Science.gov

Sample records for elektrichnogo polya na

  1. Poly(A) polymerase-based poly(A) length assay

    PubMed Central

    Patil, Deepak P.; Bakthavachalu, Baskar; Schoenberg, Daniel R.

    2013-01-01

    Summary mRNA polyadenylation functions in nuclear export, translation and stability. We describe an efficient protocol designed to assess poly(A) tail length that is based on 3' tailing by yeast poly(A) polymerase and product analysis to single-nucleotide resolution by capillary electrophoresis. PMID:24590776

  2. Spatial Reasoning and Polya's Five Planes Problem

    ERIC Educational Resources Information Center

    Madden, Sean P.; Diaz, Ricardo

    2008-01-01

    Middle and High school students of the twenty-first century possess surprising powers of spatial reasoning. They are assisted by technologies not available to earlier generations. Both of these assertions are demonstrated by students who are challenged with George Polya's classic Five Planes Problem. (Contains 5 figures.)

  3. Occlusion of the HIV poly(A) site.

    PubMed

    Weichs an der Glon, C; Monks, J; Proudfoot, N J

    1991-02-01

    To investigate the selective use of poly(A) sites in the 3' long terminal repeat (LTR) but not the 5' LTR of retroviruses, we have studied the poly(A) site of the human immunodeficiency virus (HIV-1). Using hybrid HIV/alpha-globin gene constructs, we demonstrate that the HIV poly(A) site is inactive or occluded when adjacent to an active promoter, either the homologous HIV promoter or the alpha-globin gene promoter. Furthermore, this occlusion of the HIV poly(A) site occurs over a considerable distance of up to at least 500 bp. In contrast, two nonretroviral poly(A) sites [alpha-globin and a synthetic poly(A) site] are active when close to a promoter. We also show that a short fragment of approximately 60 nucleotides containing the HIV poly(A) site is fully active when placed at the 3' end of the human alpha-globin gene or within the rabbit beta-globin gene. This result rules out the requirement of more distant upstream elements for the activity of the HIV poly(A) site, as has been suggested for other viral poly(A) sites. Finally, we show that the GT-rich downstream region of the HIV poly(A) site confers poly(A) site occlusion properties on a synthetic poly(A) site. This result focuses attention on this more variable part of a poly(A) site in retroviruses as a possible general signal for poly(A) site occlusion. PMID:1995416

  4. Journey into Problem Solving: A Gift from Polya

    NASA Astrophysics Data System (ADS)

    Lederman, Eric

    2009-02-01

    In How to Solve It, accomplished mathematician and skilled communicator George Polya describes a four-step universal solving technique designed to help students develop mathematical problem-solving skills. By providing a glimpse at the grace with which experts solve problems, Polya provides definable methods that are not exclusive to mathematicians but of interest to cognitive psychologists and problem solvers in all fields. I had the good fortune to be introduced to Polya's ideas in my first undergraduate class in physics.

  5. Presence of a polyA tail at the 3’-end of Maize rayado fino virus RNA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maize rayado fino virus (MRFV) is the type member of the genus Marafivirus in the family Tymoviridae, yet is distinct from other members of the genus in that its genome reportedly lacks a poly(A) tail at the 3’-terminus. Using naïve and targeted PCR-based approaches, we now show that the MRFV genom...

  6. Journey into Problem Solving: A Gift from Polya

    ERIC Educational Resources Information Center

    Lederman, Eric

    2009-01-01

    In "How to Solve It", accomplished mathematician and skilled communicator George Polya describes a four-step universal solving technique designed to help students develop mathematical problem-solving skills. By providing a glimpse at the grace with which experts solve problems, Polya provides definable methods that are not exclusive to…

  7. Analysis of Circadian Regulation of Poly(A) Tail Length

    PubMed Central

    Kojima, Shihoko; Green, Carla B.

    2015-01-01

    The poly(A) tail is found on the 3’-end of most eukaryotic mRNAs, and its length significantly contributes to the mRNAs half-life and translational competence. Circadian regulation of poly(A) tail length is a powerful mechanism to confer rhythmicity in gene expression post-transcriptionally, and provides a means to regulate protein levels independent of rhythmic transcription in the nucleus. Therefore, analysis of circadian poly(A) tail length regulation is important for a complete understanding of rhythmic physiology, since rhythmically expressed proteins are the ultimate mediators of rhythmic function. Nevertheless, it has previously been challenging to measure changes in poly(A) tail length, especially at a global level, due to technical constraints. However, new methodology based on differential fractionation of mRNAs based on the length of their tails has recently been developed. In this chapter, we will describe these methods as used for examining the circadian regulation of poly(A) tail length and will provide detailed experimental procedures to measure poly(A) tail length both at a the single mRNA level and the global level. Although this chapter concentrates on methods we used for analyzing poly(A) tail length in the mammalian circadian system, the methods described here can be applicable to any organisms and any biological processes. PMID:25662466

  8. Behavior of adsorbed Poly-A onto sodium montmorillonite

    NASA Astrophysics Data System (ADS)

    Palomino-Aquino, Nayeli; Negrón-Mendoza, Alicia

    2015-07-01

    The adsorption of Poly-A (a polynucleotide consisting of adenine, ribose and a phosphate group), onto a clay mineral, was studied to investigate the extent of adsorption, the site of binding, and the capacity of the clay to protect Poly-A, while it is adsorbed onto the clay, from external sources of energy. The results showed that Poly-A presented a high percentage of adsorption at the edges of the clay and that the survival of the polynucleotide was superior to irradiating the polymer in the absence of the clay.

  9. Behavior of adsorbed Poly-A onto sodium montmorillonite

    SciTech Connect

    Palomino-Aquino, Nayeli; Negrón-Mendoza, Alicia

    2015-07-23

    The adsorption of Poly-A (a polynucleotide consisting of adenine, ribose and a phosphate group), onto a clay mineral, was studied to investigate the extent of adsorption, the site of binding, and the capacity of the clay to protect Poly-A, while it is adsorbed onto the clay, from external sources of energy. The results showed that Poly-A presented a high percentage of adsorption at the edges of the clay and that the survival of the polynucleotide was superior to irradiating the polymer in the absence of the clay.

  10. Suzuki Meets Polya: Teaching Mathematics to Young Pupils.

    ERIC Educational Resources Information Center

    Hazlewood, Donald G.; And Others

    1989-01-01

    Describes how Suzuki's methods of teaching young pupils to play the violin can be combined with Polya's ideas on problem solving to teach mathematics to elementary school pupils. Six references are listed. (YP)

  11. Cap homeostasis is independent of poly(A) tail length

    PubMed Central

    Kiss, Daniel L.; Oman, Kenji M.; Dougherty, Julie A.; Mukherjee, Chandrama; Bundschuh, Ralf; Schoenberg, Daniel R.

    2016-01-01

    Cap homeostasis is a cyclical process of decapping and recapping that maintains the cap on a subset of the cytoplasmic transcriptome. Interfering with cytoplasmic capping results in the redistribution of target transcripts from polysomes to non-translating mRNPs, where they accumulate in an uncapped but nonetheless stable form. It is generally thought that decapping is preceded by shortening of the poly(A) tail to a length that can no longer support translation. Therefore recapped target transcripts would either have to undergo cytoplasmic polyadenylation or retain a reasonably long poly(A) tail if they are to return to the translating pool. In cells that are inhibited for cytoplasmic capping there is no change in the overall distribution of poly(A) lengths or in the elution profile of oligo(dT)-bound targets. Poly(A) tail lengths were similar for target mRNAs on polysomes or in non-translating mRNPs, and the presence of polyadenylated uncapped mRNA in mRNPs was confirmed by separation into capped and uncapped pools prior to assay. Finally, in silico analysis of cytoplasmic capping targets revealed significant correlations with genes encoding transcripts with uridylated or multiply modified 3′ ends, and genes possessing multiple 3′-untranslated regions (UTRs) generated by alternative cleavage and polyadenylation. PMID:26673707

  12. Reviving Polya's "Look Back" in a Singapore School

    ERIC Educational Resources Information Center

    Leong, Yew Hoong; Tay, Eng Guan; Toh, Tin Lam; Quek, Khiok Seng; Dindyal, Jaguthsing

    2011-01-01

    This study is based on the stance that Polya's "Look Back," though understudied, remains relevant to Mathematics curricula that place emphasis on problem solving. Although the Singapore Mathematics curriculum adopts the goal of teaching Look Back, research about how it is carried out in actual classroom practice is rare. In our project, we focus…

  13. Tat-dependent occlusion of the HIV poly(A) site.

    PubMed Central

    Weichs an der Glon, C; Ashe, M; Eggermont, J; Proudfoot, N J

    1993-01-01

    Retroviruses must ensure that poly(A) signals in the 3' LTR are highly active, while identical signals in the 5' LTR are inactive (occluded). In the case of HIV-1, both promoter proximity in the 5' LTR and U3 sequences in the 3' LTR may contribute to this regulation. We have discovered a novel regulatory mechanism for poly(A) site occlusion in HIV-1. When transcription initiation from the HIV promoter is activated by Tat, the HIV poly(A) site is specifically occluded, while other poly(A) sites are unaffected by Tat. Nucleotide signals associated with this Tat effect are immediately adjacent to the AAUAAA sequence of the HIV-1 poly(A) signal. These data suggest that elongating RNA polymerase II, activated by Tat specifically occludes the HIV poly(A) site. Images PMID:8491200

  14. Poly(A) Polymerase from Vaccinia Virus-Infected Cells I. Partial Purification and Characterization

    PubMed Central

    Brakel, Christine; Kates, Joseph R.

    1974-01-01

    Poly(A) polymerase activity is induced during vaccinia virus infection of HeLa cells. The enzyme is maximally induced at 3.5 h postinfection. Partial purification frees the preparation of RNase activity and RNA polymerase activity. ATP is the substrate for poly(A) synthesis. A small amount of poly(A) is produced from added adenosine diphosphate due to the production of ATP by an adenylate kinase present in the preparation. The incorporation of ATP into poly(A) is dependent on divalent cations (Mg2+ or Mn2+) and is not inhibited by UTP, CTP, or GTP. Poly(U) stimulates ATP incorporation; poly(A) and poly(C) have little effect on ATP incorporation, and poly(dT) is extremely inhibitory. RNA prepared from HeLa cells and from the partially purified poly(A) polymerase (the enzyme preparation contains endogenous RNA [Brakel and Kates]) stimulates ATP incorporation by poly(A) polymerase which was subjected to DEAE-cellulose chromatography. RNase's, pancreatic and T1, inhibit the production of poly(A). DNase has little effect. Poly(U) is able to stimulate poly(A) production in the presence of T1 RNase. PMID:4417406

  15. The Occurrence and Distribution of Poly(A) Ribonucleic Acid in Soybean

    PubMed Central

    Key, Joe L.; Silflow, Carolyn

    1975-01-01

    The occurrence and distribution of poly(A) sequences in the RNA of soybean (Glycine max var. Wayne) have been studied. Only one of the two species of AMP-rich RNA contains poly(A). D-RNA does not contain detectable poly(A) sequences. The TB-RNA is the poly(A) RNA in this system. At least a part (up to 50% or more) of the mRNA in polyribosomes contains a poly(A) sequence. The poly(A) RNA is heterodisperse in size but has a mean size of approximately 18S (2,000 nucleotides) in urea and formamide gels. The poly(A) fragment resulting from ribonuclease A and T1 digestion migrates as a broad band overlapping the 4 to 5.8S regions of the gels with a mean size of somewhat greater than 5S. No evidence was found for the occurrence of a discrete oligo(A) fragment in the poly(A) RNA; however, oligonucleotides which migrate faster than the poly(A) fraction were observed in preparations which were not bound to oligo(dT) cellulose prior to electrophoresis. This oligonucleotide region was enriched in AMP (up to about 65%) as would be expected after ribonuclease A and T1 digestion. PMID:16659304

  16. Poly(A) binding proteins: are they all created equal?

    PubMed

    Goss, Dixie J; Kleiman, Frida Esther

    2013-01-01

    The PABP family of proteins were originally thought of as a simple shield for the mRNA poly(A) tail. Years of research have shown that PABPs interact not only with the poly(A) tail, but also with specific sequences in the mRNA, having a general and specific role on the metabolism of different mRNAs. The complexity of PABPs function is increased by the interactions of PABPs with factors involved in different cellular functions. PABPs participate in all the metabolic pathways of the mRNA: polyadenylation/deadenylation, mRNA export, mRNA surveillance, translation, mRNA degradation, microRNA-associated regulation, and regulation of expression during development. In this review, we update information on the roles of PABPs and emerging data on the specific interactions of PABP homologs. Specific functions of individual members of PABPC family in development and viral infection are beginning to be elucidated. However, the interactions are complex and recent evidence for exchange of nuclear and cytoplasmic forms of the proteins, as well as post-translational modifications, emphasize the possibilities for fine-tuning the PABP metabolic network. PMID:23424172

  17. Poly(A) RNAs including coding proteins RNAs occur in plant Cajal bodies.

    PubMed

    Niedojadło, Janusz; Kubicka, Ewa; Kalich, Beata; Smoliński, Dariusz J

    2014-01-01

    The localisation of poly(A) RNA in plant cells containing either reticular (Allium cepa) or chromocentric (Lupinus luteus, Arabidopsis thaliana) nuclei was studied through in situ hybridisation. In both types of nuclei, the amount of poly(A) RNA was much greater in the nucleus than in the cytoplasm. In the nuclei, poly(A) RNA was present in structures resembling nuclear bodies. The molecular composition as well as the characteristic ultrastructure of the bodies containing poly(A) RNA demonstrated that they were Cajal bodies. We showed that some poly(A) RNAs in Cajal bodies code for proteins. However, examination of the localisation of active RNA polymerase II and in situ run-on transcription assays both demonstrated that CBs are not sites of transcription and that BrU-containing RNA accumulates in these structures long after synthesis. In addition, it was demonstrated that accumulation of poly(A) RNA occurs in the nuclei and CBs of hypoxia-treated cells. Our findings indicated that CBs may be involved in the later stages of poly(A) RNA metabolism, playing a role storage or retention. PMID:25369024

  18. Poly(A) RNAs Including Coding Proteins RNAs Occur in Plant Cajal Bodies

    PubMed Central

    Niedojadło, Janusz; Kubicka, Ewa; Kalich, Beata; Smoliński, Dariusz J.

    2014-01-01

    The localisation of poly(A) RNA in plant cells containing either reticular (Allium cepa) or chromocentric (Lupinus luteus, Arabidopsis thaliana) nuclei was studied through in situ hybridisation. In both types of nuclei, the amount of poly(A) RNA was much greater in the nucleus than in the cytoplasm. In the nuclei, poly(A) RNA was present in structures resembling nuclear bodies. The molecular composition as well as the characteristic ultrastructure of the bodies containing poly(A) RNA demonstrated that they were Cajal bodies. We showed that some poly(A) RNAs in Cajal bodies code for proteins. However, examination of the localisation of active RNA polymerase II and in situ run-on transcription assays both demonstrated that CBs are not sites of transcription and that BrU-containing RNA accumulates in these structures long after synthesis. In addition, it was demonstrated that accumulation of poly(A) RNA occurs in the nuclei and CBs of hypoxia-treated cells. Our findings indicated that CBs may be involved in the later stages of poly(A) RNA metabolism, playing a role storage or retention. PMID:25369024

  19. The Influence of SV40 polyA on Gene Expression of Baculovirus Expression Vector Systems

    PubMed Central

    Salem, Tamer Z.; Seaborn, Craig P.; Turney, Colin M.; Xue, Jianli; Shang, Hui; Cheng, Xiao-Wen

    2015-01-01

    The simian virus 40 polyadenylation signal (SV40 polyA) has been routinely inserted downstream of the polyhedrin promoter in many baculovirus expression vector systems (BEVS). In the baculovirus prototype Autographa californica multiple nucleopolyhedrovirus (AcMNPV), the polyhedrin promoter (very late promoter) transcribes its gene by a viral RNA polymerase therefore there is no supporting evidence that SV40 polyA is required for the proper gene expression under the polyhedrin promoter. Moreover, the effect of the SV40 polyA sequence on the polyhedrin promoter activity has not been tested either at its natural polyhedrin locus or in other loci in the viral genome. In order to test the significance of adding the SV40 polyA sequence on gene expression, the expression of the enhanced green fluorescent protein (egfp) was evaluated with and without the presence of SV40 polyA under the control of the polyhedrin promoter at different genomic loci (polyherin, ecdysteroid UDP-glucosyltransferase (egt), and gp37). In this study, spectrofluorometry and western blot showed reduction of EGFP protein for all recombinant viruses with SV40 polyA, whereas qPCR showed an increase in the egfp mRNA levels. Therefore, we conclude that SV40 polyA increases mRNA levels but decreases protein production in the BEVS when the polyhedrin promoter is used at different loci. This work suggests that SV40 polyA in BEVSs should be replaced by an AcMNPV late gene polyA for optimal protein production or left untouched for optimal RNA production (RNA interference applications). PMID:26659470

  20. An improved poly(A) motifs recognition method based on decision level fusion.

    PubMed

    Zhang, Shanxin; Han, Jiuqiang; Liu, Jun; Zheng, Jiguang; Liu, Ruiling

    2015-02-01

    Polyadenylation is the process of addition of poly(A) tail to mRNA 3' ends. Identification of motifs controlling polyadenylation plays an essential role in improving genome annotation accuracy and better understanding of the mechanisms governing gene regulation. The bioinformatics methods used for poly(A) motifs recognition have demonstrated that information extracted from sequences surrounding the candidate motifs can differentiate true motifs from the false ones greatly. However, these methods depend on either domain features or string kernels. To date, methods combining information from different sources have not been found yet. Here, we proposed an improved poly(A) motifs recognition method by combing different sources based on decision level fusion. First of all, two novel prediction methods was proposed based on support vector machine (SVM): one method is achieved by using the domain-specific features and principle component analysis (PCA) method to eliminate the redundancy (PCA-SVM); the other method is based on Oligo string kernel (Oligo-SVM). Then we proposed a novel machine-learning method for poly(A) motif prediction by marrying four poly(A) motifs recognition methods, including two state-of-the-art methods (Random Forest (RF) and HMM-SVM), and two novel proposed methods (PCA-SVM and Oligo-SVM). A decision level information fusion method was employed to combine the decision values of different classifiers by applying the DS evidence theory. We evaluated our method on a comprehensive poly(A) dataset that consists of 14,740 samples on 12 variants of poly(A) motifs and 2750 samples containing none of these motifs. Our method has achieved accuracy up to 86.13%. Compared with the four classifiers, our evidence theory based method reduces the average error rate by about 30%, 27%, 26% and 16%, respectively. The experimental results suggest that the proposed method is more effective for poly(A) motif recognition. PMID:25594576

  1. RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library

    PubMed Central

    Guo, Yan; Zhao, Shilin; Sheng, Quanhu; Guo, Mingsheng; Lehmann, Brian; Pietenpol, Jennifer; Samuels, David C.; Shyr, Yu

    2015-01-01

    The most popular RNA library used for RNA sequencing is the poly(A) captured RNA library. This library captures RNA based on the presence of poly(A) tails at the 3′ end. Another type of RNA library for RNA sequencing is the total RNA library which differs from the poly(A) library by capture method and price. The total RNA library costs more and its capture of RNA is not dependent on the presence of poly(A) tails. In practice, only ribosomal RNAs and small RNAs are washed out in the total RNA library preparation. To evaluate the ability of detecting RNA for both RNA libraries we designed a study using RNA sequencing data of the same two breast cancer cell lines from both RNA libraries. We found that the RNA expression values captured by both RNA libraries were highly correlated. However, the number of RNAs captured was significantly higher for the total RNA library. Furthermore, we identify several subsets of protein coding RNAs that were not captured efficiently by the poly(A) library. One of the most noticeable is the histone-encode genes, which lack the poly(A) tail. PMID:26543871

  2. The effects of Polya's heuristic and diary writing on children's problem solving

    NASA Astrophysics Data System (ADS)

    Hensberry, Karina K. R.; Jacobbe, Tim

    2012-03-01

    This paper presents the results of a study that aimed at increasing students' problem-solving skills. Polya's (1985) heuristic for problem solving was used and students were required to articulate their thought processes through the use of a structured diary. The diary prompted students to answer questions designed to engage them in the phases of Polya's (1985) heuristic. While it appeared as though most students did not internalise the diary questions, further analysis of students' responses indicated that most students showed improvement in their solution strategies. These results indicate that having students write about their thinking may be beneficial for developing their problem-solving skills.

  3. Relooking "Look Back": A Student's Attempt at Problem Solving Using Polya's Model

    ERIC Educational Resources Information Center

    Leong, Yew Hoong; Toh, Tin Lam; Tay, Eng Guan; Quek, Khiok Seng; Dindyal, Jaguthsing

    2012-01-01

    Against the backdrop of half a century of research in mathematics problem solving, Polya's last stage is especially conspicuous--by the scarcity of research on it! Much of the research focused on the first three stages (J.M. Francisco and C.A. Maher, "Conditions for promoting reasoning in problem solving: Insights from a longitudinal study," J.…

  4. The Effects of Polya's Heuristic and Diary Writing on Children's Problem Solving

    ERIC Educational Resources Information Center

    Hensberry, Karina K. R.; Jacobbe, Tim

    2012-01-01

    This paper presents the results of a study that aimed at increasing students' problem-solving skills. Polya's (1985) heuristic for problem solving was used and students were required to articulate their thought processes through the use of a structured diary. The diary prompted students to answer questions designed to engage them in the phases of…

  5. Students' Errors in Solving the Permutation and Combination Problems Based on Problem Solving Steps of Polya

    ERIC Educational Resources Information Center

    Sukoriyanto; Nusantara, Toto; Subanji; Chandra, Tjang Daniel

    2016-01-01

    This article was written based on the results of a study evaluating students' errors in problem solving of permutation and combination in terms of problem solving steps according to Polya. Twenty-five students were asked to do four problems related to permutation and combination. The research results showed that the students still did a mistake in…

  6. The Polya Tree Sampler: Towards Efficient and Automatic Independent Metropolis-Hastings Proposals

    PubMed Central

    Hanson, Timothy E.; Monteiro, João V. D.; Jara, Alejandro

    2011-01-01

    We present a simple, efficient, and computationally cheap sampling method for exploring an un-normalized multivariate density on ℝd, such as a posterior density, called the Polya tree sampler. The algorithm constructs an independent proposal based on an approximation of the target density. The approximation is built from a set of (initial) support points – data that act as parameters for the approximation – and the predictive density of a finite multivariate Polya tree. In an initial “warming-up” phase, the support points are iteratively relocated to regions of higher support under the target distribution to minimize the distance between the target distribution and the Polya tree predictive distribution. In the “sampling” phase, samples from the final approximating mixture of finite Polya trees are used as candidates which are accepted with a standard Metropolis-Hastings acceptance probability. Several illustrations are presented, including comparisons of the proposed approach to Metropolis-within-Gibbs and delayed rejection adaptive Metropolis algorithm. PMID:22135487

  7. Effect of Polya Problem-Solving Model on Senior Secondary School Students' Performance in Current Electricity

    ERIC Educational Resources Information Center

    Olaniyan, Ademola Olatide; Omosewo, Esther O.; Nwankwo, Levi I.

    2015-01-01

    This study was designed to investigate the Effect of Polya Problem-Solving Model on Senior School Students' Performance in Current Electricity. It was a quasi experimental study of non- randomized, non equivalent pre-test post-test control group design. Three research questions were answered and corresponding three research hypotheses were tested…

  8. Properties and Location of Poly(A) in Rous Sarcoma Virus RNA

    PubMed Central

    Wang, Lu-Hai; Duesberg, Peter

    1974-01-01

    The poly(A) sequence of 30 to 40S Rous sarcoma virus RNA, prepared by digestion of the RNA with RNase T1, showed a rather homogenous electrophoretic distribution in formamide-polyacrylamide gels. Its size was estimated to be about 200 AMP residues. The poly(A) appears to be located at or near the 3′ end of the 30 to 40S RNA because: (i) it contained one adenosine per 180 AMP residues, and because (ii) incubation of 30 to 40S RNA with bacterial RNase H in the presence of poly(dT) removed its poly(A) without significantly affecting its hydrodynamic or electrophoretic properties in denaturing solvents. The viral 60 to 70S RNA complex was found to consist of 30 to 40S subunits both with (65%) and without (approximately 30%) poly(A). The heteropolymeric sequences of these two species of 30 to 40S subunits have the same RNase T1-resistant oligonucleotide composition. Some, perhaps all, RNase T1-resistant oligonucleotides of 30 to 40S Rous sarcoma virus RNA appear to have a unique location relative to the poly(A) sequence, because the complexity of poly(A)-tagged fragments of 30 to 40S RNA decreased with decreasing size of the fragment. Two RNase T1-resistant oligonucleotides which distinguish sarcoma virus Prague B RNA from that of a transformation-defective deletion mutant of the same virus appear to be associated with an 11S poly(A)-tagged fragment of Prague B RNA. Thus RNA sequences concerned with cell transformation seem to be located within 5 to 10% of the 3′ terminus of Prague B RNA. Images PMID:4372409

  9. The poly(A) polymerase GLD2 is required for spermatogenesis in Drosophila melanogaster

    PubMed Central

    Sartain, Caroline V.; Cui, Jun; Meisel, Richard P.; Wolfner, Mariana F.

    2011-01-01

    The DNA of a developing sperm is normally inaccessible for transcription for part of spermatogenesis in many animals. In Drosophila melanogaster, many transcripts needed for late spermatid differentiation are synthesized in pre-meiotic spermatocytes, but are not translated until later stages. Thus, post-transcriptional control mechanisms are required to decouple transcription and translation during spermatogenesis. In the female germline, developing germ cells accomplish similar decoupling through poly(A) tail alterations to ensure that dormant transcripts are not prematurely translated: a transcript with a short poly(A) tail will remain untranslated, whereas elongating the poly(A) tail permits protein production. In Drosophila, the ovary-expressed cytoplasmic poly(A) polymerase WISPY is responsible for stage-specific poly(A) tail extension in the female germline. Here, we examine the possibility that a recently derived testis-expressed WISPY paralog, GLD2, plays a similar role in the Drosophila male germline. We show that knockdown of Gld2 transcripts causes male sterility, as GLD2-deficient males do not produce mature sperm. Spermatogenesis up to and including meiosis appears normal in the absence of GLD2, but post-meiotic spermatid development rapidly becomes abnormal. Nuclear bundling and F-actin assembly are defective in GLD2 knockdown testes and nuclei fail to undergo chromatin reorganization in elongated spermatids. GLD2 also affects the incorporation of protamines and the stability of dynamin and transition protein transcripts. Our results indicate that GLD2 is an important regulator of late spermatogenesis and is the first example of a Gld-2 family member that plays a significant role specifically in male gametogenesis. PMID:21427144

  10. Kinetic proofreading scanning models for eukaryotic translational initiation: the cap and poly(A) tail dependency of translation.

    PubMed

    Bi, X; Goss, D J

    2000-11-21

    Two simplified kinetic proofreading scanning (KPS) models were proposed to describe the 5' cap and 3' poly(A) tail dependency of eukaryotic translation initiation. In Model I, the initiation factor complex starts scanning and unwinding the secondary structure of the 5' untranslated region (UTR) from the 5' terminus of mRNA. In Model II, the initiation factor complex starts scanning from any binding site in the 5' UTR. In both models, following ATP hydrolysis, the initiation factor complex either dissociates from mRNA or continues to scan and unwind RNA secondary structure in the 5' UTR. This step repeats n times until the AUG codon is reached. These two models show very different cap and/or poly(A) tail dependency of translation initiation. The models predict that both cap and poly(A) tail dependencies of translation, and translatability of mRNAs are coupled with the structure of 5' UTR: the translation of mRNA with structured 5' UTR is strongly cap- and poly(A) tail-dependent; while translation of mRNA with unstructured 5' UTR is less cap- and poly(A) tail-dependent. We use these two models to explain: (1) the cap and poly(A) tail dependence of translation; (2) the effect of exogenous poly(A) on translation; (3) repression of host mRNA and translation of late adenovirus mRNA in the late phase of adenovirus infection; (4) repression of host mRNA and translation of Vaccinia virus mRNA in virus-infected cell; (5) heat shock repression of translation of normal mRNA and stimulation of translation of hsp mRNA; and (6) the synergistic effect of cap and poly(A) tail on stimulating translation. The kinetic proofreading scanning models provide a coherent interpretation of those phenomena. PMID:11034826

  11. Differences in behavior and activity associated with a poly(a) expansion in the dopamine transporter in Belgian Malinois.

    PubMed

    Lit, Lisa; Belanger, Janelle M; Boehm, Debby; Lybarger, Nathan; Oberbauer, Anita M

    2013-01-01

    In Belgian Malinois dogs, a 38-base pair variable number tandem repeat in the dopamine transporter gene (SLC6A3) is associated with behavior changes in Malinois. By additional sequencing in SLC6A3, we identified an intronic 12-nucleotide poly(A) insertion ("PolyA(22)") before the terminal exon that was associated with seizure, "glazing over" behaviors, and episodic biting behaviors in a sample of 138 Malinois. We next investigated whether PolyA(22) was associated with 1) increased locomotor activity and 2) response to novelty. Using a sample of 22 Malinois and 25 dogs of other breeds, dogs' activity was monitored in a novel and non-novel environment while wearing activity monitoring collars. All dogs were more active in novel compared with non-novel environments, and Malinois were more active overall than other breeds. There was an effect of PolyA(22) genotype on activity levels, and this effect appeared to underlie the difference detected between Malinois and other breeds. There was no effect of PolyA(22) genotype on the relative decrease in activity between novel and non-novel environments for either group or all dogs considered together. In addition to an association between PolyA(22) and owner reports of seizure, "glazing over" behaviors, and episodic biting behaviors, these findings support an effect of PolyA(22) on dopamine transporter function related to activity. Further investigation is required to confirm mechanistic effects of PolyA(22) on SLC6A3. The complex polygenic nature of behavior and the range of behaviors associated with this insertion predict that effects are likely also modified by additional genetic and environmental factors. PMID:24376613

  12. pEVL: A Linear Plasmid for Generating mRNA IVT Templates With Extended Encoded Poly(A) Sequences.

    PubMed

    Grier, Alexandra E; Burleigh, Stephen; Sahni, Jaya; Clough, Courtnee A; Cardot, Victoire; Choe, Dongwook C; Krutein, Michelle C; Rawlings, David J; Jensen, Michael C; Scharenberg, Andrew M; Jacoby, Kyle

    2016-01-01

    Increasing demand for large-scale synthesis of in vitro transcribed (IVT) mRNA is being driven by the increasing use of mRNA for transient gene expression in cell engineering and therapeutic applications. An important determinant of IVT mRNA potency is the 3' polyadenosine (poly(A)) tail, the length of which correlates with translational efficiency. However, present methods for generation of IVT mRNA rely on templates derived from circular plasmids or PCR products, in which homopolymeric tracts are unstable, thus limiting encoded poly(A) tail lengths to ~120 base pairs (bp). Here, we have developed a novel method for generation of extended poly(A) tracts using a previously described linear plasmid system, pJazz. We find that linear plasmids can successfully propagate poly(A) tracts up to ~500 bp in length for IVT mRNA production. We then modified pJazz by removing extraneous restriction sites, adding a T7 promoter sequence upstream from an extended multiple cloning site, and adding a unique type-IIS restriction site downstream from the encoded poly(A) tract to facilitate generation of IVT mRNA with precisely defined encoded poly(A) tracts and 3' termini. The resulting plasmid, designated pEVL, can be used to generate IVT mRNA with consistent defined lengths and terminal residue(s). PMID:27093168

  13. The murine IgM secretory poly(A) site contains dual upstream and downstream elements which affect polyadenylation.

    PubMed Central

    Phillips, C; Virtanen, A

    1997-01-01

    Regulation of polyadenylation efficiency at the secretory poly(A) site plays an essential role in gene expression at the immunoglobulin (IgM) locus. At this poly(A) site the consensus AAUAAA hexanucleotide sequence is embedded in an extended AU-rich region and there are two downstream GU-rich regions which are suboptimally placed. As these sequences are involved in formation of the polyadenylation pre-initiation complex, we examined their function in vivo and in vitro . We show that the upstream AU-rich region can function in the absence of the consensus hexanucleotide sequence both in vivo and in vitro and that both GU-rich regions are necessary for full polyadenylation activity in vivo and for formation of polyadenylation-specific complexes in vitro . Sequence comparisons reveal that: (i) the dual structure is distinct for the IgM secretory poly(A) site compared with other immunoglobulin isotype secretory poly(A) sites; (ii) the presence of an AU-rich region close to the consensus hexanucleotide is evolutionarily conserved for IgM secretory poly(A) sites. We propose that the dual structure of the IgM secretory poly(A) site provides a flexibility to accommodate changes in polyadenylation complex components during regulation of polyadenylation efficiency. PMID:9171084

  14. Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome

    PubMed Central

    Beilharz, Traude H.; Preiss, Thomas

    2007-01-01

    Control of poly(A) tail length can affect translation and stability of eukaryotic mRNAs. Although well established for individual cases, it was not known to what extent this type of adjustable gene control is used to shape expression of eukaryotic transcriptomes. Here we report on microarray-based measurements of mRNA poly(A) tail lengths and association with the poly(A)-binding protein Pab1 in S. cerevisiae, revealing extensive correlation between tail length and other physical and functional mRNA characteristics. Gene ontology analyses and further directed experiments indicate coregulation of tail length on functionally and cytotopically related mRNAs to coordinate cell-cycle progression, ribosome biogenesis, and retrotransposon expression. We show that the 3′-untranslated region drives transcript-specific adenylation control and translational efficiency of multiple mRNAs. Our findings suggest a wide-spread interdependence between 3′-untranslated region-mediated poly(A) tail length control, Pab1 binding, and mRNA translation in budding yeast. They further provide a molecular explanation for deadenylase function in the cell cycle and suggest additional cellular processes that depend on control of mRNA polyadenylation. PMID:17586758

  15. Differences in Behavior and Activity Associated with a Poly(A) Expansion in the Dopamine Transporter in Belgian Malinois

    PubMed Central

    Lit, Lisa; Belanger, Janelle M.; Boehm, Debby; Lybarger, Nathan; Oberbauer, Anita M.

    2013-01-01

    In Belgian Malinois dogs, a 38-base pair variable number tandem repeat in the dopamine transporter gene (SLC6A3) is associated with behavior changes in Malinois. By additional sequencing in SLC6A3, we identified an intronic 12-nucleotide poly(A) insertion (“PolyA(22)”) before the terminal exon that was associated with seizure, “glazing over” behaviors, and episodic biting behaviors in a sample of 138 Malinois. We next investigated whether PolyA(22) was associated with 1) increased locomotor activity and 2) response to novelty. Using a sample of 22 Malinois and 25 dogs of other breeds, dogs’ activity was monitored in a novel and non-novel environment while wearing activity monitoring collars. All dogs were more active in novel compared with non-novel environments, and Malinois were more active overall than other breeds. There was an effect of PolyA(22) genotype on activity levels, and this effect appeared to underlie the difference detected between Malinois and other breeds. There was no effect of PolyA(22) genotype on the relative decrease in activity between novel and non-novel environments for either group or all dogs considered together. In addition to an association between PolyA(22) and owner reports of seizure, “glazing over” behaviors, and episodic biting behaviors, these findings support an effect of PolyA(22) on dopamine transporter function related to activity. Further investigation is required to confirm mechanistic effects of PolyA(22) on SLC6A3. The complex polygenic nature of behavior and the range of behaviors associated with this insertion predict that effects are likely also modified by additional genetic and environmental factors. PMID:24376613

  16. RINGO/cdk1 and CPEB mediate poly(A) tail stabilization and translational regulation by ePAB

    PubMed Central

    Kim, Jong Heon; Richter, Joel D.

    2007-01-01

    One activity that controls mRNA translation in vertebrate oocytes, embryos, and neurons is cytoplasmic polyadenylation. In Xenopus oocytes, where much of the biochemistry of this process has been elucidated, nuclear pre-mRNAs containing a cytoplasmic polyadenylation element (CPE) in their 3′ untranslated regions (UTRs) have long poly(A) tails; once the RNAs are spliced and transported to the cytoplasm, the tails are shortened. Following the resumption of meiosis, the poly(A) tails are lengthened and translation ensues. CPEB is a sequence-specific RNA-binding protein that coordinates these events and does so by binding to the CPE as well as several factors including Gld2, a poly(A) polymerase, and PARN [poly(A)-specific ribonuclease], a deadenylase. Here, we show that ePAB, embryonic poly(A)-binding protein, transiently associates with the polyadenylation complex; it initially interacts with CPEB, but after polyadenylation, it binds the poly(A) tail. ePAB dissociation from CPEB is regulated by RINGO (Rapid Inducer of G2/M progression in Oocytes), a cyclin B1-like cofactor that activates cdk1, a protein kinase that phosphorylates CPEB. Subsequent ePAB binding to the poly(A) tail is necessary to protect the homopolymer from degradation by deadenylating enzymes. Poly(A)-bound ePAB also interacts with eIF4G, which instigates translation initiation of CPEB-bound mRNAs. PMID:17938241

  17. PUB1: a major yeast poly(A)+ RNA-binding protein.

    PubMed Central

    Matunis, M J; Matunis, E L; Dreyfuss, G

    1993-01-01

    The expression of RNA polymerase II transcripts can be regulated at the posttranscriptional level by RNA-binding proteins. Although extensively characterized in metazoans, relatively few RNA-binding proteins have been characterized in the yeast Saccharomyces cerevisiae. Three major proteins are cross-linked by UV light to poly(A)+ RNA in living S. cerevisiae cells. These are the 72-kDa poly(A)-binding protein and proteins of 60 and 50 kDa (S.A. Adam, T.Y. Nakagawa, M.S. Swanson, T. Woodruff, and G. Dreyfuss, Mol. Cell. Biol. 6:2932-2943, 1986). Here, we describe the 60-kDa protein, one of the major poly(A)+ RNA-binding proteins in S. cerevisiae. This protein, PUB1 [for poly(U)-binding protein 1], was purified by affinity chromatography on immobilized poly(rU), and specific monoclonal antibodies to it were produced. UV cross-linking demonstrated that PUB1 is bound to poly(A)+ RNA (mRNA or pre-mRNA) in living cells, and it was detected primarily in the cytoplasm by indirect immunofluorescence. The gene for PUB1 was cloned and sequenced, and the sequence was found to predict a 51-kDa protein with three ribonucleoprotein consensus RNA-binding domains and three glutamine- and asparagine-rich auxiliary domains. This overall structure is remarkably similar to the structures of the Drosophila melanogaster elav gene product, the human neuronal antigen HuD, and the cytolytic lymphocyte protein TIA-1. Each of these proteins has an important role in development and differentiation, potentially by affecting RNA processing. PUB1 was found to be nonessential in S. cerevisiae by gene replacement; however, further genetic analysis should reveal important features of this class of RNA-binding proteins. Images PMID:8413213

  18. Global profiling of stimulus-induced polyadenylation in cells using a poly(A) trap

    PubMed Central

    Curanovic, Dusica; Cohen, Michael; Singh, Irtisha; Slagle, Christopher E.; Leslie, Christina S.; Jaffrey, Samie R.

    2013-01-01

    Polyadenylation of mRNA leads to increased protein expression in response to diverse stimuli, but it is difficult to identify mRNAs that become polyadenylated in living cells. Here we describe a click chemistry-compatible nucleoside analog that is selectively incorporated into poly(A) tails of transcripts in cells. Next-generation sequencing of labeled mRNAs enables a transcriptome-wide profile of polyadenylation and provides insights into the mRNA sequence elements that are correlated with polyadenylation. PMID:23995769

  19. Poly(A) RNA and Paip2 act as allosteric regulators of poly(A)-binding protein.

    PubMed

    Lee, Seung Hwan; Oh, Jungsic; Park, Jonghyun; Paek, Ki Young; Rho, Sangchul; Jang, Sung Key; Lee, Jong-Bong

    2014-02-01

    When bound to the 3' poly(A) tail of mRNA, poly(A)-binding protein (PABP) modulates mRNA translation and stability through its association with various proteins. By visualizing individual PABP molecules in real time, we found that PABP, containing four RNA recognition motifs (RRMs), adopts a conformation on poly(A) binding in which RRM1 is in proximity to RRM4. This conformational change is due to the bending of the region between RRM2 and RRM3. PABP-interacting protein 2 actively disrupts the bent structure of PABP to the extended structure, resulting in the inhibition of PABP-poly(A) binding. These results suggest that the changes in the configuration of PABP induced by interactions with various effector molecules, such as poly(A) and PABP-interacting protein 2, play pivotal roles in its function. PMID:24293655

  20. Cytoplasmic Poly(A) Binding Protein C4 Serves a Critical Role in Erythroid Differentiation

    PubMed Central

    Kini, Hemant K.; Kong, Jian

    2014-01-01

    The expression of an mRNA is strongly impacted by its 3′ poly(A) tail and associated poly(A)-binding proteins (PABPs). Vertebrates encode six PABP isoforms that vary in abundance, distribution, developmental control, and subcellular localization. Here we demonstrate that the minor PABP isoform PABPC4 is expressed in erythroid cells and impacts the steady-state expression of a subset of erythroid mRNAs. Motif analyses reveal a high-value AU-rich motif in the 3′ untranslated regions (UTRs) of PABPC4-impacted mRNAs. This motif enhances the association of PABPC4 with mRNAs containing critically shortened poly(A) tails. This association may serve to protect a subset of mRNAs from accelerated decay. Finally, we demonstrate that selective depletion of PABPC4 in an erythroblast cell line inhibits terminal erythroid maturation with corresponding alterations in the erythroid gene expression. These observations lead us to conclude that PABPC4 plays an essential role in posttranscriptional control of a major developmental pathway. PMID:24469397

  1. Cytoplasmic poly(A) binding protein C4 serves a critical role in erythroid differentiation.

    PubMed

    Kini, Hemant K; Kong, Jian; Liebhaber, Stephen A

    2014-04-01

    The expression of an mRNA is strongly impacted by its 3' poly(A) tail and associated poly(A)-binding proteins (PABPs). Vertebrates encode six PABP isoforms that vary in abundance, distribution, developmental control, and subcellular localization. Here we demonstrate that the minor PABP isoform PABPC4 is expressed in erythroid cells and impacts the steady-state expression of a subset of erythroid mRNAs. Motif analyses reveal a high-value AU-rich motif in the 3' untranslated regions (UTRs) of PABPC4-impacted mRNAs. This motif enhances the association of PABPC4 with mRNAs containing critically shortened poly(A) tails. This association may serve to protect a subset of mRNAs from accelerated decay. Finally, we demonstrate that selective depletion of PABPC4 in an erythroblast cell line inhibits terminal erythroid maturation with corresponding alterations in the erythroid gene expression. These observations lead us to conclude that PABPC4 plays an essential role in posttranscriptional control of a major developmental pathway. PMID:24469397

  2. Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix

    SciTech Connect

    M Mitton-Fry; S DeGregorio; J Wang; T Steitz; J Steitz

    2011-12-31

    Kaposi's sarcoma-associated herpesvirus produces a highly abundant, nuclear noncoding RNA, polyadenylated nuclear (PAN) RNA, which contains an element that prevents its decay. The 79-nucleotide expression and nuclear retention element (ENE) was proposed to adopt a secondary structure like that of a box H/ACA small nucleolar RNA (snoRNA), with a U-rich internal loop that hybridizes to and protects the PAN RNA poly(A) tail. The crystal structure of a complex between the 40-nucleotide ENE core and oligo(A){sub 9} RNA at 2.5 angstrom resolution reveals that unlike snoRNAs, the U-rich loop of the ENE engages its target through formation of a major-groove triple helix. A-minor interactions extend the binding interface. Deadenylation assays confirm the functional importance of the triple helix. Thus, the ENE acts as an intramolecular RNA clamp, sequestering the PAN poly(A) tail and preventing the initiation of RNA decay.

  3. Contemporaneous isolation of deoxyribonucleic acid-dependent ribonucleic acid polymerase and poly(A) polymerase from rat liver mitochondria.

    PubMed Central

    Gallerani, R; di Istituto; Istituto di, Ch; Saccone, C

    1976-01-01

    1. Poly(A) polymerase and DNA-dependent RNA polymerase from rat liver mitochondria can be completely separated by using two different chromatographic procedures. 2. Poly(A) polymerase can only incorporate ATP into acid-insoluble material and strongly depends on the addition of an endogenous factor (probably containing a mixture of oligoribonucleotides), but it is not stimulated by DNA. 3. RNA polymerase is fully DNA-dependent and rifampicin-sensitive, but was not stimulated by the endogenous factor mentioned above. 4. The chromatographic behaviour of the two enzymes, together with the properties described, suggest that they represent two different protein molecules. PMID:962867

  4. Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins.

    PubMed

    Schmid, Manfred; Poulsen, Mathias Bach; Olszewski, Pawel; Pelechano, Vicent; Saguez, Cyril; Gupta, Ishaan; Steinmetz, Lars M; Moore, Claire; Jensen, Torben Heick

    2012-07-27

    Poly(A) (pA) tail binding proteins (PABPs) control mRNA polyadenylation, stability, and translation. In a purified system, S. cerevisiae PABPs, Pab1p and Nab2p, are individually sufficient to provide normal pA tail length. However, it is unknown how this occurs in more complex environments. Here we find that the nuclear exosome subunit Rrp6p counteracts the in vitro and in vivo extension of mature pA tails by the noncanonical pA polymerase Trf4p. Moreover, PABP loading onto nascent pA tails is controlled by Rrp6p; while Pab1p is the major PABP, Nab2p only associates in the absence of Rrp6p. This is because Rrp6p can interact with Nab2p and displace it from pA tails, potentially leading to RNA turnover, as evidenced for certain pre-mRNAs. We suggest that a nuclear mRNP surveillance step involves targeting of Rrp6p by Nab2p-bound pA-tailed RNPs and that pre-mRNA abundance is regulated at this level. PMID:22683267

  5. The Effects of Pair Problem Solving Technique Incorporating Polya's Problem Solving Strategy on Undergraduate Students' Performance in Chemistry

    ERIC Educational Resources Information Center

    Bilgin, Ibrahim

    2006-01-01

    The purpose of this study was to investigate the effects of pair problem solving technique incorporating Polya's problem solving strategy on undergraduate students' performance in conceptual and algorithmic questions in chemistry. The subjects of this study were 89 students enrolled from two first year chemistry classes. The experimental group was…

  6. mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development.

    PubMed

    Lim, Jaechul; Lee, Mihye; Son, Ahyeon; Chang, Hyeshik; Kim, V Narry

    2016-07-15

    Eukaryotic mRNAs are subject to multiple types of tailing that critically influence mRNA stability and translatability. To investigate RNA tails at the genomic scale, we previously developed TAIL-seq, but its low sensitivity precluded its application to biological materials of minute quantity. In this study, we report a new version of TAIL-seq (mRNA TAIL-seq [mTAIL-seq]) with enhanced sequencing depth for mRNAs (by ∼1000-fold compared with the previous version). The improved method allows us to investigate the regulation of poly(A) tails in Drosophila oocytes and embryos. We found that maternal mRNAs are polyadenylated mainly during late oogenesis, prior to fertilization, and that further modulation occurs upon egg activation. Wispy, a noncanonical poly(A) polymerase, adenylates the vast majority of maternal mRNAs, with a few intriguing exceptions such as ribosomal protein transcripts. By comparing mTAIL-seq data with ribosome profiling data, we found a strong coupling between poly(A) tail length and translational efficiency during egg activation. Our data suggest that regulation of poly(A) tails in oocytes shapes the translatomic landscape of embryos, thereby directing the onset of animal development. By virtue of the high sensitivity, low cost, technical robustness, and broad accessibility, mTAIL-seq will be a potent tool to improve our understanding of mRNA tailing in diverse biological systems. PMID:27445395

  7. Alternative poly(A) site selection in complex transcription units: means to an end?

    PubMed Central

    Edwalds-Gilbert, G; Veraldi, K L; Milcarek, C

    1997-01-01

    Many genes have been described and characterized which result in alternative polyadenylation site use at the 3'-end of their mRNAs based on the cellular environment. In this survey and summary article 95 genes are discussed in which alternative polyadenylation is a consequence of tandem arrays of poly(A) signals within a single 3'-untranslated region. An additional 31 genes are described in which polyadenylation at a promoter-proximal site competes with a splicing reaction to influence expression of multiple mRNAs. Some have a composite internal/terminal exon which can be differentially processed. Others contain alternative 3'-terminal exons, the first of which can be skipped in some cells. In some cases the mRNAs formed from these three classes of genes are differentially processed from the primary transcript during the cell cycle or in a tissue-specific or developmentally specific pattern. Immunoglobulin heavy chain genes have composite exons; regulated production of two different Ig mRNAs has been shown to involve B cell stage-specific changes in trans -acting factors involved in formation of the active polyadenylation complex. Changes in the activity of some of these same factors occur during viral infection and take-over of the cellular machinery, suggesting the potential applicability of at least some aspects of the Ig model. The differential expression of a number of genes that undergo alternative poly(A) site choice or polyadenylation/splicing competition could be regulated at the level of amounts and activities of either generic or tissue-specific polyadenylation factors and/or splicing factors. PMID:9185563

  8. Poly(A) polymerase modification and reverse transcriptase PCR amplification of environmental RNA.

    PubMed

    Botero, Lina M; D'Imperio, Seth; Burr, Mark; McDermott, Timothy R; Young, Mark; Hassett, Daniel J

    2005-03-01

    We describe a combination of two established techniques for a novel application for constructing full-length cDNA clone libraries from environmental RNA. The cDNA was cloned without the use of prescribed primers that target specific genes, and the procedure did not involve random priming. Purified RNA was first modified by addition of a poly(A) tail and then was amplified by using a commercially available reverse transcriptase PCR (RT-PCR) cDNA synthesis kit. To demonstrate the feasibility of this approach, a cDNA clone library was constructed from size-fractionated RNA (targeting 16S rRNA) purified from a geothermally heated soil in Yellowstone National Park in Wyoming. The resulting cDNA library contained clones representing Bacteria and Eukarya taxa and several mRNAs. There was no exact clone match between this library and a separate cDNA library generated from an RT-PCR performed with unmodified rRNA and Bacteria-specific forward and universal reverse primers that were designed from cultivated organisms; however, both libraries contained representatives of the Firmicutes and the alpha-Proteobacteria. Unexpectedly, there were no Archaea clones in the library generated from poly(A)-modified RNA. Additional RT-PCRs performed with universal and Archaea-biased primers and unmodified RNA demonstrated the presence of novel Archaea in the soil. Experiments with pure cultures of Sulfolobus solfataricus and Halobacterium halobium revealed that some Archaea rRNA may not be a suitable substrate for the poly(A) tail modification step. The protocol described here demonstrates the feasibility of directly accessing prokaryote RNA (rRNA and/or mRNA) in environmental samples, but the results also illustrate potentially important problems. PMID:15746328

  9. The vasopressin mRNA poly(A) tract is unusually long and increases during stimulation of vasopressin gene expression in vivo

    SciTech Connect

    Carrazana, E.J.; Pasieka, K.B.; Majzoub, J.A.

    1988-06-01

    The authors developed a method, termed an H-blot, by which the poly(A) tract of any specific mRNA may be detected by RNA filter hybridization after its removal from the body of the mRNA by a RNase H-catalyzed endonucleolytic cleavage in the 3' untranslated region. Using this method, they studied the modulation of the length of the poly(A) tract of rat vasopressin mRNA in vivo during changes in the levels of this mRNA resulting from a physiologic stimulus, osmotic stress. The poly(A) tract of hypothalamic vasopressin mRNA in hydrated rats was, quite remarkably, --250 nucleotides in length, in contrast to that of somatostatin mRNA, which was --30 nucleotides long. Vasopressin mRNA poly(A) tail length increased progressively from --250 to --400 nucleotides with the application of the hyperosmotic stimulus and declined to base line after its removal; somatostatin mRNA poly(A) tail length did not change during osmotic stress. The poly(A) tract length of total hypothalamic mRNA was between 35 and 140 nucleotides and also did not change with osmotic stress. Modulation of poly(A) tract length of specific mRNAs during stimulation of gene expression may provide an additional level of genetic regulation.

  10. The vasopressin mRNA poly(A) tract is unusually long and increases during stimulation of vasopressin gene expression in vivo.

    PubMed Central

    Carrazana, E J; Pasieka, K B; Majzoub, J A

    1988-01-01

    We developed a method, termed an H-blot, by which the poly(A) tract of any specific mRNA may be detected by RNA filter hybridization after its removal from the body of the mRNA by a RNase H-catalyzed endonucleolytic cleavage in the 3' untranslated region. Using this method, we studied the modulation of the length of the poly(A) tract of rat vasopressin mRNA in vivo during changes in the levels of this mRNA resulting from a physiologic stimulus, osmotic stress. The poly(A) tract of hypothalamic vasopressin mRNA in hydrated rats was, quite remarkably, approximately 250 nucleotides in length, in contrast to that of somatostatin mRNA, which was approximately 30 nucleotides long. Vasopressin mRNA poly(A) tail length increased progressively from approximately 250 to approximately 400 nucleotides with the application of the hyperosmotic stimulus and declined to base line after its removal; somatostatin mRNA poly(A) tail length did not change during osmotic stress. The poly(A) tract length of total hypothalamic mRNA was between 35 and 140 nucleotides and also did not change with osmotic stress. Modulation of poly(A) tract length of specific mRNAs during stimulation of gene expression may provide an additional level of genetic regulation. Images PMID:2841576

  11. Molecular recognition of poly(A) by small ligands: an alternative method of analysis reveals nanomolar, cooperative and shape-selective binding

    PubMed Central

    Çetinkol, Özgül Persil; Hud, Nicholas V.

    2009-01-01

    A few drug-like molecules have recently been found to bind poly(A) and induce a stable secondary structure (Tm ≈ 60°C), even though this RNA homopolymer is single-stranded in the absence of a ligand. Here, we report results from experiments specifically designed to explore the association of small molecules with poly(A). We demonstrate that coralyne, the first small molecule discovered to bind poly(dA), binds with unexpectedly high affinity (Ka >107 M−1), and that the crescent shape of coralyne appears necessary for poly(A) binding. We also show that the binding of similar ligands to poly(A) can be highly cooperative. For one particular ligand, at least six ligand molecules are required to stabilize the poly(A) self-structure at room temperature. This highly cooperative binding produces very sharp transitions between unstructured and structured poly(A) as a function of ligand concentration. Given the fact that junctions between Watson–Crick and A·A duplexes are tolerated, we propose that poly(A) sequence elements and appropriate ligands could be used to reversibly drive transitions in DNA and RNA-based molecular structures by simply diluting/concentrating a sample about the poly(A)-ligand ‘critical concentration’. The ligands described here may also find biological or medicinal applications, owing to the 3′-polyadenylation of mRNA in living cells. PMID:19073699

  12. Association between vitamin D receptor poly(A) polymorphism and breast cancer risk: a meta-analysis.

    PubMed

    Xu, Jinjiang; Li, Hongyu; Gu, Lixue; Zhou, Xiaoping

    2014-01-01

    Vitamin D receptor (VDR) poly(A) is a common genetic polymorphism in the VDR gene, and it has been implicated to be associated with breast cancer risk. However, previous studies on the association reported inconclusive results. We performed this meta-analysis to comprehensively assess the association. Eligible studies were searched in PubMed and EMBASE databases. Odds ratio (OR) and its 95% confidence interval (95% CI) were used for statistical analysis. A total 6,631 cases and 6,718 controls from 11 case-control studies were finally included into the meta-analysis. Meta-analysis of total eligible studies showed that VDR poly(A) polymorphism was not associated with the risk of breast cancer (S versus L: OR = 0.99, 95% CI of 0.90-1.09, P = 0.84; SS versus LL: OR = 0.96, 95% CI of 0.79-1.18, P = 0.70; SS/LS versus LL: OR = 0.96, 95% CI of 0.83-1.12, P = 0.63; SS versus LL/LS: OR = 1.00, 95% CI of 0.91-1.10, P = 0.98). Meta-analysis of studies with high quality also showed that there was no association between VDR poly(A) polymorphism and breast cancer risk. In addition, in the subgroup analysis by ethnicity, no significant association was found among Caucasians. Therefore, the meta-analysis suggests that VDR poly(A) polymorphism is not associated with the risk of breast cancer. Large well-designed studies are necessary to clarify the possible association in Asians. PMID:24037913

  13. Structure of Yeast Poly(A) Polymerase in Complex with a Peptide from Fip1, an Intrinsically Disordered Protein

    SciTech Connect

    Meinke,G.; Ezeokonkwo, C.; Balbo, P.; Stafford, W.; Moore, C.; Bohm, A.

    2008-01-01

    In yeast, the mRNA processing enzyme poly(A) polymerase is tethered to the much larger 3'-end processing complex via Fip1, a 36 kDa protein of unknown structure. We report the 2.6 Angstroms crystal structure of yeast poly(A) polymerase in complex with a peptide containing residues 80-105 of Fip1. The Fip1 peptide binds to the outside surface of the C-terminal domain of the polymerase. On the basis of this structure, we designed a mutant of the polymerase (V498Y, C485R) that is lethal to yeast. The mutant is unable to bind Fip1 but retains full polymerase activity. Fip1 is found in all eukaryotes and serves to connect poly(A) polymerase to pre-mRNA processing complexes in yeast, plants, and mammals. However, the Fip1 sequence is highly divergent, and residues on both Pap1 and Fip1 at the observed interaction surface are poorly conserved. Herein we demonstrate using analytical ultracentrifugation, circular dichroism, proteolytic studies, and other techniques that, in the absence of Pap1, Fip1 is largely, if not completely, unfolded. We speculate that flexibility may be important for Fip1's function as a molecular scaffold.

  14. Poly(A) Binding Protein 1 Enhances Cap-Independent Translation Initiation of Neurovirulence Factor from Avian Herpesvirus

    PubMed Central

    Tahiri-Alaoui, Abdessamad; Zhao, Yuguang; Sadigh, Yashar; Popplestone, James; Kgosana, Lydia; Smith, Lorraine P.; Nair, Venugopal

    2014-01-01

    Poly(A) binding protein 1 (PABP1) plays a central role in mRNA translation and stability and is a target by many viruses in diverse manners. We report a novel viral translational control strategy involving the recruitment of PABP1 to the 5' leader internal ribosome entry site (5L IRES) of an immediate-early (IE) bicistronic mRNA that encodes the neurovirulence protein (pp14) from the avian herpesvirus Marek’s disease virus serotype 1 (MDV1). We provide evidence for the interaction between an internal poly(A) sequence within the 5L IRES and PABP1 which may occur concomitantly with the recruitment of PABP1 to the poly(A) tail. RNA interference and reverse genetic mutagenesis results show that a subset of virally encoded-microRNAs (miRNAs) targets the inhibitor of PABP1, known as paip2, and therefore plays an indirect role in PABP1 recruitment strategy by increasing the available pool of active PABP1. We propose a model that may offer a mechanistic explanation for the cap-independent enhancement of the activity of the 5L IRES by recruitment of a bona fide initiation protein to the 5' end of the message and that is, from the affinity binding data, still compatible with the formation of ‘closed loop’ structure of mRNA. PMID:25503397

  15. A pollen-, ovule-, and early embryo-specific poly(A) binding protein from Arabidopsis complements essential functions in yeast.

    PubMed Central

    Belostotsky, D A; Meagher, R B

    1996-01-01

    Poly(A) tails of eukaryotic mRNAs serve as targets for regulatory proteins affecting mRNA stability and translation. Differential mRNA polyadenylation and deadenylation during gametogenesis and early development are now widely recognized as mechanisms of translational regulation in animals, but they have not been observed in plants. Here, we report that the expression of the PAB5 gene encoding one of the poly(A) binding proteins (PABPs) in Arabidopsis is restricted to pollen and ovule development and early embryogenesis. Furthermore, PAB5 is capable of rescuing a PABP-deficient yeast strain by partially restoring both poly(A) shortening and translational initiation functions of PABP. However, PAB5 did not restore the linkage of deadenylation and decapping, thus demonstrating that this function of PABP is not essential for viability. Also, like endogenous PABP, PAB5 expressed in yeast demonstrated genetic interaction with a recently characterized yeast protein SIS1, which is also involved in translational initiation. We propose that PAB5 encodes a post-transcriptional regulatory factor acting through molecular mechanisms similar to those reported for yeast PABP. This factor may have evolved further to post-transcriptionally regulate plant sexual reproduction and early development. PMID:8776896

  16. PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information

    PubMed Central

    Wu, Hao; Ji, Hongkai

    2014-01-01

    ChIP-seq is a powerful technology for detecting genomic regions where a protein of interest interacts with DNA. ChIP-seq data for mapping transcription factor binding sites (TFBSs) have a characteristic pattern: around each binding site, sequence reads aligned to the forward and reverse strands of the reference genome form two separate peaks shifted away from each other, and the true binding site is located in between these two peaks. While it has been shown previously that the accuracy and resolution of binding site detection can be improved by modeling the pattern, efficient methods are unavailable to fully utilize that information in TFBS detection procedure. We present PolyaPeak, a new method to improve TFBS detection by incorporating the peak shape information. PolyaPeak describes peak shapes using a flexible Pólya model. The shapes are automatically learnt from the data using Minorization-Maximization (MM) algorithm, then integrated with the read count information via a hierarchical model to distinguish true binding sites from background noises. Extensive real data analyses show that PolyaPeak is capable of robustly improving TFBS detection compared with existing methods. An R package is freely available. PMID:24608116

  17. The association between the poly(A) polymorphism in the VDR gene and cancer risk: a meta-analysis.

    PubMed

    Huang, Jin; Yang, Jiqiao; Wang, Haichuan; Xiong, Tianyuan; Zhang, Hongbo; Ma, Yaxian; Wang, Xiaoze; Huang, Jichong; Du, Liang

    2013-06-01

    The poly(A) polymorphism (L/S) in the VDR gene has been implicated in susceptibility of cancer, but a number of studies have reported inconclusive results. The aim of this study is to investigate the relationship between the poly(A) polymorphism in the VDR gene and cancer risk by meta-analysis. We searched PubMed database, EMBASE database, CNKI database, and Wanfang database, covering all studies until January 22, 2013. Statistical analysis was performed by using the software Revman4.2 and STATA 10.0. A total 8,186 cancer cases and 8,685 controls in 19 case-control studies from 15 studies were identified for data analysis. The results suggested that the S allele carriers (SS+SL) did not have an increased or decreased risk of cancer when compared with the homozygote LL carriers (odds ratio (OR) =0.96, 95 % CI=0.87-1.06, P=0.43 for SS+SL vs. LL). In addition, in the subgroup analysis by ethnicity and cancer type, no significant association was found among Caucasians, African-Americans, prostate cancer, or breast cancer. This current meta-analysis suggested that the poly(A) polymorphism in the VDR gene may not contribute to the risk of cancer. Future studies are needed to validate our findings. PMID:23519839

  18. Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation.

    PubMed

    Weng, Lingjie; Li, Yi; Xie, Xiaohui; Shi, Yongsheng

    2016-06-01

    mRNA alternative polyadenylation (APA) is a critical mechanism for post-transcriptional gene regulation and is often regulated in a tissue- and/or developmental stage-specific manner. An ultimate goal for the APA field has been to be able to computationally predict APA profiles under different physiological or pathological conditions. As a first step toward this goal, we have assembled a poly(A) code for predicting tissue-specific poly(A) sites (PASs). Based on a compendium of over 600 features that have known or potential roles in PAS selection, we have generated and refined a machine-learning algorithm using multiple high-throughput sequencing-based data sets of tissue-specific and constitutive PASs. This code can predict tissue-specific PASs with >85% accuracy. Importantly, by analyzing the prediction performance based on different RNA features, we found that PAS context, including the distance between alternative PASs and the relative position of a PAS within the gene, is a key feature for determining the susceptibility of a PAS to tissue-specific regulation. Our poly(A) code provides a useful tool for not only predicting tissue-specific APA regulation, but also for studying its underlying molecular mechanisms. PMID:27095026

  19. Heat shock disassembles the nucleolus and inhibits nuclear protein import and poly(A)+ RNA export.

    PubMed Central

    Liu, Y; Liang, S; Tartakoff, A M

    1996-01-01

    Heat shock causes major positive and negative changes in gene expression, drastically alters the appearance of the nucleolus and inhibits rRNA synthesis. We here show that it causes many yeast nucleolar proteins, including the fibrillarin homolog Nop1p, to relocate to the cytoplasm. Relocation depends on several proteins implicated in mRNA transport (Mtrps) and is reversible. Two observations indicate, surprisingly, that disassembly results from a reduction in Ssa protein (Hsp70) levels: (i) selective depletion of Ssa1p leads to disassembly of the nucleolus; (ii) preincubation at 37 degrees C protects the nucleolus against disassembly by heat shock, unless expression of Ssa proteins is specifically inhibited. We observed that heat shock or reduction of Ssa1p levels inhibits protein import into the nucleus and therefore we propose that inhibition of import leads to disassembly of the nucleolus. These observations provide a simple explanation of the effects of heat shock on the anatomy of the nucleolus and rRNA transcription. They also extend understanding of the path of nuclear export. Since a number of nucleoplasmic proteins also relocate upon heat shock, these observations can provide a general mechanism for regulation of gene expression. Relocation of the hnRNP-like protein Mtr13p (= Npl3p, Nop3p), explains the heat shock sensitivity of export of average poly(A)+ RNA. Strikingly, Hsp mRNA export appears not to be affected. Images PMID:8978700

  20. Entamoeba histolytica: cloning and expression of the poly(A) polymerase EhPAP.

    PubMed

    García-Vivas, Jessica; López-Camarillo, César; Azuara-Liceaga, Elisa; Orozco, Esther; Marchat, Laurence A

    2005-07-01

    In eukaryotes, polyadenylation of pre-mRNA 3' end is essential for mRNA export, stability, and translation. Here we identified and cloned a gene codifying for a putative nuclear poly(A) polymerase (EhPAP) in Entamoeba histolytica. Protein sequence alignments with eukaryotic PAPs showed that EhPAP has the RNA-binding region and the PAP central domain with the catalytic nucleotidyl transferase domain described for other nuclear PAPs. Recombinant EhPAP expressed in bacteria was used to generate specific antibodies, which recognized two EhPAP isoforms of 60 and 63kDa in nuclear and cytoplasmic extracts by Western blot assays. RT-PCR assays showed that EhPap mRNA expression varies in multidrug-resistant trophozoites growing in different emetine concentrations. Moreover, EhPap mRNA expression is about 10- and 7-fold increased in G1 and S phase, respectively, through cell cycle progression. These results suggest the existence of a link between EhPAP expression and MDR and cell cycle regulation, respectively. PMID:15955317

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

    PubMed

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

    2016-05-01

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

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

    PubMed Central

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

    2016-01-01

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

  3. Structural Basis for Dimerization and Activity of Human PAPD1 a Noncanonical Poly(A) Polymerase

    SciTech Connect

    Y Bai; S Srivastava; J Chang; J Manley; L Tong

    2011-12-31

    Poly(A) polymerases (PAPs) are found in most living organisms and have important roles in RNA function and metabolism. Here, we report the crystal structure of human PAPD1, a noncanonical PAP that can polyadenylate RNAs in the mitochondria (also known as mtPAP) and oligouridylate histone mRNAs (TUTase1). The overall structure of the palm and fingers domains is similar to that in the canonical PAPs. The active site is located at the interface between the two domains, with a large pocket that can accommodate the substrates. The structure reveals the presence of a previously unrecognized domain in the N-terminal region of PAPD1, with a backbone fold that is similar to that of RNP-type RNA binding domains. This domain (named the RL domain), together with a {beta}-arm insertion in the palm domain, contributes to dimerization of PAPD1. Surprisingly, our mutagenesis and biochemical studies show that dimerization is required for the catalytic activity of PAPD1.

  4. Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA.

    PubMed

    Wasmuth, Elizabeth V; Januszyk, Kurt; Lima, Christopher D

    2014-07-24

    The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome. PMID:25043052

  5. Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

    SciTech Connect

    Wasmuth, Elizabeth V.; Januszyk, Kurt; Lima, Christopher D.

    2014-08-20

    The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on top of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.

  6. Mitochondrial poly(A) polymerase is involved in tRNA repair

    PubMed Central

    Fiedler, Mario; Rossmanith, Walter; Wahle, Elmar; Rammelt, Christiane

    2015-01-01

    Transcription of the mitochondrial genome results in polycistronic precursors, which are processed mainly by the release of tRNAs interspersed between rRNAs and mRNAs. In many metazoan mitochondrial genomes some tRNA genes overlap with downstream genes; in the case of human mitochondria the genes for tRNATyr and tRNACys overlap by one nucleotide. It has previously been shown that processing of the common precursor releases an incomplete tRNATyr lacking the 3′-adenosine. The 3′-terminal adenosine has to be added before addition of the CCA end and subsequent aminoacylation. We show that the mitochondrial poly(A) polymerase (mtPAP) is responsible for this A addition. In vitro, a tRNATyr lacking the discriminator is a substrate for mtPAP. In vivo, an altered mtPAP protein level affected tRNATyr maturation, as shown by sequencing the 3′ ends of mitochondrial tRNAs. Complete repair could be reconstituted in vitro with three enzymes: mtPAP frequently added more than one A to the 3′ end of the truncated tRNA, and either the mitochondrial deadenylase PDE12 or the endonuclease RNase Z trimmed the oligo(A) tail to a single A before CCA addition. An enzyme machinery that evolved primarily for other purposes thus allows to tolerate the frequent evolutionary occurrence of gene overlaps. PMID:26354863

  7. Repetitive sequences in the crocodilian mitochondrial control region: poly-A sequences and heteroplasmic tandem repeats.

    PubMed

    Ray, David A; Densmore, Llewellyn D

    2003-06-01

    Heteroplasmic tandem repeats in the mitochondrial control region have been documented in a wide variety of vertebrate species. We have examined the control region from 11 species in the family Crocodylidae and identified two different types of heteroplasmic repetitive sequences in the conserved sequence block (CSB) domain-an extensive poly-A tract that appears to be involved in the formation of secondary structure and a series of tandem repeats located downstream ranging from approximately 50 to approximately 80 bp in length. We describe this portion of the crocodylian control region in detail and focus on members of the family Crocodylidae. We then address the origins of the tandemly repeated sequences in this family and suggest hypotheses to explain possible mechanisms of expansion/contraction of the sequences. We have also examined control region sequences from Alligator and Caiman and offer hypotheses for the origin of tandem repeats found in those taxa. Finally, we present a brief analysis of intraindividual and interindividual haplotype variation by examining representatives of Morelet's crocodile (Crocodylus moreletii). PMID:12716979

  8. Nanopore detachment kinetics of poly(A) binding proteins from RNA molecules reveals the critical role of C-terminus interactions.

    PubMed

    Lin, Jianxun; Fabian, Marc; Sonenberg, Nahum; Meller, Amit

    2012-03-21

    The ubiquitous and abundant cytoplasmic poly(A) binding protein (PABP) is a highly conserved multifunctional protein, many copies of which bind to the poly(A) tail of eukaryotic mRNAs to promote translation initiation. The N-terminus of PABP is responsible for the high binding specificity and affinity to poly(A), whereas the C-terminus is known to stimulate PABP multimerization on poly(A). Here, we use single-molecule nanopore force spectroscopy to directly measure interactions between poly(A) and PABPs. Both electrical and biochemical results show that the C-C domain interaction between two consecutive PABPs promotes cooperative binding. Up to now, investigators have not been able to probe the detailed polarity configuration (i.e., the internal arrangement of two PABPs on a poly(A) streak in which the C-termini face toward or away from each other). Our nanopore force spectroscopy system is able to distinguish the cooperative binding conformation from the noncooperative one. The ∼50% cooperative binding conformation of wild-type PABPs indicates that the C-C domain interaction doubles the cooperative binding probability. Moreover, the longer dissociation time of a cooperatively bound poly(A)/PABP complex as compared with a noncooperatively bound one indicates that the cooperative mode is the most stable conformation for PABPs binding onto the poly(A). However, ∼50% of the poly(A)/PABP complexes exhibit a noncooperative binding conformation, which is in line with previous studies showing that the PABP C-terminal domain also interacts with additional protein cofactors. PMID:22455926

  9. A novel nuclear pore protein Nup133p with distinct roles in poly(A)+ RNA transport and nuclear pore distribution.

    PubMed Central

    Doye, V.; Wepf, R.; Hurt, E. C.

    1994-01-01

    Temperature-sensitive nucleoporin nup49-316 mutant cells accumulate poly(A)+ RNA inside the nucleus when shifted to restrictive temperature. We performed a synthetic lethal screen with this mutant allele to identify further components of the mRNA export machinery. A synthetic lethal mutant slv21 was isolated, which exhibited a ts phenotype and showed nuclear accumulation of poly(A)+ RNA at 37 degrees C. The wild-type gene complementing slv21 was cloned and sequenced. It encodes a novel protein Nup133p which is located at the nuclear pore complex. NUP133 is not an essential gene, but cells in which NUP133 is disrupted grow slowly at permissive temperatures and stop growing at 37 degrees C. Concomitant with the growth inhibition, nup133- cells accumulate poly(A)+ RNA inside the nucleus whereas nuclear import of a karyophilic reporter protein is not altered. Strikingly, nup133- cells display extensive clustering of nuclear pore complexes at a few sites on the nuclear envelope. However, the nuclear pore clustering phenotype and intranuclear accumulation of poly(A)+ RNA are not obligatorily linked, since an amino-terminally truncated Nup133p allows normal poly(A)+ RNA export, but does not complement the clustering phenotype of nup133- cells. Images PMID:7813444

  10. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection

    PubMed Central

    2012-01-01

    Background High throughput DNA sequencing technology has enabled quantification of all the RNAs in a cell or tissue, a method widely known as RNA sequencing (RNA-Seq). However, non-coding RNAs such as rRNA are highly abundant and can consume >70% of sequencing reads. A common approach is to extract only polyadenylated mRNA; however, such approaches are blind to RNAs with short or no poly(A) tails, leading to an incomplete view of the transcriptome. Another challenge of preparing RNA-Seq libraries is to preserve the strand information of the RNAs. Design Here, we describe a procedure for preparing RNA-Seq libraries from 1 to 4 μg total RNA without poly(A) selection. Our method combines the deoxyuridine triphosphate (dUTP)/uracil-DNA glycosylase (UDG) strategy to achieve strand specificity with AMPure XP magnetic beads to perform size selection. Together, these steps eliminate gel purification, allowing a library to be made in less than two days. We barcode each library during the final PCR amplification step, allowing several samples to be sequenced in a single lane without sacrificing read length. Libraries prepared using this protocol are compatible with Illumina GAII, GAIIx and HiSeq 2000 platforms. Discussion The RNA-Seq protocol described here yields strand-specific transcriptome libraries without poly(A) selection, which provide approximately 90% mappable sequences. Typically, more than 85% of mapped reads correspond to protein-coding genes and only 6% derive from non-coding RNAs. The protocol has been used to measure RNA transcript identity and abundance in tissues from flies, mice, rats, chickens, and frogs, demonstrating its general applicability. PMID:23273270

  11. RNA Polymerase II Mutations Conferring Defects in Poly(A) Site Cleavage and Termination in Saccharomyces cerevisiae

    PubMed Central

    Kubicek, Charles E.; Chisholm, Robert D.; Takayama, Sachiko; Hawley, Diane K.

    2013-01-01

    Transcription termination by RNA polymerase (Pol) II is an essential but poorly understood process. In eukaryotic nuclei, the 3′ ends of mRNAs are generated by cleavage and polyadenylation, and the same sequence elements that specify that process are required for downstream release of the polymerase from the DNA. Although Pol II is known to bind proteins required for both events, few studies have focused on Pol II mutations as a means to uncover the mechanisms that couple polyadenylation and termination. We performed a genetic screen in the yeast Saccharomyces cerevisiae to isolate mutations in the N-terminal half of Rpb2, the second largest Pol II subunit, that conferred either a decreased or increased response to a well-characterized poly(A) site. Most of the mutant alleles encoded substitutions affecting either surface residues or conserved active site amino acids at positions important for termination by other RNA polymerases. Reverse transcription polymerase chain reaction experiments revealed that transcript cleavage at the poly(A) site was impaired in both classes of increased readthrough mutants. Transcription into downstream sequences beyond where termination normally occurs was also probed. Although most of the tested readthrough mutants showed a reduction in termination concomitant with the reduced poly(A) usage, these processes were uncoupled in at least one mutant strain. Several rpb2 alleles were found to be similar or identical to published mutants associated with defective TFIIF function. Tests of these and additional mutations known to impair Rpb2−TFIIF interactions revealed similar decreased readthrough phenotypes, suggesting that TFIIF may have a role in 3′ end formation and termination. PMID:23390594

  12. Regulation of poly(A) RNA retention in the nucleus as a survival strategy of plants during hypoxia.

    PubMed

    Niedojadło, Janusz; Dełeńko, Konrad; Niedojadło, Katarzyna

    2016-05-01

    Last finding indicates that post-transcriptional processes are significant in low-oxygen conditions, but their nature is poorly understood. Here, we localized poly(A) RNA and mRNA coding proteins involved and not involved with resistance to hypoxia in Lupinus luteus and Arabidopsis thaliana during submergence and after recovery of aerobic conditions. We showed a strong nuclear accumulation of poly(A) RNA and 6 of 7 studied mRNAs with a concurrent strong reduction in RNA polymerase II transcription during hypoxia. In this study, the nucleus did not accumulate mRNA of the ADH1 (alcohol dehydrogenase 1) gene, which is a core hypoxia gene. The RNA accumulation in the nucleus is among the mechanisms of post-transcriptional gene regulation that prevents translation. However re-aeration was accompanied by a strong increase in the amount of the mRNAs in the cytoplasm and a simultaneous decrease in nuclear mRNAs. This finding indicates that the nucleus is a storage site for those of mRNAs which are not involved in the response to hypoxia for use by the plants after the hypoxic stress. In this study, the highest intensity of RNA accumulation occurred in Cajal bodies (CBs); the intensity of accumulation was inversely correlated with transcription. Under hypoxia, ncb-1 mutants of Arabidopsis thaliana with a complete absence of CBs died sooner than wild type (WT), accompanied by a strong reduction in the level of poly(A) RNA in the nucleus. These results suggest that the CBs not only participate in the storage of the nuclear RNA, but they also could take part in its stabilization under low-oxygen conditions. PMID:27002417

  13. Identification of Endogenous mRNA-Binding Proteins in Yeast Using Crosslinking and PolyA Enrichment.

    PubMed

    Mitchell, Sarah F; Parker, Roy

    2016-01-01

    The maturation, localization, stability, and translation of messenger RNAs (mRNAs) are regulated by a wide variety of mRNA-binding proteins. Identification of the complete set of mRNA-binding proteins is a key step in understanding the regulation of gene expression. Herein, we describe a method for identifying yeast mRNA-binding proteins in a systematic manner using UV crosslinking, purification of polyA(+) mRNAs under denaturing conditions, and mass spectrometry to identify covalently bound proteins. PMID:26965264

  14. Control of translation and miRNA-dependent repression by a novel poly(A) binding protein, hnRNP-Q.

    PubMed

    Svitkin, Yuri V; Yanagiya, Akiko; Karetnikov, Alexey E; Alain, Tommy; Fabian, Marc R; Khoutorsky, Arkady; Perreault, Sandra; Topisirovic, Ivan; Sonenberg, Nahum

    2013-01-01

    Translation control often operates via remodeling of messenger ribonucleoprotein particles. The poly(A) binding protein (PABP) simultaneously interacts with the 3' poly(A) tail of the mRNA and the eukaryotic translation initiation factor 4G (eIF4G) to stimulate translation. PABP also promotes miRNA-dependent deadenylation and translational repression of target mRNAs. We demonstrate that isoform 2 of the mouse heterogeneous nuclear protein Q (hnRNP-Q2/SYNCRIP) binds poly(A) by default when PABP binding is inhibited. In addition, hnRNP-Q2 competes with PABP for binding to poly(A) in vitro. Depleting hnRNP-Q2 from translation extracts stimulates cap-dependent and IRES-mediated translation that is dependent on the PABP/poly(A) complex. Adding recombinant hnRNP-Q2 to the extracts inhibited translation in a poly(A) tail-dependent manner. The displacement of PABP from the poly(A) tail by hnRNP-Q2 impaired the association of eIF4E with the 5' m(7)G cap structure of mRNA, resulting in the inhibition of 48S and 80S ribosome initiation complex formation. In mouse fibroblasts, silencing of hnRNP-Q2 stimulated translation. In addition, hnRNP-Q2 impeded let-7a miRNA-mediated deadenylation and repression of target mRNAs, which require PABP. Thus, by competing with PABP, hnRNP-Q2 plays important roles in the regulation of global translation and miRNA-mediated repression of specific mRNAs. PMID:23700384

  15. PABP and the poly(A) tail augment microRNA repression by facilitated miRISC binding.

    PubMed

    Moretti, Francesca; Kaiser, Constanze; Zdanowicz-Specht, Agnieszka; Hentze, Matthias W

    2012-06-01

    Polyadenylated mRNAs are typically more strongly repressed by microRNAs (miRNAs) than their nonadenylated counterparts. Using a Drosophila melanogaster cell-free translation system, we found that this effect is mediated by the poly(A)-binding protein (PABP). miRNA repression was positively correlated with poly(A) tail length, but this stimulatory effect on repression was lost when translation was repressed by the tethered GW182 silencing domain rather than the miRNA-induced silencing complex (miRISC) itself. These findings are mechanistically explained by a notable function of PABP: it promotes association of miRISC with miRNA-regulated mRNAs. We also found that PABP association with mRNA rapidly diminished with miRISC recruitment and before detectable deadenylation. We integrated these data into a revised model for the function of PABP and the poly(A) tail in miRNA-mediated translational repression. PMID:22635249

  16. Rotavirus NSP3 Is a Translational Surrogate of the Poly(A) Binding Protein-Poly(A) Complex

    PubMed Central

    Gratia, Matthieu; Sarot, Emeline; Vende, Patrice; Charpilienne, Annie; Baron, Carolina Hilma; Duarte, Mariela

    2015-01-01

    ABSTRACT Through its interaction with the 5′ translation initiation factor eIF4G, poly(A) binding protein (PABP) facilitates the translation of 5′-capped and 3′-poly(A)-tailed mRNAs. Rotavirus mRNAs are capped but not polyadenylated, instead terminating in a 3′ GACC motif that is recognized by the viral protein NSP3, which competes with PABP for eIF4G binding. Upon rotavirus infection, viral, GACC-tailed mRNAs are efficiently translated, while host poly(A)-tailed mRNA translation is, in contrast, severely impaired. To explore the roles of NSP3 in these two opposing events, the translational capabilities of three capped mRNAs, distinguished by either a GACC, a poly(A), or a non-GACC and nonpoly(A) 3′ end, have been monitored after electroporation of cells expressing all rotavirus proteins (infected cells) or only NSP3 (stably or transiently transfected cells). In infected cells, we found that the magnitudes of translation induction (GACC-tailed mRNA) and translation reduction [poly(A)-tailed mRNA] both depended on the rotavirus strain used but that translation reduction not genetically linked to NSP3. In transfected cells, even a small amount of NSP3 was sufficient to dramatically enhance GACC-tailed mRNA translation and, surprisingly, to slightly favor the translation of both poly(A)- and nonpoly(A)-tailed mRNAs, likely by stabilizing the eIF4E-eIF4G interaction. These data suggest that NSP3 is a translational surrogate of the PABP-poly(A) complex; therefore, it cannot by itself be responsible for inhibiting the translation of host poly(A)-tailed mRNAs upon rotavirus infection. IMPORTANCE To control host cell physiology and to circumvent innate immunity, many viruses have evolved powerful mechanisms aimed at inhibiting host mRNA translation while stimulating translation of their own mRNAs. How rotavirus tackles this challenge is still a matter of debate. Using rotavirus-infected cells, we show that the magnitude of cellular poly(A) mRNA translation

  17. Hormonal stimulation of starfish oocytes induces partial degradation of the 3' termini of cyclin B mRNAs with oligo(U) tails, followed by poly(A) elongation.

    PubMed

    Ochi, Hiroe; Chiba, Kazuyoshi

    2016-06-01

    In yeast, plant, and mammalian somatic cells, short poly(A) tails on mRNAs are subject to uridylation, which mediates mRNA decay. Although mRNA uridylation has never been reported in animal oocytes, maternal mRNAs with short poly(A) tails are believed to be translationally repressed. In this study, we found that 96% of cyclin B mRNAs with short poly(A) tails were uridylated in starfish oocytes. Hormonal stimulation induced poly(A) elongation of cyclin B mRNA, and 62% of long adenine repeats did not contain uridine residues. To determine whether uridylated short poly(A) tails destabilize cyclin B mRNA, we developed a method for producing RNAs with the strict 3' terminal sequences of cyclin B, with or without oligo(U) tails. When we injected these synthetic RNAs into starfish oocytes prior to hormonal stimulation, we found that uridylated RNAs were as stable as nonuridylated RNAs. Following hormonal stimulation, the 3' termini of short poly(A) tails of synthesized RNAs containing oligo(U) tails were trimmed, and their poly(A) tails were subsequently elongated. These results indicate that uridylation of short poly(A) tails in cyclin B mRNA of starfish oocytes does not mediate mRNA decay; instead, hormonal stimulation induces partial degradation of uridylated short poly(A) tails in the 3'-5' direction, followed by poly(A) elongation. Oligo(U) tails may be involved in translational inactivation of mRNAs. PMID:27048146

  18. A conserved role for the zinc finger polyadenosine RNA binding protein, ZC3H14, in control of poly(A) tail length

    PubMed Central

    Kelly, Seth M.; Leung, Sara W.; Pak, ChangHui; Banerjee, Ayan; Moberg, Kenneth H.; Corbett, Anita H.

    2014-01-01

    The ZC3H14 gene, which encodes a ubiquitously expressed, evolutionarily conserved, nuclear, zinc finger polyadenosine RNA-binding protein, was recently linked to autosomal recessive, nonsyndromic intellectual disability. Although studies have been carried out to examine the function of putative orthologs of ZC3H14 in Saccharomyces cerevisiae, where the protein is termed Nab2, and Drosophila, where the protein has been designated dNab2, little is known about the function of mammalian ZC3H14. Work from both budding yeast and flies implicates Nab2/dNab2 in poly(A) tail length control, while a role in poly(A) RNA export from the nucleus has been reported only for budding yeast. Here we provide the first functional characterization of ZC3H14. Analysis of ZC3H14 function in a neuronal cell line as well as in vivo complementation studies in a Drosophila model identify a role for ZC3H14 in proper control of poly(A) tail length in neuronal cells. Furthermore, we show here that human ZC3H14 can functionally substitute for dNab2 in fly neurons and can rescue defects in development and locomotion that are present in dNab2 null flies. These rescue experiments provide evidence that this zinc finger-containing class of nuclear polyadenosine RNA-binding proteins plays an evolutionarily conserved role in controlling the length of the poly(A) tail in neurons. PMID:24671764

  19. TMV mutants with poly(A) tracts of different lengths demonstrate structural variations in 3′UTR affecting viral RNAs accumulation and symptom expression

    PubMed Central

    Guo, Song; Kierzek, Elzbieta; Chen, Gang; Zhou, Yi-Jun; Wong, Sek-Man

    2015-01-01

    The upstream pseudoknots domain (UPD) of Tobacco mosaic virus (TMV) is located at the 3′-untranslated region (UTR). It plays an important role in virus replication and translation. To determine the importance of UPD and 3′-UTR, and the effects of introduced RNA elements in TMV 3′-UTR, a series of TMV mutants with internal poly(A) tract upstream of UPD was constructed for structural analysis by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). TMV(24A+UPD) and TMV(42A+UPD) formed a similar structure as that of TMV 3′-UTR, but TMV(62A+UPD) structures altered by the introduced poly(A) tract. In addition, TMV(24A+UPD) had a higher viral RNAs accumulation than TMV in N. benthamiana protoplasts, and induced lethal symptoms in the infected plants. TMV(62A+UPD) showed a drastically reduced accumulation, its coat protein was undetectable in protoplasts, and the inoculated plants remained symptomless. This study analyzed the structures of 3′-UTR of TMV and found that the longer poly(A) tract introduced upstream of UPD reduced viral RNAs accumulation and induced milder symptoms in N. benthamiana. In conclusion, different lengths of the internal poly(A) tract introduced into the TMV 3′UTR lead to structural variations that affect virus accumulation and symptom expression. PMID:26678425

  20. Structure and Mechanism of Dimer-Monomer Transition of a Plant Poly(A)-Binding Protein upon RNA Interaction: Insights into Its Poly(A) Tail Assembly.

    PubMed

    Domingues, Mariane Noronha; Sforça, Mauricio Luis; Soprano, Adriana Santos; Lee, Jack; Souza, Tatiana de Arruda Campos Brasil de; Cassago, Alexandre; Portugal, Rodrigo Villares; Zeri, Ana Carolina de Mattos; Murakami, Mario Tyago; Sadanandom, Ari; Oliveira, Paulo Sergio Lopes de; Benedetti, Celso Eduardo

    2015-07-31

    Poly(A)-binding proteins (PABPs) play crucial roles in mRNA biogenesis, stability, transport and translational control in most eukaryotic cells. Although animal PABPs are well-studied proteins, the biological role, three-dimensional structure and RNA-binding mode of plant PABPs remain largely uncharacterized. Here, we report the structural features and RNA-binding mode of a Citrus sinensis PABP (CsPABPN1). CsPABPN1 has a domain architecture of nuclear PABPs (PABPNs) with a single RNA recognition motif (RRM) flanked by an acidic N-terminus and a GRPF-rich C-terminus. The RRM domain of CsPABPN1 displays virtually the same three-dimensional structure and poly(A)-binding mode of animal PABPNs. However, while the CsPABPN1 RRM domain specifically binds poly(A), the full-length protein also binds poly(U). CsPABPN1 localizes to the nucleus of plant cells and undergoes a dimer-monomer transition upon poly(A) interaction. We show that poly(A) binding by CsPABPN1 begins with the recognition of the RNA-binding sites RNP1 and RNP2, followed by interactions with residues of the β2 strands, which stabilize the dimer, thus leading to dimer dissociation. Like human PABPN1, CsPABPN1 also seems to form filaments in the presence of poly(A). Based on these data, we propose a structural model in which contiguous CsPABPN1 RRM monomers wrap around the RNA molecule creating a superhelical structure that could not only shield the poly(A) tail but also serve as a scaffold for the assembly of additional mRNA processing factors. PMID:26013164

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

    SciTech Connect

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

    2013-03-01

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

  2. A human mitochondrial poly(A) polymerase mutation reveals the complexities of post-transcriptional mitochondrial gene expression.

    PubMed

    Wilson, William C; Hornig-Do, Hue-Tran; Bruni, Francesco; Chang, Jeong Ho; Jourdain, Alexis A; Martinou, Jean-Claude; Falkenberg, Maria; Spåhr, Henrik; Larsson, Nils-Göran; Lewis, Richard J; Hewitt, Lorraine; Baslé, Arnaud; Cross, Harold E; Tong, Liang; Lebel, Robert R; Crosby, Andrew H; Chrzanowska-Lightowlers, Zofia M A; Lightowlers, Robert N

    2014-12-01

    The p.N478D missense mutation in human mitochondrial poly(A) polymerase (mtPAP) has previously been implicated in a form of spastic ataxia with optic atrophy. In this study, we have investigated fibroblast cell lines established from family members. The homozygous mutation resulted in the loss of polyadenylation of all mitochondrial transcripts assessed; however, oligoadenylation was retained. Interestingly, this had differential effects on transcript stability that were dependent on the particular species of transcript. These changes were accompanied by a severe loss of oxidative phosphorylation complexes I and IV, and perturbation of de novo mitochondrial protein synthesis. Decreases in transcript polyadenylation and in respiratory chain complexes were effectively rescued by overexpression of wild-type mtPAP. Both mutated and wild-type mtPAP localized to the mitochondrial RNA-processing granules thereby eliminating mislocalization as a cause of defective polyadenylation. In vitro polyadenylation assays revealed severely compromised activity by the mutated protein, which generated only short oligo(A) extensions on RNA substrates, irrespective of RNA secondary structure. The addition of LRPPRC/SLIRP, a mitochondrial RNA-binding complex, enhanced activity of the wild-type mtPAP resulting in increased overall tail length. The LRPPRC/SLIRP effect although present was less marked with mutated mtPAP, independent of RNA secondary structure. We conclude that (i) the polymerase activity of mtPAP can be modulated by the presence of LRPPRC/SLIRP, (ii) N478D mtPAP mutation decreases polymerase activity and (iii) the alteration in poly(A) length is sufficient to cause dysregulation of post-transcriptional expression and the pathogenic lack of respiratory chain complexes. PMID:25008111

  3. Target specificity among canonical nuclear poly(A) polymerases in plants modulates organ growth and pathogen response

    PubMed Central

    Vi, Son Lang; Trost, Gerda; Lange, Peggy; Czesnick, Hjördis; Rao, Nishta; Lieber, Diana; Laux, Thomas; Gray, William M.; Manley, James L.; Groth, Detlef; Kappel, Christian; Lenhard, Michael

    2013-01-01

    Polyadenylation of pre-mRNAs is critical for efficient nuclear export, stability, and translation of the mature mRNAs, and thus for gene expression. The bulk of pre-mRNAs are processed by canonical nuclear poly(A) polymerase (PAPS). Both vertebrate and higher-plant genomes encode more than one isoform of this enzyme, and these are coexpressed in different tissues. However, in neither case is it known whether the isoforms fulfill different functions or polyadenylate distinct subsets of pre-mRNAs. Here we show that the three canonical nuclear PAPS isoforms in Arabidopsis are functionally specialized owing to their evolutionarily divergent C-terminal domains. A strong loss-of-function mutation in PAPS1 causes a male gametophytic defect, whereas a weak allele leads to reduced leaf growth that results in part from a constitutive pathogen response. By contrast, plants lacking both PAPS2 and PAPS4 function are viable with wild-type leaf growth. Polyadenylation of SMALL AUXIN UP RNA (SAUR) mRNAs depends specifically on PAPS1 function. The resulting reduction in SAUR activity in paps1 mutants contributes to their reduced leaf growth, providing a causal link between polyadenylation of specific pre-mRNAs by a particular PAPS isoform and plant growth. This suggests the existence of an additional layer of regulation in plant and possibly vertebrate gene expression, whereby the relative activities of canonical nuclear PAPS isoforms control de novo synthesized poly(A) tail length and hence expression of specific subsets of mRNAs. PMID:23918356

  4. Characterization of the mouse beta maj globin transcription termination region: a spacing sequence is required between the poly(A) signal sequence and multiple downstream termination elements.

    PubMed Central

    Tantravahi, J; Alvira, M; Falck-Pedersen, E

    1993-01-01

    For the majority of mRNA encoding eukaryotic transcription units, there is little or no knowledge of the elements responsible for transcription termination or how they may interact with RNA polymerase. In this report, we have used recombinant adenovirus reporter vectors to characterize the mouse beta maj globin sequence elements that cause transcription termination. Within the globin 3' termination region, we have identified at least three sequence elements which induce significant levels of transcription termination (> 50%). The smallest functionally active element (64% termination) is 69 bp in length. The natural arrangement of these elements results in a cumulative termination which is greater than 90%. Recognition of the termination elements by RNA polymerase II depends on the presence of a functional poly(A) signal sequence. We demonstrate that efficient transcription termination depends on appropriate spacing between the poly(A) signal sequence and the termination element. Images PMID:8417354

  5. Identification and characterization of two critical sequences in SV40PolyA that activate the green fluorescent protein reporter gene.

    PubMed

    Wang, Honggang; Sun, Wuzhuang; Li, Zhu; Wang, Xiufang; Lv, Zhanjun

    2011-07-01

    Alu repeats or Line-1-ORF2 (ORF2) inhibit expression of the green fluorescent protein (GFP) gene when inserted downstream of this gene in the vector pEGFP-C1. In this work, we studied cis-acting elements that eliminated the repression of GFP gene expression induced by Alu and ORF2 and sequence characteristics of these elements. We found that sense and antisense PolyA of simian virus 40 (SV40PolyA, 240 bp) eliminated the repression of GFP gene expression when inserted between the GFP gene and the Alu (283 bp) repeats or ORF2 (3825 bp) in pAlu14 (14 tandem Alu repeats were inserted downstream of the GFP gene in the vector pEGFP-C1) or pORF2. Antisense SV40PolyA (PolyAas) induced stronger gene expression than its sense orientation (PolyA). Of four 60-bp segments of PolyAas (1F1R, 2F2R, 3F3R and 4F4R) inserted independently into pAlu14, only two (2F2R and 3F3R) eliminated the inhibition of GFP gene expression induced by Alu repeats. Deletion analysis revealed that a 17 nucleotide AT repeat (17ntAT; 5'-AAAAAAATGCTTTATTT-3') in 2F2R and the fragment 3F38d9 (5'-ATAAACAAGTTAACAACA ACAATTGCATT-3') in 3F3R were critical sequences for activating the GFP gene. Sequence and structural analyses showed that 17ntAT and 3F38d9 included imperfect palindromes and may form a variety of unstable stem-loops. We suggest that the presence of imperfect palindromes and unstable stem-loops in DNA enhancer elements plays an important role in GFP gene activation. PMID:21931509

  6. Interdomain allostery promotes assembly of the poly(A) mRNA complex with PABP and eIF4G.

    PubMed

    Safaee, Nozhat; Kozlov, Guennadi; Noronha, Anne M; Xie, Jingwei; Wilds, Christopher J; Gehring, Kalle

    2012-11-01

    Many RNA-binding proteins contain multiple single-strand nucleic acid-binding domains and assemble into large multiprotein messenger ribonucleic acid protein (mRNP) complexes. The mechanisms underlying the self-assembly of these complexes are largely unknown. In eukaryotes, the association of the translation factors polyadenylate-binding protein-1 (PABP) and eIF4G is essential for high-level expression of polyadenylated mRNAs. Here, we report the crystal structure of the ternary complex poly(A)(11)·PABP(1-190)·eIF4G(178-203) at 2.0 Å resolution. Our NMR and crystallographic data show that eIF4G interacts with the RRM2 domain of PABP. Analysis of the interaction by small-angle X-ray scattering, isothermal titration calorimetry, and electromobility shift assays reveals that this interaction is allosterically regulated by poly(A) binding to PABP. Furthermore, we have confirmed the importance of poly(A) for the endogenous PABP and eIF4G interaction in immunoprecipitation experiments using HeLa cell extracts. Our findings reveal interdomain allostery as a mechanism for cooperative assembly of RNP complexes. PMID:23041282

  7. Ribonucleotide sequences non-adjacent to poly(A) participate in the poly(A)-protein complex in 15S duck globin mRNP particles.

    PubMed Central

    Goldenberg, S; Vincent, A; Scherrer, K

    1980-01-01

    The study of the interaction between mRNA and proteins in the polyribosomal 15 S duck globin messenger ribonucleoprotein complex showed that proteins protect specific mRNA sequences against digestion by the nonspecific micrococcal nuclease (Nucleic Acids Research 6 (8) 2787, 1979). Here we report the isolation of the poly(A)-protein RNP complex from nuclease digested 15 S mRNP by two different methods: sucrose gradient sedimentation and oligo(dT)-cellulose chromatography. We show by fingerprint analysis, that aprt from the periodically fragmented poly(A) segment, mRNA sequences adjacent and non-adjacent to the poly(A) segment are protected by the poly(A) binding proteins against nuclease digestion. The duck globin poly(A)-protein RNP complex, with a sedimentation coefficient between 7 S and 10 S, shows a characteristic protein composition, with a major 73,000 MW polypeptide and some minor components. The results are discussed in view of a dynamic ribonucleoprotein structure. Images PMID:7443531

  8. The Saccharomyces cerevisiae poly(A) binding protein Pab1 as a target for eliciting stress tolerant phenotypes

    PubMed Central

    Martani, Francesca; Marano, Francesca; Bertacchi, Stefano; Porro, Danilo; Branduardi, Paola

    2015-01-01

    When exploited as cell factories, Saccharomyces cerevisiae cells are exposed to harsh environmental stresses impairing titer, yield and productivity of the fermentative processes. The development of robust strains therefore represents a pivotal challenge for the implementation of cost-effective bioprocesses. Altering master regulators of general cellular rewiring represents a possible strategy to evoke shaded potential that may accomplish the desirable features. The poly(A) binding protein Pab1, as stress granules component, was here selected as the target for obtaining widespread alterations in mRNA metabolism, resulting in stress tolerant phenotypes. Firstly, we demonstrated that the modulation of Pab1 levels improves robustness against different stressors. Secondly, the mutagenesis of PAB1 and the application of a specific screening protocol on acetic acid enriched medium allowed the isolation of the further ameliorated mutant pab1 A60-9. These findings pave the way for a novel approach to unlock industrially promising phenotypes through the modulation of a post-transcriptional regulatory element. PMID:26658950

  9. Poly(A) binding protein abundance regulates eukaryotic translation initiation factor 4F assembly in human cytomegalovirus-infected cells.

    PubMed

    McKinney, Caleb; Perez, Cesar; Mohr, Ian

    2012-04-10

    By commandeering cellular translation initiation factors, or destroying those dispensable for viral mRNA translation, viruses often suppress host protein synthesis. In contrast, cellular protein synthesis proceeds in human cytomegalovirus (HCMV)-infected cells, forcing viral and cellular mRNAs to compete for limiting translation initiation factors. Curiously, inactivating the host translational repressor 4E-BP1 in HCMV-infected cells stimulates synthesis of the cellular poly(A) binding protein (PABP), significantly increasing PABP abundance. Here, we establish that new PABP synthesis is translationally controlled by the HCMV-encoded UL38 mammalian target of rapamycin complex 1-activator. The 5' UTR within the mRNA encoding PABP contains a terminal oligopyrimidine (TOP) element found in mRNAs, the translation of which is stimulated in response to mitogenic, growth, and nutritional stimuli, and proteins encoded by TOP-containing mRNAs accumulated in HCMV-infected cells. Furthermore, UL38 expression was necessary and sufficient to regulate expression of a PABP TOP-containing reporter. Remarkably, preventing the rise in PABP abundance by RNAi impaired eIF4E binding to eIF4G, thereby reducing assembly of the multisubunit initiation factor eIF4F, viral protein production, and replication. This finding demonstrates that viruses can increase host translation initiation factor concentration to foster their replication and defines a unique mechanism whereby control of PABP abundance regulates eIF4F assembly. PMID:22431630

  10. Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs

    PubMed Central

    Bresson, Stefan M.; Hunter, Olga V.; Hunter, Allyson C.; Conrad, Nicholas K.

    2015-01-01

    The human nuclear poly(A)-binding protein PABPN1 has been implicated in the decay of nuclear noncoding RNAs (ncRNAs). In addition, PABPN1 promotes hyperadenylation by stimulating poly(A)-polymerases (PAPα/γ), but this activity has not previously been linked to the decay of endogenous transcripts. Moreover, the mechanisms underlying target specificity have remained elusive. Here, we inactivated PAP-dependent hyperadenylation in cells by two independent mechanisms and used an RNA-seq approach to identify endogenous targets. We observed the upregulation of various ncRNAs, including snoRNA host genes, primary miRNA transcripts, and promoter upstream antisense RNAs, confirming that hyperadenylation is broadly required for the degradation of PABPN1-targets. In addition, we found that mRNAs with retained introns are susceptible to PABPN1 and PAPα/γ-mediated decay (PPD). Transcripts are targeted for degradation due to inefficient export, which is a consequence of reduced intron number or incomplete splicing. Additional investigation showed that a genetically-encoded poly(A) tail is sufficient to drive decay, suggesting that degradation occurs independently of the canonical cleavage and polyadenylation reaction. Surprisingly, treatment with transcription inhibitors uncouples polyadenylation from decay, leading to runaway hyperadenylation of nuclear decay targets. We conclude that PPD is an important mammalian nuclear RNA decay pathway for the removal of poorly spliced and nuclear-retained transcripts. PMID:26484760

  11. A highly sensitive dual-readout assay based on poly(A) and gold nanoparticles for palmatine hydrochloride.

    PubMed

    Tan, Kejun; Li, Jiayu; Li, Huachun; Wang, Yingying; Yuan, Rui

    2014-03-25

    This report presents a highly sensitive, poly(A)-stabilized gold nanoparticle-based assay with dual readouts (resonance light scattering and colorimetric) for detecting palmatine hydrochloride (PaH) in real samples. The detection mechanism is based on the fact that palmatine hydrochloride has strong affinity to poly(A), which can stabilize gold nanoparticles at high ionic strength, and cause the aggregation of poly(A)-stabilized AuNPs, resulting in the enhanced resonance light scattering (RLS). At the same time, the color change of poly(A)-stabilized AuNPs solution is from red to blue via purple. Thus a highly sensitive RLS assay for PaH has been developed with a linear range of 0.023-2.5 μg/mL. The limit of detection (LOD, 3σ) is 2.3 ng/mL. In this work, the reaction mechanism of this system was investigated by scanning electron microscope (SEM), dark-field light scattering images (DLSI), dynamiclight scattering (DLS) and circular dichroism (CD). This proposed method was also applied successfully for the determination of PaH in pharmaceutical preparations and urine samples with RSD⩽4.0%. The results are in good agreement with those from the official method. PMID:24316533

  12. The role of Glu-60 in the specificity of the recombinant ribonuclease from Bacillus amyloliquefaciens (barnase) towards dinucleotides, poly(A) and RNA.

    PubMed Central

    Bastyns, K; Froeyer, M; Volckaert, G; Engelborghs, Y

    1994-01-01

    A computer model of the complex between G2'p5'G and barnase, the recombinant ribonuclease of Bacillus amyloliquefaciens, was constructed, based on the known structure of the complex RNAase T1.G2'p5'G. This model suggests that the conserved residue Glu-60 plays an important role in the specificity of barnase for guanosine. A barnase mutant was therefore made in which Glu-60 was replaced by Gln. This mutation increases the Km for the dinucleotides GpC and GpA, by a factor of 10, but does not change the kcat. For ApA, the kcat/Km decreases by a similar factor, but the individual parameters could not be determined. The mutation, however, has no influence on the kcat and the Km of barnase action towards RNA and poly(A). This demonstrates that the interactions between the substrate and the residue at position 60 must be different in the case of ApA and poly(A). For RNA, this conclusion is also likely, but not absolutely certain, because barnase/RNA might be a Briggs-Haldane type enzyme/substrate pair. Therefore, if the effect of the mutation were limited to an increase of the dissociation rate constant of the substrate (k-1), this would not be evident in Km or kcat/Km. In view of the clear cut situation with poly(A), the pH profile for and the effect of salt concentration on the kinetic parameters of the mutant barnase were studied for this substrate. The influence of salt on the Km can be interpreted via the linked function concept and shows a cooperative dissociation of 7-10 counterions upon poly(A) binding. The binding of the substrate is strongly reduced at high pH, and the pKa involved decreases strongly at high salt concentrations. Poly(A) and RNA show a pH dependency of their absorbance spectrum, indicating a pH-dependent change of base stacking, which may influence the catalytic parameters. PMID:7516656

  13. Induction and Accumulation of Heat Shock-Specific Poly(A+) RNAs and Proteins in Soybean Seedlings during Arsenite and Cadmium Treatments 1

    PubMed Central

    Edelman, Leonard; Czarnecka, Eva; Key, Joe L.

    1988-01-01

    Northern blot hybridization analyzes revealed that poly(A+) RNAs homologous to eight heat shock (HS)-specific cDNA clones were induced by arsenite (As) or Cd treatments. The mRNAs accumulated slower, and maximum accumulations were consistently lower than HS-induced levels. Prolonged treatment with low concentrations (50-100 micromolar) of As for 6 hours, or Cd for 12 hours, resulted in decreased accumulations of HS-specific mRNAs. This response resembled the `autoregulation' observed during continuous 40°C HS. However, no autoregulation was evident when soybean seedlings were exposed to high concentrations of As (250 micromolar) or Cd (1 millimolar) for 12 hours. The cDNA probe pCE54 detected a second higher molecular weight poly(A+) RNA following As or Cd treatments which accumulated concomitantly with the lower molecular weight HS-specific poly(A+) RNA. The patterns of low molecular weight HS polypeptides from in vitro translations induced by HS, As, and Cd, and analyzed by one-dimensional and two-dimensional SDS-PAGE, were similar but temporal differences were apparent. In addition to HS proteins, many control proteins were also detected in both in vitro and in vivo labeling patterns from As and, to a lesser extent, Cd treatments. The chemical agents used in this study apparently induced the accumulation and translation of HS messages in vivo but not in the selective manner as observed during HS treatment. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:16666030

  14. The 25 kDa Subunit of Cleavage Factor Im Is a RNA-Binding Protein That Interacts with the Poly(A) Polymerase in Entamoeba histolytica

    PubMed Central

    Pezet-Valdez, Marisol; Fernández-Retana, Jorge; Ospina-Villa, Juan David; Ramírez-Moreno, María Esther; Orozco, Esther; Charcas-López, Socorro; Soto-Sánchez, Jacqueline; Mendoza-Hernández, Guillermo; López-Casamicha, Mavil; López-Camarillo, César; Marchat, Laurence A.

    2013-01-01

    In eukaryotes, polyadenylation of pre-mRNA 3´ end is essential for mRNA export, stability and translation. Taking advantage of the knowledge of genomic sequences of Entamoeba histolytica, the protozoan responsible for human amoebiasis, we previously reported the putative polyadenylation machinery of this parasite. Here, we focused on the predicted protein that has the molecular features of the 25 kDa subunit of the Cleavage Factor Im (CFIm25) from other organisms, including the Nudix (nucleoside diphosphate linked to another moiety X) domain, as well as the RNA binding domain and the PAP/PAB interacting region. The recombinant EhCFIm25 protein (rEhCFIm25) was expressed in bacteria and used to generate specific antibodies in rabbit. Subcellular localization assays showed the presence of the endogenous protein in nuclear and cytoplasmic fractions. In RNA electrophoretic mobility shift assays, rEhCFIm25 was able to form specific RNA-protein complexes with the EhPgp5 mRNA 3´ UTR used as probe. In addition, Pull-Down and LC/ESI-MS/MS tandem mass spectrometry assays evidenced that the putative EhCFIm25 was able to interact with the poly(A) polymerase (EhPAP) that is responsible for the synthesis of the poly(A) tail in other eukaryotic cells. By Far-Western experiments, we confirmed the interaction between the putative EhCFIm25 and EhPAP in E. histolytica. Taken altogether, our results showed that the putative EhCFIm25 is a conserved RNA binding protein that interacts with the poly(A) polymerase, another member of the pre-mRNA 3´ end processing machinery in this protozoan parasite. PMID:23840799

  15. The 25 kDa subunit of cleavage factor Im Is a RNA-binding protein that interacts with the poly(A) polymerase in Entamoeba histolytica.

    PubMed

    Pezet-Valdez, Marisol; Fernández-Retana, Jorge; Ospina-Villa, Juan David; Ramírez-Moreno, María Esther; Orozco, Esther; Charcas-López, Socorro; Soto-Sánchez, Jacqueline; Mendoza-Hernández, Guillermo; López-Casamicha, Mavil; López-Camarillo, César; Marchat, Laurence A

    2013-01-01

    In eukaryotes, polyadenylation of pre-mRNA 3' end is essential for mRNA export, stability and translation. Taking advantage of the knowledge of genomic sequences of Entamoeba histolytica, the protozoan responsible for human amoebiasis, we previously reported the putative polyadenylation machinery of this parasite. Here, we focused on the predicted protein that has the molecular features of the 25 kDa subunit of the Cleavage Factor Im (CFIm25) from other organisms, including the Nudix (nucleoside diphosphate linked to another moiety X) domain, as well as the RNA binding domain and the PAP/PAB interacting region. The recombinant EhCFIm25 protein (rEhCFIm25) was expressed in bacteria and used to generate specific antibodies in rabbit. Subcellular localization assays showed the presence of the endogenous protein in nuclear and cytoplasmic fractions. In RNA electrophoretic mobility shift assays, rEhCFIm25 was able to form specific RNA-protein complexes with the EhPgp5 mRNA 3´ UTR used as probe. In addition, Pull-Down and LC/ESI-MS/MS tandem mass spectrometry assays evidenced that the putative EhCFIm25 was able to interact with the poly(A) polymerase (EhPAP) that is responsible for the synthesis of the poly(A) tail in other eukaryotic cells. By Far-Western experiments, we confirmed the interaction between the putative EhCFIm25 and EhPAP in E. histolytica. Taken altogether, our results showed that the putative EhCFIm25 is a conserved RNA binding protein that interacts with the poly(A) polymerase, another member of the pre-mRNA 3' end processing machinery in this protozoan parasite. PMID:23840799

  16. Regulation of poly(A) binding protein function in translation: Characterization of the Paip2 homolog, Paip2B

    PubMed Central

    Berlanga, Juan José; Baass, Alexis; Sonenberg, Nahum

    2006-01-01

    The 5′ cap and 3′ poly(A) tail of eukaryotic mRNAs act synergistically to enhance translation. This synergy is mediated via interactions between eIF4G (a component of the eIF4F cap binding complex) and poly(A) binding protein (PABP). Paip2 (PABP-interacting protein 2) binds PABP and inhibits translation both in vitro and in vivo by decreasing the affinity of PABP for polyadenylated RNA. Here, we describe the functional characteristics of Paip2B, a Paip2 homolog. A full-length brain cDNA of Paip2B encodes a protein that shares 59% identity and 80% similarity with Paip2 (Paip2A), with the highest conservation in the two PABP binding domains. Paip2B acts in a manner similar to Paip2A to inhibit translation of capped and polyadenylated mRNAs both in vitro and in vivo by displacing PABP from the poly(A) tail. Also, similar to Paip2A, Paip2B does not affect the translation mediated by the internal ribosome entry site (IRES) of hepatitis C virus (HCV). However, Paip2A and Paip2B differ with respect to both mRNA and protein distribution in different tissues and cell lines. Paip2A is more highly ubiquitinated than is Paip2B and is degraded more rapidly by the proteasome. Paip2 protein degradation may constitute a primary mechanism by which cells regulate PABP activity in translation. PMID:16804161

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

    PubMed Central

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

    2016-01-01

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

  18. Saccharomyces cerevisiae Ngl3p is an active 3′–5′ exonuclease with a specificity towards poly-A RNA reminiscent of cellular deadenylases

    PubMed Central

    Feddersen, Ane; Dedic, Emil; Poulsen, Esben G.; Schmid, Manfred; Van, Lan Bich; Jensen, Torben Heick; Brodersen, Ditlev E.

    2012-01-01

    Deadenylation is the first and rate-limiting step during turnover of mRNAs in eukaryotes. In the yeast, Saccharomyces cerevisiae, two distinct 3′–5′ exonucleases, Pop2p and Ccr4p, have been identified within the Ccr4-NOT deadenylase complex, belonging to the DEDD and Exonuclease–Endonuclease–Phosphatase (EEP) families, respectively. Ngl3p has been identified as a new member of the EEP family of exonucleases based on sequence homology, but its activity and biological roles are presently unknown. Here, we show using in vitro deadenylation assays on defined RNA species mimicking poly-A containing mRNAs that yeast Ngl3p is a functional 3′–5′ exonuclease most active at slightly acidic conditions. We further show that the enzyme depends on divalent metal ions for activity and possesses specificity towards poly-A RNA similar to what has been observed for cellular deadenylases. The results suggest that Ngl3p is naturally involved in processing of poly-adenylated RNA and provide insights into the mechanistic variations observed among the redundant set of EEP enzymes found in yeast and higher eukaryotes. PMID:21965533

  19. Phase-Specific Polypeptides and Poly(A)+ RNAs during the Cell Cycle in Synchronous Cultures of Catharanthus roseus Cells 1

    PubMed Central

    Kodama, Hiroaki; Kawakami, Naoto; Watanabe, Akira; Komamine, Atsushi

    1989-01-01

    This study shows an overall analysis of gene expression during the cell cycle in synchronous suspension cultures of Catharanthus roseus cells. First, the cellular cytoplasmic proteins were fractionated by two-dimensional gel electrophoresis and visualized by staining with silver. Seventeen polypeptides showed qualitative or quantitative changes during the cell cycle. Second, the rates of synthesis of cytoplasmic proteins were also investigated by autoradiography by labeling cells with [35S]methionine at each phase of the cell cycle. The rates of synthesis of 13 polypeptides were found to vary during the cell cycle. The silverstained electrophoretic pattern of proteins in the G2 phase in particular showed characteristic changes in levels of polypeptides, while the rates of synthesis of polypeptides synthesized during the G2 phase did not show such phase-specific changes. This result suggests that posttranslational processing of polypeptides occurs during or prior to the G2 phase. In the G1 and S phases and during cytokinesis, several other polypeptides were specifically synthesized. Finally, the variation of mRNAs was analyzed from the autoradiograms of in vitro translation products of poly(A)+ RNA isolated at each phase. Three poly(A)+ RNAs increased in amount from the G1 to the S phase and one poly (A)+ RNA increased preferentially from the G2 phase to cytokinesis. Images Figure 1 Figure 3 Figure 4 Figure 6 Figure 7 Figure 8 Figure 10 Figure 11 Figure 12 PMID:16666641

  20. Multiple forms of poly(A) polymerases purified from HeLa cells function in specific mRNA 3'-end formation.

    PubMed Central

    Ryner, L C; Takagaki, Y; Manley, J L

    1989-01-01

    Poly(A) polymerases (PAPs) from HeLa cell cytoplasmic and nuclear fractions were extensively purified by using a combination of fast protein liquid chromatography and standard chromatographic methods. Several forms of the enzyme were identified, two from the nuclear fraction (NE PAPs I and II) and one from the cytoplasmic fraction (S100 PAP). NE PAP I had chromatographic properties similar to those of S100 PAP, and both enzymes displayed higher activities in the presence of Mn2+ than in the presence of Mg2+, whereas NE PAP II was chromatographically distinct and had approximately equal levels of activity in the presence of Mn2+ and Mg2+. Each of the enzymes, when mixed with other nuclear fractions containing cleavage or specificity factors, was able to reconstitute efficient cleavage and polyadenylation of pre-mRNAs containing an AAUAAA sequence element. The PAPs alone, however, showed no preference for precursors containing an intact AAUAAA sequence over a mutated one, providing further evidence that the PAPs have no intrinsic ability to recognize poly(A) addition sites. Two additional properties of the three enzymes suggest that they are related: sedimentation in glycerol density gradients indicated that the native size of each enzyme is approximately 50 to 60 kilodaltons, and antibodies against a rat hepatoma PAP inhibited the ability of each enzyme to function in AAUAAA-dependent polyadenylation. Images PMID:2555686

  1. PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage.

    PubMed

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

    2016-04-12

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

  2. Biological activity of mRNA immobilized on nitrocellulose in NaI.

    PubMed Central

    Bresser, J; Hubbell, H R; Gillespie, D

    1983-01-01

    In 12.2 molal NaI and at 25 degrees C or below, mRNA bound to nitrocellulose while DNA and rRNA did not. Neither the poly(A) tract nor the cap were required for binding. The immobilized RNA could be translated, reverse transcribed, hybridized with radioactive probes, or released for further manipulation. mRNA was efficiently transferred from polyacrylamide to nitrocellulose in NaI. Baking was not required to fix NaI-immobilized mRNA to nitrocellulose. When cells dissolved in 12.2 molal NaI were filtered through nitrocellulose, mRNA became selectively bound (quickblot). The quick-blot system utilizing protease and detergents to prepare cells for NaI solubilization was especially suitable in quantitative, rapid screening of cells for expression of specific genes. Expression of highly repeated DNA sequences was detected in human leukemia cells. Images PMID:6579539

  3. Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases.

    PubMed Central

    Martin, G; Keller, W

    1996-01-01

    We have tested deletion and substitution mutants of bovine poly(A) polymerase, and have identified a small region that overlaps with a nuclear localization signal and binds to the RNA primer. Systematic mutagenesis of carboxylic amino acids led to the identification of three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor. Images PMID:8665867

  4. The role of the poly(A) binding protein in the assembly of the Cap-binding complex during translation initiation in plants.

    PubMed

    Gallie, Daniel R

    2014-09-01

    Translation initiation in eukaryotes requires the involvement of multiple initiation factors (eIFs) that facilitate the binding of the 40 S ribosomal subunit to an mRNA and assemble the 80 S ribosome at the correct initiation codon. eIF4F, composed of eIF4E, eIF4A, and eIF4G, binds to the 5'-cap structure of an mRNA and prepares an mRNA for recruitment of a 40 S subunit. eIF4B promotes the ATP-dependent RNA helicase activity of eIF4A and eIF4F needed to unwind secondary structure present in a 5'-leader that would otherwise impede scanning of the 40 S subunit during initiation. The poly(A) binding protein (PABP), which binds the poly(A) tail, interacts with eIF4G and eIF4B to promote circularization of an mRNA and stimulates translation by promoting 40 S subunit recruitment. Thus, these factors serve essential functions in the early steps of protein synthesis. Their assembly and function requires multiple interactions that are competitive in nature and determine the nature of interactions between the termini of an mRNA. In this review, the domain organization and partner protein interactions are presented for the factors in plants which share similarities with those in animals and yeast but differ in several important respects. The functional consequences of their interactions on factor activity are also discussed. PMID:26779409

  5. Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana

    PubMed Central

    Ramming, Anna; Kolbe, Benjamin; Vi, Son Lang; Bispo, Cláudia; Becker, Jörg D.; de Moor, Cornelia; Lenhard, Michael

    2015-01-01

    The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. PMID:26305463

  6. Selective stabilization of mammalian microRNAs by 3′ adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2

    PubMed Central

    Katoh, Takayuki; Sakaguchi, Yuriko; Miyauchi, Kenjyo; Suzuki, Takeo; Kashiwabara, Shin-ichi; Baba, Tadashi; Suzuki, Tsutomu

    2009-01-01

    The steady-state levels of microRNAs (miRNAs) and their activities are regulated by the post-transcriptional processes. It is known that 3′ ends of several miRNAs undergo post-dicing adenylation or uridylation. We isolated the liver-specific miR-122 from human hepatocytes and mouse livers. Direct analysis by mass spectrometry revealed that one variant of miR-122 has a 3′-terminal adenosine that is introduced after processing by Dicer. We identified GLD-2, which is a regulatory cytoplasmic poly(A) polymerase, as responsible for the 3′-terminal adenylation of miR-122 after unwinding of the miR-122/miR-122* duplex. In livers from GLD-2-null mice, the steady-state level of the mature form of miR-122 was specifically lower than in heterozygous mice, whereas no reduction of pre-miR-122 was observed, demonstrating that 3′-terminal adenylation by GLD-2 is required for the selective stabilization of miR-122 in the liver. PMID:19240131

  7. Site-specific cleavage of the host poly(A) binding protein by the encephalomyocarditis virus 3C proteinase stimulates viral replication.

    PubMed

    Kobayashi, Mariko; Arias, Carolina; Garabedian, Alexandra; Palmenberg, Ann C; Mohr, Ian

    2012-10-01

    Although picornavirus RNA genomes contain a 3'-terminal poly(A) tract that is critical for their replication, the impact of encephalomyocarditis virus (EMCV) infection on the host poly(A)-binding protein (PABP) remains unknown. Here, we establish that EMCV infection stimulates site-specific PABP proteolysis, resulting in accumulation of a 45-kDa N-terminal PABP fragment in virus-infected cells. Expression of a functional EMCV 3C proteinase was necessary and sufficient to stimulate PABP cleavage in uninfected cells, and bacterially expressed 3C cleaved recombinant PABP in vitro in the absence of any virus-encoded or eukaryotic cellular cofactors. N-terminal sequencing of the resulting C-terminal PABP fragment identified a 3C(pro) cleavage site on PABP between amino acids Q437 and G438, severing the C-terminal protein-interacting domain from the N-terminal RNA binding fragment. Single amino acid substitution mutants with changes at Q437 were resistant to 3C(pro) cleavage in vitro and in vivo, validating that this is the sole detectable PABP cleavage site. Finally, while ongoing protein synthesis was not detectably altered in EMCV-infected cells expressing a cleavage-resistant PABP variant, viral RNA synthesis and infectious virus production were both reduced. Together, these results establish that the EMCV 3C proteinase mediates site-specific PABP cleavage and demonstrate that PABP cleavage by 3C regulates EMCV replication. PMID:22837200

  8. Stimulation of translation by human Unr requires cold shock domains 2 and 4, and correlates with poly(A) binding protein interaction.

    PubMed

    Ray, Swagat; Anderson, Emma C

    2016-01-01

    The RNA binding protein Unr, which contains five cold shock domains, has several specific roles in post-transcriptional control of gene expression. It can act as an activator or inhibitor of translation initiation, promote mRNA turnover, or stabilise mRNA. Its role depends on the mRNA and other proteins to which it binds, which includes cytoplasmic poly(A) binding protein 1 (PABP1). Since PABP1 binds to all polyadenylated mRNAs, and is involved in translation initiation by interaction with eukaryotic translation initiation factor 4G (eIF4G), we investigated whether Unr has a general role in translational control. We found that Unr strongly stimulates translation in vitro, and mutation of cold shock domains 2 or 4 inhibited its translation activity. The ability of Unr and its mutants to stimulate translation correlated with its ability to bind RNA, and to interact with PABP1. We found that Unr stimulated the binding of PABP1 to mRNA, and that Unr was required for the stable interaction of PABP1 and eIF4G in cells. siRNA-mediated knockdown of Unr reduced the overall level of cellular translation in cells, as well as that of cap-dependent and IRES-dependent reporters. These data describe a novel role for Unr in regulating cellular gene expression. PMID:26936655

  9. Stimulation of translation by human Unr requires cold shock domains 2 and 4, and correlates with poly(A) binding protein interaction

    PubMed Central

    Ray, Swagat; Anderson, Emma C.

    2016-01-01

    The RNA binding protein Unr, which contains five cold shock domains, has several specific roles in post-transcriptional control of gene expression. It can act as an activator or inhibitor of translation initiation, promote mRNA turnover, or stabilise mRNA. Its role depends on the mRNA and other proteins to which it binds, which includes cytoplasmic poly(A) binding protein 1 (PABP1). Since PABP1 binds to all polyadenylated mRNAs, and is involved in translation initiation by interaction with eukaryotic translation initiation factor 4G (eIF4G), we investigated whether Unr has a general role in translational control. We found that Unr strongly stimulates translation in vitro, and mutation of cold shock domains 2 or 4 inhibited its translation activity. The ability of Unr and its mutants to stimulate translation correlated with its ability to bind RNA, and to interact with PABP1. We found that Unr stimulated the binding of PABP1 to mRNA, and that Unr was required for the stable interaction of PABP1 and eIF4G in cells. siRNA-mediated knockdown of Unr reduced the overall level of cellular translation in cells, as well as that of cap-dependent and IRES-dependent reporters. These data describe a novel role for Unr in regulating cellular gene expression. PMID:26936655

  10. Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation

    PubMed Central

    Li, Wencheng; You, Bei; Hoque, Mainul; Zheng, Dinghai; Luo, Wenting; Ji, Zhe; Park, Ji Yeon; Gunderson, Samuel I.; Kalsotra, Auinash; Manley, James L.; Tian, Bin

    2015-01-01

    Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage/polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1 and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI-25/68 or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly inhibiting C/P events in introns near the 5’ end of gene and U2 suppressing those in introns with features for efficient splicing. Furthermore, PABPN1 inhibits expression of transcripts with pAs near the transcription start site (TSS), a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results support an APA code where an APA event in a given cellular context is regulated by a number of parameters, including relative location to the TSS, splicing context, distance between competing pAs, surrounding cis elements and concentrations of core C/P factors. PMID:25906188

  11. A novel nuclear-encoded mitochondrial poly(A) polymerase PAPD1 is a potential candidate gene for the extreme obesity related phenotypes in mammals.

    PubMed

    Xiao, Qianjun; Wu, Xiao-Lin; Michal, Jennifer J; Reeves, Jerry J; Busboom, Jan R; Thorgaard, Gary H; Jiang, Zhihua

    2006-01-01

    People with obesity, especially extreme obesity, are at risk for many health problems. However, the responsible genes remain unknown in >95% of severe obesity cases. Our previous genome-wide scan of Wagyu x Limousin F2 cattle crosses with extreme phenotypes revealed a molecular marker significantly associated with intramuscular fat deposition. Characterization of this marker showed that it is orthologous to the human gene KIAA1462 located on HSA10p11.23, where a major quantitative trait locus for morbid obesity has been reported. The newly identified mitochondrial poly(A) polymerase associated domain containing 1 (PAPD1) gene, which is located near this marker, is particularly interesting because the polymerase is required for the polyadenylation and stabilization of mammalian mitochondrial mRNAs. In the present study, both cDNA and genomic DNA sequences were annotated for the bovine PAPD1 gene and ten genetic markers were detected in the promoter and exon 1 region. Among seven markers assayed on approximately 250 Wagyu x Limousin F2 animals, two single nucleotide polymorphisms (SNPs) in the promoter region were significantly associated with intramuscular fat (P<0.05). However, there was a significant interaction (P<0.05) between a third SNP, which causes an amino acid change in coding exon 1, and each of these two promoter SNPs on intramuscular fat deposition. In particular, the differences between double heterozygous animals at two polymorphic sites and the slim genotype animals exceeded 2.3 standard deviations for the trait in both cases. Our study provides evidence for a new mechanism--the involvement of compound heterosis in extreme obesity, which warrants further examination. PMID:16810331

  12. Differential Localization of the Two T. brucei Poly(A) Binding Proteins to the Nucleus and RNP Granules Suggests Binding to Distinct mRNA Pools

    PubMed Central

    Kramer, Susanne; Bannerman-Chukualim, Bridget; Ellis, Louise; Boulden, Elizabeth A.; Kelly, Steve; Field, Mark C.; Carrington, Mark

    2013-01-01

    The number of paralogs of proteins involved in translation initiation is larger in trypanosomes than in yeasts or many metazoan and includes two poly(A) binding proteins, PABP1 and PABP2, and four eIF4E variants. In many cases, the paralogs are individually essential and are thus unlikely to have redundant functions although, as yet, distinct functions of different isoforms have not been determined. Here, trypanosome PABP1 and PABP2 have been further characterised. PABP1 and PABP2 diverged subsequent to the differentiation of the Kinetoplastae lineage, supporting the existence of specific aspects of translation initiation regulation. PABP1 and PABP2 exhibit major differences in intracellular localization and distribution on polysome fractionation under various conditions that interfere with mRNA metabolism. Most striking are differences in localization to the four known types of inducible RNP granules. Moreover, only PABP2 but not PABP1 can accumulate in the nucleus. Taken together, these observations indicate that PABP1 and PABP2 likely associate with distinct populations of mRNAs. The differences in localization to inducible RNP granules also apply to paralogs of components of the eIF4F complex: eIF4E1 showed similar localization pattern to PABP2, whereas the localisation of eIF4E4 and eIF4G3 resembled that of PABP1. The grouping of translation initiation as either colocalizing with PABP1 or with PABP2 can be used to complement interaction studies to further define the translation initiation complexes in kinetoplastids. PMID:23382864

  13. The Novel Poly(A) Polymerase Star-PAP is a Signal-Regulated Switch at the 3′-end of mRNAs

    PubMed Central

    Li, Weimin; Laishram, Rakesh S.; Anderson, Richard A.

    2013-01-01

    The mRNA 3′-untranslated region (3′-UTR) modulates message stability, transport, intracellular location and translation. We have discovered a novel nuclear poly(A) polymerase termed Star-PAP (nuclear speckle targeted PIPKIα regulated-poly(A) polymerase) that couples with the transcriptional machinery and is regulated by the phosphoinositide lipid messenger phosphatidylinositol-4,5-bisphosphate (PI4,5P2), the central lipid in phosphoinositide signaling. PI4,5P2 is generated primarily by type I phosphatidylinositol phosphate kinases (PIPKI). Phosphoinositides are present in the nucleus including at nuclear speckles compartments separate from known membrane structures. PIPKs regulate cellular functions by interacting with PI4,5P2 effectors where PIPKs generate PI4,5P2 that then modulates the activity of the associated effectors. Nuclear PIPKIα interacts with and regulates Star-PAP, and PI4,5P2 specifically activates Star-PAP in a gene- and signaling-dependent manner. Importantly, other select signaling molecules integrated into the Star-PAP complex seem to regulate Star-PAP activities and processivities toward RNA substrates, and unique sequence elements around the Star-PAP binding sites within the 3′-UTR of target genes contribute to Star-PAP specificity for processing. Therefore, Star-PAP and its regulatory molecules form a signaling nexus at the 3′-end of target mRNAs to control the expression of select group of genes including the ones involved in stress responses. PMID:23306079

  14. The procollagen type III, alpha 1 (COL3A1) gene first intron expresses poly-A+ RNA corresponding to multiple ESTs and putative miRNAs.

    PubMed

    Sterling, Kenneth M

    2011-02-01

    The mouse COL3A1 first intron is 9684 bp. RNA's of approximately 1.6 and 3.0 kb were detected by Northern hybridization analysis of poly-A RNA from fetal mice and total RNA from suckling and adult mouse intestine using (32)P-labeled, anti-sense RNA synthesized from a mouse COL3A1 first intron, 5 prime region, 5.4 kb Xba I fragment (1655-7030 bp), recombinant plasmid (pPI5.4x). Expression of the 1.6 and 3.0 kb RNA's was significantly reduced in adult mouse intestine, indicating that these RNAs are developmentally regulated. "BLAST" analysis indicated that the mouse first intron 5 prime sequence has 94-100% identity to 13 mouse ESTs. These mouse first intron EST's lie within the 5.4 Xba I fragment of the mouse COL3A1 first intron. Two of the mouse first intron EST's have significant identity to known miRNA, mature sequences, mmu-miR-466f-3P, mmu-miR-1187, and mmu-miR-574-5P as well as others. Predicted targets for mmu-miR-466f-3P include COL1A1, COL19A1, COL11A2, COL4A1, and COL4A5 indicating that COL3A1 intronic miRNAs may regulate the expression of other collagen genes in development. PMID:21268075

  15. RBP45 and RBP47, two oligouridylate-specific hnRNP-like proteins interacting with poly(A)+ RNA in nuclei of plant cells.

    PubMed Central

    Lorković, Z J; Wieczorek Kirk, D A; Klahre, U; Hemmings-Mieszczak, M; Filipowicz, W

    2000-01-01

    Introns in plant nuclear pre-mRNAs are highly enriched in U or U + A residues and this property is essential for efficient splicing. Moreover, 3'-untranslated regions (3'-UTRs) in plant pre-mRNAs are generally UA-rich and contain sequences that are important for the polyadenylation reaction. Here, we characterize two structurally related RNA-binding proteins (RBPs) from Nicotiana plumbaginifolia, referred to as RBP45 and RBP47, having specificity for oligouridylates. Both proteins contain three RBD-type RNA-binding domains and a glutamine-rich N-terminus, and share similarity with Nam8p, a protein associated with U1 snRNP in the yeast Saccharomyces cerevisiae. Deletion analysis of RBP45 and RBP47 indicated that the presence of at least two RBD are required for interaction with RNA and that domains other than RBD do not significantly contribute to binding. mRNAs for RBP45 and RBP47 and mRNAs encoding six related proteins in Arabidopsis thaliana are constitutively expressed in different plant organs. Indirect immunofluorescence and fractionation of cell extracts showed that RBP45 and RBP47 are localized in the nucleus. In vivo UV crosslinking experiments demonstrated their association with the nuclear poly(A)+ RNA. In contrast to UBP1, another oligouridylate-binding nuclear three-RBD protein of N. plumbaginifolia (Lambermon et al., EMBO J, 2000, 19:1638-1649), RBP45 and RBP47 do not stimulate mRNA splicing and accumulation when transiently overexpressed in protoplasts. Properties of RBP45 and RBP47 suggest they represent hnRNP-proteins participating in still undefined steps of pre-mRNA maturation in plant cell nuclei. PMID:11105760

  16. mRNA Decay Proteins Are Targeted to poly(A)+ RNA and dsRNA-Containing Cytoplasmic Foci That Resemble P-Bodies in Entamoeba histolytica

    PubMed Central

    López-Rosas, Itzel; Orozco, Esther; Marchat, Laurence A.; García-Rivera, Guillermina; Guillen, Nancy; Weber, Christian; Carrillo-Tapia, Eduardo; Hernández de la Cruz, Olga; Pérez-Plasencia, Carlos; López-Camarillo, César

    2012-01-01

    In higher eukaryotes, mRNA degradation and RNA-based gene silencing occur in cytoplasmic foci referred to as processing bodies (P-bodies). In protozoan parasites, the presence of P-bodies and their putative role in mRNA decay have yet to be comprehensively addressed. Identification of P-bodies might provide information on how mRNA degradation machineries evolved in lower eukaryotes. Here, we used immunofluorescence and confocal microscopy assays to investigate the cellular localization of mRNA degradation proteins in the human intestinal parasite Entamoeba histolytica and found evidence of the existence of P-bodies. Two mRNA decay factors, namely the EhXRN2 exoribonuclease and the EhDCP2 decapping enzyme, were localized in cytoplasmic foci in a pattern resembling P-body organization. Given that amoebic foci appear to be smaller and less rounded than those described in higher eukaryotes, we have named them “P-body-like structures”. These foci contain additional mRNA degradation factors, including the EhCAF1 deadenylase and the EhAGO2-2 protein involved in RNA interference. Biochemical analysis revealed that EhCAF1 co-immunoprecipitated with EhXRN2 but not with EhDCP2 or EhAGO2-2, thus linking deadenylation to 5′-to-3′ mRNA decay. The number of EhCAF1-containing foci significantly decreased after inhibition of transcription and translation with actinomycin D and cycloheximide, respectively. Furthermore, results of RNA-FISH assays showed that (i) EhCAF1 colocalized with poly(A)+ RNA and (ii) during silencing of the Ehpc4 gene by RNA interference, EhAGO2-2 colocalized with small interfering RNAs in cytoplasmic foci. Our observation of decapping, deadenylation and RNA interference proteins within P-body-like foci suggests that these structures have been conserved after originating in the early evolution of eukaryotic lineages. To the best of our knowledge, this is the first study to report on the localization of mRNA decay proteins within P-body-like structures

  17. Replacement of the yeast TRP4 3' untranslated region by a hammerhead ribozyme results in a stable and efficiently exported mRNA that lacks a poly(A) tail.

    PubMed Central

    Düvel, Katrin; Valerius, Oliver; Mangus, David A; Jacobson, Allan; Braus, Gerhard H

    2002-01-01

    The mRNA poly(A) tail serves different purposes, including the facilitation of nuclear export, mRNA stabilization, efficient translation, and, finally, specific degradation. The posttranscriptional addition of a poly(A) tail depends on sequence motifs in the 3' untranslated region (3' UTR) of the mRNA and a complex trans-acting protein machinery. In this study, we have replaced the 3' UTR of the yeast TRP4 gene with sequences encoding a hammerhead ribozyme that efficiently cleaves itself in vivo. Expression of the TRP4-ribozyme allele resulted in the accumulation of a nonpolyadenylated mRNA. Cells expressing the TRP4-ribozyme mRNA showed a reduced growth rate due to a reduction in Trp4p enzyme activity. The reduction in enzyme activity was not caused by inefficient mRNA export from the nucleus or mRNA destabilization. Rather, analyses of mRNA association with polyribosomes indicate that translation of the ribozyme-containing mRNA is impaired. This translational defect allows sufficient synthesis of Trp4p to support growth of trp4 cells, but is, nevertheless, of such magnitude as to activate the general control network of amino acid biosynthesis. PMID:12003493

  18. Interaction between the RNA-dependent ATPase and poly(A) polymerase subunits of the TRAMP complex is mediated by short peptides and important for snoRNA processing

    PubMed Central

    Losh, Jillian S.; King, Alejandra Klauer; Bakelar, Jeremy; Taylor, Lacy; Loomis, John; Rosenzweig, Jason A.; Johnson, Sean J.; van Hoof, Ambro

    2015-01-01

    The RNA exosome is one of the main 3′ to 5′ exoribonucleases in eukaryotic cells. Although it is responsible for degradation or processing of a wide variety of substrate RNAs, it is very specific and distinguishes between substrate and non-substrate RNAs as well as between substrates that need to be 3′ processed and those that need to be completely degraded. This specificity does not appear to be determined by the exosome itself but rather by about a dozen other proteins. Four of these exosome cofactors have enzymatic activity, namely, the nuclear RNA-dependent ATPase Mtr4, its cytoplasmic paralog Ski2 and the nuclear non-canonical poly(A) polymerases, Trf4 and Trf5. Mtr4 and either Trf4 or Trf5 assemble into a TRAMP complex. However, how these enzymes assemble into a TRAMP complex and the functional consequences of TRAMP complex assembly remain unknown. Here, we identify an important interaction site between Mtr4 and Trf5, and show that disrupting the Mtr4/Trf interaction disrupts specific TRAMP and exosome functions, including snoRNA processing. PMID:25589546

  19. Poly-A binding protein-1 localization to a subset of TDP-43 inclusions in amyotrophic lateral sclerosis occurs more frequently in patients harboring an expansion in C9orf72.

    PubMed

    McGurk, Leeanne; Lee, Virginia M; Trojanowksi, John Q; Van Deerlin, Vivianna M; Lee, Edward B; Bonini, Nancy M

    2014-09-01

    Amyotrophic lateral sclerosis (ALS) is an adult-onset motor neuron disease in which the loss of spinal cord motor neurons leads to paralysis and death within a few years of clinical disease onset. In almost all cases of ALS, transactive response DNA binding protein of 43 kDa (TDP-43) forms cytoplasmic neuronal inclusions. A second causative gene for a subset of ALS is fused in sarcoma, an RNA binding protein that also forms cytoplasmic inclusions in spinal cord motor neurons. Poly-A binding protein-1 (PABP-1) is a marker of stress granules (i.e. accumulations of proteins and RNA indicative of translational arrest in cells under stress). We report on the colocalization of PABP-1 to both TDP-43 and fused-in-sarcoma inclusions in 4 patient cohorts: ALS without a mutation, ALS with an intermediate polyglutamine repeat expansion in ATXN2, ALS with a GGGGCC hexanucleotide repeat expansion in C9orf72, and ALS with basophilic inclusion body disease. Notably, PABP-1 colocalization to TDP-43 was twice as frequent in ALS with C9orf72 expansions compared to ALS with no mutation. This study highlights PABP-1 as a protein that is important to the pathology of ALS and indicates that the proteomic profile of TDP-43 inclusions in ALS may differ depending on the causative genetic mutation. PMID:25111021

  20. Both the Exact Target Site Sequence and a Long Poly(A) Tail Are Required for Precise Insertion of the 18S Ribosomal DNA-Specific Non-Long Terminal Repeat Retrotransposon R7Ag.

    PubMed

    Nichuguti, Narisu; Hayase, Mayumi; Fujiwara, Haruhiko

    2016-05-15

    Ribosomal elements (R elements) are site-specific non-long terminal repeat (LTR) retrotransposons that target ribosomal DNA (rDNA). To elucidate how R elements specifically access their target sites, we isolated and characterized the 18S rDNA-specific R element R7Ag from Anopheles gambiae Using an in vivo and ex vivo recombinant baculovirus retrotransposition system, we found that the exact host 18S rDNA sequence at the target site is essential for the precise insertion of R7Ag. In addition, a long poly(A) tail is necessary for the accurate initiation of R7Ag reverse transcription, a novel mechanism found in non-LTR elements. We further compared the subcellular localizations of proteins in R7Ag as well as R1Bm, another R element that targets 28S rDNA. Although the open reading frame 1 proteins (ORF1ps) of both R7Ag and R1Bm localized predominantly in the cytoplasm, ORF2 proteins (ORF2ps) colocalized in the nucleus with the nucleolar marker fibrillarin. The ORF1ps and ORF2ps of both R elements colocalized largely in the nuclear periphery and to a lesser extent within the nucleus. These results suggest that R7Ag and R1Bm proteins may access nucleolar rDNA targets in an ORF2p-dependent manner. PMID:26976636

  1. Interaction between the RNA-dependent ATPase and poly(A) polymerase subunits of the TRAMP complex is mediated by short peptides and important for snoRNA processing.

    PubMed

    Losh, Jillian S; King, Alejandra Klauer; Bakelar, Jeremy; Taylor, Lacy; Loomis, John; Rosenzweig, Jason A; Johnson, Sean J; van Hoof, Ambro

    2015-02-18

    The RNA exosome is one of the main 3′ to 5′ exoribonucleases in eukaryotic cells. Although it is responsible for degradation or processing of a wide variety of substrate RNAs, it is very specific and distinguishes between substrate and non-substrate RNAs as well as between substrates that need to be 3′ processed and those that need to be completely degraded. This specificity does not appear to be determined by the exosome itself but rather by about a dozen other proteins. Four of these exosome cofactors have enzymatic activity, namely, the nuclear RNA-dependent ATPase Mtr4, its cytoplasmic paralog Ski2 and the nuclear non-canonical poly(A) polymerases, Trf4 and Trf5. Mtr4 and either Trf4 or Trf5 assemble into a TRAMP complex. However, how these enzymes assemble into a TRAMP complex and the functional consequences of TRAMP complex assembly remain unknown. Here, we identify an important interaction site between Mtr4 and Trf5, and show that disrupting the Mtr4/Trf interaction disrupts specific TRAMP and exosome functions, including snoRNA processing. PMID:25589546

  2. NaCl Regulation of Tonoplast ATPase 70-Kilodalton Subunit mRNA in Tobacco Cells 1

    PubMed Central

    Narasimhan, Meena L.; Binzel, Marla L.; Perez-Prat, Eva; Chen, Zutang; Nelson, Donald E.; Singh, Narendra K.; Bressan, Ray A.; Hasegawa, Paul M.

    1991-01-01

    A cDNA clone encoding the 70-kilodalton subunit of the tobacco (Nicotiana tabacum var Wisconsin 38) tonoplast ATPase has been isolated. The 1.656 kilobase insert contains only open reading frame that represents more than 80% of the carrot cDNA coding region. The deduced amino acid sequence has greater than 95% sequence identity with the homologous carrot sequence. A transcript of approximately 2.7 kilobase was detected on Northern blots of tobacco poly(A)+ selected or total RNA using labeled probe produced from this clone. The gene was expressed throughout the growth cycle in unadapted and 428 millimolar NaCl adapted cells. Transcription of the 70-kilodalton subunit gene or mRNA stability was induced by short-term NaCl treatment in NaCl adapted cells or by abscisic acid treatment in both adapted and unadapted cells. Southern analysis indicated the presence of up to four genes encoding the 70-kilodalton subunit. ImagesFigure 2Figure 3Figure 4Figure 6 PMID:16668435

  3. Photofragmentation of Na

    SciTech Connect

    Assion, A.; Baumert, T.; Weichmann, U.; Gerber, G.

    2001-06-18

    Photofragmentation of Na{sup +}{sub 2} molecules in well prepared vibrational levels has been studied employing intense (10{sup 11}{endash}10{sup 14} W/cm{sup 2} ) and ultrashort (80fs) 790nm laser fields. Four fragmentation channels with different released kinetic energies are observed. Depending on the applied laser intensity, the fragmentation of Na{sup +}{sub 2} is governed by photodissociation on light-induced potentials and field ionization followed by Coulomb explosion. Below 1{times}10{sup 12} W /cm{sup 2} , only photodissociation on light-induced potentials is seen. For intermediate laser intensities, field ionization at large internuclear distances competes with photodissociation, thus preventing the observation of above threshold dissociation. Field ionization at small internuclear distances dominates for the highest laser intensities used.

  4. Effect of ADP on Na+-Na+ Exchange Reaction Kinetics of Na,K-ATPase

    PubMed Central

    Peluffo, R. Daniel

    2004-01-01

    The whole-cell voltage-clamp technique was used in rat cardiac myocytes to investigate the kinetics of ADP binding to phosphorylated states of Na,K-ATPase and its effects on presteady-state Na+-dependent charge movements by this enzyme. Ouabain-sensitive transient currents generated by Na,K-ATPase functioning in electroneutral Na+-Na+ exchange mode were measured at 23°C with pipette ADP concentrations ([ADP]) of up to 4.3 mM and extracellular Na+ concentrations ([Na]o) between 36 and 145 mM at membrane potentials (VM) from −160 to +80 mV. Analysis of charge-VM curves showed that the midpoint potential of charge distribution was shifted toward more positive VM both by increasing [ADP] at constant Na+o and by increasing [Na]o at constant ADP. The total quantity of mobile charge, on the other hand, was found to be independent of changes in [ADP] or [Na]o. The presence of ADP increased the apparent rate constant for current relaxation at hyperpolarizing VM but decreased it at depolarizing VM as compared to control (no added ADP), an indication that ADP binding facilitates backward reaction steps during Na+-Na+ exchange while slowing forward reactions. Data analysis using a pseudo three-state model yielded an apparent Kd of ∼6 mM for ADP binding to and release from the Na,K-ATPase phosphoenzyme; a value of 130 s−1 for k2, a rate constant that groups Na+ deocclusion/release and the enzyme conformational transition E1∼P → E2-P; a value of 162 s−1M−1 for k−2, a lumped second-order VM-independent rate constant describing the reverse reactions; and a Hill coefficient of ∼1 for Na+o binding to E2-P. The results are consistent with electroneutral release of ADP before Na+ is deoccluded and released through an ion well. The same approach can be used to study additional charge-moving reactions and associated electrically silent steps of the Na,K-pump and other transporters. PMID:15298896

  5. Na Cauda do Cometa

    NASA Astrophysics Data System (ADS)

    Voelzke, M. R.

    2009-01-01

    Quando viam um cometa, os antigos gregos imaginavam uma estrela com uma vasta cabeleira. Não à toa, a palavra deriva do termo koma, que significa cabelo. Constituídos por fragmentos de gelo e gases, os cometas possuem um núcleo sólido, que pode ter vários quilômetros de diâmetro, e uma cauda que sempre aponta na direção contrária ao Sol, devido aos ventos solares. Graças à aparência de pontos luminosos em movimento (ao contrário de outros astros, que parecem estáticos), esses corpos celestes foram interpretados por diferentes povos com muito misticismo, inspirando mitos tanto de boas-novas como de maus presságios. Conheça algumas dessas histórias:

  6. Drugs preventing Na+ and Ca2+ overload.

    PubMed

    Ravens, U; Himmel, H M

    1999-03-01

    Cardiac intracellular Na+and Ca2+homeostasis is regulated by the concerted action of ion channels, pumps and exchangers. The Na+, K+-ATPase produces the electrochemical concentration gradient for Na+, which is the driving force for Ca2+removal from the cytosol via the Na+/Ca2+exchange. Reduction of this gradient by increased intracellular Na+concentration leads to cellular Ca2+overload resulting in arrhythmias and contractile dysfunction. Na+and Ca2+overload-associated arrhythmias can be produced experimentally by inhibition of Na+efflux (digitalis-induced intoxication) and by abnormal Na+influx via modulated Na+channels (veratridine, DPI 201-106; hypoxia) or via the Na+, H+exchanger. Theoretically, blockers of Na+and Ca2+channels, inhibitors of abnormal oscillatory release of Ca2+from internal stores or modulators of the Na+, Ca2+and Na+, H+exchanger activities could protect against cellular Na+and Ca2+overload. Three exemplary drugs that prevent Na+and Ca2+overload, i.e. the benzothiazolamine R56865, the methylenephenoxydioxy-derivative CP-060S, and the benzoyl-guanidine Hoe 642, a Na+, H+exchange blocker, are briefly reviewed with respect to their efficacy on digitalis-, veratridine- and ischaemia/reperfusion-induced arrhythmias. PMID:10094840

  7. Interactions of external and internal H+ and Na+ with Na+/Na+ and Na+/H+ exchange of rabbit red cells: evidence for a common pathway.

    PubMed

    Morgan, K; Canessa, M

    1990-12-01

    We have studied the kinetic properties of rabbit red cell (RRBC) Na+/Na+ and Na+/H+ exchanges (EXC) in order to define whether or not both transport functions are conducted by the same molecule. The strategy has been to determine the interactions of Na+ and H+ at the internal (i) and external (o) sites for both exchanges modes. RRBC containing varying Nai and Hi were prepared by nystatin and DIDS treatment of acid-loaded cells. Na+/Na+ EXC was measured as Nao-stimulated Na+ efflux and Na+/H+ EXC as Nao-stimulated H+ efflux and delta pHo-stimulated Na+ influx into acid-loaded cells. The activation of Na+/Na+ EXC by Nao at pHi 7.4 did not follow simple hyperbolic kinetics. Testing of different kinetic models to obtain the best fit for the experimental data indicated the presence of high (Km 2.2 mM) and low affinity (Km 108 mM) sites for a single- or two-carrier system. The activation of Na+/H+ EXC by Nao (pHi 6.6, Nai less than 1 mM) also showed high (Km 11 mM) and low (Km 248 mM) affinity sites. External H+ competitively inhibited Na+/Na+ EXC at the low affinity Nao site (KH 52 nM) while internally H+ were competitive inhibitors (pK 6.7) at low Nai and allosteric activators (pK 7.0) at high Nai. Na+/H+ EXC was also inhibited by acid pHo and allosterically activated by Hi (pK 6.4). We also established the presence of a Nai regulatory site which activates Na+/H+ and Na+/Na+ EXC modifying the affinity for Nao of both pathways. At low Nai, Na+/Na+ EXC was inhibited by acid pHi and Na+/H+ stimulated but at high Nai, Na+/Na+ EXC was stimulated and Na+/H+ inhibited being the sum of both pathways kept constant. Both exchange modes were activated by two classes of Nao sites, cis-inhibited by external Ho, allosterically modified by the binding of H+ to a Hi regulatory site and regulated by Nai. These findings are consistent with Na+/Na+ EXC being a mode of operation of the Na+/H+ exchanger. Na+/H+ EXC was partially inhibited (80-100%) by dimethyl-amiloride (DMA) but basal or

  8. Slow inactivation of Na(+) channels.

    PubMed

    Silva, Jonathan

    2014-01-01

    Prolonged depolarizing pulses that last seconds to minutes cause slow inactivation of Na(+) channels, which regulates neuron and myocyte excitability by reducing availability of inward current. In neurons, slow inactivation has been linked to memory of previous excitation and in skeletal muscle it ensures myocytes are able to contract when K(+) is elevated. The molecular mechanisms underlying slow inactivation are unclear even though it has been studied for 50+ years. This chapter reviews what is known to date regarding the definition, measurement, and mechanisms of voltage-gated Na(+) channel slow inactivation. PMID:24737231

  9. The Shoemaker's Knife--An Approach of the Polya Type.

    ERIC Educational Resources Information Center

    Libeskind, Shlomo; Lott, Johnny W.

    1984-01-01

    Archimedes' shoemaker's knife problem is interesting in its own right and also allows the demonstration of heuristic teaching ideas and a different method of doing a routine construction. The focus in the article is on the thought processes involved and questions asked when attempting proofs with the problem. (MNS)

  10. Astrocytes generate Na+-mediated metabolic waves

    NASA Astrophysics Data System (ADS)

    Bernardinelli, Yann; Magistretti, Pierre J.; Chatton, Jean-Yves

    2004-10-01

    Glutamate-evoked Na+ increase in astrocytes has been identified as a signal coupling synaptic activity to glucose consumption. Astrocytes participate in multicellular signaling by transmitting intercellular Ca2+ waves. Here we show that intercellular Na+ waves are also evoked by activation of single cultured cortical mouse astrocytes in parallel with Ca2+ waves; however, there are spatial and temporal differences. Indeed, maneuvers that inhibit Ca2+ waves also inhibit Na+ waves; however, inhibition of the Na+/glutamate cotransporters or enzymatic degradation of extracellular glutamate selectively inhibit the Na+ wave. Thus, glutamate released by a Ca2+ wave-dependent mechanism is taken up by the Na+/glutamate cotransporters, resulting in a regenerative propagation of cytosolic Na+ increases. The Na+ wave gives rise to a spatially correlated increase in glucose uptake, which is prevented by glutamate transporter inhibition. Therefore, astrocytes appear to function as a network for concerted neurometabolic coupling through the generation of intercellular Na+ and metabolic waves.

  11. Sodium iron hexacyanoferrate with high Na content as a Na-rich cathode material for Na-ion batteries

    DOE PAGESBeta

    You, Ya; Yu, Xi -Qian; Yin, Ya -Xia; Nam, Kyung -Wan; Guo, Yu -Guo

    2014-10-27

    Owing to the worldwide abundance and low-cost of Na, room-temperature Na-ion batteries are emerging as attractive energy storage systems for large-scale grids. Increasing the Na content in cathode material is one of the effective ways to achieve high energy density. Prussian blue and its analogues (PBAs) are promising Na-rich cathode materials since they can theoretically store two Na ions per formula. However, increasing the Na content in PBAs cathode materials is a big challenge in the current. Here we show that sodium iron hexacyanoferrate with high Na content could be obtained by simply controlling the reducing agent and reaction atmospheremore » during synthesis. The Na content can reach as high as 1.63 per formula, which is the highest value for sodium iron hexacyanoferrate. This Na-rich sodium iron hexacyanoferrate demonstrates a high specific capacity of 150 mA h g-1 and remarkable cycling performance with 90% capacity retention after 200 cycles. Furthermore, the Na intercalation/de-intercalation mechanism is systematically studied by in situ Raman, X-ray diffraction and X-ray absorption spectroscopy analysis for the first time. As a result, the Na-rich sodium iron hexacyanoferrate could function as a plenteous Na reservoir and has great potential as a cathode material toward practical Na-ion batteries.« less

  12. Sodium iron hexacyanoferrate with high Na content as a Na-rich cathode material for Na-ion batteries

    SciTech Connect

    You, Ya; Yu, Xi -Qian; Yin, Ya -Xia; Nam, Kyung -Wan; Guo, Yu -Guo

    2014-10-27

    Owing to the worldwide abundance and low-cost of Na, room-temperature Na-ion batteries are emerging as attractive energy storage systems for large-scale grids. Increasing the Na content in cathode material is one of the effective ways to achieve high energy density. Prussian blue and its analogues (PBAs) are promising Na-rich cathode materials since they can theoretically store two Na ions per formula. However, increasing the Na content in PBAs cathode materials is a big challenge in the current. Here we show that sodium iron hexacyanoferrate with high Na content could be obtained by simply controlling the reducing agent and reaction atmosphere during synthesis. The Na content can reach as high as 1.63 per formula, which is the highest value for sodium iron hexacyanoferrate. This Na-rich sodium iron hexacyanoferrate demonstrates a high specific capacity of 150 mA h g-1 and remarkable cycling performance with 90% capacity retention after 200 cycles. Furthermore, the Na intercalation/de-intercalation mechanism is systematically studied by in situ Raman, X-ray diffraction and X-ray absorption spectroscopy analysis for the first time. As a result, the Na-rich sodium iron hexacyanoferrate could function as a plenteous Na reservoir and has great potential as a cathode material toward practical Na-ion batteries.

  13. The NA62 trigger system

    NASA Astrophysics Data System (ADS)

    Krivda, M.; NA62 Collaboration

    2013-08-01

    The main aim of the NA62 experiment (NA62 Technical Design Report, na62.web.cern.ch/NA62/Documents/TD_Full_doc_v1.pdf> [1]) is to study ultra-rare Kaon decays. In order to select rare events over the overwhelming background, central systems with high-performance, high bandwidth, flexibility and configurability are necessary, that minimize dead time while maximizing data collection reliability. The NA62 experiment consists of 12 sub-detector systems and several trigger and control systems, for a total channel count of less than 100,000. The GigaTracKer (GTK) has the largest number of channels (54,000), and the Liquid Krypton (LKr) calorimeter shares with it the largest raw data rate (19 GB/s). The NA62 trigger system works with 3 trigger levels. The first trigger level is based on a hardware central trigger unit, so-called L0 Trigger Processor (L0TP), and Local Trigger Units (LTU), which are all located in the experimental cavern. Other two trigger levels are based on software, and done with a computer farm located on surface. The L0TP receives information from triggering sub-detectors asynchronously via Ethernet; it processes the information, and then transmits a final trigger decision synchronously to each sub-detector through the Trigger and Timing Control (TTC) system. The interface between L0TP and the TTC system, which is used for trigger and clock distribution, is provided by the Local Trigger Unit board (LTU). The LTU can work in two modes: global and stand-alone. In the global mode, the LTU provides an interface between L0TP and TTC system. In the stand-alone mode, the LTU can fully emulate L0TP and so provides an independent way for each sub-detector for testing or calibration purposes. In addition to the emulation functionality, a further functionality is implemented that allows to synchronize the clock of the LTU with the L0TP and the TTC system. For testing and debugging purposes, a Snap Shot Memory (SSM) interface is implemented, that can work

  14. Single crystal growth of type I Na-Si clathrate by using Na-Sn flux

    NASA Astrophysics Data System (ADS)

    Morito, Haruhiko; Shimoda, Masashi; Yamane, Hisanori

    2016-09-01

    Single crystals of type I Na-Si clathrate, Na8Si46, were synthesized by heating Na, Na4Si4, and Na15Sn4 at 723 K under an Ar gas pressure of 104 Pa for 12 h. The single crystals having {110} habit planes grew up to 1.5 mm in size due to Na evaporation from a Na-Si-Sn melt with a starting compositional molar ratio of Na/Si/Sn=5.75:2:1.

  15. Europlanet NA2 Science Networking

    NASA Astrophysics Data System (ADS)

    Harri, Ari-Matti; Szego, Karoly; Genzer, Maria; Schmidt, Walter; Krupp, Norbert; Lammer, Helmut; Kallio, Esa; Haukka, Harri

    2013-04-01

    Europlanet RI / NA2 Science Networking [1] focused on determining the major goals of current and future European planetary science, relating them to the Research Infrastructure that the Europlanet RI project [2] developed, and placing them in a more global context. NA2 also enhanced the ability of European planetary scientists to participate on the global scene with their own agenda-setting projects and ideas. The Networking Activity NA2 included five working groups, aimed at identifying key science issues and producing reference books on major science themes that will bridge the gap between the results of present and past missions and the scientific preparation of the future ones. Within the Europlanet RI project (2009-2012) the NA2 and NA2-WGs organized thematic workshops, an expert exchange program and training groups to improve the scientific impact of this Infrastructure. The principal tasks addressed by NA2 were: • Science activities in support to the optimal use of data from past and present space missions, involving the broad planetary science community beyond the "space club" • Science activities in support to the preparation of future planetary missions: Earth-based preparatory observations, laboratory studies, R&D on advanced instrumentation and exploration technologies for the future, theory and modeling etc. • Develop scientific activities, joint publications, dedicated meetings, tools and services, education activities, engaging the public and industries • Update science themes and addressing the two main scientific objectives • Prepare and support workshops of the International Space Science Institute (ISSI) in Bern and • Support Trans National Activities (TNAs), Joined Research Activities (JRAs) and the Integrated and Distributed Information Service (IDIS) of the Europlanet project These tasks were achieved by WG workshops organized by the NA2 working groups, by ISSI workshops and by an Expert Exchange Program. There were 17 official WG

  16. Deliquescence of NaCl-NaNO3 and KNO3-NaNO3 Salt Mixtures at 90C

    SciTech Connect

    Carroll, S; Craig, L; Wolery, T

    2003-12-29

    We conducted reversed deliquescence experiments in saturated NaCl-NaNO3-H2O and KNO{sub 3}-NaNO{sub 3}-H{sub 2}O systems at 90 C to determine relative humidity and solution composition. NaCl, NaNO{sub 3}, and KNO{sub 3} represent members of dust salt assemblages that are likely to deliquesce and form concentrated brines on high-level radioactive waste package surfaces in a repository environment at Yucca Mountain, NV, USA. Model predictions agree with experimental results for the NaCl-NaNO{sub 3}-H{sub 2}O system, but underestimate relative humidity by as much as 8% and solution composition by as much as 50% in the KNO{sub 3}-NaNO{sub 3}-H{sub 2}O system.

  17. Na+-stimulated ATPase of alkaliphilic halotolerant cyanobacterium Aphanothece halophytica translocates Na+ into proteoliposomes via Na+ uniport mechanism

    PubMed Central

    2010-01-01

    Background When cells are exposed to high salinity conditions, they develop a mechanism to extrude excess Na+ from cells to maintain the cytoplasmic Na+ concentration. Until now, the ATPase involved in Na+ transport in cyanobacteria has not been characterized. Here, the characterization of ATPase and its role in Na+ transport of alkaliphilic halotolerant Aphanothece halophytica were investigated to understand the survival mechanism of A. halophytica under high salinity conditions. Results The purified enzyme catalyzed the hydrolysis of ATP in the presence of Na+ but not K+, Li+ and Ca2+. The apparent Km values for Na+ and ATP were 2.0 and 1.2 mM, respectively. The enzyme is likely the F1F0-ATPase based on the usual subunit pattern and the protection against N,N'-dicyclohexylcarbodiimide inhibition of ATPase activity by Na+ in a pH-dependent manner. Proteoliposomes reconstituted with the purified enzyme could take up Na+ upon the addition of ATP. The apparent Km values for this uptake were 3.3 and 0.5 mM for Na+ and ATP, respectively. The mechanism of Na+ transport mediated by Na+-stimulated ATPase in A. halophytica was revealed. Using acridine orange as a probe, alkalization of the lumen of proteoliposomes reconstituted with Na+-stimulated ATPase was observed upon the addition of ATP with Na+ but not with K+, Li+ and Ca2+. The Na+- and ATP-dependent alkalization of the proteoliposome lumen was stimulated by carbonyl cyanide m - chlorophenylhydrazone (CCCP) but was inhibited by a permeant anion nitrate. The proteoliposomes showed both ATPase activity and ATP-dependent Na+ uptake activity. The uptake of Na+ was enhanced by CCCP and nitrate. On the other hand, both CCCP and nitrate were shown to dissipate the preformed electric potential generated by Na+-stimulated ATPase of the proteoliposomes. Conclusion The data demonstrate that Na+-stimulated ATPase from A. halophytica, a likely member of F-type ATPase, functions as an electrogenic Na+ pump which transports only

  18. Thermodynamics of dissolution of lead oxide in NaOH-Na2CO3 melts

    NASA Astrophysics Data System (ADS)

    Barbin, N. M.; Barbina, T. M.

    2016-08-01

    The solubility of lead oxide in NaOH + (20%)Na2CO3 and NaOH + (40%)Na2CO3 melts was studied by the isothermal saturation method. The model mechanisms of dissolution were considered. The thermodynamic parameters were calculated.

  19. Effect of colchicine on sensitivity of duck salt gland Na,K-ATPase to Na+.

    PubMed

    Yakushev, S S; Kumskova, E M; Rubtsov, A M; Lopina, O D

    2008-09-01

    Low molecular mass proteins of the FXYD family that affect the sensitivity of Na,K-ATPase to Na+ and K+ are known to be present in Na,K-ATPases in various tissues. In particular, in Na,K-ATPase from kidney a gamma-subunit (with electrophoretic mobility corresponding to molecular mass of about 10 kD) is present, and Na,K-ATPase preparations from heart contain phospholemman (electrophoretic mobility of this protein corresponds to molecular mass of 13-14 kD), which provides for the interaction of heart Na,K-ATPase with cytoskeletal microtubules. Disruption of microtubules by colchicine removes phospholemman from heart Na,K-ATPase preparations. The goal of the present study was to reveal a low molecular mass protein (probably a member of FXYD family) in preparation of Na,K-ATPase from duck salt glands. Immunoprecipitation of solubilized duck salt gland Na,K-ATPase using antibodies against alpha1-subunit results in the coprecipitation of a 13 kD protein with the Na,K-ATPase complex. Treatment of homogenate from duck salt glands with colchicine removes this protein from the purified preparation of Na,K-ATPase. Simultaneously, we observed a decrease in the sensitivity of Na,K-ATPase to Na+ at pH 6.5. However, colchicine treatment of homogenate from rabbit kidney does not affect either the sensitivity of Na,K-ATPase obtained from this homogenate to Na+ or the content of 10 kD protein (presumably gamma-subunit). The data suggest that phospholemman (or a similar member of the FXYD family) tightly interacts with Na,K-ATPase from duck salt glands and binds it to microtubules, simultaneously participating in the regulation of the sensitivity of Na,K-ATPase to Na+. PMID:18976215

  20. Growth of binary organic NLO crystals: m.NA-p.NA and m.NA-CNA system

    NASA Technical Reports Server (NTRS)

    Singh, N. B.; Henningsen, T.; Hopkins, R. H.; Mazelsky, R.

    1993-01-01

    Experiments were carried out to grow 3.Nitroaniline (m.NA) crystals doped with 4.Nitroaniline (p.NA) and 2.chloro 4.Nitroaniline (CNA). The measured undercooling for m.NA, p.NA, and CNA were 0.21 tm K, 0.23 tm K, and 0.35 tm K respectively, where tm represents the melting temperature of the pure component. Because of the crystals' large heat of fusion and large undercooling, it was not possible to grow good quality crystals with low thermal gradients. In the conventional two-zone Bridgman furnace we had to raise the temperature of the hot zone above the decomposition temperature of CNA, p.NA, and m.NA to achieve the desired thermal gradient. To avoid decomposition, we used an unconventional Bridgman furnace. Two immiscible liquids, silicone oil and ethylene glycol, were used to build a special two-zone Bridgman furnace. A temperature gradient of 18 K/cm was achieved without exceeding the decomposition temperature of the crystal. The binary crystals, m.NA-p.NA and m.NA-CNA, were grown in centimeter size in this furnace. X-ray and optical characterization showed good optical quality.

  1. Maintaining the NA atmosphere of Mercury

    NASA Astrophysics Data System (ADS)

    Killen, R. M.; Morgan, T. H.

    1993-02-01

    The possible sources of the Na atmosphere of Mercury are calculatively studied. The likely structure, composition, and temperature of the planet's upper crust is examined along with the probable flux of Na from depth by grain boundary diffusion and by Knudsen flow. The creation of fresh regolith is considered along with mechanisms for supplying Na from the surface to the exosphere. The implications of the calculations for the probable abundances in the regolith are discussed.

  2. Maintaining the Na atmosphere of Mercury

    NASA Technical Reports Server (NTRS)

    Killen, Rosemary M.; Morgan, Thomas H.

    1993-01-01

    The possible sources of the Na atmosphere of Mercury are calculatively studied. The likely structure, composition, and temperature of the planet's upper crust is examined along with the probable flux of Na from depth by grain boundary diffusion and by Knudsen flow. The creation of fresh regolith is considered along with mechanisms for supplying Na from the surface to the exosphere. The implications of the calculations for the probable abundances in the regolith are discussed.

  3. The effect of NA vapor on the NA content of chondrules

    NASA Astrophysics Data System (ADS)

    Lewis, R. Dean; Lofgren, Gary E.; Franzen, Hugo F.; Windom, Kenneth E.

    1993-12-01

    Chondrules contain higher concentrations of volatiles (Na) than expected for melt droplets in the solar nebula. Recent studies have proposed that chondrules may have formed under non-canonical nebular conditions such as in particle/gas-rich clumps. Such chondrule formation areas may have contained significant Na vapor. To test the hypothesis of whether a Na-rich vapor would minimize Na volatilization reaction rates in a chondrule analog and maintain the Na value of the melt, experiments were designed where a Na-rich vapor could be maintained around the sample. A starting material with a melting point lower that typical chondrules was required to keep the logistics of working with Na volatilization from NaCl within the realm of feasibility. The Knippa basalt, a MgO-rich alkali olivine basalt with a melting temperature of 1325 +/- 5 C and a Na2O content of 3.05 wt%, was used as the chondrule analog. Experiments were conducted in a 1 atm, gas-mixing furnace with the fO2 controlled by a CO/CO2 gas mixture and fixed at the I-W buffer curve. To determine the extent of Na loss from the sample, initial experiments were conducted at high temperatures (1300 C - 1350 C) for duration of up to 72 h without a Na-rich vapor present. Almost all (up to 98%) Na was volatilized in runs of 72 h. Subsequent trials were conducted at 1330 C for 16 h in the presence of a Na-rich vapor, supplied by a NaCl-filled crucible placed in the bottom of the furnace. Succeeding Knudsen cell weight-loss mass-spectrometry analysis of NaCl determined the PNa for these experimental conditions to be in the 10-6 atm range. This value is considered high for nebula conditions but is still plausible for non-canonical environments. In these trials the Na2O content of the glass was maintained or in some cases increased; Na2O values ranged from 2.62% wt to 4.37% wt. The Na content of chondrules may be controlled by the Na vapor pressure in the chondrule formation region. Most heating events capable of producing

  4. NA-NET numerical analysis net

    SciTech Connect

    Dongarra, J. |; Rosener, B.

    1991-12-01

    This report describes a facility called NA-NET created to allow numerical analysts (na) an easy method of communicating with one another. The main advantage of the NA-NET is uniformity of addressing. All mail is addressed to the Internet host ``na-net.ornl.gov`` at Oak Ridge National Laboratory. Hence, members of the NA-NET do not need to remember complicated addresses or even where a member is currently located. As long as moving members change their e-mail address in the NA-NET everything works smoothly. The NA-NET system is currently located at Oak Ridge National Laboratory. It is running on the same machine that serves netlib. Netlib is a separate facility that distributes mathematical software via electronic mail. For more information on netlib consult, or send the one-line message ``send index`` to netlib{at}ornl.gov. The following report describes the current NA-NET system from both a user`s perspective and from an implementation perspective. Currently, there are over 2100 members in the NA-NET. An average of 110 mail messages pass through this facility daily.

  5. NA-NET numerical analysis net

    SciTech Connect

    Dongarra, J. . Dept. of Computer Science Oak Ridge National Lab., TN ); Rosener, B. . Dept. of Computer Science)

    1991-12-01

    This report describes a facility called NA-NET created to allow numerical analysts (na) an easy method of communicating with one another. The main advantage of the NA-NET is uniformity of addressing. All mail is addressed to the Internet host na-net.ornl.gov'' at Oak Ridge National Laboratory. Hence, members of the NA-NET do not need to remember complicated addresses or even where a member is currently located. As long as moving members change their e-mail address in the NA-NET everything works smoothly. The NA-NET system is currently located at Oak Ridge National Laboratory. It is running on the same machine that serves netlib. Netlib is a separate facility that distributes mathematical software via electronic mail. For more information on netlib consult, or send the one-line message send index'' to netlib{at}ornl.gov. The following report describes the current NA-NET system from both a user's perspective and from an implementation perspective. Currently, there are over 2100 members in the NA-NET. An average of 110 mail messages pass through this facility daily.

  6. Na+/Ca2+ exchange and Na+/K+-ATPase in the heart

    PubMed Central

    Shattock, Michael J; Ottolia, Michela; Bers, Donald M; Blaustein, Mordecai P; Boguslavskyi, Andrii; Bossuyt, Julie; Bridge, John H B; Chen-Izu, Ye; Clancy, Colleen E; Edwards, Andrew; Goldhaber, Joshua; Kaplan, Jack; Lingrel, Jerry B; Pavlovic, Davor; Philipson, Kenneth; Sipido, Karin R; Xie, Zi-Jian

    2015-01-01

    This paper is the third in a series of reviews published in this issue resulting from the University of California Davis Cardiovascular Symposium 2014: Systems approach to understanding cardiac excitation–contraction coupling and arrhythmias: Na+ channel and Na+ transport. The goal of the symposium was to bring together experts in the field to discuss points of consensus and controversy on the topic of sodium in the heart. The present review focuses on cardiac Na+/Ca2+ exchange (NCX) and Na+/K+-ATPase (NKA). While the relevance of Ca2+ homeostasis in cardiac function has been extensively investigated, the role of Na+ regulation in shaping heart function is often overlooked. Small changes in the cytoplasmic Na+ content have multiple effects on the heart by influencing intracellular Ca2+ and pH levels thereby modulating heart contractility. Therefore it is essential for heart cells to maintain Na+ homeostasis. Among the proteins that accomplish this task are the Na+/Ca2+ exchanger (NCX) and the Na+/K+ pump (NKA). By transporting three Na+ ions into the cytoplasm in exchange for one Ca2+ moved out, NCX is one of the main Na+ influx mechanisms in cardiomyocytes. Acting in the opposite direction, NKA moves Na+ ions from the cytoplasm to the extracellular space against their gradient by utilizing the energy released from ATP hydrolysis. A fine balance between these two processes controls the net amount of intracellular Na+ and aberrations in either of these two systems can have a large impact on cardiac contractility. Due to the relevant role of these two proteins in Na+ homeostasis, the emphasis of this review is on recent developments regarding the cardiac Na+/Ca2+ exchanger (NCX1) and Na+/K+ pump and the controversies that still persist in the field. PMID:25772291

  7. Epithelial Na(+) channels are regulated by flow.

    PubMed

    Satlin, L M; Sheng, S; Woda, C B; Kleyman, T R

    2001-06-01

    Na(+) absorption in the renal cortical collecting duct (CCD) is mediated by apical epithelial Na(+) channels (ENaCs). The CCD is subject to continuous variations in intraluminal flow rate that we speculate alters hydrostatic pressure, membrane stretch, and shear stress. Although ENaCs share limited sequence homology with putative mechanosensitive ion channels in Caenorhabditis elegans, controversy exists as to whether ENaCs are regulated by biomechanical forces. We examined the effect of varying the rate of fluid flow on whole cell Na(+) currents (I(Na)) in oocytes expressing mouse alpha,beta,gamma-ENaC (mENaC) and on net Na(+) absorption in microperfused rabbit CCDs. Oocytes injected with mENaC but not water responded to the initiation of superfusate flow (to 4-6 ml/min) with a reversible threefold stimulation of I(Na) without a change in reversal potential. The increase in I(Na) was variable among oocytes. CCDs responded to a threefold increase in rate of luminal flow with a twofold increase in the rate of net Na(+) absorption. An increase in luminal viscosity achieved by addition of 5% dextran to the luminal perfusate did not alter the rate of net Na(+) absorption, suggesting that shear stress does not influence Na(+) transport in the CCD. In sum, our data suggest that flow stimulation of ENaC activity and Na(+) absorption is mediated by an increase in hydrostatic pressure and/or membrane stretch. We propose that intraluminal flow rate may be an important regulator of channel activity in the CCD. PMID:11352841

  8. Reduced Na+ uptake in the NaCl-hypersensitive sos1 mutant of Arabidopsis thaliana.

    PubMed Central

    Ding, L; Zhu, J K

    1997-01-01

    Sos1 is an Arabidopsis thaliana mutant with > 20 times higher sensitivity toward Na+ inhibition due to a defective high-affinity potassium-uptake system. We report here that sos1 accumulates less Na+ than the wild type in response to NaCl stress. The Na+ contents in sos1 seedlings exposed to 25 mM NaCl for 2 or more d are about 43% lower than those in the wild type. When assayed at 20 mM external NaCl, sos1 seedlings pretreated with low potassium have 32% lower Na+ uptake than the wild type. However, little difference in Na+ uptake could be measured when the seedlings were not pretreated with low potassium. Low-potassium treatment was shown to induce high-affinity potassium-uptake activity in Arabidopsis seedlings. No substantial difference in Na+ efflux between sos1 and the wild type was detected. The results show that the reduced Na+ accumulation in sos1 is due to a lower Na+ influx rate. Therefore, the sos1 mutation appears to disrupt low-affinity Na+ uptake in addition to its impairment of high-affinity K+ uptake. PMID:9085573

  9. Inelastic processes in Na+-Ne, Na+-Ar, Ne+-Na, and Ar+-Na collisions in the energy range 0.5-14 keV

    NASA Astrophysics Data System (ADS)

    Lomsadze, R. A.; Gochitashvili, M. R.; Kezerashvili, R. Ya.

    2015-12-01

    Absolute cross sections for charge-exchange, ionization, and excitation in Na+-Ne and Na+-Ar collisions were measured in the ion energy range 0.5 -10 keV using a refined version of a capacitor method and collision and optical spectroscopy methods simultaneously in the same experimental setup. Ionization cross sections for Ne+-Na and Ar+-Na collisions are measured at energies of 2 -14 keV using a crossed-beam spectroscopy method. The experimental data and the schematic correlation diagrams are used to analyze and determine the mechanisms for these processes. For the charge-exchange process in Na+-Ar collisions two nonadiabatic regions are revealed and mechanisms responsible for these regions are explained. Structural peculiarity on the excitation function for the resonance lines of argon atoms in Na+-Ar collisions are observed and the possible mechanisms of this phenomenon are explored. The measured ionization cross sections for Na+-Ne and Ne+-Na collisions in conjunction with the Landau-Zener formula are used to determine the coupling matrix element and transition probability in a region of pseudocrossing of the potential curves.

  10. Na3DyCl6

    PubMed Central

    Schurz, Christian M.; Meyer, Gerd; Schleid, Thomas

    2011-01-01

    Single crystals of the title compound, tris­odium hexa­chloridodysprosate, Na3DyCl6, were obtained as a by-product of synthesis using dysprosium(III) chloride and sodium chloride among others. The monoclinic structure with its typical β angle close to 90° [90.823 (4)°] is isotypic with the mineral cryolite (Na3AlF6) and the high-temperature structure of the Na3 MCl6 series, with M = Eu–Lu, Y and Sc. The isolated, almost perfect [DyCl6]3− octa­hedra are inter­connected via two crystallographically different Na+ cations: while one Na+ resides on centres of symmetry (as well as Dy3+) and also builds almost perfect, isolated [NaCl6]5− octa­hedra, the other Na+ is surrounded by seven chloride anions forming a distorted [NaCl7]6− trigonal prism with just one cap as close secondary contact. PMID:21754259

  11. Na(3)DyCl(6).

    PubMed

    Schurz, Christian M; Meyer, Gerd; Schleid, Thomas

    2011-05-01

    Single crystals of the title compound, tris-odium hexa-chloridodysprosate, Na(3)DyCl(6), were obtained as a by-product of synthesis using dysprosium(III) chloride and sodium chloride among others. The monoclinic structure with its typical β angle close to 90° [90.823 (4)°] is isotypic with the mineral cryolite (Na(3)AlF(6)) and the high-temperature structure of the Na(3)MCl(6) series, with M = Eu-Lu, Y and Sc. The isolated, almost perfect [DyCl(6)](3-) octa-hedra are inter-connected via two crystallographically different Na(+) cations: while one Na(+) resides on centres of symmetry (as well as Dy(3+)) and also builds almost perfect, isolated [NaCl(6)](5-) octa-hedra, the other Na(+) is surrounded by seven chloride anions forming a distorted [NaCl(7)](6-) trigonal prism with just one cap as close secondary contact. PMID:21754259

  12. High NA Nicrostepper Final Optical Design Report

    SciTech Connect

    Hudyma, R

    1999-09-24

    The development of a new EUV high NA small-field exposure tool has been proposed for obtaining mask defect printability data in a timeframe several years before beta-tools are available. The imaging system for this new Micro-Exposure Tool (MET), would have a numerical aperture (NA) of about 0.3, similar to the NA for a beta-tool, but substantially larger than the 0.10 NA for the Engineering Test Stand (ETS) and 0.088 NA for the existing 10x Microstepper. This memorandum discusses the development and summarizes the performance of the camera for the MET and includes a listing of the design prescription, detailed analysis of the distortion, and analysis demonstrating the capability to resolution 30 nm features under the conditions of partially coherent illumination.

  13. Extracellular Na+ levels regulate formation and activity of the NaX/alpha1-Na+/K+-ATPase complex in neuronal cells

    PubMed Central

    Berret, Emmanuelle; Smith, Pascal Y.; Henry, Mélaine; Soulet, Denis; Hébert, Sébastien S.; Toth, Katalin; Mouginot, Didier; Drolet, Guy

    2014-01-01

    MnPO neurons play a critical role in hydromineral homeostasis regulation by acting as sensors of extracellular sodium concentration ([Na+]out). The mechanism underlying Na+-sensing involves Na+-flow through the NaX channel, directly regulated by the Na+/K+-ATPase α1-isoform which controls Na+-influx by modulating channel permeability. Together, these two partners form a complex involved in the regulation of intracellular sodium ([Na+]in). Here we aim to determine whether environmental changes in Na+ could actively modulate the NaX/Na+/K+-ATPase complex activity. We investigated the complex activity using patch-clamp recordings from rat MnPO neurons and Neuro2a cells. When the rats were fed with a high-salt-diet, or the [Na+] in the culture medium was increased, the activity of the complex was up-regulated. In contrast, drop in environmental [Na+] decreased the activity of the complex. Interestingly under hypernatremic condition, the colocalization rate and protein level of both partners were up-regulated. Under hyponatremic condition, only NaX protein expression was increased and the level of NaX/Na+/K+-ATPase remained unaltered. This unbalance between NaX and Na+/K+-ATPase pump proportion would induce a bigger portion of Na+/K+-ATPase-control-free NaX channel. Thus, we suggest that hypernatremic environment increases NaX/Na+/K+-ATPase α1-isoform activity by increasing the number of both partners and their colocalization rate, whereas hyponatremic environment down-regulates complex activity via a decrease in the relative number of NaX channels controlled by the pump. PMID:25538563

  14. Cytosolic Na+ Controls an Epithelial Na+ Channel Via the Go Guanine Nucleotide-Binding Regulatory Protein

    NASA Astrophysics Data System (ADS)

    Komwatana, P.; Dinudom, A.; Young, J. A.; Cook, D. I.

    1996-07-01

    In tight Na+-absorbing epithelial cells, the rate of Na+ entry through amiloride-sensitive apical membrane Na+ channels is matched to basolateral Na+ extrusion so that cell Na+ concentration and volume remain steady. Control of this process by regulation of apical Na+ channels has been attributed to changes in cytosolic Ca2+ concentration or pH, secondary to changes in cytosolic Na+ concentration, although cytosolic Cl- seems also to be involved. Using mouse mandibular gland duct cells, we now demonstrate that increasing cytosolic Na+ concentration inhibits apical Na+ channels independent of changes in cytosolic Ca2+, pH, or Cl-, and the effect is blocked by GDP-β -S, pertussis toxin, and antibodies against the α -subunits of guanine nucleotide-binding regulatory proteins (Go). In contrast, the inhibitory effect of cytosolic anions is blocked by antibodies to inhibitory guanine nucleotide-binding regulatory proteins (Gi1/Gi2. It thus appears that apical Na+ channels are regulated by Go and Gi proteins, the activities of which are controlled, respectively, by cytosolic Na+ and Cl-.

  15. Na-site substitution effects on the thermoelectric properties of NaCo2O4

    NASA Astrophysics Data System (ADS)

    Kawata, T.; Iguchi, Y.; Itoh, T.; Takahata, K.; Terasaki, I.

    1999-10-01

    The resistivity and thermopower of Na1+xCo2O4 and Na1.1-xCaxCo2O4 are measured and analyzed. In Na1+xCo2O4, whereas the resistivity increases with x, the thermopower is nearly independent of x. This suggests that the excess Na is unlikely to supply carriers, and decreases effective conduction paths in the sample. In Na1.1-xCaxCo2O4, the resistivity and the thermopower increase with x, and the Ca2+ substitution for Na+ reduces the majority carriers in NaCo2O4. This means that they are holes, which is consistent with the positive sign of the thermopower. Strong correlation in this compound is evidenced by the peculiar temperature dependence of the resistivity.

  16. Na and K Dependence of the Na/K Pump in Cystic Fibrosis Fibroblasts

    NASA Astrophysics Data System (ADS)

    Reznik, Vivian M.; Schneider, Jerry A.; Mendoza, Stanley A.

    1981-11-01

    The Na and K dependence of the Na/K pump was measured in skin fibroblasts from patients with cystic fibrosis and age/sex-matched controls. Under basal conditions, there was no difference between control and cystic fibrosis cells in protein per cell, intracellular Na and K content, or Na/K pump activity (measured as ouabain-sensitive 86Rb uptake). There was no difference in the Na dependence of the Na/K pump between cystic fibrosis cells and control cells. In cells from patients with cystic fibrosis, the Na/K pump had a significantly lower affinity for K (Km = 1.6 mM) when compared to normals (Km = 0.9 mM). This difference was demonstrated by using two independent experimental designs.

  17. Intracellular Na+ kinetically interferes with the rotation of the Na(+)-driven flagellar motors of Vibrio alginolyticus.

    PubMed

    Yoshida, S; Sugiyama, S; Hojo, Y; Tokuda, H; Imae, Y

    1990-11-25

    To understand the mechanism of Na+ movement through the force-generating units of the Na(+)-driven flagellar motors of Vibrio alginolyticus, the effect of intracellular Na+ concentration on motor rotation was investigated. Control cells containing about 50 mM Na+ showed good motility even at 10 mM Na+ in the medium, i.e. in the absence of an inwardly directed Na+ gradient. In contrast, Na(+)-loaded cells containing about 400 mM Na+ showed very poor motility at 500 mM Na+ in the medium, i.e. even in the presence of an inwardly directed Na+ gradient. The membrane potential of the cells, which is a major driving force for the motor under these conditions, was not detectably altered, and consistently with this, Na(+)-coupled sucrose transport was only partly reduced in the Na(+)-loaded cells. Motility of the Na(+)-loaded cells was restored by decreasing the intracellular Na+ concentration, and the rate of restoration of motility correlated with the rate of the Na+ decrease. These results indicate that the absolute concentration of the intracellular Na+ is a determinant of the rotation rate of the Na(+)-driven flagellar motors of V. alginolyticus. A simple explanation for this phenomenon is that the force-generating unit of the motor has an intracellular Na(+)-binding site, at which the intracellular Na+ kinetically interferes with the rate of Na+ influx for motor rotation. PMID:2243095

  18. Variational calculations of rotationally resolved infrared properties of Li 2Na +, LiNa 2+ and KLiNa +

    NASA Astrophysics Data System (ADS)

    Wang, Feng; Searles, Debra J.; von Nagy-Felsobuki, Ellak I.

    1992-10-01

    Ab initio variational rovibrational calculations have been performed for the ground electronic states of Li 2Na +, LiNa +2 and KLiNa +. Discrete potential and electric dipole moment surfaces were used to calculate rovibrational transition frequencies, absolute vibrational bands and line intensities. The variational rovibration calculations take into account a full description of the mechanical and electrical anharmonicity as well as vibration—rotation coupling effects. Absolute line intensities and square dipole matrix elements are given for some intense transitions within the P-, Q- and R-branches between the vibrational ground state and the lowest lying excited states.

  19. NMR studies on Na+ transport in Synechococcus PCC 6311

    NASA Technical Reports Server (NTRS)

    Nitschmann, W. H.; Packer, L.

    1992-01-01

    The freshwater cyanobacterium Synechococcus PCC 6311 is able to adapt to grow after sudden exposure to salt (NaCl) stress. We have investigated the mechanism of Na+ transport in these cells during adaptation to high salinity. Na+ influx under dark aerobic conditions occurred independently of delta pH or delta psi across the cytoplasmic membrane, ATPase activity, and respiratory electron transport. These findings are consistent with the existence of Na+/monovalent anion cotransport or simultaneous Na+/H+ +anion/OH- exchange. Na+ influx was dependent on Cl-, Br-, NO3-, or NO2-. No Na+ uptake occurred after addition of NaI, NaHCO3, or Na2SO4. Na+ extrusion was absolutely dependent on delta pH and on an ATPase activity and/or on respiratory electron transport. This indicates that Na+ extrusion via Na+/H+ exchange is driven by primary H+ pumps in the cytoplasmic membrane. Cells grown for 4 days in 0.5 m NaCl medium, "salt-grown cells," differ from control cells by a lower maximum velocity of Na+ influx and by lower steady-state ratios of [Na+]in/[Na+]out. These results indicate that cells grown in high-salt medium increase their capacity to extrude Na+. During salt adaptation Na+ extrusion driven by respiratory electron transport increased from about 15 to 50%.

  20. Capsazepine, a synthetic vanilloid that converts the Na,K-ATPase to Na-ATPase.

    PubMed

    Mahmmoud, Yasser A

    2008-02-01

    Capsazepine (CPZ), a synthetic capsaicin analogue, inhibits ATP hydrolysis by Na,K-ATPase in the presence but not in the absence of K(+). Studies with purified membranes revealed that CPZ reduced Na(+)-dependent phosphorylation by interference with Na(+) binding from the intracellular side of the membrane. Kinetic analyses showed that CPZ stabilized an enzyme species that constitutively occluded K(+). Low-affinity ATP interaction with the enzyme was strongly reduced after CPZ treatment; in contrast, indirectly measured interaction with ADP was much increased, which suggests that composite regulatory communication with nucleotides takes place during turnover. Studies with lipid vesicles revealed that CPZ reduced ATP-dependent digitoxigenin-sensitive (22)Na(+) influx into K(+)-loaded vesicles only at saturating ATP concentrations. The drug apparently abolishes the regulatory effect of ATP on the pump. Drawing on previous homology modeling studies of Na,K-ATPase to atomic models of sarcoplasmic reticulum Ca-ATPase and on kinetic data, we propose that CPZ uncouples an Na(+) cycle from an Na(+)/K(+) cycle in the pump. The Na(+) cycle possibly involves transport through the recently characterized Na(+)-specific site. A shift to such an uncoupled mode is believed to produce pumps mediating uncoupled Na(+) efflux by modifying the transport stoichiometry of single pump units. PMID:18230728

  1. Glutathionylation-Dependence of Na(+)-K(+)-Pump Currents Can Mimic Reduced Subsarcolemmal Na(+) Diffusion.

    PubMed

    Garcia, Alvaro; Liu, Chia-Chi; Cornelius, Flemming; Clarke, Ronald J; Rasmussen, Helge H

    2016-03-01

    The existence of a subsarcolemmal space with restricted diffusion for Na(+) in cardiac myocytes has been inferred from a transient peak electrogenic Na(+)-K(+) pump current beyond steady state on reexposure of myocytes to K(+) after a period of exposure to K(+)-free extracellular solution. The transient peak current is attributed to enhanced electrogenic pumping of Na(+) that accumulated in the diffusion-restricted space during pump inhibition in K(+)-free extracellular solution. However, there are no known physical barriers that account for such restricted Na(+) diffusion, and we examined if changes of activity of the Na(+)-K(+) pump itself cause the transient peak current. Reexposure to K(+) reproduced a transient current beyond steady state in voltage-clamped ventricular myocytes as reported by others. Persistence of it when the Na(+) concentration in patch pipette solutions perfusing the intracellular compartment was high and elimination of it with K(+)-free pipette solution could not be reconciled with restricted subsarcolemmal Na(+) diffusion. The pattern of the transient current early after pump activation was dependent on transmembrane Na(+)- and K(+) concentration gradients suggesting the currents were related to the conformational poise imposed on the pump. We examined if the currents might be accounted for by changes in glutathionylation of the β1 Na(+)-K(+) pump subunit, a reversible oxidative modification that inhibits the pump. Susceptibility of the β1 subunit to glutathionylation depends on the conformational poise of the Na(+)-K(+) pump, and glutathionylation with the pump stabilized in conformations equivalent to those expected to be imposed on voltage-clamped myocytes supported this hypothesis. So did elimination of the transient K(+)-induced peak Na(+)-K(+) pump current when we included glutaredoxin 1 in patch pipette solutions to reverse glutathionylation. We conclude that transient K(+)-induced peak Na(+)-K(+) pump current reflects the effect

  2. Dependence of Na-K pump current on internal Na+ in mammalian cardiac myocytes.

    PubMed

    Mogul, D J; Singer, D H; Ten Eick, R E

    1990-08-01

    Na-K pump current (Ipump) is a function of the intracellular Na+ concentration [( Na+]i). We examined the quantitative relationship between Ipump and [Na+]i in isolated guinea pig ventricular myocytes under steady-state conditions. [Na+]i was controlled and "clamped" at several selected concentrations using wide-tipped pipette microelectrodes, and membrane current was measured using the whole cell patch voltage-clamp technique. Ipump generated at a holding potential of -40 mV was determined by measuring the change in steady-state holding current before and during exposure to dihydroouabain (1 mM); Ipump was measured at 11 levels of [Na+]i ranging from 0 to 80 mM (n = 63) with only one measurement per cell and normalized to cell capacitance to account for differences between myocytes in sarcolemmal surface area. Ipump exhibited a nonlinear dependence on [Na+]i; a Hill analysis of the relationship yielded a half-maximal [Na+]i for pump stimulation of 43.2 mM and a Hill coefficient of 1.53. An alternative analysis of the experimental data was performed assuming that occupation of three internal binding sites by Na+ is required for enzyme turnover. Regression analysis gave the best fit when only two different binding affinities (KD) are postulated. The values are KD1 = 1 mM, KD2 = KD3 = 29 mM. From the analysis using the latter model, the level of [Na+]i at which Ipump saturated closely approximated the theoretical saturation level calculated from published estimates of pump turnover rate and density. The maximal sensitivity of the Na-K pump to changes in [Na+]i occurs when internal [Na+] is within the range for the normal resting physiological level. PMID:2167023

  3. Thermodynamic Model for the Solubility of Cr(OH)(3)(am) in Concentrated NaOH and NaOH-NaNO3 Solutions

    SciTech Connect

    Rai, Dhanpat ); Hess, Nancy J. ); Rao, Linfeng; Zhang, Zhicheng; Felmy, Andrew R. ); Moore, Dean A. ); Clark, Sue B.; Lumetta, Gregg J. )

    2001-12-01

    The objectives of this study were to develop a reliable thermodynamic model for predicting Cr(III) behavior in concentrated NaOH and in mixed NaOH-NaNO3 solutions for application to effective caustic leaching strategies for high-level tank sludges. To meet these objectives, the solubility of Cr(OH)3(am) was measured in 0.003 to 10.5 m NaOH, 3.0 m es in NaOH concentration...

  4. Nanosegregation in Na2C60

    SciTech Connect

    Klupp, G.; Kamaras, K.; Matus, P.; Kiss, L.F.; Kovats, E.; Pekker, S.; Nemes, N.M.; Quintavalle, D.; Janossy, A.

    2005-09-27

    There is continuous interest in the nature of alkali metal fullerides containing C{sub 60}{sup 4-} and C{sub 60}{sup 2-}, because these compounds are believed to be nonmagnetic Mott-Jahn-Teller insulators. This idea could be verified in the case of A4C60, but Na2C60 is more controversial. By comparing the results of infrared spectroscopy and X-ray diffraction, we found that Na2C60 is segregated into 3-10 nm large regions. The two main phases of the material are insulating C60 and metallic Na3C60. We found by neutron scattering that the diffusion of sodium ions becomes faster on heating. Above 470 K Na2C60 is homogeneous and we show IR spectroscopic evidence of a Jahn-Teller distorted C{sub 60}{sup 2-} anion.

  5. Triplet state photoassociation of LiNa

    NASA Astrophysics Data System (ADS)

    Rvachov, Timur; Jamison, Alan; Jing, Li; Jiang, Yijun; Zwierlein, Martin; Ketterle, Wolfgang

    2015-05-01

    Ultracold molecules have promise to become a useful tool for studies in quantum simulation and ultracold chemistry. We aim to produce ultracold fermionic 6Li23Na molecules in the triplet ground state. Due to the small mass, small spin-orbit coupling, and fermionic character of LiNa, the triplet ground state is expected to be long lived. We report on photoassociation spectra of LiNa to its triplet excited states from an ultracold mixture. This is the first observation of these excited triplet potentials, which have been previously difficult to observe in heat-pipe experiments due to the small spin-orbit coupling in the system. Determining the excited state potentials is a key milestone towards forming triplet ground state LiNa via two-photon STIRAP. Work supported by the NSF, AFOSR-MURI, ARO-MURI, and NSERC.

  6. Two-step melting of Na41+

    NASA Astrophysics Data System (ADS)

    Zamith, Sébastien; Labastie, Pierre; Chirot, Fabien; L'Hermite, Jean-Marc

    2010-10-01

    The heat capacity of the mass selected Na41+ cluster has been measured using a differential nanocalorimetry method. A two-peak structure appears in the heat capacity curve of Na41+, whereas Schmidt and co-workers [M. Schmidt, J. Donges, Th. Hippler, and H. Haberland, Phys. Rev. Lett. 90, 103401 (2003)] observed, within their experimental accuracy, a smooth caloric curve. They concluded from the absence of any structure that there is a second order melting transition in Na41+ with no particular feature such as premelting. The observed difference with the latter results is attributed to the better accuracy of our method owing to its differential character. The two structures in the heat capacity are ascribed to melting and premelting of Na41+. The peak at lower temperature is likely due to an anti-Mackay to Mackay solid-solid transition.

  7. Two-step melting of Na(41)(+).

    PubMed

    Zamith, Sébastien; Labastie, Pierre; Chirot, Fabien; L'hermite, Jean-Marc

    2010-10-21

    The heat capacity of the mass selected Na(41) (+) cluster has been measured using a differential nanocalorimetry method. A two-peak structure appears in the heat capacity curve of Na(41) (+), whereas Schmidt and co-workers [M. Schmidt, J. Donges, Th. Hippler, and H. Haberland, Phys. Rev. Lett. 90, 103401 (2003)] observed, within their experimental accuracy, a smooth caloric curve. They concluded from the absence of any structure that there is a second order melting transition in Na(41) (+) with no particular feature such as premelting. The observed difference with the latter results is attributed to the better accuracy of our method owing to its differential character. The two structures in the heat capacity are ascribed to melting and premelting of Na(41) (+). The peak at lower temperature is likely due to an anti-Mackay to Mackay solid-solid transition. PMID:20969397

  8. Na and K distribution in agpaitic pegmatites

    NASA Astrophysics Data System (ADS)

    Müller-Lorch, Daniel; Marks, Michael A. W.; Markl, Gregor

    2007-05-01

    Composition and zoning of amphibole in agpaitic pegmatites of the 1.16 Ga Ilímaussaq complex, South Greenland record the chemical evolution of the final stages of an already extremely fractionated melt. Our results show that the general differentiation trends found in the earlier rocks of the complex are continued in the pegmatites, albeit with some significant modifications: the dominating exchange mechanism of Na + Si ⇔ Ca + Al in the amphiboles of the magmatic stage changes to K + Si ⇔ Ca + Al and K ⇔ Na in some pegmatitic samples. Na/K ratios in amphiboles, which generally increase in the course of the Ilímaussaq fractionation, partly display a reversal during the crystallization of the most differentiated amphiboles. The alkali trends are probably related to the buffering of Na +and K +activity by the co-crystallization of albite and microcline. This buffering favors Na +in cooling fluids. This mechanism is lost when analcime replaces feldspar as a stable phase in the late stages of crystallization, e.g. due to locally elevated H 2O activity. Analcime does not incorporate significant amounts of K and accordingly, amphibole incorporates more K in analcime-bearing assemblages. The Na-K variation in amphiboles in the Ilímaussaq pegmatites allow a detailed view into the late-stage evolutionary trends of a textbook agpaitic complex. The transition from silicate melt to aqueous fluid is recorded by the change of the dominant alkali ion in the pegmatitic amphiboles from Na to K. Only in the very latest stage, virtually K-free mineral assemblages in analcime-aegirine veins support the existence of a Na-dominated aqueous fluid.

  9. Na+ reabsorption in cultured rat epididymal epithelium via the Na+/nucleoside cotransporter.

    PubMed

    Leung, G P; Cheung, K H; Tse, C M; Wong, P Y

    2001-03-01

    The effect of nucleoside on Na+ reabsorption via Na+/nucleoside cotransporter in cultured rat epididymal epithelia was studied by short-circuit current (Isc) technique. Guanosine added apically stimulated Isc in a dose-dependent manner, with a median effective concentration (EC50) of 7 +/- 2 microM (mean +/- SEM). Removal of Na+ from the apical bathing solution or pretreatment with a nonspecific Na+/nucleoside cotransporter inhibitor, phloridzin, completely blocked the Isc response to guanosine. Moreover, the guanosine response was abolished by pretreatment of the tissue with ouabain, a Na+/K+-ATPase inhibitor, suggesting the involvement of Na+/nucleoside cotransporter on the apical side and Na+/K+-ATPase on the basolateral side in Na+ reabsorption. In contrast, the Isc response to guanosine was not affected after desensitization of purinoceptors by ATP. Addition of the Na+/K+/2Cl- symport inhibitor bumetanide to the basolateral side or the nonspecific Cl- channel blocker diphenylamine-2-carboxylate to the apical side showed no effect on the Isc response to guanosine, excluding stimulation of Cl- secretion by guanosine as the cause of the guanosine-induced Isc. The Isc response to purine nucleoside (guanosine and inosine) was much higher than that to pyrimidine nucleoside (thymidine and cytidine). Consistent with substrate specificity, results of reverse transcription-polymerase chain reaction revealed mRNA for concentrative nucleoside transporter (CNT2), which is a purine nucleoside-selective Na+/nucleoside cotransporter in the epididymis, but not for CNT1. It is suggested that the Na+/nucleoside cotransporter (i.e., CNT2) may be one of the elements involved in Na+ and fluid reabsorption in the epididymis, thereby providing an optimal microenvironment for the maturation and storage of spermatozoa. PMID:11207189

  10. Deliquescence of NaCl-NaNO3, KNO3-NaNO3, and NaCl-KNO3 Salt Mixtures From 90 to 120?C

    SciTech Connect

    Carroll, S A; Craig, L; Wolery, T J

    2004-10-20

    We conducted reversed deliquescence experiments in saturated NaCl-NaNO{sub 3}-H{sub 2}O, KNO{sub 3}-NaNO{sub 3}-H{sub 2}O, and NaCl-KNO{sub 3}-H{sub 2}O systems from 90 to 120 C as a function of relative humidity and solution composition. NaCl, NaNO{sub 3}, and KNO{sub 3} represent members of dust salt assemblages that are likely to deliquesce and form concentrated brines on high-level radioactive waste package surfaces in a repository environment at Yucca Mountain, NV, USA. Discrepancy between model prediction and experimental code can be as high as 8% for relative humidity and 50% for dissolved ion concentration. The discrepancy is attributed primarily to the use of 25 C models for Cl-NO{sub 3} and K-NO{sub 3} ion interactions in the current Yucca Mountain Project high-temperature Pitzer model to describe the non-ideal behavior of these highly concentrated solutions.

  11. Determination of Na acceptor level in Na+ ion-implanted ZnO single crystal

    NASA Astrophysics Data System (ADS)

    Wang, Zheng; Liu, Huibin; He, Haiping; Huang, Jingyun; Chen, Lingxiang; Ye, Zhizhen

    2015-03-01

    Ion implantation was used to dope Na acceptor into ZnO single crystals. With three mixed implantation energies, uniform depth distribution of Na ion in the surface region (~300 nm) of ZnO bulk crystals is achieved. Via post-implantation annealing, a donor-acceptor pair recombination band is identified in the low-temperature photoluminescence spectra, from which the energy level of Na-related acceptor in single crystalline ZnO is estimated to be 300 meV. A p-n junction based on this ZnO-Na layer shows rectifying characteristics, confirming the p-type conductivity.

  12. Elastic Coulomb breakup of 34Na

    NASA Astrophysics Data System (ADS)

    Singh, G.; Shubhchintak, Chatterjee, R.

    2016-08-01

    Background: 34Na is conjectured to play an important role in the production of seed nuclei in the alternate r -process paths involving light neutron rich nuclei very near the β -stability line, and as such, it is important to know its ground state properties and structure to calculate rates of the reactions it might be involved in, in the stellar plasma. Found in the region of `island of inversion', its ground state might not be in agreement with normal shell model predictions. Purpose: The aim of this paper is to study the elastic Coulomb breakup of 34Na on 208Pb to give us a core of 33Na with a neutron and in the process we try and investigate the one neutron separation energy and the ground state configuration of 34Na. Method: A fully quantum mechanical Coulomb breakup theory within the architecture of post-form finite range distorted wave Born approximation extended to include the effects of deformation is used to research the elastic Coulomb breakup of 34Na on 208Pb at 100 MeV/u. The triple differential cross section calculated for the breakup is integrated over the desired components to find the total cross-section, momentum, and angular distributions as well as the average momenta, along with the energy-angular distributions. Results: The total one neutron removal cross section is calculated to test the possible ground state configurations of 34Na. The average momentum results along with energy-angular calculations indicate 34Na to have a halo structure. The parallel momentum distributions with narrow full widths at half-maxima signify the same. Conclusion: We have attempted to analyze the possible ground state configurations of 34Na and in congruity with the patterns in the `island of inversion' conclude that even without deformation, 34Na should be a neutron halo with a predominant contribution to its ground state most probably coming from 33Na(3 /2+)⊗ 2 p3 /2ν configuration. We also surmise that it would certainly be useful and rewarding to test our

  13. Direct Measurement of ^21Na+α Stellar Reaction

    NASA Astrophysics Data System (ADS)

    Binh Dam, Nguyen; Yamaguchi, H.; Wakabayashi, Y.; Hayakawa, S.; Hashimoto, T.; Kahl, D.; Kubono, S.; Le, H. K.; Nguyen, T. T.; Iwasa, N.; Kume, N.; Kato, S.; Teranishi, T.

    2009-10-01

    Nucleosynthesis of ^22Na is an interesting subject because of possible γ-ray observation and isotopic anomalies in presolar grain. ^22Na would have been mainly produced in the NeNa cycle. At high temperature conditions, ^21Na(α,p)^24Mg reaction could play a significant role to make flow from the NeNa cycle to the next MgAl cycle and beyond. Clearly, the ^21Na(α,p)^24Mg stellar reaction would bypass ^22Na, resulting in reduction of ^22Na production, therefore, it is strongly coupled to the Ne-E problem. It could be also important to understand the early stage of the rp-process. Experiment was performed using a 39 MeV ^21Na radioactive beam obtained by the CNS Radio Isotope Beam separator CRIB of the University of Tokyo. Both protons and alphas were measured from α+^21Na scattering with a thick ^4He gas target.

  14. Interaction of NaCl(g) and HCl(g) with condensed NA2SO4

    NASA Technical Reports Server (NTRS)

    Stearns, C. A.; Kohl, F. J.; Fryburg, G. C.; Miller, R. A.

    1977-01-01

    The interaction of Na2SO4(l) with NaCl(g), HCl(g) and H2O(g) was studied in atmospheric pressure flowing air and oxygen at Na2SO4(l) temperatures of 900 and 1000 C. Thermomicrogravimetric and high pressure mass spectrometric sampling techniques were used. Experimental results establish that previously reported enhanced rates of weight loss of Na2SO4(l) in the presence of NaCl(g) are due to the reaction: Na2SO4(c) + 2HCl(g) = 2NaCl(g) + SO2(g) + H2O(g) + 1/2O2(g) being driven to the right in flowing gas systems. The HCl(g) is the product of hydrolysis of NaCl caused by small but significant amounts of H2O(g) present in the system. Thermochemical calculations are used to show that even with sub-ppm levels of H2O(g) present, significant quantities of HCl(g) are produced.

  15. Changes in salivary [K+], [Na+] and [K+]/[Na+] with varied test demands.

    PubMed

    Richter, P; Hinton, J W; Meissner, D; Scheller, P

    1995-02-01

    It was hypothesised that choice reaction-time (CRT) testing would cause salivary [K+]/[Na+] to increase. Relative contributions of [K+] and [Na+] to ratio changes were investigated in 23 hypertensives and ten hospital staff. Changes in post-rest and post-test ionic concentrations and [K+]/[Na+], replicated earlier studies. Phasic [K+]/[Na+] changes were mainly due to [K+] changes. Significant increases in [K+] and decreases in [Na+] from a relaxed session, the day before CRT testing, to the testing session per se indicated test anticipation effects. In both groups, changes from pre-test "rest" to "on test" were significant only for [K+]. [K+] discriminated well between conditions in hypertensives. This was interpreted in terms of adaptive changes in sympathetic activation. Results show the robustness of salivary ion indices (especially of [K+]) as indicators of within-subject response to mental task demands. PMID:7537542

  16. Na-ion dynamics in Quasi-1D compound NaV2O4

    NASA Astrophysics Data System (ADS)

    Månsson, M.; Umegaki, I.; Nozaki, H.; Higuchi, Y.; Kawasaki, I.; Watanabe, I.; Sakurai, H.; Sugiyama, J.

    2014-12-01

    We have used the pulsed muon source at ISIS to study high-temperature Na-ion dynamics in the quasi-one-dimensional (Q1D) metallic antiferromagnet NaV2O4. By performing systematic zero-field and longitudinal-field measurements as a function of temperature we clearly distinguish that the hopping rate increases exponentially above Tdiff ≈ 250 K. The data is well fitted to an Arrhenius type equation typical for a diffusion process, showing that the Na-ions starts to be mobile above Tdiff. Such results make this compound very interesting for the tuning of Q1D magnetism using atomic-scale ion-texturing through the periodic potential from ordered Na-vacancies. Further, it also opens the door to possible use of NaV2O4 and related compounds in energy related applications.

  17. Concentration dependence of Li+/Na+ diffusion in manganese hexacyanoferrates

    NASA Astrophysics Data System (ADS)

    Takachi, Masamitsu; Fukuzumi, Yuya; Moritomo, Yutaka

    2016-06-01

    Manganese hexacyanoferrates (Mn-HCFs) with a jungle-gym-type structure are promising cathode materials for Li+/Na+ secondary batteries (LIBs/SIBs). Here, we investigated the diffusion constants D Li/D Na of Li+/Na+ against the Li+/Na+ concentration x Na/x Li and temperature (T) of A 1.32Mn[Fe(CN)6]0.833.6H2O (A = Li and Na). We evaluated the activation energy E\\text{a}\\text{Li}/E\\text{a}\\text{Na} of D Li/D Na against x Na/x Li. We found that E\\text{a}\\text{Na} steeply increases with x Na from 0.41 eV at x Na = 0.69 to 0.7 eV at 1.1. The increase in E\\text{a}\\text{Na} is ascribed to the occupancy effect of the Na+ site. The increase in E\\text{a}\\text{Li} is suppressed, probably because the number of Li+ sites is three times that of Na+ sites.

  18. Functional coupling of renal K+ and Na+ handling causes high blood pressure in Na+ replete mice

    PubMed Central

    Vitzthum, Helga; Seniuk, Anika; Schulte, Laura Helene; Müller, Maxie Luise; Hetz, Hannah; Ehmke, Heimo

    2014-01-01

    A network of kinases, including WNKs, SPAK and Sgk1, is critical for the independent regulation of K+ and Na+ transport in the distal nephron. Angiotensin II is thought to act as a key hormone in orchestrating these kinases to switch from K+ secretion during hyperkalaemia to Na+ reabsorption during intravascular volume depletion, thus keeping disturbances in electrolyte and blood pressure homeostasis at a minimum. It remains unclear, however, how K+ and Na+ transport are regulated during a high Na+ intake, which is associated with suppressed angiotensin II levels and a high distal tubular Na+ load. We therefore investigated the integrated blood pressure, renal, hormonal and gene and protein expression responses to large changes of K+ intake in Na+ replete mice. Both low and high K+ intake increased blood pressure and caused Na+ retention. Low K+ intake was accompanied by an upregulation of the sodium-chloride cotransporter (NCC) and its activating kinase SPAK, and inhibition of NCC normalized blood pressure. Renal responses were unaffected by angiotensin AT1 receptor antagonism, indicating that low K+ intake activates the distal nephron by an angiotensin-independent mode of action. High K+ intake was associated with elevated plasma aldosterone concentrations and an upregulation of the epithelial sodium channel (ENaC) and its activating kinase Sgk1. Surprisingly, high K+ intake increased blood pressure even during ENaC or mineralocorticoid receptor antagonism, suggesting the contribution of aldosterone-independent mechanisms. These findings show that in a Na+ replete state, changes in K+ intake induce specific molecular and functional adaptations in the distal nephron that cause a functional coupling of renal K+ and Na+ handling, resulting in Na+ retention and high blood pressure when K+ intake is either restricted or excessively increased. PMID:24396058

  19. Sodium-difluoro(oxalato)borate (NaDFOB): a new electrolyte salt for Na-ion batteries.

    PubMed

    Chen, Juner; Huang, Zhenguo; Wang, Caiyun; Porter, Spencer; Wang, Baofeng; Lie, Wilford; Liu, Hua Kun

    2015-06-18

    A new electrolyte salt, sodium-difluoro(oxalato)borate (NaDFOB), was synthesized and studied, which enables excellent reversible capacity and high rate capability when used in Na/Na0.44MnO2 half cells. NaDFOB has excellent compatibility with various common solvents used in Na-ion batteries, in strong contrast to the solvent dependent performances of NaClO4 and NaPF6. In addition, NaDFOB possesses good stability and generates no toxic or dangerous products when exposed to air and water. All these properties demonstrate that NaDFOB could be used to prepare high performance electrolytes for emerging Na-ion batteries. PMID:25987231

  20. Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state.

    PubMed

    Kanai, Ryuta; Ogawa, Haruo; Vilsen, Bente; Cornelius, Flemming; Toyoshima, Chikashi

    2013-10-10

    Na(+),K(+)-ATPase pumps three Na(+) ions out of cells in exchange for two K(+) taken up from the extracellular medium per ATP molecule hydrolysed, thereby establishing Na(+) and K(+) gradients across the membrane in all animal cells. These ion gradients are used in many fundamental processes, notably excitation of nerve cells. Here we describe 2.8 Å-resolution crystal structures of this ATPase from pig kidney with bound Na(+), ADP and aluminium fluoride, a stable phosphate analogue, with and without oligomycin that promotes Na(+) occlusion. These crystal structures represent a transition state preceding the phosphorylated intermediate (E1P) in which three Na(+) ions are occluded. Details of the Na(+)-binding sites show how this ATPase functions as a Na(+)-specific pump, rejecting K(+) and Ca(2+), even though its affinity for Na(+) is low (millimolar dissociation constant). A mechanism for sequential, cooperative Na(+) binding can now be formulated in atomic detail. PMID:24089211

  1. Role of the Na(+)-translocating NADH:quinone oxidoreductase in voltage generation and Na(+) extrusion in Vibrio cholerae.

    PubMed

    Vorburger, Thomas; Nedielkov, Ruslan; Brosig, Alexander; Bok, Eva; Schunke, Emina; Steffen, Wojtek; Mayer, Sonja; Götz, Friedrich; Möller, Heiko M; Steuber, Julia

    2016-04-01

    For Vibrio cholerae, the coordinated import and export of Na(+) is crucial for adaptation to habitats with different osmolarities. We investigated the Na(+)-extruding branch of the sodium cycle in this human pathogen by in vivo (23)Na-NMR spectroscopy. The Na(+) extrusion activity of cells was monitored after adding glucose which stimulated respiration via the Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR). In a V. cholerae deletion mutant devoid of the Na(+)-NQR encoding genes (nqrA-F), rates of respiratory Na(+) extrusion were decreased by a factor of four, but the cytoplasmic Na(+) concentration was essentially unchanged. Furthermore, the mutant was impaired in formation of transmembrane voltage (ΔΨ, inside negative) and did not grow under hypoosmotic conditions at pH8.2 or above. This growth defect could be complemented by transformation with the plasmid encoded nqr operon. In an alkaline environment, Na(+)/H(+) antiporters acidify the cytoplasm at the expense of the transmembrane voltage. It is proposed that, at alkaline pH and limiting Na(+) concentrations, the Na(+)-NQR is crucial for generation of a transmembrane voltage to drive the import of H(+) by electrogenic Na(+)/H(+) antiporters. Our study provides the basis to understand the role of the Na(+)-NQR in pathogenicity of V. cholerae and other pathogens relying on this primary Na(+) pump for respiration. PMID:26721205

  2. Na+ Inhibits the Epithelial Na+ Channel by Binding to a Site in an Extracellular Acidic Cleft*

    PubMed Central

    Kashlan, Ossama B.; Blobner, Brandon M.; Zuzek, Zachary; Tolino, Michael; Kleyman, Thomas R.

    2015-01-01

    The epithelial Na+ channel (ENaC) has a key role in the regulation of extracellular fluid volume and blood pressure. ENaC belongs to a family of ion channels that sense the external environment. These channels have large extracellular regions that are thought to interact with environmental cues, such as Na+, Cl−, protons, proteases, and shear stress, which modulate gating behavior. We sought to determine the molecular mechanism by which ENaC senses high external Na+ concentrations, resulting in an inhibition of channel activity. Both our structural model of an ENaC α subunit and the resolved structure of an acid-sensing ion channel (ASIC1) have conserved acidic pockets in the periphery of the extracellular region of the channel. We hypothesized that these acidic pockets host inhibitory allosteric Na+ binding sites. Through site-directed mutagenesis targeting the acidic pocket, we modified the inhibitory response to external Na+. Mutations at selected sites altered the cation inhibitory preference to favor Li+ or K+ rather than Na+. Channel activity was reduced in response to restraining movement within this region by cross-linking structures across the acidic pocket. Our results suggest that residues within the acidic pocket form an allosteric effector binding site for Na+. Our study supports the hypothesis that an acidic cleft is a key ligand binding locus for ENaC and perhaps other members of the ENaC/degenerin family. PMID:25389295

  3. Extracellular allosteric Na(+) binding to the Na(+),K(+)-ATPase in cardiac myocytes.

    PubMed

    Garcia, Alvaro; Fry, Natasha A S; Karimi, Keyvan; Liu, Chia-chi; Apell, Hans-Jürgen; Rasmussen, Helge H; Clarke, Ronald J

    2013-12-17

    Whole-cell patch-clamp measurements of the current, Ip, produced by the Na(+),K(+)-ATPase across the plasma membrane of rabbit cardiac myocytes show an increase in Ip over the extracellular Na(+) concentration range 0-50 mM. This is not predicted by the classical Albers-Post scheme of the Na(+),K(+)-ATPase mechanism, where extracellular Na(+) should act as a competitive inhibitor of extracellular K(+) binding, which is necessary for the stimulation of enzyme dephosphorylation and the pumping of K(+) ions into the cytoplasm. The increase in Ip is consistent with Na(+) binding to an extracellular allosteric site, independent of the ion transport sites, and an increase in turnover via an acceleration of the rate-determining release of K(+) to the cytoplasm, E2(K(+))2 → E1 + 2K(+). At normal physiological concentrations of extracellular Na(+) of 140 mM, it is to be expected that binding of Na(+) to the allosteric site would be nearly saturated. Its purpose would seem to be simply to optimize the enzyme's ion pumping rate under its normal physiological conditions. Based on published crystal structures, a possible location of the allosteric site is within a cleft between the α- and β-subunits of the enzyme. PMID:24359741

  4. Study on Na layer response to geomagnetic activities based on Odin/OSIRIS Na density data

    NASA Astrophysics Data System (ADS)

    Tsuda, Takuo; Nakamura, Takuji; Hedin, Jonas; Gumbel, Jorg; Hosokawa, Keisuke; Ejiri, Mitsumu K.; Nishiyama, Takanori; Takahashi, Toru

    2016-07-01

    The Na layer is normally distributed from 80 to 110 km, and the height range is corresponding to the ionospheric D and E region. In the polar region, the energetic particles precipitating from the magnetosphere can often penetrate into the E region and even into the D region. Thus, the influence of the energetic particles to the Na layer is one of interests in the aspect of the atmospheric composition change accompanied with the auroral activity. There are several previous studies in this issue. For example, recently, we have reported an initial result on a clear relationship between the electron density increase (due to the energetic particles) and the Na density decrease from observational data sets obtained by Na lidar, EISCAT VHF radar, and optical instruments at Tromsoe, Norway on 24-25 January 2012. However, all of the previous studies had been carried out based on case studies by ground-based lidar observations. In this study, we have performed, for the first time, statistical analysis using Na density data from 2004 to 2009 obtained with the Optical Spectrograph and InfraRed Imager System (OSIRIS) onboard Odin satellite. In the presentation, we will show relationship between the Na density and geomagnetic activities, and its latitudinal variation. Based on these results, the Na layer response to the energetic particles will be discussed.

  5. The role of Na/+/ in transport processes of bacterial membranes

    NASA Technical Reports Server (NTRS)

    Lanyi, J. K.

    1979-01-01

    Until recently it was generally held that transport in bacteria was linked exclusively to proton circulation, in contrast to most eucaryotic systems, which depended on Na(+) circulation. The present review is intended to trace recent developments which have led to the discarding of this idea. The discussion covers transport of Na(+) and other cations, effects of Na(+) and Na(+) gradients on metabolite transport, properties of Na(+)-dependent transport carriers, and evolutionary considerations of Na(+) transport. It is now apparent that the transport of Na(+) is an important part of energy metabolism in bacteria, and that Na(+) gradients as well as H(+) gradients are used in these systems for the conservation and transmission of energy. Two hypotheses are proposed to explain the evolution of Na/K systems, and it is presently difficult to decide between them.

  6. Clustered voltage-gated Na+ channels in Aplysia axons.

    PubMed

    Johnston, W L; Dyer, J R; Castellucci, V F; Dunn, R J

    1996-03-01

    Clustering of voltage-gated Na+ channels is critical for the fast saltatory conduction of action potentials in vertebrate myelinated axons. However, the mechanisms responsible for the generation and maintenance of Na+ channel clustering are not well understood. In this study we have raised an antibody against the cloned SCAP-1 voltage-gated Na+ channel of the marine invertebrate Aplysia californica and used it to examine Na+ channel localization in Aplysia ganglia and in cultured Aplysia sensory neurons. Our results show that there is a large cytoplasmic pool of Na+ channels in the soma of Aplysia neurons. Furthermore, we show that Na+ channels in Aplysia axons are not homogeneously distributed but, rather, are present in distinct clusters. Theoretical considerations indicate that Na+ channel clustering may enhance action potential conduction. We propose that clustered Na+ channels may be a fundamental property of many axons, and perhaps of many membranes that conduct Na(+)-dependent action potentials. PMID:8774441

  7. Effect of Na+ Flow on Cd2+ Block of Tetrodotoxin-resistant Na+ Channels

    PubMed Central

    Kuo, Chung-Chin; Lin, Ting-Jiun; Hsieh, Chi-Pan

    2002-01-01

    Tetrodotoxin-resistant (TTX-R) Na+ channels are 1,000-fold less sensitive to TTX than TTX-sensitive (TTX-S) Na+ channels. On the other hand, TTX-R channels are much more susceptible to external Cd2+ block than TTX-S channels. A cysteine (or serine) residue situated just next to the aspartate residue of the presumable selectivity filter “DEKA” ring of the TTX-R channel has been identified as the key ligand determining the binding affinity of both TTX and Cd2+. In this study we demonstrate that the binding affinity of Cd2+ to the TTX-R channels in neurons from dorsal root ganglia has little intrinsic voltage dependence, but is significantly influenced by the direction of Na+ current flow. In the presence of inward Na+ current, the apparent dissociation constant of Cd2+ (∼200 μM) is ∼9 times smaller than that in the presence of outward Na+ current. The Na+ flow–dependent binding affinity change of Cd2+ block is true no matter whether the direction of Na+ current is secured by asymmetrical chemical gradient (e.g., 150 mM Na+ vs. 150 mM Cs+ on different sides of the membrane, 0 mV) or by asymmetrical electrical gradient (e.g., 150 mM Na+ on both sides of the membrane, −20 mV vs. 20 mV). These findings suggest that Cd2+ is a pore blocker of TTX-R channels with its binding site located in a multiion, single-file region near the external pore mouth. Quantitative analysis of the flow dependence with the flux-coupling equation reveals that at least two Na+ ions coexist with the blocking Cd2+ ion in this pore region in the presence of 150 mM ambient Na+. Thus, the selectivity filter of the TTX-R Na+ channels in dorsal root ganglion neurons might be located in or close to a multiion single-file pore segment connected externally to a wide vestibule, a molecular feature probably shared by other voltage-gated cationic channels, such as some Ca2+ and K+ channels. PMID:12149278

  8. Synthesis of Na-A and/or Na-X zeolite/porous carbon composites from carbonized rice husk

    NASA Astrophysics Data System (ADS)

    Katsuki, Hiroaki; Komarneni, Sridhar

    2009-07-01

    Na-A and/or Na-X zeolite/porous carbon composites were prepared under hydrothermal conditions by NaOH dissolution of silica first from carbonized rice husk followed by addition of NaAlO 2 and in situ crystallization of zeolites i.e., using a two-step process. When a one-step process was used, both Na-A and Na-X zeolites crystallized on the surface of carbon. Na-A or Na-X zeolite crystals were prepared on the porous carbonized rice husk at 90 °C for 2-6 h by changing the SiO 2/Al 2O 3, H 2O/Na 2O and Na 2O/SiO 2 molar ratios of precursors in the two-step process. The surface area and NH 4+-cation exchange capacity (CEC) of Na-A zeolite/porous carbon were found to be 171 m 2/g and 506 meq/100 g, respectively, while those of Na-X zeolite/porous carbon composites were 676 m 2/g and 317 meq/100 g, respectively. Na-A and Na-X zeolites are well-known microporous and hydrophilic materials while carbonized rice husk was found to be mesoporous (pores of ˜3.9 nm) and hydrophobic. These hybrid microporous-mesoporous and hydrophilic-hydrophobic composites are expected to be useful for decontamination of metal cations as well as organic contaminants simultaneously.

  9. The solubility of Cr(OH){sub 3}(am) in concentrated NaOH and NaOH-NaNO{sub 3} solutions

    SciTech Connect

    Felmy, A.R.; Rai, D.; Fulton, R.W.

    1994-08-01

    Chromium is a major component of the Hanford waste tank sludges, and the presence of Cr in the sludges is a significant concern in the disposal of these sludges because Cr can interfere with the formation of waste glasses. One of the current pretreatment strategies for removing constituents that can interfere with glass formation, such as P and Cr, is to wash/dissolve the sludges in basic NaOH solutions. The solubility of Cr(OH){sub 3}(am) was measured in concentrated NaOH ranging in concentration from 0.1M to 6.0M and in NaOH-NaNO{sub 3} solutions with fixed NaOH concentration and variable NaNO{sub 3} concentration at room temperature (22--23 C). Equilibrium between solids and solutions was approached relatively slowly and required approximately 60--70 days before steady-state concentrations were reached. A thermodynamic model, based upon the Pitzer equations, was developed from the solubility data in NaOH, which includes only two aqueous Cr species (Cr(OH){sub 4}{sup {minus}} and NaCr(OH){sub 4}(aq)) and ion-interaction parameters for Na{sup +} with Cr(OH){sub 4}{sup {minus}}. This model was then tested in the mixed NaOH-NaNO{sub 3} solutions and found to be reliable.

  10. Laser trapping of {sup 21}Na atoms

    SciTech Connect

    Lu, Zheng-Tian

    1994-09-01

    This thesis describes an experiment in which about four thousand radioactive {sup 21}Na (t{sub l/2} = 22 sec) atoms were trapped in a magneto-optical trap with laser beams. Trapped {sup 21}Na atoms can be used as a beta source in a precision measurement of the beta-asymmetry parameter of the decay of {sup 21}Na {yields} {sup 21}Ne + {Beta}{sup +} + v{sub e}, which is a promising way to search for an anomalous right-handed current coupling in charged weak interactions. Although the number o trapped atoms that we have achieved is still about two orders of magnitude lower than what is needed to conduct a measurement of the beta-asymmetry parameter at 1% of precision level, the result of this experiment proved the feasibility of trapping short-lived radioactive atoms. In this experiment, {sup 21}Na atoms were produced by bombarding {sup 24}Mg with protons of 25 MeV at the 88 in. Cyclotron of Lawrence Berkeley Laboratory. A few recently developed techniques of laser manipulation of neutral atoms were applied in this experiment. The {sup 21}Na atoms emerging from a heated oven were first transversely cooled. As a result, the on-axis atomic beam intensity was increased by a factor of 16. The atoms in the beam were then slowed down from thermal speed by applying Zeeman-tuned slowing technique, and subsequently loaded into a magneto-optical trap at the end of the slowing path. The last two chapters of this thesis present two studies on the magneto-optical trap of sodium atoms. In particular, the mechanisms of magneto-optical traps at various laser frequencies and the collisional loss mechanisms of these traps were examined.

  11. (19)F(alpha,n)(22)Na, (22)Ne(p,n)(22)Na, and the Role of their Inverses in the Destruction of (22)Na

    NASA Astrophysics Data System (ADS)

    Wrean, Patricia Rose

    The inverses of the 19F(α,n)22Na and 22Ne(p,n)22Na reactions may be important destruction mechanisms for 22Na in neutron-rich, high-temperature or explosive nucleosynthesis. I have measured the cross sections for the 19F(α,n)22Na and 22Ne(p,n)22Na reactions from threshold to 3.1 and 5.4 MeV, respectively. The absolute efficiency of the 4π neutron detector was determined by Monte Carlo calculations and calibrated using two standard sources and two nuclear reactions. Cross sections for the inverse reactions have been calculated using the principle of detailed balance, and reaction rates for both the reactions and their inverses determined for temperatures between 0.01 and 10 GK for 19F(α,n)22Na and between 0.1 and 10 GK for 22Ne(p,n)22Na.

  12. A Selective Na(+) Aptamer Dissected by Sensitized Tb(3+) Luminescence.

    PubMed

    Zhou, Wenhu; Ding, Jinsong; Liu, Juewen

    2016-08-17

    A previous study of two RNA-cleaving DNAzymes, NaA43 and Ce13d, revealed the possibility of a common Na(+) aptamer motif. Because Na(+) binding to DNA is a fundamental biochemical problem, the interaction between Ce13d and Na(+) was studied in detail by using sensitized Tb(3+) luminescence spectroscopy. Na(+) displaces Tb(3+) from the DNAzyme, and thus quenches the emission from Tb(3+) . The overall requirement for Na(+) binding includes the hairpin and the highly conserved 16-nucleotide loop in the enzyme strand, along with a few unpaired nucleotides in the substrate. Mutation studies indicate good correlation between Na(+) binding and cleavage activity, thus suggesting a critical role of Na(+) binding for the enzyme activity. Ce13d displayed a Kd of ∼20 mm with Na(+) (other monovalent cations: 40-60 mm). The Kd values for other metal ions are mainly due to non-specific competition. With a single nucleotide mutation, the specific Na(+) binding was lost. Another mutant improved Kd to 8 mm with Na(+) . This study has demonstrated a Na(+) aptamer with important biological implications and analytical applications. It has also defined the structural requirements for Na(+) binding and produced an improved mutant. PMID:27238890

  13. Nonmagnetic Insulator State in Na1CoO2 and Phase Separation of Na Vacancies

    NASA Astrophysics Data System (ADS)

    de Vaulx, C.; Julien, M.-H.; Berthier, C.; Horvatić, M.; Bordet, P.; Simonet, V.; Chen, D. P.; Lin, C. T.

    2005-10-01

    Crystallographic, magnetic, and NMR properties of a NaxCoO2 single crystal with x≃1 are presented. We identify the stoichiometric Na1CoO2 phase, which is shown to be a nonmagnetic insulator, as expected for homogeneous planes of Co3+ ions with S=0. In addition, we present evidence that, because of slight average Na deficiency, chemical and electronic phase separation leads to a segregation of Na vacancies into the well-defined, magnetic, Na0.8CoO2 phase. The importance of phase separation is discussed in the context of magnetic order for x≃0.8 and the occurrence of a metal-insulator transition for x→1.

  14. 24Mg( p, α)21Na reaction study for spectroscopy of 21Na

    NASA Astrophysics Data System (ADS)

    Cha, S. M.; Chae, K. Y.; Kim, A.; Lee, E. J.; Ahn, S.; Bardayan, D. W.; Chipps, K. A.; Cizewski, J. A.; Howard, M. E.; Manning, B.; O'Malley, P. D.; Ratkiewicz, A.; Strauss, S.; Kozub, R. L.; Matos, M.; Pain, S. D.; Pittman, S. T.; Smith, M. S.; Peters, W. A.

    2015-10-01

    The 24Mg( p, α)21Na reaction was measured at the Holifield Radioactive Ion Beam Facility at Oak Ridge National Laboratory in order to better constrain the spins and parities of the energy levels in 21Na for the astrophysically important 17F( α, p)20Ne reaction rate calculation. 31-MeV proton beams from the 25-MV tandem accelerator and enriched 24Mg solid targets were used. Recoiling 4He particles from the 24Mg( p, α)21Na reaction were detected by a highly segmented silicon detector array which measured the yields of 4He particles over a range of angles simultaneously. A new level at 6661 ± 5 keV was observed in the present work. The extracted angular distributions for the first four levels of 21Na and the results from distorted wave Born approximation (DWBA) calculations were compared to verify and extract the angular momentum transfer.

  15. Na/beta-alumina/NaAlCl4, Cl2/C circulating cell

    NASA Astrophysics Data System (ADS)

    Cherng, Jing-Yih; Bennion, Douglas N.

    1987-09-01

    A study was made of a high specific energy battery based on a sodium negative electrode and a chlorine positive electrode with molten AlCl3-NaCl electrolyte and a solid beta alumina separator. The basic performance of a Na beta-alumina NaAlCl4, Cl2/C circulating cell at 200 C was demonstrated. This cell can be started at 150 C. The use of melting sodium chloroaluminate electrolyte overcomes some of the material problems associated with the high working temperatures of present molten salt systems, such as Na/S and LiAl/FeS, and retains the advantages of high energy density and relatively efficient electrode processes. Preliminary investigations were conducted on a sodium-chlorine static cell, material compability, electrode design, wetting, and theoretical calculations to assure a better chance of success before assembling a Na/Cl2 circulating cell. Mathematical models provide a theoretical explanation for the performance of the NaCl2 battery. The results of mathematical models match the experimental results very well. According to the result of the mathematical modeling, an output at 180 mA/sq cm and 3.2 V can be obtained with optimized cell design.

  16. Na/beta-alumina/NaAlCl4, Cl2/C circulating cell

    NASA Technical Reports Server (NTRS)

    Cherng, Jing-Yih; Bennion, Douglas N.

    1987-01-01

    A study was made of a high specific energy battery based on a sodium negative electrode and a chlorine positive electrode with molten AlCl3-NaCl electrolyte and a solid beta alumina separator. The basic performance of a Na beta-alumina NaAlCl4, Cl2/C circulating cell at 200 C was demonstrated. This cell can be started at 150 C. The use of melting sodium chloroaluminate electrolyte overcomes some of the material problems associated with the high working temperatures of present molten salt systems, such as Na/S and LiAl/FeS, and retains the advantages of high energy density and relatively efficient electrode processes. Preliminary investigations were conducted on a sodium-chlorine static cell, material compability, electrode design, wetting, and theoretical calculations to assure a better chance of success before assembling a Na/Cl2 circulating cell. Mathematical models provide a theoretical explanation for the performance of the NaCl2 battery. The results of mathematical models match the experimental results very well. According to the result of the mathematical modeling, an output at 180 mA/sq cm and 3.2 V can be obtained with optimized cell design.

  17. An enhancement to the NA4 gear vibration diagnostic parameter

    NASA Technical Reports Server (NTRS)

    Decker, Harry J.; Handschuh, Robert F.; Zakrajsek, James J.

    1994-01-01

    A new vibration diagnostic parameter for health monitoring of gears, NA4*, is proposed and tested. A recently developed gear vibration diagnostic parameter NA4 outperformed other fault detection methods at indicating the start and initial progression of damage. However, in some cases, as the damage progressed, the sensitivity of the NA4 and FM4 parameters tended to decrease and no longer indicated damage. A new parameter, NA4* was developed by enhancing NA4 to improve the trending of the parameter. This allows for the indication of damage both at initiation and also as the damage progresses. The NA4* parameter was verified and compared to the NA4 and FM4 parameters using experimental data from single mesh spur and spiral bevel gear fatigue rigs. The primary failure mode for the test cases was naturally occurring tooth surface pitting. The NA4* parameter is shown to be a more robust indicator of damage.

  18. U. S. EPA’S NA APPROACH FOR PETROLEUM HYDROCARBONS

    EPA Science Inventory

    Most evaluations of NA of petroleum hydrocarbons use geochemical data to document the NA through biodegradation. The expected trends during biodegradation (plume interior vs. background concentrations) are Dissolved oxygen concentrations below background, Nitrate concentrations ...

  19. Rescue of Na+ Affinity in Aspartate 928 Mutants of Na+,K+-ATPase by Secondary Mutation of Glutamate 314*

    PubMed Central

    Holm, Rikke; Einholm, Anja P.; Andersen, Jens P.; Vilsen, Bente

    2015-01-01

    The Na+,K+-ATPase binds Na+ at three transport sites denoted I, II, and III, of which site III is Na+-specific and suggested to be the first occupied in the cooperative binding process activating phosphorylation from ATP. Here we demonstrate that the asparagine substitution of the aspartate associated with site III found in patients with rapid-onset dystonia parkinsonism or alternating hemiplegia of childhood causes a dramatic reduction of Na+ affinity in the α1-, α2-, and α3-isoforms of Na+,K+-ATPase, whereas other substitutions of this aspartate are much less disruptive. This is likely due to interference by the amide function of the asparagine side chain with Na+-coordinating residues in site III. Remarkably, the Na+ affinity of site III aspartate to asparagine and alanine mutants is rescued by second-site mutation of a glutamate in the extracellular part of the fourth transmembrane helix, distant to site III. This gain-of-function mutation works without recovery of the lost cooperativity and selectivity of Na+ binding and does not affect the E1-E2 conformational equilibrium or the maximum phosphorylation rate. Hence, the rescue of Na+ affinity is likely intrinsic to the Na+ binding pocket, and the underlying mechanism could be a tightening of Na+ binding at Na+ site II, possibly via movement of transmembrane helix four. The second-site mutation also improves Na+,K+ pump function in intact cells. Rescue of Na+ affinity and Na+ and K+ transport by second-site mutation is unique in the history of Na+,K+-ATPase and points to new possibilities for treatment of neurological patients carrying Na+,K+-ATPase mutations. PMID:25713066

  20. Final-state symmetry of Na 1s core-shell excitons in NaCl and NaF

    SciTech Connect

    Nagle, K.P.; Seidler, G.T.; Shirley, E.L.; Fister, T.T.; Bradley, J.A.; Brown, F.C.

    2009-08-13

    We report measurements of the Na 1s contribution to the nonresonant inelastic x-ray scattering (NRIXS) from NaCl and NaF. Prior x-ray absorption studies have observed two pre-edge excitons in both materials. The momentum-transfer dependence (q dependence) of the measured NRIXS cross section and of real-space full multiple scattering and Bethe-Salpeter calculations determine that the higher-energy core excitons are s type for each material. The lower-energy core excitons contribute at most weakly to the NRIXS signal and we propose that these may be surface core excitons, as have been observed in several other alkali halides. The analysis of the orbital angular momentum of these features leads to a discussion of the limited sensitivity of NRIXS measurements to d-type final states when investigating 1s initial states. In this case the s- and p-type final density of states can be characterized by measurements at a small number of momentum transfers. This is in contrast to the case of more complex initial states for which measurements at a large number of momentum transfers are needed to separate the rich admixture of accessible and contributing final-state symmetries.

  1. Igneous origin for the NA in the cloud of Io

    NASA Astrophysics Data System (ADS)

    Johnson, M. L.; Burnett, D. S.

    1990-06-01

    Mixtures of sulfur and Na-bearing silicates were heated in evacuated silica glass capsules to temperatures between 600 C and 950 C. At or above 850 C, Na-silicate glass reacts with elemental S to form a (Na, K) sulfide. Mobilization of this phase may account for the presence of Na and K on the surface of Io, and hence in the material sputtered onto the Jovian magnetosphere.

  2. Electrical properties of Na{sub 2}US{sub 3}, NaGdS{sub 2} and NaLaS{sub 2}

    SciTech Connect

    Masuda, Hidetoshi; Fujino, Takeo; Sato, Nobuaki; Yamada, Kohta

    1999-06-01

    The electrical properties of ternary mixed sulfides Na{sub 2}US{sub 3}, NaGdS{sub 2}, and NaLaS{sub 2} were studied by measuring the electrical conductivity and Hall coefficient by the van der Pauw method in a temperature range of 17--300 K. These compounds have closely related crystal structures with nearly the same atom separations, but uranium is in a U{sup 4+} state in Na{sub 2}US{sub 3} in contrast to Ln{sup 3+} ions in NaGdS{sub 2} and NaLaS{sub 2}. The electrical conductivity was the highest for NaGdS{sub 2} (7.75 x 10{sup 2} and 11.2 x 10{sup 2} Sm{sup {minus}1} at 17 and 300 K, respectively) and the lowest for Na{sub 2}US{sub 3} (0.98 x 10{sup 2} and 1.14 x 10{sup 2} Sm{sup {minus}1} at 17 and 300 K, respectively). They showed semiconductive behavior from the temperature dependence of the electrical conductivity. The Hall coefficient showed the dominant carriers to be electrons for NaGdS{sub 2} and holes for NaLaS{sub 2} and Na{sub 2}US{sub 3}. The carrier densities were not so apart in these compounds, i.e., 0.2--0.3 x 10{sup 25} m{sup {minus}3} for NaGdS{sub 2} and {approximately}0.1 x 10{sup 25} m{sup {minus}3} for Na{sub 2}Us{sub 3}. The activation energies of conduction were very low for all three compounds, especially at low temperatures below 200 K.

  3. Glial Na(+) -dependent ion transporters in pathophysiological conditions.

    PubMed

    Boscia, Francesca; Begum, Gulnaz; Pignataro, Giuseppe; Sirabella, Rossana; Cuomo, Ornella; Casamassa, Antonella; Sun, Dandan; Annunziato, Lucio

    2016-10-01

    Sodium dynamics are essential for regulating functional processes in glial cells. Indeed, glial Na(+) signaling influences and regulates important glial activities, and plays a role in neuron-glia interaction under physiological conditions or in response to injury of the central nervous system (CNS). Emerging studies indicate that Na(+) pumps and Na(+) -dependent ion transporters in astrocytes, microglia, and oligodendrocytes regulate Na(+) homeostasis and play a fundamental role in modulating glial activities in neurological diseases. In this review, we first briefly introduced the emerging roles of each glial cell type in the pathophysiology of cerebral ischemia, Alzheimer's disease, epilepsy, Parkinson's disease, Amyotrophic Lateral Sclerosis, and myelin diseases. Then, we discussed the current knowledge on the main roles played by the different glial Na(+) -dependent ion transporters, including Na(+) /K(+) ATPase, Na(+) /Ca(2+) exchangers, Na(+) /H(+) exchangers, Na(+) -K(+) -Cl(-) cotransporters, and Na(+) - HCO3- cotransporter in the pathophysiology of the diverse CNS diseases. We highlighted their contributions in cell survival, synaptic pathology, gliotransmission, pH homeostasis, and their role in glial activation, migration, gliosis, inflammation, and tissue repair processes. Therefore, this review summarizes the foundation work for targeting Na(+) -dependent ion transporters in glia as a novel strategy to control important glial activities associated with Na(+) dynamics in different neurological disorders. GLIA 2016;64:1677-1697. PMID:27458821

  4. Homocoordination preference in NaCs and LiNa liquid alloys by first principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Costa Cabral, B. J.; Martins, J. L.

    1999-09-01

    We present structural and dynamics results based on Hellman-Feynman molecular dynamics for the liquid phase of the NaCs alloy at two Na concentrations (cNa=0.6 and 0.8) and for the Li0.61Na0.39 zero alloy at two temperatures (T=590 K and 690 K). For NaCs the calculated structure factor S(k) is in very good agreement with data from neutron scattering experiments and the partial structure factors are compared to semiexperimental, theoretical and classical molecular dynamics predictions. We predict similar values for the self-diffusion coefficients of Na and Cs atoms in the Na0.6Cs0.4 alloy. For LiNa the concentration-concentration structure factor is in good agreement with experimental data and our results for the dynamics are compared with data from classical molecular dynamics simulations.

  5. Optically pumped Na/sub 2/ laser

    SciTech Connect

    Kanorskii, S.I.; Kaslin, V.M.; Yakushev, O.F.

    1980-10-01

    A pulsed copper vapor laser emitting the 578.2 nm line was used as the pump source in achieving stimulated emission as a result of the electronic A/sup 1/..sigma../sup +//sub u/ to X/sup 1/..sigma../sup +//sub g/ transitions in the Na/sub 2/ molecule in the spectral range 0.765 to 0.804 ..mu... The average power of all the emission lines was 10 mW when the pulsed pump power was 150 W and the efficiency of conversion of the optical pump energy was about 3%. The pulse repetition frequency was 3.3 kHz. Violet diffuse radiation of the Na/sub 2/ molecules, generated by pumping with the copper vapor laser, was observed. The superradiance regime was found for some of the lines.

  6. Cardiac Na Channels: Structure to Function.

    PubMed

    DeMarco, K R; Clancy, C E

    2016-01-01

    Heart rhythms arise from electrical activity generated by precisely timed opening and closing of ion channels in individual cardiac myocytes. Opening of the primary cardiac voltage-gated sodium (NaV1.5) channel initiates cellular depolarization and the propagation of an electrical action potential that promotes coordinated contraction of the heart. The regularity of these contractile waves is critically important since it drives the primary function of the heart: to act as a pump that delivers blood to the brain and vital organs. When electrical activity goes awry during a cardiac arrhythmia, the pump does not function, the brain does not receive oxygenated blood, and death ensues. Perturbations to NaV1.5 may alter the structure, and hence the function, of the ion channel and are associated downstream with a wide variety of cardiac conduction pathologies, such as arrhythmias. PMID:27586288

  7. The complex lightcurve of 1992 NA

    NASA Technical Reports Server (NTRS)

    Wisniewski, Wieslaw Z.; Harris, A. W.

    1994-01-01

    Amor asteroid 1992 NA was monitored during three nights at a large phase angle of -65 deg. The lightcurves obtained did not reveal a repeatable curve with two maxima and two minima. However, some features suggested a periodicity with three maxima and three minima. A satisfactory composite lightcurve of this form was obtained by means of an 'eyeball' fit and by Fourier analysis. Individual and composite lightcurves are presented. The observed colors are consistent with the C class.

  8. Hybrid thermoelastic properties of NaCl

    NASA Astrophysics Data System (ADS)

    Wentzcovitch, R. M.; Marcondes, M. L.; Shukla, G.

    2015-12-01

    Despite the importance of thermoelastic properties of minerals in geophysics, their measurements at high pressures and temperatures are limited. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy and to approximations used in calculations of vibrational effects, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a hybrid scheme to reconcile calculated and measured elastic coefficients and apply it to rock-salt-type NaCl, a challenging material to describe by ab initio and an important mineral in the context of oil/gas exploration. The approach is predictive within the temperature range of validity of the quasiharmonic approximation and results are used to generate velocities of NaCl at desirable geological conditions. [1] Marcondes, M. L. & Wentzcovitch, R.M. (2015). Hybrid ab-initio/experimental thermal equations of state: application to the NaCl pressure scale, J. Appl. Phys. 117:215902.

  9. TRP-Na(+)/Ca(2+) Exchanger Coupling.

    PubMed

    Harper, Alan G S; Sage, Stewart O

    2016-01-01

    Na(+)/Ca(2+) exchangers (NCXs) have traditionally been viewed principally as a means of Ca(2+) removal from non-excitable cells. However there has recently been increasing interest in the operation of NCXs in reverse mode acting as a means of eliciting Ca(2+) entry into these cells. Reverse mode exchange requires a significant change in the normal resting transmembrane ion gradients and membrane potential, which has been suggested to occur principally via the coupling of NCXs to localised Na(+) entry through non-selective cation channels such as canonical transient receptor potential (TRPC) channels. Here we review evidence for functional or physical coupling of NCXs to non-selective cation channels, and how this affects NCX activity in non-excitable cells. In particular we focus on the potential role of nanojunctions, where the close apposition of plasma and intracellular membranes may help create the conditions needed for the generation of localised rises in Na(+) concentration that would be required to trigger reverse mode exchange. PMID:27161225

  10. Thermochemistry of binary Na-NaH and ternary Na-O-H systems and the kinetics of reaction of hydrogen/water with liquid sodium - a review

    NASA Astrophysics Data System (ADS)

    Gnanasekaran, T.

    A review of the literature data on the binary Na-H and ternary Na-O-H systems has been carried out. Influence of dissolved oxygen on Sieverts' constant for hydrogen in sodium is analysed and an expression for the variation of Sieverts' constant with oxygen concentration is derived. Data on equilibrium hydrogen partial pressures over Na(l)-NaH(s) phase mixtures are assessed and an expression for variation of Gibbs energy of formation of NaH(s) with temperature is obtained. Analysis of the phase diagram and thermochemical information on the ternary Na-O-H system has been carried out. Kinetics of the reaction of water/steam and gaseous hydrogen with liquid sodium are also presented and the need to resolve the disagreement among the literature data is brought out.

  11. A computational study of Na behavior on graphene

    NASA Astrophysics Data System (ADS)

    Malyi, Oleksandr I.; Sopiha, Kostiantyn; Kulish, Vadym V.; Tan, Teck L.; Manzhos, Sergei; Persson, Clas

    2015-04-01

    We present the first ab initio and molecular dynamics study of Na adsorption and diffusion on ideal graphene that considers Na-Na interaction and dispersion forces. From density functional theory (DFT) calculations using the generalized gradient approximation (GGA), the binding energy (vs. the vacuum reference state) of -0.75 eV is higher than the cohesive energy of Na metal (ENa metal cohesive energy (EcohDFT - D = - 1.21 eV) when dispersion correction is included (DFT-D), with Eb = -1.14 eV. Both DFT and DFT-D predict that the increase of Na concentration on graphene results in formation of Na complexes. This is evidenced by smaller Bader charge on Na atoms of Na dimer, 0.55e (0.48e for DFT) compared to 0.86e (for both DFT and DFT-D) for the single atom adsorption as well as by the formation of a Nasbnd Na bond identified by analysis of the electron density. These results suggest that ideal graphene is not a promising anode material for Na-ion batteries. Analysis of diffusion pathways for a Na dimer shows that the dimer remains stable during the diffusion, and computed migration barriers are significantly lower for the dimer than that for the single atom diffusion. This indicates that Na-Na interaction should be taken into account during the analysis of Na transport on graphene. Finally, we show that the typical defects (vacancy and divacancy) induce significant strengthening of the Nasbnd C interaction. In particular, the largest change to the interaction is computed for vacancy-defected graphene, where the found lowest binding energy (vs. the metal reference state) is about 1.15 eV (1.21 eV for DFT) lower than that for ideal graphene.

  12. Plant Defensins NaD1 and NaD2 Induce Different Stress Response Pathways in Fungi.

    PubMed

    Dracatos, Peter M; Payne, Jennifer; Di Pietro, Antonio; Anderson, Marilyn A; Plummer, Kim M

    2016-01-01

    Nicotiana alata defensins 1 and 2 (NaD1 and NaD2) are plant defensins from the ornamental tobacco that have antifungal activity against a variety of fungal pathogens. Some plant defensins interact with fungal cell wall O-glycosylated proteins. Therefore, we investigated if this was the case for NaD1 and NaD2, by assessing the sensitivity of the three Aspergillus nidulans (An) O-mannosyltransferase (pmt) knockout (KO) mutants (An∆pmtA, An∆pmtB, and An∆pmtC). An∆pmtA was resistant to both defensins, while An∆pmtC was resistant to NaD2 only, suggesting NaD1 and NaD2 are unlikely to have a general interaction with O-linked side chains. Further evidence of this difference in the antifungal mechanism was provided by the dissimilarity of the NaD1 and NaD2 sensitivities of the Fusarium oxysporum f. sp. lycopersici (Fol) signalling knockout mutants from the cell wall integrity (CWI) and high osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathways. HOG pathway mutants were sensitive to both NaD1 and NaD2, while CWI pathway mutants only displayed sensitivity to NaD2. PMID:27598152

  13. NA1, NA1, NA1-trimethylinsulin--an insulin analogue with a quaternary amino group at the A1 terminus.

    PubMed

    Drewes, S E; Magojo, H E; Gliemann, J

    1981-06-01

    By utilizing the differing reactivity of the amino groups in aqueous organic solvents, des-GlyA1-NB1,N epsilon B29-(Msc)2-insulin was prepared. Its reaction with the phenyl ester of N,N,N-trimethylglycine in the presence of N-hydroxysuccinimide afforded the crystalline NA1,NA1,NA1-trimethylinsulin analogue. In the fat cell assay this analogue has an activity of 49% and, in the mouse convulsion assay, it is 70%. PMID:7024089

  14. The unoccupied electronic structure of Na/Cu(110)

    NASA Astrophysics Data System (ADS)

    Tang, D.; Su, C.; Heskett, D.

    1993-10-01

    Using the technique of inverse photoemission spectroscopy (IPES), we have measured the unoccupied electronic states of sodium on Cu(110) as a function of Na dose on the Cu(110) surface at room temperature. An Na-induced state appears for Na coverages above 0.08 ML for normal incidence, which we assign as the Na unoccupied 3p level. A second peak appears for coverages greater than 1 ML near the overlineY point. The adsorption of Na also causes shifts and attenuation of Cu(110) surface states. We compare our results with studies of related systems.

  15. Effect of Na+ on surface fractal dimension of compacted bentonite

    NASA Astrophysics Data System (ADS)

    Xiang, G. S.; Xu, Y. F.; Jiang, H.

    2015-05-01

    Compacted Tsukinuno bentonite was immersed into NaCl solutions of different concentrations in oedometers, and the surface fractal dimension of bentonite-saline association was measured by nitrogen adsorption isotherms. The application of the Frenkel-Halsey-Hill equation and the Neimark thermodynamic method to nitrogen adsorption isotherms indicated that the surface roughness was greater for the bentonite-saline association. The surface fractal dimension of bentonite increased in the NaCl solution with low Na+ concentration, but decreased at high Na+ concentration. This process was accompanied by the same tendency in specific surface area and microporosity with the presence of Na+ coating in the clay particles.

  16. Na+ channel function, regulation, structure, trafficking and sequestration

    PubMed Central

    Chen-Izu, Ye; Shaw, Robin M; Pitt, Geoffrey S; Yarov-Yarovoy, Vladimir; Sack, Jon T; Abriel, Hugues; Aldrich, Richard W; Belardinelli, Luiz; Cannell, Mark B; Catterall, William A; Chazin, Walter J; Chiamvimonvat, Nipavan; Deschenes, Isabelle; Grandi, Eleonora; Hund, Thomas J; Izu, Leighton T; Maier, Lars S; Maltsev, Victor A; Marionneau, Celine; Mohler, Peter J; Rajamani, Sridharan; Rasmusson, Randall L; Sobie, Eric A; Clancy, Colleen E; Bers, Donald M

    2015-01-01

    This paper is the second of a series of three reviews published in this issue resulting from the University of California Davis Cardiovascular Symposium 2014: Systems approach to understanding cardiac excitation–contraction coupling and arrhythmias: Na+ channel and Na+ transport. The goal of the symposium was to bring together experts in the field to discuss points of consensus and controversy on the topic of sodium in the heart. The present review focuses on Na+ channel function and regulation, Na+ channel structure and function, and Na+ channel trafficking, sequestration and complexing. PMID:25772290

  17. Zero-gravity growth of NaF-NaCl eutectics in the NASA Skylab program

    NASA Technical Reports Server (NTRS)

    Yue, A. S.; Allen, F. G.; Yu, J. G.

    1976-01-01

    Continuous and discontinuous NaF fibers, embedded in a NaCl matrix, were produced in space and on earth. The production of continuous fibers in a eutectic mixture is attributed to the absence of convection current in the liquid during solidification in space. Image transmission and optical transmittance measurements of transverse sections of the space-grown and earth-grown ingots were made with a light microscope and a spectrometer. It is shown that better optical properties were obtained from samples grown in space. This was attributed to a better alignment of NaF fibers along the ingot axis. A new concept is advanced to explain the phenomenon of transmittance versus far infrared wavelength of the directionally solidified NaCl-NaF eutectic in terms of the two-dimensional Bragg Scattering and the polarization effect of Rayleigh scattering. This concept can be applied to other eutectic systems as long as the index of refraction of the matrix over a range of wavelengths is known. Experimental data are in agreement with the theoretical prediction.

  18. Synthesis of Na-A and/or Na-X zeolite/porous carbon composites from carbonized rice husk

    SciTech Connect

    Katsuki, Hiroaki; Komarneni, Sridhar

    2009-07-15

    Na-A and/or Na-X zeolite/porous carbon composites were prepared under hydrothermal conditions by NaOH dissolution of silica first from carbonized rice husk followed by addition of NaAlO{sub 2} and in situ crystallization of zeolites i.e., using a two-step process. When a one-step process was used, both Na-A and Na-X zeolites crystallized on the surface of carbon. Na-A or Na-X zeolite crystals were prepared on the porous carbonized rice husk at 90 deg. C for 2-6 h by changing the SiO{sub 2}/Al{sub 2}O{sub 3}, H{sub 2}O/Na{sub 2}O and Na{sub 2}O/SiO{sub 2} molar ratios of precursors in the two-step process. The surface area and NH{sub 4}{sup +}-cation exchange capacity (CEC) of Na-A zeolite/porous carbon were found to be 171 m{sup 2}/g and 506 meq/100 g, respectively, while those of Na-X zeolite/porous carbon composites were 676 m{sup 2}/g and 317 meq/100 g, respectively. Na-A and Na-X zeolites are well-known microporous and hydrophilic materials while carbonized rice husk was found to be mesoporous (pores of {approx}3.9 nm) and hydrophobic. These hybrid microporous-mesoporous and hydrophilic-hydrophobic composites are expected to be useful for decontamination of metal cations as well as organic contaminants simultaneously. - Graphical Abstract: Novel Na-X zeolite/porous carbon composite.

  19. Controls on 22Na+ Influx in Corn Roots 1

    PubMed Central

    Jacoby, Benjamin; Hanson, John B.

    1985-01-01

    We have investigated the effects of hyperpolarization and depolarization, and the presence of K+ and/or Ca2+, on 22Na+ influx into corn (Zea mays L.) root segments. In freshly excised root tissue which is injured, Na+ influx is unaffected by hyperpolarization with fusicoccin, or depolarization with uncoupler (protonophore), or by addition of K+. However, added Ca2+ suppresses Na+ influx by 60%. In washed tissue which has recovered, Na+ influx is doubled over that of freshly excised tissue, and the influx is increased by fusicoccin and suppressed by uncoupler. This energy-linked component of Na+ influx is completely eliminated by low concentrations of K+, leaving the same level and kind of Na+ influx seen in freshly excised roots. The K+-sensitive energy linkage appears to be by the carrier for active K+ influx. Calcium is equally inhibitory to Na+ influx in washed as in fresh tissue. Other divalent cations are only slightly less effective. Net Na+ uptake was about 25% of 22Na+ influx, but proportionately the response to K+ and Ca2+ was about the same. The constancy of K+-insensitive Na+ influx under conditions known to hyperpolarize and depolarize suggests that if Na+ transport is by means of a voltage-sensitive channel, the rise or fall of channel resistance must be proportional to the rise or fall in potential difference. The alternative is a passive electroneutral exchange of 22Na+ for endogenous Na+. The data suggest that an inwardly directed Na+ current is largely offset by an efflux current, giving both a small net uptake and isotopic exchange. PMID:16664165

  20. Diffuse sorption modeling: apparent H/Na, or the same, Al/Na exchange on clays.

    PubMed

    Pivovarov, Sergey

    2009-08-15

    Clay minerals are specified by permanent negative surface charge. In solutions of sodium salts, the surface of clay is covered by exchangeable sodium ions. In an acidic field (pH<4-6), sodium ions are displaced from the surface. This apparent H/Na exchange is conditioned by dissolution of alumina, followed by Al/Na exchange. Two kinds of published experimental data were considered in order to follow Al/Na exchange: the first is direct measurement of exchangeable sodium and aluminum in clay, and the second is exchange sorption of trace metal. Because of the equivalency of ionic exchange, trace metal acts as a probe, indicating the sodium content in clay. These experimental data were successfully modeled with use of the Poisson-Boltzmann equation, with the assumption that all exchange cations are located in the diffuse layer. PMID:19464695

  1. Specific oxidation pattern of soluble starch with TEMPO-NaBr-NaClO system.

    PubMed

    Hao, Jie; Lu, Jiaojiao; Xu, Naiyu; Linhardt, Robert J; Zhang, Zhenqing

    2016-08-01

    Oxidized starch, one of the most important starch derivatives, has many different properties and applications. Currently, there are two ways to produce oxidized starch, through specific and nonspecific oxidation. Specific oxidation using the stable nitroxyl radical, 2,2,6,6-tetramethyl preparidinloxy (TEMPO), with NaBr and NaClO can produce oxidized starches with different properties under good quality control. In the current study, we examine the products of specifically oxidized starch. As the amount of oxidant and the temperature, two critical factors impacting the oxidation of starch were thoroughly investigated. Analysis of the molecular weight (MW), degree of oxidization (DO) and the detailed structures of corresponding products was accomplished using gel permeation chromatography with multi-angle laser light scattering (GPC-MALLS), infrared (IR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and quadrapole time-of-flight mass spectrometry (Q/TOF-MS). According to the analytical results, the oxidation patterns of starch treated with specific oxidant TEMPO-NaBr-NaClO were established. When high amounts of oxidant was applied, more glucose residues within starch were oxidized to glucuronic acids (higher DO) and substantial degradation to starch oligosaccharides was observed. By selecting a reaction temperature of 25°C a high DO could be obtained for a given amount of oxidant. The reducing end sugar residue within oxidized starch was itself oxidized and ring opened in all TEMPO-NaBr-NaClO reactions. Furthermore, extra oxidant generated additional novel structures in the reducing end residues of some products, particularly in low temperature reactions. PMID:27112871

  2. Photoionization of the alkali dimer cations Li+2, Na+2 and LiNa+

    NASA Astrophysics Data System (ADS)

    Dumitriu, Irina; Vanne, Yulian V.; Awasthi, Manohar; Saenz, Alejandro

    2007-05-01

    Photoionization cross sections for the three alkali dimer cations (Li+2, Na+2 and LiNa+) were calculated at the equilibrium internuclear distance for parallel, perpendicular and isotropic orientations of the molecular axis with respect to the field. A model-potential method was used for the description of the cores. The influence of the model-potential parameters on the photoionization spectra was investigated. Two different methods, a time-independent and a time-dependent one, were implemented and used for computing the cross sections.

  3. Na(+),K (+)-ATPase as a docking station: protein-protein complexes of the Na(+),K (+)-ATPase.

    PubMed

    Reinhard, Linda; Tidow, Henning; Clausen, Michael J; Nissen, Poul

    2013-01-01

    The Na(+),K(+)-ATPase, or sodium pump, is well known for its role in ion transport across the plasma membrane of animal cells. It carries out the transport of Na(+) ions out of the cell and of K(+) ions into the cell and thus maintains electrolyte and fluid balance. In addition to the fundamental ion-pumping function of the Na(+),K(+)-ATPase, recent work has suggested additional roles for Na(+),K(+)-ATPase in signal transduction and biomembrane structure. Several signaling pathways have been found to involve Na(+),K(+)-ATPase, which serves as a docking station for a fast-growing number of protein interaction partners. In this review, we focus on Na(+),K(+)-ATPase as a signal transducer, but also briefly discuss other Na(+),K(+)-ATPase protein-protein interactions, providing a comprehensive overview of the diverse signaling functions ascribed to this well-known enzyme. PMID:22695678

  4. Direct Reactions with MoNA-LISA

    NASA Astrophysics Data System (ADS)

    Kuchera, Anthony

    2016-03-01

    Nuclear reactions can be used to probe the structure of nuclei. Direct reactions, which take place on short time scales, are well-suited for experiments with beams of short-lived nuclei. One such reaction is nucleon knockout where a proton or neutron is removed from the incoming beam from the interaction with a target. Single nucleon knockout reactions have been used to study the single-particle nature of nuclear wave functions. A recent experiment at the National Superconducting Cyclotron Laboratory was performed to measure cross sections from single nucleon knockout reactions for several p-shell nuclei. Detection of the residual nucleus in coincidence with any gamma rays emitted from the target allowed cross sections to ground and excited states to be measured. Together with input from reaction theory, ab initio structure theories can be tested. Simultaneously the accuracy of knockout reaction models can be validated by detecting the knocked out neutron with the Modular Neutron Array and Large multi-Institutional Scintillator Array (MoNA-LISA). Preliminary results from this experiment will be shown. Knockout reactions can also be used to populate nuclei which are neutron unbound, thus emit neutrons nearly instantaneously. The structure of these nuclei, therefore, cannot be probed with gamma ray spectroscopy. However, with large neutron detectors like MoNA-LISA the properties of these short-lived nuclei are able to be measured. Recent results using MoNA-LISA to study the structure of neutron-rich nuclei will be presented. The author would like to acknowledge support from the NNSA and NSF.

  5. Status of the NA62 Experiment

    NASA Astrophysics Data System (ADS)

    Palladino, Vito

    2016-04-01

    The rare decays {{{K}}^ + } to {π ^ + }{{ν bar ν }} are excellent processes to make tests of new physics at the highest scale complementary to LHC thanks to their theoretically cleaness. The NA62 experiment at CERN SPS aims to collect of the order of 100 events in two years of data taking, keeping the background at the level of 10%. Part of the experimental apparatus has been commissioned during a technical run in 2012. The physics prospects and the status of the experiment will be reviewed after the commissioning run of 2014 and the data taking in 2015.

  6. The NA62 spectrometer acquisition system

    NASA Astrophysics Data System (ADS)

    Azorskiy, N.; Ceccucci, A.; Bendotti, J.; Danielsson, H.; Degrange, J.; Dixon, N.; Elsha, V.; Enik, T.; Glonti, L.; Gusakov, Y.; Kakurin, S.; Kekelidze, V.; Kislov, E.; Kolesnikov, A.; Koval, M.; Lichard, P.; Madigozhin, D.; Morant, J.; Movchan, S.; Perez Gomez, F.; Palladino, V.; Polenkevich, I.; Potrebenikov, Y.; Ruggiero, G.; Samsonov, V.; Shkarovskiy, S.; Sotnikov, A.

    2016-02-01

    The NA62 low mass spectrometer consists of 7000 straw tubes operating in vacuum. The front-end electronics is directly mounted on the detector and connected by a flexible PCB. The front-end board provides the amplification, shaping, discrimination and time measurements of the analogue signals from 16 channels. After digitisation the data is sent to a VME 9U read-out board. The data, once matched with the trigger, is sent to the next step and used by the trigger level 1 algorithm. The front-end and read-out systems of the detector will be presented along with the first results of the detector performances.

  7. Minimizing Load Effects on NA4 Gear Vibration Diagnostic Parameter

    NASA Technical Reports Server (NTRS)

    Dempsey, Paula J.; Zakrajsek, James J.

    2001-01-01

    NA4 is a vibration diagnostic parameter, developed by researchers at NASA Glenn Research Center, for health monitoring of gears in helicopter transmissions. The NA4 reacts to the onset of gear pitting damage and continues to react to the damage as it spreads. This research also indicates NA4 reacts similarly to load variations. The sensitivity of NA4 to load changes will substantially affect its performance on a helicopter gearbox that experiences continuously changing load throughout its flight regimes. The parameter NA4 has been used to monitor gear fatigue tests at constant load. At constant load, NA4 effectively detects the onset of pitting damage and tracks damage severity. Previous research also shows that NA4 reacts to changes in load applied to the gears in the same way it reacts to the onset of pitting damage. The method used to calculate NA4 was modified to minimize these load effects. The modified NA4 parameter was applied to four sets of experimental data. Results indicate the modified NA4 is no longer sensitive to load changes, but remains sensitive to pitting damage.

  8. Apical Na+ permeability of frog skin during serosal Cl- replacement.

    PubMed

    Leibowich, S; DeLong, J; Civan, M M

    1988-05-01

    Gluconate substitution for serosal Cl- reduces the transepithelial short-circuit current (Isc) and depolarizes short-circuited frog skins. These effects could result either from inhibition of basolateral K+ conductance, or from two actions to inhibit both apical Na+ permeability (PapNa) and basolateral pump activity. We have addressed this question by studying whole-and split-thickness frog skins. Intracellular Na+ concentration (CcNa) and PapNa have been monitored by measuring the current-voltage relationship for apical Na+ entry. This analysis was conducted by applying trains of voltage pulses, with pulse durations of 16 to 32 msec. Estimates of PapNa and CcNa were not detectably dependent on pulse duration over the range 16 to 80 msec. Serosal Cl- replacement uniformly depolarized short-circuited tissues. The depolarization was associated with inhibition of Isc across each split skin, but only occasionally across the whole-thickness preparations. This difference may reflect the better ionic exchange between the bulk medium and the extracellular fluid in contact with the basolateral membranes, following removal of the underlying dermis in the split-skin preparations. PapNa was either unchanged or increased, and CcNa either unchanged or reduced after the anionic replacement. These data are incompatible with the concept that serosal Cl- replacement inhibits PapNa and Na,K-pump activity. Gluconate substitution likely reduces cell volume, triggering inhibition of the basolateral K+ channels, consistent with the data and conclusions of S.A. Lewis, A.G. Butt, M.J. Bowler, J.P. Leader and A.D.C. Macknight (J. Membrane Biol. 83:119-137, 1985) for toad bladder. The resulting depolarization reduces the electrical force favoring apical Na+ entry. The volume-conductance coupling serves to conserve volume by reducing K+ solute loss. Its molecular basis remains to be identified. PMID:2458472

  9. Decomposition Kinetics of Titania Slag in Eutectic NaOH-NaNO3 System

    NASA Astrophysics Data System (ADS)

    Wang, Dong; Wang, Zhi; Qi, Tao; Wang, Lina; Xue, Tianyan

    2016-02-01

    The decomposition kinetics and mechanism of titania slag in eutectic NaOH-NaNO3 system were studied in the temperature range 623 K to 723 K (350 °C to 450 °C). Decomposed products were examined using X-ray diffraction, scanning electron microscopy, and energy dispersive X-ray spectroscopy. It has been identified that the main product is Na2TiO3 and the decomposition kinetics of titania slag followed a shrinking unreacted core model. It is proposed that the chemical reaction process was the rate determining step with apparent activation energy of 62.4 kJ/mol. NaNO3 was mainly acted as oxygen carrier and mass transport agent to lower the viscosity of the system. The purity of TiO2 obtained in the product was up to 99.3 pct. A flow diagram to produce TiO2 and to recycle the media was proposed.

  10. Theoretical calculation of low-lying states of NaAr and NaXe

    NASA Technical Reports Server (NTRS)

    Laskowski, B. C.; Langhoff, S. R.; Stallcop, J. R.

    1981-01-01

    Potential curves as well as dipole moments and linking transition moments are calculated for the ground X 2 Sigma + and low lying excited A 2 Pi, B 2 Sigma +, C 2 Sigma +, (4) 2 Sigma +, (2) 2 Pi and (1) 2 Delta states of NaAr and NaXe. Calculations are performed using a self-consistent field plus configuration-interaction procedure with the core electrons replaced by an ab initio effective core potential. The potential curves obtained are found to be considerably less repulsive than the semiempirical curves of Pascale and Vandeplanque (1974) and to agree well with existing experimental data, although the binding energies of those states having potential minima due to van der Waals interactions are underestimated. Emission bands are also calculated for the X 2 Sigma + - C 2 Sigma + excimer transitions of NaAr and NaXe using the calculated transition moments and potential curves, and shown to agree well with experiment on the short-wavelength side of the maximum.

  11. Interaction of NaCl/g/ and HCl/g/ with condensed Na2SO4. [in hot corrosion processes

    NASA Technical Reports Server (NTRS)

    Stearns, C. A.; Kohl, F. J.; Fryburg, G. C.; Miller, R. A.

    1977-01-01

    Na2SO4(l)-NaCl(g) interactions were studied at a total pressure of one atmosphere of air or oxygen for various temperatures of Na2SO4(l) and for various partial pressures of NaCl(g) and H2O(g). Mass spectrometric sampling techniques were used to identify and monitor gas phase species. Continuous recording thermomicrogravimetric measurements were conducted to determine condensed phase weight change rates. Experimental measurements were supplemented with thermodynamic calculations. Numerous experiments were performed at sample temperatures of 900 and 1000 C with 300 ppm NaCl(g). In these experiments, the reproducibility of the Na2SO4 vaporization weight loss rate and initial weight gain upon addition of NaCl(g) were found to be satisfactory. It was found that the addition of NaCl(g) to air flowing over Na2SO4(l) at 900 and 1000 C enhances the rate of weight loss of the Na2SO4(l). This enhancement increases when H2O(g) is also added to the air flow.

  12. Regulation of persistent Na current by interactions between beta subunits of voltage-gated Na channels.

    PubMed

    Aman, Teresa K; Grieco-Calub, Tina M; Chen, Chunling; Rusconi, Raffaella; Slat, Emily A; Isom, Lori L; Raman, Indira M

    2009-02-18

    The beta subunits of voltage-gated Na channels (Scnxb) regulate the gating of pore-forming alpha subunits, as well as their trafficking and localization. In heterologous expression systems, beta1, beta2, and beta3 subunits influence inactivation and persistent current in different ways. To test how the beta4 protein regulates Na channel gating, we transfected beta4 into HEK (human embryonic kidney) cells stably expressing Na(V)1.1. Unlike a free peptide with a sequence from the beta4 cytoplasmic domain, the full-length beta4 protein did not block open channels. Instead, beta4 expression favored open states by shifting activation curves negative, decreasing the slope of the inactivation curve, and increasing the percentage of noninactivating current. Consequently, persistent current tripled in amplitude. Expression of beta1 or chimeric subunits including the beta1 extracellular domain, however, favored inactivation. Coexpressing Na(V)1.1 and beta4 with beta1 produced tiny persistent currents, indicating that beta1 overcomes the effects of beta4 in heterotrimeric channels. In contrast, beta1(C121W), which contains an extracellular epilepsy-associated mutation, did not counteract the destabilization of inactivation by beta4 and also required unusually large depolarizations for channel opening. In cultured hippocampal neurons transfected with beta4, persistent current was slightly but significantly increased. Moreover, in beta4-expressing neurons from Scn1b and Scn1b/Scn2b null mice, entry into inactivated states was slowed. These data suggest that beta1 and beta4 have antagonistic roles, the former favoring inactivation, and the latter favoring activation. Because increased Na channel availability may facilitate action potential firing, these results suggest a mechanism for seizure susceptibility of both mice and humans with disrupted beta1 subunits. PMID:19228957

  13. Regulation of persistent Na current by interactions between β subunits of voltage-gated Na channels

    PubMed Central

    Aman, Teresa K.; Grieco-Calub, Tina M.; Chen, Chunling; Rusconi, Raffaella; Slat, Emily A.; Isom, Lori L.; Raman, Indira M.

    2009-01-01

    The β subunits of voltage-gated Na channels (Scnxb) regulate the gating of pore-forming α subunits, as well as their trafficking and localization. In heterologous expression systems, β1, β2, and β3 subunits influence inactivation and persistent current in different ways. To test how the β4 protein regulates Na channel gating, we transfected β4 into HEK cells stably expressing NaV1.1. Unlike a free peptide with a sequence from the β4 cytoplasmic domain, the full-length β4 protein did not block open channels. Instead, β4 expression favored open states by shifting activation curves negative, decreasing the slope of the inactivation curve, and increasing the percentage of non-inactivating current. Consequently, persistent current tripled in amplitude. Expression of β1 or chimeric subunits including the β1 extracellular domain, however, favored inactivation. Co-expressing NaV1.1 and β4 with β1 produced tiny persistent currents, indicating that β1 overcomes the effects of β4 in heterotrimeric channels. In contrast, β1C121W, which contains an extracellular epilepsy-associated mutation, did not counteract the destabilization of inactivation by β4, and also required unusually large depolarizations for channel opening. In cultured hippocampal neurons transfected with β4, persistent current was slightly but significantly increased. Moreover, in β4-expressing neurons from Scn1b and Scn1b/Scn2b null mice, entry into inactivated states was slowed. These data suggest that β1 and β4 have antagonistic roles, the former favoring inactivation and the latter favoring activation. Because increased Na channel availability may facilitate action potential firing, these results suggest a mechanism for seizure susceptibility of both mice and humans with disrupted β1 subunits. PMID:19228957

  14. Pyrophosphate-Fueled Na+ and H+ Transport in Prokaryotes

    PubMed Central

    Malinen, Anssi M.; Luoto, Heidi H.

    2013-01-01

    SUMMARY In its early history, life appeared to depend on pyrophosphate rather than ATP as the source of energy. Ancient membrane pyrophosphatases that couple pyrophosphate hydrolysis to active H+ transport across biological membranes (H+-pyrophosphatases) have long been known in prokaryotes, plants, and protists. Recent studies have identified two evolutionarily related and widespread prokaryotic relics that can pump Na+ (Na+-pyrophosphatase) or both Na+ and H+ (Na+,H+-pyrophosphatase). Both these transporters require Na+ for pyrophosphate hydrolysis and are further activated by K+. The determination of the three-dimensional structures of H+- and Na+-pyrophosphatases has been another recent breakthrough in the studies of these cation pumps. Structural and functional studies have highlighted the major determinants of the cation specificities of membrane pyrophosphatases and their potential use in constructing transgenic stress-resistant organisms. PMID:23699258

  15. Electrical Resistivity of Liquid Alkali Na-based Binary Alloys

    NASA Astrophysics Data System (ADS)

    Vora, Aditya M.

    2007-11-01

    The study of the electrical resistivity rL of alkali Na-based binary alloys Na1-xLix, Na1-xKx, Na1-xRbx and Na1-xCsx have been made by well-recognized model potential of Gajjar et al. The most recent exchange and correlation functions due to Farid et al (F) and Sarkar et al (S) are used for the first time in the study of electrical resistivity of liquid binary mixtures and found suitable for such study. The results, due to the inclusion of Sarkar et al's local field correction function, are found superior to those obtained due to Farid et al's local field correction function. Electrical resistivity of Na-based binary alloys compare well with the experimental data available in the literature.

  16. Simulation of Na D emission near Europa during eclipse

    USGS Publications Warehouse

    Cassidy, T.A.; Johnson, R.E.; Geissler, P.E.; Leblanc, F.

    2008-01-01

    The Cassini imaging science subsystem observed Europa in eclipse during Cassini's Jupiter flyby. The disk-resolved observations revealed a spatially nonuniform emission in the wavelength range of 200-1050 nm (clear filters). By building on observations and simulations of Europa's Na atmosphere and torus we find that electron-excited Na in Europa's tenuous atmosphere can account for the observed emission if the Na is ejected preferentially from Europa's dark terrain. Copyright 2008 by the American Geophysical Union.

  17. Neutron diffraction studies of the Na-ion battery electrode materials NaCoCr2(PO4)3, NaNiCr2(PO4)3, and Na2Ni2Cr(PO4)3

    NASA Astrophysics Data System (ADS)

    Yahia, H. Ben; Essehli, R.; Avdeev, M.; Park, J.-B.; Sun, Y.-K.; Al-Maadeed, M. A.; Belharouak, I.

    2016-06-01

    The new compounds NaCoCr2(PO4)3, NaNiCr2(PO4)3, and Na2Ni2Cr(PO4)3 were synthesized by sol-gel method and their crystal structures were determined by using neutron powder diffraction data. These compounds were characterized by galvanometric cycling and cyclic voltammetry. NaCoCr2(PO4)3, NaNiCr2(PO4)3, and Na2Ni2Cr(PO4)3 crystallize with a stuffed α-CrPO4-type structure. The structure consists of a 3D-framework made of octahedra and tetrahedra that are sharing corners and/or edges generating channels along [100] and [010], in which the sodium atoms are located. Of significance, in the structures of NaNiCr2(PO4)3, and Na2Ni2Cr(PO4)3 a statistical disorder Ni2+/Cr3+ was observed on both the 8g and 4a atomic positions, whereas in NaCoCr2(PO4)3 the statistical disorder Co2+/Cr3+ was only observed on the 8g atomic position. When tested as negative electrode materials, NaCoCr2(PO4)3, NaNiCr2(PO4)3, and Na2Ni2Cr(PO4)3 delivered specific capacities of 352, 385, and 368 mA h g-1, respectively, which attests to the electrochemical activity of sodium in these compounds.

  18. Magnesium correction to the NaKCa chemical geothermometer

    USGS Publications Warehouse

    Fournier, R.O.; Potter, R.W., II

    1979-01-01

    Equations and graphs have been devised to correct for the adverse effects of magnesium upon the Na-K-Ca chemical geothermometer. Either the equations or graphs can be used to determine appropriate temperature corrections for given waters with calculated NaKCa temperatures > 70??C and R 50 are probably derived from relatively cool aquifers with temperatures approximately equal to the measured spring temperature, irrespective of much higher calculated Na-K-Ca temperatures. ?? 1979.

  19. Na+ Interactions with the Neutral Amino Acid Transporter ASCT1*

    PubMed Central

    Scopelliti, Amanda J.; Heinzelmann, Germano; Kuyucak, Serdar; Ryan, Renae M.; Vandenberg, Robert J.

    2014-01-01

    The alanine, serine, cysteine transporters (ASCTs) belong to the solute carrier family 1A (SLC1A), which also includes the excitatory amino acid transporters (EAATs) and the prokaryotic aspartate transporter GltPh. Acidic amino acid transport by the EAATs is coupled to the co-transport of three Na+ ions and one proton, and the counter-transport of one K+ ion. In contrast, neutral amino acid exchange by the ASCTs does not require protons or the counter-transport of K+ ions and the number of Na+ ions required is not well established. One property common to SLC1A family members is a substrate-activated anion conductance. We have investigated the number and location of Na+ ions required by ASCT1 by mutating residues in ASCT1 that correspond to residues in the EAATs and GltPh that are involved in Na+ binding. Mutations to all three proposed Na+ sites influence the binding of substrate and/or Na+, or the rate of substrate exchange. A G422S mutation near the Na2 site reduced Na+ affinity, without affecting the rate of exchange. D467T and D467A mutations in the Na1 site reduce Na+ and substrate affinity and also the rate of substrate exchange. T124A and D380A mutations in the Na3 site selectively reduce the affinity for Na+ and the rate of substrate exchange without affecting substrate affinity. In many of the mutants that reduce the rate of substrate transport the amplitudes of the substrate-activated anion conductances are not substantially affected indicating altered ion dependence for channel activation compared with substrate exchange. PMID:24808181

  20. Regulation of hamster sperm hyperactivation by extracellular Na.

    PubMed

    Takei, Gen L; Fujinoki, Masakatsu

    2016-06-01

    Mammalian sperm motility has to be hyperactivated to be fertilization-competent. Hyperactivation is regulated by extracellular environment. Osmolality of mammalian semen is higher than that in female reproductive tract; however, the effect of them on hyperactivation has not been investigated. So we investigated the effect of osmotic environment on hyperactivation using hamster spermatozoa at first. Increase in the osmolality of the media (∼370 mOsm) by increasing the concentration of NaCl (∼150 mmol/L) caused the delay of the expression of hyperactivation. When NaCl concentration varied in the same range (75-150 mmol/L) whereas the osmolality was fixed at 370 mOsm by adding mannitol, the delay of hyperactivation occurred dependent on NaCl concentration. Increase in NaCl concentration also caused suppression of curvilinear velocity, bend angle, and sliding velocity of the flagellum at the onset of incubation, suggesting that NaCl concentration affect both activation and hyperactivation in hamster spermatozoa. Hamster sperm intracellular Ca(2+) concentration decreased as extracellular NaCl concentration increased, whereas membrane potential and intracellular pH were unaffected by extracellular NaCl concentration. SN-6 and SEA0400, inhibitors of Na(+)-Ca(2+) exchanger (NCX), increased intracellular Ca(2+) and accelerated hyperactivation in the presence of 150 mmol/L NaCl. Tyrosine phosphorylation on fibrous sheath proteins was unaffected by extracellular NaCl concentration. These results suggest that extracellular Na(+) suppresses hamster sperm hyperactivation by reducing intracellular Ca(2+) via an action of NCX in a tyrosine phosphorylation-independent manner. It seems that the removal of suppression by extracellular Na(+) leads to the expression of hyperactivated motility. PMID:26952096

  1. Advanced Intermediate-Temperature Na-S Battery

    SciTech Connect

    Lu, Xiaochuan; Kirby, Brent W.; Xu, Wu; Li, Guosheng; Kim, Jin Yong; Lemmon, John P.; Sprenkle, Vincent L.; Yang, Zhenguo

    2012-11-12

    In this study, we reported an intermediate-temperature (~150°C) sodium-sulfur (Na-S) battery. With a reduced operating temperature, this novel battery can potentially reduce the cost and safety issues associated with the conventional high-temperature (300~350°C) Na-S battery. A dense β"-Al2O3 solid membrane and tetraglyme were utilized as the electrolyte separator and catholyte solvent in this battery. Solubility tests indicated that cathode mixture of Na2S4 and S exhibited extremely high solubility in tetraglyme (e.g., > 4.1 M for Na2S4 + 4 S). CV scans of Na2S4 in tetraglyme revealed two pairs of redox couples with peaks at around 2.22 and 1.75 V, corresponding to the redox reactions of polysulfide species. The discharge/charge profiles of the Na-S battery showed a slope region and a plateau, indicating multiple steps and cell reactions. In-situ Raman measurements during battery operation suggested that polysulfide species were formed in the sequence of Na2S5 + S → Na2S5 + Na2S4Na2S4 + Na2S2 during discharge and in a reverse order during charge. This battery showed dramatic improvement in rate capacity and cycling stability over room-temperature Na-S batteries, which makes it attractive for renewable energy integration and other grid related applications.

  2. Integrated Control of Na Transport along the Nephron

    PubMed Central

    Schnermann, Jürgen

    2015-01-01

    The kidney filters vast quantities of Na at the glomerulus but excretes a very small fraction of this Na in the final urine. Although almost every nephron segment participates in the reabsorption of Na in the normal kidney, the proximal segments (from the glomerulus to the macula densa) and the distal segments (past the macula densa) play different roles. The proximal tubule and the thick ascending limb of the loop of Henle interact with the filtration apparatus to deliver Na to the distal nephron at a rather constant rate. This involves regulation of both filtration and reabsorption through the processes of glomerulotubular balance and tubuloglomerular feedback. The more distal segments, including the distal convoluted tubule (DCT), connecting tubule, and collecting duct, regulate Na reabsorption to match the excretion with dietary intake. The relative amounts of Na reabsorbed in the DCT, which mainly reabsorbs NaCl, and by more downstream segments that exchange Na for K are variable, allowing the simultaneous regulation of both Na and K excretion. PMID:25098598

  3. Study of OSL in NaF: Ca,Cu

    NASA Astrophysics Data System (ADS)

    More, Y. K.; Wankhede, S. P.; Moharil, S. V.

    2013-06-01

    Sodium Fluoride containing Cu+ ions was prepared by R.A.P. followed by melt-quenching technique. Results on photo, thermo and optically stimulated luminescence in NaF:Ca,Cu are reported. OSL sensitivity of NaF:Ca,Cu is approximately 2 times than that of standard phosphor LMP. The rate of OSL depletion for 90% decay for NaF:Ca,Cu is 0.3 times as that of OSL phosphor LMP. NaF:Ca,Cu thus deserves much more attention than it has received up till now.

  4. Influenza virus neuraminidase (NA): a target for antivirals and vaccines.

    PubMed

    Jagadesh, Anitha; Salam, Abdul Ajees Abdul; Mudgal, Piya Paul; Arunkumar, Govindakarnavar

    2016-08-01

    Influenza, the most common infectious disease, poses a great threat to human health because of its highly contagious nature and fast transmissibility, often leading to high morbidity and mortality. Effective vaccination strategies may aid in the prevention and control of recurring epidemics and pandemics associated with this infectious disease. However, antigenic shifts and drifts are major concerns with influenza virus, requiring effective global monitoring and updating of vaccines. Current vaccines are standardized primarily based on the amount of hemagglutinin, a major surface antigen, which chiefly constitutes these preparations along with the varying amounts of neuraminidase (NA). Anti-influenza drugs targeting the active site of NA have been in use for more than a decade now. However, NA has not been approved as an effective antigenic component of the influenza vaccine because of standardization issues. Although some studies have suggested that NA antibodies are able to reduce the severity of the disease and induce a long-term and cross-protective immunity, a few major scientific issues need to be addressed prior to launching NA-based vaccines. Interestingly, an increasing number of studies have shown NA to be a promising target for future influenza vaccines. This review is an attempt to consolidate studies that reflect the strength of NA as a suitable vaccine target. The studies discussed in this article highlight NA as a potential influenza vaccine candidate and support taking the process of developing NA vaccines to the next stage. PMID:27255748

  5. Transcriptional regulators of Na,K-ATPase subunits

    PubMed Central

    Li, Zhiqin; Langhans, Sigrid A.

    2015-01-01

    The Na,K-ATPase classically serves as an ion pump creating an electrochemical gradient across the plasma membrane that is essential for transepithelial transport, nutrient uptake and membrane potential. In addition, Na,K-ATPase also functions as a receptor, a signal transducer and a cell adhesion molecule. With such diverse roles, it is understandable that the Na,K-ATPase subunits, the catalytic α-subunit, the β-subunit and the FXYD proteins, are controlled extensively during development and to accommodate physiological needs. The spatial and temporal expression of Na,K-ATPase is partially regulated at the transcriptional level. Numerous transcription factors, hormones, growth factors, lipids, and extracellular stimuli modulate the transcription of the Na,K-ATPase subunits. Moreover, epigenetic mechanisms also contribute to the regulation of Na,K-ATPase expression. With the ever growing knowledge about diseases associated with the malfunction of Na,K-ATPase, this review aims at summarizing the best-characterized transcription regulators that modulate Na,K-ATPase subunit levels. As abnormal expression of Na,K-ATPase subunits has been observed in many carcinoma, we will also discuss transcription factors that are associated with epithelial-mesenchymal transition, a crucial step in the progression of many tumors to malignant disease. PMID:26579519

  6. Kaolin-based geopolymers with various NaOH concentrations

    NASA Astrophysics Data System (ADS)

    Heah, C. Y.; Kamarudin, H.; Mustafa Al Bakri, A. M.; Bnhussain, M.; Luqman, M.; Khairul Nizar, I.; Ruzaidi, C. M.; Liew, Y. M.

    2013-03-01

    Kaolin geopolymers were produced by the alkali-activation of kaolin with an activator solution (a mixture of NaOH and sodium silicate solutions). The NaOH solution was prepared at a concentration of 6-14 mol/L and was mixed with the sodium silicate solution at a Na2SiO3/NaOH mass ratio of 0.24 to prepare an activator solution. The kaolin-to-activator solution mass ratio used was 0.80. This paper aimed to analyze the effect of NaOH concentration on the compressive strength of kaolin geopolymers at 80°C for 1, 2, and 3 d. Kaolin geopolymers were stable in water, and strength results showed that the kaolin binder had adequate compressive strength with 12 mol/L of NaOH concentration. When the NaOH concentration increased, the SiO2/Na2O decreased. The increased Na2O content enhanced the dissolution of kaolin as shown in X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) analyses. However, excess in this content was not beneficial for the strength development of kaolin geopolymers. In addition, there was the formation of more geopolymeric gel in 12 mol/L samples. The XRD pattern of the samples showed a higher amorphous content and a more geopolymer bonding existed as proved by FTIR analysis.

  7. The Physiological Relevance of Na+-Coupled K+-Transport.

    PubMed

    Maathuis, FJM.; Verlin, D.; Smith, F. A.; Sanders, D.; Fernandez, J. A.; Walker, N. A.

    1996-12-01

    Plant roots utilize at least two distinct pathways with high and low affinities to accumulate K+. The system for high-affinity K+ uptake, which takes place against the electrochemical K+ gradient, requires direct energization. Energization of K+ uptake via Na+ coupling has been observed in algae and was recently proposed as a mechanism for K+ uptake in wheat (Triticum aestivum L.). To investigate whether Na+ coupling has general physiological relevance in energizing K+ transport, we screened a number of species, including Arabidopsis thaliana L. Heynh. ecotype Columbia, wheat, and barley (Hordeum vulgare L.), for the presence of Na+-coupled K+ uptake. Rb+-flux analysis and electrophysiological K+-transport assays were performed in the presence and absence of Na+ and provided evidence for a coupling between K+ and Na+ transport in several aquatic species. However, all investigated terrestrial species were able to sustain growth and K+ uptake in the absence of Na+. Furthermore, the addition of Na+ was either without effect or inhibited K+ absorption. The latter characteristic was independent of growth conditions with respect to Na+ status and pH. Our results suggest that in terrestrial species Na+-coupled K+ transport has no or limited physiological relevance, whereas in certain aquatic angiosperms and algae this type of secondary transport energization plays a significant role. PMID:12226467

  8. NA Nonlinear Equation-of-state Inversion

    NASA Astrophysics Data System (ADS)

    Jackson, I.; Kennett, B. L.

    2008-12-01

    A fully non-linear inversion scheme is introduced for the determination of the parameters controlling the equation-of-state and elasticity of mineral phases using the thermodynamically consistent finite-strain formulation introduced by Stixrude & Lithgow-Bertelloni (2005). This inversion exploits a directed search in an eight-dimensional parameter space using the Neighbourhood Algorithm (NA) of Sambridge (1999) to search for the minimum of an objective function representing the misfit to multiple data sets that constrain different aspects of the mineral behaviour. No derivatives are employed and the progress towards the minimum builds on the accumulated information on the character of the parameter space acquired as the inversion progresses. When only a limited range of experimental information is available there is a strong possibility of multiple minima in the objective function, which can pose problems for conventional iterative least-squares or other gradient methods. The addition of many different styles of data tends to produce a better defined minimum. The influence of different data types can be readily assessed by allowing differential weighting. The new procedure is illustrated by application to MgO, for which extensive experimental data are available. These include the variation of relative volume V with temperature T and pressure P from both static and shock-compression experiments, acoustic measurements of compressional and shear (and hence bulk) moduli, and calorimetric determinations of entropy as a function of temperature at atmospheric pressure. Preliminary NA modeling highlighted tensions between marginally incompatible subsets of data. We therefore excluded one-atmosphere V(T) data for T ≥ 1800 K for which the quasi-harmonic approximation is inadequate (Wu et al., 2008) along with elastic moduli derived from Brillouin spectroscopy under conditions (P ≥ 14 GPa) where significant departures from hydrostatic conditions are expected. With these

  9. Na/sup +/-H/sup +/ exchange and Na/sup +/-dependent transport systems in streptozotocin diabetic rat kidneys

    SciTech Connect

    El-Seifi, S.; Freiberg, J.M.; Kinsella, F.J.; Cheng, L.; Sacktor, B.

    1987-01-01

    The streptozotocin-induced diabetic rat was used to test the hypothesis that Na/sup +/-H/sup +/ exchange activity in the proximal tubule luminal membrane would be increased in association with renal hypertrophy, altered glomerular hemodynamics, enhanced filtered load and tubular reabsorption of /sup 22/Na/sup +/, and stimulated /sup 22/Na= pump activity in the basolateral membrane, previously reported characteristics of this experimental animal model. Amiloride-sensitive H/sup +/ gradient-dependent Na/sup +/ uptake and Na/sup +/ gradient-dependent H/sup +/ flux were increased in brush-border membrane vesicles from the streptozotocin-treated animals. Na/sup +/ gradient-dependent uptakes of phosphate, D-glucose, L-proline, and myoinositol were decreased in the drug-induced diabetic animals. These membrane transport alterations were not found when the streptozotocin-diabetic animals were treated with insulin.

  10. Scintillation efficiency measurement of Na recoils in NaI(Tl) below the DAMA/LIBRA energy threshold

    NASA Astrophysics Data System (ADS)

    Xu, Jingke; Shields, Emily; Calaprice, Frank; Westerdale, Shawn; Froborg, Francis; Suerfu, Burkhant; Alexander, Thomas; Aprahamian, Ani; Back, Henning O.; Casarella, Clark; Fang, Xiao; Gupta, Yogesh K.; Ianni, Aldo; Lamere, Edward; Lippincott, W. Hugh; Liu, Qian; Lyons, Stephanie; Siegl, Kevin; Smith, Mallory; Tan, Wanpeng; Kolk, Bryant Vande

    2015-07-01

    The dark matter interpretation of the DAMA modulation signal depends on the NaI(Tl) scintillation efficiency of nuclear recoils. Previous measurements for Na recoils have large discrepancies, especially in the DAMA/LIBRA modulation energy region. We report a quenching effect measurement of Na recoils in NaI(Tl) from 3 to 52 keVnr, covering the whole DAMA/LIBRA energy region for dark matter-Na scattering interpretations. By using a low-energy, pulsed neutron beam, a double time-of-flight technique, and pulse-shape discrimination methods, we obtained the most accurate measurement of this kind for NaI(Tl) to date. The results differ significantly from the DAMA reported values at low energies but fall between the other previous measurements. We present the implications of the new quenching results for the dark matter interpretation of the DAMA modulation signal.