cold, ABA, and H2O2 suggested that they might participate in distinct signaling pathways. Our systematic analysis of MebZIPs reveals constitutive, tissue-specific and abiotic stress-responsive candidate MebZIP genes for further functional characterization in planta, yields new insights into transcriptional regulation of MebZIP genes, and lays a foundation for understanding of bZIP-mediated abiotic stress response. PMID:26947924

  14. A directional nucleation-zipping mechanism for triple helix formation.

    PubMed

    Alberti, Patrizia; Arimondo, Paola B; Mergny, Jean-Louis; Garestier, Thérèse; Hélène, Claude; Sun, Jian-Sheng

    2002-12-15

    A detailed kinetic study of triple helix formation was performed by surface plasmon resonance. Three systems were investigated involving 15mer pyrimidine oligonucleotides as third strands. Rate constants and activation energies were validated by comparison with thermodynamic values calculated from UV-melting analysis. Replacement of a T.A base pair by a C.G pair at either the 5' or the 3' end of the target sequence allowed us to assess mismatch effects and to delineate the mechanism of triple helix formation. Our data show that the association rate constant is governed by the sequence of base triplets on the 5' side of the triplex (referred to as the 5' side of the target oligopurine strand) and provides evidence that the reaction pathway for triple helix formation in the pyrimidine motif proceeds from the 5' end to the 3' end of the triplex according to the nucleation-zipping model. It seems that this is a general feature for all triple helices formation, probably due to the right-handedness of the DNA double helix that provides a stronger base stacking at the 5' than at the 3' duplex-triplex junction. Understanding the mechanism of triple helix formation is not only of fundamental interest, but may also help in designing better triple helix-forming oligonucleotides for gene targeting and control of gene expression.

  15. Protein kinase CK2 triggers cytosolic zinc signaling pathways by phosphorylation of zinc channel ZIP7.

    PubMed

    Taylor, Kathryn M; Hiscox, Stephen; Nicholson, Robert I; Hogstrand, Christer; Kille, Peter

    2012-02-07

    The transition element zinc, which has recently been identified as an intracellular second messenger, has been implicated in various signaling pathways, including those leading to cell proliferation. Zinc channels of the ZIP (ZRT1- and IRT1-like protein) family [also known as solute carrier family 39A (SLC39A)] transiently increase the cytosolic free zinc (Zn(2+)) concentration in response to extracellular signals. We show that phosphorylation of evolutionarily conserved residues in endoplasmic reticulum zinc channel ZIP7 is associated with the gated release of Zn(2+) from intracellular stores, leading to activation of tyrosine kinases and the phosphorylation of AKT and extracellular signal-regulated kinases 1 and 2. Through pharmacological manipulation, proximity ligation assay, and mutagenesis, we identified protein kinase CK2 as the kinase responsible for ZIP7 activation. Together, the present results show that transition element channels in eukaryotes can be activated posttranslationally by phosphorylation, as part of a cell signaling cascade. Our study links the regulated release of zinc from intracellular stores to phosphorylation of kinases involved in proliferative responses and cell migration, suggesting a functional role for ZIP7 and zinc signals in these events. The connection with proliferation and migration, as well as the activation of ZIP7 by CK2, a kinase that is antiapoptotic and promotes cell division, suggests that ZIP7 may provide a target for anticancer drug development.

  16. A novel bZIP gene from Tamarix hispida mediates physiological responses to salt stress in tobacco plants.

    PubMed

    Wang, Yucheng; Gao, Caiqiu; Liang, Yenan; Wang, Chao; Yang, Chuanping; Liu, Guifeng

    2010-02-15

    Basic leucine zipper proteins (bZIPs) are transcription factors that bind abscisic acid (ABA)-responsive elements (ABREs) and enable plants to withstand adverse environmental conditions. In the present study, a novel bZIP gene, ThbZIP1 was cloned from Tamarix hispida. Expression studies in T. hispida showed differential regulation of ThbZIP1 in response to treatment with NaCl, polyethylene glycol (PEG) 6000, NaHCO(3), and CdCl(2), suggesting that ThbZIP1 is involved in abiotic stress responses. To identify the physiological responses mediated by ThbZIP1, transgenic tobacco plants overexpressing exogenous ThbZIP1 were generated. Various physiological parameters related to salt stress were measured and compared between transgenic and wild type (WT) plants. Our results indicate that overexpression of ThbZIP1 can enhance the activity of both peroxidase (POD) and superoxide dismutase (SOD), and increase the content of soluble sugars and soluble proteins under salt stress conditions. These results suggest that ThbZIP1 contributes to salt tolerance by mediating signaling through multiple physiological pathways. Furthermore, ThbZIP1 confers stress tolerance to plants by enhancing reactive oxygen species (ROS) scavenging, facilitating the accumulation of compatible osmolytes, and inducing and/or enhancing the biosynthesis of soluble proteins.

  17. Bioinformatic Analyses of Subgroup-A Members of the Wheat bZIP Transcription Factor Family and Functional Identification of TabZIP174 Involved in Drought Stress Response

    PubMed Central

    Li, Xueyin; Feng, Biane; Zhang, Fengjie; Tang, Yimiao; Zhang, Liping; Ma, Lingjian; Zhao, Changping; Gao, Shiqing

    2016-01-01

    Extensive studies in Arabidopsis and rice have demonstrated that Subgroup-A members of the bZIP transcription factor family play important roles in plant responses to multiple abiotic stresses. Although common wheat (Triticum aestivum) is one of the most widely cultivated and consumed food crops in the world, there are limited investigations into Subgroup A of the bZIP family in wheat. In this study, we performed bioinformatic analyses of the 41 Subgroup-A members of the wheat bZIP family. Phylogenetic and conserved motif analyses showed that most of the Subgroup-A bZIP proteins involved in abiotic stress responses of wheat, Arabidopsis, and rice clustered in Clade A1 of the phylogenetic tree, and shared a majority of conserved motifs, suggesting the potential importance of Clade-A1 members in abiotic stress responses. Gene structure analysis showed that TabZIP genes with close phylogenetic relationships tended to possess similar exon–intron compositions, and the positions of introns in the hinge regions of the bZIP domains were highly conserved, whereas introns in the leucine zipper regions were at variable positions. Additionally, eleven groups of homologs and two groups of tandem paralogs were also identified in Subgroup A of the wheat bZIP family. Expression profiling analysis indicated that most Subgroup-A TabZIP genes were responsive to abscisic acid and various abiotic stress treatments. TabZIP27, TabZIP74, TabZIP138, and TabZIP174 proteins were localized in the nucleus of wheat protoplasts, whereas TabZIP9-GFP fusion protein was simultaneously present in the nucleus, cytoplasm, and cell membrane. Transgenic Arabidopsis overexpressing TabZIP174 displayed increased seed germination rates and primary root lengths under drought treatments. Overexpression of TabZIP174 in transgenic Arabidopsis conferred enhanced drought tolerance, and transgenic plants exhibited lower water loss rates, higher survival rates, higher proline, soluble sugar, and leaf chlorophyll

  18. Bioinformatic Analyses of Subgroup-A Members of the Wheat bZIP Transcription Factor Family and Functional Identification of TabZIP174 Involved in Drought Stress Response.

    PubMed

    Li, Xueyin; Feng, Biane; Zhang, Fengjie; Tang, Yimiao; Zhang, Liping; Ma, Lingjian; Zhao, Changping; Gao, Shiqing

    2016-01-01

    Extensive studies in Arabidopsis and rice have demonstrated that Subgroup-A members of the bZIP transcription factor family play important roles in plant responses to multiple abiotic stresses. Although common wheat (Triticum aestivum) is one of the most widely cultivated and consumed food crops in the world, there are limited investigations into Subgroup A of the bZIP family in wheat. In this study, we performed bioinformatic analyses of the 41 Subgroup-A members of the wheat bZIP family. Phylogenetic and conserved motif analyses showed that most of the Subgroup-A bZIP proteins involved in abiotic stress responses of wheat, Arabidopsis, and rice clustered in Clade A1 of the phylogenetic tree, and shared a majority of conserved motifs, suggesting the potential importance of Clade-A1 members in abiotic stress responses. Gene structure analysis showed that TabZIP genes with close phylogenetic relationships tended to possess similar exon-intron compositions, and the positions of introns in the hinge regions of the bZIP domains were highly conserved, whereas introns in the leucine zipper regions were at variable positions. Additionally, eleven groups of homologs and two groups of tandem paralogs were also identified in Subgroup A of the wheat bZIP family. Expression profiling analysis indicated that most Subgroup-A TabZIP genes were responsive to abscisic acid and various abiotic stress treatments. TabZIP27, TabZIP74, TabZIP138, and TabZIP174 proteins were localized in the nucleus of wheat protoplasts, whereas TabZIP9-GFP fusion protein was simultaneously present in the nucleus, cytoplasm, and cell membrane. Transgenic Arabidopsis overexpressing TabZIP174 displayed increased seed germination rates and primary root lengths under drought treatments. Overexpression of TabZIP174 in transgenic Arabidopsis conferred enhanced drought tolerance, and transgenic plants exhibited lower water loss rates, higher survival rates, higher proline, soluble sugar, and leaf chlorophyll

  19. Galileogenesis: A new cosmophenomenological zip code for reheating through R-parity violating coupling

    NASA Astrophysics Data System (ADS)

    Choudhury, Sayantan; Dasgupta, Arnab

    2014-05-01

    In this paper we introduce an idea of leptogenesis scenario in higher derivative gravity induced DBI Galileon framework aka Galileogenesis in presence of one-loop R-parity violating couplings in the background of a low energy effective supergravity setup derived from higher dimensional string theory framework. We have studied extensively the detailed feature of reheating constraints and the cosmophenomenological consequences of thermal gravitino dark matter in light of PLANCK and PDG data. Finally, we have also established a direct cosmophenomenological connection among dark matter relic abundance, reheating temperature and tensor-to-scalar ratio in the context of DBI Galileon inflation. Higher order correction terms in the gravity sector are introduced in the effective action as a perturbative correction to the Einstein-Hilbert counterpart coming from the computation of Conformal Field Theory disk amplitude at the two loop level [34-36]. The matter sector encounters the effect of N=1, D=4 supergravity motivated DBI Galileon interaction which is embedded in the D3 brane. Additionally, we have considered the effect of R-parity violating interactions [37-40] in the matter sector which provide a convenient framework for quantifying quark and lepton-flavor violating effects. The low energy UV protective effective action for the proposed cosmophenomenological model is described by [31,32]: S=∫d4x √{-g}[K(Φ,X)-G(Φ,X)□Φ+B1R+(B2RRαβγδ-4B3RRαβ+B4R2)+B5] where the model dependent characteristic functions K(Φ,X) and G(Φ,X) are the implicit functions of Galileon and its kinetic counterpart is X=-1/2 >g∂μΦ∂νΦ. Additionally, Bi∀i are the self-coupling constants of graviton degrees of freedom appearing via dimensional reduction from higher dimensional string theory. Specifically B5 be the effective four dimensional cosmological constant. In general, B2≠B3≠B4 which implies that the quadratic curvature terms originated from two loop correction to the CFT disk amplitudes are not topologically invariant in 4D effective theory. In Eq. (1) for potential driven DBI Galileon model once we embed DBI theory in the Galileon background we can write, K(Φ,X)=P(Φ,X)-V(Φ), where the kinetic term of the effective action is given by: P(Φ,X)=-G1/f(Φ)[√{1-2G2Xf(Φ)}-G3]-G4G(Φ,X)-2G5X with an effective Klebanov-Strassler frame function f(Φ)=(2q)-1 which characterizes the throat geometry on the D3 brane. Here Gi∀i and f2q∀q are originated from dimensional reduction. It is important to note that the functional G(ϕ,X) appearing in Eq. (1) and Eq. (2) are exactly same in the context of DBI Galileon theory. For more details on this issue see Refs. [31,32]. In the canonical limit when the contributions from the DBI Galileon sector is switched off then we get, K(ϕ,X)=X-V(ϕ), for G5=-1/2. In such a case the contributions from the higher derivative terms are highly suppressed by the UV cut-off scale of the effective theory and finally we get back the usual results as obtained from Einstein gravity. But once the contribution of DBI Galileon is switched on, the complete analysis deviates from canonical behaviour and contribution from the higher derivative gravity sector plays crucial role to change the dynamical behaviour during inflation as well as reheating.Moreover, the one-loop effective Coleman-Weinberg potential is given by [31,32]: V(Φ)=∑m=-2,m≠-12[β2m+δ2mln(Φ/M)](2m where β2m∀m are the tree level constants and δ2m∀m are originated from one-loop correction. In the present setup using Eq. (1) the Modified Friedman equation can be expressed as [31,32]: H4=ρ3/MPL2θ, where the energy density can be written in terms of DBI Galileon degrees of freedom as: ρ=2KXX-K-2GϕX-2X(1-θ)+V(ϕ). Here the subscripts represent the derivatives with respect to X and ϕ. Moreover, θ be a constant which is appearing through dimensional reduction from higher dimensional stringy setup as: θ=B1MP2+B2-4B3+B4+frac>B5MP4. In the present setup, MP=2.4×1018 GeV be the reduced Planck mass. It is important to note that the Friedman equation obtained in the present context is completely different from the Friedman equation as appearing in the context of Einstein's General Relativity which will further modifies the leptogenesis framework in the present context.To study this feature explicitly further we allow interaction of DBI Galileon scalar degrees of freedom with leptonic sector of the theory given by: LR̸int=∑k [Y1ijkνiljΦ+Y2ijkνilbarjΦ+h.c.] where the generation indices are i,j,k=1(e),2(μ),3(τ). Here after summing over all the contributions of flavor indices the corresponding charged scalar field can be written as: Φ=(Φe⊕Φμ⊕Φτ)√{3}. This induces the decay of charged DBI Galileon (Φ[Φ+,Φ-]) to the leptonic constituents through the phenomenological couplings (Y1ijk,Y2ijk). In this context these couplings violate a discrete symmetry called R-parity defined as, Rp≡(, where B,L and S are the baryon, lepton and spin angular momentum respectively. Such R-parity violating interactions in the Lagrangian (8) can be identified with the lepton number violating (LNV) MSSM flat direction LLe appearing in the superpotential as [39,40]: WR̸MSSM⊃1/2 >ɛabλLiaLjbebark+h.c. where a,b=1,2 are weak isospin indices and flatness constraint requires i

  20. bZIP17 and bZIP60 Regulate the Expression of BiP3 and Other Salt Stress Responsive Genes in an UPR-Independent Manner in Arabidopsis thaliana.

    PubMed

    Henriquez-Valencia, Carlos; Moreno, Adrian A; Sandoval-Ibañez, Omar; Mitina, Irina; Blanco-Herrera, Francisca; Cifuentes-Esquivel, Nicolas; Orellana, Ariel

    2015-08-01

    Plants can be severely affected by salt stress. Since these are sessile organisms, they have developed different cellular responses to cope with this problem. Recently, it has been described that bZIP17 and bZIP60, two ER-located transcription factors, are involved in the cellular response to salt stress. On the other hand, bZIP60 is also involved in the unfolded protein response (UPR), a signaling pathway that up-regulates the expression of ER-chaperones. Coincidentally, salt stress produces the up-regulation of BiP, one of the main chaperones located in this organelle. Then, it has been proposed that UPR is associated to salt stress. Here, by using insertional mutant plants on bZIP17 and bZIP60, we show that bZIP17 regulate the accumulation of the transcript for the chaperone BiP3 under salt stress conditions, but does not lead to the accumulation of UPR-responding genes such as the chaperones Calnexin, Calreticulin, and PDIL under salt treatments. In contrast, DTT, a known inducer of UPR, leads to the up-regulation of all these chaperones. On the other hand, we found that bZIP60 regulates the expression of some bZIP17 target genes under conditions were splicing of bZIP60 does not occur, suggesting that the spliced and unspliced forms of bZIP60 play different roles in the physiological response of the plant. Our results indicate that the ER-located transcription factors bZIP17 and bZIP60 play a role in salt stress but this response goes through a signaling pathway that is different to that triggered by the unfolded protein response.

  1. Zinc- and bicarbonate-dependent ZIP8 transporter mediates selenite uptake

    PubMed Central

    McDermott, Joseph R.; Geng, Xiangrong; Jiang, Lan; Gálvez-Peralta, Marina; Chen, Fei; Nebert, Daniel W.; Liu, Zijuan

    2016-01-01

    Selenite (HSeO3−) is a monovalent anion of the essential trace element and micronutrient selenium (Se). In therapeutic concentrations, HSeO3− has been studied for treating certain cancers, serious inflammatory disorders, and septic shock. Little is known, however, about HSeO3− uptake into mammalian cells; until now, no mammalian HSeO3− uptake transporter has been identified. The ubiquitous mammalian ZIP8 divalent cation transporter (encoded by the SLC39A8 gene) is bicarbonate-dependent, moving endogenous substrates (Zn2+, Mn2+, Fe2+ or Co2+) and nonessential metals such as Cd2+ into the cell. Herein we studied HSeO3− uptake in: human and mouse cell cultures, shRNA-knockdown experiments, Xenopus oocytes, wild-type mice and two transgenic mouse lines having genetically altered ZIP8 expression, and mouse erythrocytes ex vivo. In mammalian cell culture, excess Zn2+ levels and/or ZIP8 over-expression can be associated with diminished viability in selenite-treated cells. Intraperitoneal HSeO3− causes the largest ZIP8-dependent increases in intracellular Se content in liver, followed by kidney, heart, lung and spleen. In every model system studied, HSeO3− uptake is tightly associated with ZIP8 protein levels and sufficient Zn2+ and HCO3− concentrations, suggesting that the ZIP8-mediated electroneutral complex transported contains three ions: Zn2+/(HCO3−)(HSeO3−). Transporters having three different ions in their transport complex are not without precedent. Although there might be other HSeO3− influx transporters as yet undiscovered, data herein suggest that mammalian ZIP8 plays a major role in HSeO3− uptake. PMID:27166256

  2. Constitutive expression of the ZmZIP7 in Arabidopsis alters metal homeostasis and increases Fe and Zn content.

    PubMed

    Li, Suzhen; Zhou, Xiaojin; Zhao, Yongfeng; Li, Hongbo; Liu, Yuanfeng; Zhu, Liying; Guo, Jinjie; Huang, Yaqun; Yang, Wenzhu; Fan, Yunliu; Chen, Jingtang; Chen, Rumei

    2016-09-01

    Iron (Fe) and zinc (Zn) are important micronutrients for plant growth and development. Zinc-regulated transporters and the iron-regulated transporter-like protein (ZIP) are necessary for the homeostatic regulation of these metal micronutrients. In this study, the physiological function of ZmZIP7 which encodes a ZIP family transporter was characterized. We detected the expression profiles of ZmZIP7 in maize, and found that the accumulation of ZmZIP7 in root, stem, leaf, and seed was relatively higher than tassel and young ear. ZmZIP7 overexpression transgenic Arabidopsis lines were generated and the metal contents in transgenic and wild-type (WT) plants were examined using inductively coupled plasma atomic emission spectroscopy (ICP-OES) and Zinpyr-1 staining. Fe and Zn concentrations were elevated in the roots and shoots of ZmZIP7-overexpressing plants, while only Fe content was elevated in the seeds. We also analyzed the expression profiles of endogenous genes associated with metal homeostasis. Both endogenic Fe-deficiency inducible genes and the genes responsible for Zn and Fe transport and storage were stimulated in ZmZIP7 transgenic plants. In conclusion, ZmZIP7 encodes a functional Zn and Fe transporter, and ectopic overexpression of ZmZIP7 in Arabidopsis stimulate endogenous Fe and Zn uptake mechanisms, thereby facilitating both metal uptake and homeostasis. Our results contribute to improved understanding of ZIP family transporter functions and suggest that ZmZIP7 could be used to enhance Fe levels in grains.

  3. The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities.

    PubMed Central

    Sessa, G; Morelli, G; Ruberti, I

    1993-01-01

    The Arabidopsis Athb-1 and -2 proteins are characterized by the presence of a homeodomain (HD) with a closely linked leucine zipper motif (Zip). We have suggested that the HD-Zip motif could, via dimerization of the leucine zippers, recognize dyad-symmetric DNA sequences. Here we report an analysis of the DNA binding properties of the Athb-1 homeodomain-leucine zipper (HD-Zip-1) domain in vitro. DNA binding analysis performed using random-sequence DNA templates showed that the HD-Zip-1 domain, but not the Athb-1 HD alone, binds to DNA. The HD-Zip-1 domain recognizes a 9 bp dyad-symmetric sequence [CAAT(A/T)ATTG], as determined by selecting high-affinity binding sites from random-sequence DNA. Gel retardation assays demonstrated that the HD-Zip-1 domain binds to DNA as a dimer. Moreover, the analysis of the DNA binding activity of Athb-1 derivatives indicated that a correct spatial relationship between the HD and the Zip is essential for DNA binding. Finally, we determined that the Athb-2 HD-Zip domain recognizes a distinct 9 bp dyad-symmetric sequence [CAAT(G/C)ATTG]. A model of DNA binding by the HD-Zip proteins is proposed. Images PMID:8253077

  4. Genome-Wide Identification and Characterization of bZIP Transcription Factors in Brassica oleracea under Cold Stress

    PubMed Central

    Hwang, Indeok; Manoharan, Ranjith Kumar; Kang, Jong-Goo; Chung, Mi-Young; Kim, Young-Wook; Nou, Ill-Sup

    2016-01-01

    Cabbages (Brassica oleracea L.) are an important vegetable crop around world, and cold temperature is among the most significant abiotic stresses causing agricultural losses, especially in cabbage crops. Plant bZIP transcription factors play diverse roles in biotic/abiotic stress responses. In this study, 119 putative BolbZIP transcription factors were identified using amino acid sequences from several bZIP domain consensus sequences. The BolbZIP members were classified into 63 categories based on amino acid sequence similarity and were also compared with BrbZIP and AtbZIP transcription factors. Based on this BolbZIP identification and classification, cold stress-responsive BolbZIP genes were screened in inbred lines, BN106 and BN107, using RNA sequencing data and qRT-PCR. The expression level of the 3 genes, Bol008071, Bol033132, and Bol042729, was significantly increased in BN107 under cold conditions and was unchanged in BN106. The upregulation of these genes in BN107, a cold-susceptible inbred line, suggests that they might be significant components in the cold response. Among three identified genes, Bol033132 has 97% sequence similarity to Bra020735, which was identified in a screen for cold-related genes in B. rapa and a protein containing N-rich regions in LCRs. The results obtained in this study provide valuable information for understanding the potential function of BolbZIP transcription factors in cold stress responses. PMID:27314020

  5. Identification of Two bZIP Transcription Factors Interacting with the Promoter of Soybean Rubisco Activase Gene (GmRCAα)

    PubMed Central

    Zhang, Jinyu; Du, Hongyang; Chao, Maoni; Yin, Zhitong; Yang, Hui; Li, Yakai; Huang, Fang; Yu, Deyue

    2016-01-01

    Rubisco activase (RCA), a key photosynthetic protein, catalyses the activation of Rubisco and thus plays an important role in photosynthesis. Although the RCA gene has been characterized in a variety of species, the molecular mechanism regulating its transcription remains unclear. Our previous studies on RCA gene expression in soybean suggested that expression of this gene is regulated by trans-acting factors. In the present study, we verified activity of the GmRCAα promoter in both soybean and Arabidopsis and used a yeast one-hybrid (Y1H) system for screening a leaf cDNA expression library to identify transcription factors (TFs) interacting with the GmRCAα promoter. Four basic leucine zipper (bZIP) TFs, GmbZIP04g, GmbZIP07g, GmbZIP1, and GmbZIP71, were isolated, and GmbZIP04g and GmbZIP07g were confirmed as able to bind to a 21-nt G-box-containing sequence. Additionally, the expression patterns of GmbZIP04g, GmbZIp07g, and GmRCAα were analyzed in response to abiotic stresses and during a 24-h period. Our study will help to advance elucidation of the network regulating GmRCAα transcription. PMID:27242832

  6. Is health determined by genetic code or zip code? Measuring the health of groups and improving population health.

    PubMed

    Slade-Sawyer, Penelope

    2014-01-01

    Maintaining the optimal health of all North Carolinians is integral to the overall well-being of the state. It is not enough to have policies, initiatives, and reforms created and led by experts in health and health care. To move towards a culture that appreciates and promotes optimal population health, we also need assistance from other arenas. Data continue to suggest that domains such as education, housing, and income may be just as important, if not more important, than determinants that are usually associated with health outcomes. Thus North Carolina's leaders, professionals, and policy makers need to adopt shared responsibility for our population's health by taking a health-in-all-policies stance. Research to expand our understanding of individual and group actions that contribute to health outcomes, collaboration of partners across diverse sectors to implement evidence-based initiatives, and creative thinking and planning for future workforce needs are a few important actions. Together, these efforts can help to shift our long-standing focus on "disease care" to an upstream approach that ultimately reduces health care burdens and improves population health.

  7. Combinatorial bZIP dimers display complex DNA-binding specificity landscapes

    PubMed Central

    Rodríguez-Martínez, José A; Reinke, Aaron W; Bhimsaria, Devesh; Keating, Amy E; Ansari, Aseem Z

    2017-01-01

    How transcription factor dimerization impacts DNA-binding specificity is poorly understood. Guided by protein dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined half-sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably-spaced half-sites (12%) or ‘emergent’ sites (16%) that cannot be readily inferred from half-site preferences of partnering monomers. These binding sites were biochemically validated by EMSA-FRET analysis and validated in vivo by ChIP-seq data from human cell lines. Focusing on ATF3, we observed distinct cognate site preferences conferred by different bZIP partners, and demonstrated that genome-wide binding of ATF3 is best explained by considering many dimers in which it participates. Importantly, our compendium of bZIP-DNA interactomes predicted bZIP binding to 156 disease associated SNPs, of which only 20 were previously annotated with known bZIP motifs. DOI: http://dx.doi.org/10.7554/eLife.19272.001 PMID:28186491

  8. Beyond Molecular Codes: Simple Rules to Wire Complex Brains

    PubMed Central

    Hassan, Bassem A.; Hiesinger, P. Robin

    2015-01-01

    Summary Molecular codes, like postal zip codes, are generally considered a robust way to ensure the specificity of neuronal target selection. However, a code capable of unambiguously generating complex neural circuits is difficult to conceive. Here, we re-examine the notion of molecular codes in the light of developmental algorithms. We explore how molecules and mechanisms that have been considered part of a code may alternatively implement simple pattern formation rules sufficient to ensure wiring specificity in neural circuits. This analysis delineates a pattern-based framework for circuit construction that may contribute to our understanding of brain wiring. PMID:26451480

  9. Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity

    PubMed Central

    2011-01-01

    Background Plant HD-Zip transcription factors are modular proteins in which a homeodomain is associated to a leucine zipper. Of the four subfamilies in which they are divided, the tested members from subfamily I bind in vitro the same pseudopalindromic sequence CAAT(A/T)ATTG and among them, several exhibit similar expression patterns. However, most experiments in which HD-Zip I proteins were over or ectopically expressed under the control of the constitutive promoter 35S CaMV resulted in transgenic plants with clearly different phenotypes. Aiming to elucidate the structural mechanisms underlying such observation and taking advantage of the increasing information in databases of sequences from diverse plant species, an in silico analysis was performed. In addition, some of the results were also experimentally supported. Results A phylogenetic tree of 178 HD-Zip I proteins together with the sequence conservation presented outside the HD-Zip domains allowed the distinction of six groups of proteins. A motif-discovery approach enabled the recognition of an activation domain in the carboxy-terminal regions (CTRs) and some putative regulatory mechanisms acting in the amino-terminal regions (NTRs) and CTRs involving sumoylation and phosphorylation. A yeast one-hybrid experiment demonstrated that the activation activity of ATHB1, a member of one of the groups, is located in its CTR. Chimerical constructs were performed combining the HD-Zip domain of one member with the CTR of another and transgenic plants were obtained with these constructs. The phenotype of the chimerical transgenic plants was similar to the observed in transgenic plants bearing the CTR of the donor protein, revealing the importance of this module inside the whole protein. Conclusions The bioinformatical results and the experiments conducted in yeast and transgenic plants strongly suggest that the previously poorly analyzed NTRs and CTRs of HD-Zip I proteins play an important role in their function, hence

  10. A modified detector concept for SuperCDMS: The HiZIP and its charge performance

    SciTech Connect

    Page, Kedar Mohan

    2013-01-01

    SuperCDMS (Super Cryogenic Dark Matter Search) is a leading direct dark mat-ter search experiment which uses solid state detectors (Ge crystals) at milliKelvintemperatures to look for nuclear recoils caused by dark matter interactions in the de-tector. `Weakly Interacting Massive Particles' (WIMPs) are the most favoured darkmatter candidate particles. SuperCDMS, like many other direct dark matter searchexperiments, primarily looks for WIMPs. The measurement of both the ionizationand the lattice vibration (phonon) signals from an interaction in the detector allow itto discriminate against electron recoils which are the main source of background forWIMP detection.SuperCDMS currently operates about 9 kg of Ge detectors at the Soudan under-ground lab in northern Minnesota. In its next phase, SuperCDMS SNOLAB plansto use 100-200 kg of target mass (Ge) which would allow it to probe more of theinteresting and and as of yet unexplored parameter space for WIMPs predicted bytheoretical models. The SuperCDMS Queen's Test Facility is a detector test facilitywhich is intended to serve as detector testing and detector research and developmentpurposes for the SuperCDMS experiment.A modifed detector called the HiZIP (Half-iZIP), which is reduced in complex-ity in comparison to the currently used iZIP (interleaved Z-sensitive Ionization and Phonon mediated) detectors, is studied in this thesis. The HiZIP detector designalso serves to discriminate against background from multiple scatter events occurringclose to the surfaces in a single detector. Studies carried out to compare the surfaceevent leakage in the HiZIP detector using limited information from iZIP data takenat SuperCDMS test facility at UC Berkley produce a highly conservative upper limitof 5 out of 10,000 events at 90% condence level. This upper limit is the best amongmany different HiZIP congurations that were investigated and is comparable to theupper limit calculated for an HiZIP detector in the same way using the

  11. Cloning and molecular analysis of HlbZip1 and HlbZip2 transcription factors putatively involved in the regulation of the lupulin metabolome in hop (Humulus lupulus L.).

    PubMed

    Matousek, Jaroslav; Kocábek, Tomás; Patzak, Josef; Stehlík, Jan; Füssy, Zoltan; Krofta, Karel; Heyerick, Arne; Roldán-Ruiz, Isabel; Maloukh, Lina; De Keukeleire, Denis

    2010-01-27

    Hop (Humulus lupulus L.), the essential source of beer flavor is of interest from a medicinal perspective in view of its high content in health-beneficial terpenophenolics including prenylflavonoids. The dissection of biosynthetic pathway(s) of these compounds in lupulin glands, as well as its regulation by transcription factors (TFs), is important for efficient biotechnological manipulation of the hop metabolome. TFs of the bZIP class were preselected from the hop transcriptome using a cDNA-AFLP approach and cloned from a cDNA library based on glandular tissue-enriched hop cones. The cloned TFs HlbZIP1A and HlbZIP2 have predicted molecular masses of 27.4 and 34.2 kDa, respectively, and both are similar to the group A3 bZIP TFs according to the composition of characteristic domains. While HlbZIP1A is rather neutral (pI 6.42), HlbZIP2 is strongly basic (pI 8.51). A truncated variant of HlbZIP1 (HlbZIP1B), which is strongly basic but lacks the leucine zipper domain, has also been cloned from hop. Similar to the previously cloned HlMyb3 from hop, both bZIP TFs show a highly specific expression in lupulin glands, although low expression was observed also in other tissues including roots and immature pollen. Comparative functional analyses of HlbZip1A, HlbZip2, and subvariants of HlMyb3 were performed in a transient expression system using Nicotiana benthamiana leaf coinfiltration with Agrobacterium tumefaciens strains bearing hop TFs and selected promoters fused to the GUS reference gene. Both hop bZIP TFs and HlMyb3 mainly activated the promoters of chalcone synthase chs_H1 and the newly cloned O-methyl transferase 1 genes, while the response of the valerophenone synthase promoter to the cloned hop TFs was very low. These analyses also showed that the cloned bZIP TFs are not strictly G-box-specific. HPLC analysis of secondary metabolites in infiltrated Petunia hybrida showed that both hop bZIP TFs interfere with the accumulation and the composition of flavonol

  12. Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica).

    PubMed

    Zhang, C H; Ma, R J; Shen, Z J; Sun, X; Korir, N K; Yu, M L

    2014-04-08

    In this study, 33 homeodomain-leucine zipper (HD-ZIP) genes were identified in peach using the HD-ZIP amino acid sequences of Arabidopsis thaliana as a probe. Based on the phylogenetic analysis and the individual gene or protein characteristics, the HD-ZIP gene family in peach can be classified into 4 subfamilies, HD-ZIP I, II, III, and IV, containing 14, 7, 4, and 8 members, respectively. The most closely related peach HD-ZIP members within the same subfamilies shared very similar gene structure in terms of either intron/exon numbers or lengths. Almost all members of the same subfamily shared common motif compositions, thereby implying that the HD-ZIP proteins within the same subfamily may have functional similarity. The 33 peach HD-ZIP genes were distributed across scaffolds 1 to 7. Although the primary structure varied among HD-ZIP family proteins, their tertiary structures were similar. The results from this study will be useful in selecting candidate genes from specific subfamilies for functional analysis.

  13. The androgen-induced protein AIbZIP facilitates proliferation of prostate cancer cells through downregulation of p21 expression

    PubMed Central

    Cui, Xiang; Cui, Min; Asada, Rie; Kanemoto, Soshi; Saito, Atsushi; Matsuhisa, Koji; Kaneko, Masayuki; Imaizumi, Kazunori

    2016-01-01

    Androgen-Induced bZIP (AIbZIP) is structurally a bZIP transmembrane transcription factor belonging to the CREB/ATF family. This molecule is highly expressed in androgen-sensitive prostate cancer cells and is transcriptionally upregulated by androgen treatment. Here, we investigated molecular mechanism of androgen-dependent expression of AIbZIP and its physiological function in prostate cancer cells. Our data showed that SAM pointed domain-containing ETS transcription factor (SPDEF), which is upregulated by androgen treatment, directly activates transcription of AIbZIP. Knockdown of AIbZIP caused a significant reduction in the proliferation of androgen-sensitive prostate cancer cells with robust expression of p21. Mechanistically, we demonstrated that AIbZIP interacts with old astrocyte specifically induced substance (OASIS), which is a CREB/ATF family transcription factor, and prevents OASIS from promoting transcription of its target gene p21. These findings showed that AIbZIP induced by the androgen receptor (AR) axis plays a crucial role in the proliferation of androgen-sensitive prostate cancer cells, and could be a novel target of therapy for prostate cancer. PMID:27853318

  14. Molecular evolution and gene expression differences within the HD-Zip transcription factor family of Zea mays L.

    PubMed

    Mao, Hude; Yu, Lijuan; Li, Zhanjie; Liu, Hui; Han, Ran

    2016-04-01

    Homeodomain-leucine zipper (HD-Zip) transcription factors regulate developmental processes and stress responses in plants, and they vary widely in gene number and family structure. In this study, 55 predicted maize HD-Zip genes were systematically analyzed with respect to their phylogenetic relationships, molecular evolution, and gene expression in order to understand the functional diversification within the family. Phylogenetic analysis of HD-Zip proteins from Zea mays, Oryza sativa, Arabidopsis thaliana, Vitis vinifera, and Physcomitrella patens showed that they group into four classes. We inferred that the copy numbers of classes I and III genes were relatively conserved in all five species. The 55 maize HD-Zip genes are distributed randomly on the ten chromosomes, with 15 segmental duplication and 4 tandem duplication events, suggesting that segmental duplications were the major contributors in the expansion of the maize HD-Zip gene family. Expression analysis of the 55 maize HD-Zip genes in different tissues and drought conditions revealed differences in the expression levels and patterns between the four classes. Promoter analysis revealed that a number of stress response-, hormone response-, light response-, and development-related cis-acting elements were present in their promoters. Our results provide novel insights into the molecular evolution and gene expression within the HD-Zip gene family in maize, and provide a solid foundation for future functional study of the HD-Zip genes in maize.

  15. Phosphorylation of zinc channel ZIP7 drives MAPK, PI3K and mTOR growth and proliferation signalling.

    PubMed

    Nimmanon, T; Ziliotto, S; Morris, S; Flanagan, L; Taylor, K M

    2017-02-16

    Zinc is an essential trace element participating in diverse biological processes. Cellular zinc levels are strictly controlled by two families of transport proteins: ZIP channels (SLC39A) and ZnT transporters (SLC30A). ZIP channels increase cytosolic zinc levels by importing zinc into cells or releasing zinc from intracellular stores such as the ER. Among all the 14 human members of the ZIP family, ZIP7 is a gatekeeper of zinc release from intracellular stores, requiring post-translational activation by phosphorylation on residues S275 and S276, resulting in activation of multiple downstream pathways. Employing site-directed mutagenesis, we investigated the importance of these individual serine residues as well as other predicted phosphorylation sites on ZIP7, showing that all four sites are required for maximal ZIP7 activation. Using phosphor-protein arrays, we also discovered the major signalling pathways that were activated as a direct result of ZIP7-mediated zinc release from intracellular stores. These data reveal the role of ZIP7-mediated zinc release from intracellular stores in driving major pathways, such as MAPK, mTOR and PI3K-AKT, involved in providing cell survival and proliferation and often over activated in cancer.

  16. ZmbZIP91 regulates expression of starch synthesis-related genes by binding to ACTCAT elements in their promoters.

    PubMed

    Chen, Jiang; Yi, Qiang; Cao, Yao; Wei, Bin; Zheng, Lanjie; Xiao, Qianling; Xie, Ying; Gu, Yong; Li, Yangping; Huang, Huanhuan; Wang, Yongbin; Hou, Xianbin; Long, Tiandan; Zhang, Junjie; Liu, Hanmei; Liu, Yinghong; Yu, Guowu; Huang, Yubi

    2016-03-01

    Starch synthesis is a key process that influences crop yield and quality, though little is known about the regulation of this complex metabolic pathway. Here, we present the identification of ZmbZIP91 as a candidate regulator of starch synthesis via co-expression analysis in maize (Zea mays L.). ZmbZIP91 was strongly associated with the expression of starch synthesis genes. Reverse tanscription-PCR (RT-PCR) and RNA in situ hybridization indicated that ZmbZIP91 is highly expressed in maize endosperm, with less expression in leaves. Particle bombardment-mediated transient expression in maize endosperm and leaf protoplasts demonstrated that ZmbZIP91 could positively regulate the expression of starch synthesis genes in both leaves and endosperm. Additionally, the Arabidopsis mutant vip1 carried a mutation in a gene (VIP1) that is homologous to ZmbZIP91, displayed altered growth with less starch in leaves, and ZmbZIP91 was able to complement this phenotype, resulting in normal starch synthesis. A yeast one-hybrid experiment and EMSAs showed that ZmbZIP91 could directly bind to ACTCAT elements in the promoters of starch synthesis genes (pAGPS1, pSSI, pSSIIIa, and pISA1). These results demonstrate that ZmbZIP91 acts as a core regulatory factor in starch synthesis by binding to ACTCAT elements in the promoters of starch synthesis genes.

  17. Separable Crossover-Promoting and Crossover-Constraining Aspects of Zip1 Activity during Budding Yeast Meiosis

    PubMed Central

    Voelkel-Meiman, Karen; Johnston, Cassandra; Thappeta, Yashna; Subramanian, Vijayalakshmi V.; Hochwagen, Andreas; MacQueen, Amy J.

    2015-01-01

    Accurate chromosome segregation during meiosis relies on the presence of crossover events distributed among all chromosomes. MutSγ and MutLγ homologs (Msh4/5 and Mlh1/3) facilitate the formation of a prominent group of meiotic crossovers that mature within the context of an elaborate chromosomal structure called the synaptonemal complex (SC). SC proteins are required for intermediate steps in the formation of MutSγ-MutLγ crossovers, but whether the assembled SC structure per se is required for MutSγ-MutLγ-dependent crossover recombination events is unknown. Here we describe an interspecies complementation experiment that reveals that the mature SC is dispensable for the formation of Mlh3-dependent crossovers in budding yeast. Zip1 forms a major structural component of the budding yeast SC, and is also required for MutSγ and MutLγ-dependent crossover formation. Kluyveromyces lactis ZIP1 expressed in place of Saccharomyces cerevisiae ZIP1 in S. cerevisiae cells fails to support SC assembly (synapsis) but promotes wild-type crossover levels in those nuclei that progress to form spores. While stable, full-length SC does not assemble in S. cerevisiae cells expressing K. lactis ZIP1, aggregates of K. lactis Zip1 displayed by S. cerevisiae meiotic nuclei are decorated with SC-associated proteins, and K. lactis Zip1 promotes the SUMOylation of the SC central element protein Ecm11, suggesting that K. lactis Zip1 functionally interfaces with components of the S. cerevisiae synapsis machinery. Moreover, K. lactis Zip1-mediated crossovers rely on S. cerevisiae synapsis initiation proteins Zip3, Zip4, Spo16, as well as the Mlh3 protein, as do the crossovers mediated by S. cerevisiae Zip1. Surprisingly, however, K. lactis Zip1-mediated crossovers are largely Msh4/Msh5 (MutSγ)-independent. This separation-of-function version of Zip1 thus reveals that neither assembled SC nor MutSγ is required for Mlh3-dependent crossover formation per se in budding yeast. Our data

  18. A modified detector concept for SuperCDMS: The HiZIP and its charge performance

    NASA Astrophysics Data System (ADS)

    Page, Kedar Mohan

    SuperCDMS is a leading direct dark matter search experiment which uses solid state detectors (Ge crystals) at milliKelvin temperatures to look for nuclear recoils caused by dark matter interactions in the detector. 'Weakly Interacting Massive Particles' (WIMPs) are the most favoured dark matter candidate particles. SuperCDMS, like many other direct dark matter search experiments, primarily looks for WIMPs. The measurement of both the ionization and the lattice vibration (phonon) signals from an interaction in the detector allow it to discriminate against electron recoils which are the main source of background for WIMP detection. SuperCDMS currently operates about 9 kgs worth of germanium detectors at the Soudan underground lab in northern Minnesota. In its next phase, SuperCDMS SNOLAB, it plans to use 100-200 kg of target mass (Ge) which would allow it to probe more of the interesting and unexplored parameter space for WIMPs predicted by theoretical models. The SuperCDMS Queen's Test Facility is a detector testing facility which is intended to serve detector testing and detector research and development purposes for the SuperCDMS experiment. A modified detector called the 'HiZIP' (Half-iZIP), which is reduced in complexity in comparison to the currently used iZIP (interleaved Z-sensitive Ionization and Phonon mediated) detectors, is studied in this thesis. The HiZIP detector design also serves to discriminate against background from multiple scatter events occurring close to the surfaces in a single detector. Studies carried out to compare the surface event leakage in the HiZIP detector using limited information from iZIP data taken at SuperCDMS test facility at UC Berkley produce a highly conservative upper limit of 5 out of 10,000 events at 90% confidence level. This upper limit is the best among many different HiZIP configurations that were investigated and is comparable to the upper limit calculated for an iZIP detector in the same way using the same data. A

  19. HTLV-I Tax protein stimulation of DNA binding of bZIP proteins by enhancing dimerization.

    PubMed

    Wagner, S; Green, M R

    1993-10-15

    The Tax protein of human T cell leukemia virus type-1 (HTLV-I) transcriptionally activates the HTLV-I promoter. This activation requires binding sites for activating transcription factor (ATF) proteins, a family of cellular proteins that contain basic region-leucine zipper (bZIP) DNA binding domains. Data are presented showing that Tax increases the in vitro DNA binding activity of multiple ATF proteins. Tax also stimulated DNA binding by other bZIP proteins, but did not affect DNA binding proteins that lack a bZIP domain. The increase in DNA binding occurred because Tax promotes dimerization of the bZIP domain in the absence of DNA, and the elevated concentration of the bZIP homodimer then facilitates the DNA binding reaction. These results help explain how Tax activates viral transcription and transforms cells.

  20. Bacterial division proteins FtsZ and ZipA induce vesicle shrinkage and cell membrane invagination.

    PubMed

    Cabré, Elisa J; Sánchez-Gorostiaga, Alicia; Carrara, Paolo; Ropero, Noelia; Casanova, Mercedes; Palacios, Pilar; Stano, Pasquale; Jiménez, Mercedes; Rivas, Germán; Vicente, Miguel

    2013-09-13

    Permeable vesicles containing the proto-ring anchoring ZipA protein shrink when FtsZ, the main cell division protein, polymerizes in the presence of GTP. Shrinkage, resembling the constriction of the cytoplasmic membrane, occurs at ZipA densities higher than those found in the cell and is modulated by the dynamics of the FtsZ polymer. In vivo, an excess of ZipA generates multilayered membrane inclusions within the cytoplasm and causes the loss of the membrane function as a permeability barrier. Overproduction of ZipA at levels that block septation is accompanied by the displacement of FtsZ and two additional division proteins, FtsA and FtsN, from potential septation sites to clusters that colocalize with ZipA near the membrane. The results show that elementary constriction events mediated by defined elements involved in cell division can be evidenced both in bacteria and in vesicles.

  1. Bacterial Division Proteins FtsZ and ZipA Induce Vesicle Shrinkage and Cell Membrane Invagination*

    PubMed Central

    Cabré, Elisa J.; Sánchez-Gorostiaga, Alicia; Carrara, Paolo; Ropero, Noelia; Casanova, Mercedes; Palacios, Pilar; Stano, Pasquale; Jiménez, Mercedes; Rivas, Germán; Vicente, Miguel

    2013-01-01

    Permeable vesicles containing the proto-ring anchoring ZipA protein shrink when FtsZ, the main cell division protein, polymerizes in the presence of GTP. Shrinkage, resembling the constriction of the cytoplasmic membrane, occurs at ZipA densities higher than those found in the cell and is modulated by the dynamics of the FtsZ polymer. In vivo, an excess of ZipA generates multilayered membrane inclusions within the cytoplasm and causes the loss of the membrane function as a permeability barrier. Overproduction of ZipA at levels that block septation is accompanied by the displacement of FtsZ and two additional division proteins, FtsA and FtsN, from potential septation sites to clusters that colocalize with ZipA near the membrane. The results show that elementary constriction events mediated by defined elements involved in cell division can be evidenced both in bacteria and in vesicles. PMID:23921390

  2. A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members.

    PubMed

    Agalou, Adamantia; Purwantomo, Sigit; Overnäs, Elin; Johannesson, Henrik; Zhu, Xiaoyi; Estiati, Amy; de Kam, Rolf J; Engström, Peter; Slamet-Loedin, Inez H; Zhu, Zhen; Wang, Mei; Xiong, Lizhong; Meijer, Annemarie H; Ouwerkerk, Pieter B F

    2008-01-01

    The homeodomain leucine zipper (HD-Zip) genes encode transcription factors that have diverse functions in plant development and have often been implicated in stress adaptation. The HD-Zip genes are the most abundant group of homeobox (HB) genes in plants and do not occur in other eukaryotes. This paper describes the complete annotation of the HD-Zip families I, II and III from rice and compares these gene families with Arabidopsis in a phylogeny reconstruction. Orthologous pairs of rice and Arabidopsis HD-Zip genes were predicted based on neighbour joining and maximum parsimony (MP) trees with support of conserved intron-exon organization. Additionally, a number of HD-Zip genes appeared to be unique to rice. Searching of EST and cDNA databases and expression analysis using RT-PCR showed that 30 out of 31 predicted rice HD-Zip genes are expressed. Most HD-Zip genes were broadly expressed in mature plants and seedlings, but others showed more organ specific patterns. Like in Arabidopsis and other dicots, a subset of the rice HD-Zip I and II genes was found to be regulated by drought stress. We identified both drought-induced and drought-repressed HD-Zip genes and demonstrate that these genes are differentially regulated in drought-sensitive versus drought-tolerant rice cultivars. The drought-repressed HD-Zip family I gene, Oshox4, was selected for promoter-GUS analysis, showing that drought-responsiveness of Oshox4 is controlled by the promoter and that Oshox4 expression is predominantly vascular-specific. Loss-of-function analysis of Oshox4 revealed no specific phenotype, but overexpression analysis suggested a role for Oshox4 in elongation and maturation processes.

  3. The extracellular loop of IRT1 ZIP protein--the chosen one for zinc?

    PubMed

    Potocki, Slawomir; Valensin, Daniela; Camponeschi, Francesca; Kozlowski, Henryk

    2013-10-01

    Zinc complexes with the extracellular loop of IRT1 (iron-regulated transporter 1), a ZIP (ZRT/IRT - Related Protein) family protein from Arabidopsis thaliana, have been studied. This unstructured fragment is responsible for metal selectivity and is located between the II and III transmembrane domains of IRT1. Zinc complexes with the Ac-(95)MHVLPDSFEMLSSICLEENPWHK(117)-NH2 peptide (IRT1), revealed surprisingly high thermodynamic stability. Additionally, an N-terminal fragment of human/mouse ZIP 13 zinc transporter (MPGCPCPGCGMACPR-NH2, later called ZIP13+C), has been chosen for the thermodynamic stability comparison studies. The relative ZIP13+C stability has been shown using several Zn(2+) complexes with artificially arranged multi-cysteine sequences. An interesting coordination mode has been proposed for the IRT1-Zn(2+) complex, in which imidazoles from two histidines (His-96 and His-116), a cysteine thiolate (Cys-109) and one of a glutamic acid carboxyl group are involved. All data were collected using potentiometric, NMR and mass spectrometric methods.

  4. Mm-size bistable zipping dielectric elastomer actuators for integrated microfluidics

    NASA Astrophysics Data System (ADS)

    Maffli, Luc; Rosset, Samuel; Shea, Herbert R.

    2013-04-01

    We report on a new structure of Dielectric Elastomer Actuators (DEAs) called zipping DEAs, which have a set of unique characteristics that are a good match for the requirements of electrically-powered integrated microfluidic pumping and/or valving units as well as Braille displays. The zipping DEAs operate by pulling electrostatically an elastomer membrane in contact with the rigid sidewalls of a sloped chamber. In this work, we report on fully functional mm-size zipping DEAs that demonstrate a complete sealing of the chamber sidewalls and a tunable bistable behavior, and compare the measurements with an analytical model. Compared to our first generation of devices, we are able vary the sidewall angle and benefit therefore from more flexibility to study the requirements to make fully functional actuators. In particular, we show that with Nusil CF19 as membrane material (1.2 MPa Young's modulus), it is possible to zip completely 2.3 mm diameter chambers with 15° and 21° sidewalls angle equibiaxially prestretched to λ0=1.12 and 15° chambers with λ0=1.27.

  5. IRT-ZIP Modeling for Multivariate Zero-Inflated Count Data

    ERIC Educational Resources Information Center

    Wang, Lijuan

    2010-01-01

    This study introduces an item response theory-zero-inflated Poisson (IRT-ZIP) model to investigate psychometric properties of multiple items and predict individuals' latent trait scores for multivariate zero-inflated count data. In the model, two link functions are used to capture two processes of the zero-inflated count data. Item parameters are…

  6. Recognition of bZIP proteins by the human T-cell leukaemia virus transactivator Tax.

    PubMed

    Perini, G; Wagner, S; Green, M R

    1995-08-17

    Human T-cell leukaemia virus type I (HTLV-I) Tax protein increases the DNA binding of many cellular transcription factors that contain a basic region-leucine zipper (bZIP) DNA-binding domain. bZIP domains comprise a leucine-rich dimerization motif and a basic region that mediates DNA contact. How Tax recognizes diverse bZIPs is not understood. Here we show that no specific sequence of the leucine zipper is required for a Tax response. In contrast, the basic region is essential for the Tax-mediated DNA-binding increase, which can be eliminated by single substitutions of several conserved amino acids. Surprisingly, Tax alters the relative affinity of a bZIP for different DNA binding sites. Thus, through recognition of the conserved basic region. Tax increases DNA binding and modifies DNA site selection. Tax provides a model for how a single auxiliary factor can regulate multiple sequence-specific DNA-binding proteins.

  7. The loss of circadian PAR bZip transcription factors results in epilepsy

    PubMed Central

    Gachon, Frédéric; Fonjallaz, Philippe; Damiola, Francesca; Gos, Pascal; Kodama, Tohru; Zakany, Jozsef; Duboule, Denis; Petit, Brice; Tafti, Mehdi; Schibler, Ueli

    2004-01-01

    DBP (albumin D-site-binding protein), HLF (hepatic leukemia factor), and TEF (thyrotroph embryonic factor) are the three members of the PAR bZip (proline and acidic amino acid-rich basic leucine zipper) transcription factor family. All three of these transcriptional regulatory proteins accumulate with robust circadian rhythms in tissues with high amplitudes of clock gene expression, such as the suprachiasmatic nucleus (SCN) and the liver. However, they are expressed at nearly invariable levels in most brain regions, in which clock gene expression only cycles with low amplitude. Here we show that mice deficient for all three PAR bZip proteins are highly susceptible to generalized spontaneous and audiogenic epilepsies that frequently are lethal. Transcriptome profiling revealed pyridoxal kinase (Pdxk) as a target gene of PAR bZip proteins in both liver and brain. Pyridoxal kinase converts vitamin B6 derivatives into pyridoxal phosphate (PLP), the coenzyme of many enzymes involved in amino acid and neurotransmitter metabolism. PAR bZip-deficient mice show decreased brain levels of PLP, serotonin, and dopamine, and such changes have previously been reported to cause epilepsies in other systems. Hence, the expression of some clock-controlled genes, such as Pdxk, may have to remain within narrow limits in the brain. This could explain why the circadian oscillator has evolved to generate only low-amplitude cycles in most brain regions. PMID:15175240

  8. Theory on the Mechanism of DNA Renaturation: Stochastic Nucleation and Zipping

    PubMed Central

    Niranjani, Gnanapragasam; Murugan, Rajamanickam

    2016-01-01

    Renaturation of the complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA renaturation. According to our model there are at least three steps in the renaturation process viz. nonspecific-contact formation, correct-contact formation and nucleation, and zipping. Most of the earlier two-state models combined nucleation with nonspecific-contact formation step. In our model we suggest that it is considerably meaningful when we combine the nucleation with the zipping since nucleation is the initial step of zipping and nucleated and zipping molecules are indistinguishable. Nonspecific contact formation step is a pure three-dimensional diffusion controlled collision process. Whereas nucleation involves several rounds of one-dimensional slithering and internal displacement dynamics of one single strand of DNA on the other complementary strand in the process of searching for the correct-contact and then initiate nucleation. Upon nucleation, the stochastic zipping follows to generate a fully renatured double stranded DNA. It seems that the square-root dependency of the overall renaturation rate constant on the length of reacting single strands originates mainly from the geometric constraints in the diffusion controlled nonspecific-contact formation step. Further the inverse scaling of the renaturation rate on the viscosity of reaction medium also originates from nonspecific contact formation step. On the other hand the inverse scaling of the renaturation rate with the sequence complexity originates from the stochastic zipping which involves several rounds of crossing over the free-energy barrier at microscopic levels. When the sequence of renaturing single strands of DNA is repetitive with less complexity then the cooperative effects will not be noticeable since the parallel zipping will be a dominant enhancing

  9. Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions

    PubMed Central

    Potapov, Vladimir; Kaplan, Jenifer B.; Keating, Amy E.

    2015-01-01

    Selective dimerization of the basic-region leucine-zipper (bZIP) transcription factors presents a vivid example of how a high degree of interaction specificity can be achieved within a family of structurally similar proteins. The coiled-coil motif that mediates homo- or hetero-dimerization of the bZIP proteins has been intensively studied, and a variety of methods have been proposed to predict these interactions from sequence data. In this work, we used a large quantitative set of 4,549 bZIP coiled-coil interactions to develop a predictive model that exploits knowledge of structurally conserved residue-residue interactions in the coiled-coil motif. Our model, which expresses interaction energies as a sum of interpretable residue-pair and triplet terms, achieves a correlation with experimental binding free energies of R = 0.68 and significantly out-performs other scoring functions. To use our model in protein design applications, we devised a strategy in which synthetic peptides are built by assembling 7-residue native-protein heptad modules into new combinations. An integer linear program was used to find the optimal combination of heptads to bind selectively to a target human bZIP coiled coil, but not to target paralogs. Using this approach, we designed peptides to interact with the bZIP domains from human JUN, XBP1, ATF4 and ATF5. Testing more than 132 candidate protein complexes using a fluorescence resonance energy transfer assay confirmed the formation of tight and selective heterodimers between the designed peptides and their targets. This approach can be used to make inhibitors of native proteins, or to develop novel peptides for applications in synthetic biology or nanotechnology. PMID:25695764

  10. Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress.

    PubMed

    Banerjee, Aditya; Roychoudhury, Aryadeep

    2017-01-01

    One of the major causes of significant crop loss throughout the world is the myriad of environmental stresses including drought, salinity, cold, heavy metal toxicity, and ultraviolet-B (UV-B) rays. Plants as sessile organisms have evolved various effective mechanism which enable them to withstand this plethora of stresses. Most of such regulatory mechanisms usually follow the abscisic-acid (ABA)-dependent pathway. In this review, we have primarily focussed on the basic leucine zipper (bZIP) transcription factors (TFs) activated by the ABA-mediated signalosome. Upon perception of ABA by specialized receptors, the signal is transduced via various groups of Ser/Thr kinases, which phosphorylate the bZIP TFs. Following such post-translational modification of TFs, they are activated so that they bind to specific cis-acting sequences called abscisic-acid-responsive elements (ABREs) or GC-rich coupling elements (CE), thereby influencing the expression of their target downstream genes. Several in silico techniques have been adopted so far to predict the structural features, recognize the regulatory modification sites, undergo phylogenetic analyses, and facilitate genome-wide survey of TF under multiple stresses. Current investigations on the epigenetic regulation that controls greater accessibility of the inducible regions of DNA of the target gene to the bZIP TFs exclusively under stress situations, along with the evolved stress memory responses via genomic imprinting mechanism, have been highlighted. The potentiality of overexpression of bZIP TFs, either in a homologous or in a heterologous background, in generating transgenic plants tolerant to various abiotic stressors have also been addressed by various groups. The present review will provide a coherent documentation on the functional characterization and regulation of bZIP TFs under multiple environmental stresses, with the major goal of generating multiple-stress-tolerant plant cultivars in near future.

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    MedlinePlus

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  12. Isolation and expression analysis of 18 CsbZIP genes implicated in abiotic stress responses in the tea plant (Camellia sinensis).

    PubMed

    Cao, Hongli; Wang, Lu; Yue, Chuan; Hao, Xinyuan; Wang, Xinchao; Yang, Yajun

    2015-12-01

    Basic leucine zipper (bZIP) transcription factors (TFs) play essential roles in regulating stress processes in plants. Despite the economic importance of this woody crop, there is little information about bZIP TFs in tea plants. In this study, 18 bZIP genes were isolated from the tea plant (Camellia sinensis) and named sequentially from CsbZIP1 to CsbZIP18. According to the phylogenetic classification as in Arabidopsis, the CsbZIP genes spanned ten subgroups (Group A, B, C, D, E, F, H, I, S and K) of bZIP TFs. When analyzed for organ specific expression, all CsbZIP genes were found to be ubiquitously expressed in roots, stems, leaves and flowers. Expression analysis of CsbZIP genes in response to four abiotic stresses showed that in leaves, 9, 9, 15 and 11 CsbZIPs have 2-fold greater variation in transcript abundance under cold, exogenous ABA, high salinity and dehydration conditions, respectively. In roots, 5, 12, 14 and 11 CsbZIPs were differentially expressed under conditions of cold, exogenous ABA, high salinity and dehydration stresses. Moreover, CsbZIP genes in Groups F, H, S and K exhibited several folds up-and/or down-regulation against the above four stresses. Notably, CsbZIP18 of group K showed significant up-regulation in response to these same stresses, suggesting a vital functional role in stress response. Together, these findings increase our knowledge of bZIP TFs in the tea plant and suggest the significance of CsbZIP genes in plant abiotic responses.

  13. The Role of bZIP Transcription Factors in Green Plant Evolution: Adaptive Features Emerging from Four Founder Genes

    PubMed Central

    Schrago, Carlos Guerra; dos Santos, Renato Vicentini; Mueller-Roeber, Bernd; Vincentz, Michel

    2008-01-01

    Background Transcription factors of the basic leucine zipper (bZIP) family control important processes in all eukaryotes. In plants, bZIPs are regulators of many central developmental and physiological processes including photomorphogenesis, leaf and seed formation, energy homeostasis, and abiotic and biotic stress responses. Here we performed a comprehensive phylogenetic analysis of bZIP genes from algae, mosses, ferns, gymnosperms and angiosperms. Methodology/Principal Findings We identified 13 groups of bZIP homologues in angiosperms, three more than known before, that represent 34 Possible Groups of Orthologues (PoGOs). The 34 PoGOs may correspond to the complete set of ancestral angiosperm bZIP genes that participated in the diversification of flowering plants. Homologous genes dedicated to seed-related processes and ABA-mediated stress responses originated in the common ancestor of seed plants, and three groups of homologues emerged in the angiosperm lineage, of which one group plays a role in optimizing the use of energy. Conclusions/Significance Our data suggest that the ancestor of green plants possessed four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments. PMID:18698409

  14. Early memory formation disrupted by atypical PKC inhibitor ZIP in the medial prefrontal cortex but not hippocampus.

    PubMed

    Evuarherhe, Obaro; Barker, Gareth R I; Savalli, Giorgia; Warburton, Elizabeth C; Brown, Malcolm W

    2014-08-01

    Atypical isoforms of protein kinase C (aPKCs; particularly protein kinase M zeta: PKMζ) have been hypothesized to be necessary and sufficient for the maintenance of long-term potentiation (LTP) and long term memory by maintaining postsynaptic AMPA receptors via the GluA2 subunit. A myristoylated PKMζ pseudosubstrate peptide (ZIP) blocks PKMζ activity. We examined the actions of ZIP in medial prefrontal cortex (mPFC) and hippocampus in associative recognition memory in rats during early memory formation and memory maintenance. ZIP infusion in either hippocampus or mPFC impaired memory maintenance. However, early memory formation was impaired by ZIP in mPFC but not hippocampus; and blocking GluA2-dependent removal of AMPA receptors did not affect this impairment caused by ZIP in the mPFC. The findings indicate: (i) a difference in the actions of ZIP in hippocampus and medial prefrontal cortex, and (ii) a GluA2-independent target of ZIP (possibly PKCλ) in the mPFC during early memory formation.

  15. Zinc Transporter SLC39A7/ZIP7 Promotes Intestinal Epithelial Self-Renewal by Resolving ER Stress

    PubMed Central

    Ohashi, Wakana; Kimura, Shunsuke; Iwanaga, Toshihiko; Furusawa, Yukihiro; Irié, Tarou; Izumi, Hironori; Watanabe, Takashi; Hara, Takafumi; Ohara, Osamu; Koseki, Haruhiko; Sato, Toshiro; Robine, Sylvie; Mori, Hisashi; Hattori, Yuichi; Mishima, Kenji; Ohno, Hiroshi; Hase, Koji; Fukada, Toshiyuki

    2016-01-01

    Zinc transporters play a critical role in spatiotemporal regulation of zinc homeostasis. Although disruption of zinc homeostasis has been implicated in disorders such as intestinal inflammation and aberrant epithelial morphology, it is largely unknown which zinc transporters are responsible for the intestinal epithelial homeostasis. Here, we show that Zrt-Irt-like protein (ZIP) transporter ZIP7, which is highly expressed in the intestinal crypt, is essential for intestinal epithelial proliferation. Mice lacking Zip7 in intestinal epithelium triggered endoplasmic reticulum (ER) stress in proliferative progenitor cells, leading to significant cell death of progenitor cells. Zip7 deficiency led to the loss of Olfm4+ intestinal stem cells and the degeneration of post-mitotic Paneth cells, indicating a fundamental requirement for Zip7 in homeostatic intestinal regeneration. Taken together, these findings provide evidence for the importance of ZIP7 in maintenance of intestinal epithelial homeostasis through the regulation of ER function in proliferative progenitor cells and maintenance of intestinal stem cells. Therapeutic targeting of ZIP7 could lead to effective treatment of gastrointestinal disorders. PMID:27736879

  16. Memory Retrieval Has a Dynamic Influence on the Maintenance Mechanisms That Are Sensitive to ζ-Inhibitory Peptide (ZIP).

    PubMed

    Levitan, David; Fortis-Santiago, Yaihara; Figueroa, Joshua A; Reid, Emily E; Yoshida, Takashi; Barry, Nicholas C; Russo, Abigail; Katz, Donald B

    2016-10-12

    In neuroscientists' attempts to understand the long-term storage of memory, topics of particular importance and interest are the cellular and system mechanisms of maintenance (e.g., those sensitive to ζ-inhibitory peptide, ZIP) and those induced by memory retrieval (i.e., reconsolidation). Much is known about each of these processes in isolation, but less is known concerning how they interact. It is known that ZIP sensitivity and memory retrieval share at least some molecular targets (e.g., recycling α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid, AMPA, receptors to the plasma membrane); conversely, the fact that sensitivity to ZIP emerges only after consolidation ends suggests that consolidation (and by extension reconsolidation) and maintenance might be mutually exclusive processes, the onset of one canceling the other. Here, we use conditioned taste aversion (CTA) in rats, a cortically dependent learning paradigm, to test this hypothesis. First, we demonstrate that ZIP infusions into gustatory cortex begin interfering with CTA memory 43-45 h after memory acquisition-after consolidation ends. Next, we show that a retrieval trial administered after this time point interrupts the ability of ZIP to induce amnesia and that ZIP's ability to induce amnesia is reengaged only 45 h after retrieval. This pattern of results suggests that memory retrieval and ZIP-sensitive maintenance mechanisms are mutually exclusive and that the progression from one to the other are similar after acquisition and retrieval. They also reveal concrete differences between ZIP-sensitive mechanisms induced by acquisition and retrieval: the latency with which ZIP-sensitive mechanisms are expressed differ for the two processes.

  17. The Elucidation of the Interactome of 16 Arabidopsis bZIP Factors Reveals Three Independent Functional Networks

    PubMed Central

    Llorca, Carles Marco; Berendzen, Kenneth Wayne; Malik, Waqas Ahmed; Mahn, Stefan; Piepho, Hans-Peter; Zentgraf, Ulrike

    2015-01-01

    The function of the bZIP transcription factors is strictly dependent on their ability to dimerize. Heterodimerization has proven to be highly specific and is postulated to operate as a combinatorial mechanism allowing the generation of a large variety of dimers with unique qualities by specifically combining a small set of monomers; an assumption that has not yet been tested systematically. Here, the interaction pattern and the transactivation properties of 16 Arabidopsis thaliana bZIPs are examined in transiently transformed Arabidopsis protoplasts to deliver a perspective on the relationship between bZIP dimerization and function. An interaction matrix of bZIPs belonging to the C, G, H, and S1 bZIP groups was resolved by Bimolecular Fluorescent Complementation (BiFC) coupled to quantitative flow cytometric analysis, while an extensive GUS reporter gene assay was carried out to determine the effect of different bZIP pairs on the expression of four different known bZIP-targeted promoters. Statistical data treatment and complementary bioinformatic analysis were performed to substantiate the biological findings. According to these results, the 16 bZIPs interact in three isolated networks, within which their members dimerize non-specifically and exhibit a significant level of functional redundancy. A coherent explanation for these results is supported by in silico analysis of differences in the length, structure and composition of their leucine zippers and appears to explain their dimerization specificity and dynamics observed in vivo quite well. A model in which the bZIP networks act as functional units is proposed. PMID:26452049

  18. Isolation and characterization of a gene from Medicago sativa L., encoding a bZIP transcription factor.

    PubMed

    Li, Yan; Sun, Yan; Yang, Qingchuan; Fang, Feng; Kang, Junmei; Zhang, Tiejun

    2013-02-01

    A full-length cDNA of 1,537 nucleotides was cloned from Medicago sativa L. cv. "Zhongmu No. 1" by rapid amplification of cDNA ends. It was designated as MsZIP, encoding a protein of 340 amino acids. The protein molecular weight was 36.43 kDa, and the theoretical isoelectric point was 5.72. The MsZIP preferentially localized in nucleus and have signal peptide. Blast analysis revealed that MsZIP shared the highest homology with some bZIP proteins of M. truncatula. The transcript of MsZIP was strongly enriched in leaf compared with root and stem of mature alfalfa plants. MsZIP was strongly induced by 15 % PEG6000 (polyethylene glycol), 50 μM abscisic acid, 200 mM NaCl, 70 μM gibberellic acid, 5 mM salicylic acid and 200 μM methyl jasmonate. Physiological resistance parameters were measured in the transgenic tobacco. Malondialdehyde content, relative water content, soluble sugar content, soluble protein content and proline content in transgenic tobacco increased compared with non-transgenic tobacco under salt stress or drought stress. The results showed that accumulation of the MsZIP protein in the vegetative tissues of transgenic plants enhanced their tolerance to osmotic pressure stress. These results demonstrate a role for the MsZIP protein in stress protection and suggest the potential of the MsZIP gene for genetic engineering of salt tolerance and drought tolerance.

  19. Structure-function analysis of a novel member of the LIV-1 subfamily of zinc transporters, ZIP14.

    PubMed

    Taylor, K M; Morgan, H E; Johnson, A; Nicholson, R I

    2005-01-17

    Here, we report the first investigation of a novel member of the LZT (LIV-1 subfamily of ZIP zinc Transporters) subfamily of zinc influx transporters. LZT subfamily sequences all contain a unique and highly conserved metalloprotease motif (HEXPHEXGD) in transmembrane domain V with both histidine residues essential for zinc transport by ZIP (Zrt-, Irt-like Proteins) transporters. We investigate here whether ZIP14 (SLC39A14), lacking the initial histidine in this motif, is still able to transport zinc. We demonstrate that this plasma membrane located glycosylated protein functions as a zinc influx transporter in a temperature-dependant manner.

  20. Does it really matter that people zip through ads? Testing the effectiveness of simultaneous presentation advertising in an IDTV environment.

    PubMed

    Nam, Yoonjae; Kwon, Kyonghee H; Lee, Sungjoon

    2010-04-01

    In an IDTV environment, which facilitates self-scheduling, skipping advertisements by zipping is an emerging ad-avoidance behavior. This study explores whether an alternative ad format, called simultaneous presentation advertising (SPA), may overcome the limitations of classical sequential advertising (CSA) in controlling zipping behavior and increasing the effectiveness of ads. The experiment revealed that SPA is more effective than CSA in reducing zipping and increasing recall, but SPA was more intrusive and produced a negative product image. There was no difference regarding cognitive avoidance. This work discusses the implications of these findings in the interactive media environment.

  1. Increasing the affinity of selective bZIP-binding peptides through surface residue redesign

    PubMed Central

    Kaplan, Jenifer B; Reinke, Aaron W; Keating, Amy E

    2014-01-01

    The coiled-coil dimer is a prevalent protein interaction motif that is important for many cellular processes. The basic leucine-zipper (bZIP) transcription factors are one family of proteins for which coiled-coil mediated dimerization is essential for function, and misregulation of bZIPs can lead to disease states including cancer. This makes coiled coils attractive protein–protein interaction targets to disrupt using engineered molecules. Previous work designing peptides to compete with native coiled-coil interactions focused primarily on designing the core residues of the interface to achieve affinity and specificity. However, folding studies on the model bZIP GCN4 show that coiled-coil surface residues also contribute to binding affinity. Here we extend a prior study in which peptides were designed to bind tightly and specifically to representative members of each of 20 human bZIP families. These “anti-bZIP” peptides were designed with an emphasis on target-binding specificity, with contributions to design-target specificity and affinity engineered considering only the coiled-coil core residues. High-throughput testing using peptide arrays indicated many successes. We have now measured the binding affinities and specificities of anti-bZIPs that bind to FOS, XBP1, ATF6, and CREBZF in solution and tested whether redesigning the surface residues can increase design–target affinity. Incorporating residues that favor helix formation into the designs increased binding affinities in all cases, providing low-nanomolar binders of each target. However, changes in surface electrostatic interactions sometimes changed the binding specificity of the designed peptides. Impact Statement Designing molecules to bind native proteins is a fundamental objective in protein engineering. Ideally, designs should bind their targets both tightly and selectively. This paper reports binding affinities and specificities for computationally designed peptides that interact with human bZIP

  2. Transcriptional repression of BODENLOS by HD-ZIP transcription factor HB5 in Arabidopsis thaliana

    PubMed Central

    De Smet, Ive; Lau, Steffen; Ehrismann, Jasmin S.; Axiotis, Ioannis; Kolb, Martina; Kientz, Marika; Weijers, Dolf; Jürgens, Gerd

    2013-01-01

    In Arabidopsis thaliana, the phytohormone auxin is an important patterning agent during embryogenesis and post-embryonic development, exerting effects through transcriptional regulation. The main determinants of the transcriptional auxin response machinery are AUXIN RESPONSE FACTOR (ARF) transcription factors and AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) inhibitors. Although members of these two protein families are major developmental regulators, the transcriptional regulation of the genes encoding them has not been well explored. For example, apart from auxin-linked regulatory inputs, factors regulating the expression of the AUX/IAA BODENLOS (BDL)/IAA12 are not known. Here, it was shown that the HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP) transcription factor HOMEOBOX PROTEIN 5 (HB5) negatively regulates BDL expression, which may contribute to the spatial control of BDL expression. As such, HB5 and probably other class I HD-ZIP proteins, appear to modulate BDL-dependent auxin response. PMID:23682118

  3. Zipping and entanglement in flagellar bundle of E. coli: Role of motile cell body

    NASA Astrophysics Data System (ADS)

    Adhyapak, Tapan Chandra; Stark, Holger

    2015-11-01

    The course of a peritrichous bacterium, such as E. coli, crucially depends on the level of synchronization and self-organization of several rotating flagella. However, the rotation of each flagellum generates countermovements of the body which in turn affect the flagellar dynamics. Using a detailed numerical model of an E. coli, we demonstrate that flagellar entanglement, besides fluid flow relative to the moving body, dramatically changes the dynamics of flagella from that compared to anchored flagella. In particular, bundle formation occurs through a zipping motion in a remarkably rapid time, affected little by initial flagellar orientation. A simplified analytical model supports our observations. Finally, we illustrate how entanglement, hydrodynamic interactions, and body movement contribute to zipping and bundling.

  4. Murine chromosomal location of five bHLH-Zip transcription factor genes

    SciTech Connect

    Steingrimsson, E.; Gilbert, D.J.; Copeland, N.G.; Jenkins, N.A.

    1995-07-20

    The genes for the bHLH-Zip transcription factors Tfap4, Mxi1, Tcfeb, Usf1, and Usf2 have been mapped in mouse by interspecific backcross analysis. Mxi1, Usf1, and Usf2 have been mapped previously by in situ hybridization, but their positions on the meiotic linkage map had not been determined. The other two genes have not previously been mapped in mouse. These transcription factors belong to a growing family of transcriptional regulators, some of which are known to form a complex network of interacting proteins that control cell proliferation and apoptosis. As expected, based on mapping studies of other bHLH-Zip genes, these loci were well distributed among mouse chromosomes. In addition, some of the probes used in this study detected multiple, independently segregating loci, suggesting the possible existence of additional family members or species-specific pseudogenes. 34 refs., 1 fig., 1 tab.

  5. Identification of ZipA, a Signal Recognition Particle-Dependent Protein from Neisseria gonorrhoeae

    PubMed Central

    Du, Ying; Arvidson, Cindy Grove

    2003-01-01

    A genetic screen designed to identify proteins that utilize the signal recognition particle (SRP) for targeting in Escherichia coli was used to screen a Neisseria gonorrhoeae plasmid library. Six plasmids were identified in this screen, and each is predicted to encode one or more putative cytoplasmic membrane (CM) proteins. One of these, pSLO7, has three open reading frames (ORFs), two of which have no similarity to known proteins in GenBank other than sequences from the closely related N. meningitidis. Further analyses showed that one of these, SLO7ORF3, encodes a protein that is dependent on the SRP for localization. This gene also appears to be essential in N. gonorrhoeae since it was not possible to generate null mutations in the gene. Although appearing unique to Neisseria at the DNA sequence level, SLO7ORF3 was found to share some features with the cell division gene zipA of E. coli. These features included similar chromosomal locations (with respect to linked genes) as well as similarities in the predicted protein domain structures. Here, we show that SLO7ORF3 can complement an E. coli conditional zipA mutant and therefore encodes a functional ZipA homolog in N. gonorrhoeae. This observation is significant in that it is the first ZipA homolog identified in a non-rod-shaped organism. Also interesting is that this is the fourth cell division protein (the others are FtsE, FtsX, and FtsQ) shown to utilize the SRP for localization, which may in part explain why the genes encoding the three SRP components are essential in bacteria. PMID:12644481

  6. Phosphorylation of the Synaptonemal Complex Protein Zip1 Regulates the Crossover/Noncrossover Decision during Yeast Meiosis.

    PubMed

    Chen, Xiangyu; Suhandynata, Ray T; Sandhu, Rima; Rockmill, Beth; Mohibullah, Neeman; Niu, Hengyao; Liang, Jason; Lo, Hsiao-Chi; Miller, Danny E; Zhou, Huilin; Börner, G Valentin; Hollingsworth, Nancy M

    2015-12-01

    Interhomolog crossovers promote proper chromosome segregation during meiosis and are formed by the regulated repair of programmed double-strand breaks. This regulation requires components of the synaptonemal complex (SC), a proteinaceous structure formed between homologous chromosomes. In yeast, SC formation requires the "ZMM" genes, which encode a functionally diverse set of proteins, including the transverse filament protein, Zip1. In wild-type meiosis, Zmm proteins promote the biased resolution of recombination intermediates into crossovers that are distributed throughout the genome by interference. In contrast, noncrossovers are formed primarily through synthesis-dependent strand annealing mediated by the Sgs1 helicase. This work identifies a conserved region on the C terminus of Zip1 (called Zip1 4S), whose phosphorylation is required for the ZMM pathway of crossover formation. Zip1 4S phosphorylation is promoted both by double-strand breaks (DSBs) and the meiosis-specific kinase, MEK1/MRE4, demonstrating a role for MEK1 in the regulation of interhomolog crossover formation, as well as interhomolog bias. Failure to phosphorylate Zip1 4S results in meiotic prophase arrest, specifically in the absence of SGS1. This gain of function meiotic arrest phenotype is suppressed by spo11Δ, suggesting that it is due to unrepaired breaks triggering the meiotic recombination checkpoint. Epistasis experiments combining deletions of individual ZMM genes with sgs1-md zip1-4A indicate that Zip1 4S phosphorylation functions prior to the other ZMMs. These results suggest that phosphorylation of Zip1 at DSBs commits those breaks to repair via the ZMM pathway and provides a mechanism by which the crossover/noncrossover decision can be dynamically regulated during yeast meiosis.

  7. Phosphorylation of the Synaptonemal Complex Protein Zip1 Regulates the Crossover/Noncrossover Decision during Yeast Meiosis

    PubMed Central

    Chen, Xiangyu; Suhandynata, Ray T.; Sandhu, Rima; Rockmill, Beth; Mohibullah, Neeman; Niu, Hengyao; Liang, Jason; Lo, Hsiao-Chi; Miller, Danny E.; Zhou, Huilin; Börner, G. Valentin; Hollingsworth, Nancy M.

    2015-01-01

    Interhomolog crossovers promote proper chromosome segregation during meiosis and are formed by the regulated repair of programmed double-strand breaks. This regulation requires components of the synaptonemal complex (SC), a proteinaceous structure formed between homologous chromosomes. In yeast, SC formation requires the “ZMM” genes, which encode a functionally diverse set of proteins, including the transverse filament protein, Zip1. In wild-type meiosis, Zmm proteins promote the biased resolution of recombination intermediates into crossovers that are distributed throughout the genome by interference. In contrast, noncrossovers are formed primarily through synthesis-dependent strand annealing mediated by the Sgs1 helicase. This work identifies a conserved region on the C terminus of Zip1 (called Zip1 4S), whose phosphorylation is required for the ZMM pathway of crossover formation. Zip1 4S phosphorylation is promoted both by double-strand breaks (DSBs) and the meiosis-specific kinase, MEK1/MRE4, demonstrating a role for MEK1 in the regulation of interhomolog crossover formation, as well as interhomolog bias. Failure to phosphorylate Zip1 4S results in meiotic prophase arrest, specifically in the absence of SGS1. This gain of function meiotic arrest phenotype is suppressed by spo11Δ, suggesting that it is due to unrepaired breaks triggering the meiotic recombination checkpoint. Epistasis experiments combining deletions of individual ZMM genes with sgs1-md zip1-4A indicate that Zip1 4S phosphorylation functions prior to the other ZMMs. These results suggest that phosphorylation of Zip1 at DSBs commits those breaks to repair via the ZMM pathway and provides a mechanism by which the crossover/noncrossover decision can be dynamically regulated during yeast meiosis. PMID:26682552

  8. Zipping it up: DEAs independent of the elastomer's electric breakdown field

    NASA Astrophysics Data System (ADS)

    Gebbers, Pit; Grätzel, Chauncey; Maffli, Luc; Stamm, Christoph; Shea, Herbert

    2012-04-01

    We demonstrate here an alternative dielectric elastomer actuator (DEA) structure, which relies on the compliant nature of elastomer membranes but does not require any electric field in the elastomer. Our elastomer zipping device is a macroscopic version of the electrostatic zipping actuators common in silicon MEMS. It consists of a cm-sized metallic bottom electrode, covered by a thin insulator, on which the elastomer membrane is bonded, enclosing a tapered air gap. A compliant electrode is patterned on the lower face of the elastomer membrane. Applying a voltage between solid bottom electrode and compliant electrode leads to controlled pull-in in movement, comparable to the closing of a zipper, thus giving large strokes and forces with no electrical requirements on the elastomer since no voltage is applied across the membrane. The compliant electrodes (20 mm diameter) are produced by metal ion-implantation into the elastomer membranes. The bottom metal electrodes are coated with 10 to 30 μm of Al2O3. We report on our experimental study of membrane deflection and dynamics and discuss the effect of design parameters such as elastomer mechanical properties and actuator geometry. Membrane deflection of up to 1.4 mm was reached at only 200 V actuation voltage. The large membrane deformation achieved with this zipping actuation can be applied to applications such as pumps or tunable liquid lenses. The out-of plane movement of the membrane can be used for linear actuation.

  9. Modeling regulation of zinc uptake via ZIP transporters in yeast and plant roots.

    PubMed

    Claus, Juliane; Chavarría-Krauser, Andrés

    2012-01-01

    In yeast (Saccharomyces cerevisiae) and plant roots (Arabidopsis thaliana) zinc enters the cells via influx transporters of the ZIP family. Since zinc is both essential for cell function and toxic at high concentrations, tight regulation is essential for cell viability. We provide new insight into the underlying mechanisms, starting from a general model based on ordinary differential equations and adapting it to the specific cases of yeast and plant root cells. In yeast, zinc is transported by the transporters ZRT1 and ZRT2, which are both regulated by the zinc-responsive transcription factor ZAP1. Using biological data, parameters were estimated and analyzed, confirming the different affinities of ZRT1 and ZRT2 reported in the literature. Furthermore, our model suggests that the positive feedback in ZAP1 production has a stabilizing function at high influx rates. In plant roots, various ZIP transporters play a role in zinc uptake. Their regulation is largely unknown, but bZIP transcription factors are thought to be involved. We set up three putative models based on: an activator only, an activator with dimerization and an activator-inhibitor pair. These were fitted to measurements and analyzed. Simulations show that the activator-inhibitor model outperforms the other two in providing robust and stable homeostasis at reasonable parameter ranges.

  10. Intra-cerebellar infusion of the protein kinase Mzeta (PKMζ) inhibitor ZIP disrupts eyeblink classical conditioning

    PubMed Central

    Chihabi, Kutibh; Morielli, Anthony D.; Green, John T.

    2016-01-01

    PKM-ζ, a constitutively active N-terminal truncated form of PKC-ζ, has long been implicated in a cellular correlate of learning, long-term potentiation (LTP). Inhibition of PKM-ζ with Zeta-inhibitory peptide (ZIP) has been shown in many brain structures to disrupt maintenance of AMPA receptors, irreversibly disrupting numerous forms of learning and memory that have been maintained for weeks. Delay eyeblink conditioning (EBC) is an established model for the assessment of cerebellar learning; here, we show that PKC-ζ and PKM-ζ are highly expressed in the cerebellar cortex, with highest expression found in Purkinje cell (PC) nuclei. Despite being highly expressed in the cerebellar cortex, no studies have examined how regulation of cerebellar PKM-ζ may affect cerebellar-dependent learning and memory. Given its disruption of learning in other brain structures, we hypothesized that ZIP would also disrupt delay EBC. We have shown that infusion of ZIP into the lobulus simplex of the rat cerebellar cortex can indeed significantly disrupt delay EBC. PMID:26949968

  11. Tissue Plasminogen Activator Alters Intracellular Sequestration of Zinc through Interaction with the Transporter ZIP4

    SciTech Connect

    Emmetsberger, Jaime; Mirrione, Martine M.; Zhou, Chun; Fernandez-Monreal, Monica; Siddiq, Mustafa M.; Ji, Kyungmin; Tsirka, Stella E.

    2010-09-17

    Glutamatergic neurons contain free zinc packaged into neurotransmitter-loaded synaptic vesicles. Upon neuronal activation, the vesicular contents are released into the synaptic space, whereby the zinc modulates activity of postsynaptic neurons though interactions with receptors, transporters and exchangers. However, high extracellular concentrations of zinc trigger seizures and are neurotoxic if substantial amounts of zinc reenter the cells via ion channels and accumulate in the cytoplasm. Tissue plasminogen activator (tPA), a secreted serine protease, is also proepileptic and excitotoxic. However, tPA counters zinc toxicity by promoting zinc import back into the neurons in a sequestered form that is nontoxic. Here, we identify the zinc influx transporter, ZIP4, as the pathway through which tPA mediates the zinc uptake. We show that ZIP4 is upregulated after excitotoxin stimulation of the mouse, male and female, hippocampus. ZIP4 physically interacts with tPA, correlating with an increased intracellular zinc influx and lysosomal sequestration. Changes in prosurvival signals support the idea that this sequestration results in neuroprotection. These experiments identify a mechanism via which neurons use tPA to efficiently neutralize the toxic effects of excessive concentrations of free zinc.

  12. Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice.

    PubMed

    Lu, Guojun; Gao, Chenxi; Zheng, Xingnan; Han, Bin

    2009-02-01

    Abscisic Acid (ABA) is an important phytohormone involved in abiotic stress resistance in plants. A group of bZIP transcription factors play important roles in the ABA signaling pathway in Arabidopsis. However, little is known about the function of their orthologs in rice, where they may hold a great potential for developing drought resistant food crops. In this study, our phylogenetic analysis showed that this group of bZIPs was evolutionarily conserved between Arabidopsis and rice, which implies that they may share similar functions. We demonstrated with quantitative RT-PCR that the expressions of most of these OsbZIPs were significantly induced by ABA, ACC, and abiotic stresses. OsbZIP72, a member of this group, was proved to be an ABRE binding factor in rice using the yeast hybrid systems. We showed that it could bind to ABRE and transactivate the downstream reporter genes in yeast, and the transactivity was depending on its N-terminal region. Transgenic rice overexpressing OsbZIP72 showed a hypersensitivity to ABA, elevated levels of expression of ABA response gene such as LEAs, and an enhanced ability of drought tolerance. These results suggest that OsbZIP72 plays a positive role in drought resistance through ABA signaling, and is potential useful for engineering drought tolerant rice.

  13. Deregulation of Sucrose-Controlled Translation of a bZIP-Type Transcription Factor Results in Sucrose Accumulation in Leaves

    PubMed Central

    Lee, Sung Shin; Yang, Seung Hwan; Zhu, XuJun; Imai, Ryozo; Takahashi, Yoshihiro; Kusano, Tomonobu

    2012-01-01

    Sucrose is known to repress the translation of Arabidopsis thaliana AtbZIP11 transcript which encodes a protein belonging to the group of S (S - stands for small) basic region-leucine zipper (bZIP)-type transcription factor. This repression is called sucrose-induced repression of translation (SIRT). It is mediated through the sucrose-controlled upstream open reading frame (SC-uORF) found in the AtbZIP11 transcript. The SIRT is reported for 4 other genes belonging to the group of S bZIP in Arabidopsis. Tobacco tbz17 is phylogenetically closely related to AtbZIP11 and carries a putative SC-uORF in its 5′-leader region. Here we demonstrate that tbz17 exhibits SIRT mediated by its SC-uORF in a manner similar to genes belonging to the S bZIP group of the Arabidopsis genus. Furthermore, constitutive transgenic expression of tbz17 lacking its 5′-leader region containing the SC-uORF leads to production of tobacco plants with thicker leaves composed of enlarged cells with 3–4 times higher sucrose content compared to wild type plants. Our finding provides a novel strategy to generate plants with high sucrose content. PMID:22457737

  14. Polar Codes

    DTIC Science & Technology

    2014-12-01

    density parity check (LDPC) code, a Reed–Solomon code, and three convolutional codes. iii CONTENTS EXECUTIVE SUMMARY...the most common. Many civilian systems use low density parity check (LDPC) FEC codes, and the Navy is planning to use LDPC for some future systems...other forward error correction methods: a turbo code, a low density parity check (LDPC) code, a Reed–Solomon code, and three convolutional codes

  15. ZIP8 Zinc Transporter: Indispensable Role for Both Multiple-Organ Organogenesis and Hematopoiesis In Utero

    PubMed Central

    Gálvez-Peralta, Marina; He, Lei; Jorge-Nebert, Lucia F.; Wang, Bin; Miller, Marian L.; Eppert, Bryan L.; Afton, Scott; Nebert, Daniel W.

    2012-01-01

    Previously this laboratory characterized Slc39a8-encoded ZIP8 as a Zn2+/(HCO3–)2 symporter; yet, the overall physiological importance of ZIP8 at the whole-organism level remains unclear. Herein we describe the phenotype of the hypomorphic Slc39a8(neo/neo) mouse which has retained the neomycin-resistance gene in intron 3, hence causing significantly decreased ZIP8 mRNA and protein levels in embryo, fetus, placenta, yolk sac, and several tissues of neonates. The Slc39a8(neo) allele is associated with diminished zinc and iron uptake in mouse fetal fibroblast and liver-derived cultures; consequently, Slc39a8(neo/neo) newborns exhibit diminished zinc and iron levels in several tissues. Slc39a8(neo/neo) homozygotes from gestational day(GD)-11.5 onward are pale, growth-stunted, and die between GD18.5 and 48 h postnatally. Defects include: severely hypoplastic spleen; hypoplasia of liver, kidney, lung, and lower limbs. Histologically, Slc39a8(neo/neo) neonates show decreased numbers of hematopoietic islands in yolk sac and liver. Low hemoglobin, hematocrit, red cell count, serum iron, and total iron-binding capacity confirmed severe anemia. Flow cytometry of fetal liver cells revealed the erythroid series strikingly affected in the hypomorph. Zinc-dependent 5-aminolevulinic acid dehydratase, required for heme synthesis, was not different between Slc39a8(+/+) and Slc39a8(neo/neo) offspring. To demonstrate further that the mouse phenotype is due to ZIP8 deficiency, we bred Slc39a8(+/neo) with BAC-transgenic BTZIP8-3 line (carrying three extra copies of the Slc39a8 allele); this cross generated viable Slc39a8(neo/neo)_BTZIP8-3(+/+) pups showing none of the above-mentioned congenital defects–proving Slc39a8(neo/neo) causes the described phenotype. Our study demonstrates that ZIP8-mediated zinc transport plays an unappreciated critical role during in utero and neonatal growth, organ morphogenesis, and hematopoiesis. PMID:22563477

  16. ZIP8 zinc transporter: indispensable role for both multiple-organ organogenesis and hematopoiesis in utero.

    PubMed

    Gálvez-Peralta, Marina; He, Lei; Jorge-Nebert, Lucia F; Wang, Bin; Miller, Marian L; Eppert, Bryan L; Afton, Scott; Nebert, Daniel W

    2012-01-01

    Previously this laboratory characterized Slc39a8-encoded ZIP8 as a Zn(2+)/(HCO(3)(-))(2) symporter; yet, the overall physiological importance of ZIP8 at the whole-organism level remains unclear. Herein we describe the phenotype of the hypomorphic Slc39a8(neo/neo) mouse which has retained the neomycin-resistance gene in intron 3, hence causing significantly decreased ZIP8 mRNA and protein levels in embryo, fetus, placenta, yolk sac, and several tissues of neonates. The Slc39a8(neo) allele is associated with diminished zinc and iron uptake in mouse fetal fibroblast and liver-derived cultures; consequently, Slc39a8(neo/neo) newborns exhibit diminished zinc and iron levels in several tissues. Slc39a8(neo/neo) homozygotes from gestational day(GD)-11.5 onward are pale, growth-stunted, and die between GD18.5 and 48 h postnatally. Defects include: severely hypoplastic spleen; hypoplasia of liver, kidney, lung, and lower limbs. Histologically, Slc39a8(neo/neo) neonates show decreased numbers of hematopoietic islands in yolk sac and liver. Low hemoglobin, hematocrit, red cell count, serum iron, and total iron-binding capacity confirmed severe anemia. Flow cytometry of fetal liver cells revealed the erythroid series strikingly affected in the hypomorph. Zinc-dependent 5-aminolevulinic acid dehydratase, required for heme synthesis, was not different between Slc39a8(+/+) and Slc39a8(neo/neo) offspring. To demonstrate further that the mouse phenotype is due to ZIP8 deficiency, we bred Slc39a8(+/neo) with BAC-transgenic BTZIP8-3 line (carrying three extra copies of the Slc39a8 allele); this cross generated viable Slc39a8(neo/neo)_BTZIP8-3(+/+) pups showing none of the above-mentioned congenital defects-proving Slc39a8(neo/neo) causes the described phenotype. Our study demonstrates that ZIP8-mediated zinc transport plays an unappreciated critical role during in utero and neonatal growth, organ morphogenesis, and hematopoiesis.

  17. Clinical coding. Code breakers.

    PubMed

    Mathieson, Steve

    2005-02-24

    --The advent of payment by results has seen the role of the clinical coder pushed to the fore in England. --Examinations for a clinical coding qualification began in 1999. In 2004, approximately 200 people took the qualification. --Trusts are attracting people to the role by offering training from scratch or through modern apprenticeships.

  18. Combinatorial synthesis of substituted 3-(2-indolyl)piperidines and 2-phenyl indoles as inhibitors of ZipA-FtsZ interaction.

    PubMed

    Jennings, Lee D; Foreman, Kenneth W; Rush, Thomas S; Tsao, Desiree H H; Mosyak, Lidia; Kincaid, Scott L; Sukhdeo, Mohani N; Sutherland, Alan G; Ding, Weidong; Kenny, Cynthia Hess; Sabus, Chantel L; Liu, Hanlan; Dushin, Elizabeth G; Moghazeh, Soraya L; Labthavikul, Pornpen; Petersen, Peter J; Tuckman, Margareta; Haney, Steven A; Ruzin, Alexey V

    2004-10-01

    The ZipA-FtsZ protein-protein interaction is a potential target for antibacterial therapy. The design and parallel synthesis of a combinatorial library of small molecules, which target the FtsZ binding area on ZipA are described. Compounds were demonstrated to bind to the FtsZ binding domain of ZipA by HSQC NMR and to inhibit cell division in a cell elongation assay.

  19. HTLV-1 bZIP Factor RNA and Protein Impart Distinct Functions on T-cell Proliferation and Survival.

    PubMed

    Mitobe, Yuichi; Yasunaga, Jun-ichirou; Furuta, Rie; Matsuoka, Masao

    2015-10-01

    Infection of T cells with human T-cell leukemia virus type-1 (HTLV-1) induces clonal proliferation and is closely associated with the onset of adult T-cell leukemia-lymphoma (ATL) and inflammatory diseases. Although Tax expression is frequently suppressed in HTLV-1-infected cells, the accessory gene, HTLV-1 bZIP factor (HBZ), is continuously expressed and has been implicated in HTLV-1 pathogenesis. Here, we report that transduction of mouse T cells with specific mutants of HBZ that distinguish between its RNA and protein activity results in differential effects on T-cell proliferation and survival. HBZ RNA increased cell number by attenuating apoptosis, whereas HBZ protein induced apoptosis. However, both HBZ RNA and protein promoted S-phase entry of T cells. We further identified that the first 50 bp of the HBZ coding sequence are required for RNA-mediated cell survival. Transcriptional profiling of T cells expressing wild-type HBZ, RNA, or protein revealed that HBZ RNA is associated with genes involved in cell cycle, proliferation, and survival, while HBZ protein is more closely related to immunological properties of T cells. Specifically, HBZ RNA enhances the promoter activity of survivin, an inhibitor of apoptosis, to upregulate its expression. Inhibition of survivin using YM155 resulted in impaired proliferation of several ATL cell lines as well as a T-cell line expressing HBZ RNA. The distinct functions of HBZ RNA and protein may have several implications for the development of strategies to control the proliferation and survival mechanisms associated with HTLV-1 infection and ATL.

  20. Overexpression of the transporters AtZIP1 and AtMTP1 in cassava changes zinc accumulation and partitioning

    PubMed Central

    Gaitán-Solís, Eliana; Taylor, Nigel J.; Siritunga, Dimuth; Stevens, William; Schachtman, Daniel P.

    2015-01-01

    Zinc deficiency in humans is a serious problem worldwide with an estimated one third of populations at risk for insufficient zinc in diet, which leads to impairment of cognitive abilities and immune system function. The goal of this research was to increase the bioavailable zinc in the edible portion of cassava roots to improve the overall zinc nutrition of populations that rely on cassava as a dietary staple. To increase zinc concentrations, two Arabidopsis thaliana genes coding for ZIP1 and MTP1 were overexpressed with a tuber-specific or constitutive promoter. Eighteen transgenic events from four constructs, out of a total of 73 events generated, showed significantly higher zinc concentrations in the edible portion of the storage root compared to the non-transgenic controls. The zinc content in the transgenic lines ranged from 4 to 73 mg/kg dry weight (DW) as compared to the non-transgenic control which contained 8 mg/kg. Striking changes in whole plant phenotype such as smaller plant size and chlorotic leaves were observed in transgenic lines that over accumulated zinc. In a confined field trial five transgenic events grown for 12 months showed a range of zinc concentrations from 18 to 217 mg/kg DW. Although the overexpression of zinc transporters was successful in increasing the zinc concentrations in 25% of the transgenic lines generated, it also resulted in a decrease in plant and tuber size and overall yield due to what appears to be zinc deficiency in the aerial parts of the plant. PMID:26217349

  1. Design and synthesis of indolo[2,3-a]quinolizin-7-one inhibitors of the ZipA-FtsZ interaction.

    PubMed

    Jennings, Lee D; Foreman, Ken W; Rush, Thomas S; Tsao, Desiree H H; Mosyak, Lidia; Li, Yuanhong; Sukhdeo, Mohani N; Ding, Weidong; Dushin, Elizabeth G; Kenny, Cynthia Hess; Moghazeh, Soraya L; Petersen, Peter J; Ruzin, Alexey V; Tuckman, Margareta; Sutherland, Alan G

    2004-03-22

    The binding of FtsZ to ZipA is a potential target for antibacterial therapy. Based on a small molecule inhibitor of the ZipA-FtsZ interaction, a parallel synthesis of small molecules was initiated which targeted a key region of ZipA involved in FtsZ binding. The X-ray crystal structure of one of these molecules complexed with ZipA was solved. The structure revealed an unexpected binding mode, facilitated by desolvation of a loosely bound surface water.

  2. LiZIP3 is a cellular zinc transporter that mediates the tightly regulated import of zinc in Leishmania infantum parasites

    PubMed Central

    Carvalho, Sandra; da Silva, Rosa Barreira; Shawki, Ali; Castro, Helena; Lamy, Márcia; Eide, David; Costa, Vítor; Mackenzie, Bryan; Tomás, Ana M.

    2016-01-01

    Summary Cellular zinc homeostasis ensures that the intracellular concentration of this element is kept within limits that enable its participation in critical physiological processes without exerting toxic effects. We report here the identification and characterization of the first mediator of zinc homeostasis in Leishmania infantum, LiZIP3, a member of the ZIP family of divalent metal-ion transporters. The zinc transporter activity of LiZIP3 was first disclosed by its capacity to rescue the growth of Saccharomyces cerevisiae strains deficient in zinc acquisition. Subsequent expression of LiZIP3 in Xenopus laevis oocytes was shown to stimulate the uptake of a broad range of metal ions, among which Zn2+ was the preferred LiZIP3 substrate (K0.5 ≈ 0.1 μM). Evidence that LiZIP3 functions as a zinc importer in L. infantum came from the observations that the protein locates to the cell membrane and that its overexpression leads to augmented zinc internalization. Importantly, expression and cell-surface location of LiZIP3 are lost when parasites face high zinc bioavailability. LiZIP3 decline in response to zinc is regulated at the mRNA level in a process involving (a) short-lived protein(s). Collectively, our data reveal that LiZIP3 enables L. infantum to acquire zinc in a highly regulated manner, hence contributing to zinc homeostasis. PMID:25644708

  3. Genome-wide analyses of the bZIP family reveal their involvement in the development, ripening and abiotic stress response in banana

    PubMed Central

    Hu, Wei; Wang, Lianzhe; Tie, Weiwei; Yan, Yan; Ding, Zehong; Liu, Juhua; Li, Meiying; Peng, Ming; Xu, Biyu; Jin, Zhiqiang

    2016-01-01

    The leucine zipper (bZIP) transcription factors play important roles in multiple biological processes. However, less information is available regarding the bZIP family in the important fruit crop banana. In this study, 121 bZIP transcription factor genes were identified in the banana genome. Phylogenetic analysis showed that MabZIPs were classified into 11 subfamilies. The majority of MabZIP genes in the same subfamily shared similar gene structures and conserved motifs. The comprehensive transcriptome analysis of two banana genotypes revealed the differential expression patterns of MabZIP genes in different organs, in various stages of fruit development and ripening, and in responses to abiotic stresses, including drought, cold, and salt. Interaction networks and co-expression assays showed that group A MabZIP-mediated networks participated in various stress signaling, which was strongly activated in Musa ABB Pisang Awak. This study provided new insights into the complicated transcriptional control of MabZIP genes and provided robust tissue-specific, development-dependent, and abiotic stress-responsive candidate MabZIP genes for potential applications in the genetic improvement of banana cultivars. PMID:27445085

  4. Prion protein functions as a ferrireductase partner for ZIP14 and DMT1

    PubMed Central

    Qian, Juan; Beserra, Amber; Suda, Srinivas; Singh, Ajay; Hopfer, Ulrich; Chen, Shu G.; Garrick, Michael D.; Turner, Jerrold R.; Knutson, Mitchell D.; Singh, Neena

    2015-01-01

    Excess circulating iron is stored in the liver, and requires reduction of non-Tf-bound-iron (NTBI) and transferrin (Tf)-iron at the plasma membrane and endosomes respectively by ferrireductase (FR) proteins for transport across biological membranes through divalent metal transporters. Here, we report that prion-protein (PrPC), a ubiquitously expressed glycoprotein most abundant on neuronal cells, functions as a FR partner for divalent-metal transporter-1 (DMT1) and ZIP14. Thus, absence of PrPC in PrP-knock-out (PrP−/−) mice resulted in markedly reduced liver iron stores, a deficiency that was not corrected by chronic or acute administration of iron by the oral or intra-peritoneal routes. Likewise, preferential radiolabeling of circulating NTBI with 59Fe revealed significantly reduced uptake and storage of NTBI by the liver of PrP−/− mice relative to matched PrP+/+ controls. However, uptake, storage, and utilization of ferritin-bound iron that does not require reduction for uptake was increased in PrP−/− mice, indicating a compensatory response to the iron-deficiency. Expression of exogenous PrPC in HepG2-cells increased uptake and storage of ferric-iron (Fe3+), not ferrous-iron (Fe2+) from the medium, supporting the function of PrPC as a plasma membrane FR. Co-expression of PrPC with ZIP14 and DMT1 in HepG2 cells increased uptake of Fe3+ significantly, and surprisingly, increased the ratio of N-terminally truncated PrPC forms lacking the FR domain relative to full-length PrPC. Together, these observations indicate that PrPC promotes, and possibly regulates the uptake of NTBI through DMT1 and Zip14 via its FR activity. Implications of these observations for neuronal iron homeostasis under physiological and pathological conditions are discussed. PMID:25862412

  5. Zinc Fortification Decreases ZIP1 Gene Expression of Some Adolescent Females with Appropriate Plasma Zinc Levels

    PubMed Central

    Méndez, Rosa O.; Santiago, Alejandra; Yepiz-Plascencia, Gloria; Peregrino-Uriarte, Alma B.; de la Barca, Ana M. Calderón; García, Hugo S.

    2014-01-01

    Zinc homeostasis is achieved after intake variation by changes in the expression levels of zinc transporters. The aim of this study was to evaluate dietary intake (by 24-h recall), absorption, plasma zinc (by absorption spectrophotometry) and the expression levels (by quantitative PCR), of the transporters ZIP1 (zinc importer) and ZnT1 (zinc exporter) in peripheral white blood cells from 24 adolescent girls before and after drinking zinc-fortified milk for 27 day. Zinc intake increased (p < 0.001) from 10.5 ± 3.9 mg/day to 17.6 ± 4.4 mg/day, and its estimated absorption from 3.1 ± 1.2 to 5.3 ± 1.3 mg/day. Mean plasma zinc concentration remained unchanged (p > 0.05) near 150 µg/dL, but increased by 31 µg/dL (p < 0.05) for 6/24 adolescents (group A) and decreased by 25 µg/dL (p < 0.05) for other 6/24 adolescents (group B). Expression of ZIP1 in blood leukocytes was reduced 1.4-fold (p < 0.006) in group A, while for the expression of ZnT1 there was no difference after intervention (p = 0.39). An increase of dietary zinc after 27-days consumption of fortified-milk did not increase (p > 0.05) the plasma level of adolescent girls but for 6/24 participants from group A in spite of the formerly appropriation, which cellular zinc uptake decreased as assessed by reduction of the expression of ZIP1. PMID:24922175

  6. [HTLV-1 bZIP Factor (HBZ): Roles in HTLV-1 Oncogenesis].

    PubMed

    Wu, Wencai; Cheng, Wenzhao; Chen, Mengyun; Xu, Lingling; Zhao, Tiejun

    2016-03-01

    Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus demonstrated to be associated with human disease. Infection by the HTLV-1 can cause T-cell leukemia (ATL) in adults. HTLV-1 bZIP factor (HBZ) is a viral protein encoded by the minus strand of the HTLV-1 provirus. Among the regulatory and accessory genes of HTLV-1, HBZ is the only gene that remains intact and which is expressed consistently in all patients with ATL. Moreover, HBZ has a critical role in the leukemogenesis of ATL. Here, we review the function of HBZ in the oncogenesis of HTLV-1 and its molecular mechanism of action.

  7. Zip it!

    PubMed

    Conde, Crystal

    2012-07-01

    When it comes to enforcing HIPAA data security and privacy standards, the federal government means business. In fact, the government is conducting a national pilot program to audit 150 physicians and others that HIPAA covers as the first phase of a concerted effort to crack down on HIPAA violations.

  8. Systematic Analysis of Sequences and Expression Patterns of Drought-Responsive Members of the HD-Zip Gene Family in Maize

    PubMed Central

    Zhao, Yang; Zhou, Yuqiong; Jiang, Haiyang; Li, Xiaoyu; Gan, Defang; Peng, Xiaojian; Zhu, Suwen; Cheng, Beijiu

    2011-01-01

    Background Members of the homeodomain-leucine zipper (HD-Zip) gene family encode transcription factors that are unique to plants and have diverse functions in plant growth and development such as various stress responses, organ formation and vascular development. Although systematic characterization of this family has been carried out in Arabidopsis and rice, little is known about HD-Zip genes in maize (Zea mays L.). Methods and Findings In this study, we described the identification and structural characterization of HD-Zip genes in the maize genome. A complete set of 55 HD-Zip genes (Zmhdz1-55) were identified in the maize genome using Blast search tools and categorized into four classes (HD-Zip I-IV) based on phylogeny. Chromosomal location of these genes revealed that they are distributed unevenly across all 10 chromosomes. Segmental duplication contributed largely to the expansion of the maize HD-ZIP gene family, while tandem duplication was only responsible for the amplification of the HD-Zip II genes. Furthermore, most of the maize HD-Zip I genes were found to contain an overabundance of stress-related cis-elements in their promoter sequences. The expression levels of the 17 HD-Zip I genes under drought stress were also investigated by quantitative real-time PCR (qRT-PCR). All of the 17 maize HD-ZIP I genes were found to be regulated by drought stress, and the duplicated genes within a sister pair exhibited the similar expression patterns, suggesting their conserved functions during the process of evolution. Conclusions Our results reveal a comprehensive overview of the maize HD-Zip gene family and provide the first step towards the selection of Zmhdz genes for cloning and functional research to uncover their roles in maize growth and development. PMID:22164299

  9. Intrinsic disorder of the bacterial cell division protein ZipA: coil-to-brush conformational transition.

    PubMed

    López-Montero, Iván; López-Navajas, Pilar; Mingorance, Jesús; Rivas, Germán; Vélez, Marisela; Vicente, Miguel; Monroy, Francisco

    2013-08-01

    The full-length ZipA protein from Escherichia coli, one of the essential elements of the cell division machinery, was studied in a surface model built as adsorbed monolayers. The interplay between lateral packing and molecular conformation was probed using a combined methodology based on the scaling analysis of the surface pressure isotherms and ellipsometry measurements of the monolayer thickness. The observed behavior is compatible with the one expected for an intrinsically disordered and highly flexible protein that is preferentially structured in a random coil conformation. At low grafting densities, ZipA coils organize in a mushroom-like regime, whereas a coil-to-brush transition occurs on increasing lateral packing. The structural results suggest a functional scenario in which ZipA acts as a flexible tether anchoring bacterial proto-ring elements to the membrane during the earlier stages of division.

  10. Expression analysis of bZIP transcription factor encoding genes in response to water deficit stress in rice.

    PubMed

    Ali, Kishwar; Rai, R D; Tyagi, Aruna

    2016-05-01

    In plants, basic region/leucine zipper motif (bZIP) transcription factors regulate several developmental processes and activate genes in response to biotic and abiotic stresses. Role of stress responsive bZIP transcription factors was studied in paddy in relation to different stages of development and water deficit stress (WDS) in a drought tolerant cultivar N22 and susceptible IR 64. Further, relative water content (RWC), membrane stability index (MSI) and abscisic acid (ABA) content were measured as indices of WDS at different stages of development and levels of stress. Expression of stress responsive bZIP transcription factors was directly correlated to developmental stage and WDS and indirectly to RWC, MSI and ABA content.

  11. How water layers on graphene affect folding and adsorption of TrpZip2

    NASA Astrophysics Data System (ADS)

    Peter, Emanuel K.; Agarwal, Mrigya; Kim, BongKeun; Pivkin, Igor V.; Shea, Joan-Emma

    2014-12-01

    We present a computational study of the folding of the Trp-rich β-hairpin TrpZip2 near graphene, a surface of interest as a platform for biosensors. The protein adsorbs to the surface, populating a new bound, folded state, coexisting with extended, adsorbed conformations. Adsorption and folding are modulated by direct interactions between the indole rings of TrpZip2 and the rings on the graphene surface, as well as by indirect water-mediated interactions. In particular, we observe strong layering of water near graphene, ice-like water configurations, and the formation of short lived hydrogen-bonds between water and protein. In order to study the effect of this layering in more detail, we modified the interactions between graphene and water to obtain two extreme cases: (1) enhanced layering of water that prevents the peptide from penetrating the water layer thereby enabling it to fold to a bulk-like structure, and (2) disruption of the water layer leading to adsorption and unfolding of the protein on the surface. These studies illuminate the roles of direct and solvent mediated interactions in modulating adsorption and folding of proteins on surfaces.

  12. Zeta inhibitory peptide (ZIP) erases long-term memories in a cockroach.

    PubMed

    Deng, Zhouheng; Lubinski, Alexander J; Page, Terry L

    2015-02-01

    Recent efforts to identify the molecules that are involved in the maintenance of long-term memories in mammals have focused attention on atypical isoforms of protein kinase C (PKC). Inhibition of these kinases by either the general PKC inhibitor, chelerythrine, or the more specific inhibitor, zeta inhibitory peptide (ZIP), can abolish both long-term potentiation in the hippocampus and as well as spatial, fear, appetitive, and sensorimotor memories. These inhibitors can also abolish long-term facilitation and long-term sensitization in the mollusk Aplysia californica. We have extended these results to an insect, the cockroach Leucophaea maderae. We show that systemic injections of either chelerythrine or ZIP erase long-term olfactory memories in the cockroach, but have no effect on memory acquisition during conditioning. We also show that inhibition of either protein kinase A (PKA) or protein synthesis can block memory acquisition but neither has an effect on the memory once it is formed. The results suggest that sustaining memories in insects requires the persistent activity of one or more isoforms of PKC and point to a strong evolutionary conservation of the molecular mechanisms that underlie the persistence of long-term memories in the central nervous system.

  13. How water layers on graphene affect folding and adsorption of TrpZip2.

    PubMed

    Peter, Emanuel K; Agarwal, Mrigya; Kim, BongKeun; Pivkin, Igor V; Shea, Joan-Emma

    2014-12-14

    We present a computational study of the folding of the Trp-rich β-hairpin TrpZip2 near graphene, a surface of interest as a platform for biosensors. The protein adsorbs to the surface, populating a new bound, folded state, coexisting with extended, adsorbed conformations. Adsorption and folding are modulated by direct interactions between the indole rings of TrpZip2 and the rings on the graphene surface, as well as by indirect water-mediated interactions. In particular, we observe strong layering of water near graphene, ice-like water configurations, and the formation of short lived hydrogen-bonds between water and protein. In order to study the effect of this layering in more detail, we modified the interactions between graphene and water to obtain two extreme cases: (1) enhanced layering of water that prevents the peptide from penetrating the water layer thereby enabling it to fold to a bulk-like structure, and (2) disruption of the water layer leading to adsorption and unfolding of the protein on the surface. These studies illuminate the roles of direct and solvent mediated interactions in modulating adsorption and folding of proteins on surfaces.

  14. The Functions of Metallothionein and ZIP and ZnT Transporters: An Overview and Perspective

    PubMed Central

    Kimura, Tomoki; Kambe, Taiho

    2016-01-01

    Around 3000 proteins are thought to bind zinc in vivo, which corresponds to ~10% of the human proteome. Zinc plays a pivotal role as a structural, catalytic, and signaling component that functions in numerous physiological processes. It is more widely used as a structural element in proteins than any other transition metal ion, is a catalytic component of many enzymes, and acts as a cellular signaling mediator. Thus, it is expected that zinc metabolism and homeostasis have sophisticated regulation, and elucidating the underlying molecular basis of this is essential to understanding zinc functions in cellular physiology and pathogenesis. In recent decades, an increasing amount of evidence has uncovered critical roles of a number of proteins in zinc metabolism and homeostasis through influxing, chelating, sequestrating, coordinating, releasing, and effluxing zinc. Metallothioneins (MT) and Zrt- and Irt-like proteins (ZIP) and Zn transporters (ZnT) are the proteins primarily involved in these processes, and their malfunction has been implicated in a number of inherited diseases such as acrodermatitis enteropathica. The present review updates our current understanding of the biological functions of MTs and ZIP and ZnT transporters from several new perspectives. PMID:26959009

  15. Zinc dyshomeostasis during polymicrobial sepsis in mice involves zinc transporter Zip14 and can be overcome by zinc supplementation

    PubMed Central

    Wessels, Inga

    2015-01-01

    Integrity of the immune system is particularly dependent on the availability of zinc. Recent data suggest that zinc is involved in the development of sepsis, a life-threatening systemic inflammation with high death rates, but with limited therapeutic options. Altered cell zinc transport mechanisms could contribute to the inflammatory effects of sepsis. Zip14, a zinc importer induced by proinflammatory stimuli, could influence zinc metabolism during sepsis and serve as a target for therapy. Using cecal ligation-and-puncture (CLP) to model polymicrobial sepsis, we narrowed the function of ZIP14 to regulation of zinc homeostasis in hepatocytes, while hepatic leukocytes were mostly responsible for driving inflammation, as shown by higher expression of IL-1β, TNFα, S100A8, and matrix metalloproteinase-8. Using Zip14 knockout (KO) mice as a novel approach, we found that ablation of Zip14 produced a delay in development of leukocytosis, prevented zinc accumulation in the liver, altered the kinetics of hypozincemia, and drastically increased serum IL-6, TNFα, and IL-10 concentrations following CLP. Hence, this model revealed that the zinc transporter ZIP14 is a component of the pathway for zinc redistribution that contributes to zinc dyshomeostasis during polymicrobial sepsis. In contrast, using the identical CLP model, we found that supplemental dietary zinc reduced the severity of sepsis, as shown by amelioration of cytokines, calprotectins, and blood bacterial loads. We conclude that the zinc transporter ZIP14 influences aspects of the pathophysiology of nonlethal polymicrobial murine sepsis induced by CLP through zinc delivery. The results are promising for the use of zinc and its transporters as targets for future sepsis therapy. PMID:26272258

  16. To direct the United States Postal Service to designate a single, unique ZIP Code for Flanders, New York.

    THOMAS, 111th Congress

    Rep. Bishop, Timothy H. [D-NY-1

    2010-03-02

    05/25/2010 Referred to the Subcommittee on Federal Workforce, Post Office, and the District of Columbia. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  17. It's Not Education by Zip Code Anymore--But What is It? Conceptions of Equity under the Common Core

    ERIC Educational Resources Information Center

    Kornhaber, Mindy L.; Griffith, Kelly; Tyler, Alison

    2014-01-01

    The Common Core State Standards Initiative is a standards-based reform in which 45 U.S. states and the District of Columbia have agreed to participate. The reform seeks to anchor primary and secondary education across these states in one set of demanding, internationally benchmarked standards. Thereby, all students will be prepared for further…

  18. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are well characterized in Arabidopsis (Arabidopsis thaliana), ...

  19. Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA.

    PubMed

    Mateos-Gil, Pablo; Tsortos, Achilleas; Vélez, Marisela; Gizeli, Electra

    2016-05-05

    The sensitivity of QCM-D to molecular hydrodynamic properties is applied in this work to study conformational changes of the intrinsically disordered protein ZipA. Acoustic measurements can clearly follow ZipA's unstructured domain expansion and contraction with salt content and be correlated with changes in the hydrodynamic radius of 1.8 nm or less.

  20. BhbZIP60 from Resurrection Plant Boea hygrometrica Is an mRNA Splicing-Activated Endoplasmic Reticulum Stress Regulator Involved in Drought Tolerance

    PubMed Central

    Wang, Bo; Du, Hong; Zhang, Zhennan; Xu, Wenzhong; Deng, Xin

    2017-01-01

    Adverse environmental conditions cause endoplasmic reticulum (ER) stress in plants. To mitigate ER stress damage, ER associated transcription factors and inositol-requiring enzyme-1 (IRE1)-mediated bZIP60 mRNA splicing are activated in plants. A drought-induced gene, encoding the ortholog of AtbZIP60, was identified in the resurrection plant Boea hygrometrica, termed BhbZIP60. In response to ER stress and dehydration, BhbZIP60 mRNA can be spliced to create a frame shift in the C terminus by the excision of 23b segment in a manner of its ortholog in other plants, thus translocating to the nucleus instead of the cytoplasm. The splicing-activated BhbZIP60 (BhbZIP60S) could function in the same way as its Arabidopsis ortholog by restoring the molecular phenotype of the mutant atbzip60. When overexpressed in Arabidopsis, BhbZIP60S provided transgenic plants with enhanced tolerance to drought, tunicamycin and mannitol stresses with upregulation of the expressions of ER quality control (QC) genes (BiP2, BiP3, CNX1, and sPDI) and abscisic acid (ABA) responsive genes (RD29A, RAB18, and RD17). Furthermore, in the yeast one-hybrid system, BhbZIP60S was capable of interacting with ER stress responsive elements (ERSE and ERSE-II) that exist in the promoters of known ER-QC genes, but not binding to ABA responsive cis-elements (ABREs). Our results demonstrated that drought-induced BhbZIP60 may have a function in drought tolerance via the splicing-activated BhbZIP60S to mediate ER-QC by direct binding to the promoters of ER-QC genes. This study evidently demonstrates the involvement of ER-QC in the drought tolerance of Arabidopsis and the desiccation tolerance of the resurrection plant B. hygrometrica. PMID:28286511

  1. Generation of a Slc39a8 hypomorph mouse: Markedly decreased ZIP8 Zn{sup 2+}/(HCO{sub 3}{sup -}){sub 2} transporter expression

    SciTech Connect

    Wang, Bin; He, Lei; Dong, Hongbin; Dalton, Timothy P.; Nebert, Daniel W.

    2011-07-01

    Highlights: {yields} The mouse Slc39a8 gene encodes the ZIP8 transporter. {yields} ZIP8 functions endogenously as a electroneutral Zn{sup 2+}/(HCO{sub 3}{sup -}){sub 2} symporter. {yields} A Slc39a8(neo/neo) hypomorph mouse, due to retention of the neo mini-gene, has been created. {yields} ZIP8 expression in utero is {approx}90% decreased in all tissues examined. {yields} This mouse model will be useful for studying developmental and in utero physiological functions of ZIP8. -- Abstract: Previously this laboratory has identified the mouse Slc39a8 gene encoding the ZIP8 transporter, important in cadmium uptake. ZIP8 functions endogenously as a electroneutral Zn{sup 2+}/(HCO{sub 3}{sup -}){sub 2} symporter, moving both ions into the cell. The overall physiological importance of ZIP8 remains unclear. Herein we describe generation of a mouse line carrying the Slc39a8(neo) allele, containing the Frt-flanked neomycin-resistance (neo) mini-cassette in intron 3 and loxP sites in introns 3 and 6. Cre recombinase functions correctly in Escherichia coli and in adeno-Cre-infected mouse fetal fibroblasts, but does not function in the intact mouse for reasons not clear. Slc39a8(neo) is a hypomorphic allele, because Slc39a8(neo/neo) homozygotes exhibit dramatically decreased ZIP8 expression in embryo, fetus, and visceral yolk sac - in comparison to their littermate wild-type controls. This ZIP8 hypomorph will be instrumental in studying developmental and in utero physiological functions of the ZIP8 transporter.

  2. Characterization of a putative grapevine Zn transporter, VvZIP3, suggests its involvement in early reproductive development in Vitis vinifera L

    PubMed Central

    2012-01-01

    Background Zinc (Zn) deficiency is one of the most widespread mineral nutritional problems that affect normal development in plants. Because Zn cannot passively diffuse across cell membranes, it must be transported into intracellular compartments for all biological processes where Zn is required. Several members of the Zinc-regulated transporters, Iron-regulated transporter-like Protein (ZIP) gene family have been characterized in plants, and have shown to be involved in metal uptake and transport. This study describes the first putative Zn transporter in grapevine. Unravelling its function may explain an important symptom of Zn deficiency in grapevines, which is the production of clusters with fewer and usually smaller berries than normal. Results We identified and characterized a putative Zn transporter from berries of Vitis vinifera L., named VvZIP3. Compared to other members of the ZIP family identified in the Vitis vinifera L. genome, VvZIP3 is mainly expressed in reproductive tissue - specifically in developing flowers - which correlates with the high Zn accumulation in these organs. Contrary to this, the low expression of VvZIP3 in parthenocarpic berries shows a relationship with the lower Zn accumulation in this tissue than in normal seeded berries where its expression is induced by Zn. The predicted protein sequence indicates strong similarity with several members of the ZIP family from Arabidopsis thaliana and other species. Moreover, VvZIP3 complemented the growth defect of a yeast Zn-uptake mutant, ZHY3, and is localized in the plasma membrane of plant cells, suggesting that VvZIP3 has the function of a Zn uptake transporter. Conclusions Our results suggest that VvZIP3 encodes a putative plasma membrane Zn transporter protein member of the ZIP gene family that might play a role in Zn uptake and distribution during the early reproductive development in Vitis vinifera L., indicating that the availability of this micronutrient may be relevant for

  3. A novel strategy to produce sweeter tomato fruits with high sugar contents by fruit-specific expression of a single bZIP transcription factor gene.

    PubMed

    Sagor, G H M; Berberich, Thomas; Tanaka, Shun; Nishiyama, Manabu; Kanayama, Yoshinori; Kojima, Seiji; Muramoto, Koji; Kusano, Tomonobu

    2016-04-01

    Enhancement of sugar content and sweetness is desirable in some vegetables and in almost all fruits; however, biotechnological methods to increase sugar content are limited. Here, a completely novel methodological approach is presented that produces sweeter tomato fruits but does not have any negative effects on plant growth. Sucrose-induced repression of translation (SIRT), which is mediated by upstream open reading frames (uORFs), was initially reported in Arabidopsis AtbZIP11, a class S basic region leucine zipper (bZIP) transcription factor gene. Here, two AtbZIP11 orthologous genes, SlbZIP1 and SlbZIP2, were identified in tomato (Solanum lycopersicum). SlbZIP1 and SlbZIP2 contained four and three uORFs, respectively, in the cDNA 5'-leader regions. The second uORFs from the 5' cDNA end were conserved and involved in SIRT. Tomato plants were transformed with binary vectors in which only the main open reading frames (ORFs) of SlbZIP1 and SlbZIP2, without the SIRT-responsive uORFs, were placed under the control of the fruit-specific E8 promoter. Growth and morphology of the resulting transgenic tomato plants were comparable to those of wild-type plants. Transgenic fruits were approximately 1.5-fold higher in sugar content (sucrose/glucose/fructose) than nontransgenic tomato fruits. In addition, the levels of several amino acids, such as asparagine and glutamine, were higher in transgenic fruits than in wild-type fruits. This was expected because SlbZIP transactivates the asparagine synthase and proline dehydrogenase genes. This 'sweetening' technology is broadly applicable to other plants that utilize sucrose as a major translocation sugar.

  4. BhbZIP60 from Resurrection Plant Boea hygrometrica Is an mRNA Splicing-Activated Endoplasmic Reticulum Stress Regulator Involved in Drought Tolerance.

    PubMed

    Wang, Bo; Du, Hong; Zhang, Zhennan; Xu, Wenzhong; Deng, Xin

    2017-01-01

    Adverse environmental conditions cause endoplasmic reticulum (ER) stress in plants. To mitigate ER stress damage, ER associated transcription factors and inositol-requiring enzyme-1 (IRE1)-mediated bZIP60 mRNA splicing are activated in plants. A drought-induced gene, encoding the ortholog of AtbZIP60, was identified in the resurrection plant Boea hygrometrica, termed BhbZIP60. In response to ER stress and dehydration, BhbZIP60 mRNA can be spliced to create a frame shift in the C terminus by the excision of 23b segment in a manner of its ortholog in other plants, thus translocating to the nucleus instead of the cytoplasm. The splicing-activated BhbZIP60 (BhbZIP60S) could function in the same way as its Arabidopsis ortholog by restoring the molecular phenotype of the mutant atbzip60. When overexpressed in Arabidopsis, BhbZIP60S provided transgenic plants with enhanced tolerance to drought, tunicamycin and mannitol stresses with upregulation of the expressions of ER quality control (QC) genes (BiP2, BiP3, CNX1, and sPDI) and abscisic acid (ABA) responsive genes (RD29A, RAB18, and RD17). Furthermore, in the yeast one-hybrid system, BhbZIP60S was capable of interacting with ER stress responsive elements (ERSE and ERSE-II) that exist in the promoters of known ER-QC genes, but not binding to ABA responsive cis-elements (ABREs). Our results demonstrated that drought-induced BhbZIP60 may have a function in drought tolerance via the splicing-activated BhbZIP60S to mediate ER-QC by direct binding to the promoters of ER-QC genes. This study evidently demonstrates the involvement of ER-QC in the drought tolerance of Arabidopsis and the desiccation tolerance of the resurrection plant B. hygrometrica.

  5. Zinc Modulates Endotoxin-Induced Human Macrophage Inflammation through ZIP8 Induction and C/EBPβ Inhibition

    PubMed Central

    Pyle, Charlie J.; Akhter, Saife; Bao, ShengYing; Dodd, Claire E.

    2017-01-01

    Two vital functions of the innate immune system are to initiate inflammation and redistribute micronutrients in favor of the host. Zinc is an essential micronutrient used in host defense. The zinc importer ZIP8 is uniquely induced through stimulation of the NF-κB pathway by LPS in monocytes and functions to regulate inflammation in a zinc-dependent manner. Herein we determined the impact of zinc metabolism following LPS-induced inflammation in human macrophages. We observed that ZIP8 is constitutively expressed in resting macrophages and strikingly elevated following LPS exposure, a response that is unique compared to the 13 other known zinc import proteins. During LPS exposure, extracellular zinc concentrations within the physiological range markedly reduced IL-10 mRNA expression and protein release but increased mRNA expression of TNFα, IL-8, and IL-6. ZIP8 knockdown inhibited LPS-driven cellular accumulation of zinc and prevented zinc-dependent reduction of IL-10 release. Further, zinc supplementation reduced nuclear localization and activity of C/EBPβ, a transcription factor known to drive IL-10 expression. These studies demonstrate for the first time that zinc regulates LPS-mediated immune activation of human macrophages in a ZIP8-dependent manner, reducing IL-10. Based on these findings we predict that macrophage zinc metabolism is important in host defense against pathogens. PMID:28056086

  6. An Aspergillus nidulans bZIP response pathway hardwired for defensive secondary metabolism operates through aflR

    PubMed Central

    Yin, Wenbing; Amaike, Saori; Wohlbach, Dana J.; Gasch, Audrey P.; Chiang, Yi-Ming; Wang, Clay C.; Bok, JinWoo; Rohlfs, Marko; Keller, Nancy P.

    2012-01-01

    Summary The eukaryotic bZIP transcription factors are critical players in organismal response to environmental challenges. In fungi, the production of secondary metabolites (SMs) is hypothesized as one of the responses to environmental insults, e.g. attack by fungivorous insects, yet little data to support this hypothesis exists. Here we establish a mechanism of bZIP regulation of SMs through RsmA, a recently discovered YAP-like bZIP protein. RsmA greatly increases SM production by binding to two sites in the A. nidulans AflR promoter region, a C6 transcription factor known for activating production of the carcinogenic and anti-predation SM, sterigmatocystin (ST). Deletion of aflR in an overexpression rsmA (OE::rsmA) background not only eliminates ST production but also significantly reduces asperthecin synthesis. Furthermore, the fungivore, Folsomia candida, exhibited a distinct preference for feeding on wild type rather than an OE::rsmA strain. RsmA may thus have a critical function in mediating direct chemical resistance against predation. Taken together, these results suggest RsmA represents a bZIP pathway hardwired for defensive SM production. PMID:22283524

  7. 76 FR 75939 - ZipGlobal Holdings, Inc., Symbollon Pharmaceuticals, Inc., Microholdings US, Inc., ComCam...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-05

    ... From the Federal Register Online via the Government Publishing Office SECURITIES AND EXCHANGE COMMISSION ZipGlobal Holdings, Inc., Symbollon Pharmaceuticals, Inc., Microholdings US, Inc., ComCam.... Microholdings US, Inc. is an Oklahoma corporation with its principal place of business in Washington....

  8. Ethical coding.

    PubMed

    Resnik, Barry I

    2009-01-01

    It is ethical, legal, and proper for a dermatologist to maximize income through proper coding of patient encounters and procedures. The overzealous physician can misinterpret reimbursement requirements or receive bad advice from other physicians and cross the line from aggressive coding to coding fraud. Several of the more common problem areas are discussed.

  9. Zipping, entanglement, and the elastic modulus of aligned single-walled carbon nanotube films

    PubMed Central

    Won, Yoonjin; Gao, Yuan; Panzer, Matthew A.; Xiang, Rong; Maruyama, Shigeo; Kenny, Thomas W.; Cai, Wei; Goodson, Kenneth E.

    2013-01-01

    Reliably routing heat to and from conversion materials is a daunting challenge for a variety of innovative energy technologies––from thermal solar to automotive waste heat recovery systems––whose efficiencies degrade due to massive thermomechanical stresses at interfaces. This problem may soon be addressed by adhesives based on vertically aligned carbon nanotubes, which promise the revolutionary combination of high through-plane thermal conductivity and vanishing in-plane mechanical stiffness. Here, we report the data for the in-plane modulus of aligned single-walled carbon nanotube films using a microfabricated resonator method. Molecular simulations and electron microscopy identify the nanoscale mechanisms responsible for this property. The zipping and unzipping of adjacent nanotubes and the degree of alignment and entanglement are shown to govern the spatially varying local modulus, thereby providing the route to engineered materials with outstanding combinations of mechanical and thermal properties. PMID:24309375

  10. Divergence and Conservation of the Major UPR Branch IRE1-bZIP Signaling Pathway across Eukaryotes

    PubMed Central

    Zhang, Lingrui; Zhang, Changwei; Wang, Aiming

    2016-01-01

    The unfolded protein response (UPR) is crucial to life by regulating the cellular response to the stress in the endoplasmic reticulum (ER) imposed by abiotic and biotic cues such as heat shock and viral infection. The inositol requiring enzyme 1 (IRE1) signaling pathway activated by the IRE1-mediated unconventional splicing of HAC1 in yeast, bZIP60 in plants and XBP1 in metazoans, is the most ancient branch of the UPR. In this study, we systematically examined yeast IRE1p-HAC1, plant IRE1A/IRE1B-bZIP60 and human hIRE1-XBP1 pairs. We found that, unlike bZIP60, XBP1 is unable to functionally swap HAC1p in yeast, and that the inter-species heterotypic interactions among HAC1p, bZIP60 and XBP1 are not permitted. These data demonstrate evolutionary divergence of the downstream signaling of IRE1-bZIP. We also discovered that the dual cytosolic domains of plant IRE1s act in vivo in a mechanism consistent with IRE1p and hIRE1, and that plant IRE1B not only interacts with IRE1p but also forms typical IRE1 dynamic foci in yeast. Thus, the upstream components of the IRE1 signaling branch including IRE1 activation and action mechanisms are highly conserved. Taken together these data advance the molecular understanding of evolutionary divergence and conservation of the IRE1 signaling pathway across kingdoms. PMID:27256815

  11. Molecular cloning and characterization of a tomato cDNA encoding a systemically wound-inducible bZIP DNA-binding protein

    NASA Technical Reports Server (NTRS)

    Stankovic, B.; Vian, A.; Henry-Vian, C.; Davies, E.

    2000-01-01

    Localized wounding of one leaf in intact tomato (Lycopersicon esculentum Mill.) plants triggers rapid systemic transcriptional responses that might be involved in defense. To better understand the mechanism(s) of intercellular signal transmission in wounded tomatoes, and to identify the array of genes systemically up-regulated by wounding, a subtractive cDNA library for wounded tomato leaves was constructed. A novel cDNA clone (designated LebZIP1) encoding a DNA-binding protein was isolated and identified. This clone appears to be encoded by a single gene, and belongs to the family of basic leucine zipper domain (bZIP) transcription factors shown to be up-regulated by cold and dark treatments. Analysis of the mRNA levels suggests that the transcript for LebZIP1 is both organ-specific and up-regulated by wounding. In wounded wild-type tomatoes, the LebZIP1 mRNA levels in distant tissue were maximally up-regulated within only 5 min following localized wounding. Exogenous abscisic acid (ABA) prevented the rapid wound-induced increase in LebZIP1 mRNA levels, while the basal levels of LebZIP1 transcripts were higher in the ABA mutants notabilis (not), sitiens (sit), and flacca (flc), and wound-induced increases were greater in the ABA-deficient mutants. Together, these results suggest that ABA acts to curtail the wound-induced synthesis of LebZIP1 mRNA.

  12. B-DNA to Zip-DNA: Simulating a DNA Transition to a Novel Structure with Enhanced Charge-Transport Characteristics

    PubMed Central

    Balaeff, Alexander; Craig, Stephen L.; Beratan, David N.

    2013-01-01

    The forced extension of a DNA segment is studied in a series of steered molecular dynamics simulations, employing a broad range of pulling forces. Throughout the entire force range, the formation of a zipper-like (zip-) DNA structure is observed. In that structure, first predicted by Lohikoski et al., the bases of the DNA strands interdigitate with each other and form a single-base aromatic stack. Similar motifs, albeit only a few base pairs in extent, have been observed in experimental crystal structures. Analysis of the dynamics of structural changes in pulled DNA shows that S-form DNA, thought to be adopted by DNA under applied force, serves as an intermediate between B-DNA and zip-DNA. Therefore, the phase transition plateau observed in force–extension curves of DNA is suggested to reflect the B-DNA to zip-DNA structural transition. Electronic structure analysis of purine bases in zip-DNA indicates a several-fold to order of magnitude increase in the π–π electronic coupling among nearest-neighbor nucleobases, compared to B-DNA. We further observe that zip-DNA does not require base pair complementarity between DNA strands, and we predict that the increased electronic coupling in zip-DNA will result in a much higher rate of charge transfer through an all-purine zip-DNA compared to B-DNA of equal length. PMID:21598926

  13. Cd{sup 2+} versus Zn{sup 2+} uptake by the ZIP8 HCO{sub 3}{sup -}-dependent symporter: Kinetics, electrogenicity and trafficking

    SciTech Connect

    Liu Zhiwei; Li Hong; Soleimani, Manoocher; Girijashanker, Kuppuswami; Reed, Jodie M.; He Lei; Dalton, Timothy P.; Nebert, Daniel W.

    2008-01-25

    The mouse Slc39a8 gene encodes the ZIP8 transporter, which has been shown to be a divalent cation/HCO{sub 3}{sup -} symporter. Using ZIP8 cRNA-injected Xenopus oocyte cultures, we show herein that: [a] ZIP8-mediated cadmium (Cd{sup 2+}) and zinc (Zn{sup 2+}) uptake have V{sub max} values of 1.8 {+-} 0.08 and 1.0 {+-} 0.08 pmol/oocyte/h, and K{sub m} values of 0.48 {+-} 0.08 and 0.26 {+-} 0.09 {mu}M, respectively; [b] ZIP8-mediated Cd{sup 2+} uptake is most inhibited by Zn{sup 2+}, second-best inhibited by Cu{sup 2+}, Pb{sup 2+} and Hg{sup 2+}, and not inhibited by Mn{sup 2+} or Fe{sup 2+}; and [c] electrogenicity studies demonstrate an influx of two HCO{sub 3}{sup -} anions per one Cd{sup 2+} (or one Zn{sup 2+}) cation, i.e. electroneutral complexes. Using Madin-Darby canine kidney (MDCK) polarized epithelial cells retrovirally infected with ZIP8 cDNA and tagged with hemagglutinin at the C-terminus, we show that-similar to ZIP4-the ZIP8 eight-transmembrane protein is largely internalized during Zn{sup 2+} homeostasis, but moves predominantly to the cell surface membrane (trafficking) under conditions of Zn{sup 2+} depletion.

  14. Arabidopsis bZIP16 Transcription Factor Integrates Light and Hormone Signaling Pathways to Regulate Early Seedling Development[C][W][OA

    PubMed Central

    Hsieh, Wen-Ping; Hsieh, Hsu-Liang; Wu, Shu-Hsing

    2012-01-01

    Transcriptomic adjustment plays an important role in Arabidopsis thaliana seed germination and deetiolation in response to environmental light signals. The G-box cis-element is commonly present in promoters of genes that respond positively or negatively to the light signal. In pursuing additional transcriptional regulators that modulate light-mediated transcriptome changes, we identified bZIP16, a basic region/Leu zipper motif transcription factor, by G-box DNA affinity chromatography. We confirmed that bZIP16 has G-box–specific binding activity. Analysis of bzip16 mutants revealed that bZIP16 is a negative regulator in light-mediated inhibition of cell elongation but a positive regulator in light-regulated seed germination. Transcriptome analysis supported that bZIP16 is primarily a transcriptional repressor regulating light-, gibberellic acid (GA)–, and abscisic acid (ABA)–responsive genes. Chromatin immunoprecipitation analysis revealed that bZIP16 could directly target ABA-responsive genes and RGA-LIKE2, a DELLA gene in the GA signaling pathway. bZIP16 could also indirectly repress the expression of PHYTOCHROME INTERACTING FACTOR3-LIKE5, which encodes a basic helix-loop-helix protein coordinating hormone responses during seed germination. By repressing the expression of these genes, bZIP16 functions to promote seed germination and hypocotyl elongation during the early stages of Arabidopsis seedling development. PMID:23104829

  15. Increased expression of six ZIP family genes by zinc (Zn) deficiency is associated with enhanced uptake and root-to-shoot translocation of Zn in barley (Hordeum vulgare).

    PubMed

    Tiong, Jingwen; McDonald, Glenn; Genc, Yusuf; Shirley, Neil; Langridge, Peter; Huang, Chun Y

    2015-09-01

    Low zinc (Zn) in soils reduces yield and grain Zn content. Regulation of ZRT/IRT-like protein (ZIP) family genes is a major mechanism in plant adaptation to low and fluctuating Zn in soil. Although several Zn deficiency-inducible ZIP genes are identified in cereals, there has been no systematic study on the association of Zn deficiency-induced uptake and root-to-shoot translocation with expression of ZIP family genes. We measured Zn deficiency-induced uptake and root-to-shoot translocation of Zn in barley (Hordeum vulgare) plants by resupplying 0.5 μM Zn, and quantified the transcripts of thirteen HvZIP genes. Subcellular localization and tissue-specific expression were also determined for Zn deficiency-inducible HvZIP genes. Zn deficiency enhanced the capacity of uptake and root-to-shoot translocation of Zn, and sustained the enhanced capacity for 6 d after Zn resupply. Six HvZIP genes were highly induced in roots of Zn-deficient plants, and their proteins were localized in the plasma membrane. Tissue-specific expression in roots supports their roles in uptake and root-to-shoot translocation of Zn under low Zn conditions. Our results provide a comprehensive view on the physiological roles of ZIP genes in plant adaptation to low and fluctuating Zn in soil, and pave the way for development of new strategies to improve Zn-deficiency tolerance and biofortification in cereals.

  16. The bacterial cell-division protein ZipA and its interaction with an FtsZ fragment revealed by X-ray crystallography

    PubMed Central

    Mosyak, Lidia; Zhang, Yan; Glasfeld, Elizabeth; Haney, Steve; Stahl, Mark; Seehra, Jasbir; Somers, William S.

    2000-01-01

    In Escherichia coli, FtsZ, a homologue of eukaryotic tubulins, and ZipA, a membrane-anchored protein that binds to FtsZ, are two essential components of the septal ring structure that mediates cell division. Recent data indicate that ZipA is involved in the assembly of the ring by linking FtsZ to the cytoplasmic membrane and that the ZipA–FtsZ interaction is mediated by their C-terminal domains. We present the X-ray crystal structures of the C-terminal FtsZ-binding domain of ZipA and a complex between this domain and a C-terminal fragment of FtsZ. The ZipA domain is a six-stranded β-sheet packed against three α-helices and contains the split β–α–β motif found in many RNA-binding proteins. The uncovered side of the sheet incorporates a shallow hydrophobic cavity exposed to solvent. In the complex, the 17-residue FtsZ fragment occupies this entire cavity of ZipA and binds as an extended β-strand followed by α-helix. An alanine-scanning mutagenesis analysis of the FtsZ fragment was also performed, which shows that only a small cluster of the buried FtsZ side chains is critical in binding to ZipA. PMID:10880432

  17. Comparative study of dermal components and plasma TGF-β1 levels in Slc39a13/Zip13-KO mice

    PubMed Central

    HIROSE, Takuya; OGURA, Takayuki; TANAKA, Keisuke; MINAGUCHI, Jun; YAMAUCHI, Takeshi; FUKADA, Toshiyuki; KOYAMA, Yoh-ichi; TAKEHANA, Kazushige

    2015-01-01

    Ehlers-Danlos syndrome (EDS) is a group of disorders caused by abnormalities that are identified in the extracellular matrix. Transforming growth factor-β1 (TGF-β1) plays a crucial role in formation of the extracellular matrix. It has been reported that the loss of function of zinc transporter ZRT/IRT-like protein 13 (ZIP13) causes the spondylocheiro dysplastic form of EDS (SCD-EDS: OMIM 612350), in which dysregulation of the TGF-β1 signaling pathway is observed, although the relationship between the dermis abnormalities and peripheral TGF-β1 level has been unclear. We investigated the characteristics of the dermis of the Zip13-knockout (KO) mouse, an animal model for SCD-EDS. Both the ratio of dermatan sulfate (DS) in glycosaminoglycan (GAG) components and the amount of collagen were decreased, and there were very few collagen fibrils with diameters of more than 150 nm in Zip13-KO mice dermis. We also found that the TGF-β1 level was significantly higher in Zip13-KO mice serum. These results suggest that collagen synthesis and collagen fibril fusion might be impaired in Zip13-KO mice and that the possible decrease of decorin level by reduction of the DS ratio probably caused an increase of free TGF-β1 in Zip13-KO mice. In conclusion, skin fragility due to defective ZIP13 protein may be attributable to impaired extracellular matrix synthesis accompanied by abnormal peripheral TGF-β homeostasis. PMID:26050750

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

    PubMed Central

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

    2016-01-01

    Basic leucine zippers (bZIPs) form a large plant transcription factor family. C and S1 bZIP groups can heterodimerize, fulfilling crucial roles in seed development and stress response. S1 sequences also harbor a unique regulatory mechanism, termed Sucrose-Induced Repression of Translation (SIRT). The conservation of both C/S1 bZIP interactions and SIRT remains poorly characterized in non-model species, leaving their evolutionary origin uncertain and limiting crop research. In this work, we explored recently published plant sequencing data to establish a detailed phylogeny of C and S1 bZIPs, investigating their intertwined role in plant evolution, and the origin of SIRT. Our analyses clarified C and S1 bZIP orthology relationships in angiosperms, and identified S1 sequences in gymnosperms. We experimentally showed that the gymnosperm orthologs are regulated by SIRT, tracing back the origin of this unique regulatory mechanism to the ancestor of seed plants. Additionally, we discovered an earlier S ortholog in the charophyte algae Klebsormidium flaccidum, together with a C ortholog. This suggests that C and S groups originated by duplication from a single algal proto-C/S ancestor. Based on our observations, we propose a model wherein the C/S1 bZIP dimer network evolved in seed plants from pre-existing C/S bZIP interactions. PMID:27457880

  19. Genome-wide identification, classification and analysis of HD-ZIP gene family in citrus, and its potential roles in somatic embryogenesis regulation.

    PubMed

    Ge, Xiao-Xia; Liu, Zheng; Wu, Xiao-Meng; Chai, Li-Jun; Guo, Wen-Wu

    2015-12-10

    The homeodomain-leucine zipper (HD-Zip) transcription factors, which belong to a class of Homeobox proteins, has been reported to be involved in different biological processes of plants, including growth and development, photomorphogenesis, flowering, fruit ripening and adaptation responses to environmental stresses. In this study, 27 HD-Zip genes (CsHBs) were identified in Citrus. Based on the phylogenetic analysis and characteristics of individual gene or protein, the HD-Zip gene family in Citrus can be classified into 4 subfamilies, i.e. HD-Zip I, HD-Zip II, HD-Zip III, and HD-Zip IV containing 16, 2, 4, and 5 members respectively. The digital expression patterns of 27 HD-Zip genes were analyzed in the callus, flower, leaf and fruit of Citrus sinensis. The qRT-PCR and RT-PCR analyses of six selected HD-Zip genes were performed in six citrus cultivars with different embryogenic competence and in the embryo induction stages, which revealed that these genes were differentially expressed and might be involved in citrus somatic embryogenesis (SE). The results exhibited that the expression of CsHB1 was up-regulated in somatic embryo induction process, and its expression was higher in citrus cultivars with high embryogenic capacity than in cultivars recalcitrant to form somatic embryos. Moreover, a microsatellite site of three nucleotide repeats was found in CsHB1 gene among eighteen citrus genotypes, indicating the possible association of CsHB1 gene to the capacity of callus induction.

  20. Properties of Zip4 accumulation during zinc deficiency and its usefulness to evaluate zinc status: a study of the effects of zinc deficiency during lactation.

    PubMed

    Hashimoto, Ayako; Nakagawa, Miki; Tsujimura, Natsuki; Miyazaki, Shiho; Kizu, Kumiko; Goto, Tomoko; Komatsu, Yusuke; Matsunaga, Ayu; Shirakawa, Hitoshi; Narita, Hiroshi; Kambe, Taiho; Komai, Michio

    2016-03-01

    Systemic and cellular zinc homeostasis is elaborately controlled by ZIP and ZnT zinc transporters. Therefore, detailed characterization of their expression properties is of importance. Of these transporter proteins, Zip4 functions as the primarily important transporter to control systemic zinc homeostasis because of its indispensable function of zinc absorption in the small intestine. In this study, we closely investigated Zip4 protein accumulation in the rat small intestine in response to zinc status using an anti-Zip4 monoclonal antibody that we generated and contrasted this with the zinc-responsive activity of the membrane-bound alkaline phosphatase (ALP). We found that Zip4 accumulation is more rapid in response to zinc deficiency than previously thought. Accumulation increased in the jejunum as early as 1 day following a zinc-deficient diet. In the small intestine, Zip4 protein expression was higher in the jejunum than in the duodenum and was accompanied by reduction of ALP activity, suggesting that the jejunum can become zinc deficient more easily. Furthermore, by monitoring Zip4 accumulation levels and ALP activity in the duodenum and jejunum, we reasserted that zinc deficiency during lactation may transiently alter plasma glucose levels in the offspring in a sex-specific manner, without affecting homeostatic control of zinc metabolism. This confirms that zinc nutrition during lactation is extremely important for the health of the offspring. These results reveal that rapid Zip4 accumulation provides a significant conceptual advance in understanding the molecular basis of systemic zinc homeostatic control, and that properties of Zip4 protein accumulation are useful to evaluate zinc status closely.

  1. Genomic duplication and translocation of reactivation transactivator and bZIP-homolog genes is a conserved event in alcelaphine herpesvirus 1

    PubMed Central

    Myster, Françoise; van Beurden, Steven J.; Sorel, Océane; Suárez, Nicolás M.; Vanderplasschen, Alain; Davison, Andrew J.; Dewals, Benjamin G.

    2016-01-01

    Alcelaphine herpesvirus 1 (AlHV-1) is a gammaherpesvirus carried asymptomatically by wildebeest. Upon cross-species transmission, AlHV-1 induces malignant catarrhal fever (MCF), a fatal lymphoproliferative disease of ruminants, including cattle. The strain C500 has been cloned as an infectious, pathogenic bacterial artificial chromosome (BAC) that is used to study MCF. Although AlHV-1 infection can be established in cell culture, multiple passages in vitro cause a loss of virulence associated with rearrangements of the viral genome. Here, sequencing of the BAC clone showed that the long unique region (LUR) of the genome is nearly identical to that of the previously sequenced strain from which the BAC was derived, and identified the duplication and translocation of a region from within LUR, containing the entire coding sequences of ORF50-encoding reactivation transactivator Rta and A6-encoding bZIP protein genes. The duplicated region was further located to a position within the terminal repeat (TR) and its deletion resulted in lower ORF50 expression levels and reduced viral fitness. Finally, the presence of a similar but not identical duplication and translocation containing both genes was found in AlHV-1 strain WC11. These results indicate that selection pressure for enhanced viral fitness may drive the duplication of ORF50 and A6 in AlHV-1. PMID:27924936

  2. Sharing code.

    PubMed

    Kubilius, Jonas

    2014-01-01

    Sharing code is becoming increasingly important in the wake of Open Science. In this review I describe and compare two popular code-sharing utilities, GitHub and Open Science Framework (OSF). GitHub is a mature, industry-standard tool but lacks focus towards researchers. In comparison, OSF offers a one-stop solution for researchers but a lot of functionality is still under development. I conclude by listing alternative lesser-known tools for code and materials sharing.

  3. IRE1/bZIP60-Mediated Unfolded Protein Response Plays Distinct Roles in Plant Immunity and Abiotic Stress Responses

    PubMed Central

    Blanco, Francisca; Boatwright, Jon Lucas; Moreno, Ignacio; Jordan, Melissa R.; Chen, Yani; Brandizzi, Federica; Dong, Xinnian

    2012-01-01

    Endoplasmic reticulum (ER)-mediated protein secretion and quality control have been shown to play an important role in immune responses in both animals and plants. In mammals, the ER membrane-located IRE1 kinase/endoribonuclease, a key regulator of unfolded protein response (UPR), is required for plasma cell development to accommodate massive secretion of immunoglobulins. Plant cells can secrete the so-called pathogenesis-related (PR) proteins with antimicrobial activities upon pathogen challenge. However, whether IRE1 plays any role in plant immunity is not known. Arabidopsis thaliana has two copies of IRE1, IRE1a and IRE1b. Here, we show that both IRE1a and IRE1b are transcriptionally induced during chemically-induced ER stress, bacterial pathogen infection and treatment with the immune signal salicylic acid (SA). However, we found that IRE1a plays a predominant role in the secretion of PR proteins upon SA treatment. Consequently, the ire1a mutant plants show enhanced susceptibility to a bacterial pathogen and are deficient in establishing systemic acquired resistance (SAR), whereas ire1b is unaffected in these responses. We further demonstrate that the immune deficiency in ire1a is due to a defect in SA- and pathogen-triggered, IRE1-mediated cytoplasmic splicing of the bZIP60 mRNA, which encodes a transcription factor involved in the expression of UPR-responsive genes. Consistently, IRE1a is preferentially required for bZIP60 splicing upon pathogen infection, while IRE1b plays a major role in bZIP60 processing upon Tunicamycin (Tm)-induced stress. We also show that SA-dependent induction of UPR-responsive genes is altered in the bzip60 mutant resulting in a moderate susceptibility to a bacterial pathogen. These results indicate that the IRE1/bZIP60 branch of UPR is a part of the plant response to pathogens for which the two Arabidopsis IRE1 isoforms play only partially overlapping roles and that IRE1 has both bZIP60-dependent and bZIP60-independent functions in

  4. Genome-Wide Analysis of the bZIP Gene Family Identifies Two ABI5-Like bZIP Transcription Factors, BrABI5a and BrABI5b, as Positive Modulators of ABA Signalling in Chinese Cabbage

    PubMed Central

    Hu, Xiaochen; Sun, Congcong; Li, Yanlin; Wang, Dandan; Wang, Qinhu; Pei, Guoliang; Zhang, Yanfeng; Guo, Aiguang; Zhao, Huixian; Lu, Haibin; Mu, Xiaoqian; Hu, Jingjiang; Zhou, Xiaona; Xie, Chang Gen

    2016-01-01

    bZIP (basic leucine zipper) transcription factors coordinate plant growth and development and control responses to environmental stimuli. The genome of Chinese cabbage (Brassica rapa) encodes 136 putative bZIP transcription factors. The bZIP transcription factors in Brassica rapa (BrbZIP) are classified into 10 subfamilies. Phylogenetic relationship analysis reveals that subfamily A consists of 23 BrbZIPs. Two BrbZIPs within subfamily A, Bra005287 and Bra017251, display high similarity to ABI5 (ABA Insensitive 5). Expression of subfamily A BrbZIPs, like BrABI5a (Bra005287/BrbZIP14) and BrABI5b (Bra017251/BrbZIP13), are significantly induced by the plant hormone ABA. Subcellular localization assay reveal that both BrABI5a and BrABI5b have a nuclear localization. BrABI5a and BrABI5b could directly stimulate ABA Responsive Element-driven HIS (a HIS3 reporter gene, which confers His prototrophy) or LUC (LUCIFERASE) expression in yeast and Arabidopsis protoplast. Deletion of the bZIP motif abolished BrABI5a and BrABI5b transcriptional activity. The ABA insensitive phenotype of Arabidopsis abi5-1 is completely suppressed in transgenic lines expressing BrABI5a or BrABI5b. Overall, these results suggest that ABI5 orthologs, BrABI5a and BrABI5b, have key roles in ABA signalling in Chinese cabbage. PMID:27414644

  5. Biophysical properties of regions flanking the bHLH-Zip motif in the p22 Max protein.

    PubMed

    Pursglove, Sharon E; Fladvad, Malin; Bellanda, Massimo; Moshref, Ahmad; Henriksson, Marie; Carey, Jannette; Sunnerhagen, Maria

    2004-10-22

    The Max protein is the central dimerization partner in the Myc-Max-Mad network of transcriptional regulators, and a founding structural member of the family of basic-helix-loop-helix (bHLH)-leucine zipper (Zip) proteins. Biologically important regions flanking its bHLH-Zip motif have been disordered or absent in crystal structures. The present study shows that these regions are resistant to proteolysis in both the presence and absence of DNA, and that Max dimers containing both flanking regions have significantly higher helix content as measured by circular dichroism than that predicted from the crystal structures. Nuclear magnetic resonance measurements in the absence of DNA also support the inferred structural order. Deletion of both flanking regions is required to achieve maximal DNA affinity as measured by EMSA. Thus, the previously observed functionalities of these Max regions in DNA binding, phosphorylation, and apoptosis are suggested to be linked to structural properties.

  6. DNA binding of Jun and Fos bZip domains: homodimers and heterodimers induce a DNA conformational change in solution.

    PubMed Central

    John, M; Leppik, R; Busch, S J; Granger-Schnarr, M; Schnarr, M

    1996-01-01

    We constructed plasmids encoding the sequences for the bZip modules of c-Jun and c-Fos which could then be expressed as soluble proteins in Escherichia coli. The purified bZip modules were tested for their binding capacities of synthetic oligonucleotides containing either TRE or CRE recognition sites in electrophoretic mobility shift assays and circular dichroism (CD). Electrophoretic mobility shift assays showed that bZip Jun homodimers and bZip Jun/Fos heterodimers bind a collagenase-like TRE (CTGACTCAT) with dissociation constants of respectively 1.4 x 10(-7) M and 5 x 10(-8) M. As reported earlier [Patel et al. (1990) Nature 347, 572-575], DNA binding induces a marked change of the protein structure. However, we found that the DNA also undergoes a conformational change. This is most clearly seen with small oligonucleotides of 13 or 14 bp harboring respectively a TRE (TGACTCA) or a CRE (TGACGTCA) sequence. In this case, the positive DNA CD signal at 280 nm increases almost two-fold with a concomitant blue-shift of 3-4 nm. Within experimental error the same spectral changes are observed for TRE and CRE containing DNA fragments. The spectral changes observed with a non-specific DNA fragment are weaker and the signal of free DNA is recovered upon addition of much smaller salt concentrations than required for a specific DNA fragment. Surprisingly the spectral changes induced by Jun/Jun homodimers are not identical to those induced by Jun/Fos heterodimers. However, in both cases the increase of the positive CD band and the concomitant blue shift would be compatible with a B to A-transition of part of the binding site or a DNA conformation intermediate between the canonical A and B structures. PMID:8948639

  7. ZIP7-mediated intracellular zinc transport contributes to aberrant growth factor signaling in antihormone-resistant breast cancer Cells.

    PubMed

    Taylor, Kathryn M; Vichova, Petra; Jordan, Nicola; Hiscox, Stephen; Hendley, Rhiannon; Nicholson, Robert I

    2008-10-01

    Antiestrogens such as tamoxifen are the mainstay of treatment for estrogen receptor-positive breast cancer. However, their effectiveness is limited by the development of endocrine resistance, allowing tumor regrowth and progression. Importantly, in vitro MCF7 cell models of acquired tamoxifen resistance (TamR cells) display an aggressive, invasive phenotype in which activation of epithelial growth factor receptor/IGF-I receptor/Src signaling plays a critical role. In this study, we report that TamR cells have increased levels of zinc and zinc transporter, ZIP7 [solute carrier family 39 (zinc transporter) member 7, also known as SLC39A7], resulting in an enhanced response to exogenous zinc, which is manifested as a greatly increased growth factor receptor activation, leading to increased growth and invasion. Removal of ZIP7, using small interfering RNA, destroys this activation of epithelial growth factor receptor/IGF-I receptor/Src signaling by reducing intracellular zinc levels. Similarly, it also blocks the activation of HER2, -3, and -4. These data suggest that intracellular zinc levels may be a critical factor in determining growth factor responses and that the targeting of zinc transporters may have novel therapeutic implications. We show that ZIP7 is a critical component in the redistribution of zinc from intracellular stores to the cytoplasm and, as such, is essential for the zinc-induced inhibition of phosphatases, which leads to activation of growth factor receptors. Removal of ZIP7 therefore offers a means through which zinc-induced activation of growth factor receptors may be effectively suppressed and provides a mechanism of targeting multiple growth factor pathways, increasing tumor kill, and preventing further development of resistance in breast cancer.

  8. bZIP Transcription Factors in the Oomycete Phytophthora infestans with Novel DNA-Binding Domains Are Involved in Defense against Oxidative Stress

    PubMed Central

    Gamboa-Meléndez, Heber; Huerta, Apolonio I.

    2013-01-01

    Transcription factors of the basic leucine zipper (bZIP) family control development and stress responses in eukaryotes. To date, only one bZIP has been described in any oomycete; oomycetes are members of the stramenopile kingdom. In this study, we describe the identification of 38 bZIPs from the Phytophthora infestans genome. Half contain novel substitutions in the DNA-binding domain at a site that in other eukaryotes is reported to always be Asn. Interspecific comparisons indicated that the novel substitutions (usually Cys, but also Val and Tyr) arose after oomycetes diverged from other stramenopiles. About two-thirds of P. infestans bZIPs show dynamic changes in mRNA levels during the life cycle, with many of the genes being upregulated in sporangia, zoospores, or germinated zoospore cysts. One bZIP with the novel Cys substitution was shown to reside in the nucleus throughout growth and development. Using stable gene silencing, the functions of eight bZIPs with the Cys substitution were tested. All but one were found to play roles in protecting P. infestans from hydrogen peroxide-induced injury, and it is proposed that the novel Cys substitution serves as a redox sensor. A ninth bZIP lacking the novel Asn-to-Cys substitution, but having Cys nearby, was also shown through silencing to contribute to defense against peroxide. Little effect on asexual development, plant pathogenesis, or resistance to osmotic stress was observed in transformants silenced for any of the nine bZIPs. PMID:23975888

  9. bZIP transcription factors in the oomycete phytophthora infestans with novel DNA-binding domains are involved in defense against oxidative stress.

    PubMed

    Gamboa-Meléndez, Heber; Huerta, Apolonio I; Judelson, Howard S

    2013-10-01

    Transcription factors of the basic leucine zipper (bZIP) family control development and stress responses in eukaryotes. To date, only one bZIP has been described in any oomycete; oomycetes are members of the stramenopile kingdom. In this study, we describe the identification of 38 bZIPs from the Phytophthora infestans genome. Half contain novel substitutions in the DNA-binding domain at a site that in other eukaryotes is reported to always be Asn. Interspecific comparisons indicated that the novel substitutions (usually Cys, but also Val and Tyr) arose after oomycetes diverged from other stramenopiles. About two-thirds of P. infestans bZIPs show dynamic changes in mRNA levels during the life cycle, with many of the genes being upregulated in sporangia, zoospores, or germinated zoospore cysts. One bZIP with the novel Cys substitution was shown to reside in the nucleus throughout growth and development. Using stable gene silencing, the functions of eight bZIPs with the Cys substitution were tested. All but one were found to play roles in protecting P. infestans from hydrogen peroxide-induced injury, and it is proposed that the novel Cys substitution serves as a redox sensor. A ninth bZIP lacking the novel Asn-to-Cys substitution, but having Cys nearby, was also shown through silencing to contribute to defense against peroxide. Little effect on asexual development, plant pathogenesis, or resistance to osmotic stress was observed in transformants silenced for any of the nine bZIPs.

  10. Genome-wide characterization and expression profiling of HD-Zip gene family related to abiotic stress in cassava

    PubMed Central

    Yan, Yan; Tie, Weiwei; Xia, Zhiqiang; Wang, Wenquan; Peng, Ming; Hu, Wei; Zhang, Jiaming

    2017-01-01

    Homeodomain-leucine zipper (HD-Zip) gene family plays important roles in various abiotic stresses and hormone signaling in plants. However, no information is currently available regarding this family in cassava (Manihot esculenta), an important drought-tolerant crop in tropical and sub-tropical areas. Here, 57 HD-Zip genes (MeHDZ01-57) were identified in the cassava genome, and they were classified into four subfamilies based on phylogenetic analysis, which was further supported by their gene structure and conserved motif characteristics. Of which five gene pairs were involved in segmental duplication but none for tandem duplication, suggesting that segmental duplication was the main cause for the expansion of MeHDZ gene family in cassava. Global expression profiles revealed that MeHDZ genes were constitutively expressed, or not expressed, or tissue-specific expressed in examined tissues in both cultivated and wild subspecies. Transcriptomic analysis of three genotypes showed that most of MeHDZ genes responded differently to drought and polyethylene glycol treatments. Subsequently, quantitative RT-PCR analysis revealed comprehensive responses of twelve selected MeHDZ genes to various stimuli including cold, salt, and ABA treatments. These findings will increase our understanding of HD-Zip gene family involved in abiotic stresses and signaling transduction, and will provide a solid base for further functional characterization of MeHDZ genes in cassava. PMID:28249019

  11. The Populus Class III HD ZIP transcription factor POPCORONA affects cell differentiation during secondary growth of woody stems.

    PubMed

    Du, Juan; Miura, Eriko; Robischon, Marcel; Martinez, Ciera; Groover, Andrew

    2011-02-28

    The developmental mechanisms regulating cell differentiation and patterning during the secondary growth of woody tissues are poorly understood. Class III HD ZIP transcription factors are evolutionarily ancient and play fundamental roles in various aspects of plant development. Here we investigate the role of a Class III HD ZIP transcription factor, POPCORONA, during secondary growth of woody stems. Transgenic Populus (poplar) trees expressing either a miRNA-resistant POPCORONA or a synthetic miRNA targeting POPCORONA were used to infer function of POPCORONA during secondary growth. Whole plant, histological, and gene expression changes were compared for transgenic and wild-type control plants. Synthetic miRNA knock down of POPCORONA results in abnormal lignification in cells of the pith, while overexpression of a miRNA-resistant POPCORONA results in delayed lignification of xylem and phloem fibers during secondary growth. POPCORONA misexpression also results in coordinated changes in expression of genes within a previously described transcriptional network regulating cell differentiation and cell wall biosynthesis, and hormone-related genes associated with fiber differentiation. POPCORONA illustrates another function of Class III HD ZIPs: regulating cell differentiation during secondary growth.

  12. SnRK1-triggered switch of bZIP63 dimerization mediates the low-energy response in plants

    PubMed Central

    Mair, Andrea; Pedrotti, Lorenzo; Wurzinger, Bernhard; Anrather, Dorothea; Simeunovic, Andrea; Weiste, Christoph; Valerio, Concetta; Dietrich, Katrin; Kirchler, Tobias; Nägele, Thomas; Vicente Carbajosa, Jesús; Hanson, Johannes; Baena-González, Elena; Chaban, Christina; Weckwerth, Wolfram; Dröge-Laser, Wolfgang; Teige, Markus

    2015-01-01

    Metabolic adjustment to changing environmental conditions, particularly balancing of growth and defense responses, is crucial for all organisms to survive. The evolutionary conserved AMPK/Snf1/SnRK1 kinases are well-known metabolic master regulators in the low-energy response in animals, yeast and plants. They act at two different levels: by modulating the activity of key metabolic enzymes, and by massive transcriptional reprogramming. While the first part is well established, the latter function is only partially understood in animals and not at all in plants. Here we identified the Arabidopsis transcription factor bZIP63 as key regulator of the starvation response and direct target of the SnRK1 kinase. Phosphorylation of bZIP63 by SnRK1 changed its dimerization preference, thereby affecting target gene expression and ultimately primary metabolism. A bzip63 knock-out mutant exhibited starvation-related phenotypes, which could be functionally complemented by wild type bZIP63, but not by a version harboring point mutations in the identified SnRK1 target sites. DOI: http://dx.doi.org/10.7554/eLife.05828.001 PMID:26263501

  13. Deregulation of subcellular biometal homeostasis through loss of the metal transporter, Zip7, in a childhood neurodegenerative disorder

    PubMed Central

    2014-01-01

    Background Aberrant biometal metabolism is a key feature of neurodegenerative disorders including Alzheimer’s and Parkinson’s diseases. Metal modulating compounds are promising therapeutics for neurodegeneration, but their mechanism of action remains poorly understood. Neuronal ceroid lipofuscinoses (NCLs), caused by mutations in CLN genes, are fatal childhood neurodegenerative lysosomal storage diseases without a cure. We previously showed biometal accumulation in ovine and murine models of the CLN6 variant NCL, but the mechanism is unknown. This study extended the concept that alteration of biometal functions is involved in pathology in these disorders, and investigated molecular mechanisms underlying impaired biometal trafficking in CLN6 disease. Results We observed significant region-specific biometal accumulation and deregulation of metal trafficking pathways prior to disease onset in CLN6 affected sheep. Substantial progressive loss of the ER/Golgi-resident Zn transporter, Zip7, which colocalized with the disease-associated protein, CLN6, may contribute to the subcellular deregulation of biometal homeostasis in NCLs. Importantly, the metal-complex, ZnII(atsm), induced Zip7 upregulation, promoted Zn redistribution and restored Zn-dependent functions in primary mouse Cln6 deficient neurons and astrocytes. Conclusions This study demonstrates the central role of the metal transporter, Zip7, in the aberrant biometal metabolism of CLN6 variants of NCL and further highlights the key contribution of deregulated biometal trafficking to the pathology of neurodegenerative diseases. Importantly, our results suggest that ZnII(atsm) may be a candidate for therapeutic trials for NCLs. PMID:24581221

  14. Variation Analysis of Physiological Traits in Betula platyphylla Overexpressing TaLEA-ThbZIP Gene under Salt Stress

    PubMed Central

    Xiao, Zhenhai; Wang, Fuwei; Li, Shuchun; Zang, Lina; Zheng, Mi; Li, Ying; Qu, Guan-Zheng

    2016-01-01

    The aim of this study was to determine whether transgenic birch (Betula platyphylla) ectopic overexpressing a late embryogenesis abundant (LEA) gene and a basic leucine zipper (bZIP) gene from the salt-tolerant genus Tamarix (salt cedar) show increased tolerance to salt (NaCl) stress. Co-transfer of TaLEA and ThbZIP in birch under the control of two independent CaMV 35S promoters significantly enhanced salt stress. PCR and northern blot analyses indicated that the two genes were ectopically overexpressed in several dual-gene transgenic birch lines. We compared the effects of salt stress among three transgenic birch lines (L-4, L-5, and L-8) and wild type (WT). In all lines, the net photosynthesis values were higher before salt stress treatment than afterwards. After the salt stress treatment, the transgenic lines L-4 and L-8 showed higher values for photosynthetic traits, chlorophyll fluorescence, peroxidase and superoxide dismutase activities, and lower malondialdehyde and Na+ contents, compared with those in WT and L-5. These different responses to salt stress suggested that the transcriptional level of the TaLEA and ThbZIP genes differed among the transgenic lines, resulting in a variety of genetic and phenotypic effects. The results of this research can provide a theoretical basis for the genetic engineering of salt-tolerant trees. PMID:27802286

  15. HTLV-1 bZIP factor enhances TGF-β signaling through p300 coactivator.

    PubMed

    Zhao, Tiejun; Satou, Yorifumi; Sugata, Kenji; Miyazato, Paola; Green, Patrick L; Imamura, Takeshi; Matsuoka, Masao

    2011-08-18

    Human T-cell leukemia virus type 1 (HTLV-1) is an oncogenic retrovirus that is etiologically associated with adult T-cell leukemia. The HTLV-1 bZIP factor (HBZ), which is encoded by the minus strand of the provirus, is involved in both regulation of viral gene transcription and T-cell proliferation. We showed in this report that HBZ interacted with Smad2/3, and enhanced transforming growth factor-β (TGF-β)/Smad transcriptional responses in a p300-dependent manner. The N-terminal LXXLL motif of HBZ was responsible for HBZ-mediated TGF-β signaling activation. In a serial immunoprecipitation assay, HBZ, Smad3, and p300 formed a ternary complex, and the association between Smad3 and p300 was markedly enhanced in the presence of HBZ. In addition, HBZ could overcome the repression of the TGF-β response by Tax. Finally, HBZ expression resulted in enhanced transcription of Pdgfb, Sox4, Ctgf, Foxp3, Runx1, and Tsc22d1 genes and suppression of the Id2 gene; such effects were similar to those by TGF-β. In particular, HBZ induced Foxp3 expression in naive T cells through Smad3-dependent TGF-β signaling. Our results suggest that HBZ, by enhancing TGF-β signaling and Foxp3 expression, enables HTLV-1 to convert infected T cells into regulatory T cells, which is thought to be a critical strategy for virus persistence.

  16. SNARE Complex Zipping as a Driving Force in the Dilation of Proteinaceous Fusion Pores

    PubMed Central

    Jackson, Meyer B.

    2010-01-01

    The assembly of SNARE proteins into a tight complex has been hypothesized to drive membrane fusion. A model of the initial fusion pore as a proteinaceous channel formed by SNARE proteins places their membrane anchors in separate membranes. This leaves the possibility of a final assembly step that brings the membrane anchors together and drives fusion pore expansion. The present study develops a model for expansion in which the final SNARE complex zipping step drives a transition from a proteinaceous fusion pore to a lipidic fusion pore. An estimate of the energy released upon merger of the helical segment of the SNARE motif with the helical membrane anchor indicates that completing the assembly of a few SNARE complexes can overcome the elastic energy that opposes lipid bilayer deformation into a narrow fusion pore. The angle between the long axes of membrane anchor and SNARE motif serves as a useful reaction coordinate for this transition. Energy was calculated as a function of this angle, incorporating contributions from membrane bending, SNARE complex assembly, membrane anchor flexing, and hydrophobic interactions. The rate of this transition was evaluated as a process of diffusion over the barrier imposed by these combined energies, and the rates estimated were consistent with experimental measurements. PMID:20512644

  17. Out of field of view rejection measurements of the ZIP telescope No. 2

    NASA Astrophysics Data System (ADS)

    Wong, W. K.; Wang, D.; Murdock, T. L.

    1983-01-01

    Recent re-measurement of the Out-of Field-of View-Rejection (OFVR) characteristics of the ZIP telescope No. 2 indicated that the Point Source Power Transmittance (PSPT) was increased by as much as a factor of 400 at one off-axis source orientation in comparison with the OFVR measurement of the identical telescope three years ago. The OFVR degradation was caused by particulate contamination of the telescope optical surfaces. After cleaning of the primary mirror, the OFVR performance was restored for off-axis angles of 2 degrees to 7 degrees, but the OFVR was still degraded by a factor of 2 to 20 for off-axis angles between 8 degrees to 15 degrees. This remaining degradation was also restored after cleaning of the secondary mirror. Since the original OFVR measurement, the telescope package was opened about 10 times in a Class 100 clean room environment for integration and testing and was exposed to Class 100 environment 3 to 4 days at a time. Subsequently, the telescope was sealed and stored in an evacuated vessel at room temperature for two years.

  18. The rice bZIP transcriptional activator RITA-1 is highly expressed during seed development.

    PubMed Central

    Izawa, T; Foster, R; Nakajima, M; Shimamoto, K; Chua, N H

    1994-01-01

    Systematic protein-DNA binding studies have shown that plant basic leucine zipper (bZIP) proteins exhibit a differential binding specificity for ACGT motifs. Here, we show that the rice transcription activator-1 (RITA-1) displays a broad binding specificity for palindromic ACGT elements, being able to bind A-, C-, and G-box but not T-box elements. By using gel mobility shift assays with probes differing in sequences flanking the hexameric core, we identified high-affinity A-, C-, and G-box binding sites. Quantitative and competition DNA binding studies confirmed RITA-1 specificity for these sites. Using rice protoplasts as a transient expression system, we demonstrated that RITA-1 can transactivate reporter genes possessing high-affinity but not low-affinity RITA-1 binding sites. Our results established a direct relationship between in vivo transactivation and in vitro binding activity. Transient expression assays that demonstrated the ability of RITA-1 to transactivate a construct containing rita-1 5' flanking sequences suggest that the factor may be autoregulated. Histochemical analysis of transgenic rice plants showed that a rita-1-beta-glucuronidase transgene is expressed in aleurone and endosperm cells of developing rice seeds. We propose that RITA-1 plays a role in the regulation of rice genes expressed in developing rice seeds. PMID:7919992

  19. Challenging the paradigms of leaf evolution: Class III HD-Zips in ferns and lycophytes.

    PubMed

    Vasco, Alejandra; Smalls, Tynisha L; Graham, Sean W; Cooper, Endymion D; Wong, Gane Ka-Shu; Stevenson, Dennis W; Moran, Robbin C; Ambrose, Barbara A

    2016-11-01

    Despite the extraordinary significance leaves have for life on Earth, their origin and development remain vigorously debated. More than a century of paleobotanical, morphological, and phylogenetic research has still not resolved fundamental questions about leaves. Developmental genetic data are sparse in ferns, and comparative studies of lycophytes and seed plants have reached opposing conclusions on the conservation of a leaf developmental program. We performed phylogenetic and expression analyses of a leaf developmental regulator (Class III HD-Zip genes; C3HDZs) spanning lycophytes and ferns. We show that a duplication and neofunctionalization of C3HDZs probably occurred in the ancestor of euphyllophytes, and that there is a common leaf developmental mechanism conserved between ferns and seed plants. We show C3HDZ expression in lycophyte and fern sporangia and show that C3HDZs have conserved expression patterns during initiation of lateral primordia (leaves or sporangia). This expression is maintained throughout sporangium development in lycophytes and ferns and indicates an ancestral role of C3HDZs in sporangium development. We hypothesize that there is a deep homology of all leaves and that a sporangium-specific developmental program was coopted independently for the development of lycophyte and euphyllophyte leaves. This provides molecular genetic support for a paradigm shift in theories of lycophyte leaf evolution.

  20. Role of Homeodomain leucine zipper (HD-Zip) IV transcription factors in plant development and plant protection from deleterious environmental factors.

    PubMed

    Chew, William; Hrmova, Maria; Lopato, Sergiy

    2013-04-12

    Homeobox genes comprise an important group of genes that are responsible for regulation of developmental processes. These genes determine cell differentiation and cell fate in all eukaryotic organisms, starting from the early stages of embryo development. Homeodomain leucine zipper (HD-Zip) transcription factors are unique to the plant kingdom. Members of the HD-Zip IV subfamily have a complex domain topology and can bind several cis-elements with overlapping sequences. Many of the reported HD-Zip IV genes were shown to be specifically or preferentially expressed in plant epidermal or sub-epidermal cells. HD-Zip IV TFs were found to be associated with differentiation and maintenance of outer cell layers, and regulation of lipid biosynthesis and transport. Insights about the role of these proteins in plant cuticle formation, and hence their possible involvement in plant protection from pathogens and abiotic stresses has just started to emerge. These roles make HD-Zip IV proteins an attractive tool for genetic engineering of crop plants. To this end, there is a need for in-depth studies to further clarify the function of each HD-Zip IV subfamily member in commercially important plant species.

  1. Sharing code

    PubMed Central

    Kubilius, Jonas

    2014-01-01

    Sharing code is becoming increasingly important in the wake of Open Science. In this review I describe and compare two popular code-sharing utilities, GitHub and Open Science Framework (OSF). GitHub is a mature, industry-standard tool but lacks focus towards researchers. In comparison, OSF offers a one-stop solution for researchers but a lot of functionality is still under development. I conclude by listing alternative lesser-known tools for code and materials sharing. PMID:25165519

  2. Speech coding

    SciTech Connect

    Ravishankar, C., Hughes Network Systems, Germantown, MD

    1998-05-08

    Speech is the predominant means of communication between human beings and since the invention of the telephone by Alexander Graham Bell in 1876, speech services have remained to be the core service in almost all telecommunication systems. Original analog methods of telephony had the disadvantage of speech signal getting corrupted by noise, cross-talk and distortion Long haul transmissions which use repeaters to compensate for the loss in signal strength on transmission links also increase the associated noise and distortion. On the other hand digital transmission is relatively immune to noise, cross-talk and distortion primarily because of the capability to faithfully regenerate digital signal at each repeater purely based on a binary decision. Hence end-to-end performance of the digital link essentially becomes independent of the length and operating frequency bands of the link Hence from a transmission point of view digital transmission has been the preferred approach due to its higher immunity to noise. The need to carry digital speech became extremely important from a service provision point of view as well. Modem requirements have introduced the need for robust, flexible and secure services that can carry a multitude of signal types (such as voice, data and video) without a fundamental change in infrastructure. Such a requirement could not have been easily met without the advent of digital transmission systems, thereby requiring speech to be coded digitally. The term Speech Coding is often referred to techniques that represent or code speech signals either directly as a waveform or as a set of parameters by analyzing the speech signal. In either case, the codes are transmitted to the distant end where speech is reconstructed or synthesized using the received set of codes. A more generic term that is applicable to these techniques that is often interchangeably used with speech coding is the term voice coding. This term is more generic in the sense that the

  3. Involvement of DNA hypermethylation in down-regulation of the zinc transporter ZIP8 in cadmium-resistant metallothionein-null cells

    SciTech Connect

    Fujishiro, Hitomi; Okugaki, Satomi; Yasumitsu, Saori; Enomoto, Shuichi; Himeno, Seiichiro

    2009-12-01

    The Zrt/Irt-related protein 8 (ZIP8) encoded by slc39a8 is now emerging as an important zinc transporter involved in cellular cadmium incorporation. We have previously shown that mRNA and protein levels of ZIP8 were decreased in cadmium-resistant metallothionein-null (A7) cells, leading to a decrease in cadmium accumulation. However, the mechanism by which ZIP8 expression is suppressed in these cells remains to be elucidated. In the present study, we investigated the possibility that epigenetic silencing of the slc39a8 gene by DNA hypermethylation is involved in the down-regulation of ZIP8 expression. A7 cells showed a higher mRNA level of DNA methyltransferase 3b than parental cells. Hypermethylation of the CpG island of the slc39a8 gene was detected in A7 cells. Treatment of A7 cells with 5-aza-deoxycytidine, an inhibitor of DNA methyltransferase, caused demethylation of the CpG island of the slc39a8 gene and enhancement of mRNA and protein levels of ZIP8. In response to the recovery of ZIP8 expression, A7 cells treated with 5-aza-deoxycytidine showed an increase in cadmium accumulation and consequently an increase in sensitivity to cadmium. These results suggest that epigenetic silencing of the slc39a8 gene by DNA hypermethylation plays an important role in the down-regulation of ZIP8 in cadmium-resistant metallothionein-null cells.

  4. Expression Patterns and Correlations with Metabolic Markers of Zinc Transporters ZIP14 and ZNT1 in Obesity and Polycystic Ovary Syndrome.

    PubMed

    Maxel, Trine; Svendsen, Pernille Fog; Smidt, Kamille; Lauridsen, Jesper Krogh; Brock, Birgitte; Pedersen, Steen Bønlykke; Rungby, Jørgen; Larsen, Agnete

    2017-01-01

    Polycystic ovary syndrome (PCOS) is associated with infertility, increased androgen levels, and insulin resistance. In adipose tissue, zinc facilitates insulin signaling. Circulating zinc levels are altered in obesity, diabetes, and PCOS; and zinc supplementation can ameliorate metabolic disturbances in PCOS. In adipose tissue, expression of zinc influx transporter ZIP14 varies with body mass index (BMI), clinical markers of metabolic syndrome, and peroxisome proliferator-activated receptor gamma (PPARG). In this study, we investigated expression levels of ZIP14 and PPARG in subcutaneous adipose tissue of 36 PCOS women (17 lean and 19 obese women) compared with 23 healthy controls (7 lean and 16 obese women). Further, expression levels of zinc transporter ZIP9, a recently identified androgen receptor, and zinc efflux transporter ZNT1 were investigated, alongside lipid profile and markers of glucose metabolism [insulin degrading enzyme, retinol-binding protein 4 (RBP4), and glucose transporter 4 (GLUT4)]. We find that ZIP14 expression is reduced in obesity and positively correlates with PPARG expression, which is downregulated with increasing BMI. ZNT1 is upregulated in obesity, and both ZIP14 and ZNT1 expression significantly correlates with clinical markers of altered glucose metabolism. In addition, RBP4 and GLUT4 associate with obesity, but an association with PCOS as such was present only for PPARG and RBP4. ZIP14 and ZNT1 does not relate to clinical androgen status and ZIP9 is unaffected by all parameters investigated. In conclusion, our findings support the existence of a zinc dyshomeostasis in adipose tissue in metabolic disturbances including PCOS-related obesity.

  5. Expression Patterns and Correlations with Metabolic Markers of Zinc Transporters ZIP14 and ZNT1 in Obesity and Polycystic Ovary Syndrome

    PubMed Central

    Maxel, Trine; Svendsen, Pernille Fog; Smidt, Kamille; Lauridsen, Jesper Krogh; Brock, Birgitte; Pedersen, Steen Bønlykke; Rungby, Jørgen; Larsen, Agnete

    2017-01-01

    Polycystic ovary syndrome (PCOS) is associated with infertility, increased androgen levels, and insulin resistance. In adipose tissue, zinc facilitates insulin signaling. Circulating zinc levels are altered in obesity, diabetes, and PCOS; and zinc supplementation can ameliorate metabolic disturbances in PCOS. In adipose tissue, expression of zinc influx transporter ZIP14 varies with body mass index (BMI), clinical markers of metabolic syndrome, and peroxisome proliferator-activated receptor gamma (PPARG). In this study, we investigated expression levels of ZIP14 and PPARG in subcutaneous adipose tissue of 36 PCOS women (17 lean and 19 obese women) compared with 23 healthy controls (7 lean and 16 obese women). Further, expression levels of zinc transporter ZIP9, a recently identified androgen receptor, and zinc efflux transporter ZNT1 were investigated, alongside lipid profile and markers of glucose metabolism [insulin degrading enzyme, retinol-binding protein 4 (RBP4), and glucose transporter 4 (GLUT4)]. We find that ZIP14 expression is reduced in obesity and positively correlates with PPARG expression, which is downregulated with increasing BMI. ZNT1 is upregulated in obesity, and both ZIP14 and ZNT1 expression significantly correlates with clinical markers of altered glucose metabolism. In addition, RBP4 and GLUT4 associate with obesity, but an association with PCOS as such was present only for PPARG and RBP4. ZIP14 and ZNT1 does not relate to clinical androgen status and ZIP9 is unaffected by all parameters investigated. In conclusion, our findings support the existence of a zinc dyshomeostasis in adipose tissue in metabolic disturbances including PCOS-related obesity. PMID:28303117

  6. QR Codes

    ERIC Educational Resources Information Center

    Lai, Hsin-Chih; Chang, Chun-Yen; Li, Wen-Shiane; Fan, Yu-Lin; Wu, Ying-Tien

    2013-01-01

    This study presents an m-learning method that incorporates Integrated Quick Response (QR) codes. This learning method not only achieves the objectives of outdoor education, but it also increases applications of Cognitive Theory of Multimedia Learning (CTML) (Mayer, 2001) in m-learning for practical use in a diverse range of outdoor locations. When…

  7. Major zircon megacryst suites of the Indo-Pacific lithospheric margin (ZIP) and their petrogenetic and regional implications

    NASA Astrophysics Data System (ADS)

    Sutherland, Lin; Graham, Ian; Yaxley, Gregory; Armstrong, Richard; Giuliani, Gaston; Hoskin, Paul; Nechaev, Victor; Woodhead, Jon

    2016-04-01

    Zircon megacrysts (± gem corundum) appear in basalt fields of Indo-Pacific origin over a 12,000 km zone (ZIP) along West Pacific continental margins. Age-dating, trace element, oxygen and hafnium isotope studies on representative zircons (East Australia-Asia) indicate diverse magmatic sources. The U-Pb (249 to 1 Ma) and zircon fission track (ZFT) ages (65 to 1 Ma) suggest thermal annealing during later basalt transport, with < 1 to 203 Ma gaps between the U-Pb and ZFT ages. Magmatic growth zonation and Zr/Hf ratios (0.01-0.02) suggest alkaline magmatic sources, while Ti—in—zircon thermometry suggests that most zircons crystallized within ranges between 550 and 830 °C. Chondrite-normalised multi-element plots show variable enrichment patterns, mostly without marked Eu depletion, indicating little plagioclase fractionation in source melts. Key elements and ratios matched against zircons from magmatic rocks suggest a range of ultramafic to felsic source melts. Zircon O-isotope ratios (δ18O in the range 4 to 11‰) and initial Hf isotope ratios (ɛHf in the range +2 to +14) encompass ranges for both mantle and crustal melts. Calculated Depleted Mantle (TDM 0.03-0.56 Ga) and Crustal Residence (0.20-1.02 Ga) model ages suggest several mantle events, continental break-ups (Rodinia and Gondwana) and convergent margin collisions left imprints in the zircon source melts. East Australian ZIP sites reflect prolonged intraplate magmatism (~85 Ma), often during times of fast-migrating lithosphere. In contrast, East Asian-Russian ZIP sites reflect later basaltic magmatism (<40 Ma), often linked to episodes of back-arc rifting and spreading, slow-migrating lithosphere and slab subduction.

  8. Non-classical testosterone signaling mediated through ZIP9 stimulates claudin expression and tight junction formation in Sertoli cells.

    PubMed

    Bulldan, Ahmed; Dietze, Raimund; Shihan, Mazen; Scheiner-Bobis, Georgios

    2016-08-01

    In the classical signaling pathway, testosterone regulates gene expression by activating the cytosolic/nuclear androgen receptor. In the non-classical pathway, testosterone activates cytosolic signaling cascades that are normally triggered by growth factors. The nature of the receptor involved in this signaling pathway is a source of controversy. In the Sertoli cell line 93RS2, which lacks the classical AR, we determined that testosterone stimulates the non-classical signaling pathway, characterized by the phosphorylation of Erk1/2 and transcription factors CREB and ATF-1. We also demonstrated that testosterone increases the expression of the tight junction (TJ) proteins claudin-1 and claudin-5. Both of these proteins are known to be essential constituents of TJs between Sertoli cells, and as a consequence of their increased expression transepithelial resistance across Sertoli cell monolayers is increased. ZIP9 is a Zn(2+)transporter that was recently shown to be a membrane-bound testosterone receptor. Silencing its expression in 93RS2 Sertoli cells by siRNA completely prevents Erk1/2, CREB, and ATF-1 phosphorylation as well the stimulation of claudin-1 and -5 expression and TJ formation between neighboring cells. The study presented here demonstrates for the first time that in Sertoli cells testosterone acts through the receptor ZIP9 to trigger the non-classical signaling cascade, resulting in increased claudin expression and TJ formation. Since TJ formation is a prerequisite for the maintenance of the blood-testis barrier, the testosterone/ZIP9 effects might be significant for male physiology. Further assessment of these interactions will help to supplement our knowledge concerning the mechanism by which testosterone plays a role in male fertility.

  9. Biophysical and Mutational Analysis of the Putative bZIP Domain of Epstein-Barr Virus EBNA 3C

    PubMed Central

    West, Michelle J.; Webb, Helen M.; Sinclair, Alison J.; Woolfson, Derek N.

    2004-01-01

    Epstein-Barr virus nuclear antigen 3C (EBNA 3C) is essential for B-cell immortalization and functions as a regulator of viral and cellular transcription. EBNA 3C contains glutamine-rich and proline-rich domains and a region in the N terminus consisting of a stretch of basic residues followed by a run of leucine residues spaced seven amino acids apart. This N-terminal domain is widely believed to represent a leucine zipper dimerization motif (bZIP). We have performed the first structural and functional analysis of this motif and demonstrated that this domain is not capable of forming stable homodimers. Peptides encompassing the EBNA 3C zipper domain are approximately 54 to 67% α-helical in solution but cannot form dimers at physiologically relevant concentrations. Moreover, the EBNA 3C leucine zipper cannot functionally substitute for another homodimerizing zipper domain in domain-swapping experiments. Our data indicate, however, that the EBNA 3C zipper domain behaves as an atypical bZIP domain and is capable of self-associating to form higher-order α-helical oligomers. Using directed mutagenesis, we also identified a new role for the bZIP domain in maintaining the interaction between EBNA 3C and RBP-Jκ in vivo. Disruption of the helical nature of the zipper domain by the introduction of proline residues reduces the ability of EBNA 3C to inhibit EBNA 2 activation and interact with RBP-Jκ in vivo by 50%, and perturbation of the charge on the basic region completely abolishes this function of EBNA 3C. PMID:15308737

  10. The interaction of the Arabidopsis response regulator ARR18 with bZIP63 mediates the regulation of PROLINE DEHYDROGENASE expression.

    PubMed

    Veerabagu, Manikandan; Kirchler, Tobias; Elgass, Kirstin; Stadelhofer, Bettina; Stahl, Mark; Harter, Klaus; Mira-Rodado, Virtudes; Chaban, Christina

    2014-10-01

    As the first and rate-limiting enzyme of proline degradation, PROLINE DEHYDROGENASE1 (PDH1) is tightly regulated during plant stress responses, including induction under hypoosmolarity and repression under water deficit. The plant receptor histidine kinases AHKs, elements of the two-component system (TCS) in Arabidopsis thaliana, are proposed to function in water stress responses by regulating different stress-responsive genes. However, little information is available concerning AHK phosphorelay-mediated downstream signaling. Here we show that the Arabidopsis type-B response regulator 18 (ARR18) functions as a positive osmotic stress response regulator in Arabidopsis seeds and affects the activity of the PDH1 promoter, known to be controlled by C-group bZIP transcription factors. Moreover, direct physical interaction of ARR18 with bZIP63 was identified and shown to be dependent on phosphorylation of the conserved aspartate residue in the ARR18 receiver domain. We further show that bZIP63 itself functions as a negative regulator of seed germination upon osmotic stress. Using reporter gene assays in protoplasts, we demonstrated that ARR18 interaction negatively interferes with the transcriptional activity of bZIP63 on the PDH1 promoter. Our findings provide new insight into the function of ARR18 and bZIP63 as antagonistic regulators of gene expression in Arabidopsis.

  11. A genome-wide survey of homeodomain-leucine zipper genes and analysis of cold-responsive HD-Zip I members' expression in tomato.

    PubMed

    Zhang, Zhenzhu; Chen, Xiuling; Guan, Xin; Liu, Yang; Chen, Hongyu; Wang, Tingting; Mouekouba, Liana Dalcantara Ongouya; Li, Jingfu; Wang, Aoxue

    2014-01-01

    Homeodomain-leucine zipper (HD-Zip) proteins are a kind of transcriptional factors that play a vital role in plant growth and development. However, no detailed information of HD-Zip family in tomato has been reported till now. In this study, 51 HD-Zip genes (SlHZ01-51) in this family were identified and categorized into 4 classes by exon-intron and protein structure in tomato (Solanum lycopersicum) genome. The synthetical phylogenetic tree of tomato, Arabidopsis and rice HD-Zip genes were established for an insight into their evolutionary relationships and putative functions. The results showed that the contribution of segmental duplication was larger than that of tandem duplication for expansion and evolution of genes in this family of tomato. The expression profile results under abiotic stress suggested that all SlHZ I genes were responsive to cold stress. This study will provide a clue for the further investigation of functional identification and the role of tomato HD-Zip I subfamily in plant cold stress responses and developmental events.

  12. Chemical Emergency

    MedlinePlus

    ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store Toggle Navigation Menu ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store ...

  13. Water Safety Quiz

    MedlinePlus

    ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store Toggle Navigation Menu ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store ...

  14. American Red Cross

    MedlinePlus

    ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store Toggle Navigation Menu ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store ...

  15. Disaster Recovery Guide

    MedlinePlus

    ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store Toggle Navigation Menu ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store ...

  16. Find a Doctor

    MedlinePlus

    ... Get My Plan Info Service Status Countries ZIP Code Enter Valid ZIP Code Plans Clear Profile Find a Doctor Your health ... Live? Please enter your country and/or ZIP code Country: Zip Code: All Provider Directories I know ...

  17. Hurricane Safety

    MedlinePlus

    ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store Toggle Navigation Menu ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store ...

  18. Wildfire Preparedness

    MedlinePlus

    ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store Toggle Navigation Menu ... Espanol Local Red Cross ( ) Change Chapter Edit Zip Code Edit Zip Code Shop the Red Cross Store ...

  19. GhABF2, a bZIP transcription factor, confers drought and salinity tolerance in cotton (Gossypium hirsutum L.)

    PubMed Central

    Liang, Chengzhen; Meng, Zhaohong; Meng, Zhigang; Malik, Waqas; Yan, Rong; Lwin, Khin Myat; Lin, Fazhuang; Wang, Yuan; Sun, Guoqing; Zhou, Tao; Zhu, Tao; Li, Jianying; Jin, Shuangxia; Guo, Sandui; Zhang, Rui

    2016-01-01

    The bZIP transcription factor (TF) act as an important regulator for the abscisic acid (ABA) mediated abiotic stresses signaling pathways in plants. Here, we reported the cloning and characterization of GhABF2, encoding for typical cotton bZIP TF. Overexpression of GhABF2 significantly improved drought and salt stress tolerance both in Arabidopsis and cotton. However, silencing of GhABF2 made transgenic cotton sensitive to PEG osmotic and salt stress. Expression of GhABF2 was induced by drought and ABA treatments but repressed by high salinity. Transcriptome analysis indicated that GhABF2 increases drought and salt tolerance by regulating genes related to ABA, drought and salt response. The proline contents, activity of superoxide dismutase (SOD) and catalase (CAT) were also significantly increased in GhABF2-overexpression cottons in comparison to wild type after drought and salt treatment. Further, an increase in fiber yield under drought and saline-alkali wetland exhibited the important role of GhABF2 in enhancing the drought and salt tolerance in transgenic lines. In conclusion, manipulation of GhABF2 by biotechnological tools could be a sustainable strategy to deploy drought and salt tolerance in cotton. PMID:27713524

  20. Function of the HD-Zip I gene Oshox22 in ABA-mediated drought and salt tolerances in rice.

    PubMed

    Zhang, Shuxin; Haider, Imran; Kohlen, Wouter; Jiang, Li; Bouwmeester, Harro; Meijer, Annemarie H; Schluepmann, Henriette; Liu, Chun-Ming; Ouwerkerk, Pieter B F

    2012-12-01

    Oshox22 belongs to the homeodomain-leucine zipper (HD-Zip) family I of transcription factors, most of which have unknown functions. Here we show that the expression of Oshox22 is strongly induced by salt stress, abscisic acid (ABA), and polyethylene glycol treatment (PEG), and weakly by cold stress. Trans-activation assays in yeast and transient expression analyses in rice protoplasts demonstrated that Oshox22 is able to bind the CAAT(G/C)ATTG element and acts as a transcriptional activator that requires both the HD and Zip domains. Rice plants homozygous for a T-DNA insertion in the promoter region of Oshox22 showed reduced Oshox22 expression and ABA content, decreased sensitivity to ABA, and enhanced tolerance to drought and salt stresses at the seedling stage. In contrast, transgenic rice over-expressing Oshox22 showed increased sensitivity to ABA, increased ABA content, and decreased drought and salt tolerances. Based on these results, we conclude that Oshox22 affects ABA biosynthesis and regulates drought and salt responses through ABA-mediated signal transduction pathways.

  1. Phosphorylation Affects DNA-Binding of the Senescence-Regulating bZIP Transcription Factor GBF1

    PubMed Central

    Smykowski, Anja; Fischer, Stefan M.; Zentgraf, Ulrike

    2015-01-01

    Massive changes in the transcriptome of Arabidopsis thaliana during onset and progression of leaf senescence imply a central role for transcription factors. While many transcription factors are themselves up- or down-regulated during senescence, the bZIP transcription factor G-box-binding factor 1 (GBF1/bZIP41) is constitutively expressed in Arabidopsis leaf tissue but at the same time triggers the onset of leaf senescence, suggesting posttranscriptional mechanisms for senescence-specific GBF1 activation. Here we show that GBF1 is phosphorylated by the threonine/serine CASEIN KINASE II (CKII) in vitro and that CKII phosphorylation had a negative effect on GBF1 DNA-binding to G-boxes of two direct target genes, CATALASE2 and RBSCS1a. Phosphorylation mimicry at three serine positions in the basic region of GBF1 also had a negative effect on DNA-binding. Kinase assays revealed that CKII phosphorylates at least one serine in the basic domain but has additional phosphorylation sites outside this domain. Two different ckII α subunit1 and one α subunit2 T-DNA insertion lines showed no visible senescence phenotype, but in all lines the expression of the senescence marker gene SAG12 was remarkably diminished. A model is presented suggesting that senescence-specific GBF1 activation might be achieved by lowering the phosphorylation of GBF1 by CKII. PMID:27135347

  2. Nuclear localization of a putative Phytophthora sojae bZIP1 transcription factor is mediated by multiple targeting motifs.

    PubMed

    Fang, Yufeng; Tyler, Brett M

    2017-02-18

    Oomycetes are fungal-like eukaryotic microbes in the kingdom Stramenopila. We recently found that the oomycete plant pathogen Phytophthora sojae uses nuclear localization signals (NLSs) for translocation of proteins into the nucleus that differ from conventional well-characterized NLSs from mammals and yeast. Here we have characterized in depth the nuclear localization signals of a P. sojae basic leucine zipper transcription factor, PsbZIP1. Nuclear localization of PsbZIP1 was determined by a central conserved region overlapping the DNA binding domain. Mutational analysis of this region identified four distinct elements that contributed multiplicatively to nuclear localization, but the conserved DNA binding residues were not required. Three of the elements showed autonomous NLS activity and the fourth served as a nuclear localization enhancer. Sequences within two of the nuclear localization elements defined a new form of bipartite NLS consisting of a triplet of basic residues followed by a tail of scattered basic amino acids. This article is protected by copyright. All rights reserved.

  3. Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana.

    PubMed

    Lozano-Sotomayor, Paulina; Chávez Montes, Ricardo A; Silvestre-Vañó, Marina; Herrera-Ubaldo, Humberto; Greco, Raffaella; Pablo-Villa, Jeanneth; Galliani, Bianca M; Diaz-Ramirez, David; Weemen, Mieke; Boutilier, Kim; Pereira, Andy; Colombo, Lucia; Madueño, Francisco; Marsch-Martínez, Nayelli; de Folter, Stefan

    2016-11-01

    Here we describe an uncharacterized gene that negatively influences Arabidopsis growth and reproductive development. DRINK ME (DKM; bZIP30) is a member of the bZIP transcription factor family, and is expressed in meristematic tissues such as the inflorescence meristem (IM), floral meristem (FM), and carpel margin meristem (CMM). Altered DKM expression affects meristematic tissues and reproductive organ development, including the gynoecium, which is the female reproductive structure and is determinant for fertility and sexual reproduction. A microarray analysis indicates that DKM overexpression affects the expression of cell cycle, cell wall, organ initiation, cell elongation, hormone homeostasis, and meristem activity genes. Furthermore, DKM can interact in yeast and in planta with proteins involved in shoot apical meristem maintenance such as WUSCHEL, KNAT1/BP, KNAT2 and JAIBA, and with proteins involved in medial tissue development in the gynoecium such as HECATE, BELL1 and NGATHA1. Taken together, our results highlight the relevance of DKM as a negative modulator of Arabidopsis growth and reproductive development.

  4. ZIP2DL: An Elastic-Plastic, Large-Rotation Finite-Element Stress Analysis and Crack-Growth Simulation Program

    NASA Technical Reports Server (NTRS)

    Deng, Xiaomin; Newman, James C., Jr.

    1997-01-01

    ZIP2DL is a two-dimensional, elastic-plastic finte element program for stress analysis and crack growth simulations, developed for the NASA Langley Research Center. It has many of the salient features of the ZIP2D program. For example, ZIP2DL contains five material models (linearly elastic, elastic-perfectly plastic, power-law hardening, linear hardening, and multi-linear hardening models), and it can simulate mixed-mode crack growth for prescribed crack growth paths under plane stress, plane strain and mixed state of stress conditions. Further, as an extension of ZIP2D, it also includes a number of new capabilities. The large-deformation kinematics in ZIP2DL will allow it to handle elastic problems with large strains and large rotations, and elastic-plastic problems with small strains and large rotations. Loading conditions in terms of surface traction, concentrated load, and nodal displacement can be applied with a default linear time dependence or they can be programmed according to a user-defined time dependence through a user subroutine. The restart capability of ZIP2DL will make it possible to stop the execution of the program at any time, analyze the results and/or modify execution options and resume and continue the execution of the program. This report includes three sectons: a theoretical manual section, a user manual section, and an example manual secton. In the theoretical secton, the mathematics behind the various aspects of the program are concisely outlined. In the user manual section, a line-by-line explanation of the input data is given. In the example manual secton, three types of examples are presented to demonstrate the accuracy and illustrate the use of this program.

  5. The Zinc Concentration in the Diet and the Length of the Feeding Period Affect the Methylation Status of the ZIP4 Zinc Transporter Gene in Piglets

    PubMed Central

    Karweina, Diana; Kreuzer-Redmer, Susanne; Müller, Uwe; Franken, Tobias; Pieper, Robert; Baron, Udo; Olek, Sven; Zentek, Jürgen; Brockmann, Gudrun A.

    2015-01-01

    High doses of zinc oxide are commonly used in weaned pig diets to improve performance and health. Recent reports show that this may also lead to an imbalanced zinc homeostasis in the animal. For a better understanding of the regulatory mechanisms of different zinc intakes, we performed a feeding experiment to assess potential epigenetic regulation of the ZIP4 gene expression via DNA methylation in the small intestine of piglets. Fifty-four piglets were fed diets with 57 (LZn), 164 (NZn) or 2,425 (HZn) mg Zn/kg feed for one or four weeks. The ZIP4 expression data provided significant evidence for counter-regulation of zinc absorption with higher dietary zinc concentrations. The CpG +735 in the second exon had a 56% higher methylation in the HZn group compared to the others after one week of feeding (8.0·10-4 < p < 0.035); the methylation of this CpG was strongly negatively associated with the expression of the long ZIP4 transcripts (p < 0.007). In the LZn and NZn diets, the expression of the long ZIP4 transcripts were lower after four vs. one week of feeding (2.9·10-4 < p < 0.017). The strongest switch leading to high DNA methylation in nearly all analysed regions was dependent on feeding duration or age in all diet groups (3.7·10-10 < p < 0.099). The data suggest that DNA methylation serves as a fine-tuning mechanism of ZIP4 gene regulation to maintain zinc homeostasis. Methylation of the ZIP4 gene may play a minor role in the response to very high dietary zinc concentration, but may affect binding of alternate zinc-responsive transcription factors. PMID:26599865

  6. A new code SORD for simulation of polarized light scattering in the Earth atmosphere

    NASA Astrophysics Data System (ADS)

    Korkin, Sergey; Lyapustin, Alexei; Sinyuk, Aliaksandr; Holben, Brent

    2016-05-01

    We report a new publicly available radiative transfer (RT) code for numerical simulation of polarized light scattering in plane-parallel Earth atmosphere. Using 44 benchmark tests, we prove high accuracy of the new RT code, SORD (Successive ORDers of scattering1, 2). We describe capabilities of SORD and show run time for each test on two different machines. At present, SORD is supposed to work as part of the Aerosol Robotic NETwork3 (AERONET) inversion algorithm. For natural integration with the AERONET software, SORD is coded in Fortran 90/95. The code is available by email request from the corresponding (first) author or from ftp://climate1.gsfc.nasa.gov/skorkin/SORD/ or ftp://maiac.gsfc.nasa.gov/pub/SORD.zip

  7. Dedicated Searches for Low and High Mass Wimps with the SuperCDMS Soudan iZIP Detectors

    SciTech Connect

    Welliver, Bradford

    2016-01-01

    Recent cosmological evidence suggests most of the mass of the universe takes the form of a type of particle that we have not been able to directly detect. Nearly 80 years that have elapsed since the rst hints of this dark matter started to appear from astronomers without any direct detection. The high precision era of cosmology and unifying models of particle physics developed in the 20 th century have presented us with an exciting mystery at the intersection of these two elds that needs to be solved. SuperCDMS Soudan operates specialized germanium detectors (iZIPs) that are cooled to milliKelvin temperatures deep underground in the Soudan Underground Laboratory with the hope of detecting a rare collision between dark matter and a nucleus. A search for low-mass dark matter comes with multiple unique challenges since the background discrimination abilities of these detectors becomes less powerful at the low energies needed to probe low-mass dark matter since the signal to noise ratio deteriorates. Using a sophisticated background model via a pulse rescaling technique, SuperCDMS Soudan was able to produce a world leading exclusion limit on low-mass dark matter. Effort is to extend the analysis to higher masses require long running times during which many aspects of the detectors or the environment can change. Additional challenges are offered by the powerful background discrimination ability of the iZIP. The background distributions are well separated from the signal region, meaning most of the leakage arises from low-probability tails of the background distributions. In the absence of an enormous dataset, extrapolations from the bulk of the distribution are required. While attempting to obtain a model of gamma induced electron-recoils leaking into the signal region of the detector from high radius a curious asymmetry between the sides of the detectors was discovered potentially indicating an electronics or detector design problem. This thesis describes the physics

  8. Dedicated searches for low and high mass wimps with the SuperCDMS Soudan iZIP detectors

    NASA Astrophysics Data System (ADS)

    Welliver, Bradford C., Jr.

    Recent cosmological evidence suggests most of the mass of the universe takes the form of a type of particle that we have not been able to directly detect. Nearly 80 years that have elapsed since the first hints of this dark matter started to appear from astronomers without any direct detection. The high precision era of cosmology and unifying models of particle physics developed in the 20th century have presented us with an exciting mystery at the intersection of these two fields that needs to be solved. SuperCDMS Soudan operates specialized germanium detectors (iZIPs) that are cooled to milliKelvin temperatures deep underground in the Soudan Underground Laboratory with the hope of detecting a rare collision between dark matter and a nucleus. A search for low-mass dark matter comes with multiple unique challenges since the background discrimination abilities of these detectors becomes less powerful at the low energies needed to probe low-mass dark matter since the signal to noise ratio deteriorates. Using a sophisticated background model via a pulse rescaling technique, SuperCDMS Soudan was able to produce a world leading exclusion limit on low-mass dark matter. Effort is to extend the analysis to higher masses require long running times during which many aspects of the detectors or the environment can change. Additional challenges are offered by the powerful background discrimination ability of the iZIP. The background distributions are well separated from the signal region, meaning most of the leakage arises from low-probability tails of the background distributions. In the absence of an enormous dataset, extrapolations from the bulk of the distribution are required. While attempting to obtain a model of gamma induced electron-recoils leaking into the signal region of the detector from high radius a curious asymmetry between the sides of the detectors was discovered potentially indicating an electronics or detector design problem. This thesis describes the

  9. Intra-Amygdala ZIP Injections Impair the Memory of Learned Active Avoidance Responses and Attenuate Conditioned Taste-Aversion Acquisition in Rats

    ERIC Educational Resources Information Center

    Gamiz, Fernando; Gallo, Milagros

    2011-01-01

    We have investigated the effect of protein kinase Mzeta (PKM[zeta]) inhibition in the basolateral amygdala (BLA) upon the retention of a nonspatial learned active avoidance response and conditioned taste-aversion (CTA) acquisition in rats. ZIP (10 nmol/[mu]L) injected into the BLA 24 h after training impaired retention of a learned…

  10. Abscisic acid-dependent regulation of small rubber particle protein gene expression in Taraxacum brevicorniculatum is mediated by TbbZIP1.

    PubMed

    Fricke, Julia; Hillebrand, Andrea; Twyman, Richard M; Prüfer, Dirk; Schulze Gronover, Christian

    2013-04-01

    Natural rubber is a high-molecular-mass biopolymer found in the latex of >2,500 plant species, including Hevea brasiliensis, Parthenium argentatum and Taraxacum spp. The active sites of rubber biosynthesis are rubber particles, which comprise a hydrophobic rubber core surrounded by a phospholipid monolayer membrane containing species-dependent lipids and associated proteins. Small rubber particle proteins are the most abundant rubber particle-associated proteins in Taraxacum brevicorniculatum (TbSRPPs) and may promote rubber biosynthesis by stabilizing the rubber particle architecture. We investigated the transcriptional regulation of genes encoding SRPPs and identified a bZIP transcription factor (TbbZIP.1) similar to the Arabidopsis thaliana ABI5-ABF-AREB subfamily, which is thought to include downstream targets of ABA and/or abiotic stress-inducible protein kinases. The TbbZIP.1 gene was predominantly expressed in laticifers and regulates the expression of TbSRPP genes in an ABA-dependent manner. The individual TbSRPP genes showed distinct induction profiles, suggesting diverse roles in rubber biosynthesis and stress adaptation. The potential involvement of TbSRPPs in the adaptation of T. brevicorniculatum plants to environmental stress is discussed based on our current knowledge of the stress-response roles of SRPPs and their homologs, and the protective function of latex and rubber against pathogens. Our data suggest that TbSRPPs contribute to stress tolerance in T. brevicorniculatum and that their effects are mediated by TbbZIP.1.

  11. The contribution of the methyl groups on thymine bases to binding specificity and affinity by alanine-rich mutants of the bZIP motif.

    PubMed

    Kise, K J; Shin, J A

    2001-09-01

    We have used fluorescence anisotropy to measure in situ the thermodynamics of binding of alanine-rich mutants of the GCN4 basic region/leucine zipper (bZIP) to short DNA duplexes, in which thymines were replaced with uracils, in order to quantify the contributions of the C5 methyl group on thymines with alanine methyl side chains. We simplified the alpha-helical GCN4 bZIP by alanine substitution: 4A, 11A, and 18A contain four, 11, and 18 alanine mutations in their DNA-binding basic regions, respectively. Titration of fluorescein-labeled duplexes with increasing amounts of protein yielded dissociation constants in the low-to-mid nanomolar range for all bZIP mutants in complex with the AP-1 target site (5'-TGACTCA-3'); binding to the nonspecific control duplex was >1000-fold weaker. Small changes of <1 kcal/mol in binding free energies were observed for wild-type bZIP and 4A mutant to uracil-containing AP-1, whereas 11A and 18A bound almost equally well to native AP-1 and uracil-containing AP-1. These modest changes in binding affinities may reflect the multivalent nature of protein-DNA interactions, as our highly mutated proteins still exhibit native-like behavior. These protein mutations may compensate for changes in enthalpic and entropic contributions toward DNA-binding in order to maintain binding free energies similar to that of the native protein-DNA complex.

  12. The IRE1/bZIP60 pathway and Bax inhibitor 1 suppress systemic accumulation of potyviruses and potexviruses in Arabidopsis and Nicotiana benthamiana plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The inositol requiring enzyme (IRE1) is an endoplasmic reticulum (ER) stress sensor and when activated it splices the bZIP60 mRNA producing a truncated transcription factor that upregulates expression of genes involved in the unfolded protein response (UPR). Bax inhibitor 1 (BI-1) is another ER stre...

  13. Characterization of the bZip-type transcription factor NapA with reference to oxidative stress response in Aspergillus nidulans.

    PubMed

    Asano, Yoshihiro; Hagiwara, Daisuke; Yamashino, Takafumi; Mizuno, Takeshi

    2007-07-01

    Microorganisms growing in natural habitats are constantly confronted with a wide variety of external stresses. Here we provide several lines of experimental evidence for the thesis that the filamentous fungus Aspergillus nidulans has a homolog of the AP-1-like bZip transcription factor, which is known to play general roles in oxidative responses in many types of yeast.

  14. ZIP3D: An elastic and elastic-plastic finite-element analysis program for cracked bodies

    NASA Technical Reports Server (NTRS)

    Shivakumar, K. N.; Newman, J. C., Jr.

    1990-01-01

    ZIP3D is an elastic and an elastic-plastic finite element program to analyze cracks in three dimensional solids. The program may also be used to analyze uncracked bodies or multi-body problems involving contacting surfaces. For crack problems, the program has several unique features including the calculation of mixed-mode strain energy release rates using the three dimensional virtual crack closure technique, the calculation of the J integral using the equivalent domain integral method, the capability to extend the crack front under monotonic or cyclic loading, and the capability to close or open the crack surfaces during cyclic loading. The theories behind the various aspects of the program are explained briefly. Line-by-line data preparation is presented. Input data and results for an elastic analysis of a surface crack in a plate and for an elastic-plastic analysis of a single-edge-crack-tension specimen are also presented.

  15. Pepper CabZIP63 acts as a positive regulator during Ralstonia solanacearum or high temperature-high humidity challenge in a positive feedback loop with CaWRKY40.

    PubMed

    Shen, Lei; Liu, Zhiqin; Yang, Sheng; Yang, Tong; Liang, Jiaqi; Wen, Jiayu; Liu, Yanyan; Li, Jiazhi; Shi, Lanping; Tang, Qian; Shi, Wei; Hu, Jiong; Liu, Cailing; Zhang, Yangwen; Lin, Wei; Wang, Rongzhang; Yu, Huanxin; Mou, Shaoliang; Hussain, Ansar; Cheng, Wei; Cai, Hanyang; He, Li; Guan, Deyi; Wu, Yang; He, Shuilin

    2016-04-01

    CaWRKY40 is known to act as a positive regulator in the response of pepper (Capsicum annuum) to Ralstonia solanacearum inoculation (RSI) or high temperature-high humidity (HTHH), but the underlying mechanism remains elusive. Herein, we report that CabZIP63, a pepper bZIP family member, participates in this process by regulating the expression of CaWRKY40. CabZIP63 was found to localize in the nuclei, be up-regulated by RSI or HTHH, bind to promoters of both CabZIP63(pCabZIP63) and CaWRKY40(pCaWRKY40), and activate pCabZIP63- and pCaWRKY40-driven β-glucuronidase expression in a C- or G-box-dependent manner. Silencing of CabZIP63 by virus-induced gene silencing (VIGS) in pepper plants significantly attenuated their resistance to RSI and tolerance to HTHH, accompanied by down-regulation of immunity- or thermotolerance-associated CaPR1, CaNPR1, CaDEF1, and CaHSP24. Hypersensitive response-mediated cell death and expression of the tested immunity- and thermotolerance-associated marker genes were induced by transient overexpression (TOE) of CabZIP63, but decreased by that of CabZIP63-SRDX. Additionally, binding of CabZIP63 to pCaWRKY40 was up-regulated by RSI or HTHH, and the transcript level of CaWRKY40 and binding of CaWRKY40 to the promoters of CaPR1, CaNPR1, CaDEF1 and CaHSP24 were up-regulated by TOE of CabZIP63. On the other hand, CabZIP63 was also up-regulated transcriptionally by TOE of CaWRKY40. The data suggest collectively that CabZIP63 directly or indirectly regulates the expression of CaWRKY40 at both the transcriptional and post-transcriptional level, forming a positive feedback loop with CaWRKY40 during pepper's response to RSI or HTHH. Altogether, our data will help to elucidate the underlying mechanism of crosstalk between pepper's response to RSI and HTHH.

  16. Pepper CabZIP63 acts as a positive regulator during Ralstonia solanacearum or high temperature–high humidity challenge in a positive feedback loop with CaWRKY40

    PubMed Central

    Shen, Lei; Liu, Zhiqin; Yang, Sheng; Yang, Tong; Liang, Jiaqi; Wen, Jiayu; Liu, Yanyan; Li, Jiazhi; Shi, Lanping; Tang, Qian; Shi, Wei; Hu, Jiong; Liu, Cailing; Zhang, Yangwen; Lin, Wei; Wang, Rongzhang; Yu, Huanxin; Mou, Shaoliang; Hussain, Ansar; Cheng, Wei; Cai, Hanyang; He, Li; Guan, Deyi; Wu, Yang; He, Shuilin

    2016-01-01

    CaWRKY40 is known to act as a positive regulator in the response of pepper (Capsicum annuum) to Ralstonia solanacearum inoculation (RSI) or high temperature–high humidity (HTHH), but the underlying mechanism remains elusive. Herein, we report that CabZIP63, a pepper bZIP family member, participates in this process by regulating the expression of CaWRKY40. CabZIP63 was found to localize in the nuclei, be up-regulated by RSI or HTHH, bind to promoters of both CabZIP63 (pCabZIP63) and CaWRKY40 (pCaWRKY40), and activate pCabZIP63- and pCaWRKY40-driven β-glucuronidase expression in a C- or G-box-dependent manner. Silencing of CabZIP63 by virus-induced gene silencing (VIGS) in pepper plants significantly attenuated their resistance to RSI and tolerance to HTHH, accompanied by down-regulation of immunity- or thermotolerance-associated CaPR1, CaNPR1, CaDEF1, and CaHSP24. Hypersensitive response-mediated cell death and expression of the tested immunity- and thermotolerance-associated marker genes were induced by transient overexpression (TOE) of CabZIP63, but decreased by that of CabZIP63-SRDX. Additionally, binding of CabZIP63 to pCaWRKY40 was up-regulated by RSI or HTHH, and the transcript level of CaWRKY40 and binding of CaWRKY40 to the promoters of CaPR1, CaNPR1, CaDEF1 and CaHSP24 were up-regulated by TOE of CabZIP63. On the other hand, CabZIP63 was also up-regulated transcriptionally by TOE of CaWRKY40. The data suggest collectively that CabZIP63 directly or indirectly regulates the expression of CaWRKY40 at both the transcriptional and post-transcriptional level, forming a positive feedback loop with CaWRKY40 during pepper’s response to RSI or HTHH. Altogether, our data will help to elucidate the underlying mechanism of crosstalk between pepper’s response to RSI and HTHH. PMID:26936828

  17. Mutation in porcine Zip4-like zinc transporter is associated with pancreatic zinc concentration and apparent zinc absorption.

    PubMed

    Siebert, Felicitas; Lühken, Gesine; Pallauf, Josef; Erhardt, Georg

    2013-03-28

    The aim of the present study was to analyse the sequence variability of the porcine Zip4-like Zn transporter gene and the association of identified sequence variants with average daily gain, apparent Zn absorption, plasma Zn concentration and Zn concentration in the liver and pancreas. For the purpose of the study, two different sample sets were used. Set one, which was used for sequencing and association analysis, included mRNA from intestinal tissue from thirty-five piglets of a feeding trial. Sample set two consisted of forty-six samples of genomic DNA from sperm or tissue of wild boars and several pig breeds and was used to genotype animals of different breeds. The sequence analysis of porcine Zip4-like complementary DNA in sample set one revealed the presence of seven nucleotide substitutions. Of these, six were synonymous, whereas a substitution of A with C in exon IX (XM_001925360 c.1430A>C) causes an amino acid exchange from glutamic acid to alanine (p.Glu477Ala). The association analysis revealed no influence of the six synonymous substitutions on Zn values, but the non-synonymous nucleotide exchange significantly increased Zn concentration in the pancreas and apparent Zn absorption of the piglets in week 2 of the feeding trial. The parentage of the piglets and the genotyping results in sample set two suggest a breed-specific presence of the A allele in Piétrain for this amino acid substitution. These results indicate that genotype influences the Zn absorption abilities of individual animals, which should be taken into consideration in animal breeding as well as for the selection of experimental animals.

  18. Determinants of half-site spacing preferences that distinguish AP-1 and ATF/CREB bZIP domains.

    PubMed Central

    Kim, J; Struhl, K

    1995-01-01

    The AP-1 and ATF/CREB families of eukaryotic transcription factors are dimeric DNA-binding proteins that contain the bZIP structural motif. The AP-1 and ATF/CREB proteins are structurally related and recognize identical half-sites (TGAC), but they differ in their requirements for half-site spacing. AP-1 proteins such as yeast GCN4 preferentially bind to sequences with overlapping half-sites, whereas ATF/CREB proteins bind exclusively to sequences with adjacent half-sites. Here we investigate the distinctions between AP-1 and ATF/CREB proteins by determining the DNA-binding properties of mutant and hybrid proteins. First, analysis of GCN4-ATF1 hybrid proteins indicates that a short surface spanning the basic and fork regions of the bZIP domain is the major determinant of half-site spacing. Replacement of two GCN4 residues on this surface (Ala244 and Leu247) by their ATF1 counterparts largely converts GCN4 into a protein with ATF/CREB specificity. Secondly, analysis of a Fos derivative containing the GCN4 leucine zipper indicates that Fos represents a novel intermediate between AP-1 and ATF/CREB proteins. Thirdly, we examine the effects of mutations in the invariant arginine residue of GCN4 (Arg243) that contacts the central base pair(s) of the target sites. While most mutations abolish DNA binding, substitution of a histidine residue results in a GCN4 derivative with ATF/CREB binding specificity. These results suggest that the AP-1 and ATF/CREB proteins differ in positioning a short surface that includes the invariant arginine and that AP-1 proteins may represent a subclass (and perhaps evolutionary offshoot) of ATF/CREB proteins that can tolerate overlapping half-sites. Images PMID:7630732

  19. Error-correction coding

    NASA Technical Reports Server (NTRS)

    Hinds, Erold W. (Principal Investigator)

    1996-01-01

    This report describes the progress made towards the completion of a specific task on error-correcting coding. The proposed research consisted of investigating the use of modulation block codes as the inner code of a concatenated coding system in order to improve the overall space link communications performance. The study proposed to identify and analyze candidate codes that will complement the performance of the overall coding system which uses the interleaved RS (255,223) code as the outer code.

  20. Seasonal abscisic acid signal and a basic leucine zipper transcription factor, DkbZIP5, regulate proanthocyanidin biosynthesis in persimmon fruit.

    PubMed

    Akagi, Takashi; Katayama-Ikegami, Ayako; Kobayashi, Shozo; Sato, Akihiko; Kono, Atsushi; Yonemori, Keizo

    2012-02-01

    Proanthocyanidins (PAs) are secondary metabolites that contribute to plant protection and crop quality. Persimmon (Diospyros kaki) has a unique characteristic of accumulating large amounts of PAs, particularly in its fruit. Normal astringent-type and mutant nonastringent-type fruits show different PA accumulation patterns depending on the seasonal expression patterns of DkMyb4, which is a Myb transcription factor (TF) regulating many PA pathway genes in persimmon. In this study, attempts were made to identify the factors involved in DkMyb4 expression and the resultant PA accumulation in persimmon fruit. Treatment with abscisic acid (ABA) and an ABA biosynthesis inhibitor resulted in differential changes in the expression patterns of DkMyb4 and PA biosynthesis in astringent-type and nonastringent-type fruits depending on the development stage. To obtain an ABA-signaling TF, we isolated a full-length basic leucine zipper (bZIP) TF, DkbZIP5, which is highly expressed in persimmon fruit. We also showed that ectopic DkbZIP5 overexpression in persimmon calluses induced the up-regulation of DkMyb4 and the resultant PA biosynthesis. In addition, a detailed molecular characterization using the electrophoretic mobility shift assay and transient reporter assay indicated that DkbZIP5 recognized ABA-responsive elements in the promoter region of DkMyb4 and acted as a direct regulator of DkMyb4 in an ABA-dependent manner. These results suggest that ABA signals may be involved in PA biosynthesis in persimmon fruit via DkMyb4 activation by DkbZIP5.

  1. The Arabidopsis bZIP11 transcription factor links low-energy signalling to auxin-mediated control of primary root growth.

    PubMed

    Weiste, Christoph; Pedrotti, Lorenzo; Selvanayagam, Jebasingh; Muralidhara, Prathibha; Fröschel, Christian; Novák, Ondřej; Ljung, Karin; Hanson, Johannes; Dröge-Laser, Wolfgang

    2017-02-01

    Plants have to tightly control their energy homeostasis to ensure survival and fitness under constantly changing environmental conditions. Thus, it is stringently required that energy-consuming stress-adaptation and growth-related processes are dynamically tuned according to the prevailing energy availability. The evolutionary conserved SUCROSE NON-FERMENTING1 RELATED KINASES1 (SnRK1) and the downstream group C/S1 basic leucine zipper (bZIP) transcription factors (TFs) are well-characterised central players in plants' low-energy management. Nevertheless, mechanistic insights into plant growth control under energy deprived conditions remains largely elusive. In this work, we disclose the novel function of the low-energy activated group S1 bZIP11-related TFs as regulators of auxin-mediated primary root growth. Whereas transgenic gain-of-function approaches of these bZIPs interfere with the activity of the root apical meristem and result in root growth repression, root growth of loss-of-function plants show a pronounced insensitivity to low-energy conditions. Based on ensuing molecular and biochemical analyses, we propose a mechanistic model, in which bZIP11-related TFs gain control over the root meristem by directly activating IAA3/SHY2 transcription. IAA3/SHY2 is a pivotal negative regulator of root growth, which has been demonstrated to efficiently repress transcription of major auxin transport facilitators of the PIN-FORMED (PIN) gene family, thereby restricting polar auxin transport to the root tip and in consequence auxin-driven primary root growth. Taken together, our results disclose the central low-energy activated SnRK1-C/S1-bZIP signalling module as gateway to integrate information on the plant's energy status into root meristem control, thereby balancing plant growth and cellular energy resources.

  2. The Arabidopsis bZIP11 transcription factor links low-energy signalling to auxin-mediated control of primary root growth

    PubMed Central

    Weiste, Christoph; Pedrotti, Lorenzo; Muralidhara, Prathibha; Ljung, Karin; Dröge-Laser, Wolfgang

    2017-01-01

    Plants have to tightly control their energy homeostasis to ensure survival and fitness under constantly changing environmental conditions. Thus, it is stringently required that energy-consuming stress-adaptation and growth-related processes are dynamically tuned according to the prevailing energy availability. The evolutionary conserved SUCROSE NON-FERMENTING1 RELATED KINASES1 (SnRK1) and the downstream group C/S1 basic leucine zipper (bZIP) transcription factors (TFs) are well-characterised central players in plants’ low-energy management. Nevertheless, mechanistic insights into plant growth control under energy deprived conditions remains largely elusive. In this work, we disclose the novel function of the low-energy activated group S1 bZIP11-related TFs as regulators of auxin-mediated primary root growth. Whereas transgenic gain-of-function approaches of these bZIPs interfere with the activity of the root apical meristem and result in root growth repression, root growth of loss-of-function plants show a pronounced insensitivity to low-energy conditions. Based on ensuing molecular and biochemical analyses, we propose a mechanistic model, in which bZIP11-related TFs gain control over the root meristem by directly activating IAA3/SHY2 transcription. IAA3/SHY2 is a pivotal negative regulator of root growth, which has been demonstrated to efficiently repress transcription of major auxin transport facilitators of the PIN-FORMED (PIN) gene family, thereby restricting polar auxin transport to the root tip and in consequence auxin-driven primary root growth. Taken together, our results disclose the central low-energy activated SnRK1-C/S1-bZIP signalling module as gateway to integrate information on the plant’s energy status into root meristem control, thereby balancing plant growth and cellular energy resources. PMID:28158182

  3. Extreme Population Differences in the Human Zinc Transporter ZIP4 (SLC39A4) Are Explained by Positive Selection in Sub-Saharan Africa

    PubMed Central

    Pybus, Marc; Andrews, Glen K.; Lalueza-Fox, Carles; Comas, David; Sekler, Israel; de la Rasilla, Marco; Rosas, Antonio; Stoneking, Mark; Valverde, Miguel A.; Vicente, Rubén; Bosch, Elena

    2014-01-01

    Extreme differences in allele frequency between West Africans and Eurasians were observed for a leucine-to-valine substitution (Leu372Val) in the human intestinal zinc uptake transporter, ZIP4, yet no further evidence was found for a selective sweep around the ZIP4 gene (SLC39A4). By interrogating allele frequencies in more than 100 diverse human populations and resequencing Neanderthal DNA, we confirmed the ancestral state of this locus and found a strong geographical gradient for the derived allele (Val372), with near fixation in West Africa. In extensive coalescent simulations, we show that the extreme differences in allele frequency, yet absence of a classical sweep signature, can be explained by the effect of a local recombination hotspot, together with directional selection favoring the Val372 allele in Sub-Saharan Africans. The possible functional effect of the Leu372Val substitution, together with two pathological mutations at the same codon (Leu372Pro and Leu372Arg) that cause acrodermatitis enteropathica (a disease phenotype characterized by extreme zinc deficiency), was investigated by transient overexpression of human ZIP4 protein in HeLa cells. Both acrodermatitis mutations cause absence of the ZIP4 transporter cell surface expression and nearly absent zinc uptake, while the Val372 variant displayed significantly reduced surface protein expression, reduced basal levels of intracellular zinc, and reduced zinc uptake in comparison with the Leu372 variant. We speculate that reduced zinc uptake by the ZIP4-derived Val372 isoform may act by starving certain pathogens of zinc, and hence may have been advantageous in Sub-Saharan Africa. Moreover, these functional results may indicate differences in zinc homeostasis among modern human populations with possible relevance for disease risk. PMID:24586184

  4. Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in Sub-Saharan Africa.

    PubMed

    Engelken, Johannes; Carnero-Montoro, Elena; Pybus, Marc; Andrews, Glen K; Lalueza-Fox, Carles; Comas, David; Sekler, Israel; de la Rasilla, Marco; Rosas, Antonio; Stoneking, Mark; Valverde, Miguel A; Vicente, Rubén; Bosch, Elena

    2014-02-01

    Extreme differences in allele frequency between West Africans and Eurasians were observed for a leucine-to-valine substitution (Leu372Val) in the human intestinal zinc uptake transporter, ZIP4, yet no further evidence was found for a selective sweep around the ZIP4 gene (SLC39A4). By interrogating allele frequencies in more than 100 diverse human populations and resequencing Neanderthal DNA, we confirmed the ancestral state of this locus and found a strong geographical gradient for the derived allele (Val372), with near fixation in West Africa. In extensive coalescent simulations, we show that the extreme differences in allele frequency, yet absence of a classical sweep signature, can be explained by the effect of a local recombination hotspot, together with directional selection favoring the Val372 allele in Sub-Saharan Africans. The possible functional effect of the Leu372Val substitution, together with two pathological mutations at the same codon (Leu372Pro and Leu372Arg) that cause acrodermatitis enteropathica (a disease phenotype characterized by extreme zinc deficiency), was investigated by transient overexpression of human ZIP4 protein in HeLa cells. Both acrodermatitis mutations cause absence of the ZIP4 transporter cell surface expression and nearly absent zinc uptake, while the Val372 variant displayed significantly reduced surface protein expression, reduced basal levels of intracellular zinc, and reduced zinc uptake in comparison with the Leu372 variant. We speculate that reduced zinc uptake by the ZIP4-derived Val372 isoform may act by starving certain pathogens of zinc, and hence may have been advantageous in Sub-Saharan Africa. Moreover, these functional results may indicate differences in zinc homeostasis among modern human populations with possible relevance for disease risk.

  5. The protein phosphatase 2C clade A protein OsPP2C51 positively regulates seed germination by directly inactivating OsbZIP10.

    PubMed

    Bhatnagar, Nikita; Min, Myung-Ki; Choi, Eun-Hye; Kim, Namhyo; Moon, Seok-Jun; Yoon, Insun; Kwon, Taekryoun; Jung, Ki-Hong; Kim, Beom-Gi

    2017-03-01

    Protein phosphatase 2C clade A members are major signaling components in the ABA-dependent signaling cascade that regulates seed germination. To elucidate the role of PP2CA genes in germination of rice seed, we selected OsPP2C51, which shows highly specific expression in the embryo compared with other protein phosphatases based on microarray data. GUS histochemical assay confirmed that OsPP2C51 is expressed in the seed embryo and that this expression pattern is unique compared with those of other OsPP2CA genes. Data obtained from germination assays and alpha-amylase assays of OsPP2C51 knockout and overexpression lines suggest that OsPP2C51 positively regulates seed germination in rice. The expression of alpha-amylase synthesizing genes was high in OsPP2C51 overexpressing plants, suggesting that elevated levels of OsPP2C51 might enhance gene expression related to higher rates of seed germination. Analysis of protein interactions between ABA signaling components showed that OsPP2C51 interacts with OsPYL/RCAR5 in an ABA-dependent manner. Furthermore, interactions were observed between OsPP2C51 and SAPK2, and between OsPP2C51 and OsbZIP10 and we found out that OsPP2C51 can dephosphorylates OsbZIP10. These findings suggest the existence of a new branch in ABA signaling pathway consisting of OsPYL/RCAR-OsPP2C-bZIP apart from the previously reported OsPYL/RCAR-OsPP2C-SAPK-bZIP. Overall, our result suggests that OsPP2C51 is a positive regulator of seed germination by directly suppressing active phosphorylated OsbZIP10.

  6. Diagnostic Coding for Epilepsy.

    PubMed

    Williams, Korwyn; Nuwer, Marc R; Buchhalter, Jeffrey R

    2016-02-01

    Accurate coding is an important function of neurologic practice. This contribution to Continuum is part of an ongoing series that presents helpful coding information along with examples related to the issue topic. Tips for diagnosis coding, Evaluation and Management coding, procedure coding, or a combination are presented, depending on which is most applicable to the subject area of the issue.

  7. Model Children's Code.

    ERIC Educational Resources Information Center

    New Mexico Univ., Albuquerque. American Indian Law Center.

    The Model Children's Code was developed to provide a legally correct model code that American Indian tribes can use to enact children's codes that fulfill their legal, cultural and economic needs. Code sections cover the court system, jurisdiction, juvenile offender procedures, minor-in-need-of-care, and termination. Almost every Code section is…

  8. Phylogeny of genetic codes and punctuation codes within genetic codes.

    PubMed

    Seligmann, Hervé

    2015-03-01

    Punctuation codons (starts, stops) delimit genes, reflect translation apparatus properties. Most codon reassignments involve punctuation. Here two complementary approaches classify natural genetic codes: (A) properties of amino acids assigned to codons (classical phylogeny), coding stops as X (A1, antitermination/suppressor tRNAs insert unknown residues), or as gaps (A2, no translation, classical stop); and (B) considering only punctuation status (start, stop and other codons coded as -1, 0 and 1 (B1); 0, -1 and 1 (B2, reflects ribosomal translational dynamics); and 1, -1, and 0 (B3, starts/stops as opposites)). All methods separate most mitochondrial codes from most nuclear codes; Gracilibacteria consistently cluster with metazoan mitochondria; mitochondria co-hosted with chloroplasts cluster with nuclear codes. Method A1 clusters the euplotid nuclear code with metazoan mitochondria; A2 separates euplotids from mitochondria. Firmicute bacteria Mycoplasma/Spiroplasma and Protozoan (and lower metazoan) mitochondria share codon-amino acid assignments. A1 clusters them with mitochondria, they cluster with the standard genetic code under A2: constraints on amino acid ambiguity versus punctuation-signaling produced the mitochondrial versus bacterial versions of this genetic code. Punctuation analysis B2 converges best with classical phylogenetic analyses, stressing the need for a unified theory of genetic code punctuation accounting for ribosomal constraints.

  9. Evolution of the Class IV HD-Zip Gene Family in Streptophytes

    PubMed Central

    Zalewski, Christopher S.; Floyd, Sandra K.; Furumizu, Chihiro; Sakakibara, Keiko; Stevenson, Dennis W.; Bowman, John L.

    2013-01-01

    Class IV homeodomain leucine zipper (C4HDZ) genes are plant-specific transcription factors that, based on phenotypes in Arabidopsis thaliana, play an important role in epidermal development. In this study, we sampled all major extant lineages and their closest algal relatives for C4HDZ homologs and phylogenetic analyses result in a gene tree that mirrors land plant evolution with evidence for gene duplications in many lineages, but minimal evidence for gene losses. Our analysis suggests an ancestral C4HDZ gene originated in an algal ancestor of land plants and a single ancestral gene was present in the last common ancestor of land plants. Independent gene duplications are evident within several lineages including mosses, lycophytes, euphyllophytes, seed plants, and, most notably, angiosperms. In recently evolved angiosperm paralogs, we find evidence of pseudogenization via mutations in both coding and regulatory sequences. The increasing complexity of the C4HDZ gene family through the diversification of land plants correlates to increasing complexity in epidermal characters. PMID:23894141

  10. Basic Leucine Zipper (bZIP) Domain Transcription Factor MBZ1 Regulates Cell Wall Integrity, Spore Adherence, and Virulence in Metarhizium robertsii *

    PubMed Central

    Huang, Wei; Shang, Yanfang; Chen, Peilin; Cen, Kai; Wang, Chengshu

    2015-01-01

    Transcription factors (TFs) containing the basic leucine zipper (bZIP) domain are widely distributed in eukaryotes and display an array of distinct functions. In this study, a bZIP-type TF gene (MBZ1) was deleted and functionally characterized in the insect pathogenic fungus Metarhizium robertsii. The deletion mutant (ΔMBZ1) showed defects in cell wall integrity, adhesion to hydrophobic surfaces, and topical infection of insects. Relative to the WT, ΔMBZ1 was also impaired in growth and conidiogenesis. Examination of putative target gene expression indicated that the genes involved in chitin biosynthesis were differentially transcribed in ΔMBZ1 compared with the WT, which led to the accumulation of a higher level of chitin in mutant cell walls. MBZ1 exhibited negative regulation of subtilisin proteases, but positive control of an adhesin gene, which is consistent with the observation of effects on cell autolysis and a reduction in spore adherence to hydrophobic surfaces in ΔMBZ1. Promoter binding assays indicated that MBZ1 can bind to different target genes and suggested the possibility of heterodimer formation to increase the diversity of the MBZ1 regulatory network. The results of this study advance our understanding of the divergence of bZIP-type TFs at both intra- and interspecific levels. PMID:25673695

  11. Basic leucine zipper (bZIP) domain transcription factor MBZ1 regulates cell wall integrity, spore adherence, and virulence in Metarhizium robertsii.

    PubMed

    Huang, Wei; Shang, Yanfang; Chen, Peilin; Cen, Kai; Wang, Chengshu

    2015-03-27

    Transcription factors (TFs) containing the basic leucine zipper (bZIP) domain are widely distributed in eukaryotes and display an array of distinct functions. In this study, a bZIP-type TF gene (MBZ1) was deleted and functionally characterized in the insect pathogenic fungus Metarhizium robertsii. The deletion mutant (ΔMBZ1) showed defects in cell wall integrity, adhesion to hydrophobic surfaces, and topical infection of insects. Relative to the WT, ΔMBZ1 was also impaired in growth and conidiogenesis. Examination of putative target gene expression indicated that the genes involved in chitin biosynthesis were differentially transcribed in ΔMBZ1 compared with the WT, which led to the accumulation of a higher level of chitin in mutant cell walls. MBZ1 exhibited negative regulation of subtilisin proteases, but positive control of an adhesin gene, which is consistent with the observation of effects on cell autolysis and a reduction in spore adherence to hydrophobic surfaces in ΔMBZ1. Promoter binding assays indicated that MBZ1 can bind to different target genes and suggested the possibility of heterodimer formation to increase the diversity of the MBZ1 regulatory network. The results of this study advance our understanding of the divergence of bZIP-type TFs at both intra- and interspecific levels.

  12. The yapA Encodes bZIP Transcription Factor Involved in Stress Tolerance in Pathogenic Fungus Talaromyces marneffei

    PubMed Central

    Dankai, Wiyada; Pongpom, Monsicha; Youngchim, Sirida; Cooper, Chester R.; Vanittanakom, Nongnuch

    2016-01-01

    Talaromyces marneffei, formerly Penicillium marneffei, is a thermally dimorphic fungus. It causes a fatal disseminated disease in patients infected with the human immunodeficiency virus (HIV). Studies on the stress defense mechanism of T. marneffei can lead to a better understanding of the pathogenicity and the progression of the disease due to this fungus. The basic leucine-zipper (bZip) transcription factor gene in Saccharomyces cerevisiae, named yap1 (yeast activating protein-1), is known as a crucial central regulator of stress responses including those caused by oxidative agents, cadmium, and drugs. An ortholog of yap1, designated yapA, was identified in T. marneffei. We found that the yapA gene was involved in growth and fungal cell development. The yapA deletion mutant exhibited delays in the rate of growth, germination, and conidiation. Surprisingly, the yapA gene was also involved in the pigmentation of T. marneffei. Moreover, the mutant was sensitive to oxidative stressors such as H2O2 and menadione, similar to S. cerevisiae yap1 mutant, as well as the nitrosative stressor NaNO2. In addition, the yapA mutant demonstrated significantly decreased survival in human macrophage THP-1 compared to wild-type and complemented strains. This study reveals the role of yapA in fungal growth, cell development, stress response, and potential virulence in T. marneffei. PMID:27706212

  13. Development of T cell lymphoma in HTLV-1 bZIP factor and Tax double transgenic mice.

    PubMed

    Zhao, Tiejun; Satou, Yorifumi; Matsuoka, Masao

    2014-07-01

    Adult T-cell leukemia (ATL) is an aggressive T-cell malignancy caused by human T-cell leukemia virus type 1 (HTLV-1). ATL cells possess a CD4+ CD25+ phenotype, similar to that of regulatory T cells (Tregs). Tax has been reported to play a crucial role in the leukemogenesis of HTLV-1. The HTLV-1 bZIP factor (HBZ), which is encoded by the minus strand of the viral genomic RNA, is expressed in all ATL cases and induces neoplastic and inflammatory disease in vivo. To test whether HBZ and Tax are both required for T cell malignancy, we generated HBZ/Tax double transgenic mice in which HBZ and Tax are expressed exclusively in CD4+ T cells. Survival was much reduced in HBZ/Tax double-transgenic mice compared with wild type littermates. Transgenic expression of HBZ and Tax induced skin lesions and T-cell lymphoma in mice, resembling diseases observed in HTLV-1 infected individuals. However, Tax single transgenic mice did not develop major health problems. In addition, memory CD4+ T cells and Foxp3+ Treg cells counts were increased in HBZ/Tax double transgenic mice, and their proliferation was enhanced. There was very little difference between HBZ single and HBZ/Tax double transgenic mice. Taken together, these results show that HBZ, in addition to Tax, plays a critical role in T-cell lymphoma arising from HTLV-1 infection.

  14. High-Yield Expression in E. coli and Refolding of the bZIP Domain of Activating Transcription Factor 5

    PubMed Central

    Ciaccio, Natalie A.; Moreno, Matthew L.; Bauer, Rachel L.; Laurence, Jennifer S.

    2008-01-01

    Activating Transcription Factor 5 (ATF5) recently has been demonstrated to play a critical role in promoting the survival of human glioblastoma cells. Interference with the function of ATF5 in an in vivo rat model caused glioma cell death in primary tumors but did not affect the status of normal cells surrounding the tumor, suggesting ATF5 may prove an ideal target for anti-cancer therapy. In order to examine ATF5 as a pharmaceutical target, the protein must be produced and purified to sufficient quantity to begin analyses. Here, a procedure for expressing and refolding the bZIP domain of ATF5 in sufficient yield and final concentration to permit assay development and structural characterization of this target using solution NMR is reported. Two-dimensional NMR and circular dichrosim analyses indicate the protein exists in the partially α-helical, monomeric x-form conformation with only a small fraction of ATF5 participating in formation of higher-order structure, presumably coiled-coil homodimerization. Despite the persistence of monomers in solution even at high concentration, an electrophoretic mobility shift assay showed that ATF5 is able to bind to the cAMP response element (CRE) DNA motif. Polyacrylamide gel electrophoresis and mass spectrometry were used to confirm that ATF5 can participate in homodimer formation and that this dimerization is mediated by disulfide bond formation. PMID:18718539

  15. Accumulate repeat accumulate codes

    NASA Technical Reports Server (NTRS)

    Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

    2004-01-01

    In this paper we propose an innovative channel coding scheme called 'Accumulate Repeat Accumulate codes' (ARA). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes, thus belief propagation can be used for iterative decoding of ARA codes on a graph. The structure of encoder for this class can be viewed as precoded Repeat Accumulate (RA) code or as precoded Irregular Repeat Accumulate (IRA) code, where simply an accumulator is chosen as a precoder. Thus ARA codes have simple, and very fast encoder structure when they representing LDPC codes. Based on density evolution for LDPC codes through some examples for ARA codes, we show that for maximum variable node degree 5 a minimum bit SNR as low as 0.08 dB from channel capacity for rate 1/2 can be achieved as the block size goes to infinity. Thus based on fixed low maximum variable node degree, its threshold outperforms not only the RA and IRA codes but also the best known LDPC codes with the dame maximum node degree. Furthermore by puncturing the accumulators any desired high rate codes close to code rate 1 can be obtained with thresholds that stay close to the channel capacity thresholds uniformly. Iterative decoding simulation results are provided. The ARA codes also have projected graph or protograph representation that allows for high speed decoder implementation.

  16. Concatenated Coding Using Trellis-Coded Modulation

    NASA Technical Reports Server (NTRS)

    Thompson, Michael W.

    1997-01-01

    In the late seventies and early eighties a technique known as Trellis Coded Modulation (TCM) was developed for providing spectrally efficient error correction coding. Instead of adding redundant information in the form of parity bits, redundancy is added at the modulation stage thereby increasing bandwidth efficiency. A digital communications system can be designed to use bandwidth-efficient multilevel/phase modulation such as Amplitude Shift Keying (ASK), Phase Shift Keying (PSK), Differential Phase Shift Keying (DPSK) or Quadrature Amplitude Modulation (QAM). Performance gain can be achieved by increasing the number of signals over the corresponding uncoded system to compensate for the redundancy introduced by the code. A considerable amount of research and development has been devoted toward developing good TCM codes for severely bandlimited applications. More recently, the use of TCM for satellite and deep space communications applications has received increased attention. This report describes the general approach of using a concatenated coding scheme that features TCM and RS coding. Results have indicated that substantial (6-10 dB) performance gains can be achieved with this approach with comparatively little bandwidth expansion. Since all of the bandwidth expansion is due to the RS code we see that TCM based concatenated coding results in roughly 10-50% bandwidth expansion compared to 70-150% expansion for similar concatenated scheme which use convolution code. We stress that combined coding and modulation optimization is important for achieving performance gains while maintaining spectral efficiency.

  17. Coset Codes Viewed as Terminated Convolutional Codes

    NASA Technical Reports Server (NTRS)

    Fossorier, Marc P. C.; Lin, Shu

    1996-01-01

    In this paper, coset codes are considered as terminated convolutional codes. Based on this approach, three new general results are presented. First, it is shown that the iterative squaring construction can equivalently be defined from a convolutional code whose trellis terminates. This convolutional code determines a simple encoder for the coset code considered, and the state and branch labelings of the associated trellis diagram become straightforward. Also, from the generator matrix of the code in its convolutional code form, much information about the trade-off between the state connectivity and complexity at each section, and the parallel structure of the trellis, is directly available. Based on this generator matrix, it is shown that the parallel branches in the trellis diagram of the convolutional code represent the same coset code C(sub 1), of smaller dimension and shorter length. Utilizing this fact, a two-stage optimum trellis decoding method is devised. The first stage decodes C(sub 1), while the second stage decodes the associated convolutional code, using the branch metrics delivered by stage 1. Finally, a bidirectional decoding of each received block starting at both ends is presented. If about the same number of computations is required, this approach remains very attractive from a practical point of view as it roughly doubles the decoding speed. This fact is particularly interesting whenever the second half of the trellis is the mirror image of the first half, since the same decoder can be implemented for both parts.

  18. Discussion on LDPC Codes and Uplink Coding

    NASA Technical Reports Server (NTRS)

    Andrews, Ken; Divsalar, Dariush; Dolinar, Sam; Moision, Bruce; Hamkins, Jon; Pollara, Fabrizio

    2007-01-01

    This slide presentation reviews the progress that the workgroup on Low-Density Parity-Check (LDPC) for space link coding. The workgroup is tasked with developing and recommending new error correcting codes for near-Earth, Lunar, and deep space applications. Included in the presentation is a summary of the technical progress of the workgroup. Charts that show the LDPC decoder sensitivity to symbol scaling errors are reviewed, as well as a chart showing the performance of several frame synchronizer algorithms compared to that of some good codes and LDPC decoder tests at ESTL. Also reviewed is a study on Coding, Modulation, and Link Protocol (CMLP), and the recommended codes. A design for the Pseudo-Randomizer with LDPC Decoder and CRC is also reviewed. A chart that summarizes the three proposed coding systems is also presented.

  19. Bar Codes for Libraries.

    ERIC Educational Resources Information Center

    Rahn, Erwin

    1984-01-01

    Discusses the evolution of standards for bar codes (series of printed lines and spaces that represent numbers, symbols, and/or letters of alphabet) and describes the two types most frequently adopted by libraries--Code-A-Bar and CODE 39. Format of the codes is illustrated. Six references and definitions of terminology are appended. (EJS)

  20. Manually operated coded switch

    DOEpatents

    Barnette, Jon H.

    1978-01-01

    The disclosure relates to a manually operated recodable coded switch in which a code may be inserted, tried and used to actuate a lever controlling an external device. After attempting a code, the switch's code wheels must be returned to their zero positions before another try is made.

  1. QR Codes 101

    ERIC Educational Resources Information Center

    Crompton, Helen; LaFrance, Jason; van 't Hooft, Mark

    2012-01-01

    A QR (quick-response) code is a two-dimensional scannable code, similar in function to a traditional bar code that one might find on a product at the supermarket. The main difference between the two is that, while a traditional bar code can hold a maximum of only 20 digits, a QR code can hold up to 7,089 characters, so it can contain much more…

  2. ARA type protograph codes

    NASA Technical Reports Server (NTRS)

    Divsalar, Dariush (Inventor); Abbasfar, Aliazam (Inventor); Jones, Christopher R. (Inventor); Dolinar, Samuel J. (Inventor); Thorpe, Jeremy C. (Inventor); Andrews, Kenneth S. (Inventor); Yao, Kung (Inventor)

    2008-01-01

    An apparatus and method for encoding low-density parity check codes. Together with a repeater, an interleaver and an accumulator, the apparatus comprises a precoder, thus forming accumulate-repeat-accumulate (ARA codes). Protographs representing various types of ARA codes, including AR3A, AR4A and ARJA codes, are described. High performance is obtained when compared to the performance of current repeat-accumulate (RA) or irregular-repeat-accumulate (IRA) codes.

  3. The ERECTA, CLAVATA and class III HD-ZIP Pathways Display Synergistic Interactions in Regulating Floral Meristem Activities

    PubMed Central

    Landau, Udi; Asis, Lior; Eshed Williams, Leor

    2015-01-01

    In angiosperms, the production of flowers marks the beginning of the reproductive phase. At the emergence of flower primordia on the flanks of the inflorescence meristem, the WUSCHEL (WUS) gene, which encodes a homeodomain transcription factor starts to be expressed and establishes de novo stem cell population, founder of the floral meristem (FM). Similarly to the shoot apical meristem a precise spatial and temporal expression pattern of WUS is required and maintained through strict regulation by multiple regulatory inputs to maintain stem cell homeostasis. However, following the formation of a genetically determined fixed number of floral organs, this homeostasis is shifted towards organogenesis and the FM is terminated. In here we performed a genetic study to test how a reduction in ERECTA, CLAVATA and class III HD-ZIP pathways affects floral meristem activity and flower development. We revealed strong synergistic phenotypes of extra flower number, supernumerary whorls, total loss of determinacy and extreme enlargement of the meristem as compared to any double mutant combination indicating that the three pathways, CLV3, ER and HD-ZIPIII distinctively regulate meristem activity and that they act in parallel. Our findings yield several new insights into stem cell-driven development. We demonstrate the crucial requirement for coupling floral meristem termination with carpel formation to ensure successful reproduction in plants. We also show how regulation of meristem size and alternation in spatial structure of the meristem serve as a mechanism to determine flower organogenesis. We propose that the loss of FM determinacy due to the reduction in CLV3, ER and HD-ZIPIII activity is genetically separable from the AGAMOUS core mechanism of meristem termination. PMID:25946150

  4. Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways

    PubMed Central

    Mandel, Tali; Candela, Héctor; Landau, Udi; Asis, Lior; Zelinger, Einat; Carles, Cristel C.; Williams, Leor Eshed

    2016-01-01

    ABSTRACT The shoot apical meristem (SAM) of angiosperm plants is a small, highly organized structure that gives rise to all above-ground organs. The SAM is divided into three functional domains: the central zone (CZ) at the SAM tip harbors the self-renewing pluripotent stem cells and the organizing center, providing daughter cells that are continuously displaced into the interior rib zone (RZ) or the surrounding peripheral zone (PZ), from which organ primordia are initiated. Despite the constant flow of cells from the CZ into the RZ or PZ, and cell recruitment for primordium formation, a stable balance is maintained between the distinct cell populations in the SAM. Here we combined an in-depth phenotypic analysis with a comparative RNA-Seq approach to characterize meristems from selected combinations of clavata3 (clv3), jabba-1D (jba-1D) and erecta (er) mutants of Arabidopsis thaliana. We demonstrate that CLV3 restricts meristem expansion along the apical-basal axis, whereas class III HD-ZIP and ER pathways restrict meristem expansion laterally, but in distinct and possibly perpendicular orientations. Our k-means analysis reveals that clv3, jba-1D/+ and er lead to meristem enlargement by affecting different aspects of meristem function; for example, clv3 displays an increase in the stem cell population, whereas jba-1D/+ er exhibits an increase in mitotic activity and in the meristematic cell population. Our analyses demonstrate that a combined genetic and mRNA-Seq comparative approach provides a precise and sensitive method to identify cell type-specific transcriptomes in a small structure, such as the SAM. PMID:26989178

  5. Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways.

    PubMed

    Mandel, Tali; Candela, Héctor; Landau, Udi; Asis, Lior; Zelinger, Einat; Carles, Cristel C; Williams, Leor Eshed

    2016-05-01

    The shoot apical meristem (SAM) of angiosperm plants is a small, highly organized structure that gives rise to all above-ground organs. The SAM is divided into three functional domains: the central zone (CZ) at the SAM tip harbors the self-renewing pluripotent stem cells and the organizing center, providing daughter cells that are continuously displaced into the interior rib zone (RZ) or the surrounding peripheral zone (PZ), from which organ primordia are initiated. Despite the constant flow of cells from the CZ into the RZ or PZ, and cell recruitment for primordium formation, a stable balance is maintained between the distinct cell populations in the SAM. Here we combined an in-depth phenotypic analysis with a comparative RNA-Seq approach to characterize meristems from selected combinations of clavata3 (clv3), jabba-1D (jba-1D) and erecta (er) mutants of Arabidopsis thaliana We demonstrate that CLV3 restricts meristem expansion along the apical-basal axis, whereas class III HD-ZIP and ER pathways restrict meristem expansion laterally, but in distinct and possibly perpendicular orientations. Our k-means analysis reveals that clv3, jba-1D/+ and er lead to meristem enlargement by affecting different aspects of meristem function; for example, clv3 displays an increase in the stem cell population, whereas jba-1D/+ er exhibits an increase in mitotic activity and in the meristematic cell population. Our analyses demonstrate that a combined genetic and mRNA-Seq comparative approach provides a precise and sensitive method to identify cell type-specific transcriptomes in a small structure, such as the SAM.

  6. Efficient entropy coding for scalable video coding

    NASA Astrophysics Data System (ADS)

    Choi, Woong Il; Yang, Jungyoup; Jeon, Byeungwoo

    2005-10-01

    The standardization for the scalable extension of H.264 has called for additional functionality based on H.264 standard to support the combined spatio-temporal and SNR scalability. For the entropy coding of H.264 scalable extension, Context-based Adaptive Binary Arithmetic Coding (CABAC) scheme is considered so far. In this paper, we present a new context modeling scheme by using inter layer correlation between the syntax elements. As a result, it improves coding efficiency of entropy coding in H.264 scalable extension. In simulation results of applying the proposed scheme to encoding the syntax element mb_type, it is shown that improvement in coding efficiency of the proposed method is up to 16% in terms of bit saving due to estimation of more adequate probability model.

  7. Honesty and Honor Codes.

    ERIC Educational Resources Information Center

    McCabe, Donald; Trevino, Linda Klebe

    2002-01-01

    Explores the rise in student cheating and evidence that students cheat less often at schools with an honor code. Discusses effective use of such codes and creation of a peer culture that condemns dishonesty. (EV)

  8. Cellulases and coding sequences

    DOEpatents

    Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

    2001-02-20

    The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

  9. Cellulases and coding sequences

    DOEpatents

    Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

    2001-01-01

    The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

  10. QR Code Mania!

    ERIC Educational Resources Information Center

    Shumack, Kellie A.; Reilly, Erin; Chamberlain, Nik

    2013-01-01

    space, has error-correction capacity, and can be read from any direction. These codes are used in manufacturing, shipping, and marketing, as well as in education. QR codes can be created to produce…

  11. DIANE multiparticle transport code

    NASA Astrophysics Data System (ADS)

    Caillaud, M.; Lemaire, S.; Ménard, S.; Rathouit, P.; Ribes, J. C.; Riz, D.

    2014-06-01

    DIANE is the general Monte Carlo code developed at CEA-DAM. DIANE is a 3D multiparticle multigroup code. DIANE includes automated biasing techniques and is optimized for massive parallel calculations.

  12. The dynamic of the splicing of bZIP60 and the proteins encoded by the spliced and unspliced mRNAs reveals some unique features during the activation of UPR in Arabidopsis thaliana.

    PubMed

    Parra-Rojas, Juan; Moreno, Adrian A; Mitina, Irina; Orellana, Ariel

    2015-01-01

    The unfolded protein response (UPR) is a signaling pathway that is activated when the workload of the endoplasmic reticulum (ER) is surpassed. IRE1 is a sensor involved in triggering the UPR and plays a key role in the unconventional splicing of an mRNA leading to the formation of a transcription factor that up-regulates the transcription of genes that play a role in restoring the homeostasis in the ER. In plants, bZIP60 is the substrate for IRE1; however, questions such as what is the dynamics of the splicing of bZIP60 and the fate of the proteins encoded by the spliced and unspliced forms of the mRNA, remain unanswered. In the present work, we analyzed the processing of bZIP60 by determining the levels of the spliced form mRNA in plants exposed to different conditions that trigger UPR. The results show that induction of ER stress increases the content of the spliced form of bZIP60 (bZIP60s) reaching a maximum, that depending on the stimuli, varied between 30 min or 2 hrs. In most cases, this was followed by a decrease in the content. In contrast to other eukaryotes, the splicing never occurred to full extent. The content of bZIP60s changed among different organs upon induction of the UPR suggesting that splicing is regulated differentially throughout the plant. In addition, we analyzed the distribution of a GFP-tagged version of bZIP60 when UPR was activated. A good correlation between splicing of bZIP60 and localization of the protein in the nucleus was observed. No fluorescence was observed under basal conditions, but interestingly, the fluorescence was recovered and found to co-localize with an ER marker upon treatment with an inhibitor of the proteasome. Our results indicate that the dynamics of bZIP60, both the mRNA and the protein, are highly dynamic processes which are tissue-specific and stimulus-dependent.

  13. EMF wire code research

    SciTech Connect

    Jones, T.

    1993-11-01

    This paper examines the results of previous wire code research to determines the relationship with childhood cancer, wire codes and electromagnetic fields. The paper suggests that, in the original Savitz study, biases toward producing a false positive association between high wire codes and childhood cancer were created by the selection procedure.

  14. Universal Noiseless Coding Subroutines

    NASA Technical Reports Server (NTRS)

    Schlutsmeyer, A. P.; Rice, R. F.

    1986-01-01

    Software package consists of FORTRAN subroutines that perform universal noiseless coding and decoding of integer and binary data strings. Purpose of this type of coding to achieve data compression in sense that coded data represents original data perfectly (noiselessly) while taking fewer bits to do so. Routines universal because they apply to virtually any "real-world" data source.

  15. Mapping Local Codes to Read Codes.

    PubMed

    Bonney, Wilfred; Galloway, James; Hall, Christopher; Ghattas, Mikhail; Tramma, Leandro; Nind, Thomas; Donnelly, Louise; Jefferson, Emily; Doney, Alexander

    2017-01-01

    Background & Objectives: Legacy laboratory test codes make it difficult to use clinical datasets for meaningful translational research, where populations are followed for disease risk and outcomes over many years. The Health Informatics Centre (HIC) at the University of Dundee hosts continuous biochemistry data from the clinical laboratories in Tayside and Fife dating back as far as 1987. However, the HIC-managed biochemistry dataset is coupled with incoherent sample types and unstandardised legacy local test codes, which increases the complexity of using the dataset for reasonable population health outcomes. The objective of this study was to map the legacy local test codes to the Scottish 5-byte Version 2 Read Codes using biochemistry data extracted from the repository of the Scottish Care Information (SCI) Store.

  16. NASA. Lewis Research Center Advanced Modulation and Coding Project: Introduction and overview

    NASA Technical Reports Server (NTRS)

    Budinger, James M.

    1992-01-01

    The Advanced Modulation and Coding Project at LeRC is sponsored by the Office of Space Science and Applications, Communications Division, Code EC, at NASA Headquarters and conducted by the Digital Systems Technology Branch of the Space Electronics Division. Advanced Modulation and Coding is one of three focused technology development projects within the branch's overall Processing and Switching Program. The program consists of industry contracts for developing proof-of-concept (POC) and demonstration model hardware, university grants for analyzing advanced techniques, and in-house integration and testing of performance verification and systems evaluation. The Advanced Modulation and Coding Project is broken into five elements: (1) bandwidth- and power-efficient modems; (2) high-speed codecs; (3) digital modems; (4) multichannel demodulators; and (5) very high-data-rate modems. At least one contract and one grant were awarded for each element.

  17. Software Certification - Coding, Code, and Coders

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus; Holzmann, Gerard J.

    2011-01-01

    We describe a certification approach for software development that has been adopted at our organization. JPL develops robotic spacecraft for the exploration of the solar system. The flight software that controls these spacecraft is considered to be mission critical. We argue that the goal of a software certification process cannot be the development of "perfect" software, i.e., software that can be formally proven to be correct under all imaginable and unimaginable circumstances. More realistically, the goal is to guarantee a software development process that is conducted by knowledgeable engineers, who follow generally accepted procedures to control known risks, while meeting agreed upon standards of workmanship. We target three specific issues that must be addressed in such a certification procedure: the coding process, the code that is developed, and the skills of the coders. The coding process is driven by standards (e.g., a coding standard) and tools. The code is mechanically checked against the standard with the help of state-of-the-art static source code analyzers. The coders, finally, are certified in on-site training courses that include formal exams.

  18. Correlation between cloud thickness and brightness using Nimbus 4 THIR data /11.5-micron channel/ and ATS 3 digital data

    NASA Technical Reports Server (NTRS)

    Park, S.-U.; Sikdar, D. N.; Suomi, V. E.

    1974-01-01

    Nimbus 4 data (11.5-micron) channel and ATS 3 digitized data were analyzed for three days during April and May 1970. Cloud-top temperature, as measured by the 11.5-micron channel of the satellite radiometer, shows a close negative correlation with cloud brightness measured by the ATS 3 satellite. This is especially true in well-developed cumulonimbus clouds. An estimate of cloud heights corresponding to cloud-top temperature was obtained by using radiosonde data and radar images, and the relationships between the cloud thickness and brightness counts were derived for the cumulonimbus clouds.

  19. XSOR codes users manual

    SciTech Connect

    Jow, Hong-Nian; Murfin, W.B.; Johnson, J.D.

    1993-11-01

    This report describes the source term estimation codes, XSORs. The codes are written for three pressurized water reactors (Surry, Sequoyah, and Zion) and two boiling water reactors (Peach Bottom and Grand Gulf). The ensemble of codes has been named ``XSOR``. The purpose of XSOR codes is to estimate the source terms which would be released to the atmosphere in severe accidents. A source term includes the release fractions of several radionuclide groups, the timing and duration of releases, the rates of energy release, and the elevation of releases. The codes have been developed by Sandia National Laboratories for the US Nuclear Regulatory Commission (NRC) in support of the NUREG-1150 program. The XSOR codes are fast running parametric codes and are used as surrogates for detailed mechanistic codes. The XSOR codes also provide the capability to explore the phenomena and their uncertainty which are not currently modeled by the mechanistic codes. The uncertainty distributions of input parameters may be used by an. XSOR code to estimate the uncertainty of source terms.

  20. DLLExternalCode

    SciTech Connect

    Greg Flach, Frank Smith

    2014-05-14

    DLLExternalCode is the a general dynamic-link library (DLL) interface for linking GoldSim (www.goldsim.com) with external codes. The overall concept is to use GoldSim as top level modeling software with interfaces to external codes for specific calculations. The DLLExternalCode DLL that performs the linking function is designed to take a list of code inputs from GoldSim, create an input file for the external application, run the external code, and return a list of outputs, read from files created by the external application, back to GoldSim. Instructions for creating the input file, running the external code, and reading the output are contained in an instructions file that is read and interpreted by the DLL.

  1. Defeating the coding monsters.

    PubMed

    Colt, Ross

    2007-02-01

    Accuracy in coding is rapidly becoming a required skill for military health care providers. Clinic staffing, equipment purchase decisions, and even reimbursement will soon be based on the coding data that we provide. Learning the complicated myriad of rules to code accurately can seem overwhelming. However, the majority of clinic visits in a typical outpatient clinic generally fall into two major evaluation and management codes, 99213 and 99214. If health care providers can learn the rules required to code a 99214 visit, then this will provide a 90% solution that can enable them to accurately code the majority of their clinic visits. This article demonstrates a step-by-step method to code a 99214 visit, by viewing each of the three requirements as a monster to be defeated.

  2. Ectopic expression of a hot pepper bZIP-like transcription factor in potato enhances drought tolerance without decreasing tuber yield.

    PubMed

    Moon, Seok-Jun; Han, Se-Youn; Kim, Dool-Yi; Yoon, In Sun; Shin, Dongjin; Byun, Myung-Ok; Kwon, Hawk-Bin; Kim, Beom-Gi

    2015-11-01

    Over-expression of group A bZIP transcription factor genes in plants improves abiotic stress tolerance but usually reduces yields. Thus, there have been several efforts to overcome yield penalty in transgenic plants. In this study, we characterized that expression of the hot pepper (Capsicum annuum) gene CaBZ1, which encodes a group S bZIP transcription factor, was induced by salt and osmotic stress as well as abscisic acid (ABA). Transgenic potato (Solanum tuberosum) plants over-expressing CaBZ1 exhibited reduced rates of water loss and faster stomatal closure than non transgenic potato plants under drought and ABA treatment conditions. CaBZ1 over-expression in transgenic potato increased the expression of ABA- and stress-related genes (such as CYP707A1, CBF and NAC-like genes) and improved drought stress tolerance. Interestingly, over-expression of CaBZ1 in potato did not produce undesirable growth phenotypes in major agricultural traits such as plant height, leaf size and tuber formation under normal growth conditions. The transgenic potato plants also had higher tuber yields than non transgenic potato plants under drought stress conditions. Thus, CaBZ1 may be useful for improving drought tolerance in tuber crops. This might be the first report of the production of transgenic potato with improved tuber yields under drought conditions.

  3. An arginine to lysine substitution in the bZIP domain of an opaque-2 mutant in maize abolishes specific DNA binding.

    PubMed

    Aukerman, M J; Schmidt, R J; Burr, B; Burr, F A

    1991-02-01

    The opaque-2 (o2) locus in maize encodes a transcription factor involved in the regulation of zein storage proteins. We have shown previously that the O2 protein contains a leucine zipper domain that binds to promoters of 22-kD zein genes. In this paper we characterize an EMS-induced o2 allele, o2-676, that causes a 50% reduction in zein. We have found that the o2-676 mutant protein does not show specific recognition of zein promoter fragments because of the substitution of a lysine residue for an arginine residue within the bZIP domain of o2-676. This particular arginine is conserved within the bZIP domains of all mammalian, fungal, and plant DNA binding proteins of this class. The correlation between this mutation in o2 and the altered pattern of zein expression strongly suggests that O2 regulates transcription of certain members of the zein multigene family through direct interaction with the zein promoters and not through the transcriptional activation of some other regulator of zein gene expression.

  4. The Rice coding algorithm achieves high-performance lossless and progressive image compression based on the improving of integer lifting scheme Rice coding algorithm

    NASA Astrophysics Data System (ADS)

    Jun, Xie Cheng; Su, Yan; Wei, Zhang

    2006-08-01

    In this paper, a modified algorithm was introduced to improve Rice coding algorithm and researches of image compression with the CDF (2,2) wavelet lifting scheme was made. Our experiments show that the property of the lossless image compression is much better than Huffman, Zip, lossless JPEG, RAR, and a little better than (or equal to) the famous SPIHT. The lossless compression rate is improved about 60.4%, 45%, 26.2%, 16.7%, 0.4% on average. The speed of the encoder is faster about 11.8 times than the SPIHT's and its efficiency in time can be improved by 162%. The speed of the decoder is faster about 12.3 times than that of the SPIHT's and its efficiency in time can be rasied about 148%. This algorithm, instead of largest levels wavelet transform, has high coding efficiency when the wavelet transform levels is larger than 3. For the source model of distributions similar to the Laplacian, it can improve the efficiency of coding and realize the progressive transmit coding and decoding.

  5. Mechanical code comparator

    DOEpatents

    Peter, Frank J.; Dalton, Larry J.; Plummer, David W.

    2002-01-01

    A new class of mechanical code comparators is described which have broad potential for application in safety, surety, and security applications. These devices can be implemented as micro-scale electromechanical systems that isolate a secure or otherwise controlled device until an access code is entered. This access code is converted into a series of mechanical inputs to the mechanical code comparator, which compares the access code to a pre-input combination, entered previously into the mechanical code comparator by an operator at the system security control point. These devices provide extremely high levels of robust security. Being totally mechanical in operation, an access control system properly based on such devices cannot be circumvented by software attack alone.

  6. More box codes

    NASA Technical Reports Server (NTRS)

    Solomon, G.

    1992-01-01

    A new investigation shows that, starting from the BCH (21,15;3) code represented as a 7 x 3 matrix and adding a row and column to add even parity, one obtains an 8 x 4 matrix (32,15;8) code. An additional dimension is obtained by specifying odd parity on the rows and even parity on the columns, i.e., adjoining to the 8 x 4 matrix, the matrix, which is zero except for the fourth column (of all ones). Furthermore, any seven rows and three columns will form the BCH (21,15;3) code. This box code has the same weight structure as the quadratic residue and BCH codes of the same dimensions. Whether there exists an algebraic isomorphism to either code is as yet unknown.

  7. Generating code adapted for interlinking legacy scalar code and extended vector code

    DOEpatents

    Gschwind, Michael K

    2013-06-04

    Mechanisms for intermixing code are provided. Source code is received for compilation using an extended Application Binary Interface (ABI) that extends a legacy ABI and uses a different register configuration than the legacy ABI. First compiled code is generated based on the source code, the first compiled code comprising code for accommodating the difference in register configurations used by the extended ABI and the legacy ABI. The first compiled code and second compiled code are intermixed to generate intermixed code, the second compiled code being compiled code that uses the legacy ABI. The intermixed code comprises at least one call instruction that is one of a call from the first compiled code to the second compiled code or a call from the second compiled code to the first compiled code. The code for accommodating the difference in register configurations is associated with the at least one call instruction.

  8. Industrial Computer Codes

    NASA Technical Reports Server (NTRS)

    Shapiro, Wilbur

    1996-01-01

    This is an overview of new and updated industrial codes for seal design and testing. GCYLT (gas cylindrical seals -- turbulent), SPIRALI (spiral-groove seals -- incompressible), KTK (knife to knife) Labyrinth Seal Code, and DYSEAL (dynamic seal analysis) are covered. CGYLT uses G-factors for Poiseuille and Couette turbulence coefficients. SPIRALI is updated to include turbulence and inertia, but maintains the narrow groove theory. KTK labyrinth seal code handles straight or stepped seals. And DYSEAL provides dynamics for the seal geometry.

  9. Phonological coding during reading

    PubMed Central

    Leinenger, Mallorie

    2014-01-01

    The exact role that phonological coding (the recoding of written, orthographic information into a sound based code) plays during silent reading has been extensively studied for more than a century. Despite the large body of research surrounding the topic, varying theories as to the time course and function of this recoding still exist. The present review synthesizes this body of research, addressing the topics of time course and function in tandem. The varying theories surrounding the function of phonological coding (e.g., that phonological codes aid lexical access, that phonological codes aid comprehension and bolster short-term memory, or that phonological codes are largely epiphenomenal in skilled readers) are first outlined, and the time courses that each maps onto (e.g., that phonological codes come online early (pre-lexical) or that phonological codes come online late (post-lexical)) are discussed. Next the research relevant to each of these proposed functions is reviewed, discussing the varying methodologies that have been used to investigate phonological coding (e.g., response time methods, reading while eyetracking or recording EEG and MEG, concurrent articulation) and highlighting the advantages and limitations of each with respect to the study of phonological coding. In response to the view that phonological coding is largely epiphenomenal in skilled readers, research on the use of phonological codes in prelingually, profoundly deaf readers is reviewed. Finally, implications for current models of word identification (activation-verification model (Van Order, 1987), dual-route model (e.g., Coltheart, Rastle, Perry, Langdon, & Ziegler, 2001), parallel distributed processing model (Seidenberg & McClelland, 1989)) are discussed. PMID:25150679

  10. Tokamak Systems Code

    SciTech Connect

    Reid, R.L.; Barrett, R.J.; Brown, T.G.; Gorker, G.E.; Hooper, R.J.; Kalsi, S.S.; Metzler, D.H.; Peng, Y.K.M.; Roth, K.E.; Spampinato, P.T.

    1985-03-01

    The FEDC Tokamak Systems Code calculates tokamak performance, cost, and configuration as a function of plasma engineering parameters. This version of the code models experimental tokamaks. It does not currently consider tokamak configurations that generate electrical power or incorporate breeding blankets. The code has a modular (or subroutine) structure to allow independent modeling for each major tokamak component or system. A primary benefit of modularization is that a component module may be updated without disturbing the remainder of the systems code as long as the imput to or output from the module remains unchanged.

  11. Topological subsystem codes

    SciTech Connect

    Bombin, H.

    2010-03-15

    We introduce a family of two-dimensional (2D) topological subsystem quantum error-correcting codes. The gauge group is generated by two-local Pauli operators, so that two-local measurements are enough to recover the error syndrome. We study the computational power of code deformation in these codes and show that boundaries cannot be introduced in the usual way. In addition, we give a general mapping connecting suitable classical statistical mechanical models to optimal error correction in subsystem stabilizer codes that suffer from depolarizing noise.

  12. FAA Smoke Transport Code

    SciTech Connect

    Domino, Stefan; Luketa-Hanlin, Anay; Gallegos, Carlos

    2006-10-27

    FAA Smoke Transport Code, a physics-based Computational Fluid Dynamics tool, which couples heat, mass, and momentum transfer, has been developed to provide information on smoke transport in cargo compartments with various geometries and flight conditions. The software package contains a graphical user interface for specification of geometry and boundary conditions, analysis module for solving the governing equations, and a post-processing tool. The current code was produced by making substantial improvements and additions to a code obtained from a university. The original code was able to compute steady, uniform, isothermal turbulent pressurization. In addition, a preprocessor and postprocessor were added to arrive at the current software package.

  13. Transonic airfoil codes

    NASA Technical Reports Server (NTRS)

    Garabedian, P. R.

    1979-01-01

    Computer codes for the design and analysis of transonic airfoils are considered. The design code relies on the method of complex characteristics in the hodograph plane to construct shockless airfoil. The analysis code uses artificial viscosity to calculate flows with weak shock waves at off-design conditions. Comparisons with experiments show that an excellent simulation of two dimensional wind tunnel tests is obtained. The codes have been widely adopted by the aircraft industry as a tool for the development of supercritical wing technology.

  14. Fast Coding Unit Encoding Mechanism for Low Complexity Video Coding

    PubMed Central

    Wu, Yueying; Jia, Kebin; Gao, Guandong

    2016-01-01

    In high efficiency video coding (HEVC), coding tree contributes to excellent compression performance. However, coding tree brings extremely high computational complexity. Innovative works for improving coding tree to further reduce encoding time are stated in this paper. A novel low complexity coding tree mechanism is proposed for HEVC fast coding unit (CU) encoding. Firstly, this paper makes an in-depth study of the relationship among CU distribution, quantization parameter (QP) and content change (CC). Secondly, a CU coding tree probability model is proposed for modeling and predicting CU distribution. Eventually, a CU coding tree probability update is proposed, aiming to address probabilistic model distortion problems caused by CC. Experimental results show that the proposed low complexity CU coding tree mechanism significantly reduces encoding time by 27% for lossy coding and 42% for visually lossless coding and lossless coding. The proposed low complexity CU coding tree mechanism devotes to improving coding performance under various application conditions. PMID:26999741

  15. Fast Coding Unit Encoding Mechanism for Low Complexity Video Coding.

    PubMed

    Gao, Yuan; Liu, Pengyu; Wu, Yueying; Jia, Kebin; Gao, Guandong

    2016-01-01

    In high efficiency video coding (HEVC), coding tree contributes to excellent compression performance. However, coding tree brings extremely high computational complexity. Innovative works for improving coding tree to further reduce encoding time are stated in this paper. A novel low complexity coding tree mechanism is proposed for HEVC fast coding unit (CU) encoding. Firstly, this paper makes an in-depth study of the relationship among CU distribution, quantization parameter (QP) and content change (CC). Secondly, a CU coding tree probability model is proposed for modeling and predicting CU distribution. Eventually, a CU coding tree probability update is proposed, aiming to address probabilistic model distortion problems caused by CC. Experimental results show that the proposed low complexity CU coding tree mechanism significantly reduces encoding time by 27% for lossy coding and 42% for visually lossless coding and lossless coding. The proposed low complexity CU coding tree mechanism devotes to improving coding performance under various application conditions.

  16. Dress Codes for Teachers?

    ERIC Educational Resources Information Center

    Million, June

    2004-01-01

    In this article, the author discusses an e-mail survey of principals from across the country regarding whether or not their school had a formal staff dress code. The results indicate that most did not have a formal dress code, but agreed that professional dress for teachers was not only necessary, but showed respect for the school and had a…

  17. Lichenase and coding sequences

    DOEpatents

    Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

    2000-08-15

    The present invention provides a fungal lichenase, i.e., an endo-1,3-1,4-.beta.-D-glucanohydrolase, its coding sequence, recombinant DNA molecules comprising the lichenase coding sequences, recombinant host cells and methods for producing same. The present lichenase is from Orpinomyces PC-2.

  18. Legacy Code Modernization

    NASA Technical Reports Server (NTRS)

    Hribar, Michelle R.; Frumkin, Michael; Jin, Haoqiang; Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

    1998-01-01

    Over the past decade, high performance computing has evolved rapidly; systems based on commodity microprocessors have been introduced in quick succession from at least seven vendors/families. Porting codes to every new architecture is a difficult problem; in particular, here at NASA, there are many large CFD applications that are very costly to port to new machines by hand. The LCM ("Legacy Code Modernization") Project is the development of an integrated parallelization environment (IPE) which performs the automated mapping of legacy CFD (Fortran) applications to state-of-the-art high performance computers. While most projects to port codes focus on the parallelization of the code, we consider porting to be an iterative process consisting of several steps: 1) code cleanup, 2) serial optimization,3) parallelization, 4) performance monitoring and visualization, 5) intelligent tools for automated tuning using performance prediction and 6) machine specific optimization. The approach for building this parallelization environment is to build the components for each of the steps simultaneously and then integrate them together. The demonstration will exhibit our latest research in building this environment: 1. Parallelizing tools and compiler evaluation. 2. Code cleanup and serial optimization using automated scripts 3. Development of a code generator for performance prediction 4. Automated partitioning 5. Automated insertion of directives. These demonstrations will exhibit the effectiveness of an automated approach for all the steps involved with porting and tuning a legacy code application for a new architecture.

  19. Synthesizing Certified Code

    NASA Technical Reports Server (NTRS)

    Whalen, Michael; Schumann, Johann; Fischer, Bernd

    2002-01-01

    Code certification is a lightweight approach to demonstrate software quality on a formal level. Its basic idea is to require producers to provide formal proofs that their code satisfies certain quality properties. These proofs serve as certificates which can be checked independently. Since code certification uses the same underlying technology as program verification, it also requires many detailed annotations (e.g., loop invariants) to make the proofs possible. However, manually adding theses annotations to the code is time-consuming and error-prone. We address this problem by combining code certification with automatic program synthesis. We propose an approach to generate simultaneously, from a high-level specification, code and all annotations required to certify generated code. Here, we describe a certification extension of AUTOBAYES, a synthesis tool which automatically generates complex data analysis programs from compact specifications. AUTOBAYES contains sufficient high-level domain knowledge to generate detailed annotations. This allows us to use a general-purpose verification condition generator to produce a set of proof obligations in first-order logic. The obligations are then discharged using the automated theorem E-SETHEO. We demonstrate our approach by certifying operator safety for a generated iterative data classification program without manual annotation of the code.

  20. Coding Acoustic Metasurfaces.

    PubMed

    Xie, Boyang; Tang, Kun; Cheng, Hua; Liu, Zhengyou; Chen, Shuqi; Tian, Jianguo

    2017-02-01

    Coding acoustic metasurfaces can combine simple logical bits to acquire sophisticated functions in wave control. The acoustic logical bits can achieve a phase difference of exactly π and a perfect match of the amplitudes for the transmitted waves. By programming the coding sequences, acoustic metasurfaces with various functions, including creating peculiar antenna patterns and waves focusing, have been demonstrated.

  1. Computerized mega code recording.

    PubMed

    Burt, T W; Bock, H C

    1988-04-01

    A system has been developed to facilitate recording of advanced cardiac life support mega code testing scenarios. By scanning a paper "keyboard" using a bar code wand attached to a portable microcomputer, the person assigned to record the scenario can easily generate an accurate, complete, timed, and typewritten record of the given situations and the obtained responses.

  2. Pseudonoise code tracking loop

    NASA Technical Reports Server (NTRS)

    Laflame, D. T. (Inventor)

    1980-01-01

    A delay-locked loop is presented for tracking a pseudonoise (PN) reference code in an incoming communication signal. The loop is less sensitive to gain imbalances, which can otherwise introduce timing errors in the PN reference code formed by the loop.

  3. Evolving genetic code

    PubMed Central

    OHAMA, Takeshi; INAGAKI, Yuji; BESSHO, Yoshitaka; OSAWA, Syozo

    2008-01-01

    In 1985, we reported that a bacterium, Mycoplasma capricolum, used a deviant genetic code, namely UGA, a “universal” stop codon, was read as tryptophan. This finding, together with the deviant nuclear genetic codes in not a few organisms and a number of mitochondria, shows that the genetic code is not universal, and is in a state of evolution. To account for the changes in codon meanings, we proposed the codon capture theory stating that all the code changes are non-disruptive without accompanied changes of amino acid sequences of proteins. Supporting evidence for the theory is presented in this review. A possible evolutionary process from the ancient to the present-day genetic code is also discussed. PMID:18941287

  4. Combustion chamber analysis code

    NASA Technical Reports Server (NTRS)

    Przekwas, A. J.; Lai, Y. G.; Krishnan, A.; Avva, R. K.; Giridharan, M. G.

    1993-01-01

    A three-dimensional, time dependent, Favre averaged, finite volume Navier-Stokes code has been developed to model compressible and incompressible flows (with and without chemical reactions) in liquid rocket engines. The code has a non-staggered formulation with generalized body-fitted-coordinates (BFC) capability. Higher order differencing methodologies such as MUSCL and Osher-Chakravarthy schemes are available. Turbulent flows can be modeled using any of the five turbulent models present in the code. A two-phase, two-liquid, Lagrangian spray model has been incorporated into the code. Chemical equilibrium and finite rate reaction models are available to model chemically reacting flows. The discrete ordinate method is used to model effects of thermal radiation. The code has been validated extensively against benchmark experimental data and has been applied to model flows in several propulsion system components of the SSME and the STME.

  5. Pyramid image codes

    NASA Technical Reports Server (NTRS)

    Watson, Andrew B.

    1990-01-01

    All vision systems, both human and machine, transform the spatial image into a coded representation. Particular codes may be optimized for efficiency or to extract useful image features. Researchers explored image codes based on primary visual cortex in man and other primates. Understanding these codes will advance the art in image coding, autonomous vision, and computational human factors. In cortex, imagery is coded by features that vary in size, orientation, and position. Researchers have devised a mathematical model of this transformation, called the Hexagonal oriented Orthogonal quadrature Pyramid (HOP). In a pyramid code, features are segregated by size into layers, with fewer features in the layers devoted to large features. Pyramid schemes provide scale invariance, and are useful for coarse-to-fine searching and for progressive transmission of images. The HOP Pyramid is novel in three respects: (1) it uses a hexagonal pixel lattice, (2) it uses oriented features, and (3) it accurately models most of the prominent aspects of primary visual cortex. The transform uses seven basic features (kernels), which may be regarded as three oriented edges, three oriented bars, and one non-oriented blob. Application of these kernels to non-overlapping seven-pixel neighborhoods yields six oriented, high-pass pyramid layers, and one low-pass (blob) layer.

  6. Report number codes

    SciTech Connect

    Nelson, R.N.

    1985-05-01

    This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name.

  7. Embedded foveation image coding.

    PubMed

    Wang, Z; Bovik, A C

    2001-01-01

    The human visual system (HVS) is highly space-variant in sampling, coding, processing, and understanding. The spatial resolution of the HVS is highest around the point of fixation (foveation point) and decreases rapidly with increasing eccentricity. By taking advantage of this fact, it is possible to remove considerable high-frequency information redundancy from the peripheral regions and still reconstruct a perceptually good quality image. Great success has been obtained previously by a class of embedded wavelet image coding algorithms, such as the embedded zerotree wavelet (EZW) and the set partitioning in hierarchical trees (SPIHT) algorithms. Embedded wavelet coding not only provides very good compression performance, but also has the property that the bitstream can be truncated at any point and still be decoded to recreate a reasonably good quality image. In this paper, we propose an embedded foveation image coding (EFIC) algorithm, which orders the encoded bitstream to optimize foveated visual quality at arbitrary bit-rates. A foveation-based image quality metric, namely, foveated wavelet image quality index (FWQI), plays an important role in the EFIC system. We also developed a modified SPIHT algorithm to improve the coding efficiency. Experiments show that EFIC integrates foveation filtering with foveated image coding and demonstrates very good coding performance and scalability in terms of foveated image quality measurement.

  8. The role of a basic amino acid cluster in target site selection and non-specific binding of bZIP peptides to DNA.

    PubMed Central

    Metallo, S J; Paolella, D N; Schepartz, A

    1997-01-01

    The ability of a transcription factor to locate and bind its cognate DNA site in the presence of closely related sites and a vast array of non-specific DNA is crucial for cell survival. The CREB/ATF family of transcription factors is an important group of basic region leucine zipper (bZIP) proteins that display high affinity for the CRE site and low affinity for the closely related AP-1 site. Members of the CREB/ATF family share in common a cluster of basic amino acids at the N-terminus of their bZIP element. This basic cluster is necessary and sufficient to cause the CRE site to bend upon binding of a CREB/ATF protein. The possibility that DNA bending and CRE/AP-1 specificity were linked in CREB/ATF proteins was investigated using chimeric peptides derived from human CRE-BP1 (a member of the CREB/ATF family) and yeast GCN4, which lacks both a basic cluster and CRE/AP-1 specificity. Gain of function and loss of function experiments demonstrated that the basic cluster was not responsible for the CRE/AP-1 specificity displayed by all characterized CREB/ATF proteins. The basic cluster was, however, responsible for inducing very high affinity for non- specific DNA. It was further shown that basic cluster-containing peptides bind non-specific DNA in a random coil conformation. We postulate that the high non- specific DNA affinities of basic cluster-containing peptides result from cooperative electrostatic interactions with the phosphate backbone that do not require peptide organization. PMID:9224594

  9. The transcriptional integrator CREB-binding protein mediates positive cross talk between nuclear hormone receptors and the hematopoietic bZip protein p45/NF-E2.

    PubMed Central

    Cheng, X; Reginato, M J; Andrews, N C; Lazar, M A

    1997-01-01

    Thyroid hormone (T3) and retinoic acid (RA) play important roles in erythropoiesis. We found that the hematopoietic cell-specific bZip protein p45/NF-E2 interacts with T3 receptor (TR) and RA receptor (RAR) but not retinoid X receptor. The interaction is between the DNA-binding domain of the nuclear receptor and the leucine zipper region of p45/NF-E2 but is markedly enhanced by cognate ligand. Remarkably, ligand-dependent transactivation by TR and RAR is markedly potentiated by p45/NF-E2. This effect of p45/NF-E2 is prevented by maf-like protein p18, which functions positively as a heterodimer with p45/NF-E2 on DNA. Potentiation of hormone action by p45/NF-E2 requires its activation domain, which interacts strongly with the multifaceted coactivator cyclic AMP response element protein-binding protein (CBP). The region of CBP which interacts with p45/NF-E2 is the same interaction domain that mediates inhibition of hormone-stimulated transcription by AP1 transcription factors. Overexpression of the bZip interaction domain of CBP specifically abolishes the positive cross talk between TR and p45/NF-E2. Thus, positive cross talk between p45/NF-E2 and nuclear hormone receptors requires direct protein-protein interactions between these factors and with CBP, whose integration of positive signals from two transactivation domains provides a novel mechanism for potentiation of hormone action in hematopoietic cells. PMID:9032267

  10. Code Disentanglement: Initial Plan

    SciTech Connect

    Wohlbier, John Greaton; Kelley, Timothy M.; Rockefeller, Gabriel M.; Calef, Matthew Thomas

    2015-01-27

    The first step to making more ambitious changes in the EAP code base is to disentangle the code into a set of independent, levelized packages. We define a package as a collection of code, most often across a set of files, that provides a defined set of functionality; a package a) can be built and tested as an entity and b) fits within an overall levelization design. Each package contributes one or more libraries, or an application that uses the other libraries. A package set is levelized if the relationships between packages form a directed, acyclic graph and each package uses only packages at lower levels of the diagram (in Fortran this relationship is often describable by the use relationship between modules). Independent packages permit independent- and therefore parallel|development. The packages form separable units for the purposes of development and testing. This is a proven path for enabling finer-grained changes to a complex code.

  11. Compressible Astrophysics Simulation Code

    SciTech Connect

    Howell, L.; Singer, M.

    2007-07-18

    This is an astrophysics simulation code involving a radiation diffusion module developed at LLNL coupled to compressible hydrodynamics and adaptive mesh infrastructure developed at LBNL. One intended application is to neutrino diffusion in core collapse supernovae.

  12. Seals Flow Code Development

    NASA Technical Reports Server (NTRS)

    1991-01-01

    In recognition of a deficiency in the current modeling capability for seals, an effort was established by NASA to develop verified computational fluid dynamic concepts, codes, and analyses for seals. The objectives were to develop advanced concepts for the design and analysis of seals, to effectively disseminate the information to potential users by way of annual workshops, and to provide experimental verification for the models and codes under a wide range of operating conditions.

  13. Robust Nonlinear Neural Codes

    NASA Astrophysics Data System (ADS)

    Yang, Qianli; Pitkow, Xaq

    2015-03-01

    Most interesting natural sensory stimuli are encoded in the brain in a form that can only be decoded nonlinearly. But despite being a core function of the brain, nonlinear population codes are rarely studied and poorly understood. Interestingly, the few existing models of nonlinear codes are inconsistent with known architectural features of the brain. In particular, these codes have information content that scales with the size of the cortical population, even if that violates the data processing inequality by exceeding the amount of information entering the sensory system. Here we provide a valid theory of nonlinear population codes by generalizing recent work on information-limiting correlations in linear population codes. Although these generalized, nonlinear information-limiting correlations bound the performance of any decoder, they also make decoding more robust to suboptimal computation, allowing many suboptimal decoders to achieve nearly the same efficiency as an optimal decoder. Although these correlations are extremely difficult to measure directly, particularly for nonlinear codes, we provide a simple, practical test by which one can use choice-related activity in small populations of neurons to determine whether decoding is suboptimal or optimal and limited by correlated noise. We conclude by describing an example computation in the vestibular system where this theory applies. QY and XP was supported by a grant from the McNair foundation.

  14. Coded source neutron imaging

    SciTech Connect

    Bingham, Philip R; Santos-Villalobos, Hector J

    2011-01-01

    Coded aperture techniques have been applied to neutron radiography to address limitations in neutron flux and resolution of neutron detectors in a system labeled coded source imaging (CSI). By coding the neutron source, a magnified imaging system is designed with small spot size aperture holes (10 and 100 m) for improved resolution beyond the detector limits and with many holes in the aperture (50% open) to account for flux losses due to the small pinhole size. An introduction to neutron radiography and coded aperture imaging is presented. A system design is developed for a CSI system with a development of equations for limitations on the system based on the coded image requirements and the neutron source characteristics of size and divergence. Simulation has been applied to the design using McStas to provide qualitative measures of performance with simulations of pinhole array objects followed by a quantitative measure through simulation of a tilted edge and calculation of the modulation transfer function (MTF) from the line spread function. MTF results for both 100um and 10um aperture hole diameters show resolutions matching the hole diameters.

  15. Error coding simulations

    NASA Technical Reports Server (NTRS)

    Noble, Viveca K.

    1993-01-01

    There are various elements such as radio frequency interference (RFI) which may induce errors in data being transmitted via a satellite communication link. When a transmission is affected by interference or other error-causing elements, the transmitted data becomes indecipherable. It becomes necessary to implement techniques to recover from these disturbances. The objective of this research is to develop software which simulates error control circuits and evaluate the performance of these modules in various bit error rate environments. The results of the evaluation provide the engineer with information which helps determine the optimal error control scheme. The Consultative Committee for Space Data Systems (CCSDS) recommends the use of Reed-Solomon (RS) and convolutional encoders and Viterbi and RS decoders for error correction. The use of forward error correction techniques greatly reduces the received signal to noise needed for a certain desired bit error rate. The use of concatenated coding, e.g. inner convolutional code and outer RS code, provides even greater coding gain. The 16-bit cyclic redundancy check (CRC) code is recommended by CCSDS for error detection.

  16. Coded source neutron imaging

    NASA Astrophysics Data System (ADS)

    Bingham, Philip; Santos-Villalobos, Hector; Tobin, Ken

    2011-03-01

    Coded aperture techniques have been applied to neutron radiography to address limitations in neutron flux and resolution of neutron detectors in a system labeled coded source imaging (CSI). By coding the neutron source, a magnified imaging system is designed with small spot size aperture holes (10 and 100μm) for improved resolution beyond the detector limits and with many holes in the aperture (50% open) to account for flux losses due to the small pinhole size. An introduction to neutron radiography and coded aperture imaging is presented. A system design is developed for a CSI system with a development of equations for limitations on the system based on the coded image requirements and the neutron source characteristics of size and divergence. Simulation has been applied to the design using McStas to provide qualitative measures of performance with simulations of pinhole array objects followed by a quantitative measure through simulation of a tilted edge and calculation of the modulation transfer function (MTF) from the line spread function. MTF results for both 100μm and 10μm aperture hole diameters show resolutions matching the hole diameters.

  17. Code query by example

    NASA Astrophysics Data System (ADS)

    Vaucouleur, Sebastien

    2011-02-01

    We introduce code query by example for customisation of evolvable software products in general and of enterprise resource planning systems (ERPs) in particular. The concept is based on an initial empirical study on practices around ERP systems. We motivate our design choices based on those empirical results, and we show how the proposed solution helps with respect to the infamous upgrade problem: the conflict between the need for customisation and the need for upgrade of ERP systems. We further show how code query by example can be used as a form of lightweight static analysis, to detect automatically potential defects in large software products. Code query by example as a form of lightweight static analysis is particularly interesting in the context of ERP systems: it is often the case that programmers working in this field are not computer science specialists but more of domain experts. Hence, they require a simple language to express custom rules.

  18. Seals Code Development Workshop

    NASA Technical Reports Server (NTRS)

    Hendricks, Robert C. (Compiler); Liang, Anita D. (Compiler)

    1996-01-01

    Seals Workshop of 1995 industrial code (INDSEAL) release include ICYL, GCYLT, IFACE, GFACE, SPIRALG, SPIRALI, DYSEAL, and KTK. The scientific code (SCISEAL) release includes conjugate heat transfer and multidomain with rotordynamic capability. Several seals and bearings codes (e.g., HYDROFLEX, HYDROTRAN, HYDROB3D, FLOWCON1, FLOWCON2) are presented and results compared. Current computational and experimental emphasis includes multiple connected cavity flows with goals of reducing parasitic losses and gas ingestion. Labyrinth seals continue to play a significant role in sealing with face, honeycomb, and new sealing concepts under investigation for advanced engine concepts in view of strict environmental constraints. The clean sheet approach to engine design is advocated with program directions and anticipated percentage SFC reductions cited. Future activities center on engine applications with coupled seal/power/secondary flow streams.

  19. SAC: Sheffield Advanced Code

    NASA Astrophysics Data System (ADS)

    Griffiths, Mike; Fedun, Viktor; Mumford, Stuart; Gent, Frederick

    2013-06-01

    The Sheffield Advanced Code (SAC) is a fully non-linear MHD code designed for simulations of linear and non-linear wave propagation in gravitationally strongly stratified magnetized plasma. It was developed primarily for the forward modelling of helioseismological processes and for the coupling processes in the solar interior, photosphere, and corona; it is built on the well-known VAC platform that allows robust simulation of the macroscopic processes in gravitationally stratified (non-)magnetized plasmas. The code has no limitations of simulation length in time imposed by complications originating from the upper boundary, nor does it require implementation of special procedures to treat the upper boundaries. SAC inherited its modular structure from VAC, thereby allowing modification to easily add new physics.

  20. Autocatalysis, information and coding.

    PubMed

    Wills, P R

    2001-01-01

    Autocatalytic self-construction in macromolecular systems requires the existence of a reflexive relationship between structural components and the functional operations they perform to synthesise themselves. The possibility of reflexivity depends on formal, semiotic features of the catalytic structure-function relationship, that is, the embedding of catalytic functions in the space of polymeric structures. Reflexivity is a semiotic property of some genetic sequences. Such sequences may serve as the basis for the evolution of coding as a result of autocatalytic self-organisation in a population of assignment catalysts. Autocatalytic selection is a mechanism whereby matter becomes differentiated in primitive biochemical systems. In the case of coding self-organisation, it corresponds to the creation of symbolic information. Prions are present-day entities whose replication through autocatalysis reflects aspects of biological semiotics less obvious than genetic coding.

  1. Code inspection instructional validation

    NASA Technical Reports Server (NTRS)

    Orr, Kay; Stancil, Shirley

    1992-01-01

    The Shuttle Data Systems Branch (SDSB) of the Flight Data Systems Division (FDSD) at Johnson Space Center contracted with Southwest Research Institute (SwRI) to validate the effectiveness of an interactive video course on the code inspection process. The purpose of this project was to determine if this course could be effective for teaching NASA analysts the process of code inspection. In addition, NASA was interested in the effectiveness of this unique type of instruction (Digital Video Interactive), for providing training on software processes. This study found the Carnegie Mellon course, 'A Cure for the Common Code', effective for teaching the process of code inspection. In addition, analysts prefer learning with this method of instruction, or this method in combination with other methods. As is, the course is definitely better than no course at all; however, findings indicate changes are needed. Following are conclusions of this study. (1) The course is instructionally effective. (2) The simulation has a positive effect on student's confidence in his ability to apply new knowledge. (3) Analysts like the course and prefer this method of training, or this method in combination with current methods of training in code inspection, over the way training is currently being conducted. (4) Analysts responded favorably to information presented through scenarios incorporating full motion video. (5) Some course content needs to be changed. (6) Some content needs to be added to the course. SwRI believes this study indicates interactive video instruction combined with simulation is effective for teaching software processes. Based on the conclusions of this study, SwRI has outlined seven options for NASA to consider. SwRI recommends the option which involves creation of new source code and data files, but uses much of the existing content and design from the current course. Although this option involves a significant software development effort, SwRI believes this option

  2. Polar Code Validation

    DTIC Science & Technology

    1989-09-30

    Unclassified 2a SECURITY CLASSiF-ICATiON AUTHORIT’Y 3 DIStRIBUTION AVAILABILITY OF REPORT N,A Approved for public release; 2o DECLASSIFICAIiON DOWNGRADING SCH DI...SUMMARY OF POLAR ACHIEVEMENTS ..... .......... 3 3 . POLAR CODE PHYSICAL MODELS ..... ............. 5 3.1 PL-ASMA Su ^"ru5 I1LS SH A...11 Structure of the Bipolar Plasma Sheath Generated by SPEAR I ... ...... 1 3 The POLAR Code Wake Model: Comparison with in Situ Observations . . 23

  3. Aeroacoustic Prediction Codes

    NASA Technical Reports Server (NTRS)

    Gliebe, P; Mani, R.; Shin, H.; Mitchell, B.; Ashford, G.; Salamah, S.; Connell, S.; Huff, Dennis (Technical Monitor)

    2000-01-01

    This report describes work performed on Contract NAS3-27720AoI 13 as part of the NASA Advanced Subsonic Transport (AST) Noise Reduction Technology effort. Computer codes were developed to provide quantitative prediction, design, and analysis capability for several aircraft engine noise sources. The objective was to provide improved, physics-based tools for exploration of noise-reduction concepts and understanding of experimental results. Methods and codes focused on fan broadband and 'buzz saw' noise and on low-emissions combustor noise and compliment work done by other contractors under the NASA AST program to develop methods and codes for fan harmonic tone noise and jet noise. The methods and codes developed and reported herein employ a wide range of approaches, from the strictly empirical to the completely computational, with some being semiempirical analytical, and/or analytical/computational. Emphasis was on capturing the essential physics while still considering method or code utility as a practical design and analysis tool for everyday engineering use. Codes and prediction models were developed for: (1) an improved empirical correlation model for fan rotor exit flow mean and turbulence properties, for use in predicting broadband noise generated by rotor exit flow turbulence interaction with downstream stator vanes: (2) fan broadband noise models for rotor and stator/turbulence interaction sources including 3D effects, noncompact-source effects. directivity modeling, and extensions to the rotor supersonic tip-speed regime; (3) fan multiple-pure-tone in-duct sound pressure prediction methodology based on computational fluid dynamics (CFD) analysis; and (4) low-emissions combustor prediction methodology and computer code based on CFD and actuator disk theory. In addition. the relative importance of dipole and quadrupole source mechanisms was studied using direct CFD source computation for a simple cascadeigust interaction problem, and an empirical combustor

  4. Securing mobile code.

    SciTech Connect

    Link, Hamilton E.; Schroeppel, Richard Crabtree; Neumann, William Douglas; Campbell, Philip LaRoche; Beaver, Cheryl Lynn; Pierson, Lyndon George; Anderson, William Erik

    2004-10-01

    If software is designed so that the software can issue functions that will move that software from one computing platform to another, then the software is said to be 'mobile'. There are two general areas of security problems associated with mobile code. The 'secure host' problem involves protecting the host from malicious mobile code. The 'secure mobile code' problem, on the other hand, involves protecting the code from malicious hosts. This report focuses on the latter problem. We have found three distinct camps of opinions regarding how to secure mobile code. There are those who believe special distributed hardware is necessary, those who believe special distributed software is necessary, and those who believe neither is necessary. We examine all three camps, with a focus on the third. In the distributed software camp we examine some commonly proposed techniques including Java, D'Agents and Flask. For the specialized hardware camp, we propose a cryptographic technique for 'tamper-proofing' code over a large portion of the software/hardware life cycle by careful modification of current architectures. This method culminates by decrypting/authenticating each instruction within a physically protected CPU, thereby protecting against subversion by malicious code. Our main focus is on the camp that believes that neither specialized software nor hardware is necessary. We concentrate on methods of code obfuscation to render an entire program or a data segment on which a program depends incomprehensible. The hope is to prevent or at least slow down reverse engineering efforts and to prevent goal-oriented attacks on the software and execution. The field of obfuscation is still in a state of development with the central problem being the lack of a basis for evaluating the protection schemes. We give a brief introduction to some of the main ideas in the field, followed by an in depth analysis of a technique called 'white-boxing'. We put forth some new attacks and improvements

  5. Coding for urologic office procedures.

    PubMed

    Dowling, Robert A; Painter, Mark

    2013-11-01

    This article summarizes current best practices for documenting, coding, and billing common office-based urologic procedures. Topics covered include general principles, basic and advanced urologic coding, creation of medical records that support compliant coding practices, bundled codes and unbundling, global periods, modifiers for procedure codes, when to bill for evaluation and management services during the same visit, coding for supplies, and laboratory and radiology procedures pertinent to urology practice. Detailed information is included for the most common urology office procedures, and suggested resources and references are provided. This information is of value to physicians, office managers, and their coding staff.

  6. Accumulate Repeat Accumulate Coded Modulation

    NASA Technical Reports Server (NTRS)

    Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

    2004-01-01

    In this paper we propose an innovative coded modulation scheme called 'Accumulate Repeat Accumulate Coded Modulation' (ARA coded modulation). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes that are combined with high level modulation. Thus at the decoder belief propagation can be used for iterative decoding of ARA coded modulation on a graph, provided a demapper transforms the received in-phase and quadrature samples to reliability of the bits.

  7. Dress Codes. Legal Brief.

    ERIC Educational Resources Information Center

    Zirkel, Perry A.

    2000-01-01

    As illustrated by two recent decisions, the courts in the past decade have demarcated wide boundaries for school officials considering dress codes, whether in the form of selective prohibitions or required uniforms. Administrators must warn the community, provide legitimate justification and reasonable clarity, and comply with state law. (MLH)

  8. Dress Codes and Uniforms.

    ERIC Educational Resources Information Center

    Lumsden, Linda; Miller, Gabriel

    2002-01-01

    Students do not always make choices that adults agree with in their choice of school dress. Dress-code issues are explored in this Research Roundup, and guidance is offered to principals seeking to maintain a positive school climate. In "Do School Uniforms Fit?" Kerry White discusses arguments for and against school uniforms and summarizes the…

  9. Building Codes and Regulations.

    ERIC Educational Resources Information Center

    Fisher, John L.

    The hazard of fire is of great concern to libraries due to combustible books and new plastics used in construction and interiors. Building codes and standards can offer architects and planners guidelines to follow but these standards should be closely monitored, updated, and researched for fire prevention. (DS)

  10. Student Dress Codes.

    ERIC Educational Resources Information Center

    Uerling, Donald F.

    School officials see a need for regulations that prohibit disruptive and inappropriate forms of expression and attire; students see these regulations as unwanted restrictions on their freedom. This paper reviews court litigation involving constitutional limitations on school authority, dress and hair codes, state law constraints, and school…

  11. Video Coding for ESL.

    ERIC Educational Resources Information Center

    King, Kevin

    1992-01-01

    Coding tasks, a valuable technique for teaching English as a Second Language, are presented that enable students to look at patterns and structures of marital communication as well as objectively evaluate the degree of happiness or distress in the marriage. (seven references) (JL)

  12. Electrical Circuit Simulation Code

    SciTech Connect

    Wix, Steven D.; Waters, Arlon J.; Shirley, David

    2001-08-09

    Massively-Parallel Electrical Circuit Simulation Code. CHILESPICE is a massively-arallel distributed-memory electrical circuit simulation tool that contains many enhanced radiation, time-based, and thermal features and models. Large scale electronic circuit simulation. Shared memory, parallel processing, enhance convergence. Sandia specific device models.

  13. Multiple trellis coded modulation

    NASA Technical Reports Server (NTRS)

    Simon, Marvin K. (Inventor); Divsalar, Dariush (Inventor)

    1990-01-01

    A technique for designing trellis codes to minimize bit error performance for a fading channel. The invention provides a criteria which may be used in the design of such codes which is significantly different from that used for average white Gaussian noise channels. The method of multiple trellis coded modulation of the present invention comprises the steps of: (a) coding b bits of input data into s intermediate outputs; (b) grouping said s intermediate outputs into k groups of s.sub.i intermediate outputs each where the summation of all s.sub.i,s is equal to s and k is equal to at least 2; (c) mapping each of said k groups of intermediate outputs into one of a plurality of symbols in accordance with a plurality of modulation schemes, one for each group such that the first group is mapped in accordance with a first modulation scheme and the second group is mapped in accordance with a second modulation scheme; and (d) outputting each of said symbols to provide k output symbols for each b bits of input data.

  14. Coding Theory and Projective Spaces

    NASA Astrophysics Data System (ADS)

    Silberstein, Natalia

    2008-05-01

    The projective space of order n over a finite field F_q is a set of all subspaces of the vector space F_q^{n}. In this work, we consider error-correcting codes in the projective space, focusing mainly on constant dimension codes. We start with the different representations of subspaces in the projective space. These representations involve matrices in reduced row echelon form, associated binary vectors, and Ferrers diagrams. Based on these representations, we provide a new formula for the computation of the distance between any two subspaces in the projective space. We examine lifted maximum rank distance (MRD) codes, which are nearly optimal constant dimension codes. We prove that a lifted MRD code can be represented in such a way that it forms a block design known as a transversal design. The incidence matrix of the transversal design derived from a lifted MRD code can be viewed as a parity-check matrix of a linear code in the Hamming space. We find the properties of these codes which can be viewed also as LDPC codes. We present new bounds and constructions for constant dimension codes. First, we present a multilevel construction for constant dimension codes, which can be viewed as a generalization of a lifted MRD codes construction. This construction is based on a new type of rank-metric codes, called Ferrers diagram rank-metric codes. Then we derive upper bounds on the size of constant dimension codes which contain the lifted MRD code, and provide a construction for two families of codes, that attain these upper bounds. We generalize the well-known concept of a punctured code for a code in the projective space to obtain large codes which are not constant dimension. We present efficient enumerative encoding and decoding techniques for the Grassmannian. Finally we describe a search method for constant dimension lexicodes.

  15. Microarray hybridization analysis of light-dependent gene expression in Penicillium chrysogenum identifies bZIP transcription factor PcAtfA.

    PubMed

    Wolfers, Simon; Kamerewerd, Jens; Nowrousian, Minou; Sigl, Claudia; Zadra, Ivo; Kürnsteiner, Hubert; Kück, Ulrich; Bloemendal, Sandra

    2015-04-01

    The fungal velvet complex is a light-dependent master regulator of secondary metabolism and development in the major penicillin producer, Penicillium chrysogenum. However, the light-dependent mechanism is unclear. To identify velvet-dependent transcriptional regulators that show light-regulated expression, we performed microarray hybridizations with RNA isolated from P. chrysogenum ΔPcku70 cultures grown under 13 different long-term, light-dependent growth conditions. We compared these expression data to data from two velvet complex deletion mutants; one lacked a subunit of the velvet complex (ΔPcvelA), and the other lacked a velvet-associated protein (ΔPclaeA). We sought to identify genes that were up-regulated in light, but down-regulated in ΔPcvelA and ΔPclaeA. We identified 148 co-regulated genes that displayed this regulatory pattern. In silico analyses of the co-regulated genes identified six proteins with fungal-specific transcription factor domains. Among these, we selected the bZIP transcription factor, PcAtfA, for functional characterization in deletion and complementation strains. Our data clearly indicates that PcAtfA governs spore germination. This comparative analysis of different microarray hybridization data sets provided results that may be useful for identifying genes for future functional analyses.

  16. Roles of HTLV-1 basic Zip Factor (HBZ) in Viral Chronicity and Leukemic Transformation. Potential New Therapeutic Approaches to Prevent and Treat HTLV-1-Related Diseases.

    PubMed

    Mesnard, Jean-Michel; Barbeau, Benoit; Césaire, Raymond; Péloponèse, Jean-Marie

    2015-12-09

    More than thirty years have passed since human T-cell leukemia virus type 1 (HTLV-1) was described as the first retrovirus to be the causative agent of a human cancer, adult T-cell leukemia (ATL), but the precise mechanism behind HTLV-1 pathogenesis still remains elusive. For more than two decades, the transforming ability of HTLV-1 has been exclusively associated to the viral transactivator Tax. Thirteen year ago, we first reported that the minus strand of HTLV-1 encoded for a basic Zip factor factor (HBZ), and since then several teams have underscored the importance of this antisense viral protein for the maintenance of a chronic infection and the proliferation of infected cells. More recently, we as well as others have demonstrated that HBZ has the potential to transform cells both in vitro and in vivo. In this review, we focus on the latest progress in our understanding of HBZ functions in chronicity and cellular transformation. We will discuss the involvement of this paradigm shift of HTLV-1 research on new therapeutic approaches to treat HTLV-1-related human diseases.

  17. AtTGA4, a bZIP transcription factor, confers drought resistance by enhancing nitrate transport and assimilation in Arabidopsis thaliana.

    PubMed

    Zhong, Li; Chen, Dandan; Min, Donghong; Li, Weiwei; Xu, Zhaoshi; Zhou, Yongbin; Li, Liancheng; Chen, Ming; Ma, Youzhi

    2015-02-13

    To cope with environmental stress caused by global climate change and excessive nitrogen application, it is important to improve water and nitrogen use efficiencies in crop plants. It has been reported that higher nitrogen uptake could alleviate the damaging impact of drought stress. However, there is scant evidence to explain how nitrogen uptake affects drought resistance. In this study we observed that bZIP transcription factor AtTGA4 (TGACG motif-binding factor 4) was induced by both drought and low nitrogen stresses, and that overexpression of AtTGA4 simultaneously improved drought resistance and reduced nitrogen starvation in Arabidopsis. Following drought stress there were higher nitrogen and proline contents in transgenic AtTGA4 plants than in wild type controls, and activity of the key enzyme nitrite reductase (NIR) involved in nitrate assimilation processes was also higher. Expressions of the high-affinity nitrate transporter genes NRT2.1 and NRT2.2 and nitrate reductase genes NIA1 and NIA2 in transgenic plants were all higher than in wild type indicating that higher levels of nitrate transport and assimilation activity contributed to enhanced drought resistance of AtTGA4 transgenic plants. Thus genetic transformation with AtTGA4 may provide a new approach to simultaneously improve crop tolerance to drought and low nitrogen stresses.

  18. Modeling Associations between Principals’ Reported Indoor Environmental Quality and Students’ Self-Reported Respiratory Health Outcomes Using GLMM and ZIP Models

    PubMed Central

    Toyinbo, Oluyemi; Matilainen, Markus; Turunen, Mari; Putus, Tuula; Shaughnessy, Richard; Haverinen-Shaughnessy, Ulla

    2016-01-01

    Background: The aim of this paper was to examine associations between school building characteristics, indoor environmental quality (IEQ), and health responses using questionnaire data from both school principals and students. Methods: From 334 randomly sampled schools, 4248 sixth grade students from 297 schools participated in a questionnaire. From these schools, 134 principals returned questionnaires concerning 51 IEQ related questions of their school. Generalized linear mixed models (GLMM) were used to study the associations between IEQ indicators and existence of self-reported upper respiratory symptoms, while hierarchical Zero Inflated Poisson (ZIP)—models were used to model the number of symptoms. Results: Significant associations were established between existence of upper respiratory symptoms and unsatisfactory classroom temperature during the heating season (ORs 1.45 for too hot and cold, and 1.27 for too cold as compared to satisfactory temperature) and dampness or moisture damage during the year 2006–2007 (OR: 1.80 as compared to no moisture damage), respectively. The number of upper respiratory symptoms was significantly associated with inadequate ventilation and dampness or moisture damage. A higher number of missed school days due to respiratory infections were reported in schools with inadequate ventilation (RR: 1.16). Conclusions: The school level IEQ indicator variables described in this paper could explain a relatively large part of the school level variation observed in the self-reported upper respiratory symptoms and missed school days due to respiratory infections among students. PMID:27043595

  19. High MS-compatibility of silver nitrate-stained protein spots from 2-DE gels using ZipPlates and AnchorChips for successful protein identification.

    PubMed

    Nebrich, Grit; Herrmann, Marion; Sagi, Dijana; Klose, Joachim; Giavalisco, Patrick

    2007-05-01

    The availability of easy-to-handle, sensitive, and cost-effective protein staining protocols for 2-DE, in conjunction with a high compatibility for subsequent MS analysis, is still a prerequisite for successful proteome research. In this article we describe a quick and easy-to-use methodological protocol based on sensitive, homogeneous, and MS-compatible silver nitrate protein staining, in combination with an in-gel digestion, employing the Millipore 96-well ZipPlate system for peptide preparation. The improved quality and MS compatibility of the generated protein digests, as compared to the otherwise weakly MS-compatible silver nitrate staining, were evaluated on real tissue samples by analyzing 192 Coomassie-stained protein spots against their counterparts from a silver-stained 2-DE gel. Furthermore, the applicability of the experimental setup was evaluated and demonstrated by the analysis of a large-scale MALDI-TOF MS experiment, in which we analyzed an additional ~1000 protein spots from 2-DE gels from mouse liver and mouse brain tissue.

  20. Binary coding for hyperspectral imagery

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Chang, Chein-I.; Chang, Chein-Chi; Lin, Chinsu

    2004-10-01

    Binary coding is one of simplest ways to characterize spectral features. One commonly used method is a binary coding-based image software system, called Spectral Analysis Manager (SPAM) for remotely sensed imagery developed by Mazer et al. For a given spectral signature, the SPAM calculates its spectral mean and inter-band spectral difference and uses them as thresholds to generate a binary code word for this particular spectral signature. Such coding scheme is generally effective and also very simple to implement. This paper revisits the SPAM and further develops three new SPAM-based binary coding methods, called equal probability partition (EPP) binary coding, halfway partition (HP) binary coding and median partition (MP) binary coding. These three binary coding methods along with the SPAM well be evaluated for spectral discrimination and identification. In doing so, a new criterion, called a posteriori discrimination probability (APDP) is also introduced for performance measure.

  1. Sinusoidal transform coding

    NASA Technical Reports Server (NTRS)

    Mcaulay, Robert J.; Quatieri, Thomas F.

    1988-01-01

    It has been shown that an analysis/synthesis system based on a sinusoidal representation of speech leads to synthetic speech that is essentially perceptually indistinguishable from the original. Strategies for coding the amplitudes, frequencies and phases of the sine waves have been developed that have led to a multirate coder operating at rates from 2400 to 9600 bps. The encoded speech is highly intelligible at all rates with a uniformly improving quality as the data rate is increased. A real-time fixed-point implementation has been developed using two ADSP2100 DSP chips. The methods used for coding and quantizing the sine-wave parameters for operation at the various frame rates are described.

  2. WHPA Code available

    NASA Astrophysics Data System (ADS)

    The Wellhead Protection Area code is now available for distribution by the International Ground Water Modeling Center in Indianapolis, Ind. The WHPA code is a modular, semianalytical, groundwater flow model developed for the U.S. Environmental Protection Agency, Office of Ground Water Protection, designed to assist state and local technical staff with the task of Wellhead Protection Area (WHPA) delineation. A complete news item appeared in Eos, May 1, 1990, p. 690.The model consists of four independent, semianalytical modules that may be used to identify the areal extent of groundwater contribution to one or multiple pumping wells. One module is a general particle tracking program that may be used as a post-processor for two-dimensional, numerical models of groundwater flow. One module incorporates a Monte Carlo approach to investigate the effects of uncertain input parameters on capture zones. Multiple pumping and injection wells may be present and barrier or stream boundary conditions may be investigated.

  3. WHPA Code available

    NASA Astrophysics Data System (ADS)

    The Wellhead Protection Area (WHPA) code is now available for distribution by the International Ground Water Modeling Center in Indianapolis, Ind. The WHPA code is a modular, semi-analytical, groundwater flow model developed for the U.S. Environmental Protection Agency, Office of Ground Water Protection. It is designed to assist state and local technical staff with the task of WHPA delineation.The model consists of four independent, semi-analytical modules that may be used to identify the areal extent of groundwater contribution to one or multiple pumping wells. One module is a general particle tracking program that may be used as a post-processor for two-dimensional, numerical models of groundwater flow. One module incorporates a Monte Carlo approach to investigate the effects of uncertain input parameters on capture zones. Multiple pumping and injection wells may be present and barrier or stream boundary conditions may be investigated.

  4. Confocal coded aperture imaging

    DOEpatents

    Tobin, Jr., Kenneth William; Thomas, Jr., Clarence E.

    2001-01-01

    A method for imaging a target volume comprises the steps of: radiating a small bandwidth of energy toward the target volume; focusing the small bandwidth of energy into a beam; moving the target volume through a plurality of positions within the focused beam; collecting a beam of energy scattered from the target volume with a non-diffractive confocal coded aperture; generating a shadow image of said aperture from every point source of radiation in the target volume; and, reconstructing the shadow image into a 3-dimensional image of the every point source by mathematically correlating the shadow image with a digital or analog version of the coded aperture. The method can comprise the step of collecting the beam of energy scattered from the target volume with a Fresnel zone plate.

  5. HYCOM Code Development

    DTIC Science & Technology

    2003-02-10

    HYCOM code development Alan J. Wallcraft Naval Research Laboratory 2003 Layered Ocean Model Users’ Workshop February 10, 2003 Report Documentation...unlimited 13. SUPPLEMENTARY NOTES Layered Ocean Modeling Workshop (LOM 2003), Miami, FL, Feb 2003 14. ABSTRACT 15. SUBJECT TERMS 16. SECURITY...Kraus-Turner mixed-layer Æ Energy-Loan (passive) ice model Æ High frequency atmospheric forcing Æ New I/O scheme (.a and .b files) Æ Scalability via

  6. Reeds computer code

    NASA Technical Reports Server (NTRS)

    Bjork, C.

    1981-01-01

    The REEDS (rocket exhaust effluent diffusion single layer) computer code is used for the estimation of certain rocket exhaust effluent concentrations and dosages and their distributions near the Earth's surface following a rocket launch event. Output from REEDS is used in producing near real time air quality and environmental assessments of the effects of certain potentially harmful effluents, namely HCl, Al2O3, CO, and NO.

  7. Trajectory Code Studies, 1987

    SciTech Connect

    Poukey, J.W.

    1988-01-01

    The trajectory code TRAJ has been used extensively to study nonimmersed foilless electron diodes. The basic goal of the research is to design low-emittance injectors for electron linacs and propagation experiments. Systems studied during 1987 include Delphi, Recirc, and Troll. We also discuss a partly successful attempt to extend the same techniques to high currents (tens of kA). 7 refs., 30 figs.

  8. The PHARO Code.

    DTIC Science & Technology

    1981-11-24

    n.cet..ary ad Identfy by block nutrb.) Visible radiation Sensors Infrared radiation Line and band transitions Isophots High altitude nuclear data...radiation (watts sr) in arbitrary wavelength intervals is determined. The results are a series of " isophot " plots for rbitrariiy placed cameras or sensors...Section II. The output of the PHARO code consists of contour plots of radiative intensity (watts/cm ster) or " isophot " plots for arbitrarily placed sensors

  9. The Phantom SPH code

    NASA Astrophysics Data System (ADS)

    Price, Daniel; Wurster, James; Nixon, Chris

    2016-05-01

    I will present the capabilities of the Phantom SPH code for global simulations of dust and gas in protoplanetary discs. I will present our new algorithms for simulating both small and large grains in discs, as well as our progress towards simulating evolving grain populations and coupling with radiation. Finally, I will discuss our recent applications to HL Tau and the physics of dust gap opening.

  10. Status of MARS Code

    SciTech Connect

    N.V. Mokhov

    2003-04-09

    Status and recent developments of the MARS 14 Monte Carlo code system for simulation of hadronic and electromagnetic cascades in shielding, accelerator and detector components in the energy range from a fraction of an electronvolt up to 100 TeV are described. these include physics models both in strong and electromagnetic interaction sectors, variance reduction techniques, residual dose, geometry, tracking, histograming. MAD-MARS Beam Line Build and Graphical-User Interface.

  11. Orthopedics coding and funding.

    PubMed

    Baron, S; Duclos, C; Thoreux, P

    2014-02-01

    The French tarification à l'activité (T2A) prospective payment system is a financial system in which a health-care institution's resources are based on performed activity. Activity is described via the PMSI medical information system (programme de médicalisation du système d'information). The PMSI classifies hospital cases by clinical and economic categories known as diagnosis-related groups (DRG), each with an associated price tag. Coding a hospital case involves giving as realistic a description as possible so as to categorize it in the right DRG and thus ensure appropriate payment. For this, it is essential to understand what determines the pricing of inpatient stay: namely, the code for the surgical procedure, the patient's principal diagnosis (reason for admission), codes for comorbidities (everything that adds to management burden), and the management of the length of inpatient stay. The PMSI is used to analyze the institution's activity and dynamism: change on previous year, relation to target, and comparison with competing institutions based on indicators such as the mean length of stay performance indicator (MLS PI). The T2A system improves overall care efficiency. Quality of care, however, is not presently taken account of in the payment made to the institution, as there are no indicators for this; work needs to be done on this topic.

  12. MELCOR computer code manuals

    SciTech Connect

    Summers, R.M.; Cole, R.K. Jr.; Smith, R.C.; Stuart, D.S.; Thompson, S.L.; Hodge, S.A.; Hyman, C.R.; Sanders, R.L.

    1995-03-01

    MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the U.S. Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include: thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, and combustion; fission product release and transport; and the impact of engineered safety features on thermal-hydraulic and radionuclide behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications. This publication of the MELCOR computer code manuals corresponds to MELCOR 1.8.3, released to users in August, 1994. Volume 1 contains a primer that describes MELCOR`s phenomenological scope, organization (by package), and documentation. The remainder of Volume 1 contains the MELCOR Users Guides, which provide the input instructions and guidelines for each package. Volume 2 contains the MELCOR Reference Manuals, which describe the phenomenological models that have been implemented in each package.

  13. Bar coded retroreflective target

    DOEpatents

    Vann, Charles S.

    2000-01-01

    This small, inexpensive, non-contact laser sensor can detect the location of a retroreflective target in a relatively large volume and up to six degrees of position. The tracker's laser beam is formed into a plane of light which is swept across the space of interest. When the beam illuminates the retroreflector, some of the light returns to the tracker. The intensity, angle, and time of the return beam is measured to calculate the three dimensional location of the target. With three retroreflectors on the target, the locations of three points on the target are measured, enabling the calculation of all six degrees of target position. Until now, devices for three-dimensional tracking of objects in a large volume have been heavy, large, and very expensive. Because of the simplicity and unique characteristics of this tracker, it is capable of three-dimensional tracking of one to several objects in a large volume, yet it is compact, light-weight, and relatively inexpensive. Alternatively, a tracker produces a diverging laser beam which is directed towards a fixed position, and senses when a retroreflective target enters the fixed field of view. An optically bar coded target can be read by the tracker to provide information about the target. The target can be formed of a ball lens with a bar code on one end. As the target moves through the field, the ball lens causes the laser beam to scan across the bar code.

  14. Suboptimum decoding of block codes

    NASA Technical Reports Server (NTRS)

    Lin, Shu; Kasami, Tadao

    1991-01-01

    This paper investigates a class of decomposable codes, their distance and structural properties. it is shown that this class includes several classes of well known and efficient codes as subclasses. Several methods for constructing decomposable codes or decomposing codes are presented. A two-stage soft decision decoding scheme for decomposable codes, their translates or unions of translates is devised. This two-stage soft-decision decoding is suboptimum, and provides an excellent trade-off between the error performance and decoding complexity for codes of moderate and long block length.

  15. Preliminary Assessment of Turbomachinery Codes

    NASA Technical Reports Server (NTRS)

    Mazumder, Quamrul H.

    2007-01-01

    This report assesses different CFD codes developed and currently being used at Glenn Research Center to predict turbomachinery fluid flow and heat transfer behavior. This report will consider the following codes: APNASA, TURBO, GlennHT, H3D, and SWIFT. Each code will be described separately in the following section with their current modeling capabilities, level of validation, pre/post processing, and future development and validation requirements. This report addresses only previously published and validations of the codes. However, the codes have been further developed to extend the capabilities of the codes.

  16. Construction of new quantum MDS codes derived from constacyclic codes

    NASA Astrophysics Data System (ADS)

    Taneja, Divya; Gupta, Manish; Narula, Rajesh; Bhullar, Jaskaran

    Obtaining quantum maximum distance separable (MDS) codes from dual containing classical constacyclic codes using Hermitian construction have paved a path to undertake the challenges related to such constructions. Using the same technique, some new parameters of quantum MDS codes have been constructed here. One set of parameters obtained in this paper has achieved much larger distance than work done earlier. The remaining constructed parameters of quantum MDS codes have large minimum distance and were not explored yet.

  17. Convolutional coding techniques for data protection

    NASA Technical Reports Server (NTRS)

    Massey, J. L.

    1975-01-01

    Results of research on the use of convolutional codes in data communications are presented. Convolutional coding fundamentals are discussed along with modulation and coding interaction. Concatenated coding systems and data compression with convolutional codes are described.

  18. Combinatorial neural codes from a mathematical coding theory perspective.

    PubMed

    Curto, Carina; Itskov, Vladimir; Morrison, Katherine; Roth, Zachary; Walker, Judy L

    2013-07-01

    Shannon's seminal 1948 work gave rise to two distinct areas of research: information theory and mathematical coding theory. While information theory has had a strong influence on theoretical neuroscience, ideas from mathematical coding theory have received considerably less attention. Here we take a new look at combinatorial neural codes from a mathematical coding theory perspective, examining the error correction capabilities of familiar receptive field codes (RF codes). We find, perhaps surprisingly, that the high levels of redundancy present in these codes do not support accurate error correction, although the error-correcting performance of receptive field codes catches up to that of random comparison codes when a small tolerance to error is introduced. However, receptive field codes are good at reflecting distances between represented stimuli, while the random comparison codes are not. We suggest that a compromise in error-correcting capability may be a necessary price to pay for a neural code whose structure serves not only error correction, but must also reflect relationships between stimuli.

  19. New quantum MDS-convolutional codes derived from constacyclic codes

    NASA Astrophysics Data System (ADS)

    Li, Fengwei; Yue, Qin

    2015-12-01

    In this paper, we utilize a family of Hermitian dual-containing constacyclic codes to construct classical and quantum MDS convolutional codes. Our classical and quantum convolutional codes are optimal in the sense that they attain the classical (quantum) generalized Singleton bound.

  20. A class of constacyclic BCH codes and new quantum codes

    NASA Astrophysics Data System (ADS)

    liu, Yang; Li, Ruihu; Lv, Liangdong; Ma, Yuena

    2017-03-01

    Constacyclic BCH codes have been widely studied in the literature and have been used to construct quantum codes in latest years. However, for the class of quantum codes of length n=q^{2m}+1 over F_{q^2} with q an odd prime power, there are only the ones of distance δ ≤ 2q^2 are obtained in the literature. In this paper, by a detailed analysis of properties of q2-ary cyclotomic cosets, maximum designed distance δ _{max} of a class of Hermitian dual-containing constacyclic BCH codes with length n=q^{2m}+1 are determined, this class of constacyclic codes has some characteristic analog to that of primitive BCH codes over F_{q^2}. Then we can obtain a sequence of dual-containing constacyclic codes of designed distances 2q^2<δ ≤ δ _{max}. Consequently, new quantum codes with distance d > 2q^2 can be constructed from these dual-containing codes via Hermitian Construction. These newly obtained quantum codes have better code rate compared with those constructed from primitive BCH codes.

  1. Summary of 1990 Code Conference

    SciTech Connect

    Cooper, R.K.; Chan, Kwok-Chi D.

    1990-01-01

    The Conference on Codes and the Linear Accelerator Community was held in Los Alamos in January 1990, and had approximately 100 participants. This conference was the second in a series which has as its goal the exchange of information about codes and code practices among those writing and actually using these codes for the design and analysis of linear accelerators and their components. The first conference was held in San Diego in January 1988, and concentrated on beam dynamics codes and Maxwell solvers. This most recent conference concentrated on 3-D codes and techniques to handle the large amounts of data required for three-dimensional problems. In addition to descriptions of codes, their algorithms and implementations, there were a number of paper describing the use of many of the codes. Proceedings of both these conferences are available. 3 refs., 2 tabs.

  2. Chemical Laser Computer Code Survey,

    DTIC Science & Technology

    1980-12-01

    DOCUMENTATION: Resonator Geometry Synthesis Code Requi rement NV. L. Gamiz); Incorporate General Resonator into Ray Trace Code (W. H. Southwell... Synthesis Code Development (L. R. Stidhm) CATEGRY ATIUEOPTICS KINETICS GASOYNAM41CS None * None *iNone J.LEVEL Simrple Fabry Perot Simple SaturatedGt... Synthesis Co2de Require- ment (V L. ami l ncor~orate General Resonatorn into Ray Trace Code (W. H. Southwel) Srace Optimization Algorithms and Equations (W

  3. Energy Codes and Standards: Facilities

    SciTech Connect

    Bartlett, Rosemarie; Halverson, Mark A.; Shankle, Diana L.

    2007-01-01

    Energy codes and standards play a vital role in the marketplace by setting minimum requirements for energy-efficient design and construction. They outline uniform requirements for new buildings as well as additions and renovations. This article covers basic knowledge of codes and standards; development processes of each; adoption, implementation, and enforcement of energy codes and standards; and voluntary energy efficiency programs.

  4. Coding Issues in Grounded Theory

    ERIC Educational Resources Information Center

    Moghaddam, Alireza

    2006-01-01

    This paper discusses grounded theory as one of the qualitative research designs. It describes how grounded theory generates from data. Three phases of grounded theory--open coding, axial coding, and selective coding--are discussed, along with some of the issues which are the source of debate among grounded theorists, especially between its…

  5. IRIG Serial Time Code Formats

    DTIC Science & Technology

    2016-08-01

    TELECOMMUNICATIONS AND TIMING GROUP IRIG STANDARD 200-16 IRIG SERIAL TIME CODE FORMATS DISTRIBUTION A: APPROVED FOR...ARNOLD ENGINEERING DEVELOPMENT COMPLEX NATIONAL AERONAUTICS AND SPACE ADMINISTRATION This page intentionally left blank. IRIG SERIAL TIME CODE ...Serial Time Code Formats, RCC 200-16, August 2016 v Table of Contents Preface

  6. Coding Major Fields of Study.

    ERIC Educational Resources Information Center

    Bobbitt, L. G.; Carroll, C. D.

    The National Center for Education Statistics conducts surveys which require the coding of the respondent's major field of study. This paper presents a new system for the coding of major field of study. It operates on-line i a Computer Assisted Telephone Interview (CATI) environment and allows conversational checks to verify coding directly from…

  7. Improved code-tracking loop

    NASA Technical Reports Server (NTRS)

    Laflame, D. T.

    1980-01-01

    Delay-locked loop tracks pseudonoise codes without introducing dc timing errors, because it is not sensitive to gain imbalance between signal processing arms. "Early" and "late" reference codes pass in combined form through both arms, and each arm acts on both codes. Circuit accomodates 1 dB weaker input signals with tracking ability equal to that of tau-dither loops.

  8. Validation of the BEPLATE code

    SciTech Connect

    Giles, G.E.; Bullock, J.S.

    1997-11-01

    The electroforming simulation code BEPLATE (Boundary Element-PLATE) has been developed and validated for specific applications at Oak Ridge. New areas of application are opening up and more validations are being performed. This paper reports the validation experience of the BEPLATE code on two types of electroforms and describes some recent applications of the code.

  9. Authorship Attribution of Source Code

    ERIC Educational Resources Information Center

    Tennyson, Matthew F.

    2013-01-01

    Authorship attribution of source code is the task of deciding who wrote a program, given its source code. Applications include software forensics, plagiarism detection, and determining software ownership. A number of methods for the authorship attribution of source code have been presented in the past. A review of those existing methods is…

  10. Ptolemy Coding Style

    DTIC Science & Technology

    2014-09-05

    COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE Ptolemy Coding Style 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...lisp module for GNU Emacs that has appropriate indenting rules. This file works well with Emacs under both Unix and Windows. • testsuite/ptspell is a...Unix. It is much more liberal that the commonly used “GPL” or “ GNU Public License,” which encumbers the software and derivative works with the

  11. Structured error recovery for code-word-stabilized quantum codes

    SciTech Connect

    Li Yunfan; Dumer, Ilya; Grassl, Markus; Pryadko, Leonid P.

    2010-05-15

    Code-word-stabilized (CWS) codes are, in general, nonadditive quantum codes that can correct errors by an exhaustive search of different error patterns, similar to the way that we decode classical nonlinear codes. For an n-qubit quantum code correcting errors on up to t qubits, this brute-force approach consecutively tests different errors of weight t or less and employs a separate n-qubit measurement in each test. In this article, we suggest an error grouping technique that allows one to simultaneously test large groups of errors in a single measurement. This structured error recovery technique exponentially reduces the number of measurements by about 3{sup t} times. While it still leaves exponentially many measurements for a generic CWS code, the technique is equivalent to syndrome-based recovery for the special case of additive CWS codes.

  12. Structured error recovery for code-word-stabilized quantum codes

    NASA Astrophysics Data System (ADS)

    Li, Yunfan; Dumer, Ilya; Grassl, Markus; Pryadko, Leonid P.

    2010-05-01

    Code-word-stabilized (CWS) codes are, in general, nonadditive quantum codes that can correct errors by an exhaustive search of different error patterns, similar to the way that we decode classical nonlinear codes. For an n-qubit quantum code correcting errors on up to t qubits, this brute-force approach consecutively tests different errors of weight t or less and employs a separate n-qubit measurement in each test. In this article, we suggest an error grouping technique that allows one to simultaneously test large groups of errors in a single measurement. This structured error recovery technique exponentially reduces the number of measurements by about 3t times. While it still leaves exponentially many measurements for a generic CWS code, the technique is equivalent to syndrome-based recovery for the special case of additive CWS codes.

  13. Low Density Parity Check Codes: Bandwidth Efficient Channel Coding

    NASA Technical Reports Server (NTRS)

    Fong, Wai; Lin, Shu; Maki, Gary; Yeh, Pen-Shu

    2003-01-01

    Low Density Parity Check (LDPC) Codes provide near-Shannon Capacity performance for NASA Missions. These codes have high coding rates R=0.82 and 0.875 with moderate code lengths, n=4096 and 8176. Their decoders have inherently parallel structures which allows for high-speed implementation. Two codes based on Euclidean Geometry (EG) were selected for flight ASIC implementation. These codes are cyclic and quasi-cyclic in nature and therefore have a simple encoder structure. This results in power and size benefits. These codes also have a large minimum distance as much as d,,, = 65 giving them powerful error correcting capabilities and error floors less than lo- BER. This paper will present development of the LDPC flight encoder and decoder, its applications and status.

  14. New quantum codes constructed from quaternary BCH codes

    NASA Astrophysics Data System (ADS)

    Xu, Gen; Li, Ruihu; Guo, Luobin; Ma, Yuena

    2016-10-01

    In this paper, we firstly study construction of new quantum error-correcting codes (QECCs) from three classes of quaternary imprimitive BCH codes. As a result, the improved maximal designed distance of these narrow-sense imprimitive Hermitian dual-containing quaternary BCH codes are determined to be much larger than the result given according to Aly et al. (IEEE Trans Inf Theory 53:1183-1188, 2007) for each different code length. Thus, families of new QECCs are newly obtained, and the constructed QECCs have larger distance than those in the previous literature. Secondly, we apply a combinatorial construction to the imprimitive BCH codes with their corresponding primitive counterpart and construct many new linear quantum codes with good parameters, some of which have parameters exceeding the finite Gilbert-Varshamov bound for linear quantum codes.

  15. Quantum Codes From Cyclic Codes Over The Ring R2

    NASA Astrophysics Data System (ADS)

    Altinel, Alev; Güzeltepe, Murat

    2016-10-01

    Let R 2 denotes the ring F 2 + μF 2 + υ2 + μυF 2 + wF 2 + μwF 2 + υwF 2 + μυwF2. In this study, we construct quantum codes from cyclic codes over the ring R2, for arbitrary length n, with the restrictions μ2 = 0, υ2 = 0, w 2 = 0, μυ = υμ, μw = wμ, υw = wυ and μ (υw) = (μυ) w. Also, we give a necessary and sufficient condition for cyclic codes over R2 that contains its dual. As a final point, we obtain the parameters of quantum error-correcting codes from cyclic codes over R2 and we give an example of quantum error-correcting codes form cyclic codes over R 2.

  16. Measuring Diagnoses: ICD Code Accuracy

    PubMed Central

    O'Malley, Kimberly J; Cook, Karon F; Price, Matt D; Wildes, Kimberly Raiford; Hurdle, John F; Ashton, Carol M

    2005-01-01

    Objective To examine potential sources of errors at each step of the described inpatient International Classification of Diseases (ICD) coding process. Data Sources/Study Setting The use of disease codes from the ICD has expanded from classifying morbidity and mortality information for statistical purposes to diverse sets of applications in research, health care policy, and health care finance. By describing a brief history of ICD coding, detailing the process for assigning codes, identifying where errors can be introduced into the process, and reviewing methods for examining code accuracy, we help code users more systematically evaluate code accuracy for their particular applications. Study Design/Methods We summarize the inpatient ICD diagnostic coding process from patient admission to diagnostic code assignment. We examine potential sources of errors at each step and offer code users a tool for systematically evaluating code accuracy. Principle Findings Main error sources along the “patient trajectory” include amount and quality of information at admission, communication among patients and providers, the clinician's knowledge and experience with the illness, and the clinician's attention to detail. Main error sources along the “paper trail” include variance in the electronic and written records, coder training and experience, facility quality-control efforts, and unintentional and intentional coder errors, such as misspecification, unbundling, and upcoding. Conclusions By clearly specifying the code assignment process and heightening their awareness of potential error sources, code users can better evaluate the applicability and limitations of codes for their particular situations. ICD codes can then be used in the most appropriate ways. PMID:16178999

  17. Genetic code for sine

    NASA Astrophysics Data System (ADS)

    Abdullah, Alyasa Gan; Wah, Yap Bee

    2015-02-01

    The computation of the approximate values of the trigonometric sines was discovered by Bhaskara I (c. 600-c.680), a seventh century Indian mathematician and is known as the Bjaskara's I's sine approximation formula. The formula is given in his treatise titled Mahabhaskariya. In the 14th century, Madhava of Sangamagrama, a Kerala mathematician astronomer constructed the table of trigonometric sines of various angles. Madhava's table gives the measure of angles in arcminutes, arcseconds and sixtieths of an arcsecond. The search for more accurate formulas led to the discovery of the power series expansion by Madhava of Sangamagrama (c.1350-c. 1425), the founder of the Kerala school of astronomy and mathematics. In 1715, the Taylor series was introduced by Brook Taylor an English mathematician. If the Taylor series is centered at zero, it is called a Maclaurin series, named after the Scottish mathematician Colin Maclaurin. Some of the important Maclaurin series expansions include trigonometric functions. This paper introduces the genetic code of the sine of an angle without using power series expansion. The genetic code using square root approach reveals the pattern in the signs (plus, minus) and sequence of numbers in the sine of an angle. The square root approach complements the Pythagoras method, provides a better understanding of calculating an angle and will be useful for teaching the concepts of angles in trigonometry.

  18. FAST GYROSYNCHROTRON CODES

    SciTech Connect

    Fleishman, Gregory D.; Kuznetsov, Alexey A.

    2010-10-01

    Radiation produced by charged particles gyrating in a magnetic field is highly significant in the astrophysics context. Persistently increasing resolution of astrophysical observations calls for corresponding three-dimensional modeling of the radiation. However, available exact equations are prohibitively slow in computing a comprehensive table of high-resolution models required for many practical applications. To remedy this situation, we develop approximate gyrosynchrotron (GS) codes capable of quickly calculating the GS emission (in non-quantum regime) from both isotropic and anisotropic electron distributions in non-relativistic, mildly relativistic, and ultrarelativistic energy domains applicable throughout a broad range of source parameters including dense or tenuous plasmas and weak or strong magnetic fields. The computation time is reduced by several orders of magnitude compared with the exact GS algorithm. The new algorithm performance can gradually be adjusted to the user's needs depending on whether precision or computation speed is to be optimized for a given model. The codes are made available for users as a supplement to this paper.

  19. A novel bZIP transcription factor ClrC positively regulates multiple stress responses, conidiation and cellulase expression in Penicillium oxalicum.

    PubMed

    Lei, Yunfeng; Liu, Guodong; Yao, Guangshan; Li, Zhonghai; Qin, Yuqi; Qu, Yinbo

    2016-06-01

    Cellulase production in filamentous fungi is largely regulated at the transcriptional level, and several transcription factors have been reported to be involved in this process. In this study, we identified ClrC, a novel transcription factor in cellulase production in Penicillium oxalicum. ClrC and its orthologs have a highly conserved basic leucine zipper (bZIP) DNA binding domain, and their biological functions have not been explored. Deletion of clrC resulted in pleiotropic effects, including altered growth, reduced conidiation and increased sensitivity to oxidative and cell wall stresses. In particular, the clrC deletion mutant ΔclrC showed 46.1% ± 8.1% and 58.0% ± 8.7% decreases in production of filter paper enzyme and xylanase activities in cellulose medium, respectively. In contrast, 57.4% ± 10.0% and 70.9% ± 19.4% increased production of filter paper enzyme, and xylanase was observed in the clrC overexpressing strain, respectively. The transcription levels of major cellulase genes, as well as two cellulase transcriptional activator genes, clrB and xlnR, were significantly downregulated in ΔclrC, but substantially upregulated in clrC overexpressing strains. Furthermore, we observed that the absence of ClrC reduced full induction of cellulase expression even in the clrB overexpressing strain. These results indicated that ClrC is a novel and efficient engineering target for improving cellulolytic enzyme production in filamentous fungi.

  20. HTLV-1 bZIP Factor Enhances T-Cell Proliferation by Impeding the Suppressive Signaling of Co-inhibitory Receptors

    PubMed Central

    Shimura, Kazuya; Onishi, Chiho; Iyoda, Tomonori; Inaba, Kayo

    2017-01-01

    Human T-cell leukemia virus type 1 (HTLV-1) causes adult T-cell leukemia-lymphoma (ATL) and inflammatory diseases. To enhance cell-to-cell transmission of HTLV-1, the virus increases the number of infected cells in vivo. HTLV-1 bZIP factor (HBZ) is constitutively expressed in HTLV-1 infected cells and ATL cells and promotes T-cell proliferation. However, the detailed mechanism by which it does so remains unknown. Here, we show that HBZ enhances the proliferation of expressing T cells after stimulation via the T-cell receptor. HBZ promotes this proliferation by influencing the expression and function of multiple co-inhibitory receptors. HBZ suppresses the expression of BTLA and LAIR-1 in HBZ expressing T cells and ATL cells. Expression of T cell immunoglobulin and ITIM domain (TIGIT) and Programmed cell death 1 (PD-1) was enhanced, but their suppressive effect on T-cell proliferation was functionally impaired. HBZ inhibits the co-localization of SHP-2 and PD-1 in T cells, thereby leading to impaired inhibition of T-cell proliferation and suppressed dephosphorylation of ZAP-70 and CD3ζ. HBZ does this by interacting with THEMIS, which associates with Grb2 and SHP-2. Thus, HBZ interacts with the SHP containing complex, impedes the suppressive signal from PD-1 and TIGIT, and enhances the proliferation of T cells. Although HBZ was present in both the nucleus and the cytoplasm of T cells, HBZ was localized largely in the nucleus by suppressed expression of THEMIS by shRNA. This indicates that THEMIS is responsible for cytoplasmic localization of HBZ in T cells. Since THEMIS is expressed only in T-lineage cells, HBZ mediated inhibition of the suppressive effects of co-inhibitory receptors accounts for how HTLV-1 induces proliferation only of T cells in vivo. This study reveals that HBZ targets co-inhibitory receptors to cause the proliferation of infected cells. PMID:28046066

  1. Determinate-state convolutional codes

    NASA Technical Reports Server (NTRS)

    Collins, O.; Hizlan, M.

    1991-01-01

    A determinate state convolutional code is formed from a conventional convolutional code by pruning away some of the possible state transitions in the decoding trellis. The type of staged power transfer used in determinate state convolutional codes proves to be an extremely efficient way of enhancing the performance of a concatenated coding system. The decoder complexity is analyzed along with free distances of these new codes and extensive simulation results is provided of their performance at the low signal to noise ratios where a real communication system would operate. Concise, practical examples are provided.

  2. Circular codes, symmetries and transformations.

    PubMed

    Fimmel, Elena; Giannerini, Simone; Gonzalez, Diego Luis; Strüngmann, Lutz

    2015-06-01

    Circular codes, putative remnants of primeval comma-free codes, have gained considerable attention in the last years. In fact they represent a second kind of genetic code potentially involved in detecting and maintaining the normal reading frame in protein coding sequences. The discovering of an universal code across species suggested many theoretical and experimental questions. However, there is a key aspect that relates circular codes to symmetries and transformations that remains to a large extent unexplored. In this article we aim at addressing the issue by studying the symmetries and transformations that connect different circular codes. The main result is that the class of 216 C3 maximal self-complementary codes can be partitioned into 27 equivalence classes defined by a particular set of transformations. We show that such transformations can be put in a group theoretic framework with an intuitive geometric interpretation. More general mathematical results about symmetry transformations which are valid for any kind of circular codes are also presented. Our results pave the way to the study of the biological consequences of the mathematical structure behind circular codes and contribute to shed light on the evolutionary steps that led to the observed symmetries of present codes.

  3. Making your code citable with the Astrophysics Source Code Library

    NASA Astrophysics Data System (ADS)

    Allen, Alice; DuPrie, Kimberly; Schmidt, Judy; Berriman, G. Bruce; Hanisch, Robert J.; Mink, Jessica D.; Nemiroff, Robert J.; Shamir, Lior; Shortridge, Keith; Taylor, Mark B.; Teuben, Peter J.; Wallin, John F.

    2016-01-01

    The Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. With nearly 1,200 codes, it is the largest indexed resource for astronomy codes in existence. Established in 1999, it offers software authors a path to citation of their research codes even without publication of a paper describing the software, and offers scientists a way to find codes used in refereed publications, thus improving the transparency of the research. It also provides a method to quantify the impact of source codes in a fashion similar to the science metrics of journal articles. Citations using ASCL IDs are accepted by major astronomy journals and if formatted properly are tracked by ADS and other indexing services. The number of citations to ASCL entries increased sharply from 110 citations in January 2014 to 456 citations in September 2015. The percentage of code entries in ASCL that were cited at least once rose from 7.5% in January 2014 to 17.4% in September 2015. The ASCL's mid-2014 infrastructure upgrade added an easy entry submission form, more flexible browsing, search capabilities, and an RSS feeder for updates. A Changes/Additions form added this past fall lets authors submit links for papers that use their codes for addition to the ASCL entry even if those papers don't formally cite the codes, thus increasing the transparency of that research and capturing the value of their software to the community.

  4. Practices in Code Discoverability: Astrophysics Source Code Library

    NASA Astrophysics Data System (ADS)

    Allen, A.; Teuben, P.; Nemiroff, R. J.; Shamir, L.

    2012-09-01

    Here we describe the Astrophysics Source Code Library (ASCL), which takes an active approach to sharing astrophysics source code. ASCL's editor seeks out both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and adds entries for the found codes to the library. This approach ensures that source codes are added without requiring authors to actively submit them, resulting in a comprehensive listing that covers a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL now has over 340 codes in it and continues to grow. In 2011, the ASCL has on average added 19 codes per month. An advisory committee has been established to provide input and guide the development and expansion of the new site, and a marketing plan has been developed and is being executed. All ASCL source codes have been used to generate results published in or submitted to a refereed journal and are freely available either via a download site or from an identified source. This paper provides the history and description of the ASCL. It lists the requirements for including codes, examines the advantages of the ASCL, and outlines some of its future plans.

  5. Electromagnetic particle simulation codes

    NASA Technical Reports Server (NTRS)

    Pritchett, P. L.

    1985-01-01

    Electromagnetic particle simulations solve the full set of Maxwell's equations. They thus include the effects of self-consistent electric and magnetic fields, magnetic induction, and electromagnetic radiation. The algorithms for an electromagnetic code which works directly with the electric and magnetic fields are described. The fields and current are separated into transverse and longitudinal components. The transverse E and B fields are integrated in time using a leapfrog scheme applied to the Fourier components. The particle pushing is performed via the relativistic Lorentz force equation for the particle momentum. As an example, simulation results are presented for the electron cyclotron maser instability which illustrate the importance of relativistic effects on the wave-particle resonance condition and on wave dispersion.

  6. Telescope Adaptive Optics Code

    SciTech Connect

    Phillion, D.

    2005-07-28

    The Telescope AO Code has general adaptive optics capabilities plus specialized models for three telescopes with either adaptive optics or active optics systems. It has the capability to generate either single-layer or distributed Kolmogorov turbulence phase screens using the FFT. Missing low order spatial frequencies are added using the Karhunen-Loeve expansion. The phase structure curve is extremely dose to the theoreUcal. Secondly, it has the capability to simulate an adaptive optics control systems. The default parameters are those of the Keck II adaptive optics system. Thirdly, it has a general wave optics capability to model the science camera halo due to scintillation from atmospheric turbulence and the telescope optics. Although this capability was implemented for the Gemini telescopes, the only default parameter specific to the Gemini telescopes is the primary mirror diameter. Finally, it has a model for the LSST active optics alignment strategy. This last model is highly specific to the LSST

  7. Code lock with microcircuit

    NASA Astrophysics Data System (ADS)

    Korobka, A.; May, I.

    1985-01-01

    A code lock with a microcircuit was invented which contains only a very few components. Two DD-triggers control the state of two identical transistors. When both transistors are turned on simultaneously the transistor VS1 is turned on so that the electromagnet YA1 pulls in the bolt and the door opens. This will happen only when a logic 1 appears at the inverted output of the first trigger and at the straight output of the second one. After the door is opened, a button on it resets the contactors to return both triggers to their original state. The electromagnetic is designed to produce the necessary pull force and sufficient power when under rectified 127 V line voltage, with the neutral wire of the lock circuit always connected to the - terminal of the power supply.

  8. Peripheral coding of taste

    PubMed Central

    Liman, Emily R.; Zhang, Yali V.; Montell, Craig

    2014-01-01

    Five canonical tastes, bitter, sweet, umami (amino acid), salty and sour (acid) are detected by animals as diverse as fruit flies and humans, consistent with a near universal drive to consume fundamental nutrients and to avoid toxins or other harmful compounds. Surprisingly, despite this strong conservation of basic taste qualities between vertebrates and invertebrates, the receptors and signaling mechanisms that mediate taste in each are highly divergent. The identification over the last two decades of receptors and other molecules that mediate taste has led to stunning advances in our understanding of the basic mechanisms of transduction and coding of information by the gustatory systems of vertebrates and invertebrates. In this review, we discuss recent advances in taste research, mainly from the fly and mammalian systems, and we highlight principles that are common across species, despite stark differences in receptor types. PMID:24607224

  9. Surface acoustic wave coding for orthogonal frequency coded devices

    NASA Technical Reports Server (NTRS)

    Malocha, Donald (Inventor); Kozlovski, Nikolai (Inventor)

    2011-01-01

    Methods and systems for coding SAW OFC devices to mitigate code collisions in a wireless multi-tag system. Each device producing plural stepped frequencies as an OFC signal with a chip offset delay to increase code diversity. A method for assigning a different OCF to each device includes using a matrix based on the number of OFCs needed and the number chips per code, populating each matrix cell with OFC chip, and assigning the codes from the matrix to the devices. The asynchronous passive multi-tag system includes plural surface acoustic wave devices each producing a different OFC signal having the same number of chips and including a chip offset time delay, an algorithm for assigning OFCs to each device, and a transceiver to transmit an interrogation signal and receive OFC signals in response with minimal code collisions during transmission.

  10. Improved lossless intra coding for next generation video coding

    NASA Astrophysics Data System (ADS)

    Vanam, Rahul; He, Yuwen; Ye, Yan

    2016-09-01

    Recently, there have been efforts by the ITU-T VCEG and ISO/IEC MPEG to further improve the compression performance of the High Efficiency Video Coding (HEVC) standard for developing a potential next generation video coding standard. The exploratory codec software of this potential standard includes new coding tools for inter and intra coding. In this paper, we present a new intra prediction mode for lossless intra coding. Our new intra mode derives a prediction filter for each input pixel using its neighboring reconstructed pixels, and applies this filter to the nearest neighboring reconstructed pixels to generate a prediction pixel. The proposed intra mode is demonstrated to improve the performance of the exploratory software for lossless intra coding, yielding a maximum and average bitrate savings of 4.4% and 2.11%, respectively.

  11. Transionospheric Propagation Code (TIPC)

    SciTech Connect

    Roussel-Dupre, R.; Kelley, T.A.

    1990-10-01

    The Transionospheric Propagation Code is a computer program developed at Los Alamos National Lab to perform certain tasks related to the detection of vhf signals following propagation through the ionosphere. The code is written in Fortran 77, runs interactively and was designed to be as machine independent as possible. A menu format in which the user is prompted to supply appropriate parameters for a given task has been adopted for the input while the output is primarily in the form of graphics. The user has the option of selecting from five basic tasks, namely transionospheric propagation, signal filtering, signal processing, DTOA study, and DTOA uncertainty study. For the first task a specified signal is convolved against the impulse response function of the ionosphere to obtain the transionospheric signal. The user is given a choice of four analytic forms for the input pulse or of supplying a tabular form. The option of adding Gaussian-distributed white noise of spectral noise to the input signal is also provided. The deterministic ionosphere is characterized to first order in terms of a total electron content (TEC) along the propagation path. In addition, a scattering model parameterized in terms of a frequency coherence bandwidth is also available. In the second task, detection is simulated by convolving a given filter response against the transionospheric signal. The user is given a choice of a wideband filter or a narrowband Gaussian filter. It is also possible to input a filter response. The third task provides for quadrature detection, envelope detection, and three different techniques for time-tagging the arrival of the transionospheric signal at specified receivers. The latter algorithms can be used to determine a TEC and thus take out the effects of the ionosphere to first order. Task four allows the user to construct a table of delta-times-of-arrival (DTOAs) vs TECs for a specified pair of receivers.

  12. On multilevel block modulation codes

    NASA Technical Reports Server (NTRS)

    Kasami, Tadao; Takata, Toyoo; Fujiwara, Toru; Lin, Shu

    1991-01-01

    The multilevel (ML) technique for combining block coding and modulation is investigated. A general formulation is presented for ML modulation codes in terms of component codes with appropriate distance measures. A specific method for constructing ML block modulation codes (MLBMCs) with interdependency among component codes is proposed. Given an MLBMC C with no interdependency among the binary component codes, the proposed method gives an MLBC C-prime that has the same rate as C, a minimum squared Euclidean distance not less than that of C, a trellis diagram with the same number of states as that of C, and a smaller number of nearest-neighbor codewords than that of C. Finally, a technique is presented for analyzing the error performance of MLBMCs for an additive white Gaussian noise channel based on soft-decision maximum-likelihood decoding.

  13. QR code for medical information uses.

    PubMed

    Fontelo, Paul; Liu, Fang; Ducut, Erick G

    2008-11-06

    We developed QR code online tools, simulated and tested QR code applications for medical information uses including scanning QR code labels, URLs and authentication. Our results show possible applications for QR code in medicine.

  14. Code Speed Measuring for VC++

    DTIC Science & Technology

    2015-10-01

    UNCLASSIFIED AD-E403 688 Technical Report ARWSE-TR-14025 CODE SPEED MEASURING FOR VC++ Tom Nealis...TYPE Final 3. DATES COVERED (From – To) 4. TITLE AND SUBTITLE CODE SPEED MEASURING FOR VC++ 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...ABSTRACT It’s often important to know how fast a snippet of code executes. This information allows the coder to make important decisions

  15. Explosive Formulation Code Naming SOP

    SciTech Connect

    Martz, H. E.

    2014-09-19

    The purpose of this SOP is to provide a procedure for giving individual HME formulations code names. A code name for an individual HME formulation consists of an explosive family code, given by the classified guide, followed by a dash, -, and a number. If the formulation requires preparation such as packing or aging, these add additional groups of symbols to the X-ray specimen name.

  16. Bar-Code-Scribing Tool

    NASA Technical Reports Server (NTRS)

    Badinger, Michael A.; Drouant, George J.

    1991-01-01

    Proposed hand-held tool applies indelible bar code to small parts. Possible to identify parts for management of inventory without tags or labels. Microprocessor supplies bar-code data to impact-printer-like device. Device drives replaceable scribe, which cuts bar code on surface of part. Used to mark serially controlled parts for military and aerospace equipment. Also adapts for discrete marking of bulk items used in food and pharmaceutical processing.

  17. Upgrades to NRLMOL code

    NASA Astrophysics Data System (ADS)

    Basurto, Luis

    This project consists of performing upgrades to the massively parallel NRLMOL electronic structure code in order to enhance its performance by increasing its flexibility by: a) Utilizing dynamically allocated arrays, b) Executing in a parallel environment sections of the program that were previously executed in a serial mode, c) Exploring simultaneous concurrent executions of the program through the use of an already existing MPI environment; thus enabling the simulation of larger systems than it is currently capable of performing. Also developed was a graphical user interface that will allow less experienced users to start performing electronic structure calculations by aiding them in performing the necessary configuration of input files as well as providing graphical tools for the displaying and analysis of results. Additionally, a computational toolkit that can avail of large supercomputers and make use of various levels of approximation for atomic interactions was developed to search for stable atomic clusters and predict novel stable endohedral fullerenes. As an application of the developed computational toolkit, a search was conducted for stable isomers of Sc3N C80 fullerene. In this search, about 1.2 million isomers of C80 were optimized in various charged states at the PM6 level. Subsequently, using the selected optimized isomers of C80 in various charged state, about 10,000 isomers of Sc3N C80 were constructed which were optimized using semi-empirical PM6 quantum chemical method. A few selected lowest isomers of Sc3N C80 were optimized at the DFT level. The calculation confirms the lowest 3 isomers previously reported in literature but 4 new isomers are found within the lowest 10 isomers. Using the upgraded NRLMOL code, a study was done of the electronic structure of a multichromoric molecular complex containing two of each borondipyrromethane dye, Zn-tetraphenyl-porphyrin, bisphenyl anthracene and a fullerene. A systematic examination of the effect of

  18. The FLUKA Code: an Overview

    SciTech Connect

    Ballarini, F.; Battistoni, G.; Campanella, M.; Carboni, M.; Cerutti, F.; Empl, A.; Fasso, A.; Ferrari, A.; Gadioli, E.; Garzelli, M.V.; Lantz, M.; Liotta, M.; Mairani, A.; Mostacci, A.; Muraro, S.; Ottolenghi, A.; Pelliccioni, M.; Pinsky, L.; Ranft, J.; Roesler, S.; Sala, P.R.; /Milan U. /INFN, Milan /Pavia U. /INFN, Pavia /CERN /Siegen U. /Houston U. /SLAC /Frascati /NASA, Houston /ENEA, Frascati

    2005-11-09

    FLUKA is a multipurpose Monte Carlo code which can transport a variety of particles over a wide energy range in complex geometries. The code is a joint project of INFN and CERN: part of its development is also supported by the University of Houston and NASA. FLUKA is successfully applied in several fields, including but not only, particle physics, cosmic ray physics, dosimetry, radioprotection, hadron therapy, space radiation, accelerator design and neutronics. The code is the standard tool used at CERN for dosimetry, radioprotection and beam-machine interaction studies. Here we give a glimpse into the code physics models with a particular emphasis to the hadronic and nuclear sector.

  19. High Order Modulation Protograph Codes

    NASA Technical Reports Server (NTRS)

    Nguyen, Thuy V. (Inventor); Nosratinia, Aria (Inventor); Divsalar, Dariush (Inventor)

    2014-01-01

    Digital communication coding methods for designing protograph-based bit-interleaved code modulation that is general and applies to any modulation. The general coding framework can support not only multiple rates but also adaptive modulation. The method is a two stage lifting approach. In the first stage, an original protograph is lifted to a slightly larger intermediate protograph. The intermediate protograph is then lifted via a circulant matrix to the expected codeword length to form a protograph-based low-density parity-check code.

  20. Astrophysics Source Code Library Enhancements

    NASA Astrophysics Data System (ADS)

    Hanisch, R. J.; Allen, A.; Berriman, G. B.; DuPrie, K.; Mink, J.; Nemiroff, R. J.; Schmidt, J.; Shamir, L.; Shortridge, K.; Taylor, M.; Teuben, P. J.; Wallin, J.

    2015-09-01

    The Astrophysics Source Code Library (ASCL)1 is a free online registry of codes used in astronomy research; it currently contains over 900 codes and is indexed by ADS. The ASCL has recently moved a new infrastructure into production. The new site provides a true database for the code entries and integrates the WordPress news and information pages and the discussion forum into one site. Previous capabilities are retained and permalinks to ascl.net continue to work. This improvement offers more functionality and flexibility than the previous site, is easier to maintain, and offers new possibilities for collaboration. This paper covers these recent changes to the ASCL.

  1. The FLUKA Code: An Overview

    NASA Technical Reports Server (NTRS)

    Ballarini, F.; Battistoni, G.; Campanella, M.; Carboni, M.; Cerutti, F.; Empl, A.; Fasso, A.; Ferrari, A.; Gadioli, E.; Garzelli, M. V.; Lantz, M.; Liotta, M.; Mairani, A.; Mostacci, A.; Muraro, S.; Ottolenghi, A.; Pelliccioni, M.; Pinsky, L.; Ranft, J.; Roesler, S.; Sala, P. R.; Scannicchio, D.; Trovati, S.; Villari, R.; Wilson, T.

    2006-01-01

    FLUKA is a multipurpose Monte Carlo code which can transport a variety of particles over a wide energy range in complex geometries. The code is a joint project of INFN and CERN: part of its development is also supported by the University of Houston and NASA. FLUKA is successfully applied in several fields, including but not only, particle physics, cosmic ray physics, dosimetry, radioprotection, hadron therapy, space radiation, accelerator design and neutronics. The code is the standard tool used at CERN for dosimetry, radioprotection and beam-machine interaction studies. Here we give a glimpse into the code physics models with a particular emphasis to the hadronic and nuclear sector.

  2. Golay and other box codes

    NASA Technical Reports Server (NTRS)

    Solomon, G.

    1992-01-01

    The (24,12;8) extended Golay Code can be generated as a 6 x 4 binary matrix from the (15,11;3) BCH-Hamming Code, represented as a 5 x 3 matrix, by adding a row and a column, both of odd or even parity. The odd-parity case provides the additional 12th dimension. Furthermore, any three columns and five rows of the 6 x 4 Golay form a BCH-Hamming (15,11;3) Code. Similarly a (80,58;8) code can be generated as a 10 x 8 binary matrix from the (63,57;3) BCH-Hamming Code represented as a 9 x 7 matrix by adding a row and a column both of odd and even parity. Furthermore, any seven columns along with the top nine rows is a BCH-Hamming (53,57;3) Code. A (80,40;16) 10 x 8 matrix binary code with weight structure identical to the extended (80,40;16) Quadratic Residue Code is generated from a (63,39;7) binary cyclic code represented as a 9 x 7 matrix, by adding a row and a column, both of odd or even parity.

  3. Golay and other box codes

    NASA Technical Reports Server (NTRS)

    Solomon, G.

    1992-01-01

    The (24,12;8) extended Golay Code can be generated as a 6x4 binary matrix from the (15,11;3) BCH-Hamming Code, represented as a 5 x 3 matrix, by adding a row and a column, both of odd or even parity. The odd-parity case provides the additional 12th dimension. Furthermore, any three columns and five rows of the 6 x 4 Golay form a BCH-Hamming (15,11;3) Code. Similarly a (80,58;8) code can be generated as a 10 x 8 binary matrix from the (63,57;3) BCH-Hamming Code represented as a 9 x 7 matrix by adding a row and a column both of odd and even parity. Furthermore, any seven columns along with the top nine rows is a BCH-Hamming (63,57;3) Code. A (80,40;16) 10 x 8 matrix binary code with weight structure identical to the extended (80,40;16) Quadratic Residue Code is generated from a (63,39;7) binary cyclic code represented as a 9 x 7 matrix, by adding a row and a column, both of odd or even parity.

  4. Implementation issues in source coding

    NASA Technical Reports Server (NTRS)

    Sayood, Khalid; Chen, Yun-Chung; Hadenfeldt, A. C.

    1989-01-01

    An edge preserving image coding scheme which can be operated in both a lossy and a lossless manner was developed. The technique is an extension of the lossless encoding algorithm developed for the Mars observer spectral data. It can also be viewed as a modification of the DPCM algorithm. A packet video simulator was also developed from an existing modified packet network simulator. The coding scheme for this system is a modification of the mixture block coding (MBC) scheme described in the last report. Coding algorithms for packet video were also investigated.

  5. The KIDTALK Behavior and Language Code: Manual and Coding Protocol.

    ERIC Educational Resources Information Center

    Delaney, Elizabeth M.; Ezell, Sara S.; Solomon, Ned A.; Hancock, Terry B.; Kaiser, Ann P.

    Developed as part of the Milieu Language Teaching Project at the John F. Kennedy Center at Vanderbilt University in Nashville, Tennessee, this KIDTALK Behavior-Language Coding Protocol and manual measures behavior occurring during adult-child interactions. The manual is divided into 5 distinct sections: (1) the adult behavior codes describe…

  6. HTLV-1 bZIP Factor Impairs Anti-viral Immunity by Inducing Co-inhibitory Molecule, T Cell Immunoglobulin and ITIM Domain (TIGIT).

    PubMed

    Yasuma, Keiko; Yasunaga, Jun-ichirou; Takemoto, Keiko; Sugata, Kenji; Mitobe, Yuichi; Takenouchi, Norihiro; Nakagawa, Masanori; Suzuki, Yutaka; Matsuoka, Masao

    2016-01-01

    Human T-cell leukemia virus type 1 (HTLV-1) infects CD4+ T cells and induces proliferation of infected cells in vivo, which leads to the onset of adult T-cell leukemia (ATL) in some infected individuals. The HTLV-1 bZIP factor (HBZ) gene, which is encoded in the minus strand of HTLV-1, plays critical roles in pathogenesis. In this study, RNA-seq and ChIP-seq analyses using HBZ transduced T cells revealed that HBZ upregulates the expression and promoter acetylation levels of a co-inhibitory molecule, T cell immunoglobulin and ITIM domain (TIGIT), in addition to those of regulatory T cells related genes, Foxp3 and Ccr4. TIGIT was expressed on CD4+ T cells from HBZ-transgenic (HBZ-Tg) mice, and on ATL cells and HTLV-1 infected CD4+ T cells of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) in vivo. Expression of Blimp1 and IL-10 was upregulated in TIGIT+CD4+ cells of HBZ-Tg mice compared with TIGIT-CD4+ T cells, suggesting the correlation between TIGIT expression and IL-10 production. When CD4+ T cells from HBZ-Tg mice were stimulated with TIGIT's ligand, CD155, their production of the inhibitory cytokine IL-10 was enhanced. Furthermore, dendritic cells from HBZ-Tg mice produced high levels of IL-10 after stimulation. These data suggest that HBZ alters immune system to suppressive state via TIGIT and IL-10. Importantly, TIGIT suppressed T-cell responses to another HTLV-1 virus protein, Tax, in vitro. Blocking of TIGIT and PD-1 slightly increased anti-Tax T-cell activity in some HAM/TSP patients. These results suggest that HBZ-induced TIGIT on HTLV-1 infected cells impairs T-cell responses to viral antigens. This study shows that HBZ-induced TIGIT plays a pivotal role in attenuating host immune responses and shaping a microenvironment favorable to HTLV-1.

  7. Patched Conic Trajectory Code

    NASA Technical Reports Server (NTRS)

    Park, Brooke Anderson; Wright, Henry

    2012-01-01

    PatCon code was developed to help mission designers run trade studies on launch and arrival times for any given planet. Initially developed in Fortran, the required inputs included launch date, arrival date, and other orbital parameters of the launch planet and arrival planets at the given dates. These parameters include the position of the planets, the eccentricity, semi-major axes, argument of periapsis, ascending node, and inclination of the planets. With these inputs, a patched conic approximation is used to determine the trajectory. The patched conic approximation divides the planetary mission into three parts: (1) the departure phase, in which the two relevant bodies are Earth and the spacecraft, and where the trajectory is a departure hyperbola with Earth at the focus; (2) the cruise phase, in which the two bodies are the Sun and the spacecraft, and where the trajectory is a transfer ellipse with the Sun at the focus; and (3) the arrival phase, in which the two bodies are the target planet and the spacecraft, where the trajectory is an arrival hyperbola with the planet as the focus.

  8. Civil Code, 11 December 1987.

    PubMed

    1988-01-01

    Article 162 of this Mexican Code provides, among other things, that "Every person has the right freely, responsibly, and in an informed fashion to determine the number and spacing of his or her children." When a marriage is involved, this right is to be observed by the spouses "in agreement with each other." The civil codes of the following states contain the same provisions: 1) Baja California (Art. 159 of the Civil Code of 28 April 1972 as revised in Decree No. 167 of 31 January 1974); 2) Morelos (Art. 255 of the Civil Code of 26 September 1949 as revised in Decree No. 135 of 29 December 1981); 3) Queretaro (Art. 162 of the Civil Code of 29 December 1950 as revised in the Act of 9 January 1981); 4) San Luis Potosi (Art. 147 of the Civil Code of 24 March 1946 as revised in 13 June 1978); Sinaloa (Art. 162 of the Civil Code of 18 June 1940 as revised in Decree No. 28 of 14 October 1975); 5) Tamaulipas (Art. 146 of the Civil Code of 21 November 1960 as revised in Decree No. 20 of 30 April 1975); 6) Veracruz-Llave (Art. 98 of the Civil Code of 1 September 1932 as revised in the Act of 30 December 1975); and 7) Zacatecas (Art. 253 of the Civil Code of 9 February 1965 as revised in Decree No. 104 of 13 August 1975). The Civil Codes of Puebla and Tlaxcala provide for this right only in the context of marriage with the spouses in agreement. See Art. 317 of the Civil Code of Puebla of 15 April 1985 and Article 52 of the Civil Code of Tlaxcala of 31 August 1976 as revised in Decree No. 23 of 2 April 1984. The Family Code of Hidalgo requires as a formality of marriage a certification that the spouses are aware of methods of controlling fertility, responsible parenthood, and family planning. In addition, Article 22 the Civil Code of the Federal District provides that the legal capacity of natural persons is acquired at birth and lost at death; however, from the moment of conception the individual comes under the protection of the law, which is valid with respect to the

  9. It's (Zipped) in the Bag

    ERIC Educational Resources Information Center

    Moyer, Richard H.; Everett, Susan A.

    2011-01-01

    Plastic baggies, especially the sealable variety, seem to be a ubiquitous part of human culture. The zipper-type seal on plastic baggies is an example of an unappreciated engineering accomplishment that is relevant to everyday life. In fact, the challenge of fastening two pieces together probably dates back to the making of tools and clothing by…

  10. Coding in pigeons: Multiple-coding versus single-code/default strategies.

    PubMed

    Pinto, Carlos; Machado, Armando

    2015-05-01

    To investigate the coding strategies that pigeons may use in a temporal discrimination tasks, pigeons were trained on a matching-to-sample procedure with three sample durations (2s, 6s and 18s) and two comparisons (red and green hues). One comparison was correct following 2-s samples and the other was correct following both 6-s and 18-s samples. Tests were then run to contrast the predictions of two hypotheses concerning the pigeons' coding strategies, the multiple-coding and the single-code/default. According to the multiple-coding hypothesis, three response rules are acquired, one for each sample. According to the single-code/default hypothesis, only two response rules are acquired, one for the 2-s sample and a "default" rule for any other duration. In retention interval tests, pigeons preferred the "default" key, a result predicted by the single-code/default hypothesis. In no-sample tests, pigeons preferred the key associated with the 2-s sample, a result predicted by multiple-coding. Finally, in generalization tests, when the sample duration equaled 3.5s, the geometric mean of 2s and 6s, pigeons preferred the key associated with the 6-s and 18-s samples, a result predicted by the single-code/default hypothesis. The pattern of results suggests the need for models that take into account multiple sources of stimulus control.

  11. Cracking the bioelectric code

    PubMed Central

    Tseng, AiSun; Levin, Michael

    2013-01-01

    Patterns of resting potential in non-excitable cells of living tissue are now known to be instructive signals for pattern formation during embryogenesis, regeneration and cancer suppression. The development of molecular-level techniques for tracking ion flows and functionally manipulating the activity of ion channels and pumps has begun to reveal the mechanisms by which voltage gradients regulate cell behaviors and the assembly of complex large-scale structures. A recent paper demonstrated that a specific voltage range is necessary for demarcation of eye fields in the frog embryo. Remarkably, artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm. These data challenge the existing models of eye fate restriction and tissue competence maps, and suggest the presence of a bioelectric code—a mapping of physiological properties to anatomical outcomes. This Addendum summarizes the current state of knowledge in developmental bioelectricity, proposes three possible interpretations of the bioelectric code that functionally maps physiological states to anatomical outcomes, and highlights the biggest open questions in this field. We also suggest a speculative hypothesis at the intersection of cognitive science and developmental biology: that bioelectrical signaling among non-excitable cells coupled by gap junctions simulates neural network-like dynamics, and underlies the information processing functions required by complex pattern formation in vivo. Understanding and learning to control the information stored in physiological networks will have transformative implications for developmental biology, regenerative medicine and synthetic bioengineering. PMID:23802040

  12. Breaking the Code of Silence.

    ERIC Educational Resources Information Center

    Halbig, Wolfgang W.

    2000-01-01

    Schools and communities must break the adolescent code of silence concerning threats of violence. Schools need character education stressing courage, caring, and responsibility; regular discussions of the school discipline code; formal security discussions with parents; 24-hour hotlines; and protocols for handling reports of potential violence.…

  13. ACCELERATION PHYSICS CODE WEB REPOSITORY.

    SciTech Connect

    WEI, J.

    2006-06-26

    In the framework of the CARE HHH European Network, we have developed a web-based dynamic accelerator-physics code repository. We describe the design, structure and contents of this repository, illustrate its usage, and discuss our future plans, with emphasis on code benchmarking.

  14. Accelerator Physics Code Web Repository

    SciTech Connect

    Zimmermann, F.; Basset, R.; Bellodi, G.; Benedetto, E.; Dorda, U.; Giovannozzi, M.; Papaphilippou, Y.; Pieloni, T.; Ruggiero, F.; Rumolo, G.; Schmidt, F.; Todesco, E.; Zotter, B.W.; Payet, J.; Bartolini, R.; Farvacque, L.; Sen, T.; Chin, Y.H.; Ohmi, K.; Oide, K.; Furman, M.; /LBL, Berkeley /Oak Ridge /Pohang Accelerator Lab. /SLAC /TRIUMF /Tech-X, Boulder /UC, San Diego /Darmstadt, GSI /Rutherford /Brookhaven

    2006-10-24

    In the framework of the CARE HHH European Network, we have developed a web-based dynamic accelerator-physics code repository. We describe the design, structure and contents of this repository, illustrate its usage, and discuss our future plans, with emphasis on code benchmarking.

  15. LFSC - Linac Feedback Simulation Code

    SciTech Connect

    Ivanov, Valentin; /Fermilab

    2008-05-01

    The computer program LFSC (Code>) is a numerical tool for simulation beam based feedback in high performance linacs. The code LFSC is based on the earlier version developed by a collective of authors at SLAC (L.Hendrickson, R. McEwen, T. Himel, H. Shoaee, S. Shah, P. Emma, P. Schultz) during 1990-2005. That code was successively used in simulation of SLC, TESLA, CLIC and NLC projects. It can simulate as pulse-to-pulse feedback on timescale corresponding to 5-100 Hz, as slower feedbacks, operating in the 0.1-1 Hz range in the Main Linac and Beam Delivery System. The code LFSC is running under Matlab for MS Windows operating system. It contains about 30,000 lines of source code in more than 260 subroutines. The code uses the LIAR ('Linear Accelerator Research code') for particle tracking under ground motion and technical noise perturbations. It uses the Guinea Pig code to simulate the luminosity performance. A set of input files includes the lattice description (XSIF format), and plane text files with numerical parameters, wake fields, ground motion data etc. The Matlab environment provides a flexible system for graphical output.

  16. Indices for Testing Neural Codes

    PubMed Central

    Victor, Jonathan D.; Nirenberg, Sheila

    2009-01-01

    One of the most critical challenges in systems neuroscience is determining the neural code. A principled framework for addressing this can be found in information theory. With this approach, one can determine whether a proposed code can account for the stimulus-response relationship. Specifically, one can compare the transmitted information between the stimulus and the hypothesized neural code with the transmitted information between the stimulus and the behavioral response. If the former is smaller than the latter (i.e., if the code cannot account for the behavior), the code can be ruled out. The information-theoretic index most widely used in this context is Shannon’s mutual information. The Shannon test, however, is not ideal for this purpose: while the codes it will rule out are truly nonviable, there will be some nonviable codes that it will fail to rule out. Here we describe a wide range of alternative indices that can be used for ruling codes out. The range includes a continuum from Shannon information to measures of the performance of a Bayesian decoder. We analyze the relationship of these indices to each other and their complementary strengths and weaknesses for addressing this problem. PMID:18533812

  17. Population coding in somatosensory cortex.

    PubMed

    Petersen, Rasmus S; Panzeri, Stefano; Diamond, Mathew E

    2002-08-01

    Computational analyses have begun to elucidate which components of somatosensory cortical population activity may encode basic stimulus features. Recent results from rat barrel cortex suggest that the essence of this code is not synergistic spike patterns, but rather the precise timing of single neuron's first post-stimulus spikes. This may form the basis for a fast, robust population code.

  18. QPhiX Code Generator

    SciTech Connect

    Joo, Balint

    2014-09-16

    A simple code-generator to generate the low level code kernels used by the QPhiX Library for Lattice QCD. Generates Kernels for Wilson-Dslash, and Wilson-Clover kernels. Can be reused to write other optimized kernels for Intel Xeon Phi(tm), Intel Xeon(tm) and potentially other architectures.

  19. Using NAEYC's Code of Ethics.

    ERIC Educational Resources Information Center

    Young Children, 1995

    1995-01-01

    Considers how to deal with an ethical dilemma concerning a caregiver's dislike for a child. Recognizes that no statement in NAEYC's Code of Ethical Conduct requires that a professional must like each child, and presents some ideals and principles from the code that may guide professionals through similar situations. (BAC)

  20. Video coding with dynamic background

    NASA Astrophysics Data System (ADS)

    Paul, Manoranjan; Lin, Weisi; Lau, Chiew Tong; Lee, Bu-Sung

    2013-12-01

    Motion estimation (ME) and motion compensation (MC) using variable block size, sub-pixel search, and multiple reference frames (MRFs) are the major reasons for improved coding performance of the H.264 video coding standard over other contemporary coding standards. The concept of MRFs is suitable for repetitive motion, uncovered background, non-integer pixel displacement, lighting change, etc. The requirement of index codes of the reference frames, computational time in ME & MC, and memory buffer for coded frames limits the number of reference frames used in practical applications. In typical video sequences, the previous frame is used as a reference frame with 68-92% of cases. In this article, we propose a new video coding method using a reference frame [i.e., the most common frame in scene (McFIS)] generated by dynamic background modeling. McFIS is more effective in terms of rate-distortion and computational time performance compared to the MRFs techniques. It has also inherent capability of scene change detection (SCD) for adaptive group of picture (GOP) size determination. As a result, we integrate SCD (for GOP determination) with reference frame generation. The experimental results show that the proposed coding scheme outperforms the H.264 video coding with five reference frames and the two relevant state-of-the-art algorithms by 0.5-2.0 dB with less computational time.

  1. PARAVT: Parallel Voronoi tessellation code

    NASA Astrophysics Data System (ADS)

    González, R. E.

    2016-10-01

    In this study, we present a new open source code for massive parallel computation of Voronoi tessellations (VT hereafter) in large data sets. The code is focused for astrophysical purposes where VT densities and neighbors are widely used. There are several serial Voronoi tessellation codes, however no open source and parallel implementations are available to handle the large number of particles/galaxies in current N-body simulations and sky surveys. Parallelization is implemented under MPI and VT using Qhull library. Domain decomposition takes into account consistent boundary computation between tasks, and includes periodic conditions. In addition, the code computes neighbors list, Voronoi density, Voronoi cell volume, density gradient for each particle, and densities on a regular grid. Code implementation and user guide are publicly available at https://github.com/regonzar/paravt.

  2. Medical coding in clinical trials.

    PubMed

    Babre, Deven

    2010-01-01

    Data generated in all clinical trial are recorded on the data collection instrument Case report Form / Electronic Case Report Form by investigators located at various sites in various countries. In multicentric clinical trials since different investigator or medically qualified experts are from different sites / centers recording the medical term(s) uniformly is a big challenge. Medical coders from clinical data management team process these terms and perform medical coding. Medical coding is performed to categorize the medical terms reported appropriately so that they can be analyzed/reviewed. This article describes process which is used for medical coding in clinical data management and two most commonly used medical dictionaries MedDRA and WHO-DDE in brief. It is expected to help medical coders to understand the process of medical coding in clinical data management. Few common issues which the medical coder faces while performing medical coding, are also highlighted.

  3. Detecting non-coding selective pressure in coding regions

    PubMed Central

    Chen, Hui; Blanchette, Mathieu

    2007-01-01

    Background Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions located in intergenic or intronic regions. However, non-coding functional elements can also be located within coding region, as is common for exonic splicing enhancers, some transcription factor binding sites, and RNA secondary structure elements affecting mRNA stability, localization, or translation. Since these functional elements are located in regions that are themselves highly conserved because they are coding for a protein, they generally escaped detection by comparative genomics approaches. Results We introduce a comparative genomics approach for detecting non-coding functional elements located within coding regions. Codon evolution is modeled as a mixture of codon substitution models, where each component of the mixture describes the evolution of codons under a specific type of coding selective pressure. We show how to compute the posterior distribution of the entropy and parsimony scores under this null model of codon evolution. The method is applied to a set of growth hormone 1 orthologous mRNA sequences and a known exonic splicing elements is detected. The analysis of a set of CORTBP2 orthologous genes reveals a region of several hundred base pairs under strong non-coding selective pressure whose function remains unknown. Conclusion Non-coding functional elements, in particular those involved in post-transcriptional regulation, are likely to be much more prevalent than is currently known. With the numerous genome sequencing projects underway, comparative genomics approaches like that proposed here are likely to become increasingly powerful at detecting such elements. PMID:17288582

  4. Purification, crystallization and preliminary X-ray analysis of OsAREB8 from rice, a member of the AREB/ABF family of bZIP transcription factors, in complex with its cognate DNA.

    PubMed

    Miyazono, Ken-ichi; Koura, Tsubasa; Kubota, Keiko; Yoshida, Takuya; Fujita, Yasunari; Yamaguchi-Shinozaki, Kazuko; Tanokura, Masaru

    2012-04-01

    The AREB/ABF family of bZIP transcription factors play a key role in drought stress response and tolerance during the vegetative stage in plants. To reveal the DNA-recognition mechanism of the AREB/ABF family of proteins, the bZIP domain of OsAREB8, an AREB/ABF-family protein from Oryza sativa, was expressed in Escherichia coli, purified and crystallized with its cognate DNA. Crystals of the OsAREB8-DNA complex were obtained by the sitting-drop vapour-diffusion method at 277 K with a reservoir solution consisting of 50 mM MES pH 6.4, 29% MPD, 2 mM spermidine, 20 mM magnesium acetate and 100 mM sodium chloride. A crystal diffracted X-rays to 3.65 Å resolution and belonged to space group C222, with unit-cell parameters a = 155.1, b = 206.7, c = 38.5 Å. The crystal contained one OsAREB8-DNA complex in the asymmetric unit.

  5. BASS Code Development

    NASA Technical Reports Server (NTRS)

    Sawyer, Scott

    2004-01-01

    The BASS computational aeroacoustic code solves the fully nonlinear Euler equations in the time domain in two-dimensions. The acoustic response of the stator is determined simultaneously for the first three harmonics of the convected vortical gust of the rotor. The spatial mode generation, propagation and decay characteristics are predicted by assuming the acoustic field away from the stator can be represented as a uniform flow with small harmonic perturbations superimposed. The computed field is then decomposed using a joint temporal-spatial transform to determine the wave amplitudes as a function of rotor harmonic and spatial mode order. This report details the following technical aspects of the computations and analysis. 1) the BASS computational technique; 2) the application of periodic time shifted boundary conditions; 3) the linear theory aspects unique to rotor-stator interactions; and 4) the joint spatial-temporal transform. The computational results presented herein are twofold. In each case, the acoustic response of the stator is determined simultaneously for the first three harmonics of the convected vortical gust of the rotor. The fan under consideration here like modern fans is cut-off at +, and propagating acoustic waves are only expected at 2BPF and 3BPF. In the first case, the computations showed excellent agreement with linear theory predictions. The frequency and spatial mode order of acoustic field was computed and found consistent with linear theory. Further, the propagation of the generated modes was also correctly predicted. The upstream going waves propagated from the domain without reflection from the in ow boundary. However, reflections from the out ow boundary were noticed. The amplitude of the reflected wave was approximately 5% of the incident wave. The second set of computations were used to determine the influence of steady loading on the generated noise. Toward this end, the acoustic response was determined with three steady loading

  6. Coding for effective denial management.

    PubMed

    Miller, Jackie; Lineberry, Joe

    2004-01-01

    Nearly everyone will agree that accurate and consistent coding of diagnoses and procedures is the cornerstone for operating a compliant practice. The CPT or HCPCS procedure code tells the payor what service was performed and also (in most cases) determines the amount of payment. The ICD-9-CM diagnosis code, on the other hand, tells the payor why the service was performed. If the diagnosis code does not meet the payor's criteria for medical necessity, all payment for the service will be denied. Implementation of an effective denial management program can help "stop the bleeding." Denial management is a comprehensive process that works in two ways. First, it evaluates the cause of denials and takes steps to prevent them. Second, denial management creates specific procedures for refiling or appealing claims that are initially denied. Accurate, consistent and compliant coding is key to both of these functions. The process of proactively managing claim denials also reveals a practice's administrative strengths and weaknesses, enabling radiology business managers to streamline processes, eliminate duplicated efforts and shift a larger proportion of the staff's focus from paperwork to servicing patients--all of which are sure to enhance operations and improve practice management and office morale. Accurate coding requires a program of ongoing training and education in both CPT and ICD-9-CM coding. Radiology business managers must make education a top priority for their coding staff. Front office staff, technologists and radiologists should also be familiar with the types of information needed for accurate coding. A good staff training program will also cover the proper use of Advance Beneficiary Notices (ABNs). Registration and coding staff should understand how to determine whether the patient's clinical history meets criteria for Medicare coverage, and how to administer an ABN if the exam is likely to be denied. Staff should also understand the restrictions on use of

  7. Non-Pauli observables for CWS codes

    NASA Astrophysics Data System (ADS)

    Santiago, Douglas F. G.; Portugal, Renato; Melo, Nolmar

    2013-05-01

    It is known that nonadditive quantum codes can have higher code dimensions than stabilizer codes for the same length and minimum distance. The class of codeword stabilized codes (CWS) provides tools to obtain new nonadditive quantum codes by reducing the problem to finding nonlinear classical codes. In this work, we establish some results on the kind of non-Pauli operators that can be used as observables in the decoding scheme of CWS codes and propose a procedure to obtain those observables.

  8. ETR/ITER systems code

    SciTech Connect

    Barr, W.L.; Bathke, C.G.; Brooks, J.N.; Bulmer, R.H.; Busigin, A.; DuBois, P.F.; Fenstermacher, M.E.; Fink, J.; Finn, P.A.; Galambos, J.D.; Gohar, Y.; Gorker, G.E.; Haines, J.R.; Hassanein, A.M.; Hicks, D.R.; Ho, S.K.; Kalsi, S.S.; Kalyanam, K.M.; Kerns, J.A.; Lee, J.D.; Miller, J.R.; Miller, R.L.; Myall, J.O.; Peng, Y-K.M.; Perkins, L.J.; Spampinato, P.T.; Strickler, D.J.; Thomson, S.L.; Wagner, C.E.; Willms, R.S.; Reid, R.L.

    1988-04-01

    A tokamak systems code capable of modeling experimental test reactors has been developed and is described in this document. The code, named TETRA (for Tokamak Engineering Test Reactor Analysis), consists of a series of modules, each describing a tokamak system or component, controlled by an optimizer/driver. This code development was a national effort in that the modules were contributed by members of the fusion community and integrated into a code by the Fusion Engineering Design Center. The code has been checked out on the Cray computers at the National Magnetic Fusion Energy Computing Center and has satisfactorily simulated the Tokamak Ignition/Burn Experimental Reactor II (TIBER) design. A feature of this code is the ability to perform optimization studies through the use of a numerical software package, which iterates prescribed variables to satisfy a set of prescribed equations or constraints. This code will be used to perform sensitivity studies for the proposed International Thermonuclear Experimental Reactor (ITER). 22 figs., 29 tabs.

  9. A secure and efficient entropy coding based on arithmetic coding

    NASA Astrophysics Data System (ADS)

    Li, Hengjian; Zhang, Jiashu

    2009-12-01

    A novel security arithmetic coding scheme based on nonlinear dynamic filter (NDF) with changeable coefficients is proposed in this paper. The NDF is employed to generate the pseudorandom number generator (NDF-PRNG) and its coefficients are derived from the plaintext for higher security. During the encryption process, the mapping interval in each iteration of arithmetic coding (AC) is decided by both the plaintext and the initial values of NDF, and the data compression is also achieved with entropy optimality simultaneously. And this modification of arithmetic coding methodology which also provides security is easy to be expanded into the most international image and video standards as the last entropy coding stage without changing the existing framework. Theoretic analysis and numerical simulations both on static and adaptive model show that the proposed encryption algorithm satisfies highly security without loss of compression efficiency respect to a standard AC or computation burden.

  10. CodedStream: live media streaming with overlay coded multicast

    NASA Astrophysics Data System (ADS)

    Guo, Jiang; Zhu, Ying; Li, Baochun

    2003-12-01

    Multicasting is a natural paradigm for streaming live multimedia to multiple end receivers. Since IP multicast is not widely deployed, many application-layer multicast protocols have been proposed. However, all of these schemes focus on the construction of multicast trees, where a relatively small number of links carry the multicast streaming load, while the capacity of most of the other links in the overlay network remain unused. In this paper, we propose CodedStream, a high-bandwidth live media distribution system based on end-system overlay multicast. In CodedStream, we construct a k-redundant multicast graph (a directed acyclic graph) as the multicast topology, on which network coding is applied to work around bottlenecks. Simulation results have shown that the combination of k-redundant multicast graph and network coding may indeed bring significant benefits with respect to improving the quality of live media at the end receivers.

  11. New optimal asymmetric quantum codes constructed from constacyclic codes

    NASA Astrophysics Data System (ADS)

    Xu, Gen; Li, Ruihu; Guo, Luobin; Lü, Liangdong

    2017-02-01

    In this paper, we propose the construction of asymmetric quantum codes from two families of constacyclic codes over finite field 𝔽q2 of code length n, where for the first family, q is an odd prime power with the form 4t + 1 (t ≥ 1 is integer) or 4t ‑ 1 (t ≥ 2 is integer) and n1 = q2+1 2; for the second family, q is an odd prime power with the form 10t + 3 or 10t + 7 (t ≥ 0 is integer) and n2 = q2+1 5. As a result, families of new asymmetric quantum codes [[n,k,dz/dx

  12. State building energy codes status

    SciTech Connect

    1996-09-01

    This document contains the State Building Energy Codes Status prepared by Pacific Northwest National Laboratory for the U.S. Department of Energy under Contract DE-AC06-76RL01830 and dated September 1996. The U.S. Department of Energy`s Office of Codes and Standards has developed this document to provide an information resource for individuals interested in energy efficiency of buildings and the relevant building energy codes in each state and U.S. territory. This is considered to be an evolving document and will be updated twice a year. In addition, special state updates will be issued as warranted.

  13. Facilitating Internet-Scale Code Retrieval

    ERIC Educational Resources Information Center

    Bajracharya, Sushil Krishna

    2010-01-01

    Internet-Scale code retrieval deals with the representation, storage, and access of relevant source code from a large amount of source code available on the Internet. Internet-Scale code retrieval systems support common emerging practices among software developers related to finding and reusing source code. In this dissertation we focus on some…

  14. Bandwidth efficient coding for satellite communications

    NASA Technical Reports Server (NTRS)

    Lin, Shu; Costello, Daniel J., Jr.; Miller, Warner H.; Morakis, James C.; Poland, William B., Jr.

    1992-01-01

    An error control coding scheme was devised to achieve large coding gain and high reliability by using coded modulation with reduced decoding complexity. To achieve a 3 to 5 dB coding gain and moderate reliability, the decoding complexity is quite modest. In fact, to achieve a 3 dB coding gain, the decoding complexity is quite simple, no matter whether trellis coded modulation or block coded modulation is used. However, to achieve coding gains exceeding 5 dB, the decoding complexity increases drastically, and the implementation of the decoder becomes very expensive and unpractical. The use is proposed of coded modulation in conjunction with concatenated (or cascaded) coding. A good short bandwidth efficient modulation code is used as the inner code and relatively powerful Reed-Solomon code is used as the outer code. With properly chosen inner and outer codes, a concatenated coded modulation scheme not only can achieve large coding gains and high reliability with good bandwidth efficiency but also can be practically implemented. This combination of coded modulation and concatenated coding really offers a way of achieving the best of three worlds, reliability and coding gain, bandwidth efficiency, and decoding complexity.

  15. Internationalizing professional codes in engineering.

    PubMed

    Harris, Charles E

    2004-07-01

    Professional engineering societies which are based in the United States, such as the American Society of Mechanical Engineers (ASME, now ASME International) are recognizing that their codes of ethics must apply to engineers working throughout the world. An examination of the ethical code of the ASME International shows that its provisions pose many problems of application, especially in societies outside the United States. In applying the codes effectively in the international environment, two principal issues must be addressed. First, some Culture Transcending Guidelines must be identified and justified. Nine such guidelines are identified Second, some methods for applying the codes to particular situations must be identified Three such methods are specification, balancing, and finding a creative middle way.

  16. FLYCHK Collisional-Radiative Code

    National Institute of Standards and Technology Data Gateway

    SRD 160 FLYCHK Collisional-Radiative Code (Web, free access)   FLYCHK provides a capability to generate atomic level populations and charge state distributions for low-Z to mid-Z elements under NLTE conditions.

  17. Seals Flow Code Development 1993

    NASA Technical Reports Server (NTRS)

    Liang, Anita D. (Compiler); Hendricks, Robert C. (Compiler)

    1994-01-01

    Seals Workshop of 1993 code releases include SPIRALI for spiral grooved cylindrical and face seal configurations; IFACE for face seals with pockets, steps, tapers, turbulence, and cavitation; GFACE for gas face seals with 'lift pad' configurations; and SCISEAL, a CFD code for research and design of seals of cylindrical configuration. GUI (graphical user interface) and code usage was discussed with hands on usage of the codes, discussions, comparisons, and industry feedback. Other highlights for the Seals Workshop-93 include environmental and customer driven seal requirements; 'what's coming'; and brush seal developments including flow visualization, numerical analysis, bench testing, T-700 engine testing, tribological pairing and ceramic configurations, and cryogenic and hot gas facility brush seal results. Also discussed are seals for hypersonic engines and dynamic results for spiral groove and smooth annular seals.

  18. NFPA's Hydrogen Technologies Code Project

    SciTech Connect

    Rivkin, C. H.

    2008-12-01

    This article discusses the development of National Fire Protection Association 2 (NFPA), a comprehensive hydrogen safety code. It analyses the contents of this document with particular attention focused on new requirements for setting hydrogen storage systems. These new requirements use computational fluid dynamic modeling and risk assessment procedures to develop requirements that are based on both technical analyses and defined risk criteria. The intent is to develop requirements based on procedures that can be replicated based on the information provided in the code document. This code will require documentation of the modeling inputs and risk criteria and analyses in the supporting information. This article also includes a description of the codes and standards that address hydrogen technologies in general.

  19. Property Control through Bar Coding.

    ERIC Educational Resources Information Center

    Kingma, Gerben J.

    1984-01-01

    A public utility company uses laser wands to read bar-coded labels on furniture and equipment. The system allows an 80 percent savings of the time required to create reports for inventory control. (MLF)

  20. The moving mesh code SHADOWFAX

    NASA Astrophysics Data System (ADS)

    Vandenbroucke, B.; De Rijcke, S.

    2016-07-01

    We introduce the moving mesh code SHADOWFAX, which can be used to evolve a mixture of gas, subject to the laws of hydrodynamics and gravity, and any collisionless fluid only subject to gravity, such as cold dark matter or stars. The code is written in C++ and its source code is made available to the scientific community under the GNU Affero General Public Licence. We outline the algorithm and the design of our implementation, and demonstrate its validity through the results of a set of basic test problems, which are also part of the public version. We also compare SHADOWFAX with a number of other publicly available codes using different hydrodynamical integration schemes, illustrating the advantages and disadvantages of the moving mesh technique.

  1. Edge equilibrium code for tokamaks

    SciTech Connect

    Li, Xujing; Drozdov, Vladimir V.

    2014-01-15

    The edge equilibrium code (EEC) described in this paper is developed for simulations of the near edge plasma using the finite element method. It solves the Grad-Shafranov equation in toroidal coordinate and uses adaptive grids aligned with magnetic field lines. Hermite finite elements are chosen for the numerical scheme. A fast Newton scheme which is the same as implemented in the equilibrium and stability code (ESC) is applied here to adjust the grids.

  2. Computer-Access-Code Matrices

    NASA Technical Reports Server (NTRS)

    Collins, Earl R., Jr.

    1990-01-01

    Authorized users respond to changing challenges with changing passwords. Scheme for controlling access to computers defeats eavesdroppers and "hackers". Based on password system of challenge and password or sign, challenge, and countersign correlated with random alphanumeric codes in matrices of two or more dimensions. Codes stored on floppy disk or plug-in card and changed frequently. For even higher security, matrices of four or more dimensions used, just as cubes compounded into hypercubes in concurrent processing.

  3. Product Work Classification and Coding

    DTIC Science & Technology

    1986-06-01

    detail is much more useful in planning steel welding processes. In this regard remember that mild steel , HSLA steel , and high-yield steel (e.g. HY80 ...manufacturing facility. In Figure 2.3-2, a classification and coding system for steel parts is shown. This classification and coding system sorts steel parts...system would provide a shop which produced steel parts with a means of organizing parts. Rather than attempting to manage all of its parts as a single

  4. The Integrated TIGER Series Codes

    SciTech Connect

    Kensek, Ronald P.; Franke, Brian C.; Laub, Thomas W.

    2006-01-15

    ITS is a powerful and user-friendly software package permitting state-of-the-art Monte Carlo solution of linear time-independent coupled electron/photon radiation transport problems, with or without the presence of macroscopic electric and magnetic fields of arbitrary spatial dependence. Our goal has been to simultaneously maximize operational simplicity and physical accuracy. Through a set of preprocessor directives, the user selects one of the many ITS codes. The ease with which the makefile system is applied combines with an input scheme based on order-independent descriptive keywords that makes maximum use of defaults and intemal error checking to provide experimentalists and theorists alike with a method for the routine but rigorous solution of sophisticated radiation transport problems. Physical rigor is provided by employing accurate cross sections, sampling distributions, and physical models for describing the production and transport of the electron/photon cascade from 1.0 GeV down to 1.0 keV. The availability of source code permits the more sophisticated user to tailor the codes to specific applications and to extend the capabilities of the codes to more complex applications. Version 5.0, the latest version of ITS, contains (1) improvements to the ITS 3.0 continuous-energy codes, (2) multigroup codes with adjoint transport capabilities, (3) parallel implementations of all ITS codes, (4) a general purpose geometry engine for linking with CAD or other geometry formats, and (5) the Cholla facet geometry library. Moreover, the general user friendliness of the software has been enhanced through increased internal error checking and improved code portability.

  5. National Combustion Code: Parallel Performance

    NASA Technical Reports Server (NTRS)

    Babrauckas, Theresa

    2001-01-01

    This report discusses the National Combustion Code (NCC). The NCC is an integrated system of codes for the design and analysis of combustion systems. The advanced features of the NCC meet designers' requirements for model accuracy and turn-around time. The fundamental features at the inception of the NCC were parallel processing and unstructured mesh. The design and performance of the NCC are discussed.

  6. UNIX code management and distribution

    SciTech Connect

    Hung, T.; Kunz, P.F.

    1992-09-01

    We describe a code management and distribution system based on tools freely available for the UNIX systems. At the master site, version control is managed with CVS, which is a layer on top of RCS, and distribution is done via NFS mounted file systems. At remote sites, small modifications to CVS provide for interactive transactions with the CVS system at the master site such that remote developers are true peers in the code development process.

  7. Spaceflight Validation of Hzetrn Code

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.; Shinn, J. L.; Singleterry, R. C.; Badavi, F. F.; Badhwar, G. D.; Reitz, G.; Beaujean, R.; Cucinotta, F. A.

    1999-01-01

    HZETRN is being developed as a fast deterministic radiation transport code applicable to neutrons, protons, and multiply charged ions in the space environment. It was recently applied to 50 hours of IMP8 data measured during the August 4, 1972 solar event to map the hourly exposures within the human body under several shield configurations. This calculation required only 18 hours on a VAX 4000 machine. A similar calculation using the Monte Carlo method would have required two years of dedicated computer time. The code has been benchmarked against well documented and tested Monte Carlo proton transport codes with good success. The code will allow important trade studies to be made with relative ease due to the computational speed and will be useful in assessing design alternatives in an integrated system software environment. Since there are no well tested Monte Carlo codes for HZE particles, we have been engaged in flight validation of the HZETRN results. To date we have made comparison with TEPC, CR-39, charge particle telescopes, and Bonner spheres. This broad range of detectors allows us to test a number of functions related to differing physical processes which add to the complicated radiation fields within a spacecraft or the human body, which functions can be calculated by the HZETRN code system. In the present report we will review these results.

  8. Rotating-Pump Design Code

    NASA Technical Reports Server (NTRS)

    Walker, James F.; Chen, Shu-Cheng; Scheer, Dean D.

    2006-01-01

    Pump Design (PUMPDES) is a computer program for designing a rotating pump for liquid hydrogen, liquid oxygen, liquid nitrogen, water, methane, or ethane. Using realistic properties of these fluids provided by another program called GASPAK, this code performs a station-by-station, mean-line analysis along the pump flow path, obtaining thermodynamic properties of the pumped fluid at each station and evaluating hydraulic losses along the flow path. The variables at each station are obtained under constraints that are consistent with the underlying physical principles. The code evaluates the performance of each stage and the overall pump. In addition, by judiciously choosing the givens and the unknowns, the code can perform a geometric inverse design function: that is, it can compute a pump geometry that yields a closest approximation of given design point. The code contains two major parts: one for an axial-rotor/inducer and one for a multistage centrifugal pump. The inducer and the centrifugal pump are functionally integrated. The code can be used in designing and/or evaluating the inducer/centrifugal-pump combination or the centrifugal pump alone. The code is written in standard Fortran 77.

  9. An active Mitochondrial Complex II Present in Mature Seeds Contains an Embryo-Specific Iron–Sulfur Subunit Regulated by ABA and bZIP53 and Is Involved in Germination and Seedling Establishment

    PubMed Central

    Restovic, Franko; Espinoza-Corral, Roberto; Gómez, Isabel; Vicente-Carbajosa, Jesús; Jordana, Xavier

    2017-01-01

    Complex II (succinate dehydrogenase) is an essential mitochondrial enzyme involved in both the tricarboxylic acid cycle and the respiratory chain. In Arabidopsis thaliana, its iron–sulfur subunit (SDH2) is encoded by three genes, one of them (SDH2.3) being specifically expressed during seed maturation in the embryo. Here we show that seed SDH2.3 expression is regulated by abscisic acid (ABA) and we define the promoter region (-114 to +49) possessing all the cis-elements necessary and sufficient for high expression in seeds. This region includes between -114 and -32 three ABRE (ABA-responsive) elements and one RY-enhancer like element, and we demonstrate that these elements, although necessary, are not sufficient for seed expression, our results supporting a role for the region encoding the 5’ untranslated region (+1 to +49). The SDH2.3 promoter is activated in leaf protoplasts by heterodimers between the basic leucine zipper transcription factors bZIP53 (group S1) and bZIP10 (group C) acting through the ABRE elements, and by the B3 domain transcription factor ABA insensitive 3 (ABI3). The in vivo role of bZIP53 is further supported by decreased SDH2.3 expression in a knockdown bzip53 mutant. By using the protein synthesis inhibitor cycloheximide and sdh2 mutants we have been able to conclusively show that complex II is already present in mature embryos before imbibition, and contains mainly SDH2.3 as iron–sulfur subunit. This complex plays a role during seed germination sensu-stricto since we have previously shown that seeds lacking SDH2.3 show retarded germination and now we demonstrate that low concentrations of thenoyltrifluoroacetone, a complex II inhibitor, also delay germination. Furthermore, complex II inhibitors completely block hypocotyl elongation in the dark and seedling establishment in the light, highlighting an essential role of complex II in the acquisition of photosynthetic competence and the transition from heterotrophy to autotrophy. PMID

  10. An active Mitochondrial Complex II Present in Mature Seeds Contains an Embryo-Specific Iron-Sulfur Subunit Regulated by ABA and bZIP53 and Is Involved in Germination and Seedling Establishment.

    PubMed

    Restovic, Franko; Espinoza-Corral, Roberto; Gómez, Isabel; Vicente-Carbajosa, Jesús; Jordana, Xavier

    2017-01-01

    Complex II (succinate dehydrogenase) is an essential mitochondrial enzyme involved in both the tricarboxylic acid cycle and the respiratory chain. In Arabidopsis thaliana, its iron-sulfur subunit (SDH2) is encoded by three genes, one of them (SDH2.3) being specifically expressed during seed maturation in the embryo. Here we show that seed SDH2.3 expression is regulated by abscisic acid (ABA) and we define the promoter region (-114 to +49) possessing all the cis-elements necessary and sufficient for high expression in seeds. This region includes between -114 and -32 three ABRE (ABA-responsive) elements and one RY-enhancer like element, and we demonstrate that these elements, although necessary, are not sufficient for seed expression, our results supporting a role for the region encoding the 5' untranslated region (+1 to +49). The SDH2.3 promoter is activated in leaf protoplasts by heterodimers between the basic leucine zipper transcription factors bZIP53 (group S1) and bZIP10 (group C) acting through the ABRE elements, and by the B3 domain transcription factor ABA insensitive 3 (ABI3). The in vivo role of bZIP53 is further supported by decreased SDH2.3 expression in a knockdown bzip53 mutant. By using the protein synthesis inhibitor cycloheximide and sdh2 mutants we have been able to conclusively show that complex II is already present in mature embryos before imbibition, and contains mainly SDH2.3 as iron-sulfur subunit. This complex plays a role during seed germination sensu-stricto since we have previously shown that seeds lacking SDH2.3 show retarded germination and now we demonstrate that low concentrations of thenoyltrifluoroacetone, a complex II inhibitor, also delay germination. Furthermore, complex II inhibitors completely block hypocotyl elongation in the dark and seedling establishment in the light, highlighting an essential role of complex II in the acquisition of photosynthetic competence and the transition from heterotrophy to autotrophy.

  11. The Proteomic Code: a molecular recognition code for proteins

    PubMed Central

    Biro, Jan C

    2007-01-01

    Background The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic Code. Review The 25-year-old history of this concept is reviewed from the first independent suggestions by Biro and Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller and others, followed by the discovery of a Common Periodic Table of Codons and Nucleic Acids in 2003 and culminating in the recent conceptualization of partial complementary coding of interacting amino acids as well as the theory of the nucleic acid-assisted protein folding. Methods and conclusions A novel cloning method for the design and production of specific, high-affinity-reacting proteins (SHARP) is presented. This method is based on the concept of proteomic codes and is suitable for large-scale, industrial production of specifically interacting peptides. PMID:17999762

  12. Cleanup MAC and MBA code ATP

    SciTech Connect

    Russell, V.K.

    1994-10-17

    The K Basins Materials Accounting (MAC) and Material Balance (MBA) database system had some minor code cleanup performed to its code. This ATP describes how the code was to be tested to verify its correctness.

  13. Codes That Support Smart Growth Development

    EPA Pesticide Factsheets

    Provides examples of local zoning codes that support smart growth development, categorized by: unified development code, form-based code, transit-oriented development, design guidelines, street design standards, and zoning overlay.

  14. Tribal Green Building Administrative Code Example

    EPA Pesticide Factsheets

    This Tribal Green Building Administrative Code Example can be used as a template for technical code selection (i.e., building, electrical, plumbing, etc.) to be adopted as a comprehensive building code.

  15. 75 FR 19944 - International Code Council: The Update Process for the International Codes and Standards

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-16

    ... National Institute of Standards and Technology International Code Council: The Update Process for the International Codes and Standards AGENCY: National Institute of Standards and Technology, Commerce. ACTION: Notice. SUMMARY: The International Code Council (ICC), promulgator of the International Codes...

  16. 78 FR 18321 - International Code Council: The Update Process for the International Codes and Standards

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-26

    ... National Institute of Standards and Technology International Code Council: The Update Process for the International Codes and Standards AGENCY: National Institute of Standards and Technology, Commerce. ACTION: Notice. SUMMARY: The International Code Council (ICC), promulgator of the International Codes...

  17. Evolution of the genetic code.

    PubMed

    Davis, B K

    1999-01-01

    Comparative path lengths in amino acid biosynthesis and other molecular indicators of the timing of codon assignment were examined to reconstruct the main stages of code evolution. The codon tree obtained was rooted in the 4 N-fixing amino acids (Asp, Glu, Asn, Gln) and 16 triplets of the NAN set. This small, locally phased (commaless) code evidently arose from ambiguous translation on a poly(A) collector strand, in a surface reaction network. Copolymerisation of these amino acids yields polyanionic peptide chains, which could anchor uncharged amide residues to a positively charged mineral surface. From RNA virus structure and replication in vitro, the first genes seemed to be RNA segments spliced into tRNA. Expansion of the code reduced the risk of mutation to an unreadable codon. This step was conditional on initiation at the 5'-codon of a translated sequence. Incorporation of increasingly hydrophobic amino acids accompanied expansion. As codons of the NUN set were assigned most slowly, they received the most nonpolar amino acids. The origin of ferredoxin and Gln synthetase was traced to mid-expansion phase. Surface metabolism ceased by the end of code expansion, as cells bounded by a proteo-phospholipid membrane, with a protoATPase, had emerged. Incorporation of positively charged and aromatic amino acids followed. They entered the post-expansion code by codon capture. Synthesis of efficient enzymes with acid-base catalysis was then possible. Both types of aminoacyl-tRNA synthetases were attributed to this stage. tRNA sequence diversity and error rates in RNA replication indicate the code evolved within 20 million yr in the preIsuan era. These findings on the genetic code provide empirical evidence, from a contemporaneous source, that a surface reaction network, centred on C-fixing autocatalytic cycles, rapidly led to cellular life on Earth.

  18. NASA Rotor 37 CFD Code Validation: Glenn-HT Code

    NASA Technical Reports Server (NTRS)

    Ameri, Ali A.

    2010-01-01

    In order to advance the goals of NASA aeronautics programs, it is necessary to continuously evaluate and improve the computational tools used for research and design at NASA. One such code is the Glenn-HT code which is used at NASA Glenn Research Center (GRC) for turbomachinery computations. Although the code has been thoroughly validated for turbine heat transfer computations, it has not been utilized for compressors. In this work, Glenn-HT was used to compute the flow in a transonic compressor and comparisons were made to experimental data. The results presented here are in good agreement with this data. Most of the measures of performance are well within the measurement uncertainties and the exit profiles of interest agree with the experimental measurements.

  19. Coordinated design of coding and modulation systems

    NASA Technical Reports Server (NTRS)

    Massey, J. L.; Ancheta, T.; Johannesson, R.; Lauer, G.; Lee, L.

    1976-01-01

    The joint optimization of the coding and modulation systems employed in telemetry systems was investigated. Emphasis was placed on formulating inner and outer coding standards used by the Goddard Spaceflight Center. Convolutional codes were found that are nearly optimum for use with Viterbi decoding in the inner coding of concatenated coding systems. A convolutional code, the unit-memory code, was discovered and is ideal for inner system usage because of its byte-oriented structure. Simulations of sequential decoding on the deep-space channel were carried out to compare directly various convolutional codes that are proposed for use in deep-space systems.

  20. 76 FR 77549 - Lummi Nation-Title 20-Code of Laws-Liquor Code

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-13

    ... Bureau of Indian Affairs Lummi Nation--Title 20--Code of Laws--Liquor Code AGENCY: Bureau of Indian...--Code of Laws--Liquor Code. The Code regulates and controls the possession, sale and consumption of... this Code allows for the possession and sale of alcoholic beverages within the Lummi...

  1. International assessment of PCA codes

    SciTech Connect

    Neymotin, L.; Lui, C.; Glynn, J.; Archarya, S.

    1993-11-01

    Over the past three years (1991-1993), an extensive international exercise for intercomparison of a group of six Probabilistic Consequence Assessment (PCA) codes was undertaken. The exercise was jointly sponsored by the Commission of European Communities (CEC) and OECD Nuclear Energy Agency. This exercise was a logical continuation of a similar effort undertaken by OECD/NEA/CSNI in 1979-1981. The PCA codes are currently used by different countries for predicting radiological health and economic consequences of severe accidents at nuclear power plants (and certain types of non-reactor nuclear facilities) resulting in releases of radioactive materials into the atmosphere. The codes participating in the exercise were: ARANO (Finland), CONDOR (UK), COSYMA (CEC), LENA (Sweden), MACCS (USA), and OSCAAR (Japan). In parallel with this inter-code comparison effort, two separate groups performed a similar set of calculations using two of the participating codes, MACCS and COSYMA. Results of the intercode and inter-MACCS comparisons are presented in this paper. The MACCS group included four participants: GREECE: Institute of Nuclear Technology and Radiation Protection, NCSR Demokritos; ITALY: ENEL, ENEA/DISP, and ENEA/NUC-RIN; SPAIN: Universidad Politecnica de Madrid (UPM) and Consejo de Seguridad Nuclear; USA: Brookhaven National Laboratory, US NRC and DOE.

  2. Driver Code for Adaptive Optics

    NASA Technical Reports Server (NTRS)

    Rao, Shanti

    2007-01-01

    A special-purpose computer code for a deformable-mirror adaptive-optics control system transmits pixel-registered control from (1) a personal computer running software that generates the control data to (2) a circuit board with 128 digital-to-analog converters (DACs) that generate voltages to drive the deformable-mirror actuators. This program reads control-voltage codes from a text file, then sends them, via the computer s parallel port, to a circuit board with four AD5535 (or equivalent) chips. Whereas a similar prior computer program was capable of transmitting data to only one chip at a time, this program can send data to four chips simultaneously. This program is in the form of C-language code that can be compiled and linked into an adaptive-optics software system. The program as supplied includes source code for integration into the adaptive-optics software, documentation, and a component that provides a demonstration of loading DAC codes from a text file. On a standard Windows desktop computer, the software can update 128 channels in 10 ms. On Real-Time Linux with a digital I/O card, the software can update 1024 channels (8 boards in parallel) every 8 ms.

  3. AEST: Adaptive Eigenvalue Stability Code

    NASA Astrophysics Data System (ADS)

    Zheng, L.-J.; Kotschenreuther, M.; Waelbroeck, F.; van Dam, J. W.; Berk, H.

    2002-11-01

    An adaptive eigenvalue linear stability code is developed. The aim is on one hand to include the non-ideal MHD effects into the global MHD stability calculation for both low and high n modes and on the other hand to resolve the numerical difficulty involving MHD singularity on the rational surfaces at the marginal stability. Our code follows some parts of philosophy of DCON by abandoning relaxation methods based on radial finite element expansion in favor of an efficient shooting procedure with adaptive gridding. The δ W criterion is replaced by the shooting procedure and subsequent matrix eigenvalue problem. Since the technique of expanding a general solution into a summation of the independent solutions employed, the rank of the matrices involved is just a few hundreds. This makes easier to solve the eigenvalue problem with non-ideal MHD effects, such as FLR or even full kinetic effects, as well as plasma rotation effect, taken into account. To include kinetic effects, the approach of solving for the distribution function as a local eigenvalue ω problem as in the GS2 code will be employed in the future. Comparison of the ideal MHD version of the code with DCON, PEST, and GATO will be discussed. The non-ideal MHD version of the code will be employed to study as an application the transport barrier physics in tokamak discharges.

  4. A genetic scale of reading frame coding.

    PubMed

    Michel, Christian J

    2014-08-21

    The reading frame coding (RFC) of codes (sets) of trinucleotides is a genetic concept which has been largely ignored during the last 50 years. A first objective is the definition of a new and simple statistical parameter PrRFC for analysing the probability (efficiency) of reading frame coding (RFC) of any trinucleotide code. A second objective is to reveal different classes and subclasses of trinucleotide codes involved in reading frame coding: the circular codes of 20 trinucleotides and the bijective genetic codes of 20 trinucleotides coding the 20 amino acids. This approach allows us to propose a genetic scale of reading frame coding which ranges from 1/3 with the random codes (RFC probability identical in the three frames) to 1 with the comma-free circular codes (RFC probability maximal in the reading frame and null in the two shifted frames). This genetic scale shows, in particular, the reading frame coding probabilities of the 12,964,440 circular codes (PrRFC=83.2% in average), the 216 C(3) self-complementary circular codes (PrRFC=84.1% in average) including the code X identified in eukaryotic and prokaryotic genes (PrRFC=81.3%) and the 339,738,624 bijective genetic codes (PrRFC=61.5% in average) including the 52 codes without permuted trinucleotides (PrRFC=66.0% in average). Otherwise, the reading frame coding probabilities of each trinucleotide code coding an amino acid with the universal genetic code are also determined. The four amino acids Gly, Lys, Phe and Pro are coded by codes (not circular) with RFC probabilities equal to 2/3, 1/2, 1/2 and 2/3, respectively. The amino acid Leu is coded by a circular code (not comma-free) with a RFC probability equal to 18/19. The 15 other amino acids are coded by comma-free circular codes, i.e. with RFC probabilities equal to 1. The identification of coding properties in some classes of trinucleotide codes studied here may bring new insights in the origin and evolution of the genetic code.

  5. Roadmap to Majorana surface codes

    NASA Astrophysics Data System (ADS)

    Plugge, S.; Landau, L. A.; Sela, E.; Altland, A.; Flensberg, K.; Egger, R.

    2016-11-01

    Surface codes offer a very promising avenue towards fault-tolerant quantum computation. We argue that two-dimensional interacting networks of Majorana bound states in topological superconductor/semiconductor heterostructures hold several key advantages in that direction, concerning both the hardware realization and the actual operation of the code. We here discuss how topologically protected logical qubits in this Majorana surface code architecture can be defined, initialized, manipulated, and read out. All physical ingredients needed to implement these operations are routinely used in topologically trivial quantum devices. By means of quantum interference terms in linear conductance measurements, single-electron pumping protocols, and gate-tunable tunnel barriers, the full set of quantum gates required for universal quantum computation can be achieved. In particular, we show that designated multistep pumping sequences via tunnel-coupled quantum dots realize high-fidelity ancilla states for phase gates.

  6. ASME Code Efforts Supporting HTGRs

    SciTech Connect

    D.K. Morton

    2012-09-01

    In 1999, an international collaborative initiative for the development of advanced (Generation IV) reactors was started. The idea behind this effort was to bring nuclear energy closer to the needs of sustainability, to increase proliferation resistance, and to support concepts able to produce energy (both electricity and process heat) at competitive costs. The U.S. Department of Energy has supported this effort by pursuing the development of the Next Generation Nuclear Plant, a high temperature gas-cooled reactor. This support has included research and development of pertinent data, initial regulatory discussions, and engineering support of various codes and standards development. This report discusses the various applicable American Society of Mechanical Engineers (ASME) codes and standards that are being developed to support these high temperature gascooled reactors during construction and operation. ASME is aggressively pursuing these codes and standards to support an international effort to build the next generation of advanced reactors so that all can benefit.

  7. A coded tracking telemetry system

    USGS Publications Warehouse

    Howey, P.W.; Seegar, W.S.; Fuller, M.R.; Titus, K.; Amlaner, Charles J.

    1989-01-01

    We describe the general characteristics of an automated radio telemetry system designed to operate for prolonged periods on a single frequency. Each transmitter sends a unique coded signal to a receiving system that encodes and records only the appropriater, pre-programmed codes. A record of the time of each reception is stored on diskettes in a micro-computer. This system enables continuous monitoring of infrequent signals (e.g. one per minute or one per hour), thus extending operation life or allowing size reduction of the transmitter, compared to conventional wildlife telemetry. Furthermore, when using unique codes transmitted on a single frequency, biologists can monitor many individuals without exceeding the radio frequency allocations for wildlife.

  8. FLOWTRAN-TF code benchmarking

    SciTech Connect

    Flach, G.P.

    1990-12-01

    FLOWTRAN-TF is a two-component (air-water), two-phase thermal-hydraulics code designed for performing accident analyses of SRS reactor fuel assemblies during the Emergency Cooling System (ECS) phase of a Double Ended Guillotine Break (DEGB) Loss Of Coolant Accident (LOCA). A description of the code is given by Flach et al. (1990). This report provides benchmarking results for the version of FLOWTRAN-TF used to compute the Recommended K-Reactor Restart ECS Power Limit (Smith et al., 1990a; 1990b). Individual constitutive relations are benchmarked in Sections 2 through 5 while in Sections 6 and 7 integral code benchmarking results are presented. An overall assessment of FLOWTRAN-TF for its intended use in computing the ECS power limit completes the document.

  9. FLOWTRAN-TF code description

    SciTech Connect

    Flach, G.P.

    1990-12-01

    FLOWTRAN-TF is a two-component (air-water), two-phase thermal-hydraulics code designed for performing accident analyses of SRS reactor fuel assemblies during the Emergency Cooling System (ECS) phase of a Double Ended Guillotine Break (DEGB) Loss of Coolant Accident (LOCA). This report provides a brief description of the physical models in the version of FLOWTRAN-TF used to compute the Recommended K-Reactor Restart ECS Power Limit. This document is viewed as an interim report and should ultimately be superseded by a comprehensive user/programmer manual. In general, only high level discussions of governing equations and constitutive laws are presented. Numerical implementation of these models, code architecture and user information are not generally covered. A companion document describing code benchmarking is available.

  10. FLOWTRAN-TF code description

    SciTech Connect

    Flach, G.P.

    1991-09-01

    FLOWTRAN-TF is a two-component (air-water), two-phase thermal-hydraulics code designed for performing accident analyses of SRS reactor fuel assemblies during the Emergency Cooling System (ECS) phase of a Double Ended Guillotine Break (DEGB) Loss of Coolant Accident (LOCA). This report provides a brief description of the physical models in the version of FLOWTRAN-TF used to compute the Recommended K-Reactor Restart ECS Power Limit. This document is viewed as an interim report and should ultimately be superseded by a comprehensive user/programmer manual. In general, only high level discussions of governing equations and constitutive laws are presented. Numerical implementation of these models, code architecture and user information are not generally covered. A companion document describing code benchmarking is available.

  11. ASME Code Efforts Supporting HTGRs

    SciTech Connect

    D.K. Morton

    2011-09-01

    In 1999, an international collaborative initiative for the development of advanced (Generation IV) reactors was started. The idea behind this effort was to bring nuclear energy closer to the needs of sustainability, to increase proliferation resistance, and to support concepts able to produce energy (both electricity and process heat) at competitive costs. The U.S. Department of Energy has supported this effort by pursuing the development of the Next Generation Nuclear Plant, a high temperature gas-cooled reactor. This support has included research and development of pertinent data, initial regulatory discussions, and engineering support of various codes and standards development. This report discusses the various applicable American Society of Mechanical Engineers (ASME) codes and standards that are being developed to support these high temperature gascooled reactors during construction and operation. ASME is aggressively pursuing these codes and standards to support an international effort to build the next generation of advanced reactors so that all can benefit.

  12. ASME Code Efforts Supporting HTGRs

    SciTech Connect

    D.K. Morton

    2010-09-01

    In 1999, an international collaborative initiative for the development of advanced (Generation IV) reactors was started. The idea behind this effort was to bring nuclear energy closer to the needs of sustainability, to increase proliferation resistance, and to support concepts able to produce energy (both electricity and process heat) at competitive costs. The U.S. Department of Energy has supported this effort by pursuing the development of the Next Generation Nuclear Plant, a high temperature gas-cooled reactor. This support has included research and development of pertinent data, initial regulatory discussions, and engineering support of various codes and standards development. This report discusses the various applicable American Society of Mechanical Engineers (ASME) codes and standards that are being developed to support these high temperature gascooled reactors during construction and operation. ASME is aggressively pursuing these codes and standards to support an international effort to build the next generation of advanced reactors so that all can benefit.

  13. Verification of FANTASTIC integrated code

    NASA Technical Reports Server (NTRS)

    Chauhan, Rajinder Singh

    1987-01-01

    FANTASTIC is an acronym for Failure Analysis Nonlinear Thermal and Structural Integrated Code. This program was developed by Failure Analysis Associates, Palo Alto, Calif., for MSFC to improve the accuracy of solid rocket motor nozzle analysis. FANTASTIC has three modules: FACT - thermochemical analysis; FAHT - heat transfer analysis; and FAST - structural analysis. All modules have keywords for data input. Work is in progress for the verification of the FAHT module, which is done by using data for various problems with known solutions as inputs to the FAHT module. The information obtained is used to identify problem areas of the code and passed on to the developer for debugging purposes. Failure Analysis Associates have revised the first version of the FANTASTIC code and a new improved version has been released to the Thermal Systems Branch.

  14. The stellar atmosphere simulation code Bifrost. Code description and validation

    NASA Astrophysics Data System (ADS)

    Gudiksen, B. V.; Carlsson, M.; Hansteen, V. H.; Hayek, W.; Leenaarts, J.; Martínez-Sykora, J.

    2011-07-01

    Context. Numerical simulations of stellar convection and photospheres have been developed to the point where detailed shapes of observed spectral lines can be explained. Stellar atmospheres are very complex, and very different physical regimes are present in the convection zone, photosphere, chromosphere, transition region and corona. To understand the details of the atmosphere it is necessary to simulate the whole atmosphere since the different layers interact strongly. These physical regimes are very diverse and it takes a highly efficient massively parallel numerical code to solve the associated equations. Aims: The design, implementation and validation of the massively parallel numerical code Bifrost for simulating stellar atmospheres from the convection zone to the corona. Methods: The code is subjected to a number of validation tests, among them the Sod shock tube test, the Orzag-Tang colliding shock test, boundary condition tests and tests of how the code treats magnetic field advection, chromospheric radiation, radiative transfer in an isothermal scattering atmosphere, hydrogen ionization and thermal conduction. Results.Bifrost completes the tests with good results and shows near linear efficiency scaling to thousands of computing cores.

  15. Hybrid codes: Methods and applications

    SciTech Connect

    Winske, D. ); Omidi, N. )

    1991-01-01

    In this chapter we discuss hybrid'' algorithms used in the study of low frequency electromagnetic phenomena, where one or more ion species are treated kinetically via standard PIC methods used in particle codes and the electrons are treated as a single charge neutralizing massless fluid. Other types of hybrid models are possible, as discussed in Winske and Quest, but hybrid codes with particle ions and massless fluid electrons have become the most common for simulating space plasma physics phenomena in the last decade, as we discuss in this paper.

  16. Sensor Authentication: Embedded Processor Code

    SciTech Connect

    Svoboda, John

    2012-09-25

    Described is the c code running on the embedded Microchip 32bit PIC32MX575F256H located on the INL developed noise analysis circuit board. The code performs the following functions: Controls the noise analysis circuit board preamplifier voltage gains of 1, 10, 100, 000 Initializes the analog to digital conversion hardware, input channel selection, Fast Fourier Transform (FFT) function, USB communications interface, and internal memory allocations Initiates high resolution 4096 point 200 kHz data acquisition Computes complex 2048 point FFT and FFT magnitude. Services Host command set Transfers raw data to Host Transfers FFT result to host Communication error checking

  17. Guidelines for Coding FORTRAN Programs.

    DTIC Science & Technology

    1982-07-01

    39529 PE63759N I I CONTROLLING OFFICE NAME AND ADDRESS 12. REPORT DATE Naval Ocean Research and Development Activity July 1982 Code 320 13. NUMBER OF...Element 63759N. ,-! ri ii Contents 1. INTRODUCTION 1 1.1 Scope 1 2. CODING FORTRAN STATEMENTS 2 2.1 General Remarks and Sug- 2 gestions 2.2 FORTRAN...Assignment 11 5.3 Masking Assignment 11 5.4 Multiple Assignment 11 6. CONTROL STATEMENTS 11 6.1 GO TO Statement 11 6.1.1 Unconditional GO TO 11 Statement

  18. Radio Losses for Concatenated Codes

    NASA Astrophysics Data System (ADS)

    Shambayati, S.

    2002-07-01

    The advent of higher powered spacecraft amplifiers and better ground receivers capable of tracking spacecraft carrier signals with narrower loop bandwidths requires better understanding of the carrier tracking loss (radio loss) mechanism of the concatenated codes used for deep-space missions. In this article, we present results of simulations performed for a (7,1/2), Reed-Solomon (255,223), interleaver depth-5 concatenated code in order to shed some light on this issue. Through these simulations, we obtained the performance of this code over an additive white Gaussian noise (AWGN) channel (the baseline performance) in terms of both its frame-error rate (FER) and its bit-error rate at the output of the Reed-Solomon decoder (RS-BER). After obtaining these results, we curve fitted the baseline performance curves for FER and RS-BER and calculated the high-rate radio losses for this code for an FER of 10^(-4) and its corresponding baseline RS-BER of 2.1 x 10^(-6) for a carrier loop signal-to-noise ratio (SNR) of 14.8 dB. This calculation revealed that even though over the AWGN channel the FER value and the RS-BER value correspond to each other (i.e., these values are obtained by the same bit SNR value), the RS-BER value has higher high-rate losses than does the FER value. Furthermore, this calculation contradicted the previous assumption th at at high data rates concatenated codes have the same radio losses as their constituent convolutional codes. Our results showed much higher losses for the FER and the RS-BER (by as much as 2 dB) than for the corresponding baseline BER of the convolutional code. Further simulations were performed to investigate the effects of changes in the data rate on the code's radio losses. It was observed that as the data rate increased the radio losses for both the FER and the RS-BER approached their respective calculated high-rate values. Furthermore, these simulations showed that a simple two-parameter function could model the increase in the

  19. Coding productivity in Sydney public hospitals.

    PubMed

    Dimitropoulos, Vera; Bennett, Adam; McIntosh, Jean

    2002-01-01

    The aims of this study were to compare Sydney public hospitals regarding medical record coding times to compare observed coding times with coding times necessary to avoid backlog and to evaluate the impact on coding time of casemix complexity, coder age, experience, job satisfaction, employment status, and salary. Coding time (in minutes) for each medical record over a two-week period was documented by 61 coders employed in 13 hospitals: six principal referral (PR), six major metropolitan (MM), and one paediatric specialist (PS) hospitals. The mean coding time for each coder was estimated by averaging across coding times for all records during the two-week period. In order to compare hospital mean coding times, the hospitals were grouped into PR and MM/PS groups. The mean coding time necessary to avoid coding backlog (expected coding time) for each hospital group was based on the total number of annual separations and filled full-time equivalent coding positions. The observed mean coding time was longer in the PR group than in the MM/PS group (p = 0.019); however, the observed coding time was within the expected coding time limit in both the PR and MM/PS groups. Casemix complexity tended to influence coding time, but neither age, experience, job satisfaction, employment status nor salary had any impact. In conclusion, the expected coding times, if reliable, indicate that coders in the two hospital groups were keeping coding up-to-date. Thus, the variation between hospital groups in coding time is of little importance, given that the main objective in coding productivity is to maintain the coding workload.

  20. Multiple component codes based generalized LDPC codes for high-speed optical transport.

    PubMed

    Djordjevic, Ivan B; Wang, Ting

    2014-07-14

    A class of generalized low-density parity-check (GLDPC) codes suitable for optical communications is proposed, which consists of multiple local codes. It is shown that Hamming, BCH, and Reed-Muller codes can be used as local codes, and that the maximum a posteriori probability (MAP) decoding of these local codes by Ashikhmin-Lytsin algorithm is feasible in terms of complexity and performance. We demonstrate that record coding gains can be obtained from properly designed GLDPC codes, derived from multiple component codes. We then show that several recently proposed classes of LDPC codes such as convolutional and spatially-coupled codes can be described using the concept of GLDPC coding, which indicates that the GLDPC coding can be used as a unified platform for advanced FEC enabling ultra-high speed optical transport. The proposed class of GLDPC codes is also suitable for code-rate adaption, to adjust the error correction strength depending on the optical channel conditions.

  1. 49 CFR 178.702 - IBC codes.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false IBC codes. 178.702 Section 178.702 Transportation...-Oriented Standards § 178.702 IBC codes. (a) Intermediate bulk container code designations consist of: two... the category of intermediate bulk container. (1) IBC code number designations are as follows: Type...

  2. 32 CFR 635.19 - Offense codes.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 4 2010-07-01 2010-07-01 true Offense codes. 635.19 Section 635.19 National... INVESTIGATIONS LAW ENFORCEMENT REPORTING Offense Reporting § 635.19 Offense codes. (a) The offense code describes, as nearly as possible, the complaint or offense by using an alphanumeric code. Appendix C of AR...

  3. 7 CFR 201.24 - Code designation.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Code designation. 201.24 Section 201.24 Agriculture... REGULATIONS Labeling Agricultural Seeds § 201.24 Code designation. The code designation used in lieu of the... as may be designated by him for the purpose. When used, the code designation shall appear on...

  4. 7 CFR 201.28 - Code designation.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Code designation. 201.28 Section 201.28 Agriculture... REGULATIONS Labeling Vegetable Seeds § 201.28 Code designation. The code designation used in lieu of the full... as may be designated by him for the purpose. When used, the code designation shall appear on...

  5. An Interactive Concatenated Turbo Coding System

    NASA Technical Reports Server (NTRS)

    Liu, Ye; Tang, Heng; Lin, Shu; Fossorier, Marc

    1999-01-01

    This paper presents a concatenated turbo coding system in which a Reed-Solomon outer code is concatenated with a binary turbo inner code. In the proposed system, the outer code decoder and the inner turbo code decoder interact to achieve both good bit error and frame error performances. The outer code decoder helps the inner turbo code decoder to terminate its decoding iteration while the inner turbo code decoder provides soft-output information to the outer code decoder to carry out a reliability-based soft- decision decoding. In the case that the outer code decoding fails, the outer code decoder instructs the inner code decoder to continue its decoding iterations until the outer code decoding is successful or a preset maximum number of decoding iterations is reached. This interaction between outer and inner code decoders reduces decoding delay. Also presented in the paper are an effective criterion for stopping the iteration process of the inner code decoder and a new reliability-based decoding algorithm for nonbinary codes.

  6. Convolutional coding combined with continuous phase modulation

    NASA Technical Reports Server (NTRS)

    Pizzi, S. V.; Wilson, S. G.

    1985-01-01

    Background theory and specific coding designs for combined coding/modulation schemes utilizing convolutional codes and continuous-phase modulation (CPM) are presented. In this paper the case of r = 1/2 coding onto a 4-ary CPM is emphasized, with short-constraint length codes presented for continuous-phase FSK, double-raised-cosine, and triple-raised-cosine modulation. Coding buys several decibels of coding gain over the Gaussian channel, with an attendant increase of bandwidth. Performance comparisons in the power-bandwidth tradeoff with other approaches are made.

  7. Multichannel error correction code decoder

    NASA Technical Reports Server (NTRS)

    Wagner, Paul K.; Ivancic, William D.

    1993-01-01

    A brief overview of a processing satellite for a mesh very-small-aperture (VSAT) communications network is provided. The multichannel error correction code (ECC) decoder system, the uplink signal generation and link simulation equipment, and the time-shared decoder are described. The testing is discussed. Applications of the time-shared decoder are recommended.

  8. Tri-Coding of Information.

    ERIC Educational Resources Information Center

    Simpson, Timothy J.

    Paivio's Dual Coding Theory has received widespread recognition for its connection between visual and aural channels of internal information processing. The use of only two channels, however, cannot satisfactorily explain the effects witnessed every day. This paper presents a study suggesting the presence a third, kinesthetic channel, currently…

  9. Three-dimensional stellarator codes

    PubMed Central

    Garabedian, P. R.

    2002-01-01

    Three-dimensional computer codes have been used to develop quasisymmetric stellarators with modular coils that are promising candidates for a magnetic fusion reactor. The mathematics of plasma confinement raises serious questions about the numerical calculations. Convergence studies have been performed to assess the best configurations. Comparisons with recent data from large stellarator experiments serve to validate the theory. PMID:12140367

  10. Overview of CODE V development

    NASA Astrophysics Data System (ADS)

    Harris, Thomas I.

    1991-01-01

    This paper is part of a session that is aimed at briefly describing some of today''s optical design software packages with emphasis on the program''s philosophy and technology. CODE V is the ongoing result of a development process that began in the 1960''s it is now the result of many people''s efforts. This paper summarizes the roots of the program some of its history dominant philosophies and technologies that have contributed to its usefulness and some that drive its continued development. ROOTS OF CODE V Conceived in the early 60''s This was at a time when there was skepticism that " automatic design" could design lenses equal or better than " hand" methods. The concepts underlying CODE V and its predecessors were based on ten years of experience and exposure to the problems of a group of lens designers in a design-for-manufacture environment. The basic challenge was to show that lens design could be done better easier and faster by high quality computer-assisted design tools. The earliest development was for our own use as an engineering services organization -an in-house tool for custom design. As a tool it had to make us efficient in providing lens design and engineering services as a self-sustaining business. PHILOSOPHY OF OVTIM!ZATION IN CODE V Error function formation Based on experience as a designer we felt very strongly that there should be a clear separation of

  11. Reusable State Machine Code Generator

    NASA Astrophysics Data System (ADS)

    Hoffstadt, A. A.; Reyes, C.; Sommer, H.; Andolfato, L.

    2010-12-01

    The State Machine model is frequently used to represent the behaviour of a system, allowing one to express and execute this behaviour in a deterministic way. A graphical representation such as a UML State Chart diagram tames the complexity of the system, thus facilitating changes to the model and communication between developers and domain experts. We present a reusable state machine code generator, developed by the Universidad Técnica Federico Santa María and the European Southern Observatory. The generator itself is based on the open source project architecture, and uses UML State Chart models as input. This allows for a modular design and a clean separation between generator and generated code. The generated state machine code has well-defined interfaces that are independent of the implementation artefacts such as the middle-ware. This allows using the generator in the substantially different observatory software of the Atacama Large Millimeter Array and the ESO Very Large Telescope. A project-specific mapping layer for event and transition notification connects the state machine code to its environment, which can be the Common Software of these projects, or any other project. This approach even allows to automatically create tests for a generated state machine, using techniques from software testing, such as path-coverage.

  12. Coded continuous wave meteor radar

    NASA Astrophysics Data System (ADS)

    Vierinen, Juha; Chau, Jorge L.; Pfeffer, Nico; Clahsen, Matthias; Stober, Gunter

    2016-03-01

    The concept of a coded continuous wave specular meteor radar (SMR) is described. The radar uses a continuously transmitted pseudorandom phase-modulated waveform, which has several advantages compared to conventional pulsed SMRs. The coding avoids range and Doppler aliasing, which are in some cases problematic with pulsed radars. Continuous transmissions maximize pulse compression gain, allowing operation at lower peak power than a pulsed system. With continuous coding, the temporal and spectral resolution are not dependent on the transmit waveform and they can be fairly flexibly changed after performing a measurement. The low signal-to-noise ratio before pulse compression, combined with independent pseudorandom transmit waveforms, allows multiple geographically separated transmitters to be used in the same frequency band simultaneously without significantly interfering with each other. Because the same frequency band can be used by multiple transmitters, the same interferometric receiver antennas can be used to receive multiple transmitters at the same time. The principles of the signal processing are discussed, in addition to discussion of several practical ways to increase computation speed, and how to optimally detect meteor echoes. Measurements from a campaign performed with a coded continuous wave SMR are shown and compared with two standard pulsed SMR measurements. The type of meteor radar described in this paper would be suited for use in a large-scale multi-static network of meteor radar transmitters and receivers. Such a system would be useful for increasing the number of meteor detections to obtain improved meteor radar data products.

  13. QR Codes: Taking Collections Further

    ERIC Educational Resources Information Center

    Ahearn, Caitlin

    2014-01-01

    With some thought and direction, QR (quick response) codes are a great tool to use in school libraries to enhance access to information. From March through April 2013, Caitlin Ahearn interned at Sanborn Regional High School (SRHS) under the supervision of Pam Harland. As a result of Harland's un-Deweying of the nonfiction collection at SRHS,…

  14. Generating Constant Weight Binary Codes

    ERIC Educational Resources Information Center

    Knight, D.G.

    2008-01-01

    The determination of bounds for A(n, d, w), the maximum possible number of binary vectors of length n, weight w, and pairwise Hamming distance no less than d, is a classic problem in coding theory. Such sets of vectors have many applications. A description is given of how the problem can be used in a first-year undergraduate computational…

  15. Dress Codes and Gang Activity.

    ERIC Educational Resources Information Center

    Gluckman, Ivan B.

    1996-01-01

    Concern with school violence and efforts to reduce gang visibility at school have led to controversy about students' constitutional rights to freedom of expression. This document outlines legal precedents and offers guidelines for developing a sound school policy on dress codes. It answers the following questions: (1) Are gang clothing and symbols…

  16. AEDS Property Classification Code Manual.

    ERIC Educational Resources Information Center

    Association for Educational Data Systems, Washington, DC.

    The control and inventory of property items using data processing machines requires a form of numerical description or code which will allow a maximum of description in a minimum of space on the data card. An adaptation of a standard industrial classification system is given to cover any expendable warehouse item or non-expendable piece of…

  17. Quantum rate-distortion coding

    NASA Astrophysics Data System (ADS)

    Barnum, Howard

    2000-10-01

    I introduce rate-distortion theory for the coding of quantum information, and derive a lower bound, involving the coherent information, on the rate at which qubits must be used to store or compress an entangled quantum source with a given maximum level of distortion per source emission.

  18. Transversal Clifford gates on folded surface codes

    SciTech Connect

    Moussa, Jonathan E.

    2016-10-12

    Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surface codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. Lastly, the specific application of these codes to universal quantum computation based on qubit fusion is also discussed.

  19. Transversal Clifford gates on folded surface codes

    DOE PAGES

    Moussa, Jonathan E.

    2016-10-12

    Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surfacemore » codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. Lastly, the specific application of these codes to universal quantum computation based on qubit fusion is also discussed.« less

  20. Coded Modulations for Mobile Satellite Communication Channels

    NASA Astrophysics Data System (ADS)

    Rhee, Dojun

    1995-01-01

    The mobile satellite (MSAT) channel is subject to multipath fading, shadowing, Doppler frequency shift, and adjacent channel interference (ACI). Therefore, transmitted signals face severe amplitude and phase distortions. This dissertation investigates various high performance and low decoding complexity coded modulation schemes for reliable voice and data transmissions over the shadowed mobile satellite channel and the Rayleigh fading channel. The dissertation consists of four parts. The first part presents a systematic technique for constructing MPSK trellis coded modulation (TCM) codes for voice transmission over the MSAT channel. The multilevel coding method is used for constructing TCM codes using convolutional codes with good free branch distances as the component codes or using both convolutional and block codes as the component codes. Simulation results show that these codes achieve good coding gains over the uncoded reference system and outperform existing TCM codes with the same decoding complexity. In the second part, using the multilevel coding method, multilevel block coded modulation (BCM) codes are constructed for voice transmission over the MSAT channel. Even though BCM is generally less power efficient than TCM for AWGN channels, BCM has a great potential to compete with TCM in the MSAT channel because of its shorter decoding depth and hence more effective interleaving. Binary Reed -Muller (RM) codes of length up to 32 are used as component codes. Simulation results show that these codes achieve good coding gains over the uncoded reference system and outperform TCM codes with the same decoding complexity. In the third part, a simple and systematic technique for constructing multilevel concatenated BCM schemes for data transmission over the shadowed MSAT channel and the Rayleigh fading channel is presented. These schemes are designed to achieve high-performance or large coding gain with reduced decoding complexity. Construction is based on a

  1. Accumulate-Repeat-Accumulate-Accumulate Codes

    NASA Technical Reports Server (NTRS)

    Divsalar, Dariush; Dolinar, Samuel; Thorpe, Jeremy

    2007-01-01

    Accumulate-repeat-accumulate-accumulate (ARAA) codes have been proposed, inspired by the recently proposed accumulate-repeat-accumulate (ARA) codes. These are error-correcting codes suitable for use in a variety of wireless data-communication systems that include noisy channels. ARAA codes can be regarded as serial turbolike codes or as a subclass of low-density parity-check (LDPC) codes, and, like ARA codes they have projected graph or protograph representations; these characteristics make it possible to design high-speed iterative decoders that utilize belief-propagation algorithms. The objective in proposing ARAA codes as a subclass of ARA codes was to enhance the error-floor performance of ARA codes while maintaining simple encoding structures and low maximum variable node degree.

  2. Transversal Clifford gates on folded surface codes

    NASA Astrophysics Data System (ADS)

    Moussa, Jonathan E.

    2016-10-01

    Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surface codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. The specific application of these codes to universal quantum computation based on qubit fusion is also discussed.

  3. Letting the Data Lead the Code

    DTIC Science & Technology

    2015-08-01

    UNCLASSIFIED Page 1 of 4 UNCLASSIFIED: Distribution Statement A. Approved for public release. Letting the Data Lead the Code Darryl Bryk...used can radically simplify the code . A simple change to the way data is stored in a file can make a big difference in the code required to read it...This was made apparent recently with some Visual Basic code which would locate a list of numbers based on certain search criteria. The code was about

  4. Colour cyclic code for Brillouin distributed sensors

    NASA Astrophysics Data System (ADS)

    Le Floch, Sébastien; Sauser, Florian; Llera, Miguel; Rochat, Etienne

    2015-09-01

    For the first time, a colour cyclic coding (CCC) is theoretically and experimentally demonstrated for Brillouin optical time-domain analysis (BOTDA) distributed sensors. Compared to traditional intensity-modulated cyclic codes, the code presents an additional gain of √2 while keeping the same number of sequences as for a colour coding. A comparison with a standard BOTDA sensor is realized and validates the theoretical coding gain.

  5. The chromatin regulatory code: Beyond a histone code

    NASA Astrophysics Data System (ADS)

    Lesne, A.

    2006-03-01

    In this commentary on the contribution by Arndt Benecke in this issue, I discuss why the notion of “chromatin code” introduced and elaborated in this paper is to be preferred to that of “histone code”. Speaking of a code as regards nucleosome conformation and histone tail post-translational modifications only makes sense within the chromatin fiber, where their physico-chemical features can be translated into regulatory programs at the genome level, by means of a complex, multi-level interplay with the fiber architecture and dynamics settled in the course of Evolution. In particular, this chromatin code presumably exploits allosteric transitions of the chromatin fiber. The chromatin structure dependence of its translation suggests two alternative modes of transcription initiation regulation, also proposed in the paper by A. Benecke in this issue for interpreting strikingly bimodal micro-array data.

  6. The neuronal code(s) of the cerebellum.

    PubMed

    Heck, Detlef H; De Zeeuw, Chris I; Jaeger, Dieter; Khodakhah, Kamran; Person, Abigail L

    2013-11-06

    Understanding how neurons encode information in sequences of action potentials is of fundamental importance to neuroscience. The cerebellum is widely recognized for its involvement in the coordination of movements, which requires muscle activation patterns to be controlled with millisecond precision. Understanding how cerebellar neurons accomplish such high temporal precision is critical to understanding cerebellar function. Inhibitory Purkinje cells, the only output neurons of the cerebellar cortex, and their postsynaptic target neurons in the cerebellar nuclei, fire action potentials at high, sustained frequencies, suggesting spike rate modulation as a possible code. Yet, millisecond precise spatiotemporal spike activity patterns in Purkinje cells and inferior olivary neurons have also been observed. These results and ongoing studies suggest that the neuronal code used by cerebellar neurons may span a wide time scale from millisecond precision to slow rate modulations, likely depending on the behavioral context.

  7. Superimposed Code Theorectic Analysis of DNA Codes and DNA Computing

    DTIC Science & Technology

    2010-03-01

    that the hybridization that occurs between a DNA strand and its Watson - Crick complement can be used to perform mathematical computation. This research... Watson - Crick (WC) duplex, e.g., TCGCA TCGCA . Note that non-WC duplexes can form and such a formation is called a cross-hybridization. Cross...5’GAAAGTCGCGTA3’ Watson Crick (WC) Duplexes TACGCGACTTTC Cross Hybridized (CH) Duplexes ATTTTTGCGTTA GAAAAAGAAGAA Coding Strands for Ligation

  8. Genetic coding and gene expression - new Quadruplet genetic coding model

    NASA Astrophysics Data System (ADS)

    Shankar Singh, Rama

    2012-07-01

    Successful demonstration of human genome project has opened the door not only for developing personalized medicine and cure for genetic diseases, but it may also answer the complex and difficult question of the origin of life. It may lead to making 21st century, a century of Biological Sciences as well. Based on the central dogma of Biology, genetic codons in conjunction with tRNA play a key role in translating the RNA bases forming sequence of amino acids leading to a synthesized protein. This is the most critical step in synthesizing the right protein needed for personalized medicine and curing genetic diseases. So far, only triplet codons involving three bases of RNA, transcribed from DNA bases, have been used. Since this approach has several inconsistencies and limitations, even the promise of personalized medicine has not been realized. The new Quadruplet genetic coding model proposed and developed here involves all four RNA bases which in conjunction with tRNA will synthesize the right protein. The transcription and translation process used will be the same, but the Quadruplet codons will help overcome most of the inconsistencies and limitations of the triplet codes. Details of this new Quadruplet genetic coding model and its subsequent potential applications including relevance to the origin of life will be presented.

  9. Code-excited linear predictive coding of multispectral MR images

    NASA Astrophysics Data System (ADS)

    Hu, Jian-Hong; Wang, Yao; Cahill, Patrick

    1996-02-01

    This paper reports a multispectral code excited linear predictive coding method for the compression of well-registered multispectral MR images. Different linear prediction models and the adaptation schemes have been compared. The method which uses forward adaptive autoregressive (AR) model has proven to achieve a good compromise between performance, complexity and robustness. This approach is referred to as the MFCELP method. Given a set of multispectral images, the linear predictive coefficients are updated over non-overlapping square macroblocks. Each macro-block is further divided into several micro-blocks and, the best excitation signals for each microblock are determined through an analysis-by-synthesis procedure. To satisfy the high quality requirement for medical images, the error between the original images and the synthesized ones are further specified using a vector quantizer. The MFCELP method has been applied to 26 sets of clinical MR neuro images (20 slices/set, 3 spectral bands/slice, 256 by 256 pixels/image, 12 bits/pixel). It provides a significant improvement over the discrete cosine transform (DCT) based JPEG method, a wavelet transform based embedded zero-tree wavelet (EZW) coding method, as well as the MSARMA method we developed before.

  10. Amino acid codes in mitochondria as possible clues to primitive codes

    NASA Technical Reports Server (NTRS)

    Jukes, T. H.

    1981-01-01

    Differences between mitochondrial codes and the universal code indicate that an evolutionary simplification has taken place, rather than a return to a more primitive code. However, these differences make it evident that the universal code is not the only code possible, and therefore earlier codes may have differed markedly from the previous code. The present universal code is probably a 'frozen accident.' The change in CUN codons from leucine to threonine (Neurospora vs. yeast mitochondria) indicates that neutral or near-neutral changes occurred in the corresponding proteins when this code change took place, caused presumably by a mutation in a tRNA gene.

  11. The Mystery Behind the Code: Differentiated Instruction with Quick Response Codes in Secondary Physical Education

    ERIC Educational Resources Information Center

    Adkins, Megan; Wajciechowski, Misti R.; Scantling, Ed

    2013-01-01

    Quick response codes, better known as QR codes, are small barcodes scanned to receive information about a specific topic. This article explains QR code technology and the utility of QR codes in the delivery of physical education instruction. Consideration is given to how QR codes can be used to accommodate learners of varying ability levels as…

  12. Biological Information Transfer Beyond the Genetic Code: The Sugar Code

    NASA Astrophysics Data System (ADS)

    Gabius, H.-J.

    In the era of genetic engineering, cloning, and genome sequencing the focus of research on the genetic code has received an even further accentuation in the public eye. In attempting, however, to understand intra- and intercellular recognition processes comprehensively, the two biochemical dimensions established by nucleic acids and proteins are not sufficient to satisfactorily explain all molecular events in, for example, cell adhesion or routing. The consideration of further code systems is essential to bridge this gap. A third biochemical alphabet forming code words with an information storage capacity second to no other substance class in rather small units (words, sentences) is established by monosaccharides (letters). As hardware oligosaccharides surpass peptides by more than seven orders of magnitude in the theoretical ability to build isomers, when the total of conceivable hexamers is calculated. In addition to the sequence complexity, the use of magnetic resonance spectroscopy and molecular modeling has been instrumental in discovering that even small glycans can often reside in not only one but several distinct low-energy conformations (keys). Intriguingly, conformers can display notably different capacities to fit snugly into the binding site of nonhomologous receptors (locks). This process, experimentally verified for two classes of lectins, is termed "differential conformer selection." It adds potential for shifts of the conformer equilibrium to modulate ligand properties dynamically and reversibly to the well-known changes in sequence (including anomeric positioning and linkage points) and in pattern of substitution, for example, by sulfation. In the intimate interplay with sugar receptors (lectins, enzymes, and antibodies) the message of coding units of the sugar code is deciphered. Their recognition will trigger postbinding signaling and the intended biological response. Knowledge about the driving forces for the molecular rendezvous, i

  13. Maximal dinucleotide and trinucleotide circular codes.

    PubMed

    Michel, Christian J; Pellegrini, Marco; Pirillo, Giuseppe

    2016-01-21

    We determine here the number and the list of maximal dinucleotide and trinucleotide circular codes. We prove that there is no maximal dinucleotide circular code having strictly less than 6 elements (maximum size of dinucleotide circular codes). On the other hand, a computer calculus shows that there are maximal trinucleotide circular codes with less than 20 elements (maximum size of trinucleotide circular codes). More precisely, there are maximal trinucleotide circular codes with 14, 15, 16, 17, 18 and 19 elements and no maximal trinucleotide circular code having less than 14 elements. We give the same information for the maximal self-complementary dinucleotide and trinucleotide circular codes. The amino acid distribution of maximal trinucleotide circular codes is also determined.

  14. Quantum codes with low weight stabilizers

    NASA Astrophysics Data System (ADS)

    Kovalev, Alexey A.; Dumer, Ilya; Pryadko, Leonid P.

    2012-02-01

    We study quantum cyclic stabilizer codes whose stabilizer can be always defined by one or two stabilizer generators. Our main goal is to construct low-weight stabilizer generators that can yield quantum codes with high code rate and simple error correction. To do so, we apply the classical quaternary representation of stabilizer codes and extend our recent study of one-generator cyclic codes [1]. For any stabilizer generator of weight four or five, we formulate a necessary and sufficient condition for its commutativity. We then proceed with a design of additive cyclic codes with such generators. In some cases, we also extend our commutativity condition and code design to generators of weight six. In particular, quantum cyclic codes with stabilizers of weight four are mapped to the generalized toric codes. Here we also extend the notion of toric codes using a translationally invariant generator and periodic boundary conditions on a two dimensional lattice. Some of our numerically constructed codes can be redefined by means of Code Word Stabilized (CWS) representation [1] as quantum versions of repetition codes. We particularly concentrate on codes with a fixed nonzero rate for which the minimum distance asymptotically grows as the blocklength grows.[4pt] [1] arXiv:1108.5490v1

  15. Dual-code quantum computation model

    NASA Astrophysics Data System (ADS)

    Choi, Byung-Soo

    2015-08-01

    In this work, we propose the dual-code quantum computation model—a fault-tolerant quantum computation scheme which alternates between two different quantum error-correction codes. Since the chosen two codes have different sets of transversal gates, we can implement a universal set of gates transversally, thereby reducing the overall cost. We use code teleportation to convert between quantum states in different codes. The overall cost is decreased if code teleportation requires fewer resources than the fault-tolerant implementation of the non-transversal gate in a specific code. To analyze the cost reduction, we investigate two cases with different base codes, namely the Steane and Bacon-Shor codes. For the Steane code, neither the proposed dual-code model nor another variation of it achieves any cost reduction since the conventional approach is simple. For the Bacon-Shor code, the three proposed variations of the dual-code model reduce the overall cost. However, as the encoding level increases, the cost reduction decreases and becomes negative. Therefore, the proposed dual-code model is advantageous only when the encoding level is low and the cost of the non-transversal gate is relatively high.

  16. The EGS5 Code System

    SciTech Connect

    Hirayama, Hideo; Namito, Yoshihito; Bielajew, Alex F.; Wilderman, Scott J.; U., Michigan; Nelson, Walter R.; /SLAC

    2005-12-20

    In the nineteen years since EGS4 was released, it has been used in a wide variety of applications, particularly in medical physics, radiation measurement studies, and industrial development. Every new user and every new application bring new challenges for Monte Carlo code designers, and code refinements and bug fixes eventually result in a code that becomes difficult to maintain. Several of the code modifications represented significant advances in electron and photon transport physics, and required a more substantial invocation than code patching. Moreover, the arcane MORTRAN3[48] computer language of EGS4, was highest on the complaint list of the users of EGS4. The size of the EGS4 user base is difficult to measure, as there never existed a formal user registration process. However, some idea of the numbers may be gleaned from the number of EGS4 manuals that were produced and distributed at SLAC: almost three thousand. Consequently, the EGS5 project was undertaken. It was decided to employ the FORTRAN 77 compiler, yet include as much as possible, the structural beauty and power of MORTRAN3. This report consists of four chapters and several appendices. Chapter 1 is an introduction to EGS5 and to this report in general. We suggest that you read it. Chapter 2 is a major update of similar chapters in the old EGS4 report[126] (SLAC-265) and the old EGS3 report[61] (SLAC-210), in which all the details of the old physics (i.e., models which were carried over from EGS4) and the new physics are gathered together. The descriptions of the new physics are extensive, and not for the faint of heart. Detailed knowledge of the contents of Chapter 2 is not essential in order to use EGS, but sophisticated users should be aware of its contents. In particular, details of the restrictions on the range of applicability of EGS are dispersed throughout the chapter. First-time users of EGS should skip Chapter 2 and come back to it later if necessary. With the release of the EGS4 version

  17. Dopamine reward prediction error coding.

    PubMed

    Schultz, Wolfram

    2016-03-01

    Reward prediction errors consist of the differences between received and predicted rewards. They are crucial for basic forms of learning about rewards and make us strive for more rewards-an evolutionary beneficial trait. Most dopamine neurons in the midbrain of humans, monkeys, and rodents signal a reward prediction error; they are activated by more reward than predicted (positive prediction error), remain at baseline activity for fully predicted rewards, and show depressed activity with less reward than predicted (negative prediction error). The dopamine signal increases nonlinearly with reward value and codes formal economic utility. Drugs of addiction generate, hijack, and amplify the dopamine reward signal and induce exaggerated, uncontrolled dopamine effects on neuronal plasticity. The striatum, amygdala, and frontal cortex also show reward prediction error coding, but only in subpopulations of neurons. Thus, the important concept of reward prediction errors is implemented in neuronal hardware.

  18. Axisymmetric generalized harmonic evolution code

    SciTech Connect

    Sorkin, Evgeny

    2010-04-15

    We describe the first axisymmetric numerical code based on the generalized harmonic formulation of the Einstein equations, which is regular at the axis. We test the code by investigating gravitational collapse of distributions of complex scalar field in a Kaluza-Klein spacetime. One of the key issues of the harmonic formulation is the choice of the gauge source functions, and we conclude that a damped-wave gauge is remarkably robust in this case. Our preliminary study indicates that evolution of regular initial data leads to formation both of black holes with spherical and cylindrical horizon topologies. Intriguingly, we find evidence that near threshold for black hole formation the number of outcomes proliferates. Specifically, the collapsing matter splits into individual pulses, two of which travel in the opposite directions along the compact dimension and one which is ejected radially from the axis. Depending on the initial conditions, a curvature singularity develops inside the pulses.

  19. Multidimensional Fuel Performance Code: BISON

    SciTech Connect

    2014-09-03

    BISON is a finite element based nuclear fuel performance code applicable to a variety of fuel forms including light water reactor fuel rods, TRISO fuel particles, and metallic rod and plate fuel (Refs. [a, b, c]). It solves the fully-coupled equations of thermomechanics and species diffusion and includes important fuel physics such as fission gas release and material property degradation with burnup. BISON is based on the MOOSE framework (Ref. [d]) and can therefore efficiently solve problems on 1-, 2- or 3-D meshes using standard workstations or large high performance computers. BISON is also coupled to a MOOSE-based mesoscale phase field material property simulation capability (Refs. [e, f]). As described here, BISON includes the code library named FOX, which was developed concurrent with BISON. FOX contains material and behavioral models that are specific to oxide fuels.

  20. CBP PHASE I CODE INTEGRATION

    SciTech Connect

    Smith, F.; Brown, K.; Flach, G.; Sarkar, S.

    2011-09-30

    The goal of the Cementitious Barriers Partnership (CBP) is to develop a reasonable and credible set of software tools to predict the structural, hydraulic, and chemical performance of cement barriers used in nuclear applications over extended time frames (greater than 100 years for operating facilities and greater than 1000 years for waste management). The simulation tools will be used to evaluate and predict the behavior of cementitious barriers used in near surface engineered waste disposal systems including waste forms, containment structures, entombments, and environmental remediation. These cementitious materials are exposed to dynamic environmental conditions that cause changes in material properties via (i) aging, (ii) chloride attack, (iii) sulfate attack, (iv) carbonation, (v) oxidation, and (vi) primary constituent leaching. A set of state-of-the-art software tools has been selected as a starting point to capture these important aging and degradation phenomena. Integration of existing software developed by the CBP partner organizations was determined to be the quickest method of meeting the CBP goal of providing a computational tool that improves the prediction of the long-term behavior of cementitious materials. These partner codes were selected based on their maturity and ability to address the problems outlined above. The GoldSim Monte Carlo simulation program (GTG 2010a, GTG 2010b) was chosen as the code integration platform (Brown & Flach 2009b). GoldSim (current Version 10.5) is a Windows based graphical object-oriented computer program that provides a flexible environment for model development (Brown & Flach 2009b). The linking of GoldSim to external codes has previously been successfully demonstrated (Eary 2007, Mattie et al. 2007). GoldSim is capable of performing deterministic and probabilistic simulations and of modeling radioactive decay and constituent transport. As part of the CBP project, a general Dynamic Link Library (DLL) interface was