Sample records for cellular rna decay

  1. Identification and molecular characterization of cellular factors required for glucocorticoid receptor-mediated mRNA decay (United States)

    Park, Ok Hyun; Park, Joori; Yu, Mira; An, Hyoung-Tae; Ko, Jesang; Kim, Yoon Ki


    Glucocorticoid (GC) receptor (GR) has been shown recently to bind a subset of mRNAs and elicit rapid mRNA degradation. However, the molecular details of GR-mediated mRNA decay (GMD) remain unclear. Here, we demonstrate that GMD triggers rapid degradation of target mRNAs in a translation-independent and exon junction complex-independent manner, confirming that GMD is mechanistically distinct from nonsense-mediated mRNA decay (NMD). Efficient GMD requires PNRC2 (proline-rich nuclear receptor coregulatory protein 2) binding, helicase ability, and ATM-mediated phosphorylation of UPF1 (upstream frameshift 1). We also identify two GMD-specific factors: an RNA-binding protein, YBX1 (Y-box-binding protein 1), and an endoribonuclease, HRSP12 (heat-responsive protein 12). In particular, using HRSP12 variants, which are known to disrupt trimerization of HRSP12, we show that HRSP12 plays an essential role in the formation of a functionally active GMD complex. Moreover, we determine the hierarchical recruitment of GMD factors to target mRNAs. Finally, our genome-wide analysis shows that GMD targets a variety of transcripts, implicating roles in a wide range of cellular processes, including immune responses.

  2. Deep sequencing reveals direct targets of gammaherpesvirus-induced mRNA decay and suggests that multiple mechanisms govern cellular transcript escape.

    Directory of Open Access Journals (Sweden)

    Karen Clyde

    Full Text Available One characteristic of lytic infection with gammaherpesviruses, including Kaposi's sarcoma-associated herpesvirus (KSHV, Epstein-Barr virus (EBV and murine herpesvirus 68 (MHV68, is the dramatic suppression of cellular gene expression in a process known as host shutoff. The alkaline exonuclease proteins (KSHV SOX, MHV-68 muSOX and EBV BGLF5 have been shown to induce shutoff by destabilizing cellular mRNAs. Here we extend previous analyses of cellular mRNA abundance during lytic infection to characterize the effects of SOX and muSOX, in the absence of other viral genes, utilizing deep sequencing technology (RNA-seq. Consistent with previous observations during lytic infection, the majority of transcripts are downregulated in cells expressing either SOX or muSOX, with muSOX acting as a more potent shutoff factor than SOX. Moreover, most cellular messages fall into the same expression class in both SOX- and muSOX-expressing cells, indicating that both factors target similar pools of mRNAs. More abundant mRNAs are more efficiently downregulated, suggesting a concentration effect in transcript targeting. However, even among highly expressed genes there are mRNAs that escape host shutoff. Further characterization of select escapees reveals multiple mechanisms by which cellular genes can evade downregulation. While some mRNAs are directly refractory to SOX, the steady state levels of others remain unchanged, presumably as a consequence of downstream effects on mRNA biogenesis. Collectively, these studies lay the framework for dissecting the mechanisms underlying the susceptibility of mRNA to destruction during lytic gammaherpesvirus infection.

  3. RNA decay by messenger RNA interferases

    DEFF Research Database (Denmark)

    Christensen-Dalsgaard, Mikkel; Overgaard, Martin; Winther, Kristoffer Skovbo


    Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mRNA...... cleaving enzymes such as RelE of Escherichia coli and the corresponding antitoxin RelB. In particular, we describe a set of plasmid vectors useful for the detailed analysis of cleavage sites in model mRNAs....

  4. Diverse Strategies Used by Picornaviruses to Escape Host RNA Decay Pathways

    Directory of Open Access Journals (Sweden)

    Wendy Ullmer


    Full Text Available To successfully replicate, viruses protect their genomic material from degradation by the host cell. RNA viruses must contend with numerous destabilizing host cell processes including mRNA decay pathways and viral RNA (vRNA degradation resulting from the antiviral response. Members of the Picornaviridae family of small RNA viruses have evolved numerous diverse strategies to evade RNA decay, including incorporation of stabilizing elements into vRNA and re-purposing host stability factors. Viral proteins are deployed to disrupt and inhibit components of the decay machinery and to redirect decay machinery to the advantage of the virus. This review summarizes documented interactions of picornaviruses with cellular RNA decay pathways and processes.

  5. Importance and key events of prokaryotic RNA decay: the ultimate fate of an RNA molecule. (United States)

    Silva, Inês Jesus; Saramago, Margarida; Dressaire, Clémentine; Domingues, Susana; Viegas, Sandra Cristina; Arraiano, Cecília Maria


    RNAs are important effectors in the process of gene expression. In bacteria, constant adaptation to environmental demands is accompanied by a continual adjustment of transcripts' levels. The cellular concentration of a given RNA is the result of the balance between its synthesis and degradation. RNA degradation is a complex process encompassing multiple pathways. Ribonucleases (RNases) are the enzymes that directly process and degrade the transcripts, regulating their amounts. They are also important in quality control of RNAs by detecting and destroying defective molecules. The rate at which RNA decay occurs depends on the availability of ribonucleases and their specificities according to the sequence and/or the structural elements of the RNA molecule. Ribosome loading and the 5'-phosphorylation status can also modulate the stability of transcripts. The wide diversity of RNases present in different microorganisms is another factor that conditions the pathways and mechanisms of RNA degradation. RNases are themselves carefully regulated by distinct mechanisms. Several other factors modulate RNA degradation, namely polyadenylation, which plays a multifunctional role in RNA metabolism. Additionally, small non-coding RNAs are crucial regulators of gene expression, and can directly modulate the stability of their mRNA targets. In many cases this regulation is dependent on Hfq, an RNA binding protein which can act in concert with polyadenylation enzymes and is often necessary for the activity of sRNAs. All of the above-mentioned aspects are discussed in the present review, which also highlights the principal differences between the RNA degradation pathways for the two main Gram-negative and Gram-positive bacterial models.

  6. Attacked from All Sides: RNA Decay in Antiviral Defense

    Directory of Open Access Journals (Sweden)

    Jerome M. Molleston


    Full Text Available The innate immune system has evolved a number of sensors that recognize viral RNA (vRNA to restrict infection, yet the full spectrum of host-encoded RNA binding proteins that target these foreign RNAs is still unknown. The RNA decay machinery, which uses exonucleases to degrade aberrant RNAs largely from the 5′ or 3′ end, is increasingly recognized as playing an important role in antiviral defense. The 5′ degradation pathway can directly target viral messenger RNA (mRNA for degradation, as well as indirectly attenuate replication by limiting specific pools of endogenous RNAs. The 3′ degradation machinery (RNA exosome is emerging as a downstream effector of a diverse array of vRNA sensors. This review discusses our current understanding of the roles of the RNA decay machinery in controlling viral infection.

  7. RNA Matchmaking: Finding Cellular Pairing Partners. (United States)

    Graveley, Brenton R


    RNA structure is intimately related to function, yet methods to identify base-paired RNA strands in a transcriptome-wide manner in cells have remained elusive. One recent paper in Cell and two in Molecular Cell describe related methods to identify RNA sequences that interact in living cells, setting the stage for breakthroughs in our understanding of RNA structure and function.

  8. microRNA Decay: Refining microRNA Regulatory Activity. (United States)

    Pepin, Genevieve; Gantier, Michael P


    MicroRNAs (miRNAs) are short 19-25 nucleotide RNA molecules that impact on most biological processes by regulating the efficiency of messenger RNA (mRNA) translation. To date, most research activities have been focused on the control of miRNA expression and its functional consequences. Nonetheless, much remains unknown about the mechanisms affecting the level of specific miRNAs in the cell, a critical feature impacting their regulatory activity. This review focuses on the factors that regulate the abundance of miRNAs, including synthesis, post-transcriptional modifications, nucleases, target binding, and secretion.

  9. RNA assemblages orchestrate complex cellular processes

    DEFF Research Database (Denmark)

    Nielsen, Finn Cilius; Hansen, Heidi Theil; Christiansen, Jan


    Eukaryotic mRNAs are monocistronic, and therefore mechanisms exist that coordinate the synthesis of multiprotein complexes in order to obtain proper stoichiometry at the appropriate intracellular locations. RNA-binding proteins containing low-complexity sequences are prone to generate liquid...... droplets via liquid-liquid phase separation, and in this way create cytoplasmic assemblages of functionally related mRNAs. In a recent iCLIP study, we showed that the Drosophila RNA-binding protein Imp, which exhibits a C-terminal low-complexity sequence, increases the formation of F-actin by binding to 3......' untranslated regions of mRNAs encoding components participating in F-actin biogenesis. We hypothesize that phase transition is a mechanism the cell employs to increase the local mRNA concentration considerably, and in this way synchronize protein production in cytoplasmic territories, as discussed...

  10. mRNA decay proteins are targeted to poly(A+ RNA and dsRNA-containing cytoplasmic foci that resemble P-bodies in Entamoeba histolytica.

    Directory of Open Access Journals (Sweden)

    Itzel López-Rosas

    Full Text Available 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

  11. Using RNA as Molecular Code for Programming Cellular Function. (United States)

    Kushwaha, Manish; Rostain, William; Prakash, Satya; Duncan, John N; Jaramillo, Alfonso


    RNA is involved in a wide-range of important molecular processes in the cell, serving diverse functions: regulatory, enzymatic, and structural. Together with its ease and predictability of design, these properties can lead RNA to become a useful handle for biological engineers with which to control the cellular machinery. By modifying the many RNA links in cellular processes, it is possible to reprogram cells toward specific design goals. We propose that RNA can be viewed as a molecular programming language that, together with protein-based execution platforms, can be used to rewrite wide ranging aspects of cellular function. In this review, we catalogue developments in the use of RNA parts, methods, and associated computational models that have contributed to the programmability of biology. We discuss how RNA part repertoires have been combined to build complex genetic circuits, and review recent applications of RNA-based parts and circuitry. We explore the future potential of RNA engineering and posit that RNA programmability is an important resource for firmly establishing an era of rationally designed synthetic biology.

  12. Sensitive detection of mRNA decay products by use of reverse-ligation-mediated PCR (RL-PCR). (United States)

    Grange, Thierry


    Ligation-mediated PCR allows the detection and mapping of cleavage products of specific nucleic acid molecules out of complex nucleic acid mixtures. It can be applied to the detection of either degradation products of exogenously added nucleases in footprinting applications or natural decay products or reaction intermediates. We have developed various ligation-mediated PCR approaches to analyze mRNAs, all relying on RNA ligation, followed by reverse-transcription and PCR amplification. We have termed these approaches reverse-ligation-mediated PCR (RL-PCR). The ligation event involves either an RNA linker added to the 5'-end of cleaved RNA or RNA circularization, allowing, respectively, the mapping and quantification of the cleavage points or the simultaneous analysis of the presence or absence of the 5'-cap structure and the length of the poly(A) tail. These methods enabled us to develop a very efficient 5'-RACE procedure to map mRNA 5'-ends, to footprint in permeabilized cells the interaction of regulatory proteins with RNA, to detect the products of cellular ribozyme action and to analyze cellular decay pathways that involve deadenylation and/or decapping. I review herein the methodologic aspects and protocols of the various RL-PCR procedures we have developed.

  13. IMP3 RNP safe houses prevent miRNA-directed HMGA2 mRNA decay in cancer and development

    DEFF Research Database (Denmark)

    Jønson, Lars; Christiansen, Jan; Hansen, Thomas van Overeem;


    The IMP3 RNA-binding protein is associated with metastasis and poor outcome in human cancer. Using solid cancer transcriptome data, we found that IMP3 correlates with HMGA2 mRNA expression. Cytoplasmic IMP3 granules contain HMGA2, and IMP3 dose-dependently increases HMGA2 mRNA. HMGA2 is regulated...... that IMP3 RNPs may function as cytoplasmic safe houses and prevent miRNA-directed mRNA decay of oncogenes during tumor progression....

  14. The human nuclear poly(a-binding protein promotes RNA hyperadenylation and decay.

    Directory of Open Access Journals (Sweden)

    Stefan M Bresson

    Full Text Available Control of nuclear RNA stability is essential for proper gene expression, but the mechanisms governing RNA degradation in mammalian nuclei are poorly defined. In this study, we uncover a mammalian RNA decay pathway that depends on the nuclear poly(A-binding protein (PABPN1, the poly(A polymerases (PAPs, PAPα and PAPγ, and the exosome subunits RRP6 and DIS3. Using a targeted knockdown approach and nuclear RNA reporters, we show that PABPN1 and PAPα, redundantly with PAPγ, generate hyperadenylated decay substrates that are recognized by the exosome and degraded. Poly(A tail extension appears to be necessary for decay, as cordycepin treatment or point mutations in the PAP-stimulating domain of PABPN1 leads to the accumulation of stable transcripts with shorter poly(A tails than controls. Mechanistically, these data suggest that PABPN1-dependent promotion of PAP activity can stimulate nuclear RNA decay. Importantly, efficiently exported RNAs are unaffected by this decay pathway, supporting an mRNA quality control function for this pathway. Finally, analyses of both bulk poly(A tails and specific endogenous transcripts reveals that a subset of nuclear RNAs are hyperadenylated in a PABPN1-dependent fashion, and this hyperadenylation can be either uncoupled or coupled with decay. Our results highlight a complex relationship between PABPN1, PAPα/γ, and nuclear RNA decay, and we suggest that these activities may play broader roles in the regulation of human gene expression.

  15. Regulation of mammalian microRNA processing and function by cellular signaling and subcellular localization



    For many microRNAs, in many normal tissues and in cancer cells, the cellular levels of mature microRNAs are not simply determined by transcription of microRNA genes. This mini-review will discuss how microRNA biogenesis and function can be regulated by various nuclear and cytoplasmic processing events, including emerging evidence that microRNA pathway components can be selectively regulated by control of their subcellular localization and by modifications that occur during dynamic cellular si...

  16. Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes

    DEFF Research Database (Denmark)

    Lykke-Andersen, Søren; Chen, Yun; Ardal, Britt;


    Eukaryotic RNAs with premature termination codons (PTCs) are eliminated by nonsense-mediated decay (NMD). While human nonsense RNA degradation can be initiated either by an endonucleolytic cleavage event near the PTC or through decapping, the individual contribution of these activities on endogen......Eukaryotic RNAs with premature termination codons (PTCs) are eliminated by nonsense-mediated decay (NMD). While human nonsense RNA degradation can be initiated either by an endonucleolytic cleavage event near the PTC or through decapping, the individual contribution of these activities...... yield alternative transcript isoforms that allow for differential expression of individual coencoded snoRNAs. Based on our findings, we hypothesize that snoRNA host genes need to be highly transcribed to accommodate high levels of snoRNA production and that the expression of individual sno...

  17. Cellular Fractionation and Isolation of Chromatin-Associated RNA. (United States)

    Conrad, Thomas; Ørom, Ulf Andersson


    In eukaryotic cells, the synthesis, processing, and functions of RNA molecules are confined to distinct subcellular compartments. Biochemical fractionation of cells prior to RNA isolation thus enables the analysis of distinct steps in the lifetime of individual RNA molecules that would be masked in bulk RNA preparations from whole cells. Here, we describe a simple two-step differential centrifugation protocol for the isolation of cytoplasmic, nucleoplasmic, and chromatin-associated RNA that can be used in downstream applications such as qPCR or deep sequencing. We discuss various aspects of this fractionation protocol, which can be readily applied to many mammalian cell types. For the study of long noncoding RNAs and enhancer RNAs in regulation of transcription especially the preparation of chromatin-associated RNA can contribute significantly to further developments.

  18. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq. (United States)

    Watters, Kyle E; Abbott, Timothy R; Lucks, Julius B


    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell.

  19. Aberrant herpesvirus-induced polyadenylation correlates with cellular messenger RNA destruction.

    Directory of Open Access Journals (Sweden)

    Yeon J Lee


    Full Text Available Regulation of messenger RNA (mRNA stability plays critical roles in controlling gene expression, ensuring transcript fidelity, and allowing cells to respond to environmental cues. Unregulated enhancement of mRNA turnover could therefore dampen cellular responses to such signals. Indeed, several herpesviruses instigate widespread destruction of cellular mRNAs to block host gene expression and evade immune detection. Kaposi's sarcoma-associated herpesvirus (KSHV promotes this phenotype via the activity of its viral SOX protein, although the mechanism of SOX-induced mRNA turnover has remained unknown, given its apparent lack of intrinsic ribonuclease activity. Here, we report that KSHV SOX stimulates cellular transcriptome turnover via a unique mechanism involving aberrant polyadenylation. Transcripts in SOX-expressing cells exhibit extended poly(A polymerase II-generated poly(A tails and polyadenylation-linked mRNA turnover. SOX-induced polyadenylation changes correlate with its RNA turnover function, and inhibition of poly(A tail formation blocks SOX activity. Both nuclear and cytoplasmic poly(A binding proteins are critical cellular cofactors for SOX function, the latter of which undergoes striking nuclear relocalization by SOX. SOX-induced mRNA turnover therefore represents both a novel mechanism of host shutoff as well as a new model system to probe the regulation of poly(A tail-stimulated mRNA turnover in mammalian cells.

  20. Nonsense-mediated mRNA decay among coagulation factor genes

    Directory of Open Access Journals (Sweden)

    Shirin Shahbazi


    Full Text Available Objective(s: Haemostasis prevents blood loss following vascular injury. It depends on the unique concert of events involving platelets and specific blood proteins, known as coagulation factors. The clotting system requires precise regulation and coordinated reactions to maintain the integrity of the vasculature. Clotting insufficiency mostly occurs due to genetically inherited coagulation factor deficiencies such as hemophilia. Materials and Methods: A relevant literature search of PubMed was performed using the keywords coagulation factors, Nonsense-mediated mRNA decay and premature translation termination codons. Search limitations included English language and human-based studies. Results: Mutations that cause premature translation termination codons probably account for one-third of genetically inherited diseases. Transcripts bearing aberrant termination codons are selectively identified and eliminated by an evolutionarily conserved posttranscriptional pathway known as nonsense-mediated mRNA decay (NMD. There are many pieces of evidence of decay among coagulation factor genes. However, the hemophilia gene (F8 does not seem to be subjected to NMD. Since the F8 gene is located on the X-chromosome, a connection between X-linked traits and mRNA decay could be assumed. Conclusion: Considering that not all genes go through decay, this review focuses on the basics of the mechanism in coagulation genes. It is interesting to determine whether this translation-coupled surveillance system represents a general rule for the genes encoding components of the same physiological cascade.

  1. Do You Believe in ReincaRNAtion? Herpesviruses Reveal Connection between RNA Decay and Synthesis. (United States)

    Russo, Joseph; Wilusz, Jeffrey


    Many viruses degrade host mRNAs to reduce competition for proteins/ribosomes and promote viral gene expression. In this issue of Cell Host & Microbe, Abernathy et al. (2015) demonstrate that a herpesviral RNA endonuclease induces host transcriptional repression that is mediated through the decay factor Xrn1 and evaded by viral genes.

  2. Cellular RNA binding proteins NS1-BP and hnRNP K regulate influenza A virus RNA splicing. (United States)

    Tsai, Pei-Ling; Chiou, Ni-Ting; Kuss, Sharon; García-Sastre, Adolfo; Lynch, Kristen W; Fontoura, Beatriz M A


    Influenza A virus is a major human pathogen with a genome comprised of eight single-strand, negative-sense, RNA segments. Two viral RNA segments, NS1 and M, undergo alternative splicing and yield several proteins including NS1, NS2, M1 and M2 proteins. However, the mechanisms or players involved in splicing of these viral RNA segments have not been fully studied. Here, by investigating the interacting partners and function of the cellular protein NS1-binding protein (NS1-BP), we revealed novel players in the splicing of the M1 segment. Using a proteomics approach, we identified a complex of RNA binding proteins containing NS1-BP and heterogeneous nuclear ribonucleoproteins (hnRNPs), among which are hnRNPs involved in host pre-mRNA splicing. We found that low levels of NS1-BP specifically impaired proper alternative splicing of the viral M1 mRNA segment to yield the M2 mRNA without affecting splicing of mRNA3, M4, or the NS mRNA segments. Further biochemical analysis by formaldehyde and UV cross-linking demonstrated that NS1-BP did not interact directly with viral M1 mRNA but its interacting partners, hnRNPs A1, K, L, and M, directly bound M1 mRNA. Among these hnRNPs, we identified hnRNP K as a major mediator of M1 mRNA splicing. The M1 mRNA segment generates the matrix protein M1 and the M2 ion channel, which are essential proteins involved in viral trafficking, release into the cytoplasm, and budding. Thus, reduction of NS1-BP and/or hnRNP K levels altered M2/M1 mRNA and protein ratios, decreasing M2 levels and inhibiting virus replication. Thus, NS1-BP-hnRNPK complex is a key mediator of influenza A virus gene expression.

  3. HIV-1 TAR miRNA protects against apoptosis by altering cellular gene expression

    Directory of Open Access Journals (Sweden)

    Meiri Eti


    Full Text Available Abstract Background RNA interference is a gene regulatory mechanism that employs small RNA molecules such as microRNA. Previous work has shown that HIV-1 produces TAR viral microRNA. Here we describe the effects of the HIV-1 TAR derived microRNA on cellular gene expression. Results Using a variation of standard techniques we have cloned and sequenced both the 5' and 3' arms of the TAR miRNA. We show that expression of the TAR microRNA protects infected cells from apoptosis and acts by down-regulating cellular genes involved in apoptosis. Specifically, the microRNA down-regulates ERCC1 and IER3, protecting the cell from apoptosis. Comparison to our cloned sequence reveals possible target sites for the TAR miRNA as well. Conclusion The TAR microRNA is expressed in all stages of the viral life cycle, can be detected in latently infected cells, and represents a mechanism wherein the virus extends the life of the infected cell for the purpose of increasing viral replication.

  4. Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

    DEFF Research Database (Denmark)

    Weischenfeldt, Joachim Lütken; Waage, Johannes Eichler; Tian, Geng;


    a bioinformatic pipeline that maps RNA-seq data to a combinatorial exon database, predicts NMD-susceptibility for mRNA isoforms and calculates the distribution of major splice isoform classes. We present a catalog of NMD-regulated alternative splicing events, showing that isoforms of 30% of all expressed genes......ABSTRACT: BACKGROUND: Nonsense-mediated mRNA decay (NMD) affects the outcome of alternative splicing by degrading mRNA isoforms with premature termination codons. Splicing regulators constitute important NMD targets; however, the extent to which loss of NMD causes extensive deregulation...... of alternative splicing has not previously been assayed in a global, unbiased manner. Here, we combine mouse genetics and RNA-seq to provide the first in vivo analysis of the global impact of NMD on splicing patterns in two primary mouse tissues ablated for the NMD factor UPF2. RESULTS: We developed...

  5. A Herpesvirus Protein Selectively Inhibits Cellular mRNA Nuclear Export. (United States)

    Gong, Danyang; Kim, Yong Hoon; Xiao, Yuchen; Du, Yushen; Xie, Yafang; Lee, Kevin K; Feng, Jun; Farhat, Nisar; Zhao, Dawei; Shu, Sara; Dai, Xinghong; Chanda, Sumit K; Rana, Tariq M; Krogan, Nevan J; Sun, Ren; Wu, Ting-Ting


    Nuclear mRNA export is highly regulated to ensure accurate cellular gene expression. Viral inhibition of cellular mRNA export can enhance viral access to the cellular translation machinery and prevent anti-viral protein production but is generally thought to be nonselective. We report that ORF10 of Kaposi's sarcoma-associated herpesvirus (KSHV), a nuclear DNA virus, inhibits mRNA export in a transcript-selective manner to control cellular gene expression. Nuclear export inhibition by ORF10 requires an interaction with an RNA export factor, Rae1. Genome-wide analysis reveals a subset of cellular mRNAs whose nuclear export is blocked by ORF10 with the 3' UTRs of ORF10-targeted transcripts conferring sensitivity to export inhibition. The ORF10-Rae1 interaction is important for the virus to express viral genes and produce infectious virions. These results suggest that a nuclear DNA virus can selectively interfere with RNA export to restrict host gene expression for optimal replication.

  6. Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation. (United States)

    Puig, Sergi; Askeland, Eric; Thiele, Dennis J


    Iron (Fe) is an essential micronutrient for virtually all organisms and serves as a cofactor for a wide variety of vital cellular processes. Although Fe deficiency is the primary nutritional disorder in the world, cellular responses to Fe deprivation are poorly understood. We have discovered a posttranscriptional regulatory process controlled by Fe deficiency, which coordinately drives widespread metabolic reprogramming. We demonstrate that, in response to Fe deficiency, the Saccharomyces cerevisiae Cth2 protein specifically downregulates mRNAs encoding proteins that participate in many Fe-dependent processes. mRNA turnover requires the binding of Cth2, an RNA binding protein conserved in plants and mammals, to specific AU-rich elements in the 3' untranslated region of mRNAs targeted for degradation. These studies elucidate coordinated global metabolic reprogramming in response to Fe deficiency and identify a mechanism for achieving this by targeting specific mRNA molecules for degradation, thereby facilitating the utilization of limited cellular Fe levels.

  7. Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae. (United States)

    Harigaya, Yuriko; Parker, Roy


    The general pathways of eukaryotic mRNA decay occur via deadenylation followed by 3' to 5' degradation or decapping, although some endonuclease sites have been identified in metazoan mRNAs. To determine the role of endonucleases in mRNA degradation in Saccharomyces cerevisiae, we mapped 5' monophosphate ends on mRNAs in wild-type and dcp2 xrn1 yeast cells, wherein mRNA endonuclease cleavage products are stabilized. This led to three important observations. First, only few mRNAs that undergo low-level endonucleolytic cleavage were observed, suggesting that endonucleases are not a major contributor to yeast mRNA decay. Second, independent of known decapping enzymes, we observed low levels of 5' monophosphates on some mRNAs, suggesting that an unknown mechanism can generate 5' exposed ends, although for all substrates tested, Dcp2 was the primary decapping enzyme. Finally, we identified debranched lariat intermediates from intron-containing genes, demonstrating a significant discard pathway for mRNAs during the second step of pre-mRNA splicing, which is a potential step to regulate gene expression.

  8. Integrating mRNA Decay Information into Co-Regulation Study

    Institute of Scientific and Technical Information of China (English)

    Liang Chen; Hong-Yu Zhao


    Absolute or relative transcript amounts measured through high-throughput technologies (e.g., microarrays)are now commonly used in bioinformatics analysis, such as gene clustering and DNA binding motif finding. However,transcription rates that represent mRNA synthesis may be more relevant in these analyses. Because transcription rates are not equivalent to transcript amounts unless the mRNA degradation rates as well as other factors that affect transcript amount are identical across different genes, the use of transcription rates in bioinformatics analysis may lead to a better description of the relationships among genes and better identification of genomic signals. In this article, we propose to use experimentally measured mRNA decay rates and mRNA transcript amounts to jointly infer transcription rates, and then use the inferred transcription rates in downstream analyses. For gene expression similarity analysis, we find that there tends to be higher correlations among co-regulated genes when transcription-rate-based correlations are used compared to those based on transcript amounts. In the context of identifying DNA binding motifs, using inferred transcription rates leads to more significant findings than those based on transcript amounts. These analyses suggest that the incorporation of mRNA decay rates and the use of the inferred transcription rates can facilitate the study of gene regulations and the reconstruction of transcriptional regulatory networks.

  9. A cellular microRNA mediates antiviral defense in human cells. (United States)

    Lecellier, Charles-Henri; Dunoyer, Patrice; Arar, Khalil; Lehmann-Che, Jacqueline; Eyquem, Stephanie; Himber, Christophe; Saïb, Ali; Voinnet, Olivier


    In eukaryotes, 21- to 24-nucleotide-long RNAs engage in sequence-specific interactions that inhibit gene expression by RNA silencing. This process has regulatory roles involving microRNAs and, in plants and insects, it also forms the basis of a defense mechanism directed by small interfering RNAs that derive from replicative or integrated viral genomes. We show that a cellular microRNA effectively restricts the accumulation of the retrovirus primate foamy virus type 1 (PFV-1) in human cells. PFV-1 also encodes a protein, Tas, that suppresses microRNA-directed functions in mammalian cells and displays cross-kingdom antisilencing activities. Therefore, through fortuitous recognition of foreign nucleic acids, cellular microRNAs have direct antiviral effects in addition to their regulatory functions.

  10. Dual-acting riboswitch control of translation initiation and mRNA decay. (United States)

    Caron, Marie-Pier; Bastet, Laurène; Lussier, Antony; Simoneau-Roy, Maxime; Massé, Eric; Lafontaine, Daniel A


    Riboswitches are mRNA regulatory elements that control gene expression by altering their structure in response to specific metabolite binding. In bacteria, riboswitches consist of an aptamer that performs ligand recognition and an expression platform that regulates either transcription termination or translation initiation. Here, we describe a dual-acting riboswitch from Escherichia coli that, in addition to modulating translation initiation, also is directly involved in the control of initial mRNA decay. Upon lysine binding, the lysC riboswitch adopts a conformation that not only inhibits translation initiation but also exposes RNase E cleavage sites located in the riboswitch expression platform. However, in the absence of lysine, the riboswitch folds into an alternative conformation that simultaneously allows translation initiation and sequesters RNase E cleavage sites. Both regulatory activities can be individually inhibited, indicating that translation initiation and mRNA decay can be modulated independently using the same conformational switch. Because RNase E cleavage sites are located in the riboswitch sequence, this riboswitch provides a unique means for the riboswitch to modulate RNase E cleavage activity directly as a function of lysine. This dual inhibition is in contrast to other riboswitches, such as the thiamin pyrophosphate-sensing thiM riboswitch, which triggers mRNA decay only as a consequence of translation inhibition. The riboswitch control of RNase E cleavage activity is an example of a mechanism by which metabolite sensing is used to regulate gene expression of single genes or even large polycistronic mRNAs as a function of environmental changes.

  11. Storage of cellular 5' mRNA caps in P bodies for viral cap-snatching. (United States)

    Mir, M A; Duran, W A; Hjelle, B L; Ye, C; Panganiban, A T


    The minus strand and ambisense segmented RNA viruses include multiple important human pathogens and are divided into three families, the Orthomyxoviridae, the Bunyaviridae, and the Arenaviridae. These viruses all initiate viral transcription through the process of "cap-snatching," which involves the acquisition of capped 5' oligonucleotides from cellular mRNA. Hantaviruses are emerging pathogenic viruses of the Bunyaviridae family that replicate in the cytoplasm of infected cells. Cellular mRNAs can be actively translated in polysomes or physically sequestered in cytoplasmic processing bodies (P bodies) where they are degraded or stored for subsequent translation. Here we show that the hantavirus nucleocapsid protein binds with high affinity to the 5' cap of cellular mRNAs, protecting the 5' cap from degradation. We also show that the hantavirus nucleocapsid protein accumulates in P bodies, where it sequesters protected 5' caps. P bodies then serve as a pool of primers during the initiation of viral mRNA synthesis by the viral polymerase. We propose that minus strand segmented viruses replicating in the cytoplasm have co-opted the normal degradation machinery of P bodies for storage of cellular caps. Our data also indicate that modification of the cap-snatching model is warranted to include a role for the nucleocapsid protein in cap acquisition and storage.

  12. Cellular restriction of retrovirus particle-mediated mRNA transfer. (United States)

    Galla, Melanie; Schambach, Axel; Towers, Greg J; Baum, Christopher


    Analyzing cellular restriction mechanisms provides insight into viral replication strategies, identifies targets for antiviral drug design, and is crucial for the development of novel tools for experimental or therapeutic delivery of genetic information. We have previously shown that retroviral vector mutants that are unable to initiate reverse transcription mediate a transient expression of any sequence which replaces the gag-pol transcription unit, a process we call retrovirus particle-mediated mRNA transfer (RMT). Here, we further examined the mechanism of RMT by testing its sensitivity to cellular restriction factors and short hairpin RNAs (shRNAs). We found that both human TRIM5alpha and, to a lesser extent, Fv1 effectively restrict RMT if the RNA is delivered by a restriction-sensitive capsid. While TRIM5alpha restriction of RMT led to reduced levels of retroviral mRNA in target cells, restriction by Fv1 did not. Treatment with the proteasome inhibitor MG132 partially relieved TRIM5alpha-mediated restriction of RMT. Finally, cells expressing shRNAs specifically targeting the retroviral mRNA inhibited RMT particles, but not reverse-transcribing particles. Retroviral mRNA may thus serve as a translation template if not used as a template for reverse transcription. Our data imply that retroviral nucleic acids become accessible to host factors, including ribosomes, as a result of particle remodeling during cytoplasmic trafficking.

  13. Regulation of axon guidance by compartmentalized nonsense-mediated mRNA decay

    DEFF Research Database (Denmark)

    Colak, Dilek; Ji, Sheng-Jian; Porse, Bo T


    show that Robo3.2, a receptor for the Slit family of guidance cues, is synthesized locally within axons of commissural neurons. Robo3.2 translation is induced by floor-plate-derived signals as axons cross the spinal cord midline. Robo3.2 is also a predicted target of the nonsense-mediated mRNA decay...... (NMD) pathway. We find that NMD regulates Robo3.2 synthesis by inducing the degradation of Robo3.2 transcripts in axons that encounter the floor plate. Commissural neurons deficient in NMD proteins exhibit aberrant axonal trajectories after crossing the midline, consistent with misregulation of Robo3...

  14. Interplay between the cellular autophagy machinery and positive-stranded RNA viruses

    Institute of Scientific and Technical Information of China (English)

    Junyan Shi; Honglin Luo


    Autophagy is a conserved cellular process that acts as a key regulator in maintaining cellular homeostasis.Recent studies implicate an important role for autophagy in infection and immunity by removing invading pathogens and through modulating innate and adaptive immune responses.However,several pathogens,notably some positive-stranded RNA viruses,have subverted autophagy to their own ends.In this review,we summarize the current understanding of how viruses with a positive-stranded RNA genome interact with the host autophagy machinery to control their replication and spread.We review the mechanisms underlying the induction of autophagy and discuss the pro- and anti-viral functions of autophagy and the potential mechanisms involved.

  15. The rules and impact of nonsense-mediated mRNA decay in human cancers. (United States)

    Lindeboom, Rik G H; Supek, Fran; Lehner, Ben


    Premature termination codons (PTCs) cause a large proportion of inherited human genetic diseases. PTC-containing transcripts can be degraded by an mRNA surveillance pathway termed nonsense-mediated mRNA decay (NMD). However, the efficiency of NMD varies; it is inefficient when a PTC is located downstream of the last exon junction complex (EJC). We used matched exome and transcriptome data from 9,769 human tumors to systematically elucidate the rules of NMD targeting in human cells. An integrated model incorporating multiple rules beyond the canonical EJC model explains approximately three-fourths of the non-random variance in NMD efficiency across thousands of PTCs. We also show that dosage compensation may sometimes mask the effects of NMD. Applying the NMD model identifies signatures of both positive and negative selection on NMD-triggering mutations in human tumors and provides a classification for tumor-suppressor genes.

  16. Localization and sub-cellular shuttling of HTLV-1 tax with the miRNA machinery.

    Directory of Open Access Journals (Sweden)

    Rachel Van Duyne

    Full Text Available The innate ability of the human cell to silence endogenous retroviruses through RNA sequences encoding microRNAs, suggests that the cellular RNAi machinery is a major means by which the host mounts a defense response against present day retroviruses. Indeed, cellular miRNAs target and hybridize to specific sequences of both HTLV-1 and HIV-1 viral transcripts. However, much like the variety of host immune responses to retroviral infection, the virus itself contains mechanisms that assist in the evasion of viral inhibition through control of the cellular RNAi pathway. Retroviruses can hijack both the enzymatic and catalytic components of the RNAi pathway, in some cases to produce novel viral miRNAs that can either assist in active viral infection or promote a latent state. Here, we show that HTLV-1 Tax contributes to the dysregulation of the RNAi pathway by altering the expression of key components of this pathway. A survey of uninfected and HTLV-1 infected cells revealed that Drosha protein is present at lower levels in all HTLV-1 infected cell lines and in infected primary cells, while other components such as DGCR8 were not dramatically altered. We show colocalization of Tax and Drosha in the nucleus in vitro as well as coimmunoprecipitation in the presence of proteasome inhibitors, indicating that Tax interacts with Drosha and may target it to specific areas of the cell, namely, the proteasome. In the presence of Tax we observed a prevention of primary miRNA cleavage by Drosha. Finally, the changes in cellular miRNA expression in HTLV-1 infected cells can be mimicked by the add back of Drosha or the addition of antagomiRs against the cellular miRNAs which are downregulated by the virus.

  17. Cellular RNA is chemically modified by exposure to air pollution mixtures. (United States)

    Baldridge, Kevin C; Zavala, Jose; Surratt, Jason; Sexton, Kenneth G; Contreras, Lydia M


    RNAs are more susceptible to modifications than DNA, and chemical modifications in RNA have an effect on their structure and function. This study aimed to characterize chemical effects on total RNA in human A549 lung cells after exposure to elevated levels of major secondary air pollutants commonly found in urban locations, including ozone (O3), acrolein (ACR) and methacrolein (MACR). Enzyme-linked immunosorbent assays (ELISA) were used to measure levels of interleukin (IL)-8 in the growth media and 8-oxoguanine (8OG) levels in total cellular RNA, and lactate dehydrogenase (LDH) in the growth media was measured by a coupled enzymatic assay. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure levels of microRNA 10b (miR-10b). The study found that 1-h exposure to all tested pollutant mixtures consistently caused significant increases in the levels of 8OG in total RNA. In the case of 4 ppm O3 exposures, measured levels of IL-8, LDH and miR-10b each showed consistent trends between two independent trials, but varied among these three targets. After 1-h exposures to an ACR+MACR mixture, measured levels of IL-8, LDH and miR-10b showed variable results. For mixtures of O3+ACR+MACR, IL-8 measurements showed no change; miR-10b and LDH showed variable results. The results indicate that short-term high-concentration exposures to air pollution can cause RNA chemical modifications. Chemical modifications in RNAs could represent more consistent markers of cellular stress relative to other inflammation markers, such as IL-8 and LDH, and provide a new biomarker endpoint for mechanistic studies in toxicity of air pollution exposure.

  18. Visualization of self-delivering hydrophobically modified siRNA cellular internalization (United States)

    Ly, Socheata; Navaroli, Deanna M.; Didiot, Marie-Cécile; Cardia, James; Pandarinathan, Lakshmipathi; Alterman, Julia F.; Fogarty, Kevin; Standley, Clive; Lifshitz, Lawrence M.; Bellve, Karl D.; Prot, Matthieu; Echeverria, Dimas; Corvera, Silvia; Khvorova, Anastasia


    siRNAs are a new class of therapeutic modalities with promising clinical efficacy that requires modification or formulation for delivery to the tissue and cell of interest. Conjugation of siRNAs to lipophilic groups supports efficient cellular uptake by a mechanism that is not well characterized. Here we study the mechanism of internalization of asymmetric, chemically stabilized, cholesterol-modified siRNAs (sd-rxRNAs®) that efficiently enter cells and tissues without the need for formulation. We demonstrate that uptake is rapid with significant membrane association within minutes of exposure followed by the formation of vesicular structures and internalization. Furthermore, sd-rxRNAs are internalized by a specific class of early endosomes and show preferential association with epidermal growth factor (EGF) but not transferrin (Tf) trafficking pathways as shown by live cell TIRF and structured illumination microscopy (SIM). In fixed cells, we observe ∼25% of sd-rxRNA co-localizing with EGF and <5% with Tf, which is indicative of selective endosomal sorting. Likewise, preferential sd-rxRNA co-localization was demonstrated with EEA1 but not RBSN-containing endosomes, consistent with preferential EGF-like trafficking through EEA1-containing endosomes. sd-rxRNA cellular uptake is a two-step process, with rapid membrane association followed by internalization through a selective, saturable subset of the endocytic process. However, the mechanistic role of EEA1 is not yet known. This method of visualization can be used to better understand the kinetics and mechanisms of hydrophobic siRNA cellular uptake and will assist in further optimization of these types of compounds for therapeutic intervention. PMID:27899655

  19. The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality. (United States)

    Radhakrishnan, Aditya; Chen, Ying-Hsin; Martin, Sophie; Alhusaini, Najwa; Green, Rachel; Coller, Jeff


    A major determinant of mRNA half-life is the codon-dependent rate of translational elongation. How the processes of translational elongation and mRNA decay communicate is unclear. Here, we establish that the DEAD-box protein Dhh1p is a sensor of codon optimality that targets an mRNA for decay. First, we find mRNAs whose translation elongation rate is slowed by inclusion of non-optimal codons are specifically degraded in a Dhh1p-dependent manner. Biochemical experiments show Dhh1p is preferentially associated with mRNAs with suboptimal codon choice. We find these effects on mRNA decay are sensitive to the number of slow-moving ribosomes on an mRNA. Moreover, we find Dhh1p overexpression leads to the accumulation of ribosomes specifically on mRNAs (and even codons) of low codon optimality. Lastly, Dhh1p physically interacts with ribosomes in vivo. Together, these data argue that Dhh1p is a sensor for ribosome speed, targeting an mRNA for repression and subsequent decay.

  20. A cellular protein specifically binds to the 3'-terminal sequences of hepatitis C virus intermediate negative-strand RNA

    Institute of Scientific and Technical Information of China (English)

    王巍; 邓庆丽; 黄开红; 段朝晖; 邵静; 黄志清; 黄志明


    ObjectiveTo study the mechanism of the cellular proteins involved in the process of replication of hepatitis C virus (HCV) negative-strand RNA.MethodsUltraviolet (UV) cross-linking was used to identify the cellular proteins that would bind to the 3'-end of HCV negative-strand RNA. Competition experimentwas used to confirm the specificity of this binding, in which excess nonhomologous protein and RNA transcripts were used as competitors. The required binding sequence was determined by mapping, then the binding site was predicted through secondary structure analysis.ResultsA cellular protein of 45 kD (p45) was found to bind specifically to the 3'-endof HCV negative-strand RNA by UV cross-linking. nhomologous proteins and RNA transcripts could not compete out this binding, whereas the unlabeled 3'-endof HCV negative-strand RNA could. Mapping of the protein-binding site suggested that the 3'-end 131-278nt of HCV negative-strand RNA was the possible protein-binding region. Analysis of RNA secondary structure presumed that the potential binding site was located at 194-GAAAGAAC-201. ConclusionThe cellular protein p45 could specifically bind to the secondary structure of the 3'-end of HCV intermediate negative-strand RNA, and may play an important role in HCV RNA replication.

  1. Nonsense-meditated mRNA Decay%无义介导的mRNA降解

    Institute of Scientific and Technical Information of China (English)

    贾晓波; 胡剑


    无义介导的mRNA降解(nonsense-mediated mRNA decay,NMD)作为真核细胞中重要RNA监控机制,识别并降解开放阅读框中含有提前终止密码子(premature termination codon,PTC)的mRNA,以避免因截短的蛋白产物积累对细胞造成毒害.NMD还调控正常生理基因的表达,暗示其在真核细胞中扮演重要角色.NMD途径的关键是PTC的识别.本文通过3种模型来分别阐述发现于哺乳动物、酵母等不同有机体的识别机制.通常由NMD因子UPF1 (up-frameshift)等被招募至含PTC的mRNA上,借助这些因子组装形成“功能复合体”并激活降解.但目前对于PTC识别后的过程仍认识有限,本文通过综述NMD途径的分子机制以更好地理解其生物学意义.%Nonsense-mediated mRNA decay (NMD) is a RNA surveillance mechanism that detects the mRNAs harboring premature termination condons ( PTC ) , and triggers the degradation to prevent the accumulation of truncated and potentially harmful proteins. NMD also regulates a subset of wild-type physiological transcripts, indicating that NMD plays an important biological role in eukaryotic cells. The key of NMD pathway is PTC recognition from authentic stop condons during translation. Here we reviewed three models to elucidate different mechanisms found in mammals and invertebrates. The NMD effectors such as UPF1 ( up-frameshift) are involved in the "functional complex" assembly on PTC containing mRNA, although the details of sequential events remain to be clarified for the variety among different organisms, we present the latest progress in post-PTC recognition events to better understand the molecular mechanism of NMD pathway.

  2. Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery (United States)

    Sienski, Grzegorz; Batki, Julia; Senti, Kirsten-André; Dönertas, Derya; Tirian, Laszlo; Meixner, Katharina; Brennecke, Julius


    The repression of transposable elements in eukaryotes often involves their transcriptional silencing via targeted chromatin modifications. In animal gonads, nuclear Argonaute proteins of the PIWI clade complexed with small guide RNAs (piRNAs) serve as sequence specificity determinants in this process. How binding of nuclear PIWI–piRNA complexes to nascent transcripts orchestrates heterochromatin formation and transcriptional silencing is unknown. Here, we characterize CG9754/Silencio as an essential piRNA pathway factor that is required for Piwi-mediated transcriptional silencing in Drosophila. Ectopic targeting of Silencio to RNA or DNA is sufficient to elicit silencing independently of Piwi and known piRNA pathway factors. Instead, Silencio requires the H3K9 methyltransferase Eggless/SetDB1 for its silencing ability. In agreement with this, SetDB1, but not Su(var)3-9, is required for Piwi-mediated transcriptional silencing genome-wide. Due to its interaction with the target-engaged Piwi–piRNA complex, we suggest that Silencio acts as linker between the sequence specificity factor Piwi and the cellular heterochromatin machinery. PMID:26494711

  3. Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery. (United States)

    Sienski, Grzegorz; Batki, Julia; Senti, Kirsten-André; Dönertas, Derya; Tirian, Laszlo; Meixner, Katharina; Brennecke, Julius


    The repression of transposable elements in eukaryotes often involves their transcriptional silencing via targeted chromatin modifications. In animal gonads, nuclear Argonaute proteins of the PIWI clade complexed with small guide RNAs (piRNAs) serve as sequence specificity determinants in this process. How binding of nuclear PIWI-piRNA complexes to nascent transcripts orchestrates heterochromatin formation and transcriptional silencing is unknown. Here, we characterize CG9754/Silencio as an essential piRNA pathway factor that is required for Piwi-mediated transcriptional silencing in Drosophila. Ectopic targeting of Silencio to RNA or DNA is sufficient to elicit silencing independently of Piwi and known piRNA pathway factors. Instead, Silencio requires the H3K9 methyltransferase Eggless/SetDB1 for its silencing ability. In agreement with this, SetDB1, but not Su(var)3-9, is required for Piwi-mediated transcriptional silencing genome-wide. Due to its interaction with the target-engaged Piwi-piRNA complex, we suggest that Silencio acts as linker between the sequence specificity factor Piwi and the cellular heterochromatin machinery.

  4. The nonsense-mediated RNA decay pathway is disrupted in inflammatory myofibroblastic tumors. (United States)

    Lu, JingWei; Plank, Terra-Dawn; Su, Fang; Shi, XiuJuan; Liu, Chen; Ji, Yuan; Li, ShuaiJun; Huynh, Andrew; Shi, Chao; Zhu, Bo; Yang, Guang; Wu, YanMing; Wilkinson, Miles F; Lu, YanJun


    Inflammatory myofibroblastic tumors (IMTs) are characterized by myofibroblast proliferation and an inflammatory cell infiltrate. Little is known about the molecular pathways that precipitate IMT formation. Here, we report the identification of somatic mutations in UPF1, a gene that encodes an essential component of the nonsense-mediated RNA decay (NMD) pathway, in 13 of 15 pulmonary IMT samples. The majority of mutations occurred in a specific region of UPF1 and triggered UPF1 alternative splicing. Several mRNA targets of the NMD pathway were upregulated in IMT samples, indicating that the UPF1 mutations led to reduced NMD magnitude. These upregulated NMD targets included NIK mRNA, which encodes a potent activator of NF-κB. In human lung cells, UPF1 depletion increased expression of chemokine-encoding genes in a NIK-dependent manner. Elevated chemokines and IgE class switching events were observed in IMT samples, consistent with NIK upregulation in these tumors. Together, these results support a model in which UPF1 mutations downregulate NMD, leading to NIK-dependent NF-κB induction, which contributes to the immune infiltration that is characteristic of IMTs. The molecular link between the NMD pathway and IMTs has implications for the diagnosis and treatment of these tumors.

  5. The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigm. (United States)

    Caetano-Anollés, Gustavo; Seufferheld, Manfredo J


    The origin and evolution of modern biochemistry and cellular structure is a complex problem that has puzzled scientists for almost a century. While comparative, functional and structural genomics has unraveled considerable complexity at the molecular level, there is very little understanding of the origin, evolution and structure of the molecules responsible for cellular or viral features in life. Recent efforts, however, have dissected the emergence of the very early molecules that populated primordial cells. Deep historical signal was retrieved from a census of molecular structures and functions in thousands of nucleic acid and protein structures and hundreds of genomes using powerful phylogenomic methods. Together with structural, chemical and cell biology considerations, this information reveals that modern biochemistry is the result of the gradual evolutionary appearance and accretion of molecular parts and molecules. These patterns comply with the principle of continuity and lead to molecular and cellular complexity. Here, we review findings and report possible origins of molecular and cellular structure, the early rise of lipid biosynthetic pathways and components of cytoskeletal microstructures, the piecemeal accumulation of domains in ATP synthase complexes and the origin and evolution of the ribosome. Phylogenomic studies suggest the last universal common ancestor of life, the 'urancestor', had already developed complex cellular structure and bioenergetics. Remarkably, our findings falsify the existence of an ancient RNA world. Instead they are compatible with gradually coevolving nucleic acids and proteins in interaction with increasingly complex cofactors, lipid membrane structures and other cellular components. This changes the perception we have of the rise of modern biochemistry and prompts further analysis of the emergence of biological complexity in an ever-expanding coevolving world of macromolecules.

  6. Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq. (United States)

    Gokce, Ozgun; Stanley, Geoffrey M; Treutlein, Barbara; Neff, Norma F; Camp, J Gray; Malenka, Robert C; Rothwell, Patrick E; Fuccillo, Marc V; Südhof, Thomas C; Quake, Stephen R


    The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed ten differentiated, distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSNs) that have specific markers and that overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type-specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states.

  7. Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq

    Directory of Open Access Journals (Sweden)

    Ozgun Gokce


    Full Text Available The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed ten differentiated, distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSNs that have specific markers and that overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type-specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states.

  8. A critical role of a cellular membrane traffic protein in poliovirus RNA replication.

    Directory of Open Access Journals (Sweden)

    George A Belov


    Full Text Available Replication of many RNA viruses is accompanied by extensive remodeling of intracellular membranes. In poliovirus-infected cells, ER and Golgi stacks disappear, while new clusters of vesicle-like structures form sites for viral RNA synthesis. Virus replication is inhibited by brefeldin A (BFA, implicating some components(s of the cellular secretory pathway in virus growth. Formation of characteristic vesicles induced by expression of viral proteins was not inhibited by BFA, but they were functionally deficient. GBF1, a guanine nucleotide exchange factor for the small cellular GTPases, Arf, is responsible for the sensitivity of virus infection to BFA, and is required for virus replication. Knockdown of GBF1 expression inhibited virus replication, which was rescued by catalytically active protein with an intact N-terminal sequence. We identified a mutation in GBF1 that allows growth of poliovirus in the presence of BFA. Interaction between GBF1 and viral protein 3A determined the outcome of infection in the presence of BFA.

  9. Heritability in the efficiency of nonsense-mediated mRNA decay in humans.

    LENUS (Irish Health Repository)

    Seoighe, Cathal


    BACKGROUND: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences. PRINCIPAL FINDINGS: Using previously published Affymetrix exon microarray data from cell lines genotyped as part of the International HapMap project, we investigated whether there are heritable, inter-individual differences in the abundance of intron-containing transcripts, potentially reflecting differences in the efficiency of NMD. We identified intronic probesets using EST data and report evidence of heritability in the extent of intron expression in 56 HapMap trios. We also used a genome-wide association approach to identify genetic markers associated with intron expression. Among the top candidates was a SNP in the DCP1A gene, which forms part of the decapping complex, involved in NMD. CONCLUSIONS: While we caution that some of the apparent inter-individual difference in intron expression may be attributable to different handling or treatments of cell lines, we hypothesize that there is significant polymorphism in the process of NMD, resulting in heritable differences in the abundance of intronic mRNA. Part of this phenotype is likely to be due to a polymorphism in a decapping enzyme on human chromosome 3.

  10. Heritability in the efficiency of nonsense-mediated mRNA decay in humans

    KAUST Repository

    Seoighe, Cathal


    Background: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences. Principal Findings: Using previously published Affymetrix exon microarray data from cell lines genotyped as part of the International HapMap project, we investigated whether there are heritable, inter-individual differences in the abundance of intron-containing transcripts, potentially reflecting differences in the efficiency of NMD. We identified intronic probesets using EST data and report evidence of heritability in the extent of intron expression in 56 HapMap trios. We also used a genome-wide association approach to identify genetic markers associated with intron expression. Among the top candidates was a SNP in the DCP1A gene, which forms part of the decapping complex, involved in NMD. Conclusions: While we caution that some of the apparent inter-individual difference in intron expression may be attributable to different handling or treatments of cell lines, we hypothesize that there is significant polymorphism in the process of NMD, resulting in heritable differences in the abundance of intronic mRNA. Part of this phenotype is likely to be due to a polymorphism in a decapping enzyme on human chromosome 3. © 2010 Seoighe, Gehring.

  11. Heritability in the efficiency of nonsense-mediated mRNA decay in humans.

    Directory of Open Access Journals (Sweden)

    Cathal Seoighe

    Full Text Available BACKGROUND: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD pathway. There is evidence in the form of selective pressure for in-frame stop codons in introns and a depletion of length three introns that this is an important and conserved quality-control mechanism. Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences. PRINCIPAL FINDINGS: Using previously published Affymetrix exon microarray data from cell lines genotyped as part of the International HapMap project, we investigated whether there are heritable, inter-individual differences in the abundance of intron-containing transcripts, potentially reflecting differences in the efficiency of NMD. We identified intronic probesets using EST data and report evidence of heritability in the extent of intron expression in 56 HapMap trios. We also used a genome-wide association approach to identify genetic markers associated with intron expression. Among the top candidates was a SNP in the DCP1A gene, which forms part of the decapping complex, involved in NMD. CONCLUSIONS: While we caution that some of the apparent inter-individual difference in intron expression may be attributable to different handling or treatments of cell lines, we hypothesize that there is significant polymorphism in the process of NMD, resulting in heritable differences in the abundance of intronic mRNA. Part of this phenotype is likely to be due to a polymorphism in a decapping enzyme on human chromosome 3.

  12. Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments

    DEFF Research Database (Denmark)

    Ravenschlag, K.; Sahm, K.; Knoblauch, C.;


    The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburg-fjorden, Svalbard) a-as characterized by both fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes...... that FISH and rRNA slot blot hybridization gave comparable results. Furthermore, a combination of the two methods allowed us to calculate specific cellular rRNA contents with respect to localization in the sediment profile. The rRNA contents of Desulfosarcina-Desulfococcus cells were highest in the first 5...... mm of the sediment (0.9 and 1.4 fg, respectively) and decreased steeply with depth, indicating that maximal metabolic activity occurred close to the surface, Based on SRB cell numbers, cellular sulfate reduction rates were calculated. The rates were highest in the surface layer (0.14 fmol cell(-1...

  13. Regulation of mRNA Levels by Decay-Promoting Introns that Recruit the Exosome Specificity Factor Mmi1

    Directory of Open Access Journals (Sweden)

    Cornelia Kilchert


    Full Text Available In eukaryotic cells, inefficient splicing is surprisingly common and leads to the degradation of transcripts with retained introns. How pre-mRNAs are committed to nuclear decay is unknown. Here, we uncover a mechanism by which specific intron-containing transcripts are targeted for nuclear degradation in fission yeast. Sequence elements within these “decay-promoting” introns co-transcriptionally recruit the exosome specificity factor Mmi1, which induces degradation of the unspliced precursor and leads to a reduction in the levels of the spliced mRNA. This mechanism negatively regulates levels of the RNA helicase DDX5/Dbp2 to promote cell survival in response to stress. In contrast, fast removal of decay-promoting introns by co-transcriptional splicing precludes Mmi1 recruitment and relieves negative expression regulation. We propose that decay-promoting introns facilitate the regulation of gene expression. Based on the identification of multiple additional Mmi1 targets, including mRNAs, long non-coding RNAs, and sn/snoRNAs, we suggest a general role in RNA regulation for Mmi1 through transcript degradation.

  14. Roadmap to cellular reprogramming--manipulating transcriptional networks with DNA, RNA, proteins and small molecules. (United States)

    Wörsdörfer, P; Thier, M; Kadari, A; Edenhofer, F


    Recent reports demonstrate that the plasticity of mammalian somatic cells is much higher than previously assumed and that ectopic expression of transcription factors may have the potential to induce the conversion of any cell type into another. Fibroblast cells can be converted into embryonic stem cell-like cells, neural cells, cardiomyocytes, macrophage-like cells as well as blood progenitors. Additionally, the conversion of astrocytes into neurons or neural stem cells into monocytes has been demonstrated. Nowadays, in the era of systems biology, continuously growing holistic data sets are providing increasing insights into core transcriptional networks and cellular signaling pathways. This knowledge enables cell biologists to understand how cellular fate is determined and how it could be manipulated. As a consequence for biomedical applications, it might be soon possible to convert patient specific somatic cells directly into desired transplantable other cell types. The clinical value, however, of such reprogrammed cells is currently limited due to the invasiveness of methods applied to induce reprogramming factor activity. This review will focus on experimental strategies to ectopically induce cell fate modulators. We will emphasize those strategies that enable efficient and robust overexpression of transcription factors by minimal genetic alterations of the host genome. Furthermore, we will discuss procedures devoid of any genomic manipulation, such as the direct delivery of mRNA, proteins, or the use of small molecules. By this, we aim to give a comprehensive overview on state of the art techniques that harbor the potential to generate safe reprogrammed cells for clinical applications.

  15. Embryonic MicroRNA-369 Controls Metabolic Splicing Factors and Urges Cellular Reprograming.

    Directory of Open Access Journals (Sweden)

    Masamitsu Konno

    Full Text Available Noncoding microRNAs inhibit translation and lower the transcript stability of coding mRNA, however miR-369 s, in aberrant silencing genomic regions, stabilizes target proteins under cellular stress. We found that in vitro differentiation of embryonic stem cells led to chromatin methylation of histone H3K4 at the miR-369 region on chromosome 12qF in mice, which is expressed in embryonic cells and is critical for pluripotency. Proteomic analyses revealed that miR-369 stabilized translation of pyruvate kinase (Pkm2 splicing factors such as HNRNPA2B1. Overexpression of miR-369 stimulated Pkm2 splicing and enhanced induction of cellular reprogramming by induced pluripotent stem cell factors, whereas miR-369 knockdown resulted in suppression. Furthermore, immunoprecipitation analysis showed that the Argonaute complex contained the fragile X mental retardation-related protein 1 and HNRNPA2B1 in a miR-369-depedent manner. Our findings demonstrate a unique role of the embryonic miR-369-HNRNPA2B1 axis in controlling metabolic enzyme function, and suggest a novel pathway linking epigenetic, transcriptional, and metabolic control in cell reprogramming.

  16. Nonstop mRNA Decay: a Special Attribute of Trans-Translation Mediated Ribosome Rescue

    Directory of Open Access Journals (Sweden)

    Krithika eVenkataraman


    Full Text Available Decoding of aberrant mRNAs leads to unproductive ribosome stalling and sequestration of components of the translation machinery. Bacteria have evolved three seemingly independent pathways to resolve stalled translation complexes. The trans-translation process, orchestrated by the hybrid transfer-messenger RNA (tmRNA and its essential protein co-factor, SmpB, is the principal translation quality control system for rescuing unproductively stalled ribosomes. Two specialized alternative rescue pathways, coordinated by ArfA and ArfB, have been recently discovered. The SmpB-tmRNA mediated trans-translation pathway, in addition to re-mobilizing stalled translation complexes, co-translationally appends a degradation tag to the associated nascent polypeptides, marking them for proteolysis by various cellular proteases. Another unique feature of trans-translation, not shared by the alternative rescue pathways, is the facility to recruit RNase R for targeted degradation of nonstop mRNAs, thus preventing further futile cycles of translation. The distinct C-terminal lysine-rich (K-rich domain of RNase R is essential for its recruitment to stalled ribosomes. To gain new insights into the structure and function of RNase R, we investigated its global architecture, the spatial arrangement of its distinct domains, and the identities of key functional residues in its unique K-rich domain. Small-angle X-ray scattering (SAXS models of RNase R reveal a tri-lobed structure with flexible N- and C-terminal domains, and suggest intimate contacts between the K-rich domain and the catalytic core of the enzyme. Alanine-scanning mutagenesis of the K-rich domain, in the region spanning residues 735 and 750, has uncovered the precise amino acid determinants required for the productive engagement of RNase R on tmRNA-rescued ribosomes. Theses analyses demonstrate that alanine substitution of conserved residues E740 and K741 result in profound defects, not only in the recruitment

  17. Downregulation of microRNA-498 in colorectal cancers and its cellular effects

    Energy Technology Data Exchange (ETDEWEB)

    Gopalan, Vinod; Smith, Robert A.; Lam, Alfred K.-Y., E-mail:


    miR-498 is a non-coding RNA located intergenically in 19q13.41. Due to its predicted targeting of several genes involved in control of cellular growth, we examined the expression of miR-498 in colon cancer cell lines and a large cohort of patients with colorectal adenocarcinoma. Two colon cancer cancer cell lines (SW480 and SW48) and one normal colonic epithelial cell line (FHC) were recruited. The expression of miR-498 was tested in these cell lines by using quantitative real-time polymerase chain reaction (qRT-PCR). Tissues from 80 patients with surgical resection of colorectum (60 adenocarcinomas and 20 non-neoplastic tissues) were tested for miR-498 expression by qRT-PCR. In addition, an exogenous miR-498 (mimic) was used to detect the miRNA's effects on cell proliferation and cell cycle events in SW480 using MTT calorimetric assay and flow cytometry respectively. The colon cancer cell lines showed reduced expression of miR-498 compared to a normal colonic epithelial cell line. Mimic driven over expression of miR-498 in the SW480 cell line resulted in reduced cell proliferation and increased proportions of G2-M phase cells. In tissues, miR-498 expression was too low to be detected in all colorectal adenocarcinoma compared to non-neoplastic tissues. This suggests that the down regulation of miR-498 in colorectal cancer tissues and the direct suppressive cellular effect noted in cancer cell lines implies that miR-498 has some direct or indirect role in the pathogenesis of colorectal adenocarcinomas. - Highlights: • miR-498 is a non-coding RNA located in 19q13.41. • Colon cancer cell lines showed reduced expression of miR-498. • Mimic driven over expression of miR-498 in colon cancer cells resulted in lower cell proliferation. • miR-498 expression was down regulated in all colorectal adenocarcinoma tissues.

  18. IMP3 RNP safe houses prevent miRNA-directed HMGA2 mRNA decay in cancer and development

    DEFF Research Database (Denmark)

    Jønson, Lars; Christiansen, Jan; Hansen, Thomas van Overeem


    The IMP3 RNA-binding protein is associated with metastasis and poor outcome in human cancer. Using solid cancer transcriptome data, we found that IMP3 correlates with HMGA2 mRNA expression. Cytoplasmic IMP3 granules contain HMGA2, and IMP3 dose-dependently increases HMGA2 mRNA. HMGA2 is regulated...... embryos show dose-dependent Hmga2 mRNA downregulation. Finally, IMP3 ribonucleoproteins (RNPs) contain other let-7 target mRNAs, including LIN28B, and a global gene set enrichment analysis demonstrates that miRNA-regulated transcripts in general are upregulated following IMP3 induction. We conclude...

  19. Influence of mRNA decay rates on the computational prediction of transcription rate profiles from gene expression profiles

    Indian Academy of Sciences (India)

    Chi-Fang Chin; Arthur Chun-Chieh Shih; Kuo-Chin Fan


    The abundance of an mRNA species depends not only on the transcription rate at which it is produced, but also on its decay rate, which determines how quickly it is degraded. Both transcription rate and decay rate are important factors in regulating gene expression. With the advance of the age of genomics, there are a considerable number of gene expression datasets, in which the expression profiles of tens of thousands of genes are often non-uniformly sampled. Recently, numerous studies have proposed to infer the regulatory networks from expression profiles. Nevertheless, how mRNA decay rates affect the computational prediction of transcription rate profiles from expression profiles has not been well studied. To understand the influences, we present a systematic method based on a gene dynamic regulation model by taking mRNA decay rates, expression profiles and transcription profiles into account. Generally speaking, an expression profile can be regarded as a representation of a biological condition. The rationale behind the concept is that the biological condition is reflected in the changing of gene expression profile. Basically, the biological condition is either associated to the cell cycle or associated to the environmental stresses. The expression profiles of genes that belong to the former, so-called cell cycle data, are characterized by periodicity, whereas the expression profiles of genes that belong to the latter, so-called condition-specific data, are characterized by a steep change after a specific time without periodicity. In this paper, we examine the systematic method on the simulated expression data as well as the real expression data including yeast cell cycle data and condition-specific data (glucose-limitation data). The results indicate that mRNA decay rates do not significantly influence the computational prediction of transcription-rate profiles for cell cycle data. On the contrary, the magnitudes and shapes of transcription-rate profiles for

  20. Changes in Stoichiometry, Cellular RNA, and Alkaline Phosphatase Activity of Chlamydomonas in Response to Temperature and Nutrients (United States)

    Hessen, Dag O.; Hafslund, Ola T.; Andersen, Tom; Broch, Catharina; Shala, Nita K.; Wojewodzic, Marcin W.


    Phytoplankton may respond both to elevated temperatures and reduced nutrients by changing their cellular stoichiometry and cell sizes. Since increased temperatures often cause increased thermal stratification and reduced vertical flux of nutrients into the mixed zone, it is difficult to disentangle these drivers in nature. In this study, we used a factorial design with high and low levels of phosphorus (P) and high and low temperature to assess responses in cellular stoichiometry, levels of RNA, and alkaline phosphatase activity (APA) in the chlorophyte Chlamydomonas reinhardtii. Growth rate, C:P, C:N, N:P, RNA, and APA all responded primarily to P treatment, but except for N:P and APA, also temperature contributed significantly. For RNA, the contribution from temperature was particularly strong with higher cellular levels of RNA at low temperatures, suggesting a compensatory allocation to ribosomes to maintain protein synthesis and growth. These experiments suggest that although P-limitation is the major determinant of growth rate and cellular stoichiometry, there are pronounced effects of temperature also via interaction with P. At the ecosystem level, nutrients and temperature will thus interact, but temperatures would likely exert a stronger impact on these phytoplankton traits indirectly via its force on stratification regimes and vertical nutrient fluxes. PMID:28167934

  1. Dose point kernel for boron-11 decay and the cellular S values in boron neutron capture therapy. (United States)

    Ma, Yunzhi; Geng, JinPeng; Gao, Song; Bao, Shanglian


    The study of the radiobiology of boron neutron capture therapy is based on the cellular level dosimetry of boron-10's thermal neutron capture reaction 10B(n,alpha)7Li, in which one 1.47 MeV helium-4 ion and one 0.84 MeV lithium-7 ion are spawned. Because of the chemical preference of boron-10 carrier molecules, the dose is heterogeneously distributed in cells. In the present work, the (scaled) dose point kernel of boron-11 decay, called 11B-DPK, was calculated by GEANT4 Monte Carlo simulation code. The DPK curve drops suddenly at the radius of 4.26 microm, the continuous slowing down approximation (CSDA) range of a lithium-7 ion. Then, after a slight ascending, the curve decreases to near zero when the radius goes beyond 8.20 microm, which is the CSDA range of a 1.47 MeV helium-4 ion. With the DPK data, S values for nuclei and cells with the boron-10 on the cell surface are calculated for different combinations of cell and nucleus sizes. The S value for a cell radius of 10 microm and a nucleus radius of 5 microm is slightly larger than the value published by Tung et al. [Appl. Radiat. Isot. 61, 739-743 (2004)]. This result is potentially more accurate than the published value since it includes the contribution of a lithium-7 ion as well as the alpha particle.

  2. Sponging of Cellular Proteins by Viral RNAs


    Charley, Phillida A.; Wilusz, Jeffrey


    Viral RNAs accumulate to high levels during infection and interact with a variety of cellular factors including miRNAs and RNA-binding proteins. Although many of these interactions exist to directly modulate replication, translation and decay of viral transcripts, evidence is emerging that abundant viral RNAs may in certain cases serve as a sponge to sequester host non coding RNAs and proteins. By effectively reducing the ability of cellular RNA binding proteins to regulate host cell gene exp...

  3. A preliminary comparison of dendritic cell maturation by total cellular RNA to total cellular lysate derived from breast cancer stem cells

    Directory of Open Access Journals (Sweden)

    Phong Minh Le


    Full Text Available Introduction: Dendritic cells (DCs have been widely considered as the most potent antigen-presenting cells. As such, DC-based vaccines are regarded as a promising strategy in cancer vaccination and therapy. This study compared the maturation of DCs induced by total cellular RNA and cell lysate (i.e. nucleic acid and protein. Methods: Both total RNA and cell lysate were isolated from breast cancer stem cells (BCSCs. The lysates were used to incubate with monocyte-derived immature DCs. To track the transfection efficiency, the BCSCs were stably transfected with green fluorescent protein (GFP. The maturation of DCs was evaluated by expression of costimulatory molecules including CD40, CD80, and CD86. Transfections were confirmed by evaluating GFP expression in DCs at 24 hours post transfection. Results: The results of this study showed that GFP is expressed in DCs after both total RNA and lysate incubation. The expression of costimulatory molecules (CD40, CD80, and CD86 was significantly higher in RNA-transfected DCs than in cell lysate-primed DCs. Conclusion: Our findings suggest that total RNA primed BCSCs can be a suitable platform for DC-based vaccine therapy of breast cancer. [Biomed Res Ther 2016; 3(6.000: 679-686

  4. Mouse hepatitis coronavirus replication induces host translational shutoff and mRNA decay, with concomitant formation of stress granules and processing bodies. (United States)

    Raaben, Matthijs; Groot Koerkamp, Marian J A; Rottier, Peter J M; de Haan, Cornelis A M


    Many viruses, including coronaviruses, induce host translational shutoff, while maintaining synthesis of their own gene products. In this study we performed genome-wide microarray analyses of the expression patterns of mouse hepatitis coronavirus (MHV)-infected cells. At the time of MHV-induced host translational shutoff, downregulation of numerous mRNAs, many of which encode protein translation-related factors, was observed. This downregulation, which is reminiscent of a cellular stress response, was dependent on viral replication and caused by mRNA decay. Concomitantly, phosphorylation of the eukaryotic translation initiation factor 2alpha was increased in MHV-infected cells. In addition, stress granules and processing bodies appeared, which are sites for mRNA stalling and degradation respectively. We propose that MHV replication induces host translational shutoff by triggering an integrated stress response. However, MHV replication per se does not appear to benefit from the inhibition of host protein synthesis, at least in vitro, since viral replication was not negatively affected but rather enhanced in cells with impaired translational shutoff.

  5. Cellular delivery of siRNA mediated by fusion-active virosomes

    NARCIS (Netherlands)

    Huckriede, Anke; De Jonge, Jorgen; Holtrop, Marijke; Wilschut, Jan


    RNA interference is expected to have considerable potential for the development of novel specific therapeutic strategies. However, successful application of RNA interference in vivo will depend on the availability of efficient delivery systems for the introduction of small-interfering RNA (siRNA) in

  6. RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans (United States)

    Son, Heehwa G.; Seo, Mihwa; Ham, Seokjin; Hwang, Wooseon; Lee, Dongyeop; An, Seon Woo A.; Artan, Murat; Seo, Keunhee; Kaletsky, Rachel; Arey, Rachel N.; Ryu, Youngjae; Ha, Chang Man; Kim, Yoon Ki; Murphy, Coleen T.; Roh, Tae-Young; Nam, Hong Gil; Lee, Seung-Jae V.


    Long-lived organisms often feature more stringent protein and DNA quality control. However, whether RNA quality control mechanisms, such as nonsense-mediated mRNA decay (NMD), which degrades both abnormal as well as some normal transcripts, have a role in organismal aging remains unexplored. Here we show that NMD mediates longevity in C. elegans strains with mutations in daf-2/insulin/insulin-like growth factor 1 receptor. We find that daf-2 mutants display enhanced NMD activity and reduced levels of potentially aberrant transcripts. NMD components, including smg-2/UPF1, are required to achieve the longevity of several long-lived mutants, including daf-2 mutant worms. NMD in the nervous system of the animals is particularly important for RNA quality control to promote longevity. Furthermore, we find that downregulation of yars-2/tyrosyl-tRNA synthetase, an NMD target transcript, by daf-2 mutations contributes to longevity. We propose that NMD-mediated RNA surveillance is a crucial quality control process that contributes to longevity conferred by daf-2 mutations. PMID:28276441

  7. Coordinated function of cellular DEAD-box helicases in suppression of viral RNA recombination and maintenance of viral genome integrity.

    Directory of Open Access Journals (Sweden)

    Chingkai Chuang


    Full Text Available The intricate interactions between viruses and hosts include an evolutionary arms race and adaptation that is facilitated by the ability of RNA viruses to evolve rapidly due to high frequency mutations and genetic RNA recombination. In this paper, we show evidence that the co-opted cellular DDX3-like Ded1 DEAD-box helicase suppresses tombusviral RNA recombination in yeast model host, and the orthologous RH20 helicase functions in a similar way in plants. In vitro replication and recombination assays confirm the direct role of the ATPase function of Ded1p in suppression of viral recombination. We also present data supporting a role for Ded1 in facilitating the switch from minus- to plus-strand synthesis. Interestingly, another co-opted cellular helicase, the eIF4AIII-like AtRH2, enhances TBSV recombination in the absence of Ded1/RH20, suggesting that the coordinated actions of these helicases control viral RNA recombination events. Altogether, these helicases are the first co-opted cellular factors in the viral replicase complex that directly affect viral RNA recombination. Ded1 helicase seems to be a key factor maintaining viral genome integrity by promoting the replication of viral RNAs with correct termini, but inhibiting the replication of defective RNAs lacking correct 5' end sequences. Altogether, a co-opted cellular DEAD-box helicase facilitates the maintenance of full-length viral genome and suppresses viral recombination, thus limiting the appearance of defective viral RNAs during replication.

  8. Genetic screening of new genes responsible for cellular adaptation to hypoxia using a genome-wide shRNA library. (United States)

    Yoshino, Seiko; Hara, Toshiro; Weng, Jane S; Takahashi, Yuka; Seiki, Motoharu; Sakamoto, Takeharu


    Oxygen is a vital requirement for multi-cellular organisms to generate energy and cells have developed multiple compensatory mechanisms to adapt to stressful hypoxic conditions. Such adaptive mechanisms are intricately interconnected with other signaling pathways that regulate cellular functions such as cell growth. However, our understanding of the overall system governing the cellular response to the availability of oxygen remains limited. To identify new genes involved in the response to hypoxic stress, we have performed a genome-wide gene knockdown analysis in human lung carcinoma PC8 cells using an shRNA library carried by a lentiviral vector. The knockdown analysis was performed under both normoxic and hypoxic conditions to identify shRNA sequences enriched or lost in the resulting selected cell populations. Consequently, we identified 56 candidate genes that might contribute to the cellular response to hypoxia. Subsequent individual knockdown of each gene demonstrated that 13 of these have a significant effect upon oxygen-sensitive cell growth. The identification of BCL2L1, which encodes a Bcl-2 family protein that plays a role in cell survival by preventing apoptosis, validates the successful design of our screen. The other selected genes have not previously been directly implicated in the cellular response to hypoxia. Interestingly, hypoxia did not directly enhance the expression of any of the identified genes, suggesting that we have identified a new class of genes that have been missed by conventional gene expression analyses to identify hypoxia response genes. Thus, our genetic screening method using a genome-wide shRNA library and the newly-identified genes represent useful tools to analyze the cellular systems that respond to hypoxic stress.

  9. Manipulation of Cellular Processing Bodies and Their Constituents by Viruses


    Pattnaik, Asit K.; Dinh, Phat X.


    The processing bodies (PBs) are a form of cytoplasmic aggregates that house the cellular RNA decay machinery as well as many RNA-binding proteins and mRNAs. The PBs are constitutively present in eukaryotic cells and are involved in maintaining cellular homeostasis by regulating RNA metabolism, cell signaling, and survival. Virus infections result in modification of the PBs and their constituents. Many viruses induce compositionally altered PBs, while many others use specific components of the...

  10. Integrative analysis of miRNA and mRNA paired expression profiling of primary fibroblast derived from diabetic foot ulcers reveals multiple impaired cellular functions. (United States)

    Liang, Liang; Stone, Rivka C; Stojadinovic, Olivera; Ramirez, Horacio; Pastar, Irena; Maione, Anna G; Smith, Avi; Yanez, Vanessa; Veves, Aristides; Kirsner, Robert S; Garlick, Jonathan A; Tomic-Canic, Marjana


    Diabetic foot ulcers (DFUs) are one of the major complications of diabetes. Its molecular pathology remains poorly understood, impeding the development of effective treatments. Although it has been established that multiple cell types, including fibroblasts, keratinocytes, macrophages, and endothelial cells, all contribute to inhibition of healing, less is known regarding contributions of individual cell type. Thus, we generated primary fibroblasts from nonhealing DFUs and evaluated their cellular and molecular properties in comparison to nondiabetic foot fibroblasts (NFFs). Specifically, we analyzed both micro-RNA and mRNA expression profiles of primary DFU fibroblasts. Paired genomic analyses identified a total of 331 reciprocal miRNA-mRNA pairs including 21 miRNAs (FC > 2.0) along with 239 predicted target genes (FC > 1.5) that are significantly and differentially expressed. Of these, we focused on three miRNAs (miR-21-5p, miR-34a-5p, miR-145-5p) that were induced in DFU fibroblasts as most differentially regulated. The involvement of these microRNAs in wound healing was investigated by testing the expression of their downstream targets as well as by quantifying cellular behaviors in prospectively collected and generated cell lines from 15 patients (seven DFUF and eight NFF samples). We found large number of downstream targets of miR-21-5p, miR-34a-5p, miR-145-5p to be coordinately regulated in mRNA profiles, which was confirmed by quantitative real-time PCR. Pathway analysis on paired miRNA-mRNA profiles predicted inhibition of cell movement and cell proliferation, as well as activation of cell differentiation and senescence in DFU fibroblasts, which was confirmed by cellular assays. We concluded that induction of miR-21-5p, miR-34a-5p, miR-145-5p in DFU dermal fibroblasts plays an important role in impairing multiple cellular functions, thus contributing to overall inhibition of healing in DFUs.

  11. Changes in Cellular mRNA Stability, Splicing, and Polyadenylation through HuR Protein Sequestration by a Cytoplasmic RNA Virus

    Directory of Open Access Journals (Sweden)

    Michael D. Barnhart


    Full Text Available The impact of RNA viruses on the posttranscriptional regulation of cellular gene expression is unclear. Sindbis virus causes a dramatic relocalization of the cellular HuR protein from the nucleus to the cytoplasm in infected cells. This is to the result of the expression of large amounts of viral RNAs that contain high-affinity HuR binding sites in their 3′ UTRs effectively serving as a sponge for the HuR protein. Sequestration of HuR by Sindbis virus is associated with destabilization of cellular mRNAs that normally bind HuR and rely on it to regulate their expression. Furthermore, significant changes can be observed in nuclear alternative polyadenylation and splicing events on cellular pre-mRNAs as a result of sequestration of HuR protein by the 3′ UTR of transcripts of this cytoplasmic RNA virus. These studies suggest a molecular mechanism of virus-host interaction that probably has a significant impact on virus replication, cytopathology, and pathogenesis.

  12. Traffic jam on the cellular secretory pathway generated by a replication protein from a plant RNA virus. (United States)

    Hyodo, Kiwamu; Kaido, Masanori; Okuno, Tetsuro


    Although positive-strand RNA [(+)RNA] viruses have a limited coding capacity, they can replicate efficiently in host cells because of their ability to use host-derived proteins, membranes, lipids, and metabolites, and to rewire cellular trafficking pathways. Previously, we showed that a plant RNA virus, the Red clover necrotic mosaic virus (RCNMV), hijacked Arf1 and Sar1, which are small GTPases that regulate the biogenesis of COPI and COPII vesicles, respectively, for viral RNA replication. These small GTPases are relocated from appropriate subcellular compartments to the viral RNA replication sites by p27 replication protein, which raises the possibility that RCNMV interferes with the cellular secretory pathway. Here, we examined this possibility by using green fluorescent protein-fused rice SCAMP1 and Arabidopsis LRR84A as secretory pathway marker proteins and showed that p27 inhibited the trafficking of these proteins. RCNMV-mediated inhibition of the host secretion pathway and its possible impact on plant-virus interaction are discussed.

  13. Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation

    Directory of Open Access Journals (Sweden)

    Miller Eric S


    Full Text Available Abstract Over 50 years of biological research with bacteriophage T4 includes notable discoveries in post-transcriptional control, including the genetic code, mRNA, and tRNA; the very foundations of molecular biology. In this review we compile the past 10 - 15 year literature on RNA-protein interactions with T4 and some of its related phages, with particular focus on advances in mRNA decay and processing, and on translational repression. Binding of T4 proteins RegB, RegA, gp32 and gp43 to their cognate target RNAs has been characterized. For several of these, further study is needed for an atomic-level perspective, where resolved structures of RNA-protein complexes are awaiting investigation. Other features of post-transcriptional control are also summarized. These include: RNA structure at translation initiation regions that either inhibit or promote translation initiation; programmed translational bypassing, where T4 orchestrates ribosome bypass of a 50 nucleotide mRNA sequence; phage exclusion systems that involve T4-mediated activation of a latent endoribonuclease (PrrC and cofactor-assisted activation of EF-Tu proteolysis (Gol-Lit; and potentially important findings on ADP-ribosylation (by Alt and Mod enzymes of ribosome-associated proteins that might broadly impact protein synthesis in the infected cell. Many of these problems can continue to be addressed with T4, whereas the growing database of T4-related phage genome sequences provides new resources and potentially new phage-host systems to extend the work into a broader biological, evolutionary context.

  14. Nonsense-mediated mRNA decay controls the changes in yeast ribosomal protein pre-mRNAs levels upon osmotic stress.

    Directory of Open Access Journals (Sweden)

    Elena Garre

    Full Text Available The expression of ribosomal protein (RP genes requires a substantial part of cellular transcription, processing and translation resources. Thus, the RP expression must be tightly regulated in response to conditions that compromise cell survival. In Saccharomyces cerevisiae cells, regulation of the RP gene expression at the transcriptional, mature mRNA stability and translational levels during the response to osmotic stress has been reported. Reprogramming global protein synthesis upon osmotic shock includes the movement of ribosomes from RP transcripts to stress-induced mRNAs. Using tiling arrays, we show that osmotic stress yields a drop in the levels of RP pre-mRNAs in S. cerevisiae cells. An analysis of the tiling array data, together with transcription rates data, shows a poor correlation, indicating that the drop in the RP pre-mRNA levels is not merely a result of the lowered RP transcription rates. A kinetic study using quantitative RT-PCR confirmed the decrease in the levels of several RP-unspliced transcripts during the first 15 minutes of osmotic stress, which seems independent of MAP kinase Hog1. Moreover, we found that the mutations in the components of the nonsense-mediated mRNA decay (NMD, Upf1, Upf2, Upf3 or in exonuclease Xrn1, eliminate the osmotic stress-induced drop in RP pre-mRNAs. Altogether, our results indicate that the degradation of yeast RP unspliced transcripts by NMD increases during osmotic stress, and suggest that this might be another mechanism to control RP synthesis during the stress response.

  15. Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources.

    Directory of Open Access Journals (Sweden)

    Ravi Shah

    Full Text Available MicroRNA (miRNA expression has rapidly grown into one of the largest fields for disease characterization and development of clinical biomarkers. Consensus is lacking in regards to the optimal sample source or if different circulating sources are concordant. Here, using miRNA measurements from contemporaneously obtained whole blood- and plasma-derived RNA from 2391 individuals, we demonstrate that plasma and blood miRNA levels are divergent and may reflect different biological processes and disease associations.

  16. Picornaviruses and nuclear functions: targeting a cellular compartment distinct from the replication site of a positive-strand RNA virus. (United States)

    Flather, Dylan; Semler, Bert L


    The compartmentalization of DNA replication and gene transcription in the nucleus and protein production in the cytoplasm is a defining feature of eukaryotic cells. The nucleus functions to maintain the integrity of the nuclear genome of the cell and to control gene expression based on intracellular and environmental signals received through the cytoplasm. The spatial separation of the major processes that lead to the expression of protein-coding genes establishes the necessity of a transport network to allow biomolecules to translocate between these two regions of the cell. The nucleocytoplasmic transport network is therefore essential for regulating normal cellular functioning. The Picornaviridae virus family is one of many viral families that disrupt the nucleocytoplasmic trafficking of cells to promote viral replication. Picornaviruses contain positive-sense, single-stranded RNA genomes and replicate in the cytoplasm of infected cells. As a result of the limited coding capacity of these viruses, cellular proteins are required by these intracellular parasites for both translation and genomic RNA replication. Being of messenger RNA polarity, a picornavirus genome can immediately be translated upon entering the cell cytoplasm. However, the replication of viral RNA requires the activity of RNA-binding proteins, many of which function in host gene expression, and are consequently localized to the nucleus. As a result, picornaviruses disrupt nucleocytoplasmic trafficking to exploit protein functions normally localized to a different cellular compartment from which they translate their genome to facilitate efficient replication. Furthermore, picornavirus proteins are also known to enter the nucleus of infected cells to limit host-cell transcription and down-regulate innate antiviral responses. The interactions of picornavirus proteins and host-cell nuclei are extensive, required for a productive infection, and are the focus of this review.

  17. CBFA1 and topoisomerase I mRNA levels decline during cellular aging of human trabecular osteoblasts

    DEFF Research Database (Denmark)

    Christiansen, M; Kveiborg, Marie; Kassem, M


    In order to understand the reasons for age-related impairment of the function of bone forming osteoblasts, we have examined the steady-state mRNA levels of the transcription factor CBFA1 and topoisomerase I during cellular aging of normal human trabecular osteoblasts, by the use of semiquantitative...... reverse transcriptase-polymerase chain reaction (RT-PCR). There is a progressive and significant reduction of the CBFA1 steady-state mRNA level down to 50% during cellular aging of human osteoblasts. In comparison to the normal cells, human osteosarcoma cell lines SaOS-2 and KHOS/NP, and the SV40......-transformed human lung fibroblast cell line MRC5V2 have 20 to 40% higher levels of CBFA1 mRNA. Similar levels of CBFA1 mRNA are detectable in normal human skin fibroblasts, and these cells also exhibit an age-related decline to the same extent. In addition, the expression of topoisomerase I is reduced by 40...

  18. Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis[OPEN (United States)

    Willmann, Matthew R.


    RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5′ end to the 3′ end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of cotranslational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that cotranslational RNA decay is XRN4 dependent. Additionally, studies in plants lacking CAP BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap binding complex, reveal a role for this protein in cotranslational decay. In total, our results demonstrate the global prevalence and features of cotranslational RNA decay in a plant transcriptome. PMID:27758893

  19. Genome-wide Mapping of Cellular Protein-RNA Interactions Enabled by Chemical Crosslinking

    Institute of Scientific and Technical Information of China (English)

    Xiaoyu Li; Jinghui Song; Chengqi Yi


    RNA-protein interactions influence many biological processes. Identifying the binding sites of RNA-binding proteins (RBPs) remains one of the most fundamental and important chal-lenges to the studies of such interactions. Capturing RNA and RBPs via chemical crosslinking allows stringent purification procedures that significantly remove the non-specific RNA and protein interactions. Two major types of chemical crosslinking strategies have been developed to date, i.e., UV-enabled crosslinking and enzymatic mechanism-based covalent capture. In this review, we com-pare such strategies and their current applications, with an emphasis on the technologies themselves rather than the biology that has been revealed. We hope such methods could benefit broader audi-ence and also urge for the development of new methods to study RNA RBP interactions.

  20. Histological staining methods preparatory to laser capture microdissection significantly affect the integrity of the cellular RNA

    Directory of Open Access Journals (Sweden)

    Li Ming-Chung


    Full Text Available Abstract Background Gene expression profiling by microarray analysis of cells enriched by laser capture microdissection (LCM faces several technical challenges. Frozen sections yield higher quality RNA than paraffin-imbedded sections, but even with frozen sections, the staining methods used for histological identification of cells of interest could still damage the mRNA in the cells. To study the contribution of staining methods to degradation of results from gene expression profiling of LCM samples, we subjected pellets of the mouse plasma cell tumor cell line TEPC 1165 to direct RNA extraction and to parallel frozen sectioning for LCM and subsequent RNA extraction. We used microarray hybridization analysis to compare gene expression profiles of RNA from cell pellets with gene expression profiles of RNA from frozen sections that had been stained with hematoxylin and eosin (H&E, Nissl Stain (NS, and for immunofluorescence (IF as well as with the plasma cell-revealing methyl green pyronin (MGP stain. All RNAs were amplified with two rounds of T7-based in vitro transcription and analyzed by two-color expression analysis on 10-K cDNA microarrays. Results The MGP-stained samples showed the least introduction of mRNA loss, followed by H&E and immunofluorescence. Nissl staining was significantly more detrimental to gene expression profiles, presumably owing to an aqueous step in which RNA may have been damaged by endogenous or exogenous RNAases. Conclusion RNA damage can occur during the staining steps preparatory to laser capture microdissection, with the consequence of loss of representation of certain genes in microarray hybridization analysis. Inclusion of RNAase inhibitor in aqueous staining solutions appears to be important in protecting RNA from loss of gene transcripts.

  1. Systematic analysis of cis-elements in unstable mRNAs demonstrates that CUGBP1 is a key regulator of mRNA decay in muscle cells.

    Directory of Open Access Journals (Sweden)

    Jerome E Lee

    Full Text Available BACKGROUND: Dramatic changes in gene expression occur in response to extracellular stimuli and during differentiation. Although transcriptional effects are important, alterations in mRNA decay also play a major role in achieving rapid and massive changes in mRNA abundance. Moreover, just as transcription factor activity varies between different cell types, the factors influencing mRNA decay are also cell-type specific. PRINCIPAL FINDINGS: We have established the rates of decay for over 7000 transcripts expressed in mouse C2C12 myoblasts. We found that GU-rich (GRE and AU-rich (ARE elements are over-represented in the 3'UTRs of short-lived mRNAs and that these mRNAs tend to encode factors involved in cell cycle and transcription regulation. Stabilizing elements were also identified. By comparing mRNA decay rates in C2C12 cells with those previously measured for pluripotent and differentiating embryonic stem (ES cells, we identified several groups of transcripts that exhibit cell-type specific decay rates. Further, whereas in C2C12 cells the impact of GREs on mRNA decay appears to be greater than that of AREs, AREs are more significant in ES cells, supporting the idea that cis elements make a cell-specific contribution to mRNA stability. GREs are recognized by CUGBP1, an RNA-binding protein and instability factor whose function is affected in several neuromuscular diseases. We therefore utilized RNA immunoprecipitation followed by microarray (RIP-Chip to identify CUGBP1-associated transcripts. These mRNAs also showed dramatic enrichment of GREs in their 3'UTRs and encode proteins linked with cell cycle, and intracellular transport. Interestingly several CUGBP1 substrate mRNAs, including those encoding the myogenic transcription factors Myod1 and Myog, are also bound by the stabilizing factor HuR in C2C12 cells. Finally, we show that several CUGBP1-associated mRNAs containing 3'UTR GREs, including Myod1, are stabilized in cells depleted of CUGBP1

  2. Cockayne's syndrome: correlation of clinical features with cellular sensitivity of RNA synthesis to UV irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Lehmann, A.R.; Thompson, A.F.; Harcourt, S.A. (Medical Research Council, Brighton (United Kingdom). Cell Mutation Unit); Stefanini, Miria (Consiglio Nazionale delle Ricerche, Pavia (Italy). Ist. di Genetica Biochimica ed Evoluzionistica); Norris, P.G. (Addenbrooke' s Hospital, Cambridge (United Kingdom))


    Cockayne's syndrome (CS) is a rare autosomal recessive disorder with dwarfism, mental retardation, and otherwise clinically heterogeneous features. In cultured CS fibroblasts, the failure of RNA synthesis to recover to normal rates after UV-C irradiation provides a useful and relatively simple diagnostic test. We have measured post-UV-C RNA synthesis in 52 patients for whom a clinical diagnosis of CS was considered a possibility. Twenty-nine patients showed the defect characteristic of CS cells, and 23 had a normal response. We have attempted to correlate the cellular diagnosis with the different clinical features of the disorder. Clinical details of the patients were obtained from referring clinicians in the form of a questionnaire. Our results show that, apart from the cardinal features of dwarfism and mental retardation, sun sensitivity correlated best with a positive cellular diagnosis. Pigmentary retinopathy, gait defects, and dental caries were also good positive indicators, although several patients with a positive cellular diagnosis did not have these features. (Author).

  3. The herpes simplex virus host shutoff RNase degrades cellular and viral mRNAs made before infection but not viral mRNA made after infection. (United States)

    Taddeo, Brunella; Zhang, Weiran; Roizman, Bernard


    A herpes simplex virus tegument protein brought into the cell during infection and designated the virion host shutoff protein (VHS) is an endoribonuclease that degrades mRNA. The prevailing view for many years has been that the VHS-RNase does not discriminate between cellular and viral RNAs and that the viruses prevail because the accumulation of viral transcripts outpaces their degradation. Here we report the following. (i) The degradation of viral mRNA made during infection of Vero or HEp-2 cells proceeds at a much-reduced rate compared to that of cellular mRNA. In effect, viral mRNAs are largely stable, whereas cellular mRNAs are rapidly degraded or, in the case of AU-rich mRNA, cleaved and rendered dysfunctional. (ii) In contrast to viral mRNAs made after infection, viral mRNAs expressed by plasmids transfected into cells prior to infection are degraded after infection at a rate comparable to that of cellular mRNAs. Moreover, the mRNA encoded by the transfected plasmid is hyperadenylated in the infected cell. Hyperadenylation but not degradation of mRNAs is blocked by actinomycin D. The results indicate that VHS-mRNA discriminates between viral and cellular mRNA but only in the context of infection and that discrimination is not based on the sequence of the mRNA but most likely on one or more viral factors expressed in the infected cell.

  4. Genetics of the DST-mediated mRNA decay pathway using a transgene-based selection. (United States)

    Lidder, P; Johnson, M A; Sullivan, M L; Thompson, D M; Pérez-Amador, M A; Howard, C J; Green, P J


    mRNA sequences that control abundance, localization and translation initiation have been identified, yet the factors that recognize these sequences are largely unknown. In this report, a transgene-based strategy designed to isolate mutants of Arabidopsis thaliana that fail to recognize these sequences is described. In this strategy, a selectable gene and a screenable marker gene are put under the control of the sequence element being analysed and mutants are selected with altered abundance of the corresponding marker RNAs. The selection of mutants deficient in recognition of the DST (downstream) mRNA degradation signal is used as a test-case to illustrate some of the technical aspects that have facilitated success. Using this strategy, we report the isolation of a new mutant, dst3, deficient in the DST-mediated mRNA decay pathway. The targeted genetic strategy described circumvents certain technical limitations of biochemical approaches. Hence, it provides a means to investigate a variety of other mechanisms responsible for post-transcriptional regulation.

  5. CUGBP1 and MBNL1 preferentially bind to 3 ' UTRs and facilitate mRNA decay

    DEFF Research Database (Denmark)

    Masuda, A.; Andersen, H. S.; Doktor, T. K.


    CUGBP1 and MBNL1 are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. We globally determined the in vivo RNA-binding sites of CUGBP1 and MBNL1. Interestingly, CUGBP1 and MBNL1 are both preferentially bound to 39 UTRs. Analysis of CUGBP1...... that CUGBP1 and MBNL1 regulate alternative splicing. Screening by exon array and validation by RT-PCR revealed position dependence of CUGBP1- and MBNL1-binding sites on the resulting alternative splicing pattern. This study suggests that regulation of CUGBP1 and MBNL1 is essential for accurate control...

  6. Final report: FASEB Summer Research Conference on ''Post-transcriptional control of gene expression: Effectors of mRNA decay'' [agenda and attendees list

    Energy Technology Data Exchange (ETDEWEB)

    Maquat, Lynne


    The goal of this meeting was to provide an interactive forum for scientists working on prokaryotic and eukaryotic mRNA decay. A special seminar presented by a leader in the field of mRNA decay in S. cerevisiae focused on what is known and what needs to be determined, not only for yeast but for other organisms. The large attendance (110 participants) reflects the awareness that mRNA decay is a key player in gene regulation in a way that is affected by the many steps that precede mRNA formation. Sessions were held on the following topics: mRNA transport and mRNP; multicomponent eukaryotic nucleases; nonsense-mediated mRNA decay and nonsense-associated altered splicing; Cis-acting sequences/Trans-acting factors of mRNA decay; translational accuracy; multicomponent bacterial nucleases; interplay between mRNA polyadenylation, translation and decay in prokaryotes and prokaryotic organelles; and RNA interference and other RNA mediators of gene expression. In addition to the talks and two poster sessions, there were three round tables: (1) Does translation occur in the nucleus? (2) Differences and similarities in the mechanisms of mRNA decay in different eukaryotes, and (3) RNA surveillance in bacteria?

  7. Crystal Structure of the N-Terminal RNA Recognition Motif of mRNA Decay Regulator AUF1

    Directory of Open Access Journals (Sweden)

    Young Jun Choi


    Full Text Available AU-rich element binding/degradation factor 1 (AUF1 plays a role in destabilizing mRNAs by forming complexes with AU-rich elements (ARE in the 3′-untranslated regions. Multiple AUF1-ARE complexes regulate the translation of encoded products related to the cell cycle, apoptosis, and inflammation. AUF1 contains two tandem RNA recognition motifs (RRM and a Gln- (Q- rich domain in their C-terminal region. To observe how the two RRMs are involved in recognizing ARE, we obtained the AUF1-p37 protein covering the two RRMs. However, only N-terminal RRM (RRM1 was crystallized and its structure was determined at 1.7 Å resolution. It appears that the RRM1 and RRM2 separated before crystallization. To demonstrate which factors affect the separate RRM1-2, we performed limited proteolysis using trypsin. The results indicated that the intact proteins were cleaved by unknown proteases that were associated with them prior to crystallization. In comparison with each of the monomers, the conformations of the β2-β3 loops were highly variable. Furthermore, a comparison with the RRM1-2 structures of HuR and hnRNP A1 revealed that a dimer of RRM1 could be one of the possible conformations of RRM1-2. Our data may provide a guidance for further structural investigations of AUF1 tandem RRM repeat and its mode of ARE binding.

  8. Cellular and molecular phenotypes depending upon the RNA repair system RtcAB of Escherichia coli (United States)

    Engl, Christoph; Schaefer, Jorrit; Kotta-Loizou, Ioly; Buck, Martin


    RNA ligases function pervasively across the three kingdoms of life for RNA repair, splicing and can be stress induced. The RtcB protein (also HSPC117, C22orf28, FAAP and D10Wsu52e) is one such conserved ligase, involved in tRNA and mRNA splicing. However, its physiological role is poorly described, especially in bacteria. We now show in Escherichia coli bacteria that the RtcR activated rtcAB genes function for ribosome homeostasis involving rRNA stability. Expression of rtcAB is activated by agents and genetic lesions which impair the translation apparatus or may cause oxidative damage in the cell. Rtc helps the cell to survive challenges to the translation apparatus, including ribosome targeting antibiotics. Further, loss of Rtc causes profound changes in chemotaxis and motility. Together, our data suggest that the Rtc system is part of a previously unrecognized adaptive response linking ribosome homeostasis with basic cell physiology and behaviour. PMID:27402162

  9. The Cellular Processing Capacity Limits the Amounts of Chimeric U7 snRNA Available for Antisense Delivery. (United States)

    Eckenfelder, Agathe; Tordo, Julie; Babbs, Arran; Davies, Kay E; Goyenvalle, Aurélie; Danos, Olivier


    Many genetic diseases are induced by mutations disturbing the maturation of pre-mRNAs, often affecting splicing. Antisense oligoribonucleotides (AONs) have been used to modulate splicing thereby circumventing the deleterious effects of mutations. Stable delivery of antisense sequences is achieved by linking them to small nuclear RNA (snRNAs) delivered by viral vectors, as illustrated by studies where therapeutic exon skipping was obtained in animal models of Duchenne muscular dystrophy (DMD). Yet, clinical translation of these approaches is limited by the amounts of vector to be administered. In this respect, maximizing the amount of snRNA antisense shuttle delivered by the vector is essential. Here, we have used a muscle- and heart-specific enhancer (MHCK) to drive the expression of U7 snRNA shuttles carrying antisense sequences against the human or murine DMD pre-mRNAs. Although antisense delivery and subsequent exon skipping were improved both in tissue culture and in vivo, we observed the formation of additional U7 snRNA by-products following gene transfer. These included aberrantly 3' processed as well as unprocessed species that may arise because of the saturation of the cellular processing capacity. Future efforts to increase the amounts of functional U7 shuttles delivered into a cell will have to take this limitation into account.

  10. Opposite Prognostic Significance of Cellular and Serum Circulating MicroRNA-150 in Patients with Chronic Lymphocytic Leukemia. (United States)

    Stamatopoulos, Basile; Van Damme, Michaël; Crompot, Emerence; Dessars, Barbara; Housni, Hakim El; Mineur, Philippe; Meuleman, Nathalie; Bron, Dominique; Lagneaux, Laurence


    MicroRNAs (or miRs) play a crucial role in chronic lymphocytic leukemia (CLL) physiopathology and prognosis. In addition, circulating microRNAs in body fluids have been proposed as new biomarkers. We investigated the expression of matched cellular and serum circulating microRNA-150 by quantitative real-time PCR (qPCR) from purified CD19(+) cells or from CLL serums obtained at diagnosis in a cohort of 273/252 CLL patients with a median follow-up of 78 months (range 7-380) and correlated it to other biological or clinical parameters. We showed that miR-150 was significantly overexpressed in CLL cells/serums compared with healthy subjects (P disease aggressiveness and poor prognostic factors. In contrast, a high level of serum miR-150 was associated with tumor burden markers and some markers of poor prognosis. Similarly, cellular and serum miR-150 also predicted treatment-free survival (TFS) and overall survival (OS) in an opposite manner: patients with low cellular/serum miR-150 levels have median TFS of 40/111 months compared with high-level patients who have a median TFS of 122/60 months (P disease progression and that cellular miR-150 could be regulated by its release into the extracellular space. Cellular and serum levels of miR-150 are associated with opposite clinical prognoses and could be used to molecularly monitor disease evolution as a new prognostic factor in CLL.

  11. Knockdown of cellular RNA helicase DDX3 by short hairpin RNAs suppresses HIV-1 viral replication without inducing apoptosis. (United States)

    Ishaq, Musarat; Hu, Jiajie; Wu, Xiaoyun; Fu, Qiong; Yang, Yalin; Liu, Qingzhen; Guo, Deyin


    The targeting of a cellular co-factor, rather than the HIV-1-specific RNAs, by small interfering RNAs holds promise as the rapid mutational ability of the HIV-1 genome may obviate the potential clinical use of RNAi against this virus. The DEAD-box RNA helicase DDX3 is an essential Rev co-factor in the CRM1-Rev-RRE complex that promotes the export of unspliced and single-spliced HIV-1 RNAs from the nucleus to cytoplasm. In this report, human DDX3 was targeted by specific short hairpin RNAs, and the down-regulation of cell's endogenous DDX3 suppressed the nuclear export of unspliced HIV-1 RNAs but did not affect the cell viability. We further showed that the knockdown of cellular DDX3 could effectively inhibit the replication of HIV-1. Therefore, the current results suggest that the RNA helicase DDX3 may become a potential target by RNAi for future genetic therapy of HIV/AIDS.

  12. Cloning, Sequence Analysis and Identification of a Nonsense Mutation-mediated mRNA Decay of Porcine GSTM2 Gene

    Institute of Scientific and Technical Information of China (English)

    Jingshu HUANG; Yuanzhu XIONG; Changyan DENG; Bo ZUO; Dequan XU; Minggang LEI; Siwen JIANG


    The glutathione S-transferase mu 2 gene (GSTM2) encodes a GST functioning in the elimination of electrophilic compounds and the regulation of cell growth. In this study, the sequence of porcine GSTM2 gene that contains the complete sequence encoding a protein of 218 amino acids was cloned.The deduced amino acid sequence shared 76%, 78% and 76% identity with that of human, mouse and rat,respectively. mRNA expression analysis showed that the porcine GSTM2 gene was expressed at a high level in liver and testis, at a medium level in longissimus dorsi muscle, adipose tissue, spleen and lung, at a low level in kidney, and at a very low level in heart and embryo. A nonsense mutation (CGA→TGA) resulted from C27T substitution in the fifth exon to produce a premature translation termination codon was identified, and it was discovered that nonsense-mediated mRNA decay might have an effect on the regulation of porcine GSTM2 gene expression. This polymorphism was analyzed in Large White, Landrace, Meishan and Qingping pig populations using the Taq Ⅰ-polymerase chain reaction-restriction fragment length polymorphism method.The result showed that allele C had a higher frequency than allele T in each population.

  13. Identification and characterization of small molecules that inhibit nonsense-mediated RNA decay and suppress nonsense p53 mutations. (United States)

    Martin, Leenus; Grigoryan, Arsen; Wang, Ding; Wang, Jinhua; Breda, Laura; Rivella, Stefano; Cardozo, Timothy; Gardner, Lawrence B


    Many of the gene mutations found in genetic disorders, including cancer, result in premature termination codons (PTC) and the rapid degradation of their mRNAs by nonsense-mediated RNA decay (NMD). We used virtual library screening, targeting a pocket in the SMG7 protein, a key component of the NMD mechanism, to identify compounds that disrupt the SMG7-UPF1 complex and inhibit NMD. Several of these compounds upregulated NMD-targeted mRNAs at nanomolar concentrations, with minimal toxicity in cell-based assays. As expected, pharmacologic NMD inhibition disrupted SMG7-UPF1 interactions. When used in cells with PTC-mutated p53, pharmacologic NMD inhibition combined with a PTC "read-through" drug led to restoration of full-length p53 protein, upregulation of p53 downstream transcripts, and cell death. These studies serve as proof-of-concept that pharmacologic NMD inhibitors can restore mRNA integrity in the presence of PTC and can be used as part of a strategy to restore full-length protein in a variety of genetic diseases.

  14. Identification and characterization of small molecules that inhibit nonsense mediated RNA decay and suppress nonsense p53 mutations (United States)

    Martin, Leenus; Grigoryan, Arsen; Wang, Ding; Wang, Jinhua; Breda, Laura; Rivella, Stefano; Cardozo, Timothy; Gardner, Lawrence B.


    Many of the gene mutations found in genetic disorders, including cancer, result in premature termination codons (PTCs) and the rapid degradation of their mRNAs by nonsense mediated RNA decay (NMD). We used virtual library screening (VLS) targeting a pocket in the SMG7 protein, a key component of the NMD mechanism, to identify compounds that disrupt the SMG7-UPF1 complex and inhibit NMD. Several of these compounds upregulated NMD targeted mRNAs at nanomolar concentrations with minimal toxicity in cell based assays. As expected, pharmacological NMD inhibition disrupted SMG7-UPF1 interactions. When used in cells with PTC mutated p53, pharmacological NMD inhibition combined with a PTC “read-through” drug led to restoration of full-length p53 protein, upregulation of p53 downstream transcripts, and cell death. These studies serve as proof-of-concept that pharmacological NMD inhibitors can restore mRNA integrity in the presence of PTC and be used as part of a strategy to restore full length protein in a variety of genetic diseases. PMID:24662918

  15. Insulin Signaling Augments eIF4E-Dependent Nonsense-Mediated mRNA Decay in Mammalian Cells. (United States)

    Park, Jungyun; Ahn, Seyoung; Jayabalan, Aravinth K; Ohn, Takbum; Koh, Hyun Chul; Hwang, Jungwook


    Nonsense-mediated mRNA decay (NMD) modulates the level of mRNA harboring a premature termination codon (PTC) in a translation-dependent manner. Inhibition of translation is known to impair NMD; however, few studies have investigated the correlation between enhanced translation and increased NMD. Here, we demonstrate that insulin signaling events increase translation, leading to an increase in NMD of eIF4E-bound transcripts. We provide evidence that (i) insulin-mediated enhancement of translation augments NMD and rapamycin abrogates this enhancement; (ii) an increase in AKT phosphorylation due to inhibition of PTEN facilitates NMD; (iii) insulin stimulation increases the binding of up-frameshift factor 1 (UPF1), most likely to eIF4E-bound PTC-containing transcripts; and (iv) insulin stimulation induces the colocalization of UPF1 and eIF4E in processing bodies. These results illustrate how extracellular signaling promotes the removal of eIF4E-bound NMD targets.

  16. Transcription of human respiratory syncytial virus genome RNA in vitro: requirement of cellular factor(s).


    Barik, S


    Extracts made from human respiratory syncytial virus (RSV)-infected Hep-2 cells synthesized mRNAs encoded by all known viral genes. In contrast, RSV ribonucleoproteins purified from infected cells failed to transcribe in vitro; transcription was restored by addition of a cytoplasmic extract of uninfected Hep-2 cells, demonstrating that a cellular factor(s) has a role in RSV gene expression. Quantitation of the individual gene mRNAs transcribed in vitro revealed polarity of transcription of th...

  17. PLGA nanoparticles codeliver paclitaxel and Stat3 siRNA to overcome cellular resistance in lung cancer cells

    Directory of Open Access Journals (Sweden)

    Su WP


    Full Text Available Wen-Pin Su,1,2 Fong-Yu Cheng,3 Dar-Bin Shieh,3–6 Chen-Sheng Yeh,5–7 Wu-Chou Su1,2,81Graduate Institute of Clinical Medicine, College of Medicine, National Cheng Kung University; 2Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University; 3Institute of Oral Medicine, College of Medicine, National Cheng Kung University; 4Department of Stomatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University; 5Advanced Optoelectronic Technology Center; 6Center for Frontier Materials and Micro/Nano Science and Technology, and 7Department of Chemistry, National Cheng Kung University; 8Cancer Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.Abstract: Background: Effective cancer chemotherapy remains an important issue in cancer treatment, and signal transducer and activator of transcription-3 (Stat3 activation leads to cellular resistance of anticancer agents. Polymers are ideal vectors to carry both chemotherapeutics and small interfering ribonucleic acid (siRNA to enhance antitumor efficacy. In this paper, poly(lactic-co-glycolic acid (PLGA nanoparticles loaded with paclitaxel and Stat3 siRNA were successfully synthesized, and their applications in cancer cells were investigated.Methods: Firstly, paclitaxel was enclosed by PLGA nanoparticles through solvent evaporation. They were then coated with cationic polyethylenimine polymer (PLGA-PEI-TAX, enabling it to carry Stat3 siRNA on its surface through electrostatic interactions (PLGA-PEI-TAX-S3SI. The size, zeta potential, deliver efficacy, and release profile of the PLGA nanocomplexes were characterized in vitro. The cellular uptake, intracellular nanoparticle trajectory, and subsequent cellular events were evaluated after treatment with various PLGA nanocomplexes in human lung cancer A549 cells and A549-derived paclitaxel

  18. UPF1, a conserved nonsense-mediated mRNA decay factor, regulates cyst wall protein transcripts in Giardia lamblia.

    Directory of Open Access Journals (Sweden)

    Yi-Hsiu Chen

    Full Text Available The Giardia lamblia cyst wall is required for survival outside the host and infection. Three cyst wall protein (cwp genes identified to date are highly up-regulated during encystation. However, little is known of the molecular mechanisms governing their gene regulation. Messenger RNAs containing premature stop codons are rapidly degraded by a nonsense-mediated mRNA decay (NMD system to avoid production of non-functional proteins. In addition to RNA surveillance, NMD also regulates thousands of naturally occurring transcripts through a variety of mechanisms. It is interesting to know the NMD pathway in the primitive eukaryotes. Previously, we have found that the giardial homologue of a conserved NMD factor, UPF1, may be functionally conserved and involved in NMD and in preventing nonsense suppression. In this study, we tested the hypothesis that NMD factors can regulate some naturally occurring transcripts in G. lamblia. We found that overexpression of UPF1 resulted in a significant decrease of the levels of CWP1 and cyst formation and of the endogenous cwp1-3, and myb2 mRNA levels and stability. This indicates that NMD could contribute to the regulation of the cwp1-3 and myb2 transcripts, which are key to G. lamblia differentiation into cyst. Interestingly, we also found that UPF1 may be involved in regulation of eight other endogenous genes, including up-regulation of the translation elongation factor gene, whose product increases translation which is required for NMD. Our results indicate that NMD factor could contribute to the regulation of not only nonsense containing mRNAs, but also mRNAs of the key encystation-induced genes and other endogenous genes in the early-diverging eukaryote, G. lamblia.

  19. The interaction of the cellular export adaptor protein Aly/REF with ICP27 contributes to the efficiency of herpes simplex virus 1 mRNA export. (United States)

    Tian, Xiaochen; Devi-Rao, Gayathri; Golovanov, Alexander P; Sandri-Goldin, Rozanne M


    Herpes simplex virus 1 (HSV-1) protein ICP27 enables viral mRNA export by accessing the cellular mRNA export receptor TAP/NXF, which guides mRNA through the nuclear pore complex. ICP27 binds viral mRNAs and interacts with TAP/NXF, providing a link to the cellular mRNA export pathway. ICP27 also interacts with the mRNA export adaptor protein Aly/REF, which binds cellular mRNAs and also interacts with TAP/NXF. Studies using small interfering RNA (siRNA) knockdown indicated that Aly/REF is not required for cellular mRNA export, and similar knockdown studies during HSV-1 infection led us to conclude that Aly/REF may be dispensable for viral RNA export. Recently, the structural basis of the interaction of ICP27 with Aly/REF was elucidated at atomic resolution, and it was shown that three ICP27 residues, W105, R107, and L108, interface with the RNA recognition motif (RRM) domain of Aly/REF. Here, to determine the role the interaction of ICP27 and Aly/REF plays during infection, these residues were mutated to alanine, and a recombinant virus, WRL-A, was constructed. Virus production was reduced about 10-fold during WRL-A infection, and export of ICP27 protein and most viral mRNAs was less efficient. We conclude that interaction of ICP27 with Aly/REF contributes to efficient viral mRNA export.

  20. Interferon (IFN) and Cellular Immune Response Evoked in RNA-Pattern Sensing During Infection with Hepatitis C Virus (HCV). (United States)

    Nakai, Masato; Oshiumi, Hiroyuki; Funami, Kenji; Okamoto, Masaaki; Matsumoto, Misako; Seya, Tsukasa; Sakamoto, Naoya


    Hepatitis C virus (HCV) infects hepatocytes but not dendritic cells (DCs), but DCs effectively mature in response to HCV-infected hepatocytes. Using gene-disrupted mice and hydrodynamic injection strategy, we found the MAVS pathway to be crucial for induction of type III interferons (IFNs) in response to HCV in mouse. Human hepatocytes barely express TLR3 under non-infectious states, but frequently express it in HCV infection. Type I and III IFNs are induced upon stimulation with polyI:C, an analog of double-stranded (ds)RNA. Activation of TLR3 and the TICAM-1 pathway, followed by DC-mediated activation of cellular immunity, is augmented during exposure to viral RNA. Although type III IFNs are released from replication-competent human hepatocytes, DC-mediated CTL proliferation and NK cell activation hardly occur in response to the released type III IFNs. Yet, type I IFNs and HCV-infected hepatocytes can induce maturation of DCs in either human or mouse origin. In addition, mouse CD8+ DCs mature in response to HCV-infected hepatocytes unless the TLR3/TICAM-1 pathway is blocked. We found the exosomes containing HCV RNA in the supernatant of the HCV-infected hepatocytes act as a source of TLR3-mediated DC maturation. Here we summarize our view on the mechanism by which DCs mature to induce NK and CTL in a status of HCV infection.

  1. Luciferase mRNA Transfection of Antigen Presenting Cells Permits Sensitive Nonradioactive Measurement of Cellular and Humoral Cytotoxicity

    Directory of Open Access Journals (Sweden)

    Tana A. Omokoko


    Full Text Available Immunotherapy is rapidly evolving as an effective treatment option for many cancers. With the emerging fields of cancer vaccines and adoptive cell transfer therapies, there is an increasing demand for high-throughput in vitro cytotoxicity assays that efficiently analyze immune effector functions. The gold standard 51Cr-release assay is very accurate but has the major disadvantage of being radioactive. We reveal the development of a versatile and nonradioactive firefly luciferase in vitro transcribed (IVT RNA-based assay. Demonstrating high efficiency, consistency, and excellent target cell viability, our optimized luciferase IVT RNA is used to transfect dividing and nondividing primary antigen presenting cells. Together with the long-lasting expression and minimal background, the direct measurement of intracellular luciferase activity of living cells allows for the monitoring of killing kinetics and displays paramount sensitivity. The ability to cotransfect the IVT RNA of the luciferase reporter and the antigen of interest into the antigen presenting cells and its simple read-out procedure render the assay high-throughput in nature. Results generated were comparable to the 51Cr release and further confirmed the assay’s ability to measure antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity. The assay’s combined simplicity, practicality, and efficiency tailor it for the analysis of antigen-specific cellular and humoral effector functions during the development of novel immunotherapies.

  2. The eIF4E-Binding Protein 4E-T Is a Component of the mRNA Decay Machinery that Bridges the 5′ and 3′ Termini of Target mRNAs

    Directory of Open Access Journals (Sweden)

    Tamiko Nishimura


    Full Text Available Eukaryotic mRNA degradation often initiates with the recruitment of the CCR4-NOT deadenylase complex and decay factors to the mRNA 3′ terminus. How the 3′-proximal decay machinery interacts with the 5′-terminal cap structure in order to engender mRNA decapping and 5′–3′ degradation is unclear. Human 4E-T is an eIF4E-binding protein that has been reported to promote mRNA decay, albeit via an unknown mechanism. Here, we show that 4E-T is a component of the mRNA decay machinery and interacts with factors including DDX6, LSM14, and the LSM1-7-PAT1 complex. We also provide evidence that 4E-T associates with, and enhances the decay of, mRNAs targeted by the CCR4-NOT deadenylase complex, including microRNA targets. Importantly, we demonstrate that 4E-T must interact with eIF4E to engender mRNA decay. Taken together, our data support a model where 4E-T promotes mRNA turnover by physically linking the 3′-terminal mRNA decay machinery to the 5′ cap via its interaction with eIF4E.

  3. The application of nonsense-mediated mRNA decay inhibition to the identification of breast cancer susceptibility genes

    Directory of Open Access Journals (Sweden)

    Johnson Julie K


    Full Text Available Abstract Background Identification of novel, highly penetrant, breast cancer susceptibility genes will require the application of additional strategies beyond that of traditional linkage and candidate gene approaches. Approximately one-third of inherited genetic diseases, including breast cancer susceptibility, are caused by frameshift or nonsense mutations that truncate the protein product 1. Transcripts harbouring premature termination codons are selectively and rapidly degraded by the nonsense-mediated mRNA decay (NMD pathway. Blocking the NMD pathway in any given cell will stabilise these mutant transcripts, which can then be detected using gene expression microarrays. This technique, known as gene identification by nonsense-mediated mRNA decay inhibition (GINI, has proved successful in identifying sporadic nonsense mutations involved in many different cancer types. However, the approach has not yet been applied to identify germline mutations involved in breast cancer. We therefore attempted to use GINI on lymphoblastoid cell lines (LCLs from multiple-case, non- BRCA1/2 breast cancer families in order to identify additional high-risk breast cancer susceptibility genes. Methods We applied GINI to a total of 24 LCLs, established from breast-cancer affected and unaffected women from three multiple-case non-BRCA1/2 breast cancer families. We then used Illumina gene expression microarrays to identify transcripts stabilised by the NMD inhibition. Results The expression profiling identified a total of eight candidate genes from these three families. One gene, PPARGC1A, was a candidate in two separate families. We performed semi-quantitative real-time reverse transcriptase PCR of all candidate genes but only PPARGC1A showed successful validation by being stabilised in individuals with breast cancer but not in many unaffected members of the same family. Sanger sequencing of all coding and splice site regions of PPARGC1A did not reveal any protein

  4. Stress-induced inhibition of nonsense-mediated RNA decay regulates intracellular cystine transport and intracellular glutathione through regulation of the cystine/glutamate exchanger SLC7A11. (United States)

    Martin, L; Gardner, L B


    SLC7A11 encodes a subunit of the xCT cystine/glutamate amino-acid transport system and has a critical role in the generation of glutathione and the protection of cells from oxidative stress. Expression of SLC7A11 promotes tumorigenesis and chemotherapy resistance, but while SLC7A11 has been previously noted to be upregulated in hypoxic cells, its regulation has not been fully delineated. We have recently shown that nonsense-mediated RNA decay (NMD) is inhibited by cellular stresses generated by the tumor microenvironment, including hypoxia, and augments tumorigenesis. Here we demonstrate that the inhibition of NMD by various cellular stresses leads to the stabilization and upregulation of SLC7A11 mRNA and protein. The inhibition of NMD and upregulation of SLC7A11 augments intracellular cystine transport and increases intracellular levels of cysteine and glutathione. Accordingly, the inhibition of NMD protects cells against oxidative stress via SLC7A11 upregulation. Together our studies identify a mechanism for the dynamic regulation of SLC7A11, through the stress-inhibited regulation of NMD, and add to the growing evidence that the inhibition of NMD is an adaptive response.

  5. Adaptation of Organisms by Resonance of RNA Transcription with the Cellular Redox Cycle (United States)

    Stolc, Viktor


    Sequence variation in organisms differs across the genome and the majority of mutations are caused by oxidation, yet its origin is not fully understood. It has also been shown that the reduction-oxidation reaction cycle is the fundamental biochemical cycle that coordinates the timing of all biochemical processes in that cell, including energy production, DNA replication, and RNA transcription. It is shown that the temporal resonance of transcriptome biosynthesis with the oscillating binary state of the reduction-oxidation reaction cycle serves as a basis for non-random sequence variation at specific genome-wide coordinates that change faster than by accumulation of chance mutations. This work demonstrates evidence for a universal, persistent and iterative feedback mechanism between the environment and heredity, whereby acquired variation between cell divisions can outweigh inherited variation.

  6. MicroRNA-124 inhibits cellular proliferation and invasion by targeting Ets-1 in breast cancer. (United States)

    Li, Wentao; Zang, Wenqiao; Liu, Pei; Wang, Yuanyuan; Du, Yuwen; Chen, Xiaonan; Deng, Meng; Sun, Wencong; Wang, Lei; Zhao, Guoqiang; Zhai, Baoping


    MicroRNAs (miRNAs) are small non-coding RNAs that, by targeting certain messenger RNAs (mRNAs) for translational repression or cleavage, can regulate the expression of these genes. In addition, miRNAs may also function as oncogenes and tumor-suppressor genes, as the abnormal expression of miRNAs is associated with various human tumors. However, the effects of the expression of miR-124 in breast cancer remain unclear. The present study was conducted to study the expression of miR-124 in breast cancer, paying particular attention to miR-124's relation to the proliferation, invasion, and apoptosis in breast cancer cell MCF-7 and MDA-MB-231. Real-time quantitative RT-PCR (qRT-PCR) was performed to identify miR-124 that was down-regulated in breast cancer tissues. We also showed E26 transformation specific-1 (Ets-1) and miR-124 expression levels in breast cancer tissues that were associated with lymph node metastases. With transfected synthetic miR-124 agomir into MCF-7 and MDA-MB-231, a significant reduction (P Ets-1 as a potential major target gene of miR-124, and the result showed that miR-124 can bind to putative binding sites within the Ets-1 mRNA 3' untranslated region (UTR) to reduce its expression. Based on these findings, we propose that miR-124 and Ets-1 may serve as a therapeutic agent in breast cancer.

  7. Final Report [Regulated mRNA Decay in Arabidopsis: A global analysis of differential control by hormones and the circadian clock

    Energy Technology Data Exchange (ETDEWEB)

    Green, Pamela J.


    The long-term goal of this research was to better understand the influence of mRNA stability on gene regulation, particularly in response to hormones and the circadian clock. The primary aim of this project was to examine this using DNA microarrays, small RNA analysis and other approaches. We accomplished these objectives, although we were only able to detect small changes in mRNA stability in response to these stimuli. However, the work also contributed to a major breakthrough allowing the identification of small RNAs on a genomic scale in eukaryotes. Moreover, the project prompted us to develop a new way to analyze mRNA decay genome wide. Thus, the research was hugely successful beyond our objectives.

  8. A novel role for CARM1 in promoting nonsense-mediated mRNA decay: potential implications for spinal muscular atrophy. (United States)

    Sanchez, Gabriel; Bondy-Chorney, Emma; Laframboise, Janik; Paris, Geneviève; Didillon, Andréanne; Jasmin, Bernard J; Côté, Jocelyn


    Loss of 'Survival of Motor Neurons' (SMN) leads to spinal muscular atrophy (SMA), a disease characterized by degeneration of spinal cord alpha motor neurons, resulting in muscle weakness, paralysis and death during early childhood. SMN is required for assembly of the core splicing machinery, and splicing defects were documented in SMA. We previously uncovered that Coactivator-Associated Methyltransferase-1 (CARM1) is abnormally up-regulated in SMA, leading to mis-regulation of a number of transcriptional and alternative splicing events. We report here that CARM1 can promote decay of a premature terminating codon (PTC)-containing mRNA reporter, suggesting it can act as a mediator of nonsense-mediated mRNA decay (NMD). Interestingly, this pathway, while originally perceived as solely a surveillance mechanism preventing expression of potentially detrimental proteins, is now emerging as a highly regulated RNA decay pathway also acting on a subset of normal mRNAs. We further show that CARM1 associates with major NMD factor UPF1 and promotes its occupancy on PTC-containing transcripts. Finally, we identify a specific subset of NMD targets that are dependent on CARM1 for degradation and that are also misregulated in SMA, potentially adding exacerbated targeting of PTC-containing mRNAs to the already complex array of molecular defects associated with this disease.

  9. Disulfide-Based Poly(amido amine)s for siRNA Delivery: Effects of Structure on siRNA Complexation, Cellular Uptake, Gene Silencing and Toxicity

    NARCIS (Netherlands)

    Vader, Pieter; Aa, van der Leonardus J.; Engbersen, Johan F.J.; Storm, Gert; Schiffelers, Raymond M.


    Purpose RNA interference (RNAi) is a process by which small interfering RNAs (siRNA) induce sequence-specific gene silencing. Therefore, siRNA is an emerging promise as a novel therapeutic. In order to realize the high expectations for therapeutic applications, efficient delivery systems for siRNA

  10. The optional long 5'-untranslated region of human ACAT1 mRNAs impairs the production of ACAT1 protein by promoting its mRNA decay

    Institute of Scientific and Technical Information of China (English)

    Xiaonan Zhao; Baoliang Song; Tayuan Chang; Boliang Li; Jia Chen; Lei Lei; Guangjing Hu; Ying Xiong; Jiajia Xu; Qin Li; Xinying Yang; Catherine C.Y.Chang


    We have previously reported that human ACAT1 mRNAs produce the 50 kDa protein using the AUG1397-1399 initiation codon,and also a minor 56 kDa isoform using the upstream in-frame GGC1274-1276initiation codon.The GGC1274-1276 codon is located at the optional long 5'-untranslated region(5'-UTR,nt 1-1396)of the mRNAs.The DNA sequences corresponding to this 5'-UTR are located in two different chromosomes,7 and 1.In the current work,we report that the optional long 5'-UTR significantly impairs the production of human ACAT1 protein initiated from the AUG1397-1399 codon,mainly by promoting its mRNA decay.The western blot analyses indicated that the optional long 5'-UTR potently impaired the production of different proteins initiated from the AUG1397-1399codon,meaning that this impairing effect was not influenced by the 3'-UTR or the coding sequence of ACAT1 mRNA.The results of reverse transcription-quantitative polymerase chain reaction demonstrated that this 5'-UTR dramatically reduced the contents of its linked mRNAs.Analyses of the protein to mRNA ratios showed that this 5'-UTR mainly decreased its mRNA stability rather than altering its translational efficiency.We next performed the plasmid transfection experiments and used actinomycin D to inhibit transcription.The results showed that this 5'-UTR promoted its mRNA decay.Additional transfection and nucleofection experiments using RNAs prepared in vitro illustrated that,in both the cytoplasm and the nucleus of cells,the optional long 5'-UTR-linked mRNAs decayed faster than those without the link.Overall,our study brings new insight to the regulation of the human ACAT1 gene expression at the post-transcription level.

  11. Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria. (United States)

    Angermeyer, Angus; Crosby, Sarah C; Huber, Julie A


    In many habitats, microorganisms exhibit significant distance-decay patterns as determined by analysis of the 16S rRNA gene and various other genetic elements. However, there have been few studies that examine how the similarities of both taxonomic and functional genes co-vary over geographic distance within a group of ecologically related microbes. Here, we determined the biogeographic patterns of the functional dissimilatory sulfite reductase gene (dsrA) and the 16S rRNA gene in sulfate-reducing bacterial communities of US East Coast salt marsh sediments. Distance-decay, ordination and statistical analyses revealed that the distribution of 16S rRNA genes is strongly influenced by geographic distance and environmental factors, whereas the dsrA gene is not. Together, our results indicate that 16S rRNA genes are likely dispersal limited and under environmental selection, whereas dsrA genes appear randomly distributed and not selected for by any expected environmental variables. Selection, drift, dispersal and mutation are all factors that may help explain the decoupled biogeographic patterns for the two genes. These data suggest that both the taxonomic and functional elements of microbial communities should be considered in future studies of microbial biogeography to aid in our understanding of the diversity, distribution and function of microorganisms in the environment.

  12. Attenuation of the suppressive activity of cellular splicing factor SRSF3 by Kaposi sarcoma-associated herpesvirus ORF57 protein is required for RNA splicing. (United States)

    Majerciak, Vladimir; Lu, Mathew; Li, Xiaofan; Zheng, Zhi-Ming


    Kaposi sarcoma-associated herpesvirus (KSHV) ORF57 is a multifunctional post-transcriptional regulator essential for viral gene expression during KSHV lytic infection. ORF57 requires interactions with various cellular proteins for its function. Here, we identified serine/arginine-rich splicing factor 3 (SRSF3, formerly known as SRp20) as a cellular cofactor involved in ORF57-mediated splicing of KSHV K8β RNA. In the absence of ORF57, SRSF3 binds to a suboptimal K8β intron and inhibits K8β splicing. Knockdown of SRSF3 promotes K8β splicing, mimicking the effect of ORF57. The N-terminal half of ORF57 binds to the RNA recognition motif of SRSF3, which prevents SRSF3 from associating with the K8β intron RNA and therefore attenuates the suppressive effect of SRSF3 on K8β splicing. ORF57 also promotes splicing of heterologous non-KSHV transcripts that are negatively regulated by SRSF3, indicating that the effect of ORF57 on SRSF3 activity is independent of RNA target. SPEN proteins, previously identified as ORF57-interacting partners, suppress ORF57 splicing activity by displacing ORF57 from SRSF3-RNA complexes. In summary, we have identified modulation of SRSF3 activity as the molecular mechanism by which ORF57 promotes RNA splicing.

  13. Clathrin-dependent endocytosis plays a predominant role in cellular uptake of double-stranded RNA in the red flour beetle. (United States)

    Xiao, Da; Gao, Xiwu; Xu, Jiaping; Liang, Xiao; Li, Qingqing; Yao, Jianxiu; Zhu, Kun Yan


    RNA interference (RNAi) is a highly conserved gene regulatory mechanism in eukaryotic organisms; however, an understanding of mechanisms of cellular uptake of double-stranded RNA (dsRNA) in different organisms remains elusive. By using pharmacological inhibitors of different endocytic pathways in conjunction with RNAi of a marker gene (lethal giant larvae, TcLgl) in the red flour beetle (Tribolium castaneum), we demonstrated that two inhibitors (chlorpromazine and bafilomycin-A1) of clathrin-dependent endocytosis can nearly abolish or significantly diminish RNAi of TcLgl, whereas methyl-β-cyclodextrin and cytochalasin-D, known to inhibit other endocytic pathways, showed no effect on RNAi of TcLgl. By using Cy3-labeled TcLgl dsRNA, we observed significantly reduced cellular uptake of TcLgl dsRNA in midgut cells after larvae were injected with each of the two clathrin-dependent endocytosis inhibitors. By using an "RNAi of RNAi" strategy, we further demonstrated that suppression of each transcript of the four key genes encoding clathrin heavy chain (TcChc), clathrin coat assembly protein AP50 (TcAP50), vacuolar (H(+))-ATPase subunit H (TcVhaSFD) and a ras-related protein (TcRab7) in clathrin-dependent endocytosis by RNAi can significantly impair RNAi of TcLgl. These results support our conclusion that clathrin-dependent endocytosis is a major mechanism in cellular uptake of dsRNA in T. castaneum. Our study also provides new insights into improving RNAi efficiency by enhancing dsRNA endosomal release.

  14. Intestinal cellular localization of PCNA protein and CYP1A mRNA in Atlantic salmon Salmo salar L. exposed to a model toxicant

    Directory of Open Access Journals (Sweden)

    Olsvik Pål A


    Full Text Available Abstract Background The aim of the study was to examine the intestinal cellular localization of proliferating cell nuclear antigen (PCNA and cytochrome P450 A1 (CYP1A expression in Atlantic salmon Salmo salar L. exposed to a model toxicant. The stress response was induced by intraperitoneal injection of four salmon with a single dose (50 mg/kg of the CYP1A inducer β-naphthoflavone (BNF and intestinal tissue (mid and distal intestine; MI and DI was sampled seven days later. Samples for histology and gene transcription analysis were collected from four exposed fish and four control fish. PCNA was assessed by immunohistochemistry, CYP1A mRNA was studied by in situ hybridization (ISH and finally the transcription of five genes was quantified by real-time quantitative RT-PCR (real-time RT-PCR; two detoxifying genes (CYP1A and glutathione S-transferase; GST, a stress marker gene (heat shock protein 70; HSP70, PCNA and a gene marker of apoptosis (caspase 6A. Results PCNA protein and CYP1A mRNA were successfully localized in the intestinal cells (MI of both experimental groups. At the cellular level, BNF significantly lowered intestinal cell proliferation and increased the CYP1A mRNA levels compared to the control group. The real-time RT-PCR data, which showed an increased mRNA expression both in the MI and DI of 139- and 62-fold, respectively, confirmed the increased cellular CYP1A mRNA levels detected using ISH. HSP70 expression was also up-regulated in the exposed fish. The other examined genes did not show any differential regulation in the experimental fish group. Conclusion This study showed that CYP1A mRNA had a specific intestinal cellular transcription pattern in Atlantic salmon exposed to BNF. At the cellular level CYP1A mRNA expression was always observed at or around the cell nucleus close to the basolateral cell membrane and at the tissue level CYP1A mRNA expression was most frequently observed in the basal and apex area of the intestinal

  15. Changes in rRNA levels during stress invalidates results from mRNA blotting: Fluorescence in situ rRNA hybridization permits renormalization for estimation of cellular mRNA levels

    DEFF Research Database (Denmark)

    Hansen, M.C.; Nielsen, A.K.; Molin, Søren;


    Regulation of gene expression can be analyzed by a number of different techniques. Some techniques monitor the level of specific mRNA directly, and others monitor indirectly by determining the level of enzymes encoded by the mRNA. Each method has its own inherent way of normalization. When result...

  16. Structural basis for the recognition of cellular mRNA export factor REF by herpes viral proteins HSV-1 ICP27 and HVS ORF57. (United States)

    Tunnicliffe, Richard B; Hautbergue, Guillaume M; Kalra, Priti; Jackson, Brian R; Whitehouse, Adrian; Wilson, Stuart A; Golovanov, Alexander P


    The herpesvirus proteins HSV-1 ICP27 and HVS ORF57 promote viral mRNA export by utilizing the cellular mRNA export machinery. This function is triggered by binding to proteins of the transcription-export (TREX) complex, in particular to REF/Aly which directs viral mRNA to the TAP/NFX1 pathway and, subsequently, to the nuclear pore for export to the cytoplasm. Here we have determined the structure of the REF-ICP27 interaction interface at atomic-resolution and provided a detailed comparison of the binding interfaces between ICP27, ORF57 and REF using solution-state NMR. Despite the absence of any obvious sequence similarity, both viral proteins bind on the same site of the folded RRM domain of REF, via short but specific recognition sites. The regions of ICP27 and ORF57 involved in binding by REF have been mapped as residues 104-112 and 103-120, respectively. We have identified the pattern of residues critical for REF/Aly recognition, common to both ICP27 and ORF57. The importance of the key amino acid residues within these binding sites was confirmed by site-directed mutagenesis. The functional significance of the ORF57-REF/Aly interaction was also probed using an ex vivo cytoplasmic viral mRNA accumulation assay and this revealed that mutants that reduce the protein-protein interaction dramatically decrease the ability of ORF57 to mediate the nuclear export of intronless viral mRNA. Together these data precisely map amino acid residues responsible for the direct interactions between viral adaptors and cellular REF/Aly and provide the first molecular details of how herpes viruses access the cellular mRNA export pathway.

  17. mRNAs involved in copper homeostasis are regulated by the nonsense-mediated mRNA decay pathway depending on environmental conditions. (United States)

    Peccarelli, Megan; Scott, Taylor D; Steele, Megan; Kebaara, Bessie W


    The nonsense-mediated mRNA decay pathway (NMD) is an mRNA degradation pathway that degrades mRNAs that prematurely terminate translation. These mRNAs include mRNAs with premature termination codons as well as many natural mRNAs. In Saccharomyces cerevisiae a number of features have been shown to target natural mRNAs to NMD. However, the extent to which natural mRNAs from the same functional group are regulated by NMD and how environmental conditions influence this regulation is not known. Here, we examined mRNAs involved in copper homeostasis and are predicted to be sensitive to NMD. We found that the majority of these mRNAs have long 3'-UTRs that could target them for degradation by NMD. Analysis of one of these mRNAs, COX19, found that the long 3'-UTR contributes to regulation of this mRNA by NMD. Furthermore, we examined an additional mRNA, MAC1 under low copper conditions. We found that low copper growth conditions affect NMD sensitivity of the MAC1 mRNA demonstrating that sensitivity to NMD can be altered by environmental conditions. MAC1 is a copper sensitive transcription factor that regulates genes involved with high affinity copper transport. Our results expand our understanding of how NMD regulates mRNAs from the same functional group and how the environment influences this regulation.

  18. Cellular delivery of quantum dot-bound hybridization probe for detection of intracellular pre-microRNA using chitosan/poly(γ-glutamic acid complex as a carrier.

    Directory of Open Access Journals (Sweden)

    Yao Geng

    Full Text Available A quantum dot (QD-bound hybridization probe was designed for detection of intracellular pre-miRNA using chitosan (CS/poly(γ-glutamic acid (γ-PGA complex as a gene vector. The probe was prepared by assembling thiolated RNA to gold nanoparticle (Au NP via Au-S bond and then binding 3'-end amine of the RNA to the carboxy group capped on quantum dot surface. The QD-RNA-Au NP probe was assembled on the vector by mixing with aqueous γ-PGA solution and then CS solution to construct a gene delivery system for highly effective cellular uptake and delivery. After the probe was released from CS/γ-PGA complex to the cytoplasm by electrostatic repulsion at intracellular pH, it hybridized with pre-miRNA precursor as target. The formed product was then cleaved by RNase III Dicer, leading to the separation of QDs from Au NPs and fluorescence emission of QDs, which could be detected by confocal microscopic imaging to monitor the amount of the intracellular pre-miRNA precursor. The in vitro assays revealed that the QD-RNA-Au NP was a robust, sensitive and selective probe for quantitative detection of target pre-miRNA. Using MDA-MB231 and MCF-7 breast cancer cells as models, the relative amount of pre-miRNA let-7a could be successfully compared. Since the amount of miRNA is related to the progress and prognosis of cancer, this strategy could be expected to hold promising application potential in medical research and clinical diagnostics.

  19. The D10 Decapping Enzyme of Vaccinia Virus Contributes to Decay of Cellular and Viral mRNAs and to Virulence in Mice (United States)

    Liu, Shin-Wu; Wyatt, Linda S.; Orandle, Marlene S.; Minai, Mahnaz


    Posttranscriptional mechanisms are important for regulation of cellular and viral gene expression. The presence of the 5′ cap structure m7G(5′)ppp(5′)Nm is a general feature of mRNAs that provides protection from exoribonuclease digestion and enhances translation. Vaccinia virus and other poxviruses encode enzymes for both cap synthesis and decapping. Decapping is mediated by two related enzymes, D9 and D10, which are synthesized before and after viral DNA replication, respectively. The timing of D10 synthesis correlates better with the shutdown of host gene expression, and deletion of this gene has been shown to cause persistence of host and viral mRNAs in infected cells. Here, we constructed specific mutant viruses in which translation of D10 was prevented by stop codons or activity of D10 was abrogated by catalytic site mutations, without other genomic alterations. Both mutants formed plaques of normal size and replicated to similar extents as the parental virus in monkey epithelial cells and mouse embryonic fibroblasts. The synthesis of viral proteins was slightly delayed, and cellular and viral mRNAs persisted longer in cells infected with the mutants compared to either the parental virus or clonal revertant. Despite the mild effects in vitro, both mutants were more attenuated than the revertants in intranasal and intraperitoneal mouse models, and less infectious virus was recovered from organs. In addition, there was less lung histopathology following intranasal infection with mutant viruses. These data suggest that the D10 decapping enzyme may help restrict antiviral responses by accelerating host mRNA degradation during poxvirus infection. PMID:24155373

  20. Expression of cellular fibronectin mRNA in adult periodontitis and peri-implantitis:a real-time polymerase chain reaction study

    Institute of Scientific and Technical Information of China (English)

    Yan-Yun Wu; Huan-Huan Cao; Ning Kang; Ping Gong; Guo-Min Ou


    Cellular fibronectin (cFn) is a type of bioactive non-collagen glycoprotein regarded as the main substance used to maintain periodontal attachment. The content of cFn in some specific sites can reflect the progress of periodontitis or peri-implantitis. This study aims to evaluate the expression of cFn messenger RNA (mRNA) in tissues of adult periodontitis and peri-implantitis by real-time fluorescent quantitative polymerase chain reaction (PCR) and to determine its clinical significance. A total of 30 patients were divided into three groups of 10:healthy, adult periodontitis and peri-implantitis. Periodontal tissue biopsies (1 mm31 mm31 mm) from each patient were frozen in liquid nitrogen. Total RNA was extracted from these tissues, and the content, purity and integrity were detected. Specific primers were designed according to the sequence, and the mRNA expression levels of cellular fibronectin were detected by real-time PCR. The purity and integrity of the extracted total RNA were both high, and the specificity of amplified genes was very high with no other pollution. The mRNA expression of cFn in the adult periodontitis group (1.52660.441) was lower than that in the healthy group (3.25360.736). However, the mRNA expression of cFn in the peri-implantitis group (3.96560.537) was significantly higher than that in the healthy group. The difference revealed that although both processes were destructive inflammatory reactions in the periodontium, the pathomechanisms were different and the variation started from the transcription level of the cFn gene.

  1. Comprehensive Small RNA-Seq of Adeno-Associated Virus (AAV)-Infected Human Cells Detects Patterns of Novel, Non-Coding AAV RNAs in the Absence of Cellular miRNA Regulation (United States)

    Stutika, Catrin; Mietzsch, Mario; Gogol-Döring, Andreas; Weger, Stefan; Sohn, Madlen; Chen, Wei; Heilbronn, Regine


    Most DNA viruses express small regulatory RNAs, which interfere with viral or cellular gene expression. For adeno-associated virus (AAV), a small ssDNA virus with a complex biphasic life cycle miRNAs or other small regulatory RNAs have not yet been described. This is the first comprehensive Illumina-based RNA-Seq analysis of small RNAs expressed by AAV alone or upon co-infection with helper adenovirus or HSV. Several hotspots of AAV-specific small RNAs were detected mostly close to or within the AAV-ITR and apparently transcribed from the newly identified anti-p5 promoter. An additional small RNA hotspot was located downstream of the p40 promoter, from where transcription of non-coding RNAs associated with the inhibition of adenovirus replication were recently described. Parallel detection of known Ad and HSV miRNAs indirectly validated the newly identified small AAV RNA species. The predominant small RNAs were analyzed on Northern blots and by human argonaute protein-mediated co-immunoprecipitation. None of the small AAV RNAs showed characteristics of bona fide miRNAs, but characteristics of alternative RNA processing indicative of differentially regulated AAV promoter-associated small RNAs. Furthermore, the AAV-induced regulation of cellular miRNA levels was analyzed at different time points post infection. In contrast to other virus groups AAV infection had virtually no effect on the expression of cellular miRNA, which underscores the long-established concept that wild-type AAV infection is apathogenic. PMID:27611072

  2. Identification of Cellular Targets of MicroRNA-181a in HepG2 Cells: A New Approach for Functional Analysis of MicroRNAs. (United States)

    Tan, Jane Yi Lin; Habib, Nagy A; Chuah, York Wieo; Yau, Yin Hoe; Geifman-Shochat, Susana; Chen, Wei Ning


    MicroRNAs (miRNAs) are known to play a part in regulating important cellular processes. They generally perform their regulatory function through their binding with mRNAs, ultimately leading to a repression of target protein expression levels. However, their roles in cellular processes are poorly understood due to the limited understanding of their specific cellular targets. Aberrant levels of miRNAs have been found in hepatocellular carcinoma (HCC) including miR-181a. Using bioinformatics analysis, cyclin-dependent kinase inhibitor 1B (CDKN1β) and transcriptional factor E2F7 were identified as potential targets of miR-181a. Validation analysis using surface plasmon resonance (SPR) showed a positive binding between miR-181a and the 3'UTRs of these two potential mRNA targets. In vivo luciferase assay further confirmed the positive miR-181a:mRNA bindings, where a significant decrease in luciferase activity was detected when HepG2 cells were co-transfected with the 3'UTR-containing reporter plasmids and miR-181a. The potential impact of miR-181a binding to its specific targets on the general cellular behavior was further investigated. Results showed that miR-181a significantly activated the MAPK/JNK pathway which regulates cell proliferation, supporting our recently reported findings. Inhibition of miR-181a, on the other hand, abolished the observed activation. Our findings open up a new approach in designing targeted functional analysis of miRNAs in cellular processes, through the identification of their cellular targets.

  3. Cellular microRNA miR-181b inhibits replication of mink enteritis virus by repression of non-structural protein 1 translation. (United States)

    Sun, Jia-zeng; Wang, Jigui; Yuan, Daoli; Wang, Shuang; Li, Zhili; Yi, Bao; Mao, Yaping; Hou, Qiang; Liu, Weiquan


    Mink enteritis virus (MEV) is one of the most important viral pathogens in the mink industry. Recent studies have showed that microRNAs (miRNAs), small noncoding RNAs of length ranging from 18-23 nucleotides (nt) participate in host-pathogen interaction networks; however, whether or not miRNAs are involved in MEV infection has not been reported. Our study revealed that miRNA miR-181b inhibited replication of MEV in the feline kidney (F81) cell line by targeting the MEV non-structural protein 1 (NS1) messenger RNA (mRNA) coding region, resulting in NS1 translational repression, while MEV infection reduced miR-181b expression. This is the first description of cellular miRNAs modulating MEV infection in F81 cells, providing further insight into the mechanisms of viral infection, and may be useful in development of naturally-occurring miRNAs antiviral strategies.

  4. Nonsense-Mediated Decay of Alternative Precursor mRNA Splicing Variants Is a Major Determinant of the Arabidopsis Steady State Transcriptome[C][W (United States)

    Drechsel, Gabriele; Kahles, André; Kesarwani, Anil K.; Stauffer, Eva; Behr, Jonas; Drewe, Philipp; Rätsch, Gunnar; Wachter, Andreas


    The nonsense-mediated decay (NMD) surveillance pathway can recognize erroneous transcripts and physiological mRNAs, such as precursor mRNA alternative splicing (AS) variants. Currently, information on the global extent of coupled AS and NMD remains scarce and even absent for any plant species. To address this, we conducted transcriptome-wide splicing studies using Arabidopsis thaliana mutants in the NMD factor homologs UP FRAMESHIFT1 (UPF1) and UPF3 as well as wild-type samples treated with the translation inhibitor cycloheximide. Our analyses revealed that at least 17.4% of all multi-exon, protein-coding genes produce splicing variants that are targeted by NMD. Moreover, we provide evidence that UPF1 and UPF3 act in a translation-independent mRNA decay pathway. Importantly, 92.3% of the NMD-responsive mRNAs exhibit classical NMD-eliciting features, supporting their authenticity as direct targets. Genes generating NMD-sensitive AS variants function in diverse biological processes, including signaling and protein modification, for which NaCl stress–modulated AS-NMD was found. Besides mRNAs, numerous noncoding RNAs and transcripts derived from intergenic regions were shown to be NMD responsive. In summary, we provide evidence for a major function of AS-coupled NMD in shaping the Arabidopsis transcriptome, having fundamental implications in gene regulation and quality control of transcript processing. PMID:24163313

  5. mRNA metabolism: nonsense mediated mRNA decay as a tool for gene therapy and the role of human DIS3L2 in transcript degradation


    Amaral, Gerson Leonel Asper


    Tese de mestrado em Biologia Humana e Ambiente, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2015 A expressão génica nos eucariotas envolve uma série de passos interligados e acoplados entre si, tendo a molécula de RNA (ribonucleic acid) como mensageiro entre os grandes passos. Resumidamente, a mensagem codificada pelas bases nucleotídicas do ácido desoxirribonucleico (DNA) (deoxyribonucleic acid) é transferida para uma molécula de RNA (transcrição), que, após pr...

  6. Genome-wide measurement of RNA folding energies. (United States)

    Wan, Yue; Qu, Kun; Ouyang, Zhengqing; Kertesz, Michael; Li, Jun; Tibshirani, Robert; Makino, Debora L; Nutter, Robert C; Segal, Eran; Chang, Howard Y


    RNA structural transitions are important in the function and regulation of RNAs. Here, we reveal a layer of transcriptome organization in the form of RNA folding energies. By probing yeast RNA structures at different temperatures, we obtained relative melting temperatures (Tm) for RNA structures in over 4000 transcripts. Specific signatures of RNA Tm demarcated the polarity of mRNA open reading frames and highlighted numerous candidate regulatory RNA motifs in 3' untranslated regions. RNA Tm distinguished noncoding versus coding RNAs and identified mRNAs with distinct cellular functions. We identified thousands of putative RNA thermometers, and their presence is predictive of the pattern of RNA decay in vivo during heat shock. The exosome complex recognizes unpaired bases during heat shock to degrade these RNAs, coupling intrinsic structural stabilities to gene regulation. Thus, genome-wide structural dynamics of RNA can parse functional elements of the transcriptome and reveal diverse biological insights.

  7. TGF-β and iron differently alter HBV replication in human hepatocytes through TGF-β/BMP signaling and cellular microRNA expression.

    Directory of Open Access Journals (Sweden)

    Sun O Park

    Full Text Available The nature of host-virus interactions in hepatitis B virus infection is incompletely understood. Since soluble factors, e.g., cytokines and metals, may exacerbate liver injury in chronic hepatitis, we considered that defining the effects of receptor-mediated signaling upon viral replication will be significant. Consequently, we studied effects of iron or TGF-β-induced TGF-β/BMP signaling in the HepG2 2.2.15 cell model of hepatitis B virus replication. We found iron and TGF-β increased hepcidin mRNA expression or TGF-β receptor kinase activity, respectively, which indicated that 2.2.15 cells responded appropriately to these substances. However, iron increased but TGF-β decreased hepatitis B virus mRNA and DNA expression. TGF-β induced expression at the mRNA level of multiple TGF-β/BMP pathway genes. This change was not observed in iron-treated cells. On the other hand, presence of SMAD proteins in iron or TGF-β-treated cells, including of SMAD4, did confirm convergence of TGF-β/BMP signaling pathways under these conditions. Since transcription factors in TGF-β/BMP signaling pathways could not have directly targeted hepatitis B virus itself, we studied whether iron or TGF-β exerted their effects through alternative mechanisms, such as by involvement of antiviral cellular microRNAs. We discovered cellular microRNA expression profiles were significantly different in iron or TGF-β-treated cells compared with untreated control cells. In many cases, exposure to iron or TGF-β changed microRNA expression in opposite directions. Introduction in cells of sequences representing such differentially expressed microRNAs, e.g., hsa-miR-125a-5p and -151-5p, even reproduced effects on virus replication of iron- or TGF-β. We surmised that TGF-β/BMP pathway members, i.e., SMADs, likely governed iron or TGF-β-induced microRNA expression. Iron may have mediated Drosha/DGCR8/heme-mediated processing of microRNAs. In turn, cellular microRNAs regulated

  8. Real-time RT-PCR analysis of mRNA decay: half-life of Beta-actin mRNA in human leukemia CCRF-CEM and Nalm-6 cell lines

    Directory of Open Access Journals (Sweden)

    Barredo Julio C


    Full Text Available Abstract Background We describe an alternative method to determine mRNA half-life (t1/2 based on the Real-Time RT-PCR procedure. This approach was evaluated by using the β-actin gene as a reference molecule for measuring of mRNA stability. Results Human leukemia Nalm-6 and CCRF-CEM cells were treated with various concentrations of Actinomycin D to block transcription and aliquots were removed periodically. Total RNA was isolated and quantified using the RiboGreen® fluorescent dye with the VersaFluor Fluorometer System. One μg of total RNA was reverse transcribed and used as template for the amplification of a region of the β-actin gene (231 bp. To generate the standard curve, serial ten-fold dilutions of the pBactin-231 vector containing the cDNA amplified fragment were employed, β-actin mRNAs were quantified by Real-Time RT-PCR using the SYBR® Green I fluorogenic dye and data analyzed using the iCycle iQ system software. Using this method, the β-actin mRNA exhibited a half-life of 6.6 h and 13.5 h in Nalm-6 and CCRF-CEM cells, respectively. The t1/2 value obtained for Nalm-6 is comparable to those estimated from Northern blot studies, using normal human leukocytes (5.5 h. Conclusions We have developed a rapid, sensitive, and reliable method based on Real-Time RT-PCR for measuring mRNA half-life. Our results confirm that β-actin mRNA half-life can be affected by the cellular growth rate.

  9. Nuclear Factor 90, a cellular dsRNA binding protein inhibits the HIV Rev-export function

    Directory of Open Access Journals (Sweden)

    St-Laurent Georges


    Full Text Available Abstract Background The HIV Rev protein is known to facilitate export of incompletely spliced and unspliced viral transcripts to the cytoplasm, a necessary step in virus life cycle. The Rev-mediated nucleo-cytoplasmic transport of nascent viral transcripts, dependents on interaction of Rev with the RRE RNA structural element present in the target RNAs. The C-terminal variant of dsRNA-binding nuclear protein 90 (NF90ctv has been shown to markedly attenuate viral replication in stably transduced HIV-1 target cell line. Here we examined a mechanism of interference of viral life cycle involving Rev-NF90ctv interaction. Results Since Rev:RRE complex formations depend on protein:RNA and protein:protein interactions, we investigated whether the expression of NF90ctv might interfere with Rev-mediated export of RRE-containing transcripts. When HeLa cells expressed both NF90ctv and Rev protein, we observed that NF90ctv inhibited the Rev-mediated RNA transport. In particular, three regions of NF90ctv protein are involved in blocking Rev function. Moreover, interaction of NF90ctv with the RRE RNA resulted in the expression of a reporter protein coding sequences linked to the RRE structure. Moreover, Rev influenced the subcellular localization of NF90ctv, and this process is leptomycin B sensitive. Conclusion The dsRNA binding protein, NF90ctv competes with HIV Rev function at two levels, by competitive protein:protein interaction involving Rev binding to specific domains of NF90ctv, as well as by its binding to the RRE-RNA structure. Our results are consistent with a model of Rev-mediated HIV-1 RNA export that envisions Rev-multimerization, a process interrupted by NF90ctv.

  10. Trypanosoma brucei RNA binding proteins p34 and p37 mediate NOPP44/46 cellular localization via the exportin 1 nuclear export pathway. (United States)

    Hellman, Kristina; Prohaska, Kimberly; Williams, Noreen


    We have previously identified and characterized two novel nuclear RNA binding proteins, p34 and p37, which have been shown to interact with a family of nucleolar phosphoproteins, NOPP44/46, in Trypanosoma brucei. These proteins are nearly identical, the major difference being an 18-amino-acid insert in the N terminus of p37. In order to characterize the interaction between p34 and p37 and NOPP44/46, we have utilized an RNA interference (RNAi) cell line that specifically targets p34 and p37. Within these RNAi cells, we detected a disruption of a higher-molecular-weight complex containing NOPP44/46, as well as a dramatic increase in nuclear NOPP44/46 protein levels. We demonstrated that no change occurred in NOPP44/46 mRNA steady-state levels or stability, nor was there a change in cellular protein levels. These results led us to investigate whether p34 and p37 regulate NOPP44/46 cellular localization. Examination of the p34 and p37 amino acid sequences revealed a leucine-rich nuclear export signal, which interacts with the nuclear export factor exportin 1. Immune capture experiments demonstrated that p34, p37, and NOPP44/46 associate with exportin 1. When these experiments were performed with p34/p37 RNAi cells, NOPP44/46 no longer associated with exportin 1. Sequential immune capture experiments demonstrated that p34, p37, NOPP44/46, and exportin 1 exist in a common complex. Inhibiting exportin 1-mediated nuclear export led to an increase in nuclear NOPP44/46 proteins, indicating that they are exported from the nucleus via this pathway. Together, our results demonstrate that p34 and p37 regulate NOPP44/46 cellular localization by facilitating their association with exportin 1.

  11. The cellular RNA export receptor TAP/NXF1 is required for ICP27-mediated export of herpes simplex virus 1 RNA, but the TREX complex adaptor protein Aly/REF appears to be dispensable. (United States)

    Johnson, Lisa A; Li, Ling; Sandri-Goldin, Rozanne M


    Herpes simplex virus 1 (HSV-1) protein ICP27 has been shown to shuttle between the nucleus and cytoplasm and to bind viral RNA during infection. ICP27 was found to interact with the cellular RNA export adaptor protein Aly/REF, which is part of the TREX complex, and to relocalize Aly/REF to viral replication sites. ICP27 is exported to the cytoplasm through the export receptor TAP/NXF1, and ICP27 must be able to interact with TAP/NXF1 for efficient export of HSV-1 early and late transcripts. We examined the dynamics of ICP27 movement and its localization with respect to Aly/REF and TAP/NXF1 in living cells during viral infection. Recombinant viruses with a yellow fluorescent protein (YFP) tag on the N or C terminus of ICP27 were constructed. While the N-terminally tagged ICP27 virus behaved like wild-type HSV-1, the C-terminally tagged virus was defective in viral replication and gene expression, and ICP27 was confined to the nucleus, suggesting that the C-terminal YFP tag interfered with ICP27's C-terminal interactions, including the interaction with TAP/NXF1. To assess the role of Aly/REF and TAP/NXF1 in viral RNA export, these factors were knocked down using small interfering RNA. Knockdown of Aly/REF had little effect on the export of ICP27 or poly(A)(+) RNA during infection. In contrast, a decrease in TAP/NXF1 levels severely impaired export of ICP27 and poly(A)(+) RNA. We conclude that TAP/NXF1 is essential for ICP27-mediated export of RNA during HSV-1 infection, whereas Aly/REF may be dispensable.

  12. The RNA Polymerase II C-Terminal Domain Phosphatase-Like Protein FIERY2/CPL1 Interacts with eIF4AIII and Is Essential for Nonsense-Mediated mRNA Decay in Arabidopsis

    KAUST Repository

    Cui, Peng


    © 2016 American Society of Plant Biologists. All rights reserved. Nonsense-mediated decay (NMD) is a posttranscriptional surveillance mechanism in eukaryotes that recognizes and degrades transcripts with premature translation-termination codons. The RNA polymerase II C-terminal domain phosphatase-like protein FIERY2 (FRY2; also known as C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 [CPL1]) plays multiple roles in RNA processing in Arabidopsis thaliana. Here, we found that FRY2/CPL1 interacts with two NMD factors, eIF4AIII and UPF3, and is involved in the dephosphorylation of eIF4AIII. This dephosphorylation retains eIF4AIII in the nucleus and limits its accumulation in the cytoplasm. By analyzing RNA-seq data combined with quantitative RT-PCR validation, we found that a subset of alternatively spliced transcripts and 59-extended mRNAs with NMD-eliciting features accumulated in the fry2-1 mutant, cycloheximidetreated wild type, and upf3 mutant plants, indicating that FRY2 is essential for the degradation of these NMD transcripts.

  13. Cellular function of microRNA-15 family%microRNA-15家族功能研究进展

    Institute of Scientific and Technical Information of China (English)

    刘丽凤; 王禹


    微小RNA (microRNAs,miRNAs)是一类具有转录后调节作用的短小的内源性非编码RNA,其中miR-15家族参与凋亡、细胞分化与周期调控、应激等重要细胞功能活动的调节,并与多种人类疾病如肿瘤、心血管疾病、神经退行性疾病等相关,具有潜在的治疗前景及干预价值.本文就miR- 15家族的重要功能及治疗应用前景作一综述.%micro RNAs (miRNAs) are non-coding endogenous short RNAs which are involved in regulating gene expression at the post-transcriptional level. miR-15 family is increasingly found to play great roles in important cell processes, such as apoptosis, cell differentiation and stress response. Growing evidence indicates that miR-15 family members are implicated in tumor, cardiovascular disease and neurodegenerative disease. miRNAs have emerged as a new promising subset of therapeutic targets. The present paper re viewed the important function of miR-15 family and new approaches for miRNA-based therapy.

  14. Disregarded Effect of Biological Fluids in siRNA Delivery: Human Ascites Fluid Severely Restricts Cellular Uptake of Nanoparticles. (United States)

    Dakwar, George R; Braeckmans, Kevin; Demeester, Joseph; Ceelen, Wim; De Smedt, Stefaan C; Remaut, Katrien


    Small interfering RNA (siRNA) offers a great potential for the treatment of various diseases and disorders. Nevertheless, inefficient in vivo siRNA delivery hampers its translation into the clinic. While numerous successful in vitro siRNA delivery stories exist in reduced-protein conditions, most studies so far overlook the influence of the biological fluids present in the in vivo environment. In this study, we compared the transfection efficiency of liposomal formulations in Opti-MEM (low protein content, routinely used for in vitro screening) and human undiluted ascites fluid obtained from a peritoneal carcinomatosis patient (high protein content, representing the in vivo situation). In Opti-MEM, all formulations are biologically active. In ascites fluid, however, the biological activity of all lipoplexes is lost except for lipofectamine RNAiMAX. The drop in transfection efficiency was not correlated to the physicochemical properties of the nanoparticles, such as premature siRNA release and aggregation of the nanoparticles in the human ascites fluid. Remarkably, however, all of the formulations except for lipofectamine RNAiMAX lost their ability to be taken up by cells following incubation in ascites fluid. To take into account the possible effects of a protein corona formed around the nanoparticles, we recommend always using undiluted biological fluids for the in vitro optimization of nanosized siRNA formulations next to conventional screening in low-protein content media. This should tighten the gap between in vitro and in vivo performance of nanoparticles and ensure the optimal selection of nanoparticles for further in vivo studies.

  15. Pokeweed antiviral protein restores levels of cellular APOBEC3G during HIV-1 infection by depurinating Vif mRNA. (United States)

    Krivdova, Gabriela; Hudak, Katalin A


    Pokeweed antiviral protein (PAP) is an RNA glycosidase that inhibits production of human immunodeficiency virus type 1 (HIV-1) when expressed in human culture cells. Previously, we showed that the expression of PAP reduced the levels of several viral proteins, including virion infectivity factor (Vif). However, the mechanism causing Vif reduction and the consequences of the inhibition were not determined. Here we show that the Vif mRNA is directly depurinated by PAP. Because of depurination at two specific sites within the Vif ORF, Vif levels decrease during infections and the progeny viruses that are generated are ∼ 10-fold less infectious and compromised for proviral integration. These results are consistent with PAP activity inhibiting translation of Vif, which in turn reduces the effect of Vif to inactivate the host restriction factor APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like editing complex 3G). Our findings identify Vif mRNA as a new substrate for PAP and demonstrate that derepression of innate immunity against HIV-1 contributes to its antiviral activity.

  16. Fluorescence-Based Codetection with Protein Markers Reveals Distinct Cellular Compartments for Altered MicroRNA Expression in Solid Tumors

    DEFF Research Database (Denmark)

    Sempere, Lorenzo F.; Preis, Meir; Yezefski, Todd;


    Purpose: High-throughput profiling experiments have linked altered expression of microRNAs (miRNA) to different types of cancer. Tumor tissues are a heterogeneous mixture of not only cancer cells, but also supportive and reactive tumor microenvironment elements. To clarify the clinical significan...

  17. Modulating the RNA processing and decay by the exosome: altering Rrp44/Dis3 activity and end-product.

    Directory of Open Access Journals (Sweden)

    Filipa P Reis

    Full Text Available In eukaryotes, the exosome plays a central role in RNA maturation, turnover, and quality control. In Saccharomyces cerevisiae, the core exosome is composed of nine catalytically inactive subunits constituting a ring structure and the active nuclease Rrp44, also known as Dis3. Rrp44 is a member of the ribonuclease II superfamily of exoribonucleases which include RNase R, Dis3L1 and Dis3L2. In this work we have functionally characterized three residues located in the highly conserved RNB catalytic domain of Rrp44: Y595, Q892 and G895. To address their precise role in Rrp44 activity, we have constructed Rrp44 mutants and compared their activity to the wild-type Rrp44. When we mutated residue Q892 and tested its activity in vitro, the enzyme became slightly more active. We also showed that when we mutated Y595, the final degradation product of Rrp44 changed from 4 to 5 nucleotides. This result confirms that this residue is responsible for the stacking of the RNA substrate in the catalytic cavity, as was predicted from the structure of Rrp44. Furthermore, we also show that a strain with a mutation in this residue has a growth defect and affects RNA processing and degradation. These results lead us to hypothesize that this residue has an important biological role. Molecular dynamics modeling of these Rrp44 mutants and the wild-type enzyme showed changes that extended beyond the mutated residues and helped to explain these results.

  18. Sequence-selective recognition of double-stranded RNA and enhanced cellular uptake of cationic nucleobase and backbone-modified peptide nucleic acids. (United States)

    Hnedzko, Dziyana; McGee, Dennis W; Karamitas, Yannis A; Rozners, Eriks


    Sequence-selective recognition of complex RNAs in live cells could find broad applications in biology, biomedical research, and biotechnology. However, specific recognition of structured RNA is challenging, and generally applicable and effective methods are lacking. Recently, we found that peptide nucleic acids (PNAs) were unusually well-suited ligands for recognition of double-stranded RNAs. Herein, we report that 2-aminopyridine (M) modified PNAs and their conjugates with lysine and arginine tripeptides form strong (Ka = 9.4 to 17 × 10(7) M(-1)) and sequence-selective triple helices with RNA hairpins at physiological pH and salt concentration. The affinity of PNA-peptide conjugates for the matched RNA hairpins was unusually high compared to the much lower affinity for DNA hairpins of the same sequence (Ka = 0.05 to 1.1 × 10(7) M(-1)). The binding of double-stranded RNA by M-modified PNA-peptide conjugates was a relatively fast process (kon = 2.9 × 10(4) M(-1) sec(-1)) compared to the notoriously slow triple helix formation by oligodeoxynucleotides (kon ∼ 10(3) M(-1) sec(-1)). M-modified PNA-peptide conjugates were not cytotoxic and were efficiently delivered in the cytosol of HEK293 cells at 10 µM. Surprisingly, M-modified PNAs without peptide conjugation were also taken up by HEK293 cells, which, to the best of our knowledge, is the first example of heterocyclic base modification that enhances the cellular uptake of PNA. Our results suggest that M-modified PNA-peptide conjugates are promising probes for sequence-selective recognition of double-stranded RNA in live cells and other biological systems.

  19. mRNA expression levels in failing human hearts predict cellular electrophysiological remodeling: a population-based simulation study.

    Directory of Open Access Journals (Sweden)

    John Walmsley

    Full Text Available Differences in mRNA expression levels have been observed in failing versus non-failing human hearts for several membrane channel proteins and accessory subunits. These differences may play a causal role in electrophysiological changes observed in human heart failure and atrial fibrillation, such as action potential (AP prolongation, increased AP triangulation, decreased intracellular calcium transient (CaT magnitude and decreased CaT triangulation. Our goal is to investigate whether the information contained in mRNA measurements can be used to predict cardiac electrophysiological remodeling in heart failure using computational modeling. Using mRNA data recently obtained from failing and non-failing human hearts, we construct failing and non-failing cell populations incorporating natural variability and up/down regulation of channel conductivities. Six biomarkers are calculated for each cell in each population, at cycle lengths between 1500 ms and 300 ms. Regression analysis is performed to determine which ion channels drive biomarker variability in failing versus non-failing cardiomyocytes. Our models suggest that reported mRNA expression changes are consistent with AP prolongation, increased AP triangulation, increased CaT duration, decreased CaT triangulation and amplitude, and increased delay between AP and CaT upstrokes in the failing population. Regression analysis reveals that changes in AP biomarkers are driven primarily by reduction in I[Formula: see text], and changes in CaT biomarkers are driven predominantly by reduction in I(Kr and SERCA. In particular, the role of I(CaL is pacing rate dependent. Additionally, alternans developed at fast pacing rates for both failing and non-failing cardiomyocytes, but the underlying mechanisms are different in control and heart failure.

  20. The Cellular Processing Capacity Limits the Amounts of Chimeric U7 snRNA Available for Antisense Delivery



    Many genetic diseases are induced by mutations disturbing the maturation of pre-mRNAs, often affecting splicing. Antisense oligoribonucleotides (AONs) have been used to modulate splicing thereby circumventing the deleterious effects of mutations. Stable delivery of antisense sequences is achieved by linking them to small nuclear RNA (snRNAs) delivered by viral vectors, as illustrated by studies where therapeutic exon skipping was obtained in animal models of Duchenne muscular dystrophy (DMD)....

  1. Characterization of IRE1 ribonuclease-mediated mRNA decay in plants using transient expression analyses in rice protoplasts. (United States)

    Hayashi, Shimpei; Wakasa, Yuhya; Ozawa, Kenjirou; Takaiwa, Fumio


    In some eukaryotes, endoplasmic reticulum (ER) stress induces regulated inositol-requiring enzyme 1 (IRE1)-dependent decay (RIDD) of mRNAs. Recently, the expression levels of the mRNAs encoding some secretory proteins were reported to be downregulated by RIDD in the vegetative tissues of plants. However, the characteristics of plant RIDD have been insufficiently investigated due to difficulty of in planta analyses. Here, the RIDD susceptibilities of various mRNAs that are difficult to analyze in planta were examined using transient expression analyses of rice protoplasts. In this system, the mRNAs encoding three rice seed storage proteins (SSPs) - namely α-globulin, 16-kDa prolamin and 10-kDa prolamin - were downregulated in response to ER stress. The rapid ER stress-induced degradation of these mRNAs was repressed in cells in which the ribonuclease activity of IRE1 was specifically abolished by genome editing, suggesting that the mRNAs encoding certain SSPs are strong targets of RIDD. Furthermore, we investigated whether these RIDD targets are substrates of the IRE1 ribonuclease using a recombinant IRE1 protein, and identified candidate IRE1-mediated cleavage sites. Overall, the results demonstrate the existence of a post-transcriptional mechanism of regulation of SSPs, and illustrate the basic and multifaceted characteristics of RIDD in higher plants.

  2. Carpenter syndrome: extended RAB23 mutation spectrum and analysis of nonsense-mediated mRNA decay. (United States)

    Jenkins, Dagan; Baynam, Gareth; De Catte, Luc; Elcioglu, Nursel; Gabbett, Michael T; Hudgins, Louanne; Hurst, Jane A; Jehee, Fernanda Sarquis; Oley, Christine; Wilkie, Andrew O M


    Carpenter syndrome, a rare autosomal recessive disorder characterized by a combination of craniosynostosis, polysyndactyly, obesity, and other congenital malformations, is caused by mutations in RAB23, encoding a member of the Rab-family of small GTPases. In 15 out of 16 families previously reported, the disease was caused by homozygosity for truncating mutations, and currently only a single missense mutation has been identified in a compound heterozygote. Here, we describe a further 8 independent families comprising 10 affected individuals with Carpenter syndrome, who were positive for mutations in RAB23. We report the first homozygous missense mutation and in-frame deletion, highlighting key residues for RAB23 function, as well as the first splice-site mutation. Multi-suture craniosynostosis and polysyndactyly have been present in all patients described to date, and abnormal external genitalia have been universal in boys. High birth weight was not evident in the current group of patients, but further evidence for laterality defects is reported. No genotype-phenotype correlations are apparent. We provide experimental evidence that transcripts encoding truncating mutations are subject to nonsense-mediated decay, and that this plays an important role in the pathogenesis of many RAB23 mutations. These observations refine the phenotypic spectrum of Carpenter syndrome and offer new insights into molecular pathogenesis.

  3. Modified-chitosan/siRNA nanoparticles downregulate cellular CDX2 expression and cross the gastric mucus barrier.

    Directory of Open Access Journals (Sweden)

    Ana Sadio

    Full Text Available Development of effective non-viral vectors is of crucial importance in the implementation of RNA interference in clinical routine. The localized delivery of siRNAs to the gastrointestinal mucosa is highly desired but faces specific problems such as the stability in gastric acidity conditions and the presence of the mucus barrier. CDX2 is a transcription factor critical for intestinal differentiation being involved in the initiation and maintenance of gastrointestinal diseases. Specifically, it is the trigger of gastric intestinal metaplasia which is a precursor lesion of gastric cancer. Its expression is also altered in colorectal cancer, where it may constitute a lineage-survival oncogene. Our main objective was to develop a nanoparticle-delivery system of siRNA targeting CDX2 using modified chitosan as a vector. CDX2 expression was assessed in gastric carcinoma cell lines and nanoparticles behaviour in gastrointestinal mucus was tested in mouse explants. We show that imidazole-modified chitosan and trimethylchitosan/siRNA nanoparticles are able to downregulate CDX2 expression and overpass the gastric mucus layer but not colonic mucus. This system might constitute a potential therapeutic approach to treat CDX2-dependent gastric lesions.

  4. Cellular microRNA miR-181b inhibits replication of mink enteritis virus by repression of non-structural protein 1 translation.

    Directory of Open Access Journals (Sweden)

    Jia-zeng Sun

    Full Text Available Mink enteritis virus (MEV is one of the most important viral pathogens in the mink industry. Recent studies have showed that microRNAs (miRNAs, small noncoding RNAs of length ranging from 18-23 nucleotides (nt participate in host-pathogen interaction networks; however, whether or not miRNAs are involved in MEV infection has not been reported. Our study revealed that miRNA miR-181b inhibited replication of MEV in the feline kidney (F81 cell line by targeting the MEV non-structural protein 1 (NS1 messenger RNA (mRNA coding region, resulting in NS1 translational repression, while MEV infection reduced miR-181b expression. This is the first description of cellular miRNAs modulating MEV infection in F81 cells, providing further insight into the mechanisms of viral infection, and may be useful in development of naturally-occurring miRNAs antiviral strategies.

  5. RNA granules


    Anderson, Paul; Kedersha, Nancy


    Cytoplasmic RNA granules in germ cells (polar and germinal granules), somatic cells (stress granules and processing bodies), and neurons (neuronal granules) have emerged as important players in the posttranscriptional regulation of gene expression. RNA granules contain various ribosomal subunits, translation factors, decay enzymes, helicases, scaffold proteins, and RNA-binding proteins, and they control the localization, stability, and translation of their RNA cargo. We review the relationshi...

  6. MicroRNA Profiling of the Effect of the Heptapeptide Angiotensin-(1-7) in A549 Lung Tumor Cells Reveals a Role for miRNA149-3p in Cellular Migration Processes (United States)

    da Silva, Brenda de Oliveira; Lima, Kelvin Furtado; Gonçalves, Letícia Rocha; da Silveira, Marina Bonfogo; Moraes, Karen C. M.


    Lung cancer is one of the most frequent types of cancer in humans and a leading cause of death worldwide. The high mortality rates are correlated with late diagnosis, which leads to high rates of metastasis found in patients. Thus, despite all the improvement in therapeutic approaches, the development of new drugs that control cancer cell migration and metastasis are required. The heptapeptide angiotensin-(1–7) [ang-(1–7)] has demonstrated the ability to control the growth rates of human lung cancer cells in vitro and in vivo, and the elucidation of central elements that control the fine-tuning of cancer cells migration in the presence of the ang-(1–7), will support the development of new therapeutic approaches. Ang-(1–7) is a peptide hormone of the renin-angiotensin system (RAS) and this study investigates the modulatory effect of the heptapeptide on the expression pattern of microRNAs (miRNAs) in lung tumor cells, to elucidate mechanistic concerns about the effect of the peptide in the control of tumor migratory processes. Our primary aim was to compare the miRNA profiling between treated and untreated-heptapeptide cells to characterize the relevant molecule that modulates cellular migration rates. The analyses selected twenty one miRNAs, which are differentially expressed between the groups; however, statistical analyses indicated miRNA-149-3p as a relevant molecule. Once functional analyses were performed, we demonstrated that miRNA-149-3p plays a role in the cellular migration processes. This information could be useful for future investigations on drug development. PMID:27598578

  7. The expanding functions of cellular helicases: the tombusvirus RNA replication enhancer co-opts the plant eIF4AIII-like AtRH2 and the DDX5-like AtRH5 DEAD-box RNA helicases to promote viral asymmetric RNA replication.

    Directory of Open Access Journals (Sweden)

    Nikolay Kovalev


    Full Text Available Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication. Several of the co-opted host factors bind to the viral RNA, which plays multiple roles, including mRNA function, as an assembly platform for the viral replicase (VRC, template for RNA synthesis, and encapsidation during infection. It is likely that remodeling of the viral RNAs and RNA-protein complexes during the switch from one step to another requires RNA helicases. In this paper, we have discovered a second group of cellular RNA helicases, including the eIF4AIII-like yeast Fal1p and the DDX5-like Dbp3p and the orthologous plant AtRH2 and AtRH5 DEAD box helicases, which are co-opted by tombusviruses. Unlike the previously characterized DDX3-like AtRH20/Ded1p helicases that bind to the 3' terminal promoter region in the viral minus-strand (-RNA, the other class of eIF4AIII-like RNA helicases bind to a different cis-acting element, namely the 5' proximal RIII(- replication enhancer (REN element in the TBSV (-RNA. We show that the binding of AtRH2 and AtRH5 helicases to the TBSV (-RNA could unwind the dsRNA structure within the RIII(- REN. This unique characteristic allows the eIF4AIII-like helicases to perform novel pro-viral functions involving the RIII(- REN in stimulation of plus-strand (+RNA synthesis. We also show that AtRH2 and AtRH5 helicases are components of the tombusvirus VRCs based on co-purification experiments. We propose that eIF4AIII-like helicases destabilize dsRNA replication intermediate within the RIII(- REN that promotes bringing the 5' and 3' terminal (-RNA sequences in close vicinity via long-range RNA-RNA base pairing. This newly formed RNA structure promoted by eIF4AIII helicase together with AtRH20 helicase might facilitate the recycling of the viral replicases for multiple rounds of (+-strand synthesis, thus resulting in asymmetrical viral replication.

  8. Nonsense-mediated mRNA decay was demonstrated in two hypofibrinogenemias caused by heterozygous nonsense mutations of FGG, Shizuoka III and Kanazawa II. (United States)

    Soya, Keisuke; Takezawa, Yuka; Okumura, Nobuo; Terasawa, Fumiko


    We report two novel hypofibrinogenemias, Shizuoka III and Kanazawa II, which are caused by heterozygous mutations in FGG. Shizuoka III showed c.147delT and 147_149insACA in FGG exon 3 and a subsequent frameshift mutation, resulting in mature protein γ23X (native protein: γ49X), and Kanazawa II showed c.1205G>A in FGG exon 9, resulting in γ376X (native protein: γ402X). To determine whether the truncated γ-chains, γ23X and γ376X, were synthesized and participated in the assembly of fibrinogen, mutant-type cDNA vectors were transfected into Chinese hamster ovary (CHO) cells. Significant levels of mutant fibrinogen were not detected by ELISA in the culture media and cell lysates. Immunoblot analysis of cell lysates revealed that the mutant γ-chain of γ376X was observed but intact fibrinogen was not. On the other hand, mutant γ-chain was not observed in γ23X-expressing cells. To demonstrate the involvement of the mechanisms of nonsense-mediated mRNA decay (NMD), we cloned wild- and mutant-type mini-genes containing γ23 or γ376 codon and transfected these into CHO cell lines in the absence or presence of cycloheximide as an NMD inhibitor. mRNA levels were determined using real-time quantitative RT-PCR in CHO cells. In the absence of cycloheximide, levels of mRNAs transcribed from the mutant gene were lower than from the wild-type gene whereas, in the presence of cycloheximide, levels of mRNAs transcribed from the mutant gene increased dose-dependently. Finally, these results demonstrated that mRNAs containing γ23X or γ376X are degraded by the NMD system and translation of the truncated γ-chain polypeptide decrease in patients' hepatocytes, resulting in hypofibrinogenemias.

  9. Two novel exonic point mutations in HEXA identified in a juvenile Tay-Sachs patient: role of alternative splicing and nonsense-mediated mRNA decay. (United States)

    Levit, A; Nutman, D; Osher, E; Kamhi, E; Navon, R


    We have identified three mutations in the beta-hexoseaminidase A (HEXA) gene in a juvenile Tay-Sachs disease (TSD) patient, which exhibited a reduced level of HEXA mRNA. Two mutations are novel, c.814G>A (p.Gly272Arg) and c.1305C>T (p.=), located in exon 8 and in exon 11, respectively. The third mutation, c.1195A>G (p.Asn399Asp) in exon 11, has been previously characterized as a common polymorphism in African-Americans. Hex A activity measured in TSD Glial cells, transfected with HEXA cDNA constructs bearing these mutations, was unaltered from the activity level measured in normal HEXA cDNA. Analysis of RT-PCR products revealed three aberrant transcripts in the patient, one where exon 8 was absent, one where exon 11 was absent and a third lacking both exons 10 and 11. All three novel transcripts contain frameshifts resulting in premature termination codons (PTCs). Transfection of mini-gene constructs carrying the c.814G>A and c.1305C>T mutations proved that the two mutations result in exon skipping. mRNAs that harbor a PTC are detected and degraded by the nonsense-mediated mRNA decay (NMD) pathway to prevent synthesis of abnormal proteins. However, although NMD is functional in the patient's fibroblasts, aberrant transcripts are still present. We suggest that the level of correctly spliced transcripts as well as the efficiency in which NMD degrade the PTC-containing transcripts, apparently plays an important role in the phenotype severity of the unique patient and thus should be considered as a potential target for drug therapy.

  10. A case of pancreatic agenesis and congenital heart defects with a novel GATA6 nonsense mutation: evidence of haploinsufficiency due to nonsense-mediated mRNA decay. (United States)

    Suzuki, Shigeru; Nakao, Atsushi; Sarhat, Ashoor R; Furuya, Akiko; Matsuo, Kumihiro; Tanahashi, Yusuke; Kajino, Hiroki; Azuma, Hiroshi


    Recently, GATA6 heterozygous loss-of-function mutations were reported to cause pancreatic agenesis and congenital heart defects (PACHD [OMIM:600001]). However, the molecular mechanisms resulting from premature termination codons have not been examined in this disorder. The objective of this study was to perform a genetic analysis of a patient with PACHD. A female patient presented with ventricular septal defect, patent ductus arteriosus, and congenital diaphragmatic hernia at birth. Permanent neonatal diabetes mellitus and pancreatic exocrine deficiency due to pancreatic agenesis was diagnosed at 1 month of age. PCR-direct sequencing of GATA6 revealed that the patient is heterozygous for a novel de novo nonsense mutation of c.1477C>T, p. Arg493X in exon 5. RT-PCR direct sequencing of the RT-PCR products of total RNA from peripheral blood of the patient for the region encompassing exons 4-6 revealed only the wild-type allele. This finding provides the evidence for the occurrence of nonsense-mediated mRNA decay (NMD) in the p.Arg493X mutation. Quantitative RT-PCR analysis revealed that the expression of GATA6 transcript in the patient was less than half compared with normal control samples. This is the first evidence that GATA6 haploinsufficiency is caused by NMD in vivo, and we conclude that GATA6 haploinsufficiency causes not only PACHD but may affect other organs derived from the endoderm. Further screenings of GATA6 mutations in patients with various forms of diabetes and/or congenital heart disease with other visceral malformation may reveal the impact of GATA6 mutations on diabetes and congenital malformation.

  11. Genome-wide siRNA screen identifies the retromer as a cellular entry factor for human papillomavirus. (United States)

    Lipovsky, Alex; Popa, Andreea; Pimienta, Genaro; Wyler, Michael; Bhan, Ashima; Kuruvilla, Leena; Guie, Marie-Aude; Poffenberger, Adrian C; Nelson, Christian D S; Atwood, Walter J; DiMaio, Daniel


    Despite major advances in our understanding of many aspects of human papillomavirus (HPV) biology, HPV entry is poorly understood. To identify cellular genes required for HPV entry, we conducted a genome-wide screen for siRNAs that inhibited infection of HeLa cells by HPV16 pseudovirus. Many retrograde transport factors were required for efficient infection, including multiple subunits of the retromer, which initiates retrograde transport from the endosome to the trans-Golgi network (TGN). The retromer has not been previously implicated in virus entry. Furthermore, HPV16 capsid proteins arrive in the TGN/Golgi in a retromer-dependent fashion during entry, and incoming HPV proteins form a stable complex with retromer subunits. We propose that HPV16 directly engages the retromer at the early or late endosome and traffics to the TGN/Golgi via the retrograde pathway during cell entry. These results provide important insights into HPV entry, identify numerous potential antiviral targets, and suggest that the role of the retromer in infection by other viruses should be assessed.

  12. Potential toxic effect of trifloxystrobin on cellular microstructure, mRNA expression and antioxidant enzymes in Chlorella vulgaris. (United States)

    Shen, Yu-Feng; Liu, Lei; Gong, Yu-Xin; Zhu, Bin; Liu, Guang-Lu; Wang, Gao-Xue


    This study investigated the effects of trifloxystrobin that one strobilurin used widely in the world as an effective fungicidal agent to control Asian soybean rust on aquatic unicellular algae Chlorella vulgaris. We determined the potential toxic effect of trifloxystrobin on C. vulgaris, and found median inhibition concentration (IC(50)) value 255.58 (95% confidence interval, 207.81-330.29)μgL(-1). In addition, the algal cells were obviously depressed or shrunk at different concentrations by electron microscopy. In the study, a real-time polymerase chain reaction (PCR) assay showed changes in transcript abundances of three photosynthetic genes, psaB, psbC, and rbcL, and one energy gene, ATPs. The results showed that trifloxystrobin reduced the transcript abundances of the three genes and enhanced expression of ATPs after 48 and 96 h. The lowest abundances of psaB, psbC and rbcL transcripts in response to trifloxystrobin exposure were 58%, 79% and 60% of those of the control, respectively. For the potential toxic influences, trifloxystrobin could decrease the soluble protein and total antioxidant contents (T-AOC), and increase superoxide dismutase (SOD) and peroxidase (POD) activity with a gradual concentration-response relationship. Overall, the present study demonstrated that trifloxystrobin could affect the activities of antioxidant enzymes, disrupts photosynthesis in C. vulgaris, and damage cellular structure.

  13. Progress on Cis-acting Regulatory Elements in Nonsense-mediated mRNA Decay%NMD作用的顺式调控元件

    Institute of Scientific and Technical Information of China (English)

    黄峙; 周天鸿; 郭宝江


    真核生物利用无义介导的mRNA降解(nonsense-mediated mRNA decay,NMD),对含有提前终止密码子(premature termination codons,PTC)的异常转录产物进行快速清除,防止毒害性截短蛋白(truncated proteins)的产生,是真核生物重要的mRNA监视机制.NMD作用的启动与多种顺式调控元件有关,它们包括:提前终止密码子的标识;PTC下游特定位置的序列元件,在酵母细胞称为DSE(downstream sequence element,DSE),在哺乳动物细胞主要为内含子剪接依赖性序列元件(exon-exon junction,EEJ);稳定作用元件(stabilizer elements,STE)对NMD作用的阻抑调节;以及其他与NMD作用相关的序列,如poly(A)延长、5'-UTR的uORF(upstream open reading frame,uORF)和程序化核糖体移码(programmed -1 ribosomal frameshift,-1 PRF)信号序列等.NMD途径中的这些顺式调控元件可能是分子遗传调控的关键靶点.

  14. Distinct Effects of Allelic NFIX Mutations on Nonsense-Mediated mRNA Decay Engender Either a Sotos-like or a Marshall-Smith Syndrome (United States)

    Malan, Valérie; Rajan, Diana; Thomas, Sophie; Shaw, Adam C.; Louis dit Picard, Hélène; Layet, Valérie; Till, Marianne; van Haeringen, Arie; Mortier, Geert; Nampoothiri, Sheela; Pušeljić, Silvija; Legeai-Mallet, Laurence; Carter, Nigel P.; Vekemans, Michel; Munnich, Arnold; Hennekam, Raoul C.; Colleaux, Laurence; Cormier-Daire, Valérie


    By using a combination of array comparative genomic hybridization and a candidate gene approach, we identified nuclear factor I/X (NFIX) deletions or nonsense mutation in three sporadic cases of a Sotos-like overgrowth syndrome with advanced bone age, macrocephaly, developmental delay, scoliosis, and unusual facies. Unlike the aforementioned human syndrome, Nfix-deficient mice are unable to gain weight and die in the first 3 postnatal weeks, while they also present with a spinal deformation and decreased bone mineralization. These features prompted us to consider NFIX as a candidate gene for Marshall-Smith syndrome (MSS), a severe malformation syndrome characterized by failure to thrive, respiratory insufficiency, accelerated osseous maturation, kyphoscoliosis, osteopenia, and unusual facies. Distinct frameshift and splice NFIX mutations that escaped nonsense-mediated mRNA decay (NMD) were identified in nine MSS subjects. NFIX belongs to the Nuclear factor one (NFI) family of transcription factors, but its specific function is presently unknown. We demonstrate that NFIX is normally expressed prenatally during human brain development and skeletogenesis. These findings demonstrate that allelic NFIX mutations trigger distinct phenotypes, depending specifically on their impact on NMD. PMID:20673863

  15. VHL Frameshift Mutation as Target of Nonsense-Mediated mRNA Decay in Drosophila melanogaster and Human HEK293 Cell Line

    Directory of Open Access Journals (Sweden)

    Lucia Micale


    Full Text Available There are many well-studied examples of human phenotypes resulting from nonsense or frameshift mutations that are modulated by Nonsense-Mediated mRNA Decay (NMD, a process that typically degrades transcripts containing premature termination codons (PTCs in order to prevent translation of unnecessary or aberrant transcripts. Different types of germline mutations in the VHL gene cause the von Hippel-Lindau disease, a dominantly inherited familial cancer syndrome with a marked phenotypic variability and age-dependent penetrance. By generating the Drosophila UAS:Upf1D45B line we showed the possible involvement of NMD mechanism in the modulation of the c.172delG frameshift mutation located in the exon 1 of Vhl gene. Further, by Quantitative Real-time PCR (QPCR we demonstrated that the corresponding c.163delG human mutation is targeted by NMD in human HEK 293 cells. The UAS:Upf1D45B line represents a useful system to identify novel substrates of NMD pathway in Drosophila melanogaster. Finally, we suggest the possible role of NMD on the regulation of VHL mutations.

  16. Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study.

    Directory of Open Access Journals (Sweden)

    Cyril Dalmasso

    Full Text Available Previous studies of the HIV-1 disease have shown that HLA and Chemokine receptor genetic variants influence disease progression and early viral load. We performed a Genome Wide Association study in a cohort of 605 HIV-1-infected seroconverters for detection of novel genetic factors that influence plasma HIV-RNA and cellular HIV-DNA levels. Most of the SNPs strongly associated with HIV-RNA levels were localised in the 6p21 major histocompatibility complex (MHC region and were in the vicinity of class I and III genes. Moreover, protective alleles for four disease-associated SNPs in the MHC locus (rs2395029, rs13199524, rs12198173 and rs3093662 were strikingly over-represented among forty-five Long Term HIV controllers. Furthermore, we show that the HIV-DNA levels (reflecting the HIV reservoir are associated with the same four SNPs, but also with two additional SNPs on chromosome 17 (rs6503919; intergenic region flanked by the DDX40 and YPEL2 genes and chromosome 8 (rs2575735; within the Syndecan 2 gene. Our data provide evidence that the MHC controls both HIV replication and HIV reservoir. They also indicate that two additional genomic loci may influence the HIV reservoir.

  17. Dual role of TRBP in HIV replication and RNA interference: viral diversion of a cellular pathway or evasion from antiviral immunity?

    Directory of Open Access Journals (Sweden)

    Clerzius Guerline


    Full Text Available Abstract Increasing evidence indicates that RNA interference (RNAi may be used to provide antiviral immunity in mammalian cells. Human micro (miRNAs can inhibit the replication of a primate virus, whereas a virally-encoded miRNA from HIV inhibits its own replication. Indirect proof comes from RNAi suppressors encoded by mammalian viruses. Influenza NS1 and Vaccinia E3L proteins can inhibit RNAi in plants, insects and worms. HIV-1 Tat protein and Adenovirus VA RNAs act as RNAi suppressors in mammalian cells. Surprisingly, many RNAi suppressors are also inhibitors of the interferon (IFN-induced protein kinase R (PKR but the potential overlap between the RNAi and the IFN pathways remains to be determined. The link between RNAi as an immune response and the IFN pathway may be formed by a cellular protein, TRBP, which has a dual role in HIV replication and RNAi. TRBP has been isolated as an HIV-1 TAR RNA binding protein that increases HIV expression and replication by inhibiting PKR and by increasing translation of structured RNAs. A recent report published in the Journal of Virology shows that the poor replication of HIV in astrocytes is mainly due to a heightened PKR response that can be overcome by supplying TRBP exogenously. In two recent papers published in Nature and EMBO Reports, TRBP is now shown to interact with Dicer and to be required for RNAi mediated by small interfering (si and micro (miRNAs. The apparent discrepancy between TRBP requirement in RNAi and in HIV replication opens the hypotheses that RNAi may be beneficial for HIV-1 replication or that HIV-1 may evade the RNAi restriction by diverting TRBP from Dicer and use it for its own benefit.

  18. RNA interference-mediated targeting of human cytomegalovirus immediate-early or early gene products inhibits viral replication with differential effects on cellular functions. (United States)

    Xiaofei, E; Stadler, Bradford M; Debatis, Michelle; Wang, Shixia; Lu, Shan; Kowalik, Timothy F


    Viral drug toxicity, resistance, and an increasing immunosuppressed population warrant continued research into new avenues for limiting diseases associated with human cytomegalovirus (HCMV). In this study, a small interfering RNA (siRNA), siX3, was designed to target coding sequences within shared exon 3 of UL123 and UL122 transcripts encoding IE1 and IE2 immediate-early proteins of HCMV. Pretreatment of cells with siX3 reduced the levels of viral protein expression, DNA replication, and progeny virus production compared to control siRNA. Two siRNAs against UL54 and overlapping transcripts (UL55-57) were compared to siX3 in HCMV infection and were also found to be effective at inhibiting HCMV replication. Further investigation into the effects of the siRNAs on viral replication showed that pretreatment with each of the siRNAs resulted in an inhibition in the formation of mature replication compartments. The ability of these siRNAs to prevent or reduce certain cytopathic effects associated with HCMV infection was also examined. Infected cells pretreated with siX3, but not siUL54, retained promyelocytic leukemia (PML) protein in cellular PML bodies, an essential component of this host intrinsic antiviral defense. DNA damage response proteins, which are localized in nuclear viral replication compartments, were reduced in the siX3- and siUL54-treated cells. siX3, but not siUL54, prevented DNA damage response signaling early after infection. Therapeutic efficacy was demonstrated by treating cells with siRNAs after HCMV replication had commenced. Together, these findings suggest that siRNAs targeting exon 3 of the major IE genes or the UL54-57 transcripts be further studied for their potential development into anti-HCMV therapeutics.

  19. The miRNA Profile of Platelets Stored in a Blood Bank and Its Relation to Cellular Damage from Storage. (United States)

    Pontes, Thaís Brilhante; Moreira-Nunes, Caroline de Fátima Aquino; Maués, Jersey Heitor da Silva; Lamarão, Letícia Martins; de Lemos, José Alexandre Rodrigues; Montenegro, Raquel Carvalho; Burbano, Rommel Mário Rodriguez


    Millions of blood products are transfused each year, and many lives are directly affected by transfusion. Platelet concentrate (PC) is one of the main products derived from blood. Even under good storage conditions, PC is likely to suffer cell damage. The shape of platelets changes after 5 to 7 days of storage at 22°C. Taking into consideration that some platelet proteins undergo changes in their shape and functionality during PC storage. Sixteen PC bags were collected and each PC bag tube was cut into six equal pieces to perform experiments with platelets from six different days of storage. Thus, on the first day of storage, 1/6 of the tube was used for miRNA extraction, and the remaining 5/6 was stored under the same conditions until extraction of miRNAs on each the following five days. Samples were sequenced on an Illumina Platform to demonstrate the most highly expressed miRNAs. Three miRNAs, mir127, mir191 and mir320a were validated by real-time quantitative PCR (RQ-PCR) in 100 PC bags tubes. Our method suggests, the use of the miRNAs mir127 and mir320a as biomarkers to assess the "validity period" of PC bags stored in blood banks for long periods. Thus, bags can be tested on the 5th day of storage for the relative expression levels of mir127 and mir320a. Thus, we highlight candidate miRNAs as biomarkers of storage damage that can be used as tools to evaluate the quality of stored PC. The use of miRNAs as biomarkers of damage is unprecedented and will contribute to improved quality of blood products for transfusions.

  20. Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives

    Directory of Open Access Journals (Sweden)

    Jozef Julian Bujarski


    Full Text Available RNA recombination is one of the driving forces of genetic variability in (+-strand RNA viruses. Various types of RNA-RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings along with nonreplicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (i How various factors modulate the ability of viral replicase to switch templates, (ii What is the intracellular location of RNA-RNA template switchings, (iii Mechanisms and factors responsible for non-replicative RNA recombination, (iv Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (v What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.

  1. The D10 Decapping Enzyme of Vaccinia Virus Contributes to Decay of Cellular and Viral mRNAs and to Virulence in Mice



    Posttranscriptional mechanisms are important for regulation of cellular and viral gene expression. The presence of the 5′ cap structure m7G(5′)ppp(5′)Nm is a general feature of mRNAs that provides protection from exoribonuclease digestion and enhances translation. Vaccinia virus and other poxviruses encode enzymes for both cap synthesis and decapping. Decapping is mediated by two related enzymes, D9 and D10, which are synthesized before and after viral DNA replication, respectively. The timin...

  2. ACTH Action on Messenger RNA Stability Mechanisms (United States)

    Desroches-Castan, Agnès; Feige, Jean-Jacques; Cherradi, Nadia


    The regulation of mRNA stability has emerged as a critical control step in dynamic gene expression. This process occurs in response to modifications of the cellular environment, including hormonal variations, and regulates the expression of subsets of proteins whose levels need to be rapidly adjusted. Modulation of messenger RNA stability is usually mediated by stabilizing or destabilizing RNA-binding proteins (RNA-BP) that bind to the 3′-untranslated region regulatory motifs, such as AU-rich elements (AREs). Destabilizing ARE-binding proteins enhance the decay of their target transcripts by recruiting the mRNA decay machineries. Failure of such mechanisms, in particular misexpression of RNA-BP, has been linked to several human diseases. In the adrenal cortex, the expression and activity of mRNA stability regulatory proteins are still understudied. However, ACTH- or cAMP-elicited changes in the expression/phosphorylation status of the major mRNA-destabilizing protein TIS11b/BRF1 or in the subcellular localization of the stabilizing protein Human antigen R have been reported. They suggest that this level of regulation of gene expression is also important in endocrinology.

  3. MiRNA-205 modulates cellular invasion and migration via regulating zinc finger E-box binding homeobox 2 expression in esophageal squamous cell carcinoma cells

    Directory of Open Access Journals (Sweden)

    Yamashita Shunichi


    Full Text Available Abstract Background Esophageal squamous cell carcinoma (ESCC is often diagnosed at later stages until they are incurable. MicroRNA (miR is a small, non-coding RNA that negatively regulates gene expression mainly via translational repression. Accumulating evidence indicates that deregulation of miR is associated with human malignancies including ESCC. The aim of this study was to identify miR that could be specifically expressed and exert distinct biological actions in ESCC. Methods Total RNA was extracted from ESCC cell lines, OE21 and TE10, and a non-malignant human esophageal squamous cell line, Het-1A, and subjected to microarray analysis. Expression levels of miR that showed significant differences between the 2 ESCC and Het-1A cells based on the comprehensive analysis were analyzed by the quantitative reverse transcriptase (RT-PCR method. Then, functional analyses, including cellular proliferation, apoptosis and Matrigel invasion and the wound healing assay, for the specific miR were conducted. Using ESCC tumor samples and paired surrounding non-cancerous tissue obtained endoscopically, the association with histopathological differentiation was examined with quantitative RT-PCR. Results Based on the miR microarray analysis, there were 14 miRs that showed significant differences (more than 2-fold in expression between the 2 ESCC cells and non-malignant Het-1A. Among the significantly altered miRs, miR-205 expression levels were exclusively higher in 5 ESCC cell lines examined than any other types of malignant cell lines and Het-1A. Thus, miR-205 could be a specific miR in ESCC. Modulation of miR-205 expression by transfection with its precursor or anti-miR-205 inhibitor did not affect ESCC cell proliferation and apoptosis, but miR-205 was found to be involved in cell invasion and migration. Western blot revealed that knockdown of miR-205 expression in ESCC cells substantially enhanced expression of zinc finger E-box binding homeobox 2

  4. Retraction Statement: 'MicroRNA-218 increases cellular sensitivity to Rapamycin via targeting Rictor in cervical cancer' by Li J, Wang J, Wang Y, Qiu H. (United States)


    The above article from APMIS, published online on 24 April 2015 in Wiley Online Library ( and in Volume 123, pp. 562-570, has been retracted by agreement between the authors, the journal Editors in Chief, Professors Bodil Norrild, Ben Vainer and Elisabeth Ralfkiaer, and John Wiley & Sons Ltd. The article has been retracted due to errors in the reported results. In this study, the authors used HeLa and SiHa cell lines to investigate the biological roles of miR-218. However, subsequently it emerged that the two cell lines were contaminated in the laboratory by other unknown cell lines. When repeating the experiments, it was found that the functions of miR-218 were not as significant as had been previously reported, especially its effects on rapamycin sensitivity. Reference Li J, Li X, Wang J, Wang Y, Qiu H. MicroRNA-218 increases cellular sensitivity to Rapamycin via targeting Rictor in cervical cancer. APMIS 2015; 123:562-570. doi: 10.1111/apm.12387.

  5. mRNA for N-Bak, a neuron-specific BH3-only splice isoform of Bak, escapes nonsense-mediated decay and is translationally repressed in the neurons. (United States)

    Jakobson, M; Lintulahti, A; Arumäe, U


    mRNA for neuronal Bak (N-Bak), a splice variant of pro-apoptotic Bcl-2 family member Bak is expressed in the neurons. Surprisingly the endogeneous N-Bak protein cannot be demonstrated in the neurons, although the antibodies recognize N-Bak protein from in vitro translation or transiently transfected cells. As N-Bak mRNA contains premature termination codon (PTC) at 89 nucleotides upstream from the last exon-exon junction, it could be degraded by nonsense-mediated decay (NMD) during the pioneer round of translation thus explaining the absence of the protein. We show here that the endogeneous neuronal N-Bak mRNA is not the NMD substrate, as it is not accumulating by cycloheximide treatment, it has a long lifetime, and even prevention of PTC by interfering with the alternative splicing did not lead to translation of the Bak mRNA. N-Bak protein is also not revealed by proteasome inhibitors. Our data suggest strong translational arrest of N-Bak mRNA in the neurons. We show that this arrest is partially mediated by 5'-untranslated region of Bak mRNA and it is not released during mitochondrial apoptosis.

  6. Herpes Simplex Virus 1 Infection Alters the mRNA Translation Processing in L-02 Cells

    Institute of Scientific and Technical Information of China (English)

    Min HONG; Yan-chun CHE; Gui-zhen TANG; Wei CUN; Xue-mei ZHANG; Long-ding LIU; Qi-han LI


    HSV-1 infection-mediated regulation of mRNA translation in host cells is a systematic and complicated process. Investigation of the details of this mechanism will facilitate understanding of biological variations in the viral replication process and host cells. In this study, a comparative proteomics technology platform was applied by two-dimension electrophoresis of HSV-1 infected normal human L-02 cell and control cell lysates. The observed protein spots were analyzed qualitatively and quantitatively by the PDQuest software package. A number of the different observed protein spots closely associated with cellular protein synthesis were identified by matrix-assisted laser-desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS). The expression levels of the RPLP1 protein, which is required for mRNA translation, and KHSRP protein, which is involved in rapid decay of mRNA, were up-regulated, whereas the expression level of RNP H2, which is involved in positive regulation on the mRNA splicing process, was down-regulated. All of these results suggest that HSV-1 infection can influence cellular protein synthesis via modulation of cellular regulatory proteins involved in RNA splicing, translation and decay, resulting in optimisation of viral protein synthesis when cellular protein synthesis is shut off. Although there is need for further investigations regarding the detailed mechanisms of cellular protein control, our studies provide new insight into the targeting of varied virus signaling pathways involved in host cellular protein synthesis.

  7. Viral Evasion and Manipulation of Host RNA Quality Control Pathways. (United States)

    Hogg, J Robert


    Viruses have evolved diverse strategies to maximize the functional and coding capacities of their genetic material. Individual viral RNAs are often used as substrates for both replication and translation and can contain multiple, sometimes overlapping open reading frames. Further, viral RNAs engage in a wide variety of interactions with both host and viral proteins to modify the activities of important cellular factors and direct their own trafficking, packaging, localization, stability, and translation. However, adaptations increasing the information density of small viral genomes can have unintended consequences. In particular, viral RNAs have developed features that mark them as potential targets of host RNA quality control pathways. This minireview focuses on ways in which viral RNAs run afoul of the cellular mRNA quality control and decay machinery, as well as on strategies developed by viruses to circumvent or exploit cellular mRNA surveillance.

  8. The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production

    DEFF Research Database (Denmark)

    Schmid, Manfred; Olszewski, Pawel; Pelechano, Vicent;


    Polyadenylation of mRNA is a key step in eukaryotic gene expression. However, despite the major impact of poly(A) tails on mRNA metabolism, the precise roles of poly(A)-binding proteins (PABPs) in nuclear mRNA biogenesis remain elusive. Here, we demonstrate that rapid nuclear depletion of the S....... cerevisiae PABP Nab2p leads to a global loss of cellular mRNA, but not of RNA lacking poly(A) tails. Disappearance of mRNA is a nuclear event, but not due to decreased transcription. Instead, the absence of Nab2p results in robust nuclear mRNA decay by the ribonucleolytic RNA exosome in a polyadenylation......-dependent process. We conclude that Nab2p is required to protect early mRNA and therefore constitutes a crucial nuclear mRNA biogenesis factor....

  9. CD11b/CD18 (Mac-1) is a novel surface receptor for extracellular double-stranded RNA to mediate cellular inflammatory responses. (United States)

    Zhou, Hui; Liao, Jieying; Aloor, Jim; Nie, Hui; Wilson, Belinda C; Fessler, Michael B; Gao, Hui-Ming; Hong, Jau-Shyong


    During viral infection, extracellular dsRNA is a potent signaling molecule that activates many innate immune cells, including macrophages. TLR3 is a well-known receptor for extracellular dsRNA, and internalization of extracellular dsRNA is required for endosomal TLR3 activation. Preserved inflammatory responses of TLR3-deficient macrophages to extracellular dsRNA strongly support a TLR3-independent mechanism in dsRNA-mediated immune responses. The present study demonstrated that CD11b/CD18 (Mac-1 [macrophage-1 Ag]), a surface integrin receptor, recognized extracellular dsRNA and induced macrophage immune responses. CD11b deficiency reduced inflammatory cytokine induction elicited by polyinosinic:polycytidylic acid (poly I:C; a synthetic dsRNA) in mouse sera and livers, as well as in cultured peritoneal macrophages. dsRNA-binding assay and confocal immunofluorescence showed that Mac-1, especially the CD11b subunit, interacted and colocalized with poly I:C on the surface of macrophages. Further mechanistic studies revealed two distinct signaling events following dsRNA recognition by Mac-1. First, Mac-1 facilitated poly I:C internalization through the activation of PI3K signaling and enhanced TLR3-dependent activation of IRF3 in macrophages. Second, poly I:C induced activation of phagocyte NADPH oxidase in a TLR3-independent, but Mac-1-dependent, manner. Subsequently, phagocyte NADPH oxidase-derived intracellular reactive oxygen species activated MAPK and NF-κB pathways. Our results indicate that extracellular dsRNA activates Mac-1 to enhance TLR3-dependent signaling and to trigger TLR3-independent, but Mac-1-dependent, inflammatory oxidative signaling, identifying a novel mechanistic basis for macrophages to recognize extracellular dsRNA to regulate innate immune responses. This study identifies Mac-1 as a novel surface receptor for extracellular dsRNA and implicates it as a potential therapeutic target for virus-related inflammatory diseases.

  10. Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay

    Directory of Open Access Journals (Sweden)

    Zavolan Mihaela


    Full Text Available Abstract Background In addition to acting as an RNA quality control pathway, nonsense-mediated mRNA decay (NMD plays roles in regulating normal gene expression. In particular, the extent to which alternative splicing is coupled to NMD and the roles of NMD in regulating uORF containing transcripts have been a matter of debate. Results In order to achieve a greater understanding of NMD regulated gene expression we used 2D-DiGE proteomics technology to examine the changes in protein expression induced in HeLa cells by UPF1 knockdown. QPCR based validation of the corresponding mRNAs, in response to both UPF1 knockdown and cycloheximide treatment, identified 17 bona fide NMD targets. Most of these were associated with bioinformatically predicted NMD activating features, predominantly upstream open reading frames (uORFs. Strikingly, however, the majority of transcripts up-regulated by UPF1 knockdown were either insensitive to, or even down-regulated by, cycloheximide treatment. Furthermore, the mRNA abundance of several down-regulated proteins failed to change upon UPF1 knockdown, indicating that UPF1's role in regulating mRNA and protein abundance is more complex than previously appreciated. Among the bona fide NMD targets, we identified a highly conserved AS-NMD event within the 3' UTR of the HNRNPA2B1 gene. Overexpression of GFP tagged hnRNP A2 resulted in a decrease in endogenous hnRNP A2 and B1 mRNA with a concurrent increase in the NMD sensitive isoforms. Conclusions Despite the large number of changes in protein expression upon UPF1 knockdown, a relatively small fraction of them can be directly attributed to the action of NMD on the corresponding mRNA. From amongst these we have identified a conserved AS-NMD event within HNRNPA2B1 that appears to mediate autoregulation of HNRNPA2B1 expression levels.

  11. The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions. (United States)

    Beckmann, Benedikt M; Castello, Alfredo; Medenbach, Jan


    Post-transcriptional regulation of gene expression plays a critical role in almost all cellular processes. Regulation occurs mostly by RNA-binding proteins (RBPs) that recognise RNA elements and form ribonucleoproteins (RNPs) to control RNA metabolism from synthesis to decay. Recently, the repertoire of RBPs was significantly expanded owing to methodological advances such as RNA interactome capture. The newly identified RNA binders are involved in diverse biological processes and belong to a broad spectrum of protein families, many of them exhibiting enzymatic activities. This suggests the existence of an extensive crosstalk between RNA biology and other, in principle unrelated, cell functions such as intermediary metabolism. Unexpectedly, hundreds of new RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. Despite the many functions that have been attributed to RNA, our understanding of RNPs is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (RNA-determined RNPs) are abundant and offer an alternative explanation for the surprising lack of classical RBDs in many RNA-interacting proteins. Moreover, RNAs can act as scaffolds to orchestrate and organise protein networks and directly control their activity, suggesting that nucleic acids might play an important regulatory role in many cellular processes, including metabolism.

  12. Nuclear export of human hepatitis B virus core protein and pregenomic RNA depends on the cellular NXF1-p15 machinery. (United States)

    Yang, Ching-Chun; Huang, Er-Yi; Li, Hung-Cheng; Su, Pei-Yi; Shih, Chiaho


    Hepatitis B virus (HBV) core protein (HBc) can shuttle between nucleus and cytoplasm. Cytoplasm-predominant HBc is clinically associated with severe liver inflammation. Previously, we found that HBc arginine-rich domain (ARD) can associate with a host factor NXF1 (TAP) by coimmunoprecipitation. It is well known that NXF1-p15 heterodimer can serve as a major export receptor of nuclear mRNA as a ribonucleoprotein complex (RNP). In the NXF1-p15 pathway, TREX (transcription/export) complex plays an important role in coupling nuclear pre-mRNA processing with mRNA export in mammalian cells. Here, we tested the hypothesis whether HBc and HBV specific RNA can be exported via the TREX and NXF1-p15 mediated pathway. We demonstrated here that HBc can physically and specifically associate with TREX components, and the NXF1-p15 export receptor by coimmunoprecipitation. Accumulation of HBc protein in the nucleus can be induced by the interference with TREX and NXF1-p15 mediated RNA export machinery. HBV transcripts encodes a non-spliced 3.5 kb pregenomic RNA (pgRNA) which can serve as a template for reverse transcription. Cytoplasmic HBV pgRNA appeared to be reduced by siRNA treatment specific for the NXF1-p15 complex by quantitative RT-qPCR and Northern blot analyses. This result suggests that the pgRNA was also exported via the NXF1-p15 machinery. We entertain the hypothesis that HBc protein can be exported as an RNP cargo via the mRNA export pathway by hijacking the TREX and NXF1-p15 complex. In our current and previous studies, HBc is not required for pgRNA accumulation in the cytoplasm. Furthermore, HBc ARD can mediate nuclear export of a chimeric protein containing HBc ARD in a pgRNA-independent manner. Taken together, it suggests that while both pgRNA and HBc protein exports are dependent on NXF1-p15, they are using the same export machinery in a manner independent of each other.

  13. RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction. (United States)

    Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong


    Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (, an RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA-RNA interactions and 1619 RNA-protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA-RNA/RNA-protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA-RNA/RNA-protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network.

  14. Convivial Decay

    DEFF Research Database (Denmark)

    Cohn, Marisa


    in the life of infrastructure we can observe common issues associated with aging infrastructures – hardware’s material decay, programming languages and software tools reaching end of support, obsolete managerial methodologies, etc. Such a case of infrastructural decay reveals how work of infrastructure...... maintenance may reach the limits of repair and shift from repair-as-sustaining into a mode of repair- into-decay, actively working towards the end-of-life. What this reveals is that, rather than infrastructural decay being a natural by-product of time’s passing, there is active work that goes into producing......This paper discusses the empirical case of an aging and obsolescent infrastructure supporting a space science mission that is currently approaching a known end. Such a case contributes to our understanding of the degrading path at the end-of-life of an infrastructure. During this later stage...

  15. miRNA array analysis determines miR-205 is overexpressed in head and neck squamous cell carcinoma and enhances cellular proliferation

    Directory of Open Access Journals (Sweden)

    Howard JD


    Full Text Available MicroRNAs (miRNAs play a critical role in cell cycle and pro-survival signal regulation. Consequently, their deregulation can enhance tumorigenesis and cancer progression. In the current investigation, we determined whether cancer- or human papillomavirus (HPV-specific miRNA deregulation could further elucidate signal transduction events unique to head and neck squamous cell carcinoma (HNSCC. Twenty-nine newly diagnosed HNSCC tumors (HPV-positive: 14, HPV-negative: 15 and four normal mucosa samples were analyzed for global miRNA expression. Differential miRNA expression analysis concluded HNSCC is characterized by a general upregulation of miRNAs compared to normal mucosa. Additionally, miR-449a and miR-129-3p were statistically significant miRNAs differentially expressed between HPV-positive and HPV-negative HNSCC. The upregulation of miR-449a was also validated within an independent dataset obtained from TCGA containing 279 HNSCCs and 39 normal adjacent mucosa samples. To gain a better understanding of miRNA-mediated cell cycle deregulation in HNSCC, we functionally evaluated miR-205, a transcript upregulated in our cancer-specific analysis and a putative regulator of E2F1. Modulation of miR-205 with a miRNA mimic and inhibitor revealed miR-205 is capable of regulating E2F1 expression in HNSCC and overexpression of this transcript enhances proliferation. This study demonstrates miRNA expression is highly deregulated in HNSCC and functional evaluations of these miRNAs may reveal novel HPV context dependent mechanisms in this disease.

  16. Proton Decay


    Hikosaka, Koki


    We discuss the status of supersymmetric grand unified theories [SUSY GUTs] with regards to the observation of proton decay. In this talk we focus on SUSY GUTs in 4 dimensions. We outline the major theoretical uncertainties present in the calculation of the proton lifetime and then present our best estimate of an absolute upper bound on the predicted proton lifetime. Towards the end, we consider some new results in higher dimensional GUTs and the ramifications for proton decay.

  17. Cellular identity of an 18S rRNA gene sequence clade within the class Kinetoplastea: the novel genus Actuariola gen. nov. (Neobodonida) with description of the type species Actuariola framvarensis sp. nov. (United States)

    Stoeck, Thorsten; Schwarz, M V Julian; Boenigk, Jens; Schweikert, Michael; von der Heyden, Sophie; Behnke, Anke


    Environmental molecular surveys of microbial diversity have uncovered a vast number of novel taxonomic units in the eukaryotic tree of life that are exclusively known by their small-subunit (SSU) rRNA gene signatures. In this study, we reveal the cellular and taxonomic identity of a novel eukaryote SSU rRNA gene sequence clade within the Kinetoplastea. Kinetoplastea are ubiquitously distributed flagellated protists of high ecological and medical importance. We isolated an organism from the oxic-anoxic interface of the anoxic Framvaren Fjord (Norway), which branches within an unidentified kinetoplastean sequence clade. Ultrastructural studies revealed a typical cellular organization that characterized the flagellated isolate as a member of the order Neobodonida Vickerman 2004, which contains five genera. The isolate differed in several distinctive characters from Dimastigella, Cruzella, Rhynchobodo and Rhynchomonas. The arrangement of the microtubular rod that supports the apical cytostome and the cytopharynx differed from the diagnosis of the fifth described genus (Neobodo Vickerman 2004) within the order Neobodonida. On the basis of both molecular and microscopical data, a novel genus within the order Neobodonida, Actuariola gen. nov., is proposed. Here, we characterize its type species, Actuariola framvarensis sp. nov., and provide an in situ tool to access the organism in nature and study its ecology.

  18. Cellular glutathione content modulates the effect of andrographolide on β-naphthoflavone-induced CYP1A1 mRNA expression in mouse hepatocytes. (United States)

    Kondo, Sachiko; Chatuphonprasert, Waranya; Jaruchotikamol, Atika; Sakuma, Tsutomu; Nemoto, Nobuo


    We previously reported that andrographolide (Andro), a major bioactive constituent of Andrographis paniculata, synergistically enhanced the inducible expression of CYP1A1 mRNA. In this study, although the synergism was confirmed at 24h after the start of treatment with Andro and β-naphthoflavone (βNF), a CYP1A inducer, the expression was profoundly suppressed at an earlier phase, namely at 6-12h, when the βNF-induced expression peaked. Although oxidized glutathione (GSSG) levels were higher in co-treated cells at 6 and 24h, levels of reactive oxygen species varied depending on the treatment period and species, indicating no relation to the synergistic expression of CYP1A1 mRNA. Glutathione (GSH) and N-acetyl-l-cysteine (NAC) significantly enhanced the βNF-induced expression, and partly reversed the suppressive effect of Andro in the early phase. At 24h, the addition of GSH or NAC had no effect on βNF-induced CYP1A1 mRNA expression, but significantly reduced the synergistic effect of Andro. The synergistic effect was enhanced by l-buthionine-(S,R)-sulfoximine, a GSH depleter. Furthermore, H(2)O(2) and ascorbic acid further modified the profile of synergism of Andro on βNF-inducible CYP1A1 mRNA expression. These results suggest that GSH status might be involved in βNF-induced CYP1A1 mRNA expression, and the interaction of Andro with GSH might modulate the expression.

  19. SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample.

    Directory of Open Access Journals (Sweden)

    Jesse M Gray

    Full Text Available mRNA synthesis, processing, and destruction involve a complex series of molecular steps that are incompletely understood. Because the RNA intermediates in each of these steps have finite lifetimes, extensive mechanistic and dynamical information is encoded in total cellular RNA. Here we report the development of SnapShot-Seq, a set of computational methods that allow the determination of in vivo rates of pre-mRNA synthesis, splicing, intron degradation, and mRNA decay from a single RNA-Seq snapshot of total cellular RNA. SnapShot-Seq can detect in vivo changes in the rates of specific steps of splicing, and it provides genome-wide estimates of pre-mRNA synthesis rates comparable to those obtained via labeling of newly synthesized RNA. We used SnapShot-Seq to investigate the origins of the intrinsic bimodality of metazoan gene expression levels, and our results suggest that this bimodality is partly due to spillover of transcriptional activation from highly expressed genes to their poorly expressed neighbors. SnapShot-Seq dramatically expands the information obtainable from a standard RNA-Seq experiment.

  20. mRNA decay during herpes simplex virus (HSV) infections: mutations that affect translation of an mRNA influence the sites at which it is cleaved by the HSV virion host shutoff (Vhs) protein. (United States)

    Shiflett, Lora A; Read, G Sullivan


    During lytic infections, the herpes simplex virus (HSV) virion host shutoff (Vhs) endoribonuclease degrades many host and viral mRNAs. Within infected cells it cuts mRNAs at preferred sites, including some in regions of translation initiation. Vhs binds the translation initiation factors eIF4H, eIF4AI, and eIF4AII, suggesting that its mRNA degradative function is somehow linked to translation. To explore how Vhs is targeted to preferred sites, we examined the in vitro degradation of a target mRNA in rabbit reticulocyte lysates containing in vitro-translated Vhs. Vhs caused rapid degradation of mRNAs beginning with cleavages at sites in the first 250 nucleotides, including a number near the start codon and in the 5' untranslated region. Ligation of the ends to form a circular mRNA inhibited Vhs cleavage at the same sites at which it cuts capped linear molecules. This was not due to an inability to cut any circular RNA, since Vhs cuts circular mRNAs containing an encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES) at the same sites as linear molecules with the IRES. Cutting linear mRNAs at preferred sites was augmented by the presence of a 5' cap. Moreover, mutations that altered the 5' proximal AUG abolished Vhs cleavage at nearby sites, while mutations that changed sequences surrounding the AUG to improve their match to the Kozak consensus sequence enhanced Vhs cutting near the start codon. The results indicate that mutations in an mRNA that affect its translation affect the sites at which it is cut by Vhs and suggest that Vhs is directed to its preferred cut sites during translation initiation.

  1. Pseudouridine and N-6 methyladenosine modifications weaken PUF protein/RNA interactions. (United States)

    Vaidyanathan, Pavanapuresan P; AlSadhan, Ishraq; Merriman, Dawn K; Al-Hashimi, Hashim; Herschlag, Daniel


    RNA modifications are ubiquitous in biology, with over 100 distinct modifications. While the vast majority were identified and characterized on abundant non-coding RNA such as tRNA and rRNA, the advent of sensitive sequencing-based approaches has led to the discovery of extensive and regulated modification of eukaryotic messenger RNAs as well. The two most abundant mRNA modifications -pseudouridine (Ψ) and N-6 methyladenosine (m6A)- affect diverse cellular processes including mRNA splicing, localization, translation, and decay and modulate RNA structure. Here, we test the hypothesis that RNA modifications directly affect interactions between RNA-binding proteins and target RNA. We show that Ψ and m6A weaken the binding of the human single-stranded RNA binding protein Pumilio 2 (hPUM2) to its consensus motif, with individual modifications having effects up to ~3 fold and multiple modifications giving larger effects. While there are likely to be some cases where RNA modifications essentially fully ablate protein binding, here we see modest responses that may be more common. Such modest effects could nevertheless profoundly alter the complex landscape of RNA:protein interactions, and the quantitative rather than qualitative nature of these effects underscores the need for quantitative, systems-level accounting of RNA:protein interactions to understand post-transcriptional regulation.

  2. Memory loss in old rats is associated with brain mitochondrial decay and RNA/DNA oxidation: Partial reversal by feeding acetyl-l-carnitine and/or R-α-lipoic acid (United States)

    Liu, Jiankang; Head, Elizabeth; Gharib, Afshin M.; Yuan, Wenjun; Ingersoll, Russell T.; Hagen, Tory M.; Cotman, Carl W.; Ames, Bruce N.


    Accumulation of oxidative damage to mitochondria, protein, and nucleic acid in the brain may lead to neuronal and cognitive dysfunction. The effects on cognitive function, brain mitochondrial structure, and biomarkers of oxidative damage were studied after feeding old rats two mitochondrial metabolites, acetyl-l-carnitine (ALCAR) [0.5% or 0.2% (wt/vol) in drinking water], and/or R-α-lipoic acid (LA) [0.2% or 0.1% (wt/wt) in diet]. Spatial memory was assessed by using the Morris water maze; temporal memory was tested by using the peak procedure (a time-discrimination procedure). Dietary supplementation with ALCAR and/or LA improved memory, the combination being the most effective for two different tests of spatial memory (P < 0.05; P < 0.01) and for temporal memory (P < 0.05). Immunohistochemical analysis showed that oxidative damage to nucleic acids (8-hydroxyguanosine and 8-hydroxy-2′-deoxyguanosine) increased with age in the hippocampus, a region important for memory. Oxidative damage to nucleic acids occurred predominantly in RNA. Dietary administration of ALCAR and/or LA significantly reduced the extent of oxidized RNA, the combination being the most effective. Electron microscopic studies in the hippocampus showed that ALCAR and/or LA reversed age-associated mitochondrial structural decay. These results suggest that feeding ALCAR and LA to old rats improves performance on memory tasks by lowering oxidative damage and improving mitochondrial function. PMID:11854529

  3. Arabidopsis Plants Having Defects in Nonsense-mediated mRNA Decay Factors UPF1,UPF2, and UPF3 Show Photoperiod-dependent Phenotypes in Development and Stress Responses

    Institute of Scientific and Technical Information of China (English)

    Chuan Shi; lan T. Baldwin; Jianqiang Wu


    Nonsense-mediated mRNA decay (NMD) is an important mRNA quality surveillance pathway in all eukaryotes that eliminates aberrant mRNAs derived from various sources.Three NMD factor proteins,UPF1,UPF2,and UPF3 are required for the NMD process and were found to be also involved in certain stress responses in mammalian and yeast cells.Using Arabidopsis thaliana mutants of UPF1 and UPF3 and UPF2-silenced lines (irUPF2),we examined the involvement of UPF1,UPF2,and UPF3 in development and in response to stresses,wounding and infection by Pseudomonas syringae pv.tomato strain DC3000.Under the long (16 h) photoperiod condition,Arabidopsis having a defect in NMD factors exhibited altered morphologies of various organs,disturbed homeostasis of wounding-induced jasmonic acid and pathogen-elicited salicylic acid,and abnormal wounding- and methyl jasmonate-induced changes in the transcript levels of two defense-related genes,LOX2 and VSP2.Importantly,when plants were cultivated under the short (10 h) photoperiod condition,mutants of UPF1 and UPF3 and irUPF2 showed smaller differences from the wild-type plants in growth and stress-induced responses.These data suggest a complex regulatory network,likely composed of light signaling and NMD factor-mediated pathways,in influencing plant development and adaption to environmental stresses.

  4. A non-proteolytic role for ubiquitin in deadenylation of MHC-I mRNA by the RNA-binding E3-ligase MEX-3C (United States)

    Cano, Florencia; Rapiteanu, Radu; Sebastiaan Winkler, G.; Lehner, Paul J.


    The regulation of protein and mRNA turnover is essential for many cellular processes. We recently showed that ubiquitin—traditionally linked to protein degradation—directly regulates the degradation of mRNAs through the action of a newly identified family of RNA-binding E3 ubiquitin ligases. How ubiquitin regulates mRNA decay remains unclear. Here, we identify a new role for ubiquitin in regulating deadenylation, the initial and often rate-limiting step in mRNA degradation. MEX-3C, a canonical member of this family of RNA-binding ubiquitin ligases, associates with the cytoplasmic deadenylation complexes and ubiquitinates CNOT7(Caf1), the main catalytic subunit of the CCR4-NOT deadenylation machinery. We establish a new role for ubiquitin in regulating MHC-I mRNA deadenylation as ubiquitination of CNOT7 by MEX-3C regulates its deadenylation activity and is required for MHC-I mRNA degradation. Since neither proteasome nor lysosome inhibitors rescued MEX-3C-mediated MHC-I mRNA degradation, our findings suggest a new non-proteolytic function for ubiquitin in the regulation of mRNA decay. PMID:26471122

  5. The CELF1 RNA-Binding Protein Regulates Decay of Signal Recognition Particle mRNAs and Limits Secretion in Mouse Myoblasts (United States)

    Russo, Joseph; Lee, Jerome E.; López, Carolina M.; Anderson, John; Nguyen, Thuy-mi P.; Heck, Adam M.; Wilusz, Jeffrey


    We previously identified several mRNAs encoding components of the secretory pathway, including signal recognition particle (SRP) subunit mRNAs, among transcripts associated with the RNA-binding protein CELF1. Through immunoprecipitation of RNAs crosslinked to CELF1 in myoblasts and in vitro binding assays using recombinant CELF1, we now provide evidence that CELF1 directly binds the mRNAs encoding each of the subunits of the SRP. Furthermore, we determined the half-lives of the Srp transcripts in control and CELF1 knockdown myoblasts. Our results indicate CELF1 is a destabilizer of at least five of the six Srp transcripts and that the relative abundance of the SRP proteins is out of balance when CELF1 is depleted. CELF1 knockdown myoblasts exhibit altered secretion of a luciferase reporter protein and are impaired in their ability to migrate and close a wound, consistent with a defect in the secreted extracellular matrix. Importantly, similar defects in wound healing are observed when SRP subunit imbalance is induced by over-expression of SRP68. Our studies support the existence of an RNA regulon containing Srp mRNAs that is controlled by CELF1. One implication is that altered function of CELF1 in myotonic dystrophy may contribute to changes in the extracellular matrix of affected muscle through defects in secretion. PMID:28129347

  6. RNA. Introduction. (United States)

    Bao, Marie Z; Kruger, Robert P; Rivas, Fabiola; Smith, Orla; Szewczak, Lara


    Two scientists walk into a bar. After a pint and an exchange of pleasantries, one says to the other, "Where do you come from? Scientifically, I mean." The queried scientist responds, "Out of the RNA world." "Don't we all," the asker responds chuckling. Fifteen years ago, the joke would have been made with a nod to the notion that life arose from an RNA-based precursor, the so-called "RNA world." Yet had this conversation happened last week, the scientists would also be grinning in appreciation of the extent to which contemporary cellular biology is steeped in all things RNA. Ours is truly an RNA world.In this year's special review issue, the Cell editorial team has brought together articles focused on RNA in the modern world, providing perspectives on classical and emerging areas of inquiry. We extend our thanks to the many distinguished experts who contributed their time and effort as authors and reviewers to make the issue informative, thought-provoking, and timely. We hope that this collection of articles, written as we stand on the verge of a new wave of RNA biology, edifies and inspires by revealing the inner workings of these versatile molecules and by highlighting the next key questions that need to be addressed as we strive to understand the full functional scope of RNA in cells.

  7. APOBEC3G induces a hypermutation gradient: purifying selection at multiple steps during HIV-1 replication results in levels of G-to-A mutations that are high in DNA, intermediate in cellular viral RNA, and low in virion RNA

    Directory of Open Access Journals (Sweden)

    Pathak Vinay K


    Full Text Available Abstract Background Naturally occurring Vif variants that are unable to inhibit the host restriction factor APOBEC3G (A3G have been isolated from infected individuals. A3G can potentially induce G-to-A hypermutation in these viruses, and hypermutation could contribute to genetic variation in HIV-1 populations through recombination between hypermutant and wild-type genomes. Thus, hypermutation could contribute to the generation of immune escape and drug resistant variants, but the genetic contribution of hypermutation to the viral evolutionary potential is poorly understood. In addition, the mechanisms by which these viruses persist in the host despite the presence of A3G remain unknown. Results To address these questions, we generated a replication-competent HIV-1 Vif mutant in which the A3G-binding residues of Vif, Y40RHHY44, were substituted with five alanines. As expected, the mutant was severely defective in an A3G-expressing T cell line and exhibited a significant delay in replication kinetics. Analysis of viral DNA showed the expected high level of G-to-A hypermutation; however, we found substantially reduced levels of G-to-A hypermutation in intracellular viral RNA (cRNA, and the levels of G-to-A mutations in virion RNA (vRNA were even further reduced. The frequencies of hypermutation in DNA, cRNA, and vRNA were 0.73%, 0.12%, and 0.05% of the nucleotides sequenced, indicating a gradient of hypermutation. Additionally, genomes containing start codon mutations and early termination codons within gag were isolated from the vRNA. Conclusion These results suggest that sublethal levels of hypermutation coupled with purifying selection at multiple steps during the early phase of viral replication lead to the packaging of largely unmutated genomes, providing a mechanism by which mutant Vif variants can persist in infected individuals. The persistence of genomes containing mutated gag genes despite this selection pressure indicates that dual

  8. B decays

    CERN Document Server

    Stone, Sheldon


    This book reviews the study of b quarks and also looks at the implications of future studies. The most important observations thus far - including measurement of the ""B"" lifetime and observations of b -> u transitions - as well as the more mundane results of hadronic and semileptonic transitions are described in detail by experimentalists who have been closely involved with the measurements. Theoretical progress in understanding b quark decays, including the mechanisms of hadronic and semileptonic decays, are described. Synthesizing the experimental and theoretical information, the authors d

  9. B decays

    CERN Document Server

    Stone, Sheldon


    The study of b quarks has now reached a stage where it is useful to review what has been learned so far and also to look at the implications of future studies. The most important observations thus far - measurement of the "B" lifetime, B 0 - B 0 mixing, and the observation of b? u transitions, as well as more mundane results on hadronic and semileptonic transitions - are described in detail by experimentalists who have been closely involved with the measurements. Theoretical progress in understanding b quark decays, including the mechanisms of hadronic and semileptonic decays, are described. S

  10. Cellular automata

    CERN Document Server

    Codd, E F


    Cellular Automata presents the fundamental principles of homogeneous cellular systems. This book discusses the possibility of biochemical computers with self-reproducing capability.Organized into eight chapters, this book begins with an overview of some theorems dealing with conditions under which universal computation and construction can be exhibited in cellular spaces. This text then presents a design for a machine embedded in a cellular space or a machine that can compute all computable functions and construct a replica of itself in any accessible and sufficiently large region of t

  11. Functional high-throughput screening identifies the miR-15 microRNA family as cellular restriction factors for Salmonella infection. (United States)

    Maudet, Claire; Mano, Miguel; Sunkavalli, Ushasree; Sharan, Malvika; Giacca, Mauro; Förstner, Konrad U; Eulalio, Ana


    Increasing evidence suggests an important role for miRNAs in the molecular interplay between bacterial pathogens and host cells. Here we perform a fluorescence microscopy-based screen using a library of miRNA mimics and demonstrate that miRNAs modulate Salmonella infection. Several members of the miR-15 miRNA family were among the 17 miRNAs that more efficiently inhibit Salmonella infection. We discovered that these miRNAs are downregulated during Salmonella infection, through the inhibition of the transcription factor E2F1. Analysis of miR-15 family targets revealed that derepression of cyclin D1 and the consequent promotion of G1/S transition are crucial for Salmonella intracellular proliferation. In addition, Salmonella induces G2/M cell cycle arrest in infected cells, further promoting its replication. Overall, these findings uncover a mechanism whereby Salmonella renders host cells more susceptible to infection by controlling cell cycle progression through the active modulation of host cell miRNAs.

  12. Triggering of RNA interference with RNA-RNA, RNA-DNA, and DNA-RNA nanoparticles. (United States)

    Afonin, Kirill A; Viard, Mathias; Kagiampakis, Ioannis; Case, Christopher L; Dobrovolskaia, Marina A; Hofmann, Jen; Vrzak, Ashlee; Kireeva, Maria; Kasprzak, Wojciech K; KewalRamani, Vineet N; Shapiro, Bruce A


    Control over cellular delivery of different functionalities and their synchronized activation is a challenging task. We report several RNA and RNA/DNA-based nanoparticles designed to conditionally activate the RNA interference in various human cells. These nanoparticles allow precise control over their formulation, stability in blood serum, and activation of multiple functionalities. Importantly, interferon and pro-inflammatory cytokine activation assays indicate the significantly lower responses for DNA nanoparticles compared to the RNA counterparts, suggesting greater potential of these molecules for therapeutic use.

  13. Massive bowel resection upregulates the intestinal mRNA expression levels of cellular retinol-binding protein II and apolipoprotein A-IV and alters the intestinal vitamin A status in rats. (United States)

    Hebiguchi, Taku; Mezaki, Yoshihiro; Morii, Mayako; Watanabe, Ryo; Yoshikawa, Kiwamu; Miura, Mitsutaka; Imai, Katsuyuki; Senoo, Haruki; Yoshino, Hiroaki


    Short bowel (SB) syndrome causes the malabsorption of various nutrients. Among these, vitamin A is important for a number of physiological activities. Vitamin A is absorbed by epithelial cells of the small intestine and is discharged into the lymphatic vessels as a component of chylomicrons and is delivered to the liver. In the present study, we used a rat model of SB syndrome in order to assess its effects on the expression of genes associated with the absorption, transport and metabolism of vitamin A. In the rats with SB, the intestinal mRNA expression levels of cellular retinol-binding protein II (CRBP II, gene symbol Rbp2) and apolipoprotein A-IV (gene symbol Apoa4) were higher than those in the sham-operated rats, as shown by RT-qPCR. Immunohistochemical analysis revealed that absorptive epithelial cells stained positive for both CRBP II and lecithin retinol acyltransferase, which are both required for the effective esterification of vitamin A. In the rats with SB, the retinol content in the ileum and the retinyl ester content in the jejunum were lower than those in the sham-operated rats, as shown by quantitative analysis of retinol and retinyl esters by high performance liquid chromatography. These results suggest that the elevated mRNA expression levels of Rbp2 and Apoa4 in the rats with SB contribute to the effective esterification and transport of vitamin A.

  14. The structure and function of the rous sarcoma virus RNA stability element. (United States)

    Withers, Johanna B; Beemon, Karen L


    For simple retroviruses, such as the Rous sarcoma virus (RSV), post-transcriptional control elements regulate viral RNA splicing, export, stability, and packaging into virions. These RNA sequences interact with cellular host proteins to regulate and facilitate productive viral infections. One such element, known as the RSV stability element (RSE), is required for maintaining stability of the full-length unspliced RNA. This viral RNA serves as the mRNA for the Gag and Pol proteins and also as the genome packaged in progeny virions. When the RSE is deleted from the viral RNA, the unspliced RNA becomes unstable and is degraded in a Upf1-dependent manner. Current evidence suggests that the RSE inhibits recognition of the viral gag termination codon by the nonsense-mediated mRNA decay (NMD) pathway. We believe that the RSE acts as an insulator to NMD, thereby preventing at least one of the required functional steps that target an mRNA for degradation. Here, we discuss the history of the RSE and the current model of how the RSE is interacting with cellular NMD factors.

  15. Long non-coding RNA lnc-MX1-1 is associated with poor clinical features and promotes cellular proliferation and invasiveness in prostate cancer. (United States)

    Jiang, Chen-Yi; Gao, Yuan; Wang, Xing-Jie; Ruan, Yuan; Bei, Xiao-Yu; Wang, Xiao-Hai; Jing, Yi-Feng; Zhao, Wei; Jiang, Qi; Li, Jia; Han, Bang-Min; Xia, Shu-Jie; Zhao, Fu-Jun


    Long non-coding RNAs (lncRNAs) are emerging as key molecules in human cancer genesis and progression, including prostate cancer. Large amount of lncRNAs have been found that differentially expressed between prostate cancer tissues and normal prostate tissues. Whether these lncRNAs could serve as a novel biomarker for prostate cancer diagnosis or prognosis, and their biological functions in prostate cancer need further investigation. In the present study, we identified that lncRNA lnc-MX1-1 is over-expressed in prostate cancer tissues compared with their adjacent normal prostate tissues by gene expression array profiling. The expression of lnc-MX1-1 in 60 prostate cancer cases was determined by real-time quantitative PCR and the correlations between lnc-MX1-1 expression and patients' clinical features were further analyzed. Next, we impaired lnc-MX1-1 expression using RNAi in LNCaP and 22Rv1 prostate cancer cells to explore the effects of lnc-MX1-1 on proliferation and invasiveness of the cells. Our results showed that there was a significant association between over-expression of lnc-MX1-1 and patients' clinical features such as PSA, Gleason score, metastasis, and recurrence free survival. Moreover, knockdown of lnc-MX1-1 reduced both proliferation and invasiveness of LNCaP and 22Rv1 cells. In conclusion, the results suggest that lnc-MX1-1 may serve as a potential biomarker and therapeutic target for prostate cancer.

  16. Cellular Telephone

    Institute of Scientific and Technical Information of China (English)



    Cellular phones, used in automobiles, airliners, and passenger trains, are basically low-power radiotelephones. Calls go through radio transmitters that are located within small geographical units called cells. Because each cell’s signals are too weak to interfere with those of other cells operating on the same fre-

  17. RNA-modifying enzymes. (United States)

    Ferré-D'Amaré, Adrian R


    A bewildering number of post-transcriptional modifications are introduced into cellular RNAs by enzymes that are often conserved among archaea, bacteria and eukaryotes. The modifications range from those with well-understood functions, such as tRNA aminoacylation, to widespread but more mysterious ones, such as pseudouridylation. Recent structure determinations have included two types of RNA nucleobase modifying enzyme: pseudouridine synthases and tRNA guanine transglycosylases.

  18. Semileptonic Decays

    Energy Technology Data Exchange (ETDEWEB)

    Luth, Vera G.; /SLAC


    The following is an overview of the measurements of the CKM matrix elements |V{sub cb}| and |V{sub ub}| that are based on detailed studies of semileptonic B decays by the BABAR and Belle Collaborations and major advances in QCD calculations. In addition, a new and improved measurement of the ratios R(D{sup (*)}) = {Beta}({bar B} {yields} D{sup (*)}{tau}{sup -}{bar {nu}}{sub {tau}})/{Beta}({bar B} {yields} D{sup (*)}{ell}{sup -}{bar {nu}}{sub {ell}}) is presented. Here D{sup (*)} refers to a D or a D* meson and {ell} is either e or {mu}. The results, R(D) = 0.440 {+-} 0.058 {+-} 0.042 and R(D*) = 0.332 {+-} 0.024 {+-} 0.018, exceed the Standard Model expectations by 2.0{sigma} and 2.7{sigma}, respectively. Taken together, they disagree with these expectations at the 3.4{sigma} level. The excess of events cannot be explained by a charged Higgs boson in the type II two-Higgs-doublet model.

  19. Cellular functions of the microprocessor. (United States)

    Macias, Sara; Cordiner, Ross A; Cáceres, Javier F


    The microprocessor is a complex comprising the RNase III enzyme Drosha and the double-stranded RNA-binding protein DGCR8 (DiGeorge syndrome critical region 8 gene) that catalyses the nuclear step of miRNA (microRNA) biogenesis. DGCR8 recognizes the RNA substrate, whereas Drosha functions as an endonuclease. Recent global analyses of microprocessor and Dicer proteins have suggested novel functions for these components independent of their role in miRNA biogenesis. A HITS-CLIP (high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation) experiment designed to identify novel substrates of the microprocessor revealed that this complex binds and regulates a large variety of cellular RNAs. The microprocessor-mediated cleavage of several classes of RNAs not only regulates transcript levels, but also modulates alternative splicing events, independently of miRNA function. Importantly, DGCR8 can also associate with other nucleases, suggesting the existence of alternative DGCR8 complexes that may regulate the fate of a subset of cellular RNAs. The aim of the present review is to provide an overview of the diverse functional roles of the microprocessor.

  20. Simultaneous RNA-DNA FISH. (United States)

    Lai, Lan-Tian; Meng, Zhenyu; Shao, Fangwei; Zhang, Li-Feng


    A highly useful tool for studying lncRNAs is simultaneous RNA-DNA FISH, which reveals the localization and quantitative information of RNA and DNA in cellular contexts. However, a simple combination of RNA FISH and DNA FISH often generates disappointing results because the fragile RNA signals are often damaged by the harsh conditions used in DNA FISH for denaturing the DNA. Here, we describe a robust and simple RNA-DNA FISH protocol, in which amino-labeled nucleic acid probes are used for RNA FISH. The method is suitable to detect single-RNA molecules simultaneously with DNA.

  1. Stochastic Kinetics of Nascent RNA (United States)

    Xu, Heng; Skinner, Samuel O.; Sokac, Anna Marie; Golding, Ido


    The stochastic kinetics of transcription is typically inferred from the distribution of RNA numbers in individual cells. However, cellular RNA reflects additional processes downstream of transcription, hampering this analysis. In contrast, nascent (actively transcribed) RNA closely reflects the kinetics of transcription. We present a theoretical model for the stochastic kinetics of nascent RNA, which we solve to obtain the probability distribution of nascent RNA per gene. The model allows us to evaluate the kinetic parameters of transcription from single-cell measurements of nascent RNA. The model also predicts surprising discontinuities in the distribution of nascent RNA, a feature which we verify experimentally.

  2. Generation of siRNA Nanosheets for Efficient RNA Interference (United States)

    Kim, Hyejin; Lee, Jae Sung; Lee, Jong Bum


    After the discovery of small interference RNA (siRNA), nanostructured siRNA delivery systems have been introduced to achieve an efficient regulation of the target gene expression. Here we report a new siRNA-generating two dimensional nanostructure in a formation of nanosized sheet. Inspired by tunable mechanical and functional properties of the previously reported RNA membrane, siRNA nanosized sheets (siRNA-NS) with multiple Dicer cleavage sites were prepared. The siRNA-NS has two dimensional structure, providing a large surface area for Dicer to cleave the siRNA-NS for the generation of functional siRNAs. Furthermore, downregulation of the cellular target gene expression was achieved by delivery of siRNA-NS without chemical modification of RNA strands or conjugation to other substances.

  3. Proteins involved in the degradation of cytoplasmic mRNA in the major eukaryotic model systems. (United States)

    Siwaszek, Aleksandra; Ukleja, Marta; Dziembowski, Andrzej


    The process of mRNA decay and surveillance is considered to be one of the main posttranscriptional gene expression regulation platforms in eukaryotes. The degradation of stable, protein-coding transcripts is normally initiated by removal of the poly(A) tail followed by 5'-cap hydrolysis and degradation of the remaining mRNA body by Xrn1. Alternatively, the exosome complex degrades mRNA in the 3'>5'direction. The newly discovered uridinylation-dependent pathway, which is present in many different organisms, also seems to play a role in bulk mRNA degradation. Simultaneously, to avoid the synthesis of incorrect proteins, special cellular machinery is responsible for the removal of faulty transcripts via nonsense-mediated, no-go, non-stop or non-functional 18S rRNA decay. This review is focused on the major eukaryotic cytoplasmic mRNA degradation pathways showing many similarities and pointing out main differences between the main model-species: yeast, Drosophila, plants and mammals.

  4. Methods for RNA Analysis

    DEFF Research Database (Denmark)

    Olivarius, Signe

    While increasing evidence appoints diverse types of RNA as key players in the regulatory networks underlying cellular differentiation and metabolism, the potential functions of thousands of conserved RNA structures encoded in mammalian genomes remain to be determined. Since the functions of most...... RNAs rely on interactions with proteins, the establishment of protein-binding profiles is essential for the characterization of RNAs. Aiming to facilitate RNA analysis, this thesis introduces proteomics- as well as transcriptomics-based methods for the functional characterization of RNA. First, RNA......-protein pulldown combined with mass spectrometry analysis is applied for in vivo as well as in vitro identification of RNA-binding proteins, the latter succeeding in verifying known RNA-protein interactions. Secondly, acknowledging the significance of flexible promoter usage for the diversification...

  5. iRNA-seq

    DEFF Research Database (Denmark)

    Madsen, Jesper Grud Skat; Schmidt, Søren Fisker; Larsen, Bjørk Ditlev;


    RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we...... have developed an easy, sensitive and accurate novel computational method, IRNA-SEQ: , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using...... current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all...

  6. decays to baryons

    Indian Academy of Sciences (India)

    Torsten Leddig


    From inclusive measurements, it is known that about 7% of all mesons decay into final states with baryons. In these decays, some striking features become visible compared to mesonic decays. The largest branching fractions come with quite moderate multiplicities of 3–4 hadrons. We note that two-body decays to baryons are suppressed relative to three- and four-body decays. In most of these analyses, the invariant baryon–antibaryon mass shows an enhancement near the threshold. We propose a phenomenological interpretation of this quite common feature of hadronization to baryons.

  7. Weak decays. [Lectures, phenomenology

    Energy Technology Data Exchange (ETDEWEB)

    Wojcicki, S.


    Lectures are given on weak decays from a phenomenological point of view, emphasizing new results and ideas and the relation of recent results to the new standard theoretical model. The general framework within which the weak decay is viewed and relevant fundamental questions, weak decays of noncharmed hadrons, decays of muons and the tau, and the decays of charmed particles are covered. Limitation is made to the discussion of those topics that either have received recent experimental attention or are relevant to the new physics. (JFP) 178 references

  8. RNA Interference (United States)

    ... NIGMS Home > Science Education > RNA Interference Fact Sheet RNA Interference Fact Sheet Tagline (Optional) Middle/Main Content Area What is RNA interference? RNA interference (RNAi) is a natural process ...

  9. RNA helicases


    Owttrim, George W.


    Similar to proteins, RNA molecules must fold into the correct conformation and associate with protein complexes in order to be functional within a cell. RNA helicases rearrange RNA secondary structure and RNA-protein interactions in an ATP-dependent reaction, performing crucial functions in all aspects of RNA metabolism. In prokaryotes, RNA helicase activity is associated with roles in housekeeping functions including RNA turnover, ribosome biogenesis, translation and small RNA metabolism. In...

  10. RNA topology


    Frank-Kamenetskii, Maxim D.


    A new variety on non-coding RNA has been discovered by several groups: circular RNA (circRNA). This discovery raises intriguing questions about the possibility of the existence of knotted RNA molecules and the existence of a new class of enzymes changing RNA topology, RNA topoisomerases.

  11. Relationship between the expression of long-non-coding RNA ( lncRNA ) HOTAIR and cellular radiosensitivity in esophageal squamous cell carcinoma%食管鳞癌细胞HOTAIR mRNA表达水平与放射敏感性之间关系

    Institute of Scientific and Technical Information of China (English)

    达春丽; 王若峥; 李瑜; 李亚伟; 刘凯


    Objective To investigate the relationship between the expression level of HOTAIR and cellular radiosensitivity in esophageal squamous cell carcinoma (ESCC). Methods Four ESCC cell lines ( K150, K450, TE-1, and Eca109 ) were used in this study. Quantitative real-time polymerase chain reaction was applied to measure the expression level of HOTAIR in the above cell lines;colony-forming assay was applied to measure the survival fraction of different cells irradiated by different doses of X-ray. The t-test or analysis of variance was applied for analysis of differences. The correlation analysis was used by Pearson methods. Results The four cell lines all showed high expression levels of HOTAIR and radioresistance. Compared with the other three cell lines, Eca109 had a lower expression level of HOTAIR, a lower survival fraction at each radiation dose point, and significantly lower D0 and Dq . The mRNA expression level of HOTAIR and radiosensitivity were K150cellular radiosensitivity, and the expression level of HOTAIR may be an indicator to predict cellular radiosensitivity.%目的 分析细胞内HOTAIR mRNA表达水平与食管鳞癌细胞放射敏感性之间的关系.方法 以4种食管鳞癌细胞( K150、K450、TE-1、Eca109细胞)为研究对象. 采用qRT-PCR检测细胞中HOTAIR mRNA表达水平,采用平板克隆形成实验检测不同剂量X射线照射下的存活分数( SF).采用t检验或方差分析差异,Pearson法进行相关分析. 结果 4种细胞均呈现HOTAIR mRNA高表达及放射抵抗性,其中 Eca109 细胞表达水平最低,每个剂量点 SF 也最低, D0、Dq 值也均最低.HOTAIR mRNA表达水平和放射敏感

  12. Roseovarius antarcticus sp. nov., isolated from a decayed whale bone. (United States)

    Deng, Sangsang; Jiang, Fan; Chang, Xulu; Qu, Zhihao; Ren, Lvzhi; Zhang, Yumin; Kan, Wenjing; Da, Xuyang; Qiu, Xia; Kim, Myongchol; Fang, Chengxiang; Peng, Fang


    A pale yellow, ovoid- to rod-shaped and budding bacterium, designated strain M-S13-148(T), was isolated from a decayed bone of whale from the eastern coast of King George Island, South Shetlands, Antarctica. Strain M-S13-148(T) exhibited motility, aerobic growth and was Gram-stain-negative. Strain M-S13-148(T) was positive for catalase and oxidase. Growth was observed at pH 6.0-9.0, at 4-42 °C and with 0-14% (w/v) NaCl. The novel strain contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unknown phospholipid as the major polar lipids. The dominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), (58.8%) and C16 : 0 (11.7%). The respiratory quinone was Q-10 and the DNA G + C content was 60.9 mol%. Neighbour-joining, maximum-likelihood and minimum-evolution phylogenetic trees, based on 16S rRNA gene sequences, indicated that strain M-S13-148(T) belonged to the genus Roseovarius and was most closely related to Roseovarius nanhaiticus CCTCC AB 208317(T) (93.72% 16S rRNA gene sequence similarity). The 16S rRNA gene sequence similarity with respect to members of the genus Roseovarius ranged from 91.81 to 93.94%. On the basis of phenotypic, molecular and chemotaxonomic characteristics, strain M-S13-148 is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius antarcticus sp. nov., is proposed. The type strain is M-S13-148(T) ( = CCTCC AB2014072(T) = LMG 28420(T)).

  13. Effective Majorana neutrino decay

    Energy Technology Data Exchange (ETDEWEB)

    Duarte, Lucia [Instituto de Fisica, Facultad de Ingenieria,Universidad de la Republica, Montevideo (Uruguay); Romero, Ismael; Peressutti, Javier; Sampayo, Oscar A. [Universidad Nacional de Mar del Plata, Departamento de Fisica, Instituto de Investigaciones Fisicas de Mar del Plata (IFIMAR) CONICET, UNMDP, Mar del Plata (Argentina)


    We study the decay of heavy sterile Majorana neutrinos according to the interactions obtained from an effective general theory. We describe the two- and three-body decays for a wide range of neutrino masses. The results obtained and presented in this work could be useful for the study of the production and detection of these particles in a variety of high energy physics experiments and astrophysical observations. We show in different figures the dominant branching ratios and the total decay width. (orig.)

  14. 5-azacytidine inhibits nonsense-mediated decay in a MYC-dependent fashion. (United States)

    Bhuvanagiri, Madhuri; Lewis, Joe; Putzker, Kerstin; Becker, Jonas P; Leicht, Stefan; Krijgsveld, Jeroen; Batra, Richa; Turnwald, Brad; Jovanovic, Bogdan; Hauer, Christian; Sieber, Jana; Hentze, Matthias W; Kulozik, Andreas E


    Nonsense-mediated RNA decay (NMD) is an RNA-based quality control mechanism that eliminates transcripts bearing premature translation termination codons (PTC). Approximately, one-third of all inherited disorders and some forms of cancer are caused by nonsense or frame shift mutations that introduce PTCs, and NMD can modulate the clinical phenotype of these diseases. 5-azacytidine is an analogue of the naturally occurring pyrimidine nucleoside cytidine, which is approved for the treatment of myelodysplastic syndrome and myeloid leukemia. Here, we reveal that 5-azacytidine inhibits NMD in a dose-dependent fashion specifically upregulating the expression of both PTC-containing mutant and cellular NMD targets. Moreover, this activity of 5-azacytidine depends on the induction of MYC expression, thus providing a link between the effect of this drug and one of the key cellular pathways that are known to affect NMD activity. Furthermore, the effective concentration of 5-azacytidine in cells corresponds to drug levels used in patients, qualifying 5-azacytidine as a candidate drug that could potentially be repurposed for the treatment of Mendelian and acquired genetic diseases that are caused by PTC mutations.

  15. Characterizing the transcriptome upon depletion of RNA processing factors

    DEFF Research Database (Denmark)

    Herudek, Jan

    The human genome is pervasively transcribed and produces an enormous amount of non-coding RNA (ncRNA). Compared to protein-coding transcripts, many classes of ncRNAs are very unstable and rapidly degraded by the RNA decay machinery. The RNA exosome complex is a main RNA ‘degrader’ in the human nu...... this method with CRISPR/Cas9 genome editing to pursue rapid depletion of endogenous protein. Applying this technology, I aim to study dynamics of the RNA decay machinery and obtain a deeper understanding of recently characterized ncRNAs....

  16. Rare Semileptonic Charm Decays

    CERN Document Server

    de Boer, Stefan


    An analysis of charm mesons decaying semileptonically via Flavor Changing Neutral Currents is presented. We calculate the Wilson coefficients within the Standard Model. A window in the decay distribution, where physics beyond the Standard Model could be measured is identified. Exemplary, we study effects of leptoquark models.

  17. Double beta decay experiments

    CERN Document Server

    Barabash, A S


    The present status of double beta decay experiments is reviewed. The results of the most sensitive experiments are discussed. Proposals for future double beta decay experiments with a sensitivity to the $$ at the level of (0.01--0.1) eV are considered.

  18. Observation of semileptonic decay (United States)

    Albrecht, H.; Cronström, H. I.; Ehrlichmann, H.; Hamacher, T.; Hofmann, R. P.; Kirchhoff, T.; Nau, A.; Nowak, S.; Reidenbach, M.; Reiner, R.; Schröder, H.; Schulz, H. D.; Walter, M.; Wurth, R.; Appuhn, R. D.; Hast, C.; Kolanoski, H.; Lange, A.; Lindner, A.; Mankel, R.; Schieber, M.; Siegmund, T.; Spaan, B.; Thurn, H.; Töpfer, D.; Walther, A.; Wegener, D.; Paulini, M.; Reim, K.; Wegener, H.; Mundt, R.; Oest, T.; Schmidt-Parzefall, W.; Funk, W.; Stiewe, J.; Werner, S.; Ehret, K.; Hölscher, A.; Hofmann, W.; Hüpper, A.; Khan, S.; Knöpfle, K. T.; Spengler, J.; Britton, D. I.; Charlesworth, C. E. K.; Edwards, K. W.; Hyatt, E. R. F.; Kapitza, H.; Krieger, P.; Macfarlane, D. B.; Patel, P. M.; Prentice, J. D.; Saull, P. R. B.; Seidel, S. C.; Tzamariudaki, K.; van de Water, R. G.; Yoon, T.-S.; Reβing, D.; Schmidtler, M.; Schneider, M.; Schubert, K. R.; Strahl, K.; Waldi, R.; Weseler, S.; Kernel, G.; Križan, P.; Križnič, E.; Podobnik, T.; Živko, T.; Jönsson, L.; Balagura, V.; Belyaev, I.; Danilov, M.; Droutskoy, A.; Golutvin, A.; Gorelov, I.; Kostina, G.; Lubimov, V.; Murat, P.; Pakhlov, P.; Ratnikov, F.; Semenov, S.; Shibaev, V.; Soloshenko, V.; Tichomirov, I.; Zaitsev, Yu.; Argus Collaboration


    Observation of the semileptonic decay of the charmed baryon ? in the decay channel ? has been made using the ARGUS detector at the e+e- storage ring DORIS II at DESY. The cross section times branching ratio was found to be ?.

  19. Some aspects of RNA repair and editing

    Directory of Open Access Journals (Sweden)

    Kovalchuk M. V.


    Full Text Available All cellular RNA molecules are damaged at the scale of DNA molecules, or even more. In the present review the RNA damaging agents, some mechanisms of RNA repair and editing, their difference from DNA repair mechanisms have been discussed.

  20. RNA tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology. (United States)

    Ishikawa, Junya; Furuta, Hiroyuki; Ikawa, Yoshiya


    RNA molecules are versatile biomaterials that act not only as DNA-like genetic materials but also have diverse functions in regulation of cellular biosystems. RNA is capable of regulating gene expression by sequence-specific hybridization. This feature allows the design of RNA-based artificial gene regulators (riboregulators). RNA can also build complex two-dimensional (2D) and 3D nanostructures, which afford protein-like functions and make RNA an attractive material for nanobiotechnology. RNA tectonics is a methodology in RNA nanobiotechnology for the design and construction of RNA nanostructures/nanoobjects through controlled self-assembly of modular RNA units (tectoRNAs). RNA nanostructures designed according to the concept of RNA tectonics are also attractive as tools in synthetic biology, but in vivo RNA tectonics is still in the early stages. This review presents a summary of the achievements of RNA tectonics and its related researches in vitro, and also introduces recent developments that facilitated the use of RNA nanostructures in bacterial cells.

  1. Interferon gamma, interleukin 4 and transforming growth factor beta in experimental autoimmune encephalomyelitis in Lewis rats: dynamics of cellular mRNA expression in the central nervous system and lymphoid cells

    DEFF Research Database (Denmark)

    Issazadeh-Navikas, Shohreh; Mustafa, M; Ljungdahl, A;


    The potential role of certain important immunoregulatory and effector cytokines in autoimmune neuroinflammation have been studied. We have examined the expression of mRNA, with in situ hybridization, of interferon gamma (IFN-gamma), interleukin 4 (IL-4) and transforming growth factor beta (TGF...

  2. A versatile assay for RNA-binding proteins in living cells. (United States)

    Strein, Claudia; Alleaume, Anne-Marie; Rothbauer, Ulrich; Hentze, Matthias W; Castello, Alfredo


    RNA-binding proteins (RBPs) control RNA fate from synthesis to decay. Since their cellular expression levels frequently do not reflect their in vivo activity, methods are needed to assess the steady state RNA-binding activity of RBPs as well as their responses to stimuli. While electrophoresis mobility shift assays (EMSA) have been used for such determinations, their results serve at best as proxies for the RBP activities in living cells. Here, we describe a quantitative dual fluorescence method to analyze protein-mRNA interactions in vivo. Known or candidate RBPs are fused to fluorescent proteins (eGFP, YFP), expressed in cells, cross-linked in vivo to RNA by ultraviolet light irradiation, and immunoprecipitated, after lysis, with a single chain antibody fragment directed against eGFP (GFP-binding protein, GBP). Polyadenylated RNA-binding activity of fusion proteins is assessed by hybridization with an oligo(DT) probe coupled with a red fluorophore. Since UV light is directly applied to living cells, the assay can be used to monitor dynamic changes in RNA-binding activities in response to biological or pharmacological stimuli. Notably, immunoprecipitation and hybridization can also be performed with commercially available GBP-coupled 96-well plates (GFP-multiTrap), allowing highly parallel RNA-binding measurements in a single experiment. Therefore, this method creates the possibility to conduct in vivo high-throughput RNA-binding assays. We believe that this fast and simple radioactivity-free method will find many useful applications in RNA biology.

  3. HIV-1 infection induces changes in expression of cellular splicing factors that regulate alternative viral splicing and virus production in macrophages

    Directory of Open Access Journals (Sweden)

    Purcell Damian FJ


    Full Text Available Abstract Background Macrophages are important targets and long-lived reservoirs of HIV-1, which are not cleared of infection by currently available treatments. In the primary monocyte-derived macrophage model of infection, replication is initially productive followed by a decline in virion output over ensuing weeks, coincident with a decrease in the levels of the essential viral transactivator protein Tat. We investigated two possible mechanisms in macrophages for regulation of viral replication, which appears to be primarily regulated at the level of tat mRNA: 1 differential mRNA stability, used by cells and some viruses for the rapid regulation of gene expression and 2 control of HIV-1 alternative splicing, which is essential for optimal viral replication. Results Following termination of transcription at increasing times after infection in macrophages, we found that tat mRNA did indeed decay more rapidly than rev or nef mRNA, but with similar kinetics throughout infection. In addition, tat mRNA decayed at least as rapidly in peripheral blood lymphocytes. Expression of cellular splicing factors in uninfected and infected macrophage cultures from the same donor showed an inverse pattern over time between enhancing factors (members of the SR family of RNA binding proteins and inhibitory factors (members of the hnRNP family. While levels of the SR protein SC35 were greatly up-regulated in the first week or two after infection, hnRNPs of the A/B and H groups were down-regulated. Around the peak of virus production in each culture, SC35 expression declined to levels in uninfected cells or lower, while the hnRNPs increased to control levels or above. We also found evidence for increased cytoplasmic expression of SC35 following long-term infection. Conclusion While no evidence of differential regulation of tat mRNA decay was found in macrophages following HIV-1 infection, changes in the balance of cellular splicing factors which regulate alternative

  4. Messenger RNA surveillance: neutralizing natural nonsense

    DEFF Research Database (Denmark)

    Weischelfeldt, Joachim Lütken; Lykke-Andersen, Jens; Porse, Bo


    Messenger RNA transcripts that contain premature stop codons are degraded by a process termed nonsense-mediated mRNA decay (NMD). Although previously thought of as a pathway that rids the cell of non-functional mRNAs arising from mutations and processing errors, new research suggests a more general...

  5. Weak Decay of Hypernuclei

    CERN Document Server

    Alberico, W M


    The focus of these Lectures is on the weak decay modes of hypernuclei, with special attention to Lambda-hypernuclei. The subject involves many fields of modern theoretical and experimental physics, from nuclear structure to the fundamental constituents of matter and their interactions. The various weak decay modes of Lambda-hypernuclei are described: the mesonic mode and the non-mesonic ones. The latter are the dominant decay channels of medium--heavy hypernuclei, where, on the contrary, the mesonic decay is disfavoured by Pauli blocking effect on the outgoing nucleon. In particular, one can distinguish between one-body and two-body induced decays. Theoretical models employed to evaluate the (partial and total) decay widths of hypernuclei are illustrated, and their results compared with existing experimental data. Open problems and recent achievements are extensively discussed, in particular the determination of the ratio Gamma_n/Gamma_p, possible tests of the Delta I=1/2 rule in non-mesonic decays and the pu...

  6. Axions from wall decay

    Energy Technology Data Exchange (ETDEWEB)

    Chang, S; Hagmann, C; Sikivie, P


    The authors discuss the decay of axion walls bounded by strings and present numerical simulations of the decay process. In these simulations, the decay happens immediately, in a time scale of order the light travel time, and the average energy of the radiated axions is {approx_equal} 7m{sub a} for v{sub a}/m{sub a} {approx_equal} 500. is found to increase approximately linearly with ln(v{sub a}/m{sub a}). Extrapolation of this behavior yields {approx_equal} 60 m{sub a} in axion models of interest.

  7. Rare decays at LHCb

    CERN Document Server

    Lafferty, George


    We review recent results from the LHCb experiment on studies of particle decays that are forbidden or rare in the Standard Model. The studies include searches for lepton flavour violating decays of the $\\tau$ lepton and the $B$ and $D$ mesons, and of $B$ and $D$ meson decays that would be mediated by Majorana neutrinos. Results are also presented for the rare processes $B_s \\to \\mu^+\\mu^-$ and $B^0 \\to \\mu^+\\mu^-$, $D^0 \\to \\pi^+\\pi^-\\mu^+\\mu^-$, $b \\to s\\gamma$ transitions, and $B \\to K^{(*)}\\mu^+\\mu^-$.

  8. Ab initio RNA folding. (United States)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela


    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  9. RNA Crystallization (United States)

    Golden, Barbara L.; Kundrot, Craig E.


    RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

  10. Weak decays and double beta decay

    Energy Technology Data Exchange (ETDEWEB)

    Nicholson, H.W.


    Work to measure the ..sigma../sup +/ 0 degree differential cross section in the reaction K/sup -/p ..-->.. ..sigma../sup +/..pi../sup -/ at several incident K/sup -/ momenta between 600 and 800 MeV/c as well as the asymmetries in the decays of polarized ..sigma../sup +/'s into protons and neutral pions and of polarized ..sigma../sup -/'s into neutrons and negative pions in collaboration with experimenters from Yale, Brookhaven, and the University of Pittsburgh (Brookhaven experiment 702) has been completed. Data from this experiment is currently being analyzed at Yale. Work is currently underway to develop and construct an experiment to search for neutrinoless double beta decay in thin foils of Mo/sup 100/ in collaboration with experimenters from Lawrence Berkeley Laboratory. Development work on the solid state silicon detectors should be complete in the next six months and construction should e well underway within the next year.

  11. Non-leptonic decays of beauty decays

    CERN Document Server

    Bigi, Ikaros I; Shifman, M; Uraltsev, N; Vainshtein, A I


    "Anyone who keeps the ability to see beauty never grows old" (Franz Kafka). In the last few years considerable progress has been achieved in our understanding of the decays of heavy flavour hadrons. One can now calculate inclusive transition rates in QCD proper through an expansion in inverse powers of the heavy flavour quark mass without recourse to phenomenological assumptions. The non-perturbative contributions are treated systematically in this way; they are found to produce corrections of order a few percent in beauty decays, i.e. typically somewhat smaller than the perturbative corrections. One finds, among other things: (a) The lifetime of $B^-$ mesons is predicted to be longer than that of $B^0$ mesons by several percent. (b) The QCD prediction for the semileptonic branching ratio of $B$ mesons appears to exceed present experimental values.

  12. The Lsm1-7-Pat1 complex promotes viral RNA translation and replication by differential mechanisms. (United States)

    Jungfleisch, Jennifer; Chowdhury, Ashis; Alves-Rodrigues, Isabel; Tharun, Sundaresan; Díez, Juana


    The Lsm1-7-Pat1 complex binds to the 3' end of cellular mRNAs and promotes 3' end protection and 5'-3' decay. Interestingly, this complex also specifically binds to cis-acting regulatory sequences of viral positive-strand RNA genomes promoting their translation and subsequent recruitment from translation to replication. Yet, how the Lsm1-7-Pat1 complex regulates these two processes remains elusive. Here, we show that Lsm1-7-Pat1 complex acts differentially in these processes. By using a collection of well-characterized lsm1 mutant alleles and a system that allows the replication of Brome mosaic virus (BMV) in yeast we show that the Lsm1-7-Pat1 complex integrity is essential for both, translation and recruitment. However, the intrinsic RNA-binding ability of the complex is only required for translation. Consistent with an RNA-binding-independent function of the Lsm1-7-Pat1 complex on BMV RNA recruitment, we show that the BMV 1a protein, the sole viral protein required for recruitment, interacts with this complex in an RNA-independent manner. Together, these results support a model wherein Lsm1-7-Pat1 complex binds consecutively to BMV RNA regulatory sequences and the 1a protein to promote viral RNA translation and later recruitment out of the host translation machinery to the viral replication complexes.

  13. The number of regulatory T cells in transbronchial lung allograft biopsies is related to FoxP3 mRNA levels in bronchoalveolar lavage fluid and to the degree of acute cellular rejection

    DEFF Research Database (Denmark)

    Krustrup, Dorrit; Madsen, Caroline B; Iversen, Martin;


    The transcription factor Forkhead Box P3 (FoxP3) is a marker of regulatory T cells (Tregs) - a subset of T cells known to suppress a wide range of immune responses. These cells are considered to be pivotal for the induction of tolerance to donor antigens in human allografts. We aimed to correlate...... the number of lymphocytes expressing FoxP3 in transbronchial biopsies from lung allografts with the FoxP3 expression in bronchoalveolar lavage fluid (BALF). In addition, we aimed to correlate the number of FoxP3+ cells in transbronchial biopsies with the degree of acute cellular rejection in lung allografts....

  14. Decay ring design

    CERN Document Server

    Chancé, A; Bouquerel, E; Hancock, S; Jensen, E

    The study of the neutrino oscillation between its different flavours needs pureand very intense fluxes of high energy, well collimated neutrinos with a welldetermined energy spectrum. A dedicated machine seems to be necessarynowadays to reach the required flux. A new concept based on the β-decayof radioactive ions which were accelerated in an accelerator chain was thenproposed. After ion production, stripping, bunching and acceleration, the unstableions are then stored in a racetrack-shaped superconducting decay ring.Finally, the ions are accumulated in the decay ring until being lost. The incomingbeam is merged to the stored beam by using a specific RF system, whichwill be presented here.We propose here to study some aspects of the decay ring, such as its opticalproperties, its RF system or the management of the losses which occur in thering (mainly by decay or by collimation).

  15. Neutrinoless double beta decay

    Indian Academy of Sciences (India)

    Kai Zuber


    The physics potential of neutrinoless double beta decay is discussed. Furthermore, experimental considerations as well as the current status of experiments are presented. Finally, an outlook towards the future, work on nuclear matrix elements and alternative processes is given.

  16. Inflaton decay in supergravity

    Energy Technology Data Exchange (ETDEWEB)

    Endo, M.; Takahashi, F. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Yanagida, T.T. [Tokyo Univ. (Japan). Dept. of Physics]|[Tokyo Univ. (Japan). Research Center for the Early Universe


    We discuss inflaton decay in supergravity, taking account of the gravitational effects. It is shown that, if the inflaton has a nonzero vacuum expectation value, it generically couples to any matter fields that appear in the superpotential at the tree level, and to any gauge sectors through anomalies in the supergravity. Through these processes, the inflaton generically decays into the supersymmetry breaking sector, producing many gravitinos. The inflaton also directly decays into a pair of the gravitinos. We derive constraints on both inflation models and supersymmetry breaking scenarios for avoiding overproduction of the gravitinos. Furthermore, the inflaton naturally decays into the visible sector via the top Yukawa coupling and SU(3){sub C} gauge interactions. (orig.)


    Energy Technology Data Exchange (ETDEWEB)



    Lepton flavor violation (LFV) experiments have probed sensitivities corresponding to mass scales of well over 100 TeV, making life difficult for models predicting accessible LFV in kaon decay and discouraging new dedicated experiments of this type.

  18. CLEO Results B Decays

    CERN Document Server

    Cassel, David G


    Measurements of many Standard Model constants are clouded by uncertainties in nonperturbative QCD parameters that relate measurable quantities to the underlying parton-level processes. Generally these QCD parameters have been obtained from model calculations with large uncertainties that are difficult to quantify. The CLEO Collaboration has taken a major step towards reducing these uncertainties in determining the CKM matrix elements Vcb and Vub using new measurements of the branching fraction and photon energy spectrum of B -> s gamma decays. This report includes: the new CLEO measurements of B -> s gamma decays, Vcb, and Vub; the first results from CLEO III data -- studies of B -> K pi, pi pi, and K Kbar decays; mention of some other recent CLEO B decay results; and plans for operating CESR and CLEO in the charm threshold region.

  19. Flat Cellular (UMTS) Networks

    NARCIS (Netherlands)

    Bosch, H.G.P.; Samuel, L.G.; Mullender, S.J.; Polakos, P.; Rittenhouse, G.


    Traditionally, cellular systems have been built in a hierarchical manner: many specialized cellular access network elements that collectively form a hierarchical cellular system. When 2G and later 3G systems were designed there was a good reason to make system hierarchical: from a cost-perspective i

  20. Laser assisted {alpha} decay

    Energy Technology Data Exchange (ETDEWEB)

    Castaneda Cortes, Hector Mauricio


    Excited or short-lived nuclei often decay by emitting alpha particles that are assumed to be preformed inside the nucleus and confined in the nuclear potential well. In this picture, {alpha} decay refers to the tunneling of the alpha particle through the potential barrier. In this thesis we investigate for the first time how strong laser fields can assist the tunneling of the alpha particle and thus influence the nuclear decay. Generally speaking, laser-assisted {alpha} decay can be described as laser-assisted tunneling of a quasistationary state, i.e, a slowly decaying state. Our theoretical treatment is developed starting from the complex trajectory formulation of the well-known strong-field approximation used to describe laser-induced ionization. We extend this formulation and develop a method to treat the decay of quasistationary states. The effect of both static and optical and X-ray monochromatic fields on the lifetimes and {alpha}-particle emission spectra are investigated for a number of {alpha}-emitting nuclei. We find that even at strong intensities, the laser-induced acceleration of the {alpha} decay is negligible, ranging from a relative modification in the decay rate of 10{sup -3} for static fields of electric field strengths of 10{sup 15} V/m, to 10{sup -8} for strong optical fields with intensities of 10{sup 22} W/cm{sup 2}, and to 10{sup -6} for strong X-ray fields with laser intensities around 10{sup 24} W/cm{sup 2}. However, the effect of the external field is visible in the spectrum of emitted alpha particles, leading in the case of optical fields even to rescattering phenomena for intensities approaching 6 x 10{sup 22} W/cm{sup 2}. The dynamics of the alpha particle in laser fields of intensities below the rescattering limit is investigated.

  1. Solar Neutrino Decay

    CERN Document Server

    Acker, A; Acker, Andy; Pakvasa, Sandip


    We re-examine the neutrino decay solution to the solar neutrino problem in light of the new data from Gallex II and Kamiokande III. We compare the experimental data with the solar models of Bahcall and Pinsonneault and Turck-Chieze and find that neutrino decay is ruled out as a solution to the solar neutrino problem at better than the 98\\% c.l. even when solar model uncertainties are taken into account.

  2. Open Flavor Strong Decays (United States)

    García-Tecocoatzi, H.; Bijker, R.; Ferretti, J.; Galatà, G.; Santopinto, E.


    In this contribution, we discuss the results of a QM calculation of the open-flavor strong decays of **** light nucleon resonances. These are the results of a recent calculation, where we used a modified ^3P_0 model for the amplitudes and the U(7) algebraic model and the hypercentral quark model to predict the baryon spectrum. The decay amplitudes are compared with the existing experimental data.

  3. Streamer chamber: pion decay

    CERN Multimedia


    The real particles produced in the decay of a positive pion can be seen in this image from a streamer chamber. Streamer chambers consist of a gas chamber through which a strong pulsed electric field is passed, creating sparks as a charged particle passes through it. A magnetic field is added to cause the decay products to follow curved paths so that their charge and momentum can be measured.

  4. Aspects of B decays

    Energy Technology Data Exchange (ETDEWEB)

    Faller, Sven


    B-meson decays are a good probe for testing the flavour sector of the standard model of particle physics. The standard model describes at present all experimental data satisfactorily, although some ''tensions'' exist, i.e. two to three sigma deviations from the predictions, in particular in B decays. The arguments against the standard model are thus purely theoretical. These tensions between experimental data and theoretical predictions provide an extension of the standard model by new physics contributions. Within the flavour sector main theoretical uncertainties are related to the hadronic matrix elements. For exclusive semileptonic anti B {yields} D{sup (*)}l anti {nu} decays QCD sum rule techniques, which are suitable for studying hadronic matrix elements, however, with substantial, but estimable hadronic uncertainties, are used. The exploration of new physics effects in B-meson decays is done in an twofold way. In exclusive semileptonic anti B {yields} D{sup (*)}l anti {nu} decays the effect of additional right-handed vector as well as left- and right-handed scalar and tensor hadronic current structures in the decay rates and the form factors are studied at the non-recoil point. As a second approach one studied the non-leptonic B{sup 0}{sub s}{yields}J/{psi}{phi} and B{sup 0}{yields}J/{psi}K{sub S,L} decays discussing CP violating effects in the time-dependent decay amplitudes by considering new physics phase in the B{sup 0}- anti B{sup 0} mixing phase. (orig.)

  5. Regulation of the stability of poly(I)xpoly(C)-induced human fibroblast interferon mRNA: selective inactivation of interferon mRNA and lack of involvement of 2',5'-oligo(A) synthetase activation during the shutoff of interferon production. (United States)

    Sehgal, P B; Gupta, S L


    The inactivation of interferon mRNA during the shutoff phase of interferon production in poly(I)xpoly(C)-induced human fibroblast cultures is selective. We have determined that the shutoff of interferon production, which takes place from 3 to 8 hr after the beginning of induction, is not associated with an appreciable declined in the rate of bulk cellular protein synthesis or of cellular protein secretion. While the amount of translatable interferon mRNA declined markedly during the shutoff phase, the level of translatable bulk cellular mRNA and the stability of [3H]uridine-labeled mRNA were unaffected. Superinduction with actinomycin D selectively stabilized interferon mRNA with no apparent effect on the stability of bulk cellular mRNA. Furthermore, an activation of the 2',5'-oligo(A) synthetase/endonuclease system does not appear to be involved in the shutoff phenomenon. Uninduced FS-4 cells contained a low basal level of 2'5'-oligo(A) synthetase activity, which was unchanged in poly(I)xpoly(C)-induced cells during the shutoff phase. Treatment of FS-4 cells with interferon for 16-18 hr prior to induction increased the enzyme activity by approximately 200-fold. However, this did not inhibit interferon production after induction with poly(I)xpoly(C) alone or after superinduction with cycloheximide or actinomycin D or both. Furthermore, the rates of decay of interferon production were comparable in cells with either a basal or an increased level of 2',5'-oligo(A) synthetase. Thus a 200-fold increase in 2',5'-oligo(A) synthetase level did not affect either the stability of interferon mRNA or the efficacy of interferon superinduction by metabolic inhibitors.

  6. Molecular Beacons: Powerful Tools for Imaging RNA in Living Cells


    Ricardo Monroy-Contreras; Luis Vaca


    Recent advances in RNA functional studies highlights the pivotal role of these molecules in cell physiology. Diverse methods have been implemented to measure the expression levels of various RNA species, using either purified RNA or fixed cells. Despite the fact that fixed cells offer the possibility to observe the spatial distribution of RNA, assays with capability to real-time monitoring RNA transport into living cells are needed to further understand the role of RNA dynamics in cellular fu...

  7. Posttranscriptional regulation of GAP-43 gene expression in PC12 cells through protein kinase C-dependent stabilization of the mRNA. (United States)

    Perrone-Bizzozero, N I; Cansino, V V; Kohn, D T


    We have previously shown that nerve growth factor (NGF) selectively stabilizes the GAP-43 mRNA in PC12 cells. To study the cellular mechanisms for this post-transcriptional control and to determine the contribution of mRNA stability to GAP-43 gene expression, we examined the effects of several agents that affect PC12 cell differentiation on the level of induction and rate of degradation of the GAP-43 mRNA. The NGF-mediated increase in GAP-43 mRNA levels and neurite outgrowth was mimicked by the phorbol ester TPA, but not by dibutyryl cAMP or the calcium ionophore A12783. Downregulation of protein kinase C (PKC) by high doses of phorbol esters or selective PKC inhibitors prevented the induction of this mRNA by NGF, suggesting that NGF and TPA act through a common PKC-dependent pathway. In mRNA decay studies, phorbol esters caused a selective 6-fold increase in the half-life of the GAP-43 mRNA, which accounts for most of the induction of this mRNA by TPA. The phorbol ester-induced stabilization of GAP-43 mRNA was blocked by the protein kinase inhibitor polymyxin B and was partially inhibited by dexamethasone, an agent that blocks GAP-43 expression and neuronal differentiation in PC12 cells. In contrast, the rates of degradation and the levels of the GAP-43 mRNA in control and TPA-treated cells were not affected by cycloheximide treatment. Thus, changes in GAP-43 mRNA turnover do not appear to require continuous protein synthesis. In conclusion, these data suggest that PKC activity regulates the levels of the GAP-43 mRNA in PC12 cells through a novel, translation-independent mRNA stabilization mechanism.

  8. Overview of MicroRNA Biology



    In considering an overview of microRNA biology, it is useful to consider microRNAs as a part of cellular communication. At the simplest level, microRNAs act to decrease the expression of mRNAs that contain stretches of sequence complementary to the microRNA. This function can be likened to the function of endogenous or synthetic short interfering RNA (siRNA). However, microRNA function is more complicated and nuanced than this ‘on-off’ model would suggest. Further, many microRNA targets are t...

  9. RNA Origami

    DEFF Research Database (Denmark)

    Sparvath, Steffen Lynge


    for biosensorer,  der kan spore enten microRNA’er eller små molekyler, eksemplificeret ved S-adenosylmethionin (SAM). Slutteligt indikerer foreløbige resultater, at apta-FRET SAM sensoren kan udtrykkes i Escherichia coli-celler, hvilket viser, at RNA-origami arkitekturen muliggør cotransskriptionel foldning af......RNA-nanoteknologi feltet har demonstreret alsidigheden af RNA som byggemateriale, og rationelt designede RNA-nanostrukturer er blevet brugt i udviklingen af strukturelle platforme og dynamiske anordninger med anvendelser både in vitro og in vivo. Naturlige RNA-strukturer foldes cotransskriptionelt...... fra en enkelt RNA-streng, og udfører en lang række komplekse cellulære funktioner. Mange af funktionerne er blevet udnyttet til at skabe funktionelle RNA-baserede nanoapparater, men den nuværende litteratur giver kun få eksempler på cotranskriptionel produktion af RNA-nanostrukturer. I 2014...

  10. Exponential Decay of Correlations for the Strongly Coupled Toom Model

    CERN Document Server

    de Maere, Augustin


    We prove that, for the two-dimensional probabilistic cellular automaton of Toom in the low-noise regime, there are two classes of initial measures, each of which converges exponentially fast toward one of the two natural invariant measures. We also show that these two invariant measures have exponential decay of correlations in space and in time and are strongly mixing.

  11. RNA genetics

    Energy Technology Data Exchange (ETDEWEB)

    Domingo, E. (Instituto de Biologia Molecular, Facultad de Ciencias, Universidad Autonoma de Madrid, Canto Blanco, Madrid (ES)); Holland, J.J. (California Univ., San Diego, La Jolla, CA (USA). Dept. of Biology); Ahlquist, P. (Wisconsin Univ., Madison, WI (USA). Dept. of Plant Pathology)


    This book contains the proceedings on RNA genetics: RNA-directed virus replication Volume 1. Topics covered include: Replication of the poliovirus genome; Influenza viral RNA transcription and replication; and Relication of the reoviridal: Information derived from gene cloning and expression.

  12. Application of Live-Cell RNA Imaging Techniques to the Study of Retroviral RNA Trafficking

    Directory of Open Access Journals (Sweden)

    Darrin V. Bann


    Full Text Available Retroviruses produce full-length RNA that serves both as a genomic RNA (gRNA, which is encapsidated into virus particles, and as an mRNA, which directs the synthesis of viral structural proteins. However, we are only beginning to understand the cellular and viral factors that influence trafficking of retroviral RNA and the selection of the RNA for encapsidation or translation. Live cell imaging studies of retroviral RNA trafficking have provided important insight into many aspects of the retrovirus life cycle including transcription dynamics, nuclear export of viral RNA, translational regulation, membrane targeting, and condensation of the gRNA during virion assembly. Here, we review cutting-edge techniques to visualize single RNA molecules in live cells and discuss the application of these systems to studying retroviral RNA trafficking.

  13. Beta and muon decays

    Energy Technology Data Exchange (ETDEWEB)

    Galindo, A.; Pascual, P.


    These notes represent a series of lectures delivered by the authors in the Junta de Energia Nuclear, during the Spring term of 1965. They were devoted to graduate students interested in the Theory of Elementary Particles. Special emphasis was focussed into the computational problems. Chapter I is a review of basic principles (Dirac equation, transition probabilities, final state interactions.) which will be needed later. In Chapter II the four-fermion punctual Interaction is discussed, Chapter III is devoted to the study of beta-decay; the main emphasis is given to the deduction of the formulae corresponding to electron-antineutrino correlation, electron energy spectrum, lifetimes, asymmetry of electrons emitted from polarized nuclei, electron and neutrino polarization and time reversal invariance in beta decay. In Chapter IV we deal with the decay of polarized muons with radiative corrections. Chapter V is devoted to an introduction to C.V.C. theory. (Author)

  14. Suppressed Charmed B Decay

    Energy Technology Data Exchange (ETDEWEB)

    Snoek, Hella Leonie [Vrije Univ., Amsterdam (Netherlands)


    This thesis describes the measurement of the branching fractions of the suppressed charmed B0 → D*- a0+ decays and the non-resonant B0 → D*- ηπ+ decays in approximately 230 million Υ(4S) → B$\\bar{B}$ events. The data have been collected with the BABAR detector at the PEP-II B factory at the Stanford Linear Accelerator Center in California. Theoretical predictions of the branching fraction of the B0 → D*- a{sub 0}+ decays show large QCD model dependent uncertainties. Non-factorizing terms, in the naive factorization model, that can be calculated by QCD factorizing models have a large impact on the branching fraction of these decay modes. The predictions of the branching fractions are of the order of 10-6. The measurement of the branching fraction gives more insight into the theoretical models. In general a better understanding of QCD models will be necessary to conduct weak interaction physics at the next level. The presence of CP violation in electroweak interactions allows the differentiation between matter and antimatter in the laws of physics. In the Standard Model, CP violation is incorporated in the CKM matrix that describes the weak interaction between quarks. Relations amongst the CKM matrix elements are used to present the two relevant parameters as the apex of a triangle (Unitarity Triangle) in a complex plane. The over-constraining of the CKM triangle by experimental measurements is an important test of the Standard Model. At this moment no stringent direct measurements of the CKM angle γ, one of the interior angles of the Unitarity Triangle, are available. The measurement of the angle γ can be performed using the decays of neutral B mesons. The B0 → D*- a0+ decay is sensitive to the angle γ and, in comparison to the current decays that are being employed, could significantly

  15. Holographic Glueball Decay

    CERN Document Server

    Brünner, Frederic; Rebhan, Anton


    We announce new results on glueball decay rates in the Sakai-Sugimoto model, a realization of holographic QCD from first principles that has only one coupling constant and an overall mass scale as free parameters. We extend a previous investigation by Hashimoto, Tan, and Terashima who have considered the lowest scalar glueball which arises from a somewhat exotic polarization of supergravity modes and whose mass is uncomfortably small in comparison with lattice results. On the other hand, the scalar glueball dual to the dilaton turns out to have a mass of about twice the mass of the rho meson (1487 MeV), very close to the scalar meson $f_0(1500)$ that is frequently interpreted as predominantly glue. Calculating the decay rate into two pions we find a surprisingly good agreement with experimental data for the $f_0(1500)$. We have also obtained decay widths for tensor and excited scalar glueballs, indicating universal narrowness.

  16. RNA epigenetics


    Liu, Nian; Pan, Tao


    Mammalian messenger and long non-coding RNA contain tens of thousands of post-transcriptional chemical modifications. Among these, the N6-methyl-adenosine (m6A) modification is the most abundant and can be removed by specific mammalian enzymes. M6A modification is recognized by families of RNA binding proteins that affect many aspects of mRNA function. mRNA/lncRNA modification represents another layer of epigenetic regulation of gene expression, analogous to DNA methylation and histone modifi...

  17. Flavor changing nucleon decay (United States)

    Maekawa, Nobuhiro; Muramatsu, Yu


    Recent discovery of neutrino large mixings implies the large mixings in the diagonalizing matrices of 5 bar fields in SU (5) grand unified theory (GUT), while the diagonalizing matrices of 10 fields of SU (5) are expected to have small mixings like Cabibbo-Kobayashi-Maskawa matrix. We calculate the predictions of flavor changing nucleon decays (FCND) in SU (5), SO (10), and E6 GUT models which have the above features for mixings. We found that FCND can be the main decay mode and play an important role to test GUT models.

  18. The sweet side of RNA regulation: glyceraldehyde-3-phosphate dehydrogenase as a noncanonical RNA-binding protein. (United States)

    White, Michael R; Garcin, Elsa D


    The glycolytic protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has a vast array of extraglycolytic cellular functions, including interactions with nucleic acids. GAPDH has been implicated in the translocation of transfer RNA (tRNA), the regulation of cellular messenger RNA (mRNA) stability and translation, as well as the regulation of replication and gene expression of many single-stranded RNA viruses. A growing body of evidence supports GAPDH-RNA interactions serving as part of a larger coordination between intermediary metabolism and RNA biogenesis. Despite the established role of GAPDH in nucleic acid regulation, it is still unclear how and where GAPDH binds to its RNA targets, highlighted by the absence of any conserved RNA-binding sequences. This review will summarize our current understanding of GAPDH-mediated regulation of RNA function. WIREs RNA 2016, 7:53-70. doi: 10.1002/wrna.1315 For further resources related to this article, please visit the WIREs website.

  19. Tat RNA silencing suppressor activity contributes to perturbation of lymphocyte miRNA by HIV-1

    Directory of Open Access Journals (Sweden)

    Yu Lianbo


    Full Text Available Abstract Background MicroRNA (miRNA-mediated RNA silencing is integral to virtually every cellular process including cell cycle progression and response to virus infection. The interplay between RNA silencing and HIV-1 is multifaceted, and accumulating evidence posits a strike-counterstrike interface that alters the cellular environment to favor virus replication. For instance, miRNA-mediated RNA silencing of HIV-1 translation is antagonized by HIV-1 Tat RNA silencing suppressor activity. The activity of HIV-1 accessory proteins Vpr/Vif delays cell cycle progression, which is a process prominently modulated by miRNA. The expression profile of cellular miRNA is altered by HIV-1 infection in both cultured cells and clinical samples. The open question stands of what, if any, is the contribution of Tat RNA silencing suppressor activity or Vpr/Vif activity to the perturbation of cellular miRNA by HIV-1. Results Herein, we compared the perturbation of miRNA expression profiles of lymphocytes infected with HIV-1NL4-3 or derivative strains that are deficient in Tat RNA silencing suppressor activity (Tat K51A substitution or ablated of the vpr/vif open reading frames. Microarrays recapitulated the perturbation of the cellular miRNA profile by HIV-1 infection. The miRNA expression trends overlapped ~50% with published microarray results on clinical samples from HIV-1 infected patients. Moreover, the number of miRNA perturbed by HIV-1 was largely similar despite ablation of Tat RSS activity and Vpr/Vif; however, the Tat RSS mutation lessened HIV-1 downregulation of twenty-two miRNAs. Conclusions Our study identified miRNA expression changes attributable to Tat RSS activity in HIV-1NL4-3. The results accomplish a necessary step in the process to understand the interface of HIV-1 with host RNA silencing activity. The overlap in miRNA expression trends observed between HIV-1 infected CEMx174 lymphocytes and primary cells supports the utility of cultured

  20. Transfer RNA and human disease

    Directory of Open Access Journals (Sweden)

    Jamie A Abbott


    Full Text Available Pathological mutations in tRNA genes and tRNA processing enzymes are numerous and result in very complicated clinical phenotypes. Mitochondrial tRNA (mt-tRNA genes are hotspots for pathological mutations and over 200 mt-tRNA mutations have been linked to various disease states. Often these mutations prevent tRNA aminoacylation. Disrupting this primary function affects protein synthesis and the expression, folding, and function of oxidative phosphorylation enzymes. Mitochondrial tRNA mutations manifest in a wide panoply of diseases related to cellular energetics, including COX deficiency (cytochrome C oxidase, mitochondrial myopathy, MERRF (Myoclonic Epilepsy with Ragged Red Fibers, and MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes. Diseases caused by mt-tRNA mutations can also affect very specific tissue types, as in the case of neurosensory non-syndromic hearing loss and pigmentary retinopathy, diabetes mellitus, and hypertrophic cardiomyopathy. Importantly, mitochondrial heteroplasmy plays a role in disease severity and age of onset as well. Not surprisingly, mutations in enzymes that modify cytoplasmic and mitochondrial tRNAs are also linked to a diverse range of clinical phenotypes. In addition to compromised aminoacylation of the tRNAs, mutated modifying enzymes can also impact tRNA expression and abundance, tRNA modifications, tRNA folding, and even tRNA maturation (e.g., splicing. Some of these pathological mutations in tRNAs and processing enzymes are likely to affect non-canonical tRNA functions, and contribute to the diseases without significantly impacting on translation. This chapter will review recent literature on the relation of mitochondrial and cytoplasmic tRNA, and enzymes that process tRNAs, to human disease. We explore the mechanisms involved in the clinical presentation of these various diseases with an emphasis on neurological disease.

  1. MicroRNA: Potential Targets for the Development of Novel Drugs?


    Wei WU


    MicroRNA (miRNA) is an endogenous non-protein coding small RNA molecule that negatively regulates gene expression by the degradation of messenger RNA (mRNA) or the suppression of mRNA translation. miRNA plays important roles in physiologic processes such as cellular development, differentiation, proliferation, apoptosis, and stem cell self-renewal. Studies show that deregulation of miRNA expression is closely associated with tumorigenicity, invasion, and metastasis. The functionality of aberr...

  2. Reversible quantum cellular automata

    CERN Document Server

    Schumacher, B


    We define quantum cellular automata as infinite quantum lattice systems with discrete time dynamics, such that the time step commutes with lattice translations and has strictly finite propagation speed. In contrast to earlier definitions this allows us to give an explicit characterization of all local rules generating such automata. The same local rules also generate the global time step for automata with periodic boundary conditions. Our main structure theorem asserts that any quantum cellular automaton is structurally reversible, i.e., that it can be obtained by applying two blockwise unitary operations in a generalized Margolus partitioning scheme. This implies that, in contrast to the classical case, the inverse of a nearest neighbor quantum cellular automaton is again a nearest neighbor automaton. We present several construction methods for quantum cellular automata, based on unitaries commuting with their translates, on the quantization of (arbitrary) reversible classical cellular automata, on quantum c...

  3. Molecular kinesis in cellular function and plasticity. (United States)

    Tiedge, H; Bloom, F E; Richter, D


    Intracellular transport and localization of cellular components are essential for the functional organization and plasticity of eukaryotic cells. Although the elucidation of protein transport mechanisms has made impressive progress in recent years, intracellular transport of RNA remains less well understood. The National Academy of Sciences Colloquium on Molecular Kinesis in Cellular Function and Plasticity therefore was devised as an interdisciplinary platform for participants to discuss intracellular molecular transport from a variety of different perspectives. Topics covered at the meeting included RNA metabolism and transport, mechanisms of protein synthesis and localization, the formation of complex interactive protein ensembles, and the relevance of such mechanisms for activity-dependent regulation and synaptic plasticity in neurons. It was the overall objective of the colloquium to generate momentum and cohesion for the emerging research field of molecular kinesis.

  4. The upstream open reading frame of cyclin-dependent kinase inhibitor 1A mRNA negatively regulates translation of the downstream main open reading frame

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kyoung Mi; Cho, Hana [School of Life Sciences and Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Kim, Yoon Ki, E-mail: [School of Life Sciences and Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of)


    Highlights: Black-Right-Pointing-Pointer CDKN1A mRNA is a bona fide NMD substrate. Black-Right-Pointing-Pointer The uORF of CDKN1A mRNA is efficiently translated. Black-Right-Pointing-Pointer Translation of downstream main ORF is negatively regulated by translation of uORF in CDKN1A mRNA. -- Abstract: The first round of translation occurs on mRNAs bound by nuclear cap-binding complex (CBC), which is composed of nuclear cap-binding protein 80 and 20 (CBP80/20). During this round of translation, aberrant mRNAs are recognized and downregulated in abundance by nonsense-mediated mRNA decay (NMD), which is one of the mRNA quality control mechanisms. Here, our microarray analysis reveals that the level of cyclin-dependent kinase inhibitor 1A (CDKN1A; also known as Waf1/p21) mRNAs increases in cells depleted of cellular NMD factors. Intriguingly, CDKN1A mRNA contains an upstream open reading frame (uORF), which is a NMD-inducing feature. Using chimeric reporter constructs, we find that the uORF of CDKN1A mRNA negatively modulates translation of the main downstream ORF. These findings provide biological insights into the possible role of NMD in diverse biological pathways mediated by CDKN1A.

  5. RNA interference-mediated simultaneous silencing of four genes using cross-shaped RNA. (United States)

    Lee, Tae Yeon; Chang, Chan Il; Lee, Dooyoung; Hong, Sun Woo; Shin, Chanseok; Li, Chiang J; Kim, Soyoun; Haussecker, Dirk; Lee, Dong-Ki


    The structural flexibility of RNA interference (RNAi)-triggering nucleic acids suggests that the design of unconventional RNAi trigger structures with novel features is possible. Here, we report a cross-shaped RNA duplex structure, termed quadruple interfering RNA (qiRNA), with multiple target gene silencing activity. qiRNA triggers the simultaneous down-regulation of four cellular target genes via an RNAi mechanism. In addition, qiRNA shows enhanced intracellular delivery and target gene silencing over conventional siRNA when complexed with jetPEI, a linear polyethyleneimine (PEI). We also show that the long antisense strand of qiRNA is incorporated intact into an RNA-induced silencing complex (RISC). This novel RNA scaffold further expands the repertoire of RNAi-triggering molecular structures and could be used in the development of therapeutics for various diseases including viral infections and cancer.

  6. Rare B decays at LEP

    CERN Document Server

    Kluit, P M


    The results of the LEP experiments for rare B decays will be reviewed, covering hadronic final states, radiative and other rare decays and results for the inclusive charmless branching ratio. (8 refs).

  7. Designing synthetic RNA for delivery by nanoparticles (United States)

    Jedrzejczyk, Dominika; Gendaszewska-Darmach, Edyta; Pawlowska, Roza; Chworos, Arkadiusz


    The rapid development of synthetic biology and nanobiotechnology has led to the construction of various synthetic RNA nanoparticles of different functionalities and potential applications. As they occur naturally, nucleic acids are an attractive construction material for biocompatible nanoscaffold and nanomachine design. In this review, we provide an overview of the types of RNA and nucleic acid’s nanoparticle design, with the focus on relevant nanostructures utilized for gene-expression regulation in cellular models. Structural analysis and modeling is addressed along with the tools available for RNA structural prediction. The functionalization of RNA-based nanoparticles leading to prospective applications of such constructs in potential therapies is shown. The route from the nanoparticle design and modeling through synthesis and functionalization to cellular application is also described. For a better understanding of the fate of targeted RNA after delivery, an overview of RNA processing inside the cell is also provided.

  8. Analysis of extracellular RNA by digital PCR

    Directory of Open Access Journals (Sweden)

    Kenji eTakahashi


    Full Text Available The transfer of extracellular RNA is emerging as an important mechanism for intracellular communication. The ability for the transfer of functionally active RNA molecules from one cell to another within vesicles such as exosomes enables a cell to modulate cellular signaling and biological processes within recipient cells. The study of extracellular RNA requires sensitive methods for the detection of these molecules. In this methods article, we will describe protocols for the detection of such extracellular RNA using sensitive detection technologies such as digital PCR. These protocols should be valuable to researchers interested in the role and contribution of extracellular RNA to tumor cell biology.

  9. CP-violations in decays

    Indian Academy of Sciences (India)

    Y Sakai


    Recent results on CP-violation measurements in decays from energy asymmetric -factory experiments are reported. Thanks to large accumulated data samples, CP-violations in decays in mixing-decay interference and direct CP-violation are now firmly established. The measurements of three angles of the unitarity triangle from CP-violations of decays are quite consistent with the Standard Model expectations. These results strongly support the validity of the Kobayashi-Maskawa prescription of CP-violation.

  10. Fundamental Limits to Cellular Sensing (United States)

    ten Wolde, Pieter Rein; Becker, Nils B.; Ouldridge, Thomas E.; Mugler, Andrew


    In recent years experiments have demonstrated that living cells can measure low chemical concentrations with high precision, and much progress has been made in understanding what sets the fundamental limit to the precision of chemical sensing. Chemical concentration measurements start with the binding of ligand molecules to receptor proteins, which is an inherently noisy process, especially at low concentrations. The signaling networks that transmit the information on the ligand concentration from the receptors into the cell have to filter this receptor input noise as much as possible. These networks, however, are also intrinsically stochastic in nature, which means that they will also add noise to the transmitted signal. In this review, we will first discuss how the diffusive transport and binding of ligand to the receptor sets the receptor correlation time, which is the timescale over which fluctuations in the state of the receptor, arising from the stochastic receptor-ligand binding, decay. We then describe how downstream signaling pathways integrate these receptor-state fluctuations, and how the number of receptors, the receptor correlation time, and the effective integration time set by the downstream network, together impose a fundamental limit on the precision of sensing. We then discuss how cells can remove the receptor input noise while simultaneously suppressing the intrinsic noise in the signaling network. We describe why this mechanism of time integration requires three classes (groups) of resources—receptors and their integration time, readout molecules, energy—and how each resource class sets a fundamental sensing limit. We also briefly discuss the scheme of maximum-likelihood estimation, the role of receptor cooperativity, and how cellular copy protocols differ from canonical copy protocols typically considered in the computational literature, explaining why cellular sensing systems can never reach the Landauer limit on the optimal trade

  11. RNA fluorescence with light-up aptamers (United States)

    Ouellet, Jonathan


    Seeing is not only believing; it also includes understanding. Cellular imaging with GFP in live cells has been transformative in many research fields. Modulation of cellular regulation is tightly regulated and innovative imaging technologies contribute to further understand cellular signaling and physiology. New types of genetically encoded biosensors have been developed over the last decade. They are RNA aptamers that bind with their cognate fluorogen ligands and activate their fluorescence. The emergence and the evolution of these RNA aptamers as well as their conversion into a wide spectrum of applications are examined in a global way.

  12. RNA structural analysis by evolving SHAPE chemistry. (United States)

    Spitale, Robert C; Flynn, Ryan A; Torre, Eduardo A; Kool, Eric T; Chang, Howard Y


    RNA is central to the flow of biological information. From transcription to splicing, RNA localization, translation, and decay, RNA is intimately involved in regulating every step of the gene expression program, and is thus essential for health and understanding disease. RNA has the unique ability to base-pair with itself and other nucleic acids to form complex structures. Hence the information content in RNA is not simply its linear sequence of bases, but is also encoded in complex folding of RNA molecules. A general chemical functionality that all RNAs have is a 2'-hydroxyl group in the ribose ring, and the reactivity of the 2'-hydroxyl in RNA is gated by local nucleotide flexibility. In other words, the 2'-hydroxyl is reactive at single-stranded and conformationally flexible positions but is unreactive at nucleotides constrained by base-pairing. Recent efforts have been focused on developing reagents that modify RNA as a function of RNA 2' hydroxyl group reactivity. Such RNA structure probing techniques can be read out by primer extension in experiments termed RNA SHAPE (selective 2'- hydroxyl acylation and primer extension). Herein, we describe the efforts devoted to the design and utilization of SHAPE probes for characterizing RNA structure. We also describe current technological advances that are being applied to utilize SHAPE chemistry with deep sequencing to probe many RNAs in parallel. The merging of chemistry with genomics is sure to open the door to genome-wide exploration of RNA structure and function.

  13. Heterogeneous cellular networks

    CERN Document Server

    Hu, Rose Qingyang


    A timely publication providing coverage of radio resource management, mobility management and standardization in heterogeneous cellular networks The topic of heterogeneous cellular networks has gained momentum in industry and the research community, attracting the attention of standardization bodies such as 3GPP LTE and IEEE 802.16j, whose objectives are looking into increasing the capacity and coverage of the cellular networks. This book focuses on recent progresses,  covering the related topics including scenarios of heterogeneous network deployment, interference management i

  14. siRNA and miRNA processing: new functions for Cajal bodies. (United States)

    Pontes, Olga; Pikaard, Craig S


    In diverse eukaryotes, micro-RNAs (miRNAs) and small interfering RNAs (siRNAs) regulate important processes that include mRNA inactivation, viral defense, chromatin modification, and transposon silencing. Recently, nucleolus-associated Cajal bodies in plants have been implicated as sites of siRNA and miRNA biogenesis, whereas in animals siRNA and miRNA dicing occurs in the cytoplasm. The plant nucleolus also contains proteins of the nonsense-mediated mRNA decay pathway that in animals are found associated with cytoplasmic processing bodies (P-bodies). P-bodies also function in the degradation of mRNAs subjected to miRNA and siRNA targeting. Collectively, these observations suggest interesting variations in the way siRNAs and miRNAs can accomplish their similar functions in plants and animals.

  15. Decay constants in geochronology

    Institute of Scientific and Technical Information of China (English)

    IgorM.Villa; PaulR.Renne


    Geologic time is fundamental to the Earth Sciences, and progress in many disciplines depends critically on our ability to measure time with increasing accuracy and precision. Isotopic geochronology makes use of the decay of radioactive nuclides as a help to quantify the histories of rock, minerals, and other materials. Both accuracy and precision of radioisotopic ages are, at present, limited by those of radioactive decay constants. Modem mass spectrometers can measure isotope ratios with a precision of 10-4 or better. On the other hand, the uncertainties associated with direct half-life determinations are, in most cases, still at the percent level. The present short note briefly summarizes progress and problems that have been encountered during the Working Group's activity.

  16. Decay of Hoyle state

    Indian Academy of Sciences (India)

    S Bhattacharya; T K Rana; C Bhattacharya; S Kundu; K Banerjee; T K Ghosh; G Mukherjee; R Pandey; P Roy


    The prediction of Hoyle state was necessitated to explain the abundance of carbon, which is crucial for the existence of life on Earth and is the stepping stone for understanding the abundance of other heavier elements. After the experimental confirmation of its existence, soon it was realized that the Hoyle state was `different’ from other excited states of carbon, which led to intense theoretical and experimental activities over the past few decades to understand its structure. In recent times, precision, high statistics experiments on the decay of Hoyle state have been performed at the Variable Energy Cyclotron Centre, to determine the quantitative contributions of various direct 3 decay mechanisms of the Hoyle state. The present results have been critically compared with those obtained in other recent experiments and their implications have been discussed.

  17. Electroweak penguin B decays

    CERN Document Server

    Nikodem, Thomas


    Flavour Changing Neutral Currents (FCNC) are sensitive probes for physics beyond the Standard Model (SM), so-called New Physics. An example of a FCNC is the $b \\to s$ quark transition described by the electroweak penguin Feynman diagram shown in Figure 1. In the SM such FCNC are only allowed with a loop structure (as e:g: shown in the figure) and not by tree level processes. In the loops heavy particles appear virtually and do not need to be on shell. Therefore also not yet discovered heavy particles with up to a mass $\\mathcal{O}$(TeV) could virtually contribute significantly to observables. Several recent measurements of electroweak penguin B decays exhibit interesting tensions with SM predictions, most prominently in the angular observable $P'_5$ 5 of the decay $B^0 \\to K^{*0} \\mu^+ \\mu^1$[1], which triggered a lot of discussion in the theory community [2]-[14].

  18. Teleportation via decay

    Indian Academy of Sciences (India)

    S Bose; P L Knight; M B Plenio; V Vedral


    We present a rare example of a decay mechanism playing a constructive role in quantum information processing. We show how the state of an atom trapped in a cavity can be teleported to a second atom trapped in a distant cavity by the joint detection of photon leakage from the cavities. The scheme, which is probabilistic, requires only a single three level atom in a cavity. We also show how this scheme can be modified to a teleportation with insurance.

  19. Charmless B decays

    Directory of Open Access Journals (Sweden)

    Martens Aurélien


    Full Text Available During 2011, LHCb has collected an integrated luminosity of 1.1 fb−1, giving rise to a large variety of measurements. Amongst these, measurements of CP violation in B decays play a central role. In particular CP violation measurements in charmless transitions of B mesons are of interest since they provide new or improved constraints on new physics contributions. These proceedings concentrate on LHCb results made publicin the first half of the year 2012.

  20. Decays of s neutrinos

    CERN Document Server

    Barradas, J E


    Based on the Minimal Supersymmetric Standard Model (MSSM), we discussed possible two body decay modes for the s neutrino v, one charged and other neutral: v -> l sub x sub 1 sup + sup - and v -> vx sub 1 sup 0 , respectively. Exploring a range of possible values for its mass, and for the chargino x sub i sup + sup - and neutralino x sub j sup 0 masses as well. We present the specific calculation for branching ratios, which are analyzed numerically. (Author)

  1. RNA oxidation

    DEFF Research Database (Denmark)

    Kjaer, L. K.; Cejvanovic, V.; Henriken, T.


    RNA modification has attracted increasing interest as it is realized that epitranscriptomics is important in disease development. In type 2 diabetes we have suggested that high urinary excretion of 8-oxo-2'-Guanosine (8oxoGuo), as a measure of global RNA oxidation, is associated with poor survival.......9 significant hazard ratio for death compared with the quartile with the lowest 8oxoGuo excretion when adjusted for age, sex, BMI, smoker status, s-HbA1c, urine protein excretion and s-cholesterol. We conclude that it is now established that RNA oxidation is an independent risk factor for death in type 2...... diabetes. In agreement with our previous finding, DNA oxidation did not show any prognostic value. RNA oxidation represents oxidative stress intracellularly, presumably predominantly in the cytosol. The mechanism of RNA oxidation is not clear, but hypothesized to result from mitochondrial dysfunction...

  2. Multifluid magnetohydrodynamic turbulent decay

    CERN Document Server

    Downes, Turlough P


    It is generally believed that turbulence has a significant impact on the dynamics and evolution of molecular clouds and the star formation which occurs within them. Non-ideal magnetohydrodynamic effects are known to influence the nature of this turbulence. We present the results of a suite of 512-cubed resolution simulations of the decay of initially super-Alfvenic and supersonic fully multifluid MHD turbulence. We find that ambipolar diffusion increases the rate of decay of the turbulence while the Hall effect has virtually no impact. The decay of the kinetic energy can be fitted as a power-law in time and the exponent is found to be -1.34 for fully multifluid MHD turbulence. The power spectra of density, velocity and magnetic field are all steepened significantly by the inclusion of non-ideal terms. The dominant reason for this steepening is ambipolar diffusion with the Hall effect again playing a minimal role except at short length scales where it creates extra structure in the magnetic field. Interestingl...

  3. Radioactive decay data tables

    Energy Technology Data Exchange (ETDEWEB)

    Kocher, D.C.


    The estimation of radiation dose to man from either external or internal exposure to radionuclides requires a knowledge of the energies and intensities of the atomic and nuclear radiations emitted during the radioactive decay process. The availability of evaluated decay data for the large number of radionuclides of interest is thus of fundamental importance for radiation dosimetry. This handbook contains a compilation of decay data for approximately 500 radionuclides. These data constitute an evaluated data file constructed for use in the radiological assessment activities of the Technology Assessments Section of the Health and Safety Research Division at Oak Ridge National Laboratory. The radionuclides selected for this handbook include those occurring naturally in the environment, those of potential importance in routine or accidental releases from the nuclear fuel cycle, those of current interest in nuclear medicine and fusion reactor technology, and some of those of interest to Committee 2 of the International Commission on Radiological Protection for the estimation of annual limits on intake via inhalation and ingestion for occupationally exposed individuals.

  4. Nanostructured cellular networks. (United States)

    Moriarty, P; Taylor, M D R; Brust, M


    Au nanocrystals spin-coated onto silicon from toluene form cellular networks. A quantitative statistical crystallography analysis shows that intercellular correlations drive the networks far from statistical equilibrium. Spin-coating from hexane does not produce cellular structure, yet a strong correlation is retained in the positions of nanocrystal aggregates. Mechanisms based on Marangoni convection alone cannot account for the variety of patterns observed, and we argue that spinodal decomposition plays an important role in foam formation.

  5. RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs. (United States)

    Simon, Anne E; Gehrke, Lee


    The rugged nature of the RNA structural free energy landscape allows cellular RNAs to respond to environmental conditions or fluctuating levels of effector molecules by undergoing dynamic conformational changes that switch on or off activities such as catalysis, transcription or translation. Infectious RNAs must also temporally control incompatible activities and rapidly complete their life cycle before being targeted by cellular defenses. Viral genomic RNAs must switch between translation and replication, and untranslated subviral RNAs must control other activities such as RNA editing or self-cleavage. Unlike well characterized riboswitches in cellular RNAs, the control of infectious RNA activities by altering the configuration of functional RNA domains has only recently been recognized. In this review, we will present some of these molecular rearrangements found in RNA viruses, viroids and virus-associated RNAs, relating how these dynamic regions were discovered, the activities that might be regulated, and what factors or conditions might cause a switch between conformations.

  6. Column: Factors Affecting Data Decay

    Directory of Open Access Journals (Sweden)

    Kevin Fairbanks


    Full Text Available In nuclear physics, the phrase decay rate is used to denote the rate that atoms and other particles spontaneously decompose. Uranium-235 famously decays into a variety of daughter isotopes including Thorium and Neptunium, which themselves decay to others. Decay rates are widely observed and wildly different depending on many factors, both internal and external. U-235 has a half-life of 703,800,000 years, for example, while free neutrons have a half-life of 611 seconds and neutrons in an atomic nucleus are stable.We posit that data in computer systems also experiences some kind of statistical decay process and thus also has a discernible decay rate. Like atomic decay, data decay fluctuates wildly. But unlike atomic decay, data decay rates are the result of so many different interplaying processes that we currently do not understand them well enough to come up with quantifiable numbers. Nevertheless, we believe that it is useful to discuss some of the factors that impact the data decay rate, for these factors frequently determine whether useful data about a subject can be recovered by forensic investigation.(see PDF for full column

  7. Molecular and cellular aspects of mental retardation in the Fragile X syndrome: from gene mutation/s to spine dysmorphogenesis. (United States)

    De Rubeis, Silvia; Fernández, Esperanza; Buzzi, Andrea; Di Marino, Daniele; Bagni, Claudia


    The Fragile X syndrome (FXS) is the most frequent form of inherited mental retardation and also considered a monogenic cause of Autism Spectrum Disorder. FXS symptoms include neurodevelopmental delay, anxiety, hyperactivity, and autistic-like behavior. The disease is due to mutations or loss of the Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein abundant in the brain and gonads, the two organs mainly affected in FXS patients. FMRP has multiple functions in RNA metabolism, including mRNA decay, dendritic targeting of mRNAs, and protein synthesis. In neurons lacking FMRP, a wide array of mRNAs encoding proteins involved in synaptic structure and function are altered. As a result of this complex dysregulation, in the absence of FMRP, spine morphology and functioning is impaired. Consistently, model organisms for the study of the syndrome recapitulate the phenotype observed in FXS patients, such as dendritic spine anomalies and defects in learning. Here, we review the fundamentals of genetic and clinical aspects of FXS, devoting a specific attention to ASD comorbidity and FXS-related diseases. We also review the current knowledge on FMRP functions through structural, molecular, and cellular findings. Finally, we discuss the neuroanatomical, electrophysiological, and behavioral defects caused by FMRP loss, as well as the current treatments able to partially revert some of the FXS abnormalities.

  8. The RNA interference revolution

    Directory of Open Access Journals (Sweden)

    G. Lenz


    Full Text Available The discovery of double-stranded RNA-mediated gene silencing has rapidly led to its use as a method of choice for blocking a gene, and has turned it into one of the most discussed topics in cell biology. Although still in its infancy, the field of RNA interference has already produced a vast array of results, mainly in Caenorhabditis elegans, but recently also in mammalian systems. Micro-RNAs are short hairpins of RNA capable of blocking translation, which are transcribed from genomic DNA and are implicated in several aspects from development to cell signaling. The present review discusses the main methods used for gene silencing in cell culture and animal models, including the selection of target sequences, delivery methods and strategies for a successful silencing. Expected developments are briefly discussed, ranging from reverse genetics to therapeutics. Thus, the development of the new paradigm of RNA-mediated gene silencing has produced two important advances: knowledge of a basic cellular mechanism present in the majority of eukaryotic cells and access to a potent and specific new method for gene silencing.

  9. Primer-Dependent and Primer-Independent Initiation of Double Stranded RNA Synthesis by Purified Arabidopsis RNA-Dependent RNA Polymerases RDR2 and RDR6 (United States)

    Devert, Anthony; Fabre, Nicolas; Floris, Maïna; Canard, Bruno; Robaglia, Christophe; Crété, Patrice


    Cellular RNA-dependent RNA polymerases (RDRs) are fundamental components of RNA silencing in plants and many other eukaryotes. In Arabidopsis thaliana genetic studies have demonstrated that RDR2 and RDR6 are involved in the synthesis of double stranded RNA (dsRNA) from single stranded RNA (ssRNA) targeted by RNA silencing. The dsRNA is subsequently cleaved by the ribonuclease DICER-like into secondary small interfering RNAs (siRNAs) that reinforce and/or maintain the silenced state of the target RNA. Models of RNA silencing propose that RDRs could use primer-independent and primer-dependent initiation to generate dsRNA from a transcript targeted by primary siRNA or microRNA (miRNA). However, the biochemical activities of RDR proteins are still partly understood. Here, we obtained active recombinant RDR2 and RDR6 in a purified form. We demonstrate that RDR2 and RDR6 have primer-independent and primer-dependent RNA polymerase activities with different efficiencies. We further show that RDR2 and RDR6 can initiate dsRNA synthesis either by elongation of 21- to 24- nucleotides RNAs hybridized to complementary RNA template or by elongation of self-primed RNA template. These findings provide new insights into our understanding of the molecular mechanisms of RNA silencing in plants. PMID:25793874

  10. Is Radioactive Decay Really Exponential?

    CERN Document Server

    Aston, Philip J


    Radioactive decay of an unstable isotope is widely believed to be exponential. This view is supported by experiments on rapidly decaying isotopes but is more difficult to verify for slowly decaying isotopes. The decay of 14C can be calibrated over a period of 12,550 years by comparing radiocarbon dates with dates obtained from dendrochronology. It is well known that this approach shows that radiocarbon dates of over 3,000 years are in error, which is generally attributed to past variation in atmospheric levels of 14C. We note that predicted atmospheric variation (assuming exponential decay) does not agree with results from modelling, and that theoretical quantum mechanics does not predict exact exponential decay. We give mathematical arguments that non-exponential decay should be expected for slowly decaying isotopes and explore the consequences of non-exponential decay. We propose an experimental test of this prediction of non-exponential decay for 14C. If confirmed, a foundation stone of current dating meth...

  11. Analysis of MicroRNA Niches: Techniques to Measure Extracellular MicroRNA and Intracellular MicroRNA In Situ (United States)

    Parikh, Victoria N.; Chan, Stephen Y.


    MicroRNA (miRNA) are small, non-coding RNA molecules that negatively regulate gene expression and control a wide range of cellular processes. Extracellular forms of miRNA circulating in the bloodstream (circulating miRNA, c-miRNA) are of increasing interest for their potential as biomarkers and long-range physiological signaling molecules. Precise measurement of intracellular miRNA expression is possible but can be challenging, especially in the context of specialized tissue niches in vivo. The accurate measurement of extracellular miRNA presents other obstacles stemming from their low concentrations and confounding sources of intracellular miRNA that contaminate RNA extraction protocols. Here, we describe multiple methods to isolate extracellular miRNA from cell culture media, serum, and plasma in order to accurately measure their variable expression under different conditions. We additionally describe an in situ staining protocol designed not only to quantify, but also to localize miRNA in formalin-fixed paraffin-embedded (FFPE) tissue, that may prove useful in describing the action of c-miRNA before they leave their tissue of origin and after they potentially arrive at their target destination. PMID:23719949

  12. Rare B Decays

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, P.D.; /Victoria U.


    Recent results from Belle and BaBar on rare B decays involving flavor-changing neutral currents or purely leptonic final states are presented. Measurements of the CP asymmetries in B {yields} K*{gamma} and b {yields} s{gamma} are reported. Also reported are updated limits on B{sup +} {yields} K{sup +}{nu}{bar {nu}}, B{sup +} {yields} {tau}{sup +}{nu}, B{sup +} {yields} {mu}{sup +}{nu} and the recent measurement of B {yields} X{sub s}{ell}{sup +}{ell}{sup -}.

  13. The mechanism of nonsense-mediated mRNA decay


    Costa, Nuno Filipe Teixeira


    Trabalho de investigação desenvolvido no Departamento de Genética Humana do Instituto Nacional de Saúde Doutor Ricardo Jorge. [PT] A expressão genética representa uma das vias mais complexas e importantes para a célula, que culminam na síntese proteica. Como tal, quaisquer erros que possam surgir durante estes eventos podem ser rapidamente amplificados e terem um impacto severo na célula. Portanto surgiram diversos mecanismos de controlo de qualidade para assegurar a fidelidade da expr...

  14. Emerging connections between RNA and autophagy

    DEFF Research Database (Denmark)

    Frankel, Lisa B; Lubas, Michal; Lund, Anders H


    Macroautophagy/autophagy is a key catabolic process, essential for maintaining cellular homeostasis and survival through the removal and recycling of unwanted cellular material. Emerging evidence has revealed intricate connections between the RNA and autophagy research fields. While a majority...... of studies have focused on protein, lipid and carbohydrate catabolism via autophagy, accumulating data supports the view that several types of RNA and associated ribonucleoprotein complexes are specifically recruited to phagophores (precursors to autophagosomes) and subsequently degraded in the lysosome....../vacuole. Moreover, recent studies have revealed a substantial number of novel autophagy regulators with RNA-related functions, indicating roles for RNA and associated proteins not only as cargo, but also as regulators of this process. In this review, we discuss widespread evidence of RNA catabolism via autophagy...

  15. Fast production of homogeneous recombinant RNA--towards large-scale production of RNA

    NARCIS (Netherlands)

    Nelissen, F.H.; Leunissen, E.H.P.; Laar, L. van de; Tessari, M.; Heus, H.A.; Wijmenga, S.S.


    In the past decades, RNA molecules have emerged as important players in numerous cellular processes. To understand these processes at the molecular and atomic level, large amounts of homogeneous RNA are required for structural, biochemical and pharmacological investigations. Such RNAs are generally

  16. Epigenetics and Cellular Metabolism (United States)

    Xu, Wenyi; Wang, Fengzhong; Yu, Zhongsheng; Xin, Fengjiao


    Living eukaryotic systems evolve delicate cellular mechanisms for responding to various environmental signals. Among them, epigenetic machinery (DNA methylation, histone modifications, microRNAs, etc.) is the hub in transducing external stimuli into transcriptional response. Emerging evidence reveals the concept that epigenetic signatures are essential for the proper maintenance of cellular metabolism. On the other hand, the metabolite, a main environmental input, can also influence the processing of epigenetic memory. Here, we summarize the recent research progress in the epigenetic regulation of cellular metabolism and discuss how the dysfunction of epigenetic machineries influences the development of metabolic disorders such as diabetes and obesity; then, we focus on discussing the notion that manipulating metabolites, the fuel of cell metabolism, can function as a strategy for interfering epigenetic machinery and its related disease progression as well. PMID:27695375

  17. Architected Cellular Materials (United States)

    Schaedler, Tobias A.; Carter, William B.


    Additive manufacturing enables fabrication of materials with intricate cellular architecture, whereby progress in 3D printing techniques is increasing the possible configurations of voids and solids ad infinitum. Examples are microlattices with graded porosity and truss structures optimized for specific loading conditions. The cellular architecture determines the mechanical properties and density of these materials and can influence a wide range of other properties, e.g., acoustic, thermal, and biological properties. By combining optimized cellular architectures with high-performance metals and ceramics, several lightweight materials that exhibit strength and stiffness previously unachievable at low densities were recently demonstrated. This review introduces the field of architected materials; summarizes the most common fabrication methods, with an emphasis on additive manufacturing; and discusses recent progress in the development of architected materials. The review also discusses important applications, including lightweight structures, energy absorption, metamaterials, thermal management, and bioscaffolds.

  18. Cellular blue naevus

    Directory of Open Access Journals (Sweden)

    Mittal R


    Full Text Available A 31-year-old man had asymptomatic, stationary, 1.5X2 cm, shiny, smooth, dark blue nodule on dorsum of right hand since 12-14 years. In addition he had developed extensive eruption of yellow to orange papulonodular lesions on extensors of limbs and buttocks since one and half months. Investigations confirmed that yellow papules were xanthomatosis and he had associated diabetes mellitus and hyperlipidaemia. Biopsy of blue nodule confirmed the clinical diagnosis of cellular blue naevus. Cellular blue naevus is rare and its association with xanthomatosis and diabetes mellitus were interesting features of above patients which is being reported for its rarity.

  19. Novel Immune-Modulating Cellular Vaccine for Prostate Cancer Immunotherapy (United States)


    AWARD NUMBER: W81XWH-13-1-0423 TITLE: Novel Immune-Modulating Cellular Vaccine for Prostate Cancer Immunotherapy PRINCIPAL INVESTIGATOR: Smita...SUBTITLE 5a. CONTRACT NUMBER W81XWH-13-1-0423 Novel Immune-Modulating Cellular Vaccine for Prostate Cancer Immunotherapy 5b. GRANT NUMBER 5c...immune checkpoint blockade, local CTLA-4 modulation, prostate cancer immunotherapy , prostatic acid phosphatase (PAP), RNA-based vaccines 16

  20. Advances in imaging RNA in plants

    DEFF Research Database (Denmark)

    Christensen, Nynne Meyn; Oparka, Karl J.; Tilsner, Jens


    Increasing evidence shows that many RNAs are targeted to specific locations within cells, and that RNA-processing pathways occur in association with specific subcellular structures. Compartmentation of mRNA translation and RNA processing helps to assemble large RNA–protein complexes, while RNA...... targeting allows local protein synthesis and the asymmetric distribution of transcripts during cell polarisation. In plants, intercellular RNA trafficking also plays an additional role in plant development and pathogen defence. Methods that allow the visualisation of RNA sequences within a cellular context......, and preferably at subcellular resolution, can help to answer important questions in plant cell and developmental biology. Here, we summarise the approaches currently available for localising RNA in vivo and address the specific limitations inherent with plant systems....

  1. Decoherence delays false vacuum decay


    Bachlechner, Thomas C.


    We show that gravitational interactions between massless thermal modes and a nucleating Coleman-de Luccia bubble may lead to efficient decoherence and strongly suppress metastable vacuum decay for bubbles that are small compared to the Hubble radius. The vacuum decay rate including gravity and thermal photon interactions has the exponential scaling $\\Gamma\\sim\\Gamma_{CDL}^{2}$, where $\\Gamma_{CDL}$ is the Coleman-de Luccia decay rate neglecting photon interactions. For the lowest metastable i...

  2. Higgs decay to fermions (CMS)

    CERN Document Server

    Saxena, Pooja


    A search for high mass Higgs boson of the MSSM decaying into two fermions using the first 2015 data at 13 TeV is presented. The four final decay channels of mu \\tau_h, e \\tau_h, \\tau_h \\tau_h and e mu is used. The limits on production cross section times branching ratio has been set.Other results from Run1 and different searches and measurements involving Higgs decays fermions will also be reviewed.

  3. Self-assembled RNA interference microsponges for efficient siRNA delivery. (United States)

    Lee, Jong Bum; Hong, Jinkee; Bonner, Daniel K; Poon, Zhiyong; Hammond, Paula T


    The encapsulation and delivery of short interfering RNA (siRNA) has been realized using lipid nanoparticles, cationic complexes, inorganic nanoparticles, RNA nanoparticles and dendrimers. Still, the instability of RNA and the relatively ineffectual encapsulation process of siRNA remain critical issues towards the clinical translation of RNA as a therapeutic. Here we report the synthesis of a delivery vehicle that combines carrier and cargo: RNA interference (RNAi) polymers that self-assemble into nanoscale pleated sheets of hairpin RNA, which in turn form sponge-like microspheres. The RNAi-microsponges consist entirely of cleavable RNA strands, and are processed by the cell's RNA machinery to convert the stable hairpin RNA to siRNA only after cellular uptake, thus inherently providing protection for siRNA during delivery and transport to the cytoplasm. More than half a million copies of siRNA can be delivered to a cell with the uptake of a single RNAi-microsponge. The approach could lead to novel therapeutic routes for siRNA delivery.

  4. RNA structure prediction: progress and perspective

    CERN Document Server

    Shi, Ya-Zhou; Wang, Feng-Hua; Tan, Zhi-Jie


    Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction models have been developed in recent years. In this review, the progress in computational models for RNA structure prediction is introduced and the distinguishing features of many outstanding algorithms are discussed, emphasizing three dimensional (3D) structure prediction. A promising coarse-grained model for predicting RNA 3D structure, stability and salt effect is also introduced briefly. Finally, we discuss the major challenges in the RNA 3D structure modeling.

  5. miRNA Isolation from FFPET Specimen: A Technical Comparison of miRNA and Total RNA Isolation Methods. (United States)

    Nagy, Zsófia Brigitta; Wichmann, Barnabás; Kalmár, Alexandra; Barták, Barbara Kinga; Tulassay, Zsolt; Molnár, Béla


    MiRNA remain stable for detection and PCR-based amplification in FFPE tissue samples. Several miRNA extraction kits are available, however miRNA fraction, as part of total RNA can be isolated using total RNA purification methods, as well. Our primary aim was to compare four different miRNA and total RNA isolation methods from FFPE tissues. Further purposes were to evaluate quantitatively and qualitatively the yield of the isolated miRNA. MiRNAs were isolated from normal colorectal cancer FFPE specimens from the same patients. Two miRNA isolation kits (High Pure miRNA Isolation Kit, miRCURY™ RNA Isolation Kit) and two total RNA isolation kits were compared (High Pure RNA Paraffin Kit, MagNA Pure 96 Cellular RNA LV Kit). Quantity and quality were determined, expression analysis was performed by real-time PCR using qPCR Human Panel I + II (Exiqon) method detecting 742 human miRNAs in parallel. The yield of total RNA was found to be higher than miRNA purification protocols (in CRC: Ex: 0203 ± 0021 μg; HPm: 1,45 ± 0,8 μg; HPp: 21,36 ± 4,98 μg; MP: 8,6 ± 5,1 μg). MiRNAs were detected in lower relative quantity of total RNA compared to the miRNA kits. Higher number of miRNAs could be detected by the miRNA isolation kits in comparison to the total RNA isolation methods. (Ex: 497 ± 16; HPm: 542 ± 11; HPp: 332 ± 36; MP: 295 ± 74). Colon specific miRNAs (miR-21-5p;-34-5p) give satisfying results by miRNA isolation kits. Although miRNA can be detected also after total RNA isolation methods, for reliable and reproducible miRNA expression profiling the use of miRNA isolation kits are more suitable.

  6. Cellular rehabilitation of photobiomodulation (United States)

    Liu, Timon Cheng-Yi; Yuan, Jian-Qin; Wang, Yan-Fang; Xu, Xiao-Yang; Liu, Song-Hao


    Homeostasis is a term that refers to constancy in a system. A cell in homeostasis normally functions. There are two kinds of processes in the internal environment and external environment of a cell, the pathogenic processes (PP) which disrupts the old homeostasis (OH), and the sanogenetic processes (SP) which restores OH or establishes a new homeostasis (NH). Photobiomodualtion (PBM), the cell-specific effects of low intensity monochromatic light or low intensity laser irradiation (LIL) on biological systems, is a kind of modulation on PP or SP so that there is no PBM on a cell in homeostasis. There are two kinds of pathways mediating PBM, the membrane endogenetic chromophores mediating pathways which often act through reactive oxygen species, and membrane proteins mediating pathways which often enhance cellular SP so that it might be called cellular rehabilitation. The cellular rehabilitation of PBM will be discussed in this paper. It is concluded that PBM might modulate the disruption of cellular homeostasis induced by pathogenic factors such as toxin until OH has been restored or NH has been established, but can not change homeostatic processes from one to another one.

  7. Cellular Response to Irradiation

    Institute of Scientific and Technical Information of China (English)

    LIU Bo; YAN Shi-Wei


    To explore the nonlinear activities of the cellular signaling system composed of one transcriptional arm and one protein-interaction arm, we use an irradiation-response module to study the dynamics of stochastic interactions.It is shown that the oscillatory behavior could be described in a unified way when the radiation-derived signal and noise are incorporated.

  8. The emerging role of RNA editing in plasticity. (United States)

    Rosenthal, Joshua J C


    All true metazoans modify their RNAs by converting specific adenosine residues to inosine. Because inosine binds to cytosine, it is a biological mimic for guanosine. This subtle change, termed RNA editing, can have diverse effects on various RNA-mediated cellular pathways, including RNA interference, innate immunity, retrotransposon defense and messenger RNA recoding. Because RNA editing can be regulated, it is an ideal tool for increasing genetic diversity, adaptation and environmental acclimation. This review will cover the following themes related to RNA editing: (1) how it is used to modify different cellular RNAs, (2) how frequently it is used by different organisms to recode mRNA, (3) how specific recoding events regulate protein function, (4) how it is used in adaptation and (5) emerging evidence that it can be used for acclimation. Organismal biologists with an interest in adaptation and acclimation, but with little knowledge of RNA editing, are the intended audience.

  9. RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. (United States)

    Pefanis, Evangelos; Wang, Jiguang; Rothschild, Gerson; Lim, Junghyun; Kazadi, David; Sun, Jianbo; Federation, Alexander; Chao, Jaime; Elliott, Oliver; Liu, Zhi-Ping; Economides, Aris N; Bradner, James E; Rabadan, Raul; Basu, Uttiya


    We have ablated the cellular RNA degradation machinery in differentiated B cells and pluripotent embryonic stem cells (ESCs) by conditional mutagenesis of core (Exosc3) and nuclear RNase (Exosc10) components of RNA exosome and identified a vast number of long non-coding RNAs (lncRNAs) and enhancer RNAs (eRNAs) with emergent functionality. Unexpectedly, eRNA-expressing regions accumulate R-loop structures upon RNA exosome ablation, thus demonstrating the role of RNA exosome in resolving deleterious DNA/RNA hybrids arising from active enhancers. We have uncovered a distal divergent eRNA-expressing element (lncRNA-CSR) engaged in long-range DNA interactions and regulating IgH 3' regulatory region super-enhancer function. CRISPR-Cas9-mediated ablation of lncRNA-CSR transcription decreases its chromosomal looping-mediated association with the IgH 3' regulatory region super-enhancer and leads to decreased class switch recombination efficiency. We propose that the RNA exosome protects divergently transcribed lncRNA expressing enhancers by resolving deleterious transcription-coupled secondary DNA structures, while also regulating long-range super-enhancer chromosomal interactions important for cellular function.

  10. RNA recognition by a human antibody against brain cytoplasmic 200 RNA. (United States)

    Jung, Euihan; Lee, Jungmin; Hong, Hyo Jeong; Park, Insoo; Lee, Younghoon


    Diverse functional RNAs participate in a wide range of cellular processes. The RNA structure is critical for function, either on its own or as a complex form with proteins and other ligands. Therefore, analysis of the RNA conformation in cells is essential for understanding their functional mechanisms. However, no appropriate methods have been established as yet. Here, we developed an efficient strategy for panning and affinity maturation of anti-RNA human monoclonal antibodies from a naïve antigen binding fragment (Fab) combinatorial phage library. Brain cytoplasmic 200 (BC200) RNA, which is also highly expressed in some tumors, was used as an RNA antigen. We identified MabBC200-A3 as the optimal binding antibody. Mutagenesis and SELEX experiments showed that the antibody recognized a domain of BC200 in a structure- and sequence-dependent manner. Various breast cancer cell lines were further examined for BC200 RNA expression using conventional hybridization and immunoanalysis with MabBC200-A3 to see whether the antibody specifically recognizes BC200 RNA among the total purified RNAs. The amounts of antibody-recognizable BC200 RNA were consistent with hybridization signals among the cell lines. Furthermore, the antibody was able to discriminate BC200 RNA from other RNAs, supporting the utility of this antibody as a specific RNA structure-recognizing probe. Intriguingly, however, when permeabilized cells were subjected to immunoanalysis instead of purified total RNA, the amount of antibody-recognizable RNA was not correlated with the cellular level of BC200 RNA, indicating that BC200 RNA exists as two distinct forms (antibody-recognizable and nonrecognizable) in breast cancer cells and that their distribution depends on the cell type. Our results clearly demonstrate that anti-RNA antibodies provide an effective novel tool for detecting and analyzing RNA conformation.

  11. Polarization in heavy quark decays

    Energy Technology Data Exchange (ETDEWEB)

    Alimujiang, K.


    In this thesis I concentrate on the angular correlations in top quark decays and their order (NLO) QCD corrections. I also discuss the leading.order (LO) angular correlations in unpolarized and polarized hyperon decays. In the first part of the thesis I calculate the angular correlation between the top quark spin and the momentum of decay products in the rest frame decay of a polarized top quark into a charged Higgs boson and a bottom quark in Two-Higgs-Doublet-Models: t({up_arrow}) {yields} b + H{sup +}. I provide closed form formulae for the O({alpha}{sub s}) radiative corrections to the unpolarized and the polar correlation functions for m{sub b}{ne}0 and m{sub b}=0. In the second part I concentrate on the semileptonic rest frame decay of a polarized top quark into a bottom quark and a lepton pair: t({up_arrow}){yields}X{sub b}+l{sup +}+{nu}{sub l}. I present closed form expressions for the O({alpha}{sub s}) radiative corrections to the unpolarized part and the polar and azimuthal correlations for m{sub b}{ne}0 and m{sub b}=0. In the last part I turn to the angular distribution in semileptonic hyperon decays. Using the helicity method I derive complete formulas for the leading order joint angular decay distributions occurring in semileptonic hyperon decays including lepton mass and polarization effects. (orig.)

  12. CP violation in kaon decays

    CERN Document Server

    D'Ambrosio, G


    We review the Standard Model predictions of CP violation in kaon decays. We present an elementary introduction to Chiral Perturbation Theory, four--quark effective hamiltonians and the relation among them. Particular attention is devoted to $K\\to 3\\pi$, $K\\to 2\\pi \\gamma$ and $K\\to \\pi \\bar{f} f$ decays.

  13. Welding the CNGS decay tube

    CERN Multimedia

    Maximilien Brice


    3.6 km of welds were required for the 1 km long CERN Neutrinos to Gran Sasso (CNGS) decay tube, in which particles produced in the collision with a proton and a graphite target will decay into muons and muon neutrinos. Four highly skilled welders performed this delicate task.

  14. Strong decays of qqq baryons

    CERN Document Server

    Bijker, R; Leviatan, A


    We study strong decays of nonstrange baryons by making use of the algebraic approach to hadron structure. Within this framework we derive closed expressions for decay widths in an elementary-meson emission model and use these to analyze the experimental data for $N^* \\rightarrow N + \\pi$, $N^* + \\pi$, $\\Delta^* \\rightarrow \\Delta + \\pi$ and $\\Delta^* \\rightarrow \\Delta +

  15. Eukaryotic protein domains as functional units of cellular evolution

    DEFF Research Database (Denmark)

    Jin, Jing; Xie, Xueying; Chen, Chen;


    domain compositions and functional properties, termed "domain clubs," which we use to compare multiple eukaryotic proteomes. This analysis shows that different domain types can take distinct evolutionary trajectories, which correlate with the conservation, gain, expansion, or decay of particular...... of different domain types to assess the molecular compartment occupied by each domain. This reveals that specific subsets of domains demarcate particular cellular processes, such as growth factor signaling, chromatin remodeling, apoptotic and inflammatory responses, or vesicular trafficking. We suggest...

  16. Molecular and Cellular Signaling

    CERN Document Server

    Beckerman, Martin


    A small number of signaling pathways, no more than a dozen or so, form a control layer that is responsible for all signaling in and between cells of the human body. The signaling proteins belonging to the control layer determine what kinds of cells are made during development and how they function during adult life. Malfunctions in the proteins belonging to the control layer are responsible for a host of human diseases ranging from neurological disorders to cancers. Most drugs target components in the control layer, and difficulties in drug design are intimately related to the architecture of the control layer. Molecular and Cellular Signaling provides an introduction to molecular and cellular signaling in biological systems with an emphasis on the underlying physical principles. The text is aimed at upper-level undergraduates, graduate students and individuals in medicine and pharmacology interested in broadening their understanding of how cells regulate and coordinate their core activities and how diseases ...

  17. Transcriptome-wide dynamics of RNA pseudouridylation. (United States)

    Karijolich, John; Yi, Chengqi; Yu, Yi-Tao


    Pseudouridylation is the most abundant internal post-transcriptional modification of stable RNAs, with fundamental roles in the biogenesis and function of spliceosomal small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNAs). Recently, the first transcriptome-wide maps of RNA pseudouridylation were published, greatly expanding the catalogue of known pseudouridylated RNAs. These data have further implicated RNA pseudouridylation in the cellular stress response and, moreover, have established that mRNAs are also targets of pseudouridine synthases, potentially representing a novel mechanism for expanding the complexity of the cellular proteome.

  18. Environment Aware Cellular Networks

    KAUST Repository

    Ghazzai, Hakim


    The unprecedented rise of mobile user demand over the years have led to an enormous growth of the energy consumption of wireless networks as well as the greenhouse gas emissions which are estimated currently to be around 70 million tons per year. This significant growth of energy consumption impels network companies to pay huge bills which represent around half of their operating expenditures. Therefore, many service providers, including mobile operators, are looking for new and modern green solutions to help reduce their expenses as well as the level of their CO2 emissions. Base stations are the most power greedy element in cellular networks: they drain around 80% of the total network energy consumption even during low traffic periods. Thus, there is a growing need to develop more energy-efficient techniques to enhance the green performance of future 4G/5G cellular networks. Due to the problem of traffic load fluctuations in cellular networks during different periods of the day and between different areas (shopping or business districts and residential areas), the base station sleeping strategy has been one of the main popular research topics in green communications. In this presentation, we present several practical green techniques that provide significant gains for mobile operators. Indeed, combined with the base station sleeping strategy, these techniques achieve not only a minimization of the fossil fuel consumption but also an enhancement of mobile operator profits. We start with an optimized cell planning method that considers varying spatial and temporal user densities. We then use the optimal transport theory in order to define the cell boundaries such that the network total transmit power is reduced. Afterwards, we exploit the features of the modern electrical grid, the smart grid, as a new tool of power management for cellular networks and we optimize the energy procurement from multiple energy retailers characterized by different prices and pollutant

  19. Semileptonic and leptonic $B$ decays, circa 2016

    CERN Document Server

    Ricciardi, Giulia


    We summarize the status of semileptonic and leptonic $B$ decays, including $|V_{cb}|$ and $|V_{ub}|$ exclusive and inclusive determinations, decays to excited states of the charm meson spectrum and decays into $\\tau$ leptons.

  20. Engineering Structurally Interacting RNA (sxRNA) (United States)

    Doyle, Francis; Lapsia, Sameer; Spadaro, Salvatore; Wurz, Zachary E.; Bhaduri-McIntosh, Sumita; Tenenbaum, Scott A.


    RNA-based three-way junctions (3WJs) are naturally occurring structures found in many functional RNA molecules including rRNA, tRNA, snRNA and ribozymes. 3WJs are typically characterized as resulting from an RNA molecule folding back on itself in cis but could also form in trans when one RNA, for instance a microRNA binds to a second structured RNA, such as a mRNA. Trans-3WJs can influence the final shape of one or both of the RNA molecules and can thus provide a means for modulating the availability of regulatory motifs including potential protein or microRNA binding sites. Regulatory 3WJs generated in trans represent a newly identified regulatory category that we call structurally interacting RNA or sxRNA for convenience. Here we show that they can be rationally designed using familiar cis-3WJ examples as a guide. We demonstrate that an sxRNA “bait” sequence can be designed to interact with a specific microRNA “trigger” sequence, creating a regulatable RNA-binding protein motif that retains its functional activity. Further, we show that when placed downstream of a coding sequence, sxRNA can be used to switch “ON” translation of that sequence in the presence of the trigger microRNA and the amount of translation corresponded with the amount of microRNA present. PMID:28350000

  1. Screening of Modified RNA duplexes

    DEFF Research Database (Denmark)

    Schyth, Brian Dall; Bramsen, Jesper Bertram; Kjems, Jørgen

    Because of sequence specific gene targeting activity siRNAs are regarded as promising active compounds in gene medicine. But one serious problem with delivering siRNAs as treatment is the now well-established non-specific activities of some RNA duplexes. Cellular reactions towards double stranded...... RNAs include the 2´-5´ oligoadenylate synthetase system, the protein kinase R, RIG-I and Toll-like receptor activated pathways all resulting in antiviral defence mechanism. We have previously shown that antiviral innate immune reactions against double stranded RNAs could be detected in vivo as partial...... protection against a fish pathogenic virus. This protection corresponded with an interferon response in the fish. Here we use this fish model to screen siRNAs containing various chemical modifications of the RNA backbone for their antiviral activity, the overall aim being identification of an siRNA form...

  2. The nucleolus—guardian of cellular homeostasis and genome integrity. (United States)

    Grummt, Ingrid


    All organisms sense and respond to conditions that stress their homeostasis by downregulating the synthesis of rRNA and ribosome biogenesis, thus designating the nucleolus as the central hub in coordinating the cellular stress response. One of the most intriguing roles of the nucleolus, long regarded as a mere ribosome-producing factory, is its participation in monitoring cellular stress signals and transmitting them to the RNA polymerase I (Pol I) transcription machinery. As rRNA synthesis is a most energy-consuming process, switching off transcription of rRNA genes is an effective way of saving the energy required to maintain cellular homeostasis during acute stress. The Pol I transcription machinery is the key convergence point that collects and integrates a vast array of information from cellular signaling cascades to regulate ribosome production which, in turn, guides cell growth and proliferation. This review focuses on the mechanisms that link cell physiology to rDNA silencing, a prerequisite for nucleolar integrity and cell survival.

  3. Detection of the expression of cellular fetal hemoglobin gamma chain messenger RNA(HbF-γmRNA)in maternal circulation for non-invasive prenatal diagnosis%应用原位PCR检测母体循环中胎儿遗传信息HbF γ mRNA的表达

    Institute of Scientific and Technical Information of China (English)

    汤冬玲; 周新; 李艳; 郑芳; 李从荣


    目的 原位PCR是一种直接在细胞或组织材料标本上原位扩增目的DNA或RNA片段,并在原位检测扩增产物,从而进行细胞内特定核酸序列检出及定位的分子技术.胎儿血红蛋白(fetal hemoglobin,Hbr)(α2γ2)是胎儿红细胞中一种主要的胞浆蛋白,依据其特有的发育规律,拟从转录水平的角度,采用高灵敏度的反转录聚合酶链反应(RT-PCR)结合原位杂交技术,深入探讨胎儿血红蛋白γ mRNA在孕妇外周血中的表达机理.方法 取EDTA抗凝的孕妇静脉血5 ml.PBS稀释后,经淋巴细胞分离液分离获取单个核细胞层.PBS洗3次,离心后将沉淀涂片在经多聚赖氨酸处理的栽玻片上,10%缓冲中性甲醛固定,PBS洗3次,蛋白酶K消化,PBS洗3次,气干.用地高辛标记的脱氧三磷酸尿苷掺入的原位RT-PCR的方法进行检测,经25轮PCR循环后,用碱性磷酸酶标记的抗地高辛抗体检测扩增产物,显色镜检,分析36例孕妇外周血中胎儿血红蛋白γ基因的表达情况.结果 靶序列的原位RT-PCR结果显示,36例孕妇外周血中有30例标本中可定位检测到胞核、胞浆内的蓝紫色的阳性信号,符合率为83.33%,在孕妇外周血和初产妇的脐血的有核红细胞的胞浆内均可检测到DIG标记的HbF-γ mRNA蓝紫色信号,而正常人外周血则无此信号.结论 原位RT-PCR将PCR技术的高效扩增与细胞定位相结合,在细胞原位检测低拷贝mRNA,具有敏感性高、特异性强的特点,能从分子水平上定位定量检测HbF-γ mRNA的表达,该基因仅在孕妇外周血中表达,未孕女性未见其表达,提示HbF-γ mRNA可能为孕妇外周血中的一种新的靶标,为无创性产前诊断提供线索和思路.

  4. Nonleptonic Bc→VV decays (United States)

    Kar, Susmita; Dash, P. C.; Priyadarsini, M.; Naimuddin, Sk.; Barik, N.


    We study the exclusive nonleptonic Bc→VV decays, within the factorization approximation, in the framework of the relativistic independent quark model, based on a confining potential in the scalar-vector harmonic form. The weak form factors are extracted from the overlap integral of meson wave functions derived in the relativistic independent quark model. The predicted branching ratios for different Bc-meson decays are obtained in a wide range, from a tiny value of O(10-6) for Bc→D*D(s)* to a large value of 24.32% for Bc→Bs*ρ-, in general agreement with other dynamical-quark-model predictions. The decay modes Bc→Bs*ρ- and Bc→B*ρ- with high branching ratios of 24.32% and 1.73%, respectively, obtained in this model should be detectable at the LHC and Tevatron in the near future. The b→c, u induced decays are predicted predominantly in the longitudinal mode, whereas the c¯→s¯, d¯ induced decays are obtained in a slightly higher transverse mode. The CP-odd fractions (R⊥) for different decay modes are predicted and those for color-favored Bc→D*D*, D*Ds* decays indicate significant CP violation in this sector.

  5. MIRD radionuclide data and decay schemes

    CERN Document Server

    Eckerman, Keith F


    For all physicians, scientists, and physicists working in the nuclear medicine field, the MIRD: Radionuclide Data and Decay Schemes updated edition is an essential sourcebook for radiation dosimetry and understanding the properties of radionuclides. Includes CD Table of Contents Decay schemes listed by atomic number Radioactive decay processes Serial decay schemes Decay schemes and decay tables This essential reference for nuclear medicine physicians, scientists and physicists also includes a CD with tabulations of the radionuclide data necessary for dosimetry calculations.

  6. Functional characterization of the Drosophila MRP (mitochondrial RNA processing) RNA gene. (United States)

    Schneider, Mary D; Bains, Anupinder K; Rajendra, T K; Dominski, Zbigniew; Matera, A Gregory; Simmonds, Andrew J


    MRP RNA is a noncoding RNA component of RNase mitochondrial RNA processing (MRP), a multi-protein eukaryotic endoribonuclease reported to function in multiple cellular processes, including ribosomal RNA processing, mitochondrial DNA replication, and cell cycle regulation. A recent study predicted a potential Drosophila ortholog of MRP RNA (CR33682) by computer-based genome analysis. We have confirmed the expression of this gene and characterized the phenotype associated with this locus. Flies with mutations that specifically affect MRP RNA show defects in growth and development that begin in the early larval period and end in larval death during the second instar stage. We present several lines of evidence demonstrating a role for Drosophila MRP RNA in rRNA processing. The nuclear fraction of Drosophila MRP RNA localizes to the nucleolus. Further, a mutant strain shows defects in rRNA processing that include a defect in 5.8S rRNA processing, typical of MRP RNA mutants in other species, as well as defects in early stages of rRNA processing.

  7. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. (United States)

    Bosson, Andrew D; Zamudio, Jesse R; Sharp, Phillip A


    Target competition (ceRNA crosstalk) within miRNA-regulated gene networks has been proposed to influence biological systems. To assess target competition, we characterize and quantitate miRNA networks in two cell types. Argonaute iCLIP reveals that hierarchical binding of high- to low-affinity miRNA targets is a key characteristic of in vivo activity. Quantification of cellular miRNA and mRNA/ncRNA target pool levels indicates that miRNA:target pool ratios and an affinity partitioned target pool accurately predict in vivo Ago binding profiles and miRNA susceptibility to target competition. Using single-cell reporters, we directly test predictions and estimate that ?3,000 additional high-affinity target sites can affect active miRNA families with low endogenous miRNA:target ratios, such as miR-92/25. In contrast, the highly expressed miR-294 and let-7 families are not susceptible to increases of nearly 10,000 sites. These results show differential susceptibility based on endogenous miRNA:target pool ratios and provide a physiological context for ceRNA competition in vivo.

  8. Regulation of pri-miRNA processing by a long noncoding RNA transcribed from an ultraconserved region. (United States)

    Liz, Julia; Portela, Anna; Soler, Marta; Gómez, Antonio; Ling, Hui; Michlewski, Gracjan; Calin, George A; Guil, Sònia; Esteller, Manel


    Noncoding RNAs (ncRNAs) control cellular programs by affecting protein-coding genes, but evidence increasingly points to their involvement in a network of ncRNA-ncRNA interactions. Here, we show that a long ncRNA, Uc.283+A, controls pri-miRNA processing. Regulation requires complementarity between the lower stem region of the pri-miR-195 transcript and an ultraconserved sequence in Uc.283+A, which prevents pri-miRNA cleavage by Drosha. Mutation of the site in either RNA molecule uncouples regulation in vivo and in vitro. We propose a model in which lower-stem strand invasion by Uc.283+A impairs microprocessor recognition and efficient pri-miRNA cropping. In addition to identifying a case of RNA-directed regulation of miRNA biogenesis, our study reveals regulatory networks involving different ncRNA classes of importance in cancer.

  9. Composition and conservation of the mRNA-degrading machinery in bacteria

    Directory of Open Access Journals (Sweden)

    Kaberdin Vladimir R


    Full Text Available Abstract RNA synthesis and decay counteract each other and therefore inversely regulate gene expression in pro- and eukaryotic cells by controlling the steady-state level of individual transcripts. Genetic and biochemical data together with recent in depth annotation of bacterial genomes indicate that many components of the bacterial RNA decay machinery are evolutionarily conserved and that their functional analogues exist in organisms belonging to all kingdoms of life. Here we briefly review biological functions of essential enzymes, their evolutionary conservation and multienzyme complexes that are involved in mRNA decay in Escherichia coli and discuss their conservation in evolutionarily distant bacteria.

  10. Charm counting in b decays

    CERN Document Server

    Buskulic, Damir; Décamp, D; Ghez, P; Goy, C; Lees, J P; Lucotte, A; Minard, M N; Nief, J Y; Odier, P; Pietrzyk, B; Casado, M P; Chmeissani, M; Crespo, J M; Delfino, M C; Efthymiopoulos, I; Fernández, E; Fernández-Bosman, M; Carrido, L; Juste, A; Martínez, M; Orteu, S; Padilla, C; Park, I C; Pascual, A; Perlas, J A; Riu, I; Sánchez, F; Teubert, F; Colaleo, A; Creanza, D; De Palma, M; Gelao, G; Girone, M; Iaselli, Giuseppe; Maggi, G; Maggi, M; Marinelli, N; Nuzzo, S; Ranieri, A; Raso, G; Ruggieri, F; Selvaggi, G; Silvestris, L; Tempesta, P; Tricomi, A; Zito, G; Huang, X; Lin, J; Ouyang, Q; Wang, T; Xie, Y; Xu, R; Xue, S; Zhang, J; Zhang, L; Zhao, W; Alemany, R; Bazarko, A O; Bonvicini, G; Bright-Thomas, P G; Cattaneo, M; Cerutti, F; Comas, P; Coyle, P; Drevermann, H; Forty, Roger W; Frank, M; Hagelberg, R; Harvey, J; Janot, P; Jost, B; Kneringer, E; Knobloch, J; Lehraus, Ivan; Lutters, G; Martin, E B; Mato, P; Minten, Adolf G; Miquel, R; Mir, L M; Moneta, L; Oest, T; Pacheco, A; Pusztaszeri, J F; Ranjard, F; Rensing, P E; Rizzo, G; Rolandi, Luigi; Schlatter, W D; Schmelling, M; Schmitt, M; Schneider, O; Tejessy, W; Tomalin, I R; Venturi, A; Wachsmuth, H W; Wagner, A; Ajaltouni, Ziad J; Barrès, A; Boyer, C; Falvard, A; Gay, P; Guicheney, C; Henrard, P; Jousset, J; Michel, B; Monteil, S; Montret, J C; Pallin, D; Perret, P; Podlyski, F; Proriol, J; Rosnet, P; Rossignol, J M; Fearnley, Tom; Hansen, J B; Hansen, J D; Hansen, J R; Hansen, P H; Nilsson, B S; Rensch, B; Wäänänen, A; Kyriakis, A; Markou, C; Simopoulou, Errietta; Siotis, I; Vayaki, Anna; Zachariadou, K; Blondel, A; Bonneaud, G R; Brient, J C; Bourdon, P; Rougé, A; Rumpf, M; Valassi, Andrea; Verderi, M; Videau, H L; Candlin, D J; Parsons, M I; Focardi, E; Parrini, G; Corden, M; Georgiopoulos, C H; Jaffe, D E; Antonelli, A; Bencivenni, G; Bologna, G; Bossi, F; Campana, P; Capon, G; Casper, David William; Chiarella, V; Felici, G; Laurelli, P; Mannocchi, G; Murtas, F; Murtas, G P; Passalacqua, L; Pepé-Altarelli, M; Curtis, L; Dorris, S J; Halley, A W; Knowles, I G; Lynch, J G; O'Shea, V; Raine, C; Reeves, P; Scarr, J M; Smith, K; Teixeira-Dias, P; Thompson, A S; Thomson, F; Thorn, S; Turnbull, R M; Becker, U; Geweniger, C; Graefe, G; Hanke, P; Hansper, G; Hepp, V; Kluge, E E; Putzer, A; Schmidt, M; Sommer, J; Tittel, K; Werner, S; Wunsch, M; Abbaneo, D; Beuselinck, R; Binnie, David M; Cameron, W; Dornan, Peter J; Moutoussi, A; Nash, J; Sedgbeer, J K; Stacey, A M; Williams, M D; Dissertori, G; Girtler, P; Kuhn, D; Rudolph, G; Betteridge, A P; Bowdery, C K; Colrain, P; Crawford, G; Finch, A J; Foster, F; Hughes, G; Sloan, Terence; Williams, M I; Galla, A; Giehl, I; Greene, A M; Hoffmann, C; Jakobs, K; Kleinknecht, K; Quast, G; Renk, B; Rohne, E; Sander, H G; Van Gemmeren, P; Zeitnitz, C; Aubert, Jean-Jacques; Bencheikh, A M; Benchouk, C; Bonissent, A; Bujosa, G; Calvet, D; Carr, J; Diaconu, C A; Etienne, F; Konstantinidis, N P; Payre, P; Rousseau, D; Talby, M; Sadouki, A; Thulasidas, M; Trabelsi, K; Aleppo, M; Ragusa, F; Bauer, C; Berlich, R; Blum, Walter; Büscher, V; Dietl, H; Dydak, Friedrich; Ganis, G; Gotzhein, C; Kroha, H; Lütjens, G; Lutz, Gerhard; Männer, W; Moser, H G; Richter, R H; Rosado-Schlosser, A; Schael, S; Settles, Ronald; Seywerd, H C J; Saint-Denis, R; Stenzel, H; Wiedenmann, W; Wolf, G; Boucrot, J; Callot, O; Choi, Y; Cordier, A; Davier, M; Duflot, L; Grivaz, J F; Heusse, P; Höcker, A; Jacholkowska, A; Jacquet, M; Kim, D W; Le Diberder, F R; Lefrançois, J; Lutz, A M; Nikolic, I A; Park, H J; Schune, M H; Simion, S; Veillet, J J; Videau, I; Zerwas, D; Azzurri, P; Bagliesi, G; Batignani, G; Bettarini, S; Bozzi, C; Calderini, G; Carpinelli, M; Ciocci, M A; Ciulli, V; Dell'Orso, R; Fantechi, R; Ferrante, I; Foà, L; Forti, F; Giassi, A; Giorgi, M A; Gregorio, A; Ligabue, F; Lusiani, A; Marrocchesi, P S; Messineo, A; Palla, Fabrizio; Sanguinetti, G; Sciabà, A; Spagnolo, P; Steinberger, Jack; Tenchini, Roberto; Tonelli, G; Vannini, C; Verdini, P G; Blair, G A; Bryant, L M; Chambers, J T; Gao, Y; Green, M G; Medcalf, T; Perrodo, P; Strong, J A; Von Wimmersperg-Töller, J H; Botterill, David R; Clifft, R W; Edgecock, T R; Haywood, S; Maley, P; Norton, P R; Thompson, J C; Wright, A E; Bloch-Devaux, B; Colas, P; Emery, S; Kozanecki, Witold; Lançon, E; Lemaire, M C; Locci, E; Pérez, P; Rander, J; Renardy, J F; Roussarie, A; Schuller, J P; Schwindling, J; Trabelsi, A; Vallage, B; Black, S N; Dann, J H; Johnson, R P; Kim, H Y; Litke, A M; McNeil, M A; Taylor, G; Booth, C N; Boswell, R; Brew, C A J; Cartwright, S L; Combley, F; Köksal, A; Lehto, M H; Newton, W M; Reeve, J; Thompson, L F; Böhrer, A; Brandt, S; Cowan, G D; Grupen, Claus; Minguet-Rodríguez, J A; Rivera, F; Saraiva, P; Smolik, L; Stephan, F; Apollonio, M; Bosisio, L; Della Marina, R; Giannini, G; Gobbo, B; Musolino, G; Rothberg, J E; Wasserbaech, S R; Armstrong, S R; Elmer, P; Feng, Z; Ferguson, D P S; Gao, Y S; González, S; Grahl, J; Greening, T C; Hayes, O J; Hu, H; McNamara, P A; Nachtman, J M; Orejudos, W; Pan, Y B; Saadi, Y; Scott, I J; Walsh, A M; Walsh, J; Wu, X; Yamartino, J M; Zheng, M; Zobernig, G


    The inclusive production of charmed particles in Z -> bb decays has been measured from the yield of D^0, D^+, D^+_s and Lambda_{c}^+ decays in a sample of qq events with high b purity collected with the ALEPH detector from 1992 to 1995. From these measurements, adding the charmonia production rate and an estimate of the charmed strange baryon contribution, the average number of charm quarks per b decay is determined to be n_c = 1.230 \\pm 0.036 \\pm 0.038 \\pm 0.053 where the uncertainties are due to statistics, systematic effects and branching ratios, respectively.

  11. Decays of the b quark (United States)

    Thorndike, Edward H.; Poling, Ronald A.


    Recent experimental results on the decay of b-flavored hadrons are reviewed. Substantial progress has been made in the study of exclusive and inclusive B-meson decays, as well as in the theoretical understanding of these processes. The two most prominent developments are the continuing failure to observe evidence of decays of the b quark to a u quark rather than a c quark, and the surprisingly high level of B 0- overlineB0 mi xing which has recently been reported by the ARGUS collaboration. Notwithstanding these results, we conclude that the health of the Standard Model is excellent.

  12. Inconclusive Inclusive Nonleptonic $B$ Decays

    CERN Document Server

    Falk, A F; Dunietz, Isard; Falk, Adam F.; Wise, Mark B.; Dunietz, Isard


    We reconsider the conflict between recent calculations of the semileptonic branching ratio of the $B$ meson and the experimentally measured rate. Such calculations depend crucially on the application of ``local duality'' in nonleptonic decays, and we discuss the relation of this assumption to the weaker assumptions required to compute the semileptonic decay rate. We suggest that the discrepancy between theory and experiment might be due to the channel with two charm quarks in the final state, either because of a small value for $m_c$ or because of a failure of local duality. We examine the experimental consequences of such solutions for the charm multiplicity in $B$ decays.

  13. Inconclusive inclusive nonleptonic B decays

    CERN Document Server

    Falk, A F; Dunietz, Isard; Adam F Falk; Mark B Wise; Isard Dunietz


    We reconsider the conflict between recent calculations of the semileptonic branching ratio of the B meson and the experimentally measured rate. Such calculations depend crucially on the application of ``local duality'' in nonleptonic decays, and we discuss the relation of this assumption to the weaker assumptions required to compute the semileptonic decay rate. We suggest that the discrepancy between theory and experiment might be due to the channel with two charm quarks in the final state, either because of a small value for m_c or because of a failure of local duality. We examine the experimental consequences of such solutions for the charm multiplicity in B decays.

  14. Cusp effects in meson decays

    CERN Document Server

    Kubis, Bastian


    The pion mass difference generates a pronounced cusp in the pi0 pi0 invariant mass distribution of K+ --> pi0 pi0 pi+ decays. As originally pointed out by Cabibbo, an accurate measurement of the cusp may allow one to pin down the S-wave pion-pion scattering lengths to high precision. We present the non-relativistic effective field theory framework that permits to determine the structure of this cusp in a straightforward manner, including the effects of radiative corrections. Applications of the same formalism to other decay channels, in particular eta and eta' decays, are also discussed.

  15. Effects of MicroRNA-153 on the Expression of Its Target Gene Downstream Signaling Molecule GSK-3β and on the Cellular Anti-Injury Ability%MicroRNA-153对靶基因下游信号分子GSK-3β表达水平及细胞抗损伤能力的影响

    Institute of Scientific and Technical Information of China (English)

    梁春联; 朱华; 黄澜; 许艳峰; 邓巍; 马春梅; 刘颖; 秦川


    Objective Mir-153 can negatively regulate the expression of APP and APLP2 protein, the crucial Alzheimer' s disease related genes, and consequently lower the level of their intracellular degradation fragment (intracellular domains, ICDs). Considering the transcriptional activity and pro-apoptotic role of ICDs, the aim of this study was to explore the effect of mir-153 on the expression of GSK-3β, the downstream signaling molecule of the two target genes, and on the ability of cells against damage stress to further identify the role of mir-153 in Alzheimer' s disease.Methods A stably transfected cell line over-expressing mir-153 was developed and mir-153 transgenic mice were generated. Western blot was used to detect the expression of phosphorylated GSK-3β, Tau and their total protein in the cells and mice. The mir-153 stably transfected cells were treated with Aβ42peptide and H202. respectively, to determine the changes of cell viability by MTS and analyze the cell apoptosis by flow cytometry. Results The expression of phosphorylated GSK-3β and it's total protein were decreased and the phosphorylation of Tau was reduced in the mir-153 stably transfected cells. The expression of phosphorylated GSK-3β and it' s total protein were down-regulated and the level of phosphorylated Tau and its total protein were not significantly changed in the brain of mir-153 transgenic mice. Under the treatment of Aβ42 peptide and H2O2, the viability of mir-153 stably transfected cells were clearly decreased and the apoptosis level of the cells was increased. Conclusion Mir-153 can negatively regulate the expression of GSK-3β, the downstream signaling molecule of its target genes. Over-expressed mir-153 lowers the cellular anti-injury ability.%目的 mir-153可负调控阿尔茨海默病(Alzheimer'S disease,AD)主要致病基因APP及APLP2的蛋白表达,降低其胞内降解片段(intracellular domains,ICDs)的生成.因ICDs具有转录活化及促凋亡

  16. Cellular communication through light.

    Directory of Open Access Journals (Sweden)

    Daniel Fels

    Full Text Available Information transfer is a fundamental of life. A few studies have reported that cells use photons (from an endogenous source as information carriers. This study finds that cells can have an influence on other cells even when separated with a glass barrier, thereby disabling molecule diffusion through the cell-containing medium. As there is still very little known about the potential of photons for intercellular communication this study is designed to test for non-molecule-based triggering of two fundamental properties of life: cell division and energy uptake. The study was performed with a cellular organism, the ciliate Paramecium caudatum. Mutual exposure of cell populations occurred under conditions of darkness and separation with cuvettes (vials allowing photon but not molecule transfer. The cell populations were separated either with glass allowing photon transmission from 340 nm to longer waves, or quartz being transmittable from 150 nm, i.e. from UV-light to longer waves. Even through glass, the cells affected cell division and energy uptake in neighboring cell populations. Depending on the cuvette material and the number of cells involved, these effects were positive or negative. Also, while paired populations with lower growth rates grew uncorrelated, growth of the better growing populations was correlated. As there were significant differences when separating the populations with glass or quartz, it is suggested that the cell populations use two (or more frequencies for cellular information transfer, which influences at least energy uptake, cell division rate and growth correlation. Altogether the study strongly supports a cellular communication system, which is different from a molecule-receptor-based system and hints that photon-triggering is a fine tuning principle in cell chemistry.

  17. Cellular automata: structures


    Ollinger, Nicolas


    Jury : François Blanchard (Rapporteur), Marianne Delorme (Directeur), Jarkko Kari (Président), Jacques Mazoyer (Directeur), Dominique Perrin, Géraud Sénizergues (Rapporteur); Cellular automata provide a uniform framework to study an important problem of "complex systems" theory: how and why do system with a easily understandable -- local -- microscopic behavior can generate a more complicated -- global -- macroscopic behavior? Since its introduction in the 40s, a lot of work has been done to ...

  18. Engineering Cellular Metabolism

    DEFF Research Database (Denmark)

    Nielsen, Jens; Keasling, Jay


    Metabolic engineering is the science of rewiring the metabolism of cells to enhance production of native metabolites or to endow cells with the ability to produce new products. The potential applications of such efforts are wide ranging, including the generation of fuels, chemicals, foods, feeds...... of metabolic engineering and will discuss how new technologies can enable metabolic engineering to be scaled up to the industrial level, either by cutting off the lines of control for endogenous metabolism or by infiltrating the system with disruptive, heterologous pathways that overcome cellular regulation....

  19. Failover in cellular automata

    CERN Document Server

    Kumar, Shailesh


    A cellular automata (CA) configuration is constructed that exhibits emergent failover. The configuration is based on standard Game of Life rules. Gliders and glider-guns form the core messaging structure in the configuration. The blinker is represented as the basic computational unit, and it is shown how it can be recreated in case of a failure. Stateless failover using primary-backup mechanism is demonstrated. The details of the CA components used in the configuration and its working are described, and a simulation of the complete configuration is also presented.

  20. Quantitative proteomics reveals cellular targets of celastrol.

    Directory of Open Access Journals (Sweden)

    Jakob Hansen

    Full Text Available Celastrol, a natural substance isolated from plant extracts used in traditional Chinese medicine, has been extensively investigated as a possible drug for treatment of cancer, autoimmune diseases, and protein misfolding disorders. Although studies focusing on celastrol's effects in specific cellular pathways have revealed a considerable number of targets in a diverse array of in vitro models there is an essential need for investigations that can provide a global view of its effects. To assess cellular effects of celastrol and to identify target proteins as biomarkers for monitoring treatment regimes, we performed large-scale quantitative proteomics in cultured human lymphoblastoid cells, a cell type that can be readily prepared from human blood samples. Celastrol substantially modified the proteome composition and 158 of the close to 1800 proteins with robust quantitation showed at least a 1.5 fold change in protein levels. Up-regulated proteins play key roles in cytoprotection with a prominent group involved in quality control and processing of proteins traversing the endoplasmic reticulum. Increased levels of proteins essential for the cellular protection against oxidative stress including heme oxygenase 1, several peroxiredoxins and thioredoxins as well as proteins involved in the control of iron homeostasis were also observed. Specific analysis of the mitochondrial proteome strongly indicated that the mitochondrial association of certain antioxidant defense and apoptosis-regulating proteins increased in cells exposed to celastrol. Analysis of selected mRNA transcripts showed that celastrol activated several different stress response pathways and dose response studies furthermore showed that continuous exposure to sub-micromolar concentrations of celastrol is associated with reduced cellular viability and proliferation. The extensive catalog of regulated proteins presented here identifies numerous cellular effects of celastrol and constitutes

  1. Decoherence delays false vacuum decay (United States)

    Bachlechner, Thomas C.


    We show that gravitational interactions between massless thermal modes and a nucleating Coleman-de Luccia bubble may lead to efficient decoherence and strongly suppress metastable vacuum decay for bubbles that are small compared to the Hubble radius. The vacuum decay rate including gravity and thermal photon interactions has the exponential scaling \\Gamma \\sim \\Gamma _{CDL}^{2}, where ΓCDL is the Coleman-de Luccia decay rate neglecting photon interactions. For the lowest metastable initial state an efficient quantum Zeno effect occurs due to thermal radiation of temperatures as low as the de Sitter temperature. This strong decoherence effect is a consequence of gravitational interactions with light external mode. We argue that efficient decoherence does not occur for the case of Hawking-Moss decay. This observation is consistent with requirements set by Poincaré recurrence in de Sitter space.

  2. Decoherence delays false vacuum decay

    CERN Document Server

    Bachlechner, Thomas C


    We show that gravitational interactions between thermal de Sitter photons and a nucleating Coleman-de Luccia bubble lead to efficient decoherence and strongly suppress metastable vacuum decay for bubbles that are small compared to the Hubble radius. The vacuum decay rate including gravity and photon interactions has the exponential scaling $\\Gamma\\sim \\Gamma_{0}^{2}$, where $\\Gamma_{0}$ is the Coleman-de Luccia decay rate neglecting photon interactions. This strong decoherence effect is a generic consequence of gravitational interactions with light external modes. We argue that efficient decoherence does not occur for the case of Hawking-Moss decay. This observation is consistent with requirements set by Poincare recurrence in de Sitter space.

  3. Questions Students Ask: Beta Decay. (United States)

    Koss, Jordan; Hartt, Kenneth


    Answers a student's question about the emission of a positron from a nucleus. Discusses the problem from the aspects of the uncertainty principle, beta decay, the Fermi Theory, and modern physics. (YP)

  4. \\tau lepton decays and CVC


    Cherepanov, V. A.; Eidelman, S. I.


    We use experimental data on $e^+e^- \\to \\eta (\\eta^{\\prime})\\pi^+\\pi^-$ and conservation of vector current to estimate the branching fractions of $\\tau^-$ decay to $\\eta (\\eta^{\\prime})\\pi^-\\pi^0\

  5. Higher Order Top Squark Decays

    CERN Document Server

    Porod, Werner


    Within the Minimal Supersymmetric Standard Model we study the three bod= y decay of the lighter top squark into a b-quark, a W-boson and the lightes= t neutralino and compare this decay with the flavour changing two body deca= y of the lighter top squark into a c-quark and the lightest neutralino. We do = this for scenarios where two body decays at tree level are forbidden for the l= ight top squark. We give the complete analysis for the three body and compare = it with the mentioned two body decay. We discuss our numerical results in vi= ew of the upgraded Tevatron, the LHC and a 500~GeV $e^+ e^-$ Linear Collider.

  6. The Search for Proton Decay. (United States)

    Marshak, Marvin L.


    Provides the rationale for and examples of experiments designed to test the stability of protons and bound neutrons. Also considers the unification question, cosmological implications, current and future detectors, and current status of knowledge on proton decay. (JN)

  7. CP violation in sbottom decays (United States)

    Deppisch, Frank F.; Kittel, Olaf


    We study CP asymmetries in two-body decays of bottom squarks into charginos and top quarks. These asymmetries probe the SUSY CP phases of the sbottom and the chargino sector in the Minimal Supersymmetric Standard Model (MSSM). We identify the MSSM parameter space where the CP asymmetries are sizeable. As a result, potentially detectable CP asymmetries in sbottom decays are found, which motivates further detailed experimental studies for probing the SUSY CP phases at the LHC.

  8. $\\Upsilon$ production in Z Decays

    CERN Document Server

    Acciarri, M; Aguilar-Benítez, M; Ahlen, S P; Alcaraz, J; Alemanni, G; Allaby, James V; Aloisio, A; Alverson, G; Alviggi, M G; Ambrosi, G; Anderhub, H; Andreev, V P; Angelescu, T; Anselmo, F; Arefev, A; Azemoon, T; Aziz, T; Bagnaia, P; Baksay, L; Banerjee, S; Banerjee, Sw; Banicz, K; Barczyk, A; Barillère, R; Barone, L; Bartalini, P; Baschirotto, A; Basile, M; Battiston, R; Bay, A; Becattini, F; Becker, U; Behner, F; Berdugo, J; Berges, P; Bertucci, B; Betev, B L; Bhattacharya, S; Biasini, M; Biland, A; Bilei, G M; Blaising, J J; Blyth, S C; Bobbink, Gerjan J; Böck, R K; Böhm, A; Boldizsar, L; Borgia, B; Boucham, A; Bourilkov, D; Bourquin, Maurice; Boutigny, D; Braccini, S; Branson, J G; Brigljevic, V; Brock, I C; Buffini, A; Buijs, A; Burger, J D; Burger, W J; Busenitz, J K; Cai, X D; Campanelli, M; Capell, M; Cara Romeo, G; Carlino, G; Cartacci, A M; Casaus, J; Castellini, G; Cavallari, F; Cavallo, N; Cecchi, C; Cerrada-Canales, M; Cesaroni, F; Chamizo-Llatas, M; Chang, Y H; Chaturvedi, U K; Chekanov, S V; Chemarin, M; Chen, A; Chen, G; Chen, G M; Chen, H F; Chen, H S; Chen, M; Chiefari, G; Chien, C Y; Cifarelli, Luisa; Cindolo, F; Civinini, C; Clare, I; Clare, R; Cohn, H O; Coignet, G; Colijn, A P; Colino, N; Commichau, V; Costantini, S; Cotorobai, F; de la Cruz, B; Csilling, Akos; Dai, T S; D'Alessandro, R; De Asmundis, R; Degré, A; Deiters, K; Denes, P; De Notaristefani, F; DiBitonto, Daryl; Diemoz, M; Van Dierendonck, D N; Di Lodovico, F; Dionisi, C; Dittmar, Michael; Dominguez, A; Doria, A; Dorne, I; Dova, M T; Drago, E; Duchesneau, D; Duinker, P; Durán, I; Dutta, S; Easo, S; Efremenko, Yu V; El-Mamouni, H; Engler, A; Eppling, F J; Erné, F C; Ernenwein, J P; Extermann, Pierre; Fabre, M; Faccini, R; Falciano, S; Favara, A; Fay, J; Fedin, O; Felcini, Marta; Fenyi, B; Ferguson, T; Ferroni, F; Fesefeldt, H S; Fiandrini, E; Field, J H; Filthaut, Frank; Fisher, P H; Fisk, I; Forconi, G; Fredj, L; Freudenreich, Klaus; Furetta, C; Galaktionov, Yu; Ganguli, S N; García-Abia, P; Gau, S S; Gentile, S; Gerald, J; Gheordanescu, N; Giagu, S; Goldfarb, S; Goldstein, J; Gong, Z F; Gougas, Andreas; Gratta, Giorgio; Grünewald, M W; Gupta, V K; Gurtu, A; Gutay, L J; Hartmann, B; Hasan, A; Hatzifotiadou, D; Hebbeker, T; Hervé, A; Van Hoek, W C; Hofer, H; Hong, S J; Hoorani, H; Hou, S R; Hu, G; Innocente, Vincenzo; Jenkes, K; Jin, B N; Jones, L W; de Jong, P; Josa-Mutuberria, I; Kasser, A; Khan, R A; Kamrad, D; Kamyshkov, Yu A; Kapustinsky, J S; Karyotakis, Yu; Kaur, M; Kienzle-Focacci, M N; Kim, D; Kim, D H; Kim, J K; Kim, S C; Kim, Y G; Kinnison, W W; Kirkby, A; Kirkby, D; Kirkby, Jasper; Kiss, D; Kittel, E W; Klimentov, A; König, A C; Kopp, A; Korolko, I; Koutsenko, V F; Krämer, R W; Krenz, W; Kunin, A; Ladrón de Guevara, P; Landi, G; Lapoint, C; Lassila-Perini, K M; Laurikainen, P; Lebeau, M; Lebedev, A; Lebrun, P; Lecomte, P; Lecoq, P; Le Coultre, P; Leggett, C; Le Goff, J M; Leiste, R; Leonardi, E; Levchenko, P M; Li Chuan; Lin, C H; Lin, W T; Linde, Frank L; Lista, L; Liu, Z A; Lohmann, W; Longo, E; Lu, W; Lü, Y S; Lübelsmeyer, K; Luci, C; Luckey, D; Luminari, L; Lustermann, W; Ma Wen Gan; Maity, M; Majumder, G; Malgeri, L; Malinin, A; Maña, C; Mangeol, D J J; Mangla, S; Marchesini, P A; Marin, A; Martin, J P; Marzano, F; Massaro, G G G; McNally, D; Mele, S; Merola, L; Meschini, M; Metzger, W J; Von der Mey, M; Mi, Y; Mihul, A; Van Mil, A J W; Mirabelli, G; Mnich, J; Molnár, P; Monteleoni, B; Moore, R; Morganti, S; Moulik, T; Mount, R; Müller, S; Muheim, F; Muijs, A J M; Nahn, S; Napolitano, M; Nessi-Tedaldi, F; Newman, H; Niessen, T; Nippe, A; Nisati, A; Nowak, H; Oh, Yu D; Opitz, H; Organtini, G; Ostonen, R; Palomares, C; Pandoulas, D; Paoletti, S; Paolucci, P; Park, H K; Park, I H; Pascale, G; Passaleva, G; Patricelli, S; Paul, T; Pauluzzi, M; Paus, C; Pauss, Felicitas; Peach, D; Pei, Y J; Pensotti, S; Perret-Gallix, D; Petersen, B; Petrak, S; Pevsner, A; Piccolo, D; Pieri, M; Pinto, J C; Piroué, P A; Pistolesi, E; Plyaskin, V; Pohl, M; Pozhidaev, V; Postema, H; Produit, N; Prokofev, D; Prokofiev, D O; Rahal-Callot, G; Raja, N; Rancoita, P G; Rattaggi, M; Raven, G; Razis, P A; Read, K; Ren, D; Rescigno, M; Reucroft, S; Van Rhee, T; Riemann, S; Riles, K; Robohm, A; Rodin, J; Roe, B P; Romero, L; Rosier-Lees, S; Rosselet, P; Van Rossum, W; Roth, S; Rubio, Juan Antonio; Ruschmeier, D; Rykaczewski, H; Salicio, J; Sánchez, E; Sanders, M P; Sarakinos, M E; Sarkar, S; Sassowsky, M; Sauvage, G; Schäfer, C; Shchegelskii, V; Schmidt-Kärst, S; Schmitz, D; Schmitz, P; Schneegans, M; Scholz, N; Schopper, Herwig Franz; Schotanus, D J; Schwenke, J; Schwering, G; Sciacca, C; Sciarrino, D; Servoli, L; Shevchenko, S; Shivarov, N; Shoutko, V; Shukla, J; Shumilov, E; Shvorob, A V; Siedenburg, T; Son, D; Sopczak, André; Soulimov, V; Smith, B; Spillantini, P; Steuer, M; Stickland, D P; Stone, H; Stoyanov, B; Strässner, A; Strauch, K; Sudhakar, K; Sultanov, G G; Sun, L Z; Susinno, G F; Suter, H; Swain, J D; Tang, X W; Tauscher, Ludwig; Taylor, L; Ting, Samuel C C; Ting, S M; Tonutti, M; Tonwar, S C; Tóth, J; Tully, C; Tuchscherer, H; Tung, K L; Uchida, Y; Ulbricht, J; Uwer, U; Valente, E; Van de Walle, R T; Vesztergombi, G; Vetlitskii, I; Viertel, Gert M; Vivargent, M; Völkert, R; Vogel, H; Vogt, H; Vorobev, I; Vorobyov, A A; Vorvolakos, A; Wadhwa, M; Wallraff, W; Wang, J C; Wang, X L; Wang, Z M; Weber, A; Wittgenstein, F; Wu, S X; Wynhoff, S; Xu, J; Xu, Z Z; Yang, B Z; Yang, C G; Yao, X Y; Ye, J B; Yeh, S C; You, J M; Zalite, A; Zalite, Yu; Zemp, P; Zeng, Y; Zhang, Z; Zhang, Z P; Zhou, B; Zhou, Y; Zhu, G Y; Zhu, R Y; Zichichi, Antonino; Ziegler, F


    We have searched for evidence of Upsilon production in 3.5 million hadronic Z decays collected by the L3 detector at LEP in 1991-1995. No signals are observed for the decay chain Z -> Upsilon X; Upsilon -> l+l- (l= e, mu), therefore upper limits at the 95% confidence level are set on the following Z branching fractions: BR (Z -> Upsilon(1S) X) Upsilon(2S) X) Upsilon(3S) X) < 9.4 x 10**-5.

  9. Strange decays from strange resonances

    CERN Document Server

    Bijker, R


    We discuss the mass spectrum and strong decays of baryon resonances belonging to the N, Delta, Sigma, Lambda, Xi and Omega families in a collective string-like model for the nucleon. We find good overall agreement with the available data. Systematic discrepancies are found for lowlying S-wave states, in particular in the strong decays of N(1535), N(1650), Sigma(1750), Lambda(1405), Lambda(1670) and Lambda(1800).

  10. Strange decays from strange resonances

    Energy Technology Data Exchange (ETDEWEB)

    Bijker, R. [Instituto de Ciencias Nucleares, Universidad Nacional Autonoma de Mexico, A.P. 70-543, 04510 Mexico D.F. (Mexico); Leviatan, A. [Racah Institute of Physics, The Hebrew University, Jerusalem 91904 (Israel)


    We discuss the mass spectrum and strong decays of baryon resonances belonging to the N, {delta}, {sigma}, {lambda}, {xi} and {omega} families in a collective string- like model for the nucleon. We find good overall agreement with the available data. Systematic discrepancies are found for low-lying S-wave states, in particular in the strong decays of N(1535), N(1650), {sigma}(1750), {lambda}{sup *}(1405), {lambda}(1670) and {lambda}(1800). (Author)

  11. CP violation in sbottom decays

    CERN Document Server

    Deppisch, Frank F


    We study CP asymmetries in two-body decays of bottom squarks into charginos and tops. These asymmetries probe the SUSY CP phases of the sbottom and the chargino sector in the Minimal Supersymmetric Standard Model. We identify the MSSM parameter space where the CP asymmetries are sizeable, and analyze the feasibility of their observation at the LHC. As a result, potentially detectable CP asymmetries in sbottom decays are found, which motivates further detailed experimental studies for probing the SUSY CP phases.

  12. $D$ leptonic and semileptonic decays

    CERN Document Server

    Ma, Hailong


    Based on 2.92 fb$^{-1}$ data taken at the center-of-mass energy $\\sqrt s=3.773$ GeV with the BESIII detector, we report recent results on the decay constant $f_{D^+}$, the hadronic form factors, as well as the quark mixing matrix elements $|V_{cs(d)}|$, which are extracted from analyses of the leptonic decay $D^+ \\to \\mu^+\

  13. Multiboson production in W' decays

    CERN Document Server

    Aguilar-Saavedra, J A


    In models with an extra $\\text{SU}(2)_R$ gauge group and an extended scalar sector, the cascade decays of the $W'$ boson can provide various multiboson signals. In particular, diboson decays $W' \\to WZ$ can be suppressed while $W' \\to WZX$, with $X$ one of the scalars present in the model, can reach branching ratios around 4%. We discuss these multiboson signals focusing on possible interpretations of the ATLAS excess in fat jet pair production.

  14. Cyclin-dependent kinase 9 links RNA polymerase II transcription to processing of ribosomal RNA. (United States)

    Burger, Kaspar; Mühl, Bastian; Rohrmoser, Michaela; Coordes, Britta; Heidemann, Martin; Kellner, Markus; Gruber-Eber, Anita; Heissmeyer, Vigo; Strässer, Katja; Eick, Dirk


    Ribosome biogenesis is a process required for cellular growth and proliferation. Processing of ribosomal RNA (rRNA) is highly sensitive to flavopiridol, a specific inhibitor of cyclin-dependent kinase 9 (Cdk9). Cdk9 has been characterized as the catalytic subunit of the positive transcription elongation factor b (P-TEFb) of RNA polymerase II (RNAPII). Here we studied the connection between RNAPII transcription and rRNA processing. We show that inhibition of RNAPII activity by α-amanitin specifically blocks processing of rRNA. The block is characterized by accumulation of 3' extended unprocessed 47 S rRNAs and the entire inhibition of other 47 S rRNA-specific processing steps. The transcription rate of rRNA is moderately reduced after inhibition of Cdk9, suggesting that defective 3' processing of rRNA negatively feeds back on RNAPI transcription. Knockdown of Cdk9 caused a strong reduction of the levels of RNAPII-transcribed U8 small nucleolar RNA, which is essential for 3' rRNA processing in mammalian cells. Our data demonstrate a pivotal role of Cdk9 activity for coupling of RNAPII transcription with small nucleolar RNA production and rRNA processing.

  15. RNA topology remoulds electrostatic stabilization of viruses

    CERN Document Server

    Erdemci-Tandogan, Gonca; van der Schoot, Paul; Podgornik, Rudolf; Zandi, Roya


    Simple RNA viruses efficiently encapsulate their genome into a nano-sized protein shell-the capsid. Spontaneous co-assembly of the genome and the capsid proteins is driven predominantly by electrostatic interactions between the negatively charged RNA and the positively charged inner capsid wall. Using field theoretic formulation we show that the inherently branched RNA secondary structure allows viruses to {\\sl maximize} the amount of encapsulated genome and make assembly more efficient, allowing viral RNAs to out-compete cellular RNAs during replication in infected host cells.

  16. Annexin A2 binds RNA and reduces the frameshifting efficiency of infectious bronchitis virus.

    Directory of Open Access Journals (Sweden)

    Hoyun Kwak

    Full Text Available Annexin A2 (ANXA2 is a protein implicated in diverse cellular functions, including exocytosis, DNA synthesis and cell proliferation. It was recently proposed to be involved in RNA metabolism because it was shown to associate with some cellular mRNA. Here, we identified ANXA2 as a RNA binding protein (RBP that binds IBV (Infectious Bronchitis Virus pseudoknot RNA. We first confirmed the binding of ANXA2 to IBV pseudoknot RNA by ultraviolet crosslinking and showed its binding to RNA pseudoknot with ANXA2 protein in vitro and in the cells. Since the RNA pseudoknot located in the frameshifting region of IBV was used as bait for cellular RBPs, we tested whether ANXA2 could regulate the frameshfting of IBV pseudoknot RNA by dual luciferase assay. Overexpression of ANXA2 significantly reduced the frameshifting efficiency from IBV pseudoknot RNA and knockdown of the protein strikingly increased the frameshifting efficiency. The results suggest that ANXA2 is a cellular RBP that can modulate the frameshifting efficiency of viral RNA, enabling it to act as an anti-viral cellular protein, and hinting at roles in RNA metabolism for other cellular mRNAs.

  17. Micro-RNA - A potential for forensic science? (United States)

    Courts, Cornelius; Madea, Burkhard


    Micro-RNAs (miRNAs) are a class of small non-coding RNA (ncRNA) molecules with a length of 18 to 24 nucleotides which play an essential regulative role for many cellular processes. Whereas mRNA-analysis has become a well established technique in many forensic laboratories, micro-RNA has only recently been introduced to forensic science. Herein we provide a short outline of biogenesis, mode of function and regulation of miRNAs and take a look at tissue and cell specific miRNA expression. After recapitulating the role of mRNA analysis in forensic science we compare it to miRNA analysis and discuss the results of two recent studies applying miRNA analysis to a forensic research setting. We conclude that analysis of miRNA and perhaps small non-coding RNAs in general clearly has potential for forensic applications and merits attention of forensic scientists.

  18. Heavy hadron decays with conserved heavy flavour

    Energy Technology Data Exchange (ETDEWEB)

    Faller, Sven; Mannel, Thomas [Theoretische Physik 1, Naturwissenschaftlich-Technische Fakultaet, Universitaet Siegen, Walter-Flex-Strasse 3, D-57068 Siegen (Germany)


    We investigate the decays of heavy hadrons where the heavy quark acts as a spectator and the light quark decays in a weak transition. For these s → u or d → u decays we show that the decay rates can be reliably computed.

  19. Cellular image classification

    CERN Document Server

    Xu, Xiang; Lin, Feng


    This book introduces new techniques for cellular image feature extraction, pattern recognition and classification. The authors use the antinuclear antibodies (ANAs) in patient serum as the subjects and the Indirect Immunofluorescence (IIF) technique as the imaging protocol to illustrate the applications of the described methods. Throughout the book, the authors provide evaluations for the proposed methods on two publicly available human epithelial (HEp-2) cell datasets: ICPR2012 dataset from the ICPR'12 HEp-2 cell classification contest and ICIP2013 training dataset from the ICIP'13 Competition on cells classification by fluorescent image analysis. First, the reading of imaging results is significantly influenced by one’s qualification and reading systems, causing high intra- and inter-laboratory variance. The authors present a low-order LP21 fiber mode for optical single cell manipulation and imaging staining patterns of HEp-2 cells. A focused four-lobed mode distribution is stable and effective in optical...

  20. Multiuser Cellular Network

    CERN Document Server

    Bao, Yi; Chen, Ming


    Modern radio communication is faced with a problem about how to distribute restricted frequency to users in a certain space. Since our task is to minimize the number of repeaters, a natural idea is enlarging coverage area. However, coverage has restrictions. First, service area has to be divided economically as repeater's coverage is limited. In this paper, our fundamental method is to adopt seamless cellular network division. Second, underlying physics content in frequency distribution problem is interference between two close frequencies. Consequently, we choose a proper frequency width of 0.1MHz and a relevantly reliable setting to apply one frequency several times. We make a few general assumptions to simplify real situation. For instance, immobile users yield to homogenous distribution; repeaters can receive and transmit information in any given frequency in duplex operation; coverage is mainly decided by antenna height. Two models are built up to solve 1000 users and 10000 users situations respectively....

  1. Engineering Cellular Metabolism. (United States)

    Nielsen, Jens; Keasling, Jay D


    Metabolic engineering is the science of rewiring the metabolism of cells to enhance production of native metabolites or to endow cells with the ability to produce new products. The potential applications of such efforts are wide ranging, including the generation of fuels, chemicals, foods, feeds, and pharmaceuticals. However, making cells into efficient factories is challenging because cells have evolved robust metabolic networks with hard-wired, tightly regulated lines of communication between molecular pathways that resist efforts to divert resources. Here, we will review the current status and challenges of metabolic engineering and will discuss how new technologies can enable metabolic engineering to be scaled up to the industrial level, either by cutting off the lines of control for endogenous metabolism or by infiltrating the system with disruptive, heterologous pathways that overcome cellular regulation.

  2. Enhanced cellular delivery of cell-penetrating peptide-peptide nucleic acid conjugates by photochemical internalization

    DEFF Research Database (Denmark)

    Shiraishi, Takehiko; Nielsen, Peter E


    )) or tetraphenylporphyrin tetrasulfonic acid (TPPS). Cellular uptake of the PNA conjugates were evaluated by using a sensitive cellular method with HeLa pLuc705 cells based on the splicing correction of luciferase gene by targeting antisense oligonucleotides to a cryptic splice site of the mutated luciferase gene....... The cellular efficacy of CPP conjugates were evaluated by measuring luciferase activity as a result of splicing correction and was also confirmed by RT-PCR analysis of luciferase pre-mRNA....

  3. Kaons in flavour tagged B decays (United States)

    Albrecht, H.; Ehrlichmann, H.; Hamacher, T.; Hofmann, R. P.; Kirchhoff, T.; Nau, A.; Nowak, S.; Schröder, H.; Schulz, H. D.; Walter, M.; Wurth, R.; Hast, C.; Kolanoski, H.; Kosche, A.; Lange, A.; Lindner, A.; Mankel, R.; Schieber, M.; Siegmund, T.; Spaan, B.; Thurn, H.; Töpfer, D.; Wegener, D.; Bittner, M.; Eckstein, P.; Paulini, M. G.; Reim, K.; Wegener, H.; Mundt, R.; Oest, T.; Reiner, R.; Schmidt-Parzefall, W.; Funk, W.; Stiewe, J.; Werner, S.; Ehret, K.; Hofmann, W.; Hüpper, A.; Khan, S.; Knöpfle, K. T.; Seeger, M.; Spengler, J.; Britton, D. I.; Charlesworth, C. E. K.; Edwards, K. W.; Hyatt, E. R. F.; Kapitza, H.; Krieger, P.; Macfarlane, D. B.; Patel, P. M.; Prentice, J. D.; Saull, P. R. B.; Tzamariudaki, K.; van de Water, R. G.; Yoon, T.-S.; Reßing, D.; Schmidtler, M.; Schneider, M.; Schubert, K. R.; Strahl, K.; Waldi, R.; Weseler, S.; Kernel, G.; Križan, P.; Križnič, E.; Podobnik, T.; Živko, T.; Cronström, H. I.; Jönsson, L.; Balagura, V.; Belyaev, I.; Chechelnitsky, S.; Danilov, M.; Droutskoy, A.; Gershtein, Yu.; Golutvin, A.; Kostina, G.; Litvintsev, D.; Lubimov, V.; Pakhlov, P.; Ratnikov, F.; Semenov, S.; Snizhko, A.; Soloshenko, V.; Tichomirov, I.; Zaitsev, Yu.


    Using the ARGUS detector at the e + e - storage ring DORIS II, flavour-dependent kaon production in B meson decays has been studied. Using the leptons as flavour tags, it has been possible to separately measure the multiplicities of K +, K - and K {/s 0} in inclusive B decays and in semileptonic B decays. The kaon production in semileptonic B decays was further used to estimate the ratio of charmed decays over all decays, and thus also the fraction of charmless B decays.

  4. A deep phylogeny of viral and cellular right-hand polymerases. (United States)

    Černý, Jiří; Černá Bolfíková, Barbora; de A Zanotto, Paolo M; Grubhoffer, Libor; Růžek, Daniel


    Right-hand polymerases are important players in genome replication and repair in cellular organisms as well as in viruses. All right-hand polymerases are grouped into seven related protein families: viral RNA-dependent RNA polymerases, reverse transcriptases, single-subunit RNA polymerases, and DNA polymerase families A, B, D, and Y. Although the evolutionary relationships of right-hand polymerases within each family have been proposed, evolutionary relationships between families remain elusive because their sequence similarity is too low to allow classical phylogenetic analyses. The structure of viral RNA-dependent RNA polymerases recently was shown to be useful in inferring their evolution. Here, we address evolutionary relationships between right-hand polymerase families by combining sequence and structure information. We used a set of 22 viral and cellular polymerases representing all right-hand polymerase families with known protein structure. In contrast to previous studies, which focused only on the evolution of particular families, the current approach allowed us to present the first robust phylogenetic analysis unifying evolution of all right-hand polymerase families. All polymerase families branched into discrete lineages, following a fairly robust adjacency pattern. Only single-subunit RNA polymerases formed an inner group within DNA polymerase family A. RNA-dependent RNA polymerases of RNA viruses and reverse transcriptases of retroviruses formed two sister groups and were distinguishable from all other polymerases. DNA polymerases of DNA bacteriophages did not form a monophyletic group and are phylogenetically mixed with cellular DNA polymerase families A and B. Based on the highest genetic variability and structural simplicity, we assume that RNA-dependent RNA polymerases are the most ancient group of right-hand polymerases, in agreement with the RNA World hypothesis, because RNA-dependent RNA polymerases are enzymes that could serve in replication of

  5. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice


    RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...... in three dimensions (3D) and used as building blocks assembled manually during a bioinformatic interactive process. Comparing the models to the corresponding crystal structures has validated the method as being powerful to predict the RNA topology and architecture while being less accurate regarding...

  6. In-trap decay spectroscopy for {beta}{beta} decays

    Energy Technology Data Exchange (ETDEWEB)

    Brunner, Thomas


    The presented work describes the implementation of a new technique to measure electron-capture (EC) branching ratios (BRs) of intermediate nuclei in {beta}{beta} decays. This technique has been developed at TRIUMF in Vancouver, Canada. It facilitates one of TRIUMF's Ion Traps for Atomic and Nuclear science (TITAN), the Electron Beam Ion Trap (EBIT) that is used as a spectroscopy Penning trap. Radioactive ions, produced at the radioactive isotope facility ISAC, are injected and stored in the spectroscopy Penning trap while their decays are observed. A key feature of this technique is the use of a strong magnetic field, required for trapping. It radially confines electrons from {beta} decays along the trap axis while X-rays, following an EC, are emitted isotropically. This provides spatial separation of X-ray and {beta} detection with almost no {beta}-induced background at the X-ray detector, allowing weak EC branches to be measured. Furthermore, the combination of several traps allows one to isobarically clean the sample prior to the in-trap decay spectroscopy measurement. This technique has been developed to measure ECBRs of transition nuclei in {beta}{beta} decays. Detailed knowledge of these electron capture branches is crucial for a better understanding of the underlying nuclear physics in {beta}{beta} decays. These branches are typically of the order of 10{sup -5} and therefore difficult to measure. Conventional measurements suffer from isobaric contamination and a dominating {beta} background at theX-ray detector. Additionally, X-rays are attenuated by the material where the radioactive sample is implanted. To overcome these limitations, the technique of in-trap decay spectroscopy has been developed. In this work, the EBIT was connected to the TITAN beam line and has been commissioned. Using the developed beam diagnostics, ions were injected into the Penning trap and systematic studies on injection and storage optimization were performed. Furthermore, Ge

  7. Analysis of the RNA Content of the Yeast "Saccharomyces Cerevisiae" (United States)

    Deutch, Charles E.; Marshall, Pamela A.


    In this article, the authors describe an interconnected set of relatively simple laboratory experiments in which students determine the RNA content of yeast cells and use agarose gel electrophoresis to separate and analyze the major species of cellular RNA. This set of experiments focuses on RNAs from the yeast "Saccharomyces cerevisiae", a…

  8. [Ubiquitous Ribonucleic Acid:miRNA is the Ubiquitin of RNA]. (United States)

    Zheng, Xiao-fei


    Small RNAs, especially microRNAs (miRNAs),widely exist in eukaryotic cells, with their main functions being regulating gene expression and function of target molecules through the degradation of cellular target RNAs by the ribonuclease-based system. Ubiquitins and ubiquitin-like proteins are polypeptides that exist in most eukaryotic cells, and their main function is almost to regulate protein level through the degradation of cellular proteins by ubiquitin proteasome system. Small RNAs, including miRNAs,and ubiquitins or ubiquitin-like proteins have similarities in many aspects although small RNAs and ubiquitin or ubiquitin-like proteins interact different substrates respectively. Therefore, miRNAs can be defined as ubiquitra (ubiquitous ribonucleic acid, ubiquitra or uRNA), and the other small RNAs can be defined as ubiquitra-like RNA or uRNA-like RNA. The concept of ubiquitra may be applied for explaining the biological essence of small RNAs diversity.

  9. Decays of the vector glueball

    CERN Document Server

    Giacosa, Francesco; Janowski, Stanislaus


    We calculate two- and three-body decays of the (lightest) vector glueball into (pseudo)scalar, (axial-)vector, as well as pseudovector and excited vector mesons. By setting the mass of this yet hypothetical vector glueball to 3.8 GeV as predicted by Lattice QCD, many branching ratios can be computed and represent a parameter-free prediction of our approach. We find that the decay mode $\\omega\\pi\\pi$ should be one of the largest (both through the decay chain $\\mathcal{O}\\rightarrow b_{1}\\pi\\rightarrow$ $\\omega\\pi\\pi$ and through the direct coupling $\\mathcal{O}\\rightarrow\\omega\\pi\\pi$)$.$ Similarly, the (direct and indirect) decay into $\\pi KK^{\\ast}(892)$ is sizable. Moreover, the decays into $\\rho\\pi$ and $K^{\\ast}(892)K$ are, although subleading, possible and could play a role in explaining the $\\rho\\pi$ puzzle of the charmonium state $\\psi(2S)$ thank to a (small) mixing with the vector glueball. The vector glueball can be directly formed at the ongoing BESIII experiment as well as at the future PANDA exper...

  10. Time evolution of cascade decay

    CERN Document Server

    Boyanovsky, Daniel


    We study non-perturbatively the time evolution of cascade decay for generic fields $\\pi \\rightarrow \\phi_1\\phi_2\\rightarrow \\phi_2\\chi_1\\chi_2$ and obtain the time dependence of amplitudes and populations for the resonant and final states. We analyze in detail the different time scales and the manifestation of unitary time evolution in the dynamics of production and decay of resonant intermediate and final states. The probability of occupation (population) ``flows'' as a function of time from the initial to the final states. When the decay width of the parent particle $\\Gamma_\\pi$ is much larger than that of the intermediate resonant state $\\Gamma_{\\phi_1}$ there is a ``bottleneck'' in the flow, the population of resonant states builds up to a maximum at $t^* = \\ln[\\Gamma_\\pi/\\Gamma_{\\phi_1}]/(\\Gamma_\\pi-\\Gamma_{\\phi_1})$ nearly saturating unitarity and decays to the final state on the longer time scale $1/\\Gamma_{\\phi_1}$. As a consequence of the wide separation of time scales in this case the cascade decay ...

  11. RNA targeting by small molecules: Binding of protoberberine, benzophenanthridine and aristolochia alkaloids to various RNA structures

    Indian Academy of Sciences (India)

    Gopinatha Suresh Kumar


    Studies on RNA targeting by small molecules to specifically control certain cellular functions is an area of remarkable current interest. For this purpose, a basic understanding of the molecular aspects of the interaction of small molecules with various RNA structures is essential. Alkaloids are a group of natural products with potential therapeutic utility, and very recently, their interaction with many RNA structures have been reported. Especially noteworthy are the protoberberines and aristolochia alkaloids distributed widely in many botanical families. Many of the alkaloids of these group exhibit excellent binding affinity to many RNA structures that may be exploited to develop RNA targeted therapeutics. This review attempts to present the current status on the understanding of the interaction of these alkaloids with various RNA structures, mainly highlighting the biophysical aspects.

  12. Multiple functions of DDX3 RNA helicase in gene regulation, tumorigenesis, and viral infection



    The DEAD-box RNA helicase DDX3 is a multifunctional protein involved in all aspects of RNA metabolism, including transcription, splicing, mRNA nuclear export, translation, RNA decay and ribosome biogenesis. In addition, DDX3 is also implicated in cell cycle regulation, apoptosis, Wnt-β-catenin signaling, tumorigenesis, and viral infection. Notably, recent studies suggest that DDX3 is a component of anti-viral innate immune signaling pathways. Indeed, DDX3 contributes to enhance the induction ...

  13. Interplay between inflammation and cellular stress triggered by Flaviviridae viruses

    Directory of Open Access Journals (Sweden)

    Ana Luiza Chaves Valadão


    Full Text Available Flaviviruses, from Flaviviridae virus family, comprises several human pathogens, including Dengue, Zika, Yellow Fever, West Nile and Japanese Encephalitis viruses. Those are enveloped, single-stranded positive sense RNA viruses, and replicate mostly in intracellular compartments associated to endoplasmic reticulum (ER and Golgi complex. Virus replication results in abundant viral RNAs and proteins, which are recognized by cellular mechanisms evolved to prevent virus infection, resulting in inflammation and stress responses. Virus RNA molecules are sensed by Toll-like receptors (TLRs, RIG-I-like receptors (RIG-I and MDA5 and RNA-dependent protein kinases (PKR, inducing the production of inflammatory mediators and interferons. Simultaneously, the synthesis of virus RNA and proteins are distinguished in different compartments such as mitochondria, ER and cytoplasmic granules, triggering intracellular stress pathways, including oxidative stress, UPR pathway, and stress granules assembly. Here, we review the new findings that connect the inflammatory pathways to cellular stress sensors and the strategies of Flaviviridae members to counteract these cellular mechanisms and escape immune response.

  14. Interplay between Inflammation and Cellular Stress Triggered by Flaviviridae Viruses (United States)

    Valadão, Ana L. C.; Aguiar, Renato S.; de Arruda, Luciana B.


    The Flaviviridae family comprises several human pathogens, including Dengue, Zika, Yellow Fever, West Nile, Japanese Encephalitis viruses, and Hepatitis C Virus. Those are enveloped, single-stranded positive sense RNA viruses, which replicate mostly in intracellular compartments associated to endoplasmic reticulum (ER) and Golgi complex. Virus replication results in abundant viral RNAs and proteins, which are recognized by cellular mechanisms evolved to prevent virus infection, resulting in inflammation and stress responses. Virus RNA molecules are sensed by Toll-like receptors (TLRs), RIG-I-like receptors (RIG-I and MDA5) and RNA-dependent protein kinases (PKR), inducing the production of inflammatory mediators and interferons. Simultaneously, the synthesis of virus RNA and proteins are distinguished in different compartments such as mitochondria, ER and cytoplasmic granules, triggering intracellular stress pathways, including oxidative stress, unfolded protein response pathway, and stress granules assembly. Here, we review the new findings that connect the inflammatory pathways to cellular stress sensors and the strategies of Flaviviridae members to counteract these cellular mechanisms and escape immune response. PMID:27610098

  15. RNA Replicons - A New Approach for Influenza Virus Immunoprophylaxis

    Directory of Open Access Journals (Sweden)

    Gert Zimmer


    Full Text Available RNA replicons are derived from either positive- or negative-strand RNA viruses. They represent disabled virus vectors that are not only avirulent, but also unable to revert to virulence. Due to autonomous RNA replication, RNA replicons are able to drive high level, cytosolic expression of recombinant antigens stimulating both the humoral and the cellular branch of the immune system. This review provides an update on the available literature covering influenza virus vaccines based on RNA replicons. The pros and cons of these vaccine strategies will be discussed and future perspectives disclosed.

  16. The exosome and RNA quality control in the nucleus


    Vanacova, Stepanka; Stef, Richard


    To control the quality of RNA biogenesis in the nucleus, cells use sophisticated molecular machines. These machines recognize and degrade not only RNA trimmings—the leftovers of RNA processing—but also incorrectly processed RNAs that contain defects. By using this mechanism, cells ensure that only high-quality RNAs are engaged in protein synthesis and other cellular processes. The exosome—a complex of several exoribonucleolytic and RNA-binding proteins—is the central 3′-end RNA degradation an...

  17. Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes

    NARCIS (Netherlands)

    Mokry, Michal; Hatzis, Pantelis; Schuijers, Jurian; Lansu, Nico; Ruzius, Frans-Paul; Clevers, Hans; Cuppen, Edwin


    Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RN

  18. Conceptual modeling in systems biology fosters empirical findings: the mRNA lifecycle.

    Directory of Open Access Journals (Sweden)

    Dov Dori

    Full Text Available One of the main obstacles to understanding complex biological systems is the extent and rapid evolution of information, way beyond the capacity individuals to manage and comprehend. Current modeling approaches and tools lack adequate capacity to model concurrently structure and behavior of biological systems. Here we propose Object-Process Methodology (OPM, a holistic conceptual modeling paradigm, as a means to model both diagrammatically and textually biological systems formally and intuitively at any desired number of levels of detail. OPM combines objects, e.g., proteins, and processes, e.g., transcription, in a way that is simple and easily comprehensible to researchers and scholars. As a case in point, we modeled the yeast mRNA lifecycle. The mRNA lifecycle involves mRNA synthesis in the nucleus, mRNA transport to the cytoplasm, and its subsequent translation and degradation therein. Recent studies have identified specific cytoplasmic foci, termed processing bodies that contain large complexes of mRNAs and decay factors. Our OPM model of this cellular subsystem, presented here, led to the discovery of a new constituent of these complexes, the translation termination factor eRF3. Association of eRF3 with processing bodies is observed after a long-term starvation period. We suggest that OPM can eventually serve as a comprehensive evolvable model of the entire living cell system. The model would serve as a research and communication platform, highlighting unknown and uncertain aspects that can be addressed empirically and updated consequently while maintaining consistency.

  19. Tensor interactions and {tau} decays

    Energy Technology Data Exchange (ETDEWEB)

    Godina Nava, J.J.; Lopez Castro, G. [Departamento de Fisica, Cinvestav del IPN, Apartado Postal 14-740, 07000 Mexico, D.F. (Mexico)


    We study the effects of charged tensor weak currents on the strangeness-changing decays of the {tau} lepton. First, we use the available information on the {ital K}{sub {ital e}3}{sup +} form factors to obtain {ital B}({tau}{sup {minus}}{r_arrow}{ital K}{sup {minus}}{pi}{sup 0}{nu}{sub {tau}}){similar_to}10{sup {minus}4} when the {ital K}{pi} system is produced in an antisymmetric tensor configuration. Then we propose a mechanism for the direct production of the {ital K}{sub 2}{sup *}(1430) in {tau} decays. Using the current upper limit on this decay we set a bound on the symmetric tensor interactions.

  20. Charmless B decays involving baryons (United States)

    Gronau, Michael; Rosner, Jonathan L.


    Predictions are made for the fraction of B-meson decays involving specific final states of NN¯+nπ (n>=0), as functions of (a) decay dynamics, (b) models for multipion production, (c) the isospin of the final state, and (d) the ratio ||Vbu/Vbc|| of Kobayashi-Maskawa matrix elements. From recent observations of B+-->pp¯π+(+c.c.) and B0-->pp¯π+π- by the ARGUS Collaboration, it is concluded that ||Vbu/Vbc||>~0.08, similar to the ARGUS Collaboration's own estimate of 0.07. However, a more likely value for this ratio is near its present experimental upper limit. Predictions are made for further final states in NN¯+nπ and in other charmless B decays. We also comment briefly on prospects for observing CP violation in B-->NN¯+nπ.

  1. Decay spectroscopy of $^{178}$Au

    CERN Document Server

    Whitmore, B

    In this thesis, the neutron-deficient nucleus $^{178}$Au is investigated through decay spectroscopy. Si and HPGe detectors were used to analyse the decay radiation of $^{178}$Au and its daughter nuclei. Previous studies have been unable to distinguish decay radiation from different isomeric states of this nucleus. This thesis represents the first time such isomeric discrimination has been achieved, and presents tentative spin assignments of both the ground state and an isomer. The neutron-deficient gold isotopes are an area of interest for the study of shape coexistence. This is the phenomenon exhibited by nuclei able to exist at a number of close lying energy minima, each reflecting a distinct type of deformation. It is hoped that studies such as this can help identify the evolution of nuclear deformation in this region of the nuclear chart.

  2. Proton decay and grand unification

    CERN Document Server

    Senjanovic, Goran


    I review the theoretical and experimental status of proton decay theory and experiment. Regarding theory, I focus mostly, but not only, on grand unification. I discuss only the minimal, well established SU(5) and SO(10) models, both ordinary and supersymmetric. I show how the minimal realistic extensions of the original Georgi - Glashow model can lead to interesting LHC physics, and I demonstrate that the minimal supersymmetric SU(5) theory is in perfect accord with experiment. Since no universally accepted model has of yet emerged, I discuss the effective operator analysis of proton decay and some related predictions from a high scale underlying theory. A strong case is made for the improvement of experimental limits, or better the search of, two body neutron decay modes into charged kaons and charged leptons. Their discovery would necessarily imply a low energy physics since they practically vanish in any theory with a desert in energies between M_W and M_GUT.

  3. Lepton flavor violating quarkonium decays

    CERN Document Server

    Hazard, Derek E


    We argue that lepton flavor violating (LFV) decays $M \\to \\ell_1 \\overline \\ell_2$ of quarkonium states $M$ with different quantum numbers could be used to put constraints on the Wilson coefficients of effective operators describing LFV interactions at low energy scales. We note that restricted kinematics of the two-body quarkonium decays allows us to select operators with particular quantum numbers, significantly reducing the reliance on the single operator dominance assumption that is prevalent in constraining parameters of the effective LFV Lagrangian. We shall also argue that studies of radiative lepton flavor violating $M \\to \\gamma \\ell_1 \\overline \\ell_2$ decays could provide important complementary access to those effective operators.

  4. Composite Taus and Higgs Decays

    CERN Document Server

    Carmona, Adrian


    In this talk, we describe the effects of extended fermion sectors, respecting custodial symmetry, on Higgs production and decay. The resulting protection for the Z->b_L b_L and Z->\\tau_R \\tau_R decays allows for potentially interesting signals in Higgs physics, while maintaining the good agreement of the Standard Model with precision tests. The setups can be motivated as the low energy effective theories of the composite Higgs models MCHM_5 and MCHM_10, where the spectra can be identified with the light custodians present in these theories. We will show that these describe the relevant physics in the fermion sectors in a simplified and transparent way. In contrast to previous studies of composite models, the impact of a realistic lepton sector on the Higgs decays is taken into account.

  5. Overview of kaon decay physics

    CERN Document Server

    Peccei, Roberto D


    After a brief history of the insights gained from Kaon physics, the potential of Kaon decays for probing lepton number violation is discussed. Present tests of CTP and of Quantum Mechanics in the neutral Kaon sector are then reviewed and the potential of the Frascati \\Phi factory for doing incisive tests in this area is emphasized. The rest of this overview focuses on CP violating effects in the Kaon system. Although present observations of CP violation are perfectly consistent with the CKM model, we emphasize the theoretical and experimental difficulties which must be faced to establish this conclusively. In so doing, theoretical predictions and experimental prospects for detecting \\Delta S=1 CP violation through measurements of \\epsilon^\\prime/\\epsilon and of rare K decays are reviewed. The importance of looking for evidence for non-CKM CP-violating phases, through a search for a non-vanishing transverse muon polarization in K_{\\mu 3} decays, is also stressed.

  6. Hybrid Exotic Meson Decay Width

    CERN Document Server

    Cook, M S


    We present results of a decay width calculation for a hybrid exotic meson(h, JPC=1-+) in the decay channel h to pi+a1. This calculation uses quenched lattice QCD and Luescher's finite box method. Operators for the h and pi+a1 states are used in a correlation matrix which was expanded by varying the smearing and fuzzing levels at source and sink points. Scattering phase shifts for a discrete set of relative pi+a1 momenta are determined using eigenvalues of the correlation matrix and formulae derived by Luescher. The phase shift data is very sparse, but fits to a Breit-Wigner model are made, resulting in a decay width of about 80 MeV.

  7. Favipiravir (T-705), a novel viral RNA polymerase inhibitor


    Furuta, Yousuke; Gowen, Brian B.; Takahashi, Kazumi; Shiraki, Kimiyasu; Smee, Donald F.; Barnard, Dale L.


    Favipiravir (T-705; 6-fluoro-3-hydroxy-2-pyrazinecarboxamide) is an antiviral drug that selectively inhibits the RNA-dependent RNA polymerase of influenza virus. It is phosphoribosylated by cellular enzymes to its active form, favipiravir-ribofuranosyl-5′-triphosphate (RTP). Its antiviral effect is attenuated by the addition of purine nucleic acids, indicating the viral RNA polymerase mistakenly recognizes favipiravir-RTP as a purine nucleotide. Favipiravir is active against a broad range of ...

  8. Cellular bioluminescence imaging. (United States)

    Welsh, David K; Noguchi, Takako


    Bioluminescence imaging of live cells has recently been recognized as an important alternative to fluorescence imaging. Fluorescent probes are much brighter than bioluminescent probes (luciferase enzymes) and, therefore, provide much better spatial and temporal resolution and much better contrast for delineating cell structure. However, with bioluminescence imaging there is virtually no background or toxicity. As a result, bioluminescence can be superior to fluorescence for detecting and quantifying molecules and their interactions in living cells, particularly in long-term studies. Structurally diverse luciferases from beetle and marine species have been used for a wide variety of applications, including tracking cells in vivo, detecting protein-protein interactions, measuring levels of calcium and other signaling molecules, detecting protease activity, and reporting circadian clock gene expression. Such applications can be optimized by the use of brighter and variously colored luciferases, brighter microscope optics, and ultrasensitive, low-noise cameras. This article presents a review of how bioluminescence differs from fluorescence, its applications to cellular imaging, and available probes, optics, and detectors. It also gives practical suggestions for optimal bioluminescence imaging of single cells.

  9. Cellular neurothekeoma with melanocytosis. (United States)

    Wu, Ren-Chin; Hsieh, Yi-Yueh; Chang, Yi-Chin; Kuo, Tseng-Tong


    Cellular neurothekeoma (CNT) is a benign dermal tumor mainly affecting the head and neck and the upper extremities. It is characterized histologically by interconnecting fascicles of plump spindle or epithelioid cells with ample cytoplasm infiltrating in the reticular dermis. The histogenesis of CNT has been controversial, although it is generally regarded as an immature counterpart of classic/myxoid neurothekeoma, a tumor with nerve sheath differentiation. Two rare cases of CNT containing melanin-laden cells were described. Immunohistochemical study with NKI/C3, vimentin, epithelial membrane antigen, smooth muscle antigen, CD34, factor XIIIa, collagen type IV, S100 protein and HMB-45 was performed. Both cases showed typical growth pattern of CNT with interconnecting fascicles of epithelioid cells infiltrating in collagenous stroma. One of the nodules contained areas exhibiting atypical cytological features. Melanin-laden epithelioid or dendritic cells were diffusely scattered throughout one nodule, and focally present in the peripheral portion of the other nodule. Both nodules were strongly immunoreactive to NKI/C3 and vimentin, but negative to all the other markers employed. CNT harboring melanin-laden cells may pose diagnostic problems because of their close resemblance to nevomelanocytic lesions and other dermal mesenchymal tumors. These peculiar cases may also provide further clues to the histogenesis of CNT.

  10. NF90 in Posttranscriptional Gene Regulation and MicroRNA Biogenesis



    Gene expression patterns are effectively regulated by turnover and translation regulatory (TTR) RNA-binding proteins (RBPs). The TTR-RBPs control gene expression at posttranscriptional levels, such as pre-mRNA splicing, mRNA cytoplasmic export, turnover, storage, and translation. Double-stranded RNA binding proteins (DSRBPs) are known to regulate many processes of cellular metabolism, including transcriptional control, translational control, mRNA processing and localization. Nuclear factor 90...

  11. Involvement of Noxa in mediating cellular ER stress responses to lytic virus infection



    Noxa is a Bcl-2 homology domain-containing pro-apoptotic mitochondrial protein. Noxa mRNA and protein expression are upregulated by dsRNA or virus, and ectopic Noxa expression enhances cellular sensitivity to virus or dsRNA-induced apoptosis. Here we demonstrate that Noxa null baby mouse kidney (BMK) cells are deficient in normal cytopathic response to lytic viruses, and that reconstitution of the knockout cells with wild type Noxa restored normal cytopathic responses. Noxa regulation by viru...

  12. Decay of Quantum Accelerator Modes

    CERN Document Server

    Sheinman, M; Guarneri, I; Rebuzzini, L; Fishman, Shmuel; Guarneri, Italo; Rebuzzini, Laura; Sheinman, Michael


    Experimentally observable Quantum Accelerator Modes are used as a test case for the study of some general aspects of quantum decay from classical stable islands immersed in a chaotic sea. The modes are shown to correspond to metastable states, analogous to the Wannier-Stark resonances. Different regimes of tunneling, marked by different quantitative dependence of the lifetimes on 1/hbar, are identified, depending on the resolution of KAM substructures that is achieved on the scale of hbar. The theory of Resonance Assisted Tunneling introduced by Brodier, Schlagheck, and Ullmo [9], is revisited, and found to well describe decay whenever applicable.

  13. Luminescence decay of porous silicon (United States)

    Chen, X.; Uttamchandani, D.; Sander, D.; O'Donnell, K. P.


    The luminescence decay pattern of porous silicon samples prepared by electrochemical etching is characterised experimentally by a non-exponential profile, a strong dependence on temperature and an absence of spectral diffusion. We describe this luminescence as carrier-dopping-assisted recombination. Following the correlation function approach to non-dispersive transport developed by Scher and co-workers [Physics Today 41 (1991) 26], we suggest a simple derivation of analytical functions which accurately describes the anomalous luminescence decay of porous silicon, and show that this model includes exponential and Kohlrausch [Pogg. Ann. Phys. 119 (1863) 352] (stretched-exponential) relaxations as special cases.

  14. Alternative mRNA fates identified in microRNA-associated transcriptome analysis

    Directory of Open Access Journals (Sweden)

    Carroll Adam P


    Full Text Available Abstract Background MicroRNA (miRNA are small non-coding RNA molecules which function as nucleic acid-based specificity factors in the universal RNA binding complex known as the RNA induced silencing complex (RISC. In the canonical gene-silencing pathway, these activated RISC particles are associated with RNA decay and gene suppression, however, there is evidence to suggest that in some circumstances they may also stabilise their target RNA and even enhance translation. To further explore the role of miRNA in this context, we performed a genome-wide expression analysis to investigate the molecular consequences of bidirectional modulation of the disease-associated miRNAs miR-181b and miR-107 in multiple human cell lines. Results This data was subjected to pathways analysis and correlated against miRNA targets predicted through seed region homology. This revealed a large number of both conserved and non-conserved miRNA target genes, a selection of which were functionally validated through reporter gene assays. Contrary to expectation we also identified a significant proportion of predicted target genes with both conserved and non-conserved recognition elements that were positively correlated with the modulated miRNA. Finally, a large proportion of miR-181b associated genes devoid of the corresponding miRNA recognition element, were enriched with binding motifs for the E2F1 transcription factor, which is encoded by a miR-181b target gene. Conclusions These findings suggest that miRNA regulate target genes directly through interactions with both conserved and non-conserved target recognition elements, and can lead to both a decrease and increase in transcript abundance. They also multiply their influence through interaction with transcription factor genes exemplified by the observed miR-181b/E2F1 relationship.

  15. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Xiaofei [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036 (China); Deng, Ping; Cui, Hongguang [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); Wang, Aiming, E-mail: [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada)


    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  16. Human Enterovirus Nonstructural Protein 2CATPase Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone.

    Directory of Open Access Journals (Sweden)

    Hongjie Xia


    Full Text Available RNA helicases and chaperones are the two major classes of RNA remodeling proteins, which function to remodel RNA structures and/or RNA-protein interactions, and are required for all aspects of RNA metabolism. Although some virus-encoded RNA helicases/chaperones have been predicted or identified, their RNA remodeling activities in vitro and functions in the viral life cycle remain largely elusive. Enteroviruses are a large group of positive-stranded RNA viruses in the Picornaviridae family, which includes numerous important human pathogens. Herein, we report that the nonstructural protein 2CATPase of enterovirus 71 (EV71, which is the major causative pathogen of hand-foot-and-mouth disease and has been regarded as the most important neurotropic enterovirus after poliovirus eradication, functions not only as an RNA helicase that 3'-to-5' unwinds RNA helices in an adenosine triphosphate (ATP-dependent manner, but also as an RNA chaperone that destabilizes helices bidirectionally and facilitates strand annealing and complex RNA structure formation independently of ATP. We also determined that the helicase activity is based on the EV71 2CATPase middle domain, whereas the C-terminus is indispensable for its RNA chaperoning activity. By promoting RNA template recycling, 2CATPase facilitated EV71 RNA synthesis in vitro; when 2CATPase helicase activity was impaired, EV71 RNA replication and virion production were mostly abolished in cells, indicating that 2CATPase-mediated RNA remodeling plays a critical role in the enteroviral life cycle. Furthermore, the RNA helicase and chaperoning activities of 2CATPase are also conserved in coxsackie A virus 16 (CAV16, another important enterovirus. Altogether, our findings are the first to demonstrate the RNA helicase and chaperoning activities associated with enterovirus 2CATPase, and our study provides both in vitro and cellular evidence for their potential roles during viral RNA replication. These findings

  17. Phenotypic MicroRNA Microarrays



    Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the bio...

  18. Cellular and Matrix Contributions to Tissue Construct Stiffness Increase with Cellular Concentration (United States)

    Marquez, J. Pablo; Genin, Guy M.; Pryse, Kenneth M.; Elson, Elliot L.


    The mechanics of bio-artificial tissue constructs result from active and passive contributions of cells and extracellular matrix (ECM). We delineated these for a fibroblast-populated matrix (FPM) consisting of chick embryo fibroblast cells in a type I collagen ECM through mechanical testing, mechanical modeling, and selective biochemical elimination of tissue components. From a series of relaxation tests, we found that contributions to overall tissue mechanics from both cells and ECM increase exponentially with the cell concentration. The force responses in these relaxation tests exhibited a logarithmic decay over the 3600 second test duration. The amplitudes of these responses were nearly linear with the amplitude of the applied stretch. The active component of cellular forces rose dramatically for FPMs containing higher cell concentrations. PMID:16874557

  19. Direct translocation as major cellular uptake for CADY self-assembling peptide-based nanoparticles.

    Directory of Open Access Journals (Sweden)

    Anna Rydström

    Full Text Available Cell penetrating peptides constitute a potent approach to overcome the limitations of in vivo siRNA delivery. We recently proposed a peptide-based nanoparticle system, CADY, for efficient delivery of siRNA into numerous cell lines. CADY is a secondary amphipathic peptide that forms stable complexes with siRNA thereby improving both their cellular uptake and biological response. With the aim of understanding the cellular uptake mechanism of CADY:siRNA complexes, we have combined biochemical, confocal and electron microscopy approaches. In the present work, we provide evidence that the major route for CADY:siRNA cellular uptake involves direct translocation through the membrane but not the endosomal pathway. We have demonstrated that CADY:siRNA complexes do not colocalize with most endosomal markers and remain fully active in the presence of inhibitors of the endosomal pathway. Moreover, neither electrostatic interactions with cell surface heparan sulphates nor membrane potential are essential for CADY:siRNA cell entry. In contrast, we have shown that CADY:siRNA complexes clearly induce a transient cell membrane permeabilization, which is rapidly restored by cell membrane fluidity. Therefore, we propose that direct translocation is the major gate for cell entry of CADY:siRNA complexes. Membrane perturbation and uptake are driven mainly by the ability of CADY to interact with phospholipids within the cell membrane, followed by rapid localization of the complex in the cytoplasm, without affecting cell integrity or viability.

  20. Inhibition of hepatitis C virus RNA replication by short hairpin RNA synthesized by T7 RNA polymerase in hepatitis C virus subgenomic replicons. (United States)

    Hamazaki, Hiroyuki; Ujino, Saneyuki; Miyano-Kurosaki, Naoko; Shimotohno, Kunitada; Takaku, Hiroshi


    RNA interference (RNAi) is a cellular process that induces gene silencing by which small duplexes of RNA specifically target a homologous sequence for cleavage by cellular ribonucleases. Here, to test the RNAi method for blocking hepatitis C virus (HCV) RNA replication, we created four short hairpin RNAs (shRNAs) targeting the HCV internal ribosome entry site/Core gene transcript using T7 RNA polymerase. shRNA suppressed the replication of HCV RNA in the HCV replicon. On the other hand, short interfering RNAs synthesized using the T7 RNA polymerase system trigger a potent induction of interferon-alpha and -beta in a variety of cells. We examined whether the shRNAs synthesized using the T7 RNA polymerase system activated double-stranded RNA-dependent protein kinase, 2'-5' oligoadenylate synthetase, or interferon-regulatory factor-3. Our results demonstrated that the T7-transcribed shRNA did not activate these proteins in Huh-7 cells and the HCV replicon. These shRNAs are a promising new strategy for anti-HCV gene therapeutics.

  1. Free fall and cellular automata

    Directory of Open Access Journals (Sweden)

    Pablo Arrighi


    Full Text Available Three reasonable hypotheses lead to the thesis that physical phenomena can be described and simulated with cellular automata. In this work, we attempt to describe the motion of a particle upon which a constant force is applied, with a cellular automaton, in Newtonian physics, in Special Relativity, and in General Relativity. The results are very different for these three theories.

  2. About Strongly Universal Cellular Automata

    Directory of Open Access Journals (Sweden)

    Maurice Margenstern


    Full Text Available In this paper, we construct a strongly universal cellular automaton on the line with 11 states and the standard neighbourhood. We embed this construction into several tilings of the hyperbolic plane and of the hyperbolic 3D space giving rise to strongly universal cellular automata with 10 states.

  3. Reactive Programming of Cellular Automata


    Boussinot, Frédéric


    Implementation of cellular automata using reactive programming gives a way to code cell behaviors in an abstract and modular way. Multiprocessing also becomes possible. The paper describes the implementation of cellular automata with the reactive programming language LOFT, a thread-based extension of C. Self replicating loops considered in artificial life are coded to show the interest of the approach.

  4. Superheavy elements and decay properties

    Indian Academy of Sciences (India)

    K P Santhosh


    The decay properties of the isotopes of = 115, 117, 118 and 119 have been extensively investigated, focussing on the newly synthesized isotopes within the Coulomb and proximity potential model for deformed nuclei (CPPMDN). The half-lives have also been evaluated using the Viola–Seaborg systematic (VSS) and the analytical formulae of Royer and it can be seen that our calculated values match well with these theoretical values. The mode of decay of these isotopes has also been studied by calculating the spontaneous fission half-lives. Thus, we have predicted 4 chains from 287115, 3 chains from 288115, 3 chains from 293117, 4 chains from 294117 and 3 chains from 294118 and, it can be seen that our predictions on the decay chains also match well with the experimental observations. The study on = 119 has predicted six consistent chains from 292−295119, 5 chains from 296119, 4 chains from 297119 and 3 chains from 298,299119. Thus, through our study on isotopes of = 115, 117, 118 and 119 superheavy nuclei, we could predict the range of isotopes that may be detectable using decay and we hope that the findings on the isotopes of = 119 will provide a new guide for future experiments.

  5. Hadronic B Decays in PQCD

    CERN Document Server

    Mishima, S


    I review recent progress on exclusive hadronic B meson decays in the perturbative QCD approach, with focus on puzzles in the branching ratios and the CP asymmetries of the B -> pi K and B -> pi pi modes, and polarization fractions in B -> VV modes.

  6. Rare decays of b hadrons

    CERN Document Server

    Koppenburg, Patrick; Smizanska, Maria


    Rare decays of b hadrons provide a powerful way of identifying contributions from physics beyond the Standard Model, in particular from new hypothetical particles too heavy to be produced at colliders. The most relevant experimental measurements are reviewed and possible interpretations are briefly discussed.

  7. Higgs Decay to Two Photons


    Marciano, William J.; Zhang, Cen; Willenbrock, Scott


    The amplitude for Higgs decay to two photons is calculated in renormalizable and unitary gauges using dimensional regularization at intermediate steps. The result is finite, gauge independent, and in agreement with previously published results. The large Higgs mass limit is examined using the Goldstone-boson equivalence theorem as a check on the use of dimensional regularization and to explain the absence of decoupling.

  8. Rare B decays at CDF

    Energy Technology Data Exchange (ETDEWEB)

    Farrington, Sinead M.; /Liverpool U.


    The confidence level limits of the CDF search for the B{sub s}{sup 0} and B{sub d}{sup 0} {yields} {mu}{sup +}{mu}{sup -} rare decays and the branching ratio measurement of B{sub s}{sup 0} {yields} D{sub s}{sup +} D{sub s}{sup -} are presented.

  9. Salt decay of Morley limestone

    NARCIS (Netherlands)

    Nijland, T.G.; Van Hees, R.P.J.


    Salt weathering is one of the main causes of decay of natural stone, and by consequence a major problem to the conservation of cultural heritage. In the present case, the performance of Morley limestone from the Département Meuse, France, as a replacement stone under saltloaded conditions is evaluat

  10. Beta decay of Cu-56

    NARCIS (Netherlands)

    Borcea, R; Aysto, J; Caurier, E; Dendooven, P; Doring, J; Gierlik, M; Gorska, M; Grawe, H; Hellstrom, M; Janas, Z; Jokinen, A; Karny, M; Kirchner, R; La Commara, M; Langanke, K; Martinez-Pinedo, G; Mayet, P; Nieminen, A; Nowacki, F; Penttila, H; Plochocki, A; Rejmund, M; Roeckl, E; Schlegel, C; Schmidt, K; Schwengner, R; Sawicka, M


    The proton-rich isotope Cu-56 was produced at the GSI On-Line Mass Separator by means of the Si-28(S-32, p3n) fusion-evaporation reaction. Its beta -decay properties were studied by detecting beta -delayed gamma rays and protons. A half-Life of 93 +/- 3 ms was determined for Cu-56. Compared to the p

  11. Decay Constants of Vector Mesons

    Institute of Scientific and Technical Information of China (English)

    LI Heng-Mei; WAN Shao-Long


    @@ The light vector mesons are studied within the framework of the Bethe-Salpeter equation with the vector-vectortype flat-bottom potential The Bethe-Salpeter wavefunctions and the decay constants of the vector mesons are obtained. All the obtained results, fρ, fφ, and fΚ* , are in agreement with the experimental values, respectively.

  12. MIMO Communication for Cellular Networks

    CERN Document Server

    Huang, Howard; Venkatesan, Sivarama


    As the theoretical foundations of multiple-antenna techniques evolve and as these multiple-input multiple-output (MIMO) techniques become essential for providing high data rates in wireless systems, there is a growing need to understand the performance limits of MIMO in practical networks. To address this need, MIMO Communication for Cellular Networks presents a systematic description of MIMO technology classes and a framework for MIMO system design that takes into account the essential physical-layer features of practical cellular networks. In contrast to works that focus on the theoretical performance of abstract MIMO channels, MIMO Communication for Cellular Networks emphasizes the practical performance of realistic MIMO systems. A unified set of system simulation results highlights relative performance gains of different MIMO techniques and provides insights into how best to use multiple antennas in cellular networks under various conditions. MIMO Communication for Cellular Networks describes single-user,...

  13. Extracellular RNA Communication (ExRNA) (United States)

    Federal Laboratory Consortium — Until recently, scientists believed RNA worked mostly inside the cell that produced it. Some types of RNA help translate genes into proteins that are necessary for...

  14. RNA chaperones encoded by RNA viruses

    Institute of Scientific and Technical Information of China (English)

    Jie Yang; Hongjie Xia; Qi Qian; Xi Zhou


    RNAs are functionally diverse macromolecules whose proper functions rely strictly upon their correct tertiary structures. However, because of their high structural flexibility, correct folding of RNAs is challenging and slow. Therefore, cells and viruses encode a variety of RNA remodeling proteins, including helicases and RNA chaperones. In RNA viruses, these proteins are believed to play pivotal roles in all the processes involving viral RNAs during the life cycle. RNA helicases have been studied extensively for decades, whereas RNA chaperones, particularly virus-encoded RNA chaperones, are often overlooked. This review describes the activities of RNA chaperones encoded by RNA viruses, particularly the ones identified and characterized in recent years, and the functions of these proteins in different steps of viral life cycles, and presents an overview of this unique group of proteins.

  15. NeuN/Rbfox3 nuclear and cytoplasmic isoforms differentially regulate alternative splicing and nonsense-mediated decay of Rbfox2.

    Directory of Open Access Journals (Sweden)

    B Kate Dredge

    Full Text Available Anti-NeuN (Neuronal Nuclei is a monoclonal antibody used extensively to specifically detect post-mitotic neurons. Anti-NeuN reactivity is predominantly nuclear; by western it detects multiple bands ranging in molecular weight from 45 kDa to >75 kDa. Expression screening putatively identified R3hdm2 as NeuN; however immunoprecipitation and mass spectrometry of the two major NeuN species at 45-50 kDa identified both as the RNA binding protein Rbfox3 (a member of the Fox family of alternative splicing factors, confirming and extending the identification of the 45 kDa band as Rbfox3 by Kim et al. Mapping of the anti-NeuN reactive epitopes in both R3hdm2 and Rbfox3 reveals a common proline- and glutamine-rich domain that lies at the N-terminus of the Rbfox3 protein. Our data suggests that alternative splicing of the Rbfox3 pre-mRNA itself leads to the production of four protein isoforms that migrate in the 45-50 kDa range, and that one of these splicing choices regulates Rbfox3/NeuN sub-cellular steady-state distribution, through the addition or removal of a short C-terminal extension containing the second half of a bipartite hydrophobic proline-tyrosine nuclear localization signal. Rbfox3 regulates alternative splicing of the Rbfox2 pre-mRNA, producing a message encoding a dominant negative form of the Rbfox2 protein. We show here that nuclear Rbfox3 isoforms can also enhance the inclusion of cryptic exons in the Rbfox2 mRNA, resulting in nonsense-mediated decay of the message, thereby contributing to the negative regulation of Rbfox2 by Rbfox3 through a novel mechanism.

  16. Cellular Deconstruction: Finding Meaning in Individual Cell Variation. (United States)

    Eberwine, James; Kim, Junhyong


    The advent of single cell transcriptome analysis has permitted the discovery of cell-to-cell variation in transcriptome expression of even presumptively identical cells. We hypothesize that this variability reflects a many-to-one relation between transcriptome states and the phenotype of a cell. In this relation, the molecular ratios of the subsets of RNA are determined by the stoichiometric constraints of the cell systems, which underdetermine the transcriptome state. Furthermore, the variability is, in part, induced by the tissue context and is important for system-level function. This theory is analogous to theories of literary deconstruction, where multiple 'signifiers' work in opposition to one another to create meaning. By analogy, transcriptome phenotypes should be defined as subsets of RNAs comprising selected RNA systems where the system-associated RNAs are balanced with each other to produce the associated cellular function. This idea provides a framework for understanding cellular heterogeneity in phenotypic responses to variant conditions, such as disease challenge.

  17. Modeling In Vitro Cellular Responses to Silver Nanoparticles

    Directory of Open Access Journals (Sweden)

    Dwaipayan Mukherjee


    Full Text Available Engineered nanoparticles (NPs have been widely demonstrated to induce toxic effects to various cell types. In vitro cell exposure systems have high potential for reliable, high throughput screening of nanoparticle toxicity, allowing focusing on particular pathways while excluding unwanted effects due to other cells or tissue dosimetry. The work presented here involves a detailed biologically based computational model of cellular interactions with NPs; it utilizes measurements performed in human cell culture systems in vitro, to develop a mechanistic mathematical model that can support analysis and prediction of in vivo effects of NPs. The model considers basic cellular mechanisms including proliferation, apoptosis, and production of cytokines in response to NPs. This new model is implemented for macrophages and parameterized using in vitro measurements of changes in cellular viability and mRNA levels of cytokines: TNF, IL-1b, IL-6, IL-8, and IL-10. The model includes in vitro cellular dosimetry due to nanoparticle transport and transformation. Furthermore, the model developed here optimizes the essential cellular parameters based on in vitro measurements, and provides a “stepping stone” for the development of more advanced in vivo models that will incorporate additional cellular and NP interactions.

  18. Resistance to PVY using siRNA in transgenic potatoes(Abstract) (United States)

    Virus resistance by expression of viral coat protein (CP) is well documented. The role of small RNAs (sRNA) in virus suppression has only more recently begun to be elucidated. Many sRNAs are involved in gene regulation and referred to as micro RNA (miRNA). Taking advantage of the cellular mechanism ...

  19. Structures of two exonucleases involved in controlled RNA turnover in yeast

    DEFF Research Database (Denmark)

    Jonstrup, Anette Thyssen; Midtgaard, Søren Fuglsang; Van, Lan Bich;

    The precise regulation of the cellular levels of different RNA species is important for cell function as well as securing the integrity of each individual RNA. Central to both these processes is the degradation of RNA, either as a means of decreasing the level of particular RNAs or as a way to ge...

  20. Albumin pre-coating enhances intracellular siRNA delivery of multifunctional amphiphile/siRNA nanoparticles

    Directory of Open Access Journals (Sweden)

    Kummitha CM


    Full Text Available China M Kummitha, Anthony S Malamas, Zheng-Rong LuDepartment of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USAAbstract: Nonspecific association of serum molecules with short-interfering RNA (siRNA nanoparticles can change their physiochemical characteristics, and results in reduced cellular uptake in the target tissue during the systemic siRNA delivery process. Serum albumin is the most abundant protein in the body and has been used to modify the surface of nanoparticles, to inhibit association of other serum molecules. Here, we hypothesized that surface modification of lipid-based nanoparticular siRNA delivery systems with albumin could prevent their interaction with serum proteins, and improve intracellular uptake. In this study, we investigated the influence of albumin on the stability and intracellular siRNA delivery of the targeted siRNA nanoparticles of a polymerizable and pH-sensitive multifunctional surfactant N-(1-aminoethyliminobis[N-(oleoylcysteinylhistinyl-1-aminoethylpropionamide] (EHCO in serum. Serum resulted in a significant increase in the size of targeted EHCO/siRNA nanoparticles and inhibited cellular uptake of the nanoparticles. Coating of targeted EHCO/siRNA nanoparticles with bovine serum albumin at 9.4 µM prior to cell transfection improved cellular uptake and gene silencing efficacy of EHCO/siRNA targeted nanoparticles in serum-containing media, as compared with the uncoated nanoparticles. At a proper concentration, albumin has the potential to minimize interactions of serum proteins with siRNA nanoparticles for effective systemic in vivo siRNA delivery.Keywords: multifunctional, lipid nanoparticles, RNA interference, pH-sensitive amphiphile, siRNA

  1. Neutron Beta Decay Studies with Nab

    CERN Document Server

    Baeßler, S; Alonzi, L P; Balascuta, S; Barrón-Palos, L; Bowman, J D; Bychkov, M A; Byrne, J; Calarco, J R; Chupp, T; Vianciolo, T V; Crawford, C; Frlež, E; Gericke, M T; Glück, F; Greene, G L; Grzywacz, R K; Gudkov, V; Harrison, D; Hersman, F W; Ito, T; Makela, M; Martin, J; McGaughey, P L; McGovern, S; Page, S; Penttilä, S I; Počanić, D; Rykaczewski, K P; Salas-Bacci, A; Tompkins, Z; Wagner, D; Wilburn, W S; Young, A R


    Precision measurements in neutron beta decay serve to determine the coupling constants of beta decay and allow for several stringent tests of the standard model. This paper discusses the design and the expected performance of the Nab spectrometer.

  2. Cellular Plasticity and Heterogeneity of EGFR Mutant Lung Cancer (United States)


    transition occurs is unknown. In this proposal, we are studying the molecular and cellular mechanisms that cause this transition to occur in...weekly cancer center and pathology grand rounds amongst others. d. How were the results disseminated to communities of interest? Nothing to report...process and obtain high quality data recently. Therefore, we will be performing RNA sequencing on samples of EGFR mutant SCLC in the next couple of

  3. Long-term RNA persistence in postmortem contexts

    DEFF Research Database (Denmark)

    Fordyce, Sarah Louise; Kampmann, Marie-Louise; van Doorn, Nienke L


    Ribonucleic acids (RNA) are generally considered fragile molecules that are readily degraded. However, there is growing documentation of long-term (from days to centuries) RNA persistence in a variety of contexts and tissue types, and as such a number of academic disciplines are beginning...... to exploit degraded RNA. While the reasons for its survival are not fully understood, there are several plausible mechanisms that would safeguard this molecule against degradation. However, after examining the literature available on the postmortem instability and decay mechanisms of RNA, it has become clear...... that limited experimental studies and no reviews offer an overview of these mechanisms. Hence in this review we outline molecular reasons for RNA surviving long-term postmortem, and provide specific examples of RNA survival in forensic, archival and archaeological contexts. A better understanding...

  4. Rhabdomyosarcoma: Advances in Molecular and Cellular Biology

    Directory of Open Access Journals (Sweden)

    Xin Sun


    Full Text Available Rhabdomyosarcoma (RMS is the most common soft tissue malignancy in childhood and adolescence. The two major histological subtypes of RMS are alveolar RMS, driven by the fusion protein PAX3-FKHR or PAX7-FKHR, and embryonic RMS, which is usually genetically heterogeneous. The prognosis of RMS has improved in the past several decades due to multidisciplinary care. However, in recent years, the treatment of patients with metastatic or refractory RMS has reached a plateau. Thus, to improve the survival rate of RMS patients and their overall well-being, further understanding of the molecular and cellular biology of RMS and identification of novel therapeutic targets are imperative. In this review, we describe the most recent discoveries in the molecular and cellular biology of RMS, including alterations in oncogenic pathways, miRNA (miR, in vivo models, stem cells, and important signal transduction cascades implicated in the development and progression of RMS. Furthermore, we discuss novel potential targeted therapies that may improve the current treatment of RMS.

  5. RNA interference in neuroscience: progress and challenges. (United States)

    Miller, Victor M; Paulson, Henry L; Gonzalez-Alegre, Pedro


    1.RNA interference (RNAi) is a recently discovered biological pathway that mediates post-transcriptional gene silencing. The process of RNAi is orchestrated by an increasingly well-understood cellular machinery. 2. The common entry point for both natural and engineered RNAi are double stranded RNA molecules known as short interfering RNAs (siRNAs), that mediate the sequence-specific identification and degradation of the targeted messenger RNA (mRNA). The study and manipulation of these siRNAs has recently revolutionized biomedical research. 3. In this review, we first provide a brief overview of the process of RNAi, focusing on its potential role in brain function and involvement in neurological disease. We then describe the methods developed to manipulate RNAi in the laboratory and its applications to neuroscience. Finally, we focus on the potential therapeutic application of RNAi to neurological disease.

  6. Search for hadronic b yields u decays

    Energy Technology Data Exchange (ETDEWEB)

    Albrecht, H.; Glaeser, R.; Harder, G.; Krueger, A.; Nilsson, A.W.; Nippe, A.; Oest, T.; Reidenbach, M.; Schaefer, M.; Schmidt-Parzefall, W.; Schroeder, H.; Schulz, H.D.; Sefkow, F.; Wurth, R. (Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany, F.R.)); Appuhn, R.D.; Drescher, A.; Hast, C.; Herrera, G.; Kolanoski, H.; Lange, A.; Lindner, A.; Mankel, R.; Scheck, H.; Schweda, G.; Spaan, B.; Walther, A.; Wegener, D. (Dortmund Univ. (Germany, F.R.). Inst. fuer Physik); Paulini, M.; Reim, K.; Volland, U.; Wegener, H. (Erlangen-Nuernberg Univ., Erlangen (Germany, F.R.). Physikalisches Inst.); Funk, W.; Stiewe, J.; Werner, S. (Heidelberg Univ. (Germany, F.R.). Inst. fuer Hochenergiephysik); Ball, S.; Gabriel, J.C.; Geyer, C.; Hoelscher, A.; Hofmann, W.; Holzer, B.; Khan, S.; Spengler, J. (Max-Planck-Institut fuer Kernphysik, Heidelberg (Germany, F.R.)); Charlesworth, C.E.K.; Krieger, P.; Kutschke, R.; Orr, R.S.; Parsons, J.A.; Prentice, J.D.; Seidel, S.C.; Swain, J.D.; Yoon, T.S. (; ARGUS Collaboration


    Using the ARGUS detector at the e{sup +}e{sup -} storgage ring DORIS II at DESY, we searched for b{yields}u transitions in exclusive hadronic B meson decays. A systematic analysis of B decays into pions has been performed for decay modes with 2-7 pions in the final state. In none of the decays a positive signal was observed. The upper limits obtained on various branching ratios are consistent with the current model predictions. (orig.).

  7. Search for hadronic b-->u decays (United States)

    Albrecht, H.; Gläser, R.; Harder, G.; Krüger, A.; Nilsson, A. W.; Nippe, A.; Oest, T.; Reidenbach, M.; Schäfer, M.; Schmidt-Parzefall, W.; Schröder, H.; Schulz, H. D.; Sefkow, F.; Wurth, R.; Appuhn, R. D.; Drescher, A.; Hast, C.; Herrera, G.; Kolanoski, H.; Lange, A.; Lindner, A.; Mankel, R.; Scheck, H.; Schweda, G.; Spaan, B.; Walther, A.; Wegener, D.; Paulini, M.; Reim, K.; Volland, U.; Wegener, H.; Funk, W.; Stiewe, J.; Werner, S.; Ball, S.; Gabriel, J. C.; Geyer, C.; Hölscher, A.; Hofmann, W.; Holzer, B.; Khan, S.; Spengler, J.; Charlesworth, C. E. K.; Edwards, K. W.; Frisken, W. R.; Kapitza, H.; Krieger, P.; Kutschke, R.; Macfarlene, D. B.; McLean, K. W.; Orr, R. S.; Parsons, J. A.; Patel, P. M.; Prentice, J. D.; Seidel, S. C.; Swain, J. D.; Tsipolitis, G.; Tzamariudaki, K.; Yoon, T.-S.; Ruf, T.; Schael, S.; Schubert, K. R.; Strahl, K.; Waldi, R.; Weseler, S.; Boštjančič, B.; Kernel, G.; Križan, P.; Križnič, E.; Cronström, H. I.; Jönsson, L.; Babaev, A.; Danilo, M.; Fominykh, B.; Golutvin, A.; Gorelov, I.; Lubimov, V.; Rostovtsev, A.; Semenov, A.; Semenov, S.; Shevchenko, V.; Soloshenko, V.; Tchistilin, V.; Tichomirov, I.; Zaitsev, Yu.; Childers, R.; Darden, C. W.; Argus Collaboration


    Using the ARGUS detector at the e +e - storage ring DORIS II at DESY, we searched for b→u transitions in exclusive hadronic B meson decays. A systematic analysis of B decays into pions has been performed for decay modes with 2-7 pions in the final state. In none of the decays a positive signal was observed. The upper limits obtained on various branching ratios are consistent with the current model predictions.

  8. Gaussian Confinement in a Jkj Decay Model (United States)

    da Silva, Mario L. L.; Hadjimichef, Dimiter; Vasconcellos, Cesar A. Z.

    In microscopic decay models, one attempts to describe hadron strong decays in terms of quark and gluon degrees of freedom. We begin by assuming that strong decays are driven by the same interquark Hamiltonian which determines the spectrum, and that it incorporates gaussian confinement. An A → BC decay matrix element of the JKJ Hamiltonian involves a pair-production current matrix elements times a scatering matrix element. Diagrammatically this corresponds to an interaction between an initial line and produced pair.

  9. Cellular systems biology profiling applied to cellular models of disease. (United States)

    Giuliano, Kenneth A; Premkumar, Daniel R; Strock, Christopher J; Johnston, Patricia; Taylor, Lansing


    Building cellular models of disease based on the approach of Cellular Systems Biology (CSB) has the potential to improve the process of creating drugs as part of the continuum from early drug discovery through drug development and clinical trials and diagnostics. This paper focuses on the application of CSB to early drug discovery. We discuss the integration of protein-protein interaction biosensors with other multiplexed, functional biomarkers as an example in using CSB to optimize the identification of quality lead series compounds.

  10. Probing dimensionality beyond the linear sequence of mRNA. (United States)

    Del Campo, Cristian; Ignatova, Zoya


    mRNA is a nexus entity between DNA and translating ribosomes. Recent developments in deep sequencing technologies coupled with structural probing have revealed new insights beyond the classic role of mRNA and place it more centrally as a direct effector of a variety of processes, including translation, cellular localization, and mRNA degradation. Here, we highlight emerging approaches to probe mRNA secondary structure on a global transcriptome-wide level and compare their potential and resolution. Combined approaches deliver a richer and more complex picture. While our understanding on the effect of secondary structure for various cellular processes is quite advanced, the next challenge is to unravel more complex mRNA architectures and tertiary interactions.

  11. Cellular identity at the single-cell level. (United States)

    Coskun, Ahmet F; Eser, Umut; Islam, Saiful


    A single cell creates surprising heterogeneity in a multicellular organism. While every organismal cell shares almost an identical genome, molecular interactions in cells alter the use of DNA sequences to modulate the gene of interest for specialization of cellular functions. Each cell gains a unique identity through molecular coding across the DNA, RNA, and protein conversions. On the other hand, loss of cellular identity leads to critical diseases such as cancer. Most cell identity dissection studies are based on bulk molecular assays that mask differences in individual cells. To probe cell-to-cell variability in a population, we discuss single cell approaches to decode the genetic, epigenetic, transcriptional, and translational mechanisms for cell identity formation. In combination with molecular instructions, the physical principles behind cell identity determination are examined. Deciphering and reprogramming cellular types impact biology and medicine.

  12. Light-quark decays in heavy hadrons (United States)

    Faller, Sven; Mannel, Thomas


    We consider weak decays of heavy hadrons (bottom and charmed) where the heavy quark acts as a spectator. These decays are heavily phase-space suppressed but may become experimentally accessible in the near future. These decays may be interesting as a QCD laboratory to study the behaviour of the light quarks in the colour-background field of the heavy spectator.

  13. Light-quark decays in heavy hadrons

    Energy Technology Data Exchange (ETDEWEB)

    Faller, Sven, E-mail:; Mannel, Thomas, E-mail:


    We consider weak decays of heavy hadrons (bottom and charmed) where the heavy quark acts as a spectator. These decays are heavily phase-space suppressed but may become experimentally accessible in the near future. These decays may be interesting as a QCD laboratory to study the behaviour of the light quarks in the colour-background field of the heavy spectator.

  14. Light-Quark Decays in Heavy Hadrons

    CERN Document Server

    Faller, Sven


    We consider weak decays of heavy hadrons (bottom and charmed) where the heavy quark acts as a spectator. Theses decays are heavily phase-space suppressed but may become experimentally accessible in the near future. These decays are interesting as a QCD laboratory to study the behaviour of the light quarks in the colour-background field of the heavy spectator.

  15. Beauty baryon decays: a theoretical overview (United States)

    Wang, Yu-Ming


    I overview the theoretical status and recent progress on the calculations of beauty baryon decays focusing on the QCD aspects of the exclusive semi-leptonic Λb → plμ decay at large recoil and theoretical challenges of radiative and electro-weak penguin decays Λb → Λγ,Λl+l-.

  16. Recent results on semileptonic decays at BABAR (United States)

    Serrano, J.; Babar Collaboration


    Some recent BABAR results on semileptonic decays are presented. They focus on the determination of the CKM matrix elements |V| and |V| in inclusive and exclusive b→uℓν and b→cℓν decays, and on form factors measurement in exclusive c→sℓν decays.

  17. Decay of eigenfunctions of elliptic PDE's

    DEFF Research Database (Denmark)

    Herbst, Ira; Skibsted, Erik

    We study exponential decay of eigenfunctions of self-adjoint higher order elliptic operators on Rd. We show that the possible critical decay rates are determined algebraically. In addition we show absence of super-exponentially decaying eigenfunctions and a refined exponential upper bound....

  18. Self-amplifying mRNA vaccines. (United States)

    Brito, Luis A; Kommareddy, Sushma; Maione, Domenico; Uematsu, Yasushi; Giovani, Cinzia; Berlanda Scorza, Francesco; Otten, Gillis R; Yu, Dong; Mandl, Christian W; Mason, Peter W; Dormitzer, Philip R; Ulmer, Jeffrey B; Geall, Andrew J


    This chapter provides a brief introduction to nucleic acid-based vaccines and recent research in developing self-amplifying mRNA vaccines. These vaccines promise the flexibility of plasmid DNA vaccines with enhanced immunogenicity and safety. The key to realizing the full potential of these vaccines is efficient delivery of nucleic acid to the cytoplasm of a cell, where it can amplify and express the encoded antigenic protein. The hydrophilicity and strong net negative charge of RNA impedes cellular uptake. To overcome this limitation, electrostatic complexation with cationic lipids or polymers and physical delivery using electroporation or ballistic particles to improve cellular uptake has been evaluated. This chapter highlights the rapid progress made in using nonviral delivery systems for RNA-based vaccines. Initial preclinical testing of self-amplifying mRNA vaccines has shown nonviral delivery to be capable of producing potent and robust innate and adaptive immune responses in small animals and nonhuman primates. Historically, the prospect of developing mRNA vaccines was uncertain due to concerns of mRNA instability and the feasibility of large-scale manufacturing. Today, these issues are no longer perceived as barriers in the widespread implementation of the technology. Currently, nonamplifying mRNA vaccines are under investigation in human clinical trials and can be produced at a sufficient quantity and quality to meet regulatory requirements. If the encouraging preclinical data with self-amplifying mRNA vaccines are matched by equivalently positive immunogenicity, potency, and tolerability in human trials, this platform could establish nucleic acid vaccines as a versatile new tool for human immunization.

  19. The emerging role of triple helices in RNA biology. (United States)

    Conrad, Nicholas K


    The ability of RNA to form sophisticated secondary and tertiary structures enables it to perform a wide variety of cellular functions. One tertiary structure, the RNA triple helix, was first observed in vitro over 50 years ago, but biological activities for triple helices are only beginning to be appreciated. The recent determination of several RNA structures has implicated triple helices in distinct biological functions. For example, the SAM-II riboswitch forms a triple helix that creates a highly specific binding pocket for S-adenosylmethionine. In addition, a triple helix in the conserved pseudoknot domain of the telomerase-associated RNA TER is essential for telomerase activity. A viral RNA cis-acting RNA element called the ENE contributes to the nuclear stability of a viral noncoding RNA by forming a triple helix with the poly(A) tail. Finally, a cellular noncoding RNA, MALAT1, includes a triple helix at its 3'-end that contributes to RNA stability, but surprisingly also supports translation. These examples highlight the diverse roles that RNA triple helices play in biology. Moreover, the dissection of triple helix mechanisms has the potential to uncover fundamental pathways in cell biology.

  20. ppGpp: magic beyond RNA polymerase. (United States)

    Dalebroux, Zachary D; Swanson, Michele S


    During stress, bacteria undergo extensive physiological transformations, many of which are coordinated by ppGpp. Although ppGpp is best known for enhancing cellular resilience by redirecting the RNA polymerase (RNAP) to certain genes, it also acts as a signal in many other cellular processes in bacteria. After a brief overview of ppGpp biosynthesis and its impact on promoter selection by RNAP, we discuss how bacteria exploit ppGpp to modulate the synthesis, stability or activity of proteins or regulatory RNAs that are crucial in challenging environments, using mechanisms beyond the direct regulation of RNAP activity.

  1. Vitamin D and the RNA transcriptome: more than mRNA regulation

    Directory of Open Access Journals (Sweden)

    Moray J Campbell


    Full Text Available The GRCh37.p13 primary assembly of the human genome contains 20805 protein coding mRNA, and 37147 non-protein coding genes and pseudogenes that as a result of RNA processing and editing generate 196501 gene transcripts. Given the size and diversity of the human transcriptome, it is timely to revisit what is known of VDR function in the regulation and targeting of transcription.Early transcriptomic studies using microarray approaches focused on the protein coding mRNA that were regulated by the VDR, usually following treatment with ligand. These studies quickly established the approxamte size, and surprising diversity of the VDR transcriptome, revealing it to be highly heterogenous and cell type and time dependent. With the discovery of microRNA, investigators also considered VDR regulation of these non-protein coding RNA. Again, cell and time dependency has emerged. Attempts to integrate mRNA and miRNA regulation patterns are beginning to reveal patterns of co-regulation and interaction that allow for greater control of mRNA expression, and the capacity to govern more complex cellular events. As the awareness of the diversity of non-coding RNA increases, it is evident that VDR actions are mediated through these molecules also. Key knowledge gaps remain over the VDR transcriptome. The causes for the cell and type dependent transcriptional heterogenetiy remain enigmatic. ChIP-Seq approaches have confirmed that VDR binding choices differ very significantly by cell type, but as yet the underlying causes distilling VDR binding choices are unclear. Similarly, it is clear that many of the VDR binding sites are non-canonical in nature but again the mechanisms underlying these interactions are unclear. Finally, although alternative splicing is clearly a very significant process in cellular transcriptional control, the lack of RNA-Seq data centered on VDR function are currently limiting the global assessment of the VDR transcriptome. VDR focused research

  2. Structural imprints in vivo decode RNA regulatory mechanisms (United States)

    Spitale, Robert C.; Flynn, Ryan A.; Zhang, Qiangfeng Cliff; Crisalli, Pete; Lee, Byron; Jung, Jong-Wha; Kuchelmeister, Hannes Y.; Batista, Pedro J.; Torre, Eduardo A.; Kool, Eric T.; Chang, Howard Y.


    Visualizing the physical basis for molecular behaviour inside living cells is a great challenge for biology. RNAs are central to biological regulation, and the ability of RNA to adopt specific structures intimately controls every step of the gene expression program. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles include only two of the four nucleotides that make up RNA. Here we present a novel biochemical approach, in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. icSHAPE of the mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguish different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro conditions, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA-binding proteins or RNA-modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N6-methyladenosine (m6A) modification genome wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.

  3. Neutrino mass from triton decay (United States)

    Weinheimer, Christian


    Since the discovery of neutrino flavor oscillation in different fields and by many different experiments we believe that neutrinos have non-vanishing masses in contrast to their current description within the Standard Model of particle physics. However, the absolute values of the neutrino masses, which are as important for particle physics as they are for cosmology and astrophysics, cannot be determined by oscillation experiments alone. There are a few ways to determine the neutrino mass scale, but the only model-independent method is the investigation of the electron energy spectrum of a β decay near its endpoint with tritium being the ideal isotope for the classical spectrometer set-up. The tritium β decay experiments at Mainz and Troitsk have recently been finished. At Mainz all relevant systematic uncertainties have been investigated by dedicated experiments yielding an upper limit of m(ν)MAC-E-Filter type. The recent achievements in test experiments show, that this very challenging experiment is feasible.

  4. $\\tau$ decays with neutral kaons

    CERN Document Server

    Abbiendi, G.; Akesson, P.F.; Alexander, G.; Allison, John; Anderson, K.J.; Arcelli, S.; Asai, S.; Ashby, S.F.; Axen, D.; Azuelos, G.; Bailey, I.; Ball, A.H.; Barberio, E.; Barlow, Roger J.; Batley, J.R.; Baumann, S.; Behnke, T.; Bell, Kenneth Watson; Bella, G.; Bellerive, A.; Bentvelsen, S.; Bethke, S.; Betts, S.; Biebel, O.; Biguzzi, A.; Bloodworth, I.J.; Bock, P.; Bohme, J.; Boeriu, O.; Bonacorsi, D.; Boutemeur, M.; Braibant, S.; Bright-Thomas, P.; Brigliadori, L.; Brown, Robert M.; Burckhart, H.J.; Capiluppi, P.; Carnegie, R.K.; Carter, A.A.; Carter, J.R.; Chang, C.Y.; Charlton, David G.; Chrisman, D.; Ciocca, C.; Clarke, P.E.L.; Clay, E.; Cohen, I.; Conboy, J.E.; Cooke, O.C.; Couchman, J.; Couyoumtzelis, C.; Coxe, R.L.; Cuffiani, M.; Dado, S.; Dallavalle, G.Marco; Dallison, S.; Davis, R.; de Roeck, A.; Dervan, P.; Desch, K.; Dienes, B.; Dixit, M.S.; Donkers, M.; Dubbert, J.; Duchovni, E.; Duckeck, G.; Duerdoth, I.P.; Estabrooks, P.G.; Etzion, E.; Fabbri, F.; Fanfani, A.; Fanti, M.; Faust, A.A.; Feld, L.; Ferrari, P.; Fiedler, F.; Fierro, M.; Fleck, I.; Frey, A.; Furtjes, A.; Futyan, D.I.; Gagnon, P.; Gary, J.W.; Gaycken, G.; Geich-Gimbel, C.; Giacomelli, G.; Giacomelli, P.; Gingrich, D.M.; Glenzinski, D.; Goldberg, J.; Gorn, W.; Grandi, C.; Graham, K.; Gross, E.; Grunhaus, J.; Gruwe, M.; Hajdu, C.; Hanson, G.G.; Hansroul, M.; Hapke, M.; Harder, K.; Harel, A.; Hargrove, C.K.; Harin-Dirac, M.; Hauschild, M.; Hawkes, C.M.; Hawkings, R.; Hemingway, R.J.; Herten, G.; Heuer, R.D.; Hildreth, M.D.; Hill, J.C.; Hobson, P.R.; Hocker, James Andrew; Hoffman, Kara Dion; Homer, R.J.; Honma, A.K.; Horvath, D.; Hossain, K.R.; Howard, R.; Huntemeyer, P.; Igo-Kemenes, P.; Imrie, D.C.; Ishii, K.; Jacob, F.R.; Jawahery, A.; Jeremie, H.; Jimack, M.; Jones, C.R.; Jovanovic, P.; Junk, T.R.; Kanaya, N.; Kanzaki, J.; Karapetian, G.; Karlen, D.; Kartvelishvili, V.; Kawagoe, K.; Kawamoto, T.; Kayal, P.I.; Keeler, R.K.; Kellogg, R.G.; Kennedy, B.W.; Kim, D.H.; Klier, A.; Kobayashi, T.; Kobel, M.; Kokott, T.P.; Kolrep, M.; Komamiya, S.; Kowalewski, Robert V.; Kress, T.; Krieger, P.; von Krogh, J.; Kuhl, T.; Kupper, M.; Kyberd, P.; Lafferty, G.D.; Landsman, H.; Lanske, D.; Lauber, J.; Lawson, I.; Layter, J.G.; Lellouch, D.; Letts, J.; Levinson, L.; Liebisch, R.; Lillich, J.; List, B.; Littlewood, C.; Lloyd, A.W.; Lloyd, S.L.; Loebinger, F.K.; Long, G.D.; Losty, M.J.; Lu, J.; Ludwig, J.; Macchiolo, A.; Macpherson, A.; Mader, W.; Mannelli, M.; Marcellini, S.; Marchant, T.E.; Martin, A.J.; Martin, J.P.; Martinez, G.; Mashimo, T.; Mattig, Peter; McDonald, W.John; McKenna, J.; Mckigney, E.A.; McMahon, T.J.; McPherson, R.A.; Meijers, F.; Mendez-Lorenzo, P.; Merritt, F.S.; Mes, H.; Meyer, I.; Michelini, A.; Mihara, S.; Mikenberg, G.; Miller, D.J.; Mohr, W.; Montanari, A.; Mori, T.; Nagai, K.; Nakamura, I.; Neal, H.A.; Nisius, R.; O'Neale, S.W.; Oakham, F.G.; Odorici, F.; Ogren, H.O.; Okpara, A.; Oreglia, M.J.; Orito, S.; Pasztor, G.; Pater, J.R.; Patrick, G.N.; Patt, J.; Perez-Ochoa, R.; Petzold, S.; Pfeifenschneider, P.; Pilcher, J.E.; Pinfold, J.; Plane, David E.; Poli, B.; Polok, J.; Przybycien, M.; Quadt, A.; Rembser, C.; Rick, H.; Robins, S.A.; Rodning, N.; Roney, J.M.; Rosati, S.; Roscoe, K.; Rossi, A.M.; Rozen, Y.; Runge, K.; Runolfsson, O.; Rust, D.R.; Sachs, K.; Saeki, T.; Sahr, O.; Sang, W.M.; Sarkisian, E.K.G.; Sbarra, C.; Schaile, A.D.; Schaile, O.; Scharff-Hansen, P.; Schieck, J.; Schmitt, S.; Schoning, A.; Schroder, Matthias; Schumacher, M.; Schwick, C.; Scott, W.G.; Seuster, R.; Shears, T.G.; Shen, B.C.; Shepherd-Themistocleous, C.H.; Sherwood, P.; Siroli, G.P.; Skuja, A.; Smith, A.M.; Snow, G.A.; Sobie, R.; Soldner-Rembold, S.; Spagnolo, S.; Sproston, M.; Stahl, A.; Stephens, K.; Stoll, K.; Strom, David M.; Strohmer, R.; Surrow, B.; Talbot, S.D.; Taras, P.; Tarem, S.; Teuscher, R.; Thiergen, M.; Thomas, J.; Thomson, M.A.; Torrence, E.; Towers, S.; Trefzger, T.; Trigger, I.; Trocsanyi, Z.; Tsur, E.; Turner-Watson, M.F.; Ueda, I.; Van Kooten, Rick J.; Vannerem, P.; Verzocchi, M.; Voss, H.; Wackerle, F.; Waller, D.; Ward, C.P.; Ward, D.R.; Watkins, P.M.; Watson, A.T.; Watson, N.K.; Wells, P.S.; Wengler, T.; Wermes, N.; Wetterling, D.; White, J.S.; Wilson, G.W.; Wilson, J.A.; Wyatt, T.R.; Yamashita, S.; Zacek, V.; Zer-Zion, D.


    The branching ratio of the tau lepton to a neutral K meson is measured from a sample of approximately 200,000 tau decays recorded by the OPAL detector at centre-of-mass energies near the Z0 resonance. The measurement is based on two samples which identify one-prong tau decays with KL and KS mesons. The combined branching ratios are measured to be B(tau- -->pi- K0bar nutau) = (9.33+-0.68+-0.49)x10^-3 B(tau- -->pi- K0bar [>=1pi0] nutau) = (3.24+-0.74+-0.66)x10^-3 B(tau- -->K- K0bar [>=0pi0] nutau) = (3.30+-0.55+-0.39)x10^-3 where the first error is statistical and the second systematic.

  5. Rare Decays of the $\\eta^{'}$

    CERN Document Server

    Briere, R A; Ford, W T; Gritsan, A; Krieg, H; Roy, J D; Smith, J G; Alexander, J P; Baker, R; Bebek, C; Berger, B E; Berkelman, K; Blanc, F; Boisvert, V; Cassel, David G; Dickson, M; Von Dombrowski, S; Drell, P S; Ecklund, K M; Ehrlich, R; Foland, A D; Gaidarev, P B; Galik, R S; Gibbons, L K; Gittelman, B; Gray, S W; Hartill, D L; Heltsley, B K; Hopman, P I; Jones, C D; Kreinick, D L; Lee, T; Liu, Y; Meyer, T O; Mistry, N B; Ng, C R; Nordberg, E; Patterson, J R; Peterson, D; Riley, D; Thayer, J G; Thies, P G; Valant-Spaight, B L; Warburton, A; Avery, P; Lohner, M; Prescott, C; Rubiera, A I; Yelton, J; Zheng, J; Brandenburg, G; Ershov, A; Gao, Y S; Kim, D Y J; Wilson, R; Browder, T E; Li, Y; Rodríguez, J L; Yamamoto, H; Bergfeld, T; Eisenstein, B I; Ernst, J; Gladding, G E; Gollin, G D; Hans, R M; Johnson, E; Karliner, I; Marsh, M A; Palmer, M; Plager, C; Sedlack, C; Selen, M; Thaler, J J; Williams, J; Edwards, K W; Janicek, R; Patel, P M; Sadoff, A J; Ammar, R; Baringer, P; Bean, A; Besson, D; Coppage, D; Davis, R; Kotov, S A; Kravchenko, I V; Kwak, N; Zhao, X; Anderson, S; Frolov, V V; Kubota, Y; Lee, S J; Mahapatra, R; O'Neill, J J; Poling, R A; Riehle, T; Smith, A; Ahmed, S; Alam, M S; Athar, S B; Jian, L; Ling, L; Mahmood, A H; Saleem, M; Timm, S; Wappler, F; Anastassov, A; Duboscq, J E; Gan, K K; Gwon, C; Hart, T; Honscheid, K; Kagan, H; Kass, R; Lorenc, J; Schwarthoff, H; Spencer, M B; Von Törne, E; Zoeller, M M; Richichi, S J; Severini, H; Skubic, P L; Undrus, A E; Bishai, M; Chen, S; Fast, J; Hinson, J W; Lee, J; Menon, N; Miller, D H; Shibata, E I; Shipsey, I P J; Kwon, Y; Lyon, A L; Thorndike, E H; Jessop, C P; Lingel, K; Marsiske, H; Perl, Martin Lewis; Savinov, V; Ugolini, D W; Zhou, X; Coan, T E; Fadeev, V; Korolkov, I Ya; Maravin, Y; Narsky, I; Stroynowski, R; Ye, J; Wlodek, T; Artuso, M; Ayad, R; Dambasuren, E; Kopp, S E; Majumder, G; Moneti, G C; Mountain, R; Schuh, S; Skwarnicki, T; Stone, S; Titov, A; Viehhauser, G; Wang, J C; Wolf, A; Wu, J; Csorna, S E; McLean, K W; Marka, S; Xu, Z; Godang, R; Kinoshita, K; Lai, I C; Pomianowski, P A; Schrenk, S; Bonvicini, G; Cinabro, D; Greene, R; Perera, L P; Zhou, G J; Chan, S; Eigen, G; Lipeles, E; Schmidtler, M; Shapiro, A; Sun, W M; Urheim, J; Weinstein, A J; Würthwein, F; Jaffe, D E; Masek, G E; Paar, H P; Potter, E M; Prell, S; Sharma, V; Asner, D M; Eppich, A; Gronberg, J B; Hill, T S; Lange, D J; Morrison, R J; Nelson, T K; Richman, J D; Roberts, D


    We have searched for the rare decays of the eta prime meson to e+ e- eta, e+ e- pizero, e+ e- gamma, and e mu in hadronic events at the CLEO II detector. The search is conducted on 4.80 fb^-1 of e+ e- collisions at the Cornell Electron Storage Ring. We find no signal in any of these modes, and set 90% confidence level upper limits on their branching fractions of 2.4 X 10^-3, 1.4 X 10^-3, 0.9 X 10^-3, and 4.7 X 10^-4, respectively. We also investigate the Dalitz plot of the common decay of the eta prime to pi+ pi- eta. We fit the matrix element with the Particle Data Group parameterization and find Re(alpha) = -0.021 +- 0.025, where alpha is a linear function of the kinetic energy of the eta.

  6. Orthopositronium Decay Spectrum using NRQED

    CERN Document Server

    Ruiz-Femenia, P D


    As noticed in Ref.[1], the Ore-Powell's classical calculation of the o-Ps -> 3 gamma decay amplitude does not fulfill Low's theorem requirements for the low energy end of the photon spectrum. We reanalyze the implications of Low's theorem applied to this decay considering the interplay between the soft photon limit and the energy scales present in the e+e- system. For energetic photons, the spectrum agrees with the Ore-Powell result, but deviates from it when the photon energy is comparable to the positronium binding energy. In this region it is found that bound states effects are essential to reach agreement with Low's theorem and can be accounted for in the framework of non-relativistic QED.

  7. Entanglement entropy in particle decay

    CERN Document Server

    Lello, Louis; Holman, Richard


    The decay of a parent particle into two or more daughter particles results in an entangled quantum state, as a consequence of conservation laws in the decay process. We use the Wigner-Weisskopf formalism to construct an approximation to this state that evolves in time in a {\\em manifestly unitary} way. We then construct the entanglement entropy for one of the daughter particles by use of the reduced density matrix obtained by tracing out the unobserved states and follow its time evolution. We find that it grows over a time scale determined by the lifetime of the parent particle to a maximum, which when the width of the parent particle is narrow, describes the phase space distribution of maximally entangled Bell-like states.

  8. Measurement of $\\psip$ Radiative Decays


    Ablikim, M.; J.Z. Bai; Ban, Y.; Collaboration, BES


    Using 14 million psi(2S) events accumulated at the BESII detector, we report first measurements of branching fractions or upper limits for psi(2S) decays into gamma ppbar, gamma 2(pi^+pi^-), gamma K_s K^-pi^++c.c., gamma K^+ K^- pi^+pi^-, gamma K^{*0} K^- pi^+ +c.c., gamma K^{*0}\\bar K^{*0}, gamma pi^+pi^- p pbar, gamma 2(K^+K^-), gamma 3(pi^+pi^-), and gamma 2(pi^+pi^-)K^+K^- with the invariant mass of hadrons below 2.9GeV/c^2. We also report branching fractions of psi(2S) decays into 2(pi^+...

  9. Lyapunov decay in quantum irreversibility. (United States)

    García-Mata, Ignacio; Roncaglia, Augusto J; Wisniacki, Diego A


    The Loschmidt echo--also known as fidelity--is a very useful tool to study irreversibility in quantum mechanics due to perturbations or imperfections. Many different regimes, as a function of time and strength of the perturbation, have been identified. For chaotic systems, there is a range of perturbation strengths where the decay of the Loschmidt echo is perturbation independent, and given by the classical Lyapunov exponent. But observation of the Lyapunov decay depends strongly on the type of initial state upon which an average is carried out. This dependence can be removed by averaging the fidelity over the Haar measure, and the Lyapunov regime is recovered, as has been shown for quantum maps. In this work, we introduce an analogous quantity for systems with infinite dimensional Hilbert space, in particular the quantum stadium billiard, and we show clearly the universality of the Lyapunov regime.

  10. UA1: Z particle decay

    CERN Multimedia


    A colour treated picture of the computer reconstruction of the real particle tracks emerging from a high energy proton-antiproton collision recorded in the UA1 detector at the SPS (converted to act as a collider). This picture shows the production of a Z particle that has decayed into a high energy electron and positron flying off in opposite directions (in yellow). The UA1 detector ran on the SPS accelerator at CERN between 1981 and 1993.

  11. Future double beta decay experiments

    Energy Technology Data Exchange (ETDEWEB)

    Piquemal, F. [Laboratoire Souterrain de Modane, Modane (France); Centre d' Etudes Nucleaire, Bordeaux-Gradignan (France)


    The search of neutrinoless double beta decay is very challenging because of the expected half-life of the process and the backgrounds from the natural radioactivity. Many projects exist to try to reach a sensitivity of ∼50 meV on the effective neutrino mass corresponding to a mass of isotopes of ∼100 kg. In this article some of the futur projects are presented.

  12. Proton Decay Searches with DUNE (United States)

    Wood, Kevin


    The Deep Underground Neutrino Experiment (DUNE) will be comprised of a beam line and near detector complex at Fermilab, Illinois as well as a massive far detector located 1300 km away at Sanford Underground Research Facility (SURF), South Dakota. To achieve its rich physics program, DUNE plans to construct a 40kt fiducial volume Liquid Argon Time Projection Chamber (LArTPC) far detector almost a mile underground. The size, location, and technology of the proposed far detector make it an attractive tool to search for proton decay, which has yet to be observed. Observation of such a rare event requires high sensitivity to the signal and high background rejection rate. A particular background of interest arises from cosmic muons interacting with rock surrounding the detector and producing a variety of particles which can enter the detector and leave signatures similar to that of proton decay. In order to keep this background to a reasonable level without sacrificing signal acceptance efficiency, precise tracking, made possible by the LArTPC technology, is required. Precise 3D localization of proton decay events relies on the detector's ability to identify the prompt emission of scintillation light from proton decay events as the t0-defining signal. Therefore, low background rate and high detection efficiency of this light are the crucial to the search. This work examines these characteristics in a detailed Monte Carlo simulation using DUNE`s far detector reference design and demonstrates a high signal efficiency while keeping the expected number of cosmogenic background events sufficiently low.

  13. Optical spectroscopy and tooth decay (United States)

    Misra, P.; De, T.; Singh, R.


    Optical spectroscopy in the ultraviolet, visible and mid-infrared spectral regions has been used to discriminate between healthy and diseased teeth of patients in the age range 15-75 years. Spectral scans of absorbance versus wavenumber and fluorescence intensity versus wavelength have been recorded and investigated for caries and periodontal disease. Such optical diagnostics can prove very useful in the early detection and treatment of tooth decay.

  14. Decays of the tau lepton

    Energy Technology Data Exchange (ETDEWEB)

    Burchat, P.R.


    Previous measurements of the branching fractions of the tau lepton result in a discrepancy between the inclusive branching fraction and the sum of the exclusive branching fractions to final states containing one charged particle. The sum of the exclusive branching fractions is significantly smaller than the inclusive branching fraction. In this analysis, the branching fractions for all the major decay modes are measured simultaneously with the sum of the branching fractions constrained to be one. The branching fractions are measured using an unbiased sample of tau decays, with little background, selected from 207 pb/sup -1/ of data accumulated with the Mark II detector at the PEP e/sup +/e/sup -/ storage ring. The sample is selected using the decay products of one member of the ..gamma../sup +/..gamma../sup -/ pair produced in e/sup +/e/sup -/ annihilation to identify the event and then including the opposite member of the pair in the sample. The sample is divided into subgroups according to charged and neutral particle multiplicity, and charged particle identification. The branching fractions are simultaneously measured using an unfold technique and a maximum likelihood fit. The results of this analysis indicate that the discrepancy found in previous experiments is possibly due to two sources. First, the leptonic branching fractions measured in this analysis are about one standard deviation higher than the world average. The measured leptonic branching fractions correspond to a tau lifetime of (3.0 +- 0.2) x 10/sup -13/ s. Secondly, the total branching fraction to one charged hadron plus at least one neutral particle is measured to be (7 +- 3)% higher than the branching fraction expected from a combination of previous measurements and theoretical predictions. It is shown that decay modes involving the eta are not expected to contribute more than 3% to this excess.

  15. Digging the CNGS decay tunnel

    CERN Multimedia

    Patrice Loiez


    Products of the collision between a proton beam and a graphite target will pass through a horn containing an electric field that will produce a focused beam. These particles will decay into muon neutrinos within the tunnel that is being constructed in these images. The neutrinos will then travel 730 km to Gran Sasso in Italy where huge detectors will observe the beam to study a process called neutrino oscillation.

  16. Applying the breaks on gene expression - mRNA deadenylation by Pop2p

    DEFF Research Database (Denmark)

    Andersen, Kasper Røjkjær; Jonstrup, Anette Thyssen; Van, Lan Bich;

    When driving a car, control of the brakes is just as important as control of the accelerator pedal. Likewise, in gene expression, regulation of mRNA degradation is as important as regulation of its synthesis (Mühlemann, 2005). The rate-determining step of mRNA decay in eukaryotes seems to be the ...

  17. A Course in Cellular Bioengineering. (United States)

    Lauffenburger, Douglas A.


    Gives an overview of a course in chemical engineering entitled "Cellular Bioengineering," dealing with how chemical engineering principles can be applied to molecular cell biology. Topics used are listed and some key references are discussed. Listed are 85 references. (YP)

  18. Energy profile and secondary structure impact shRNA efficacy

    Directory of Open Access Journals (Sweden)

    Zeng Xiao


    Full Text Available Abstract Background RNA interference (RNAi is a cellular mechanism in which a short/small double stranded RNA induces the degradation of its sequence specific target mRNA, leading to specific gene silencing. Since its discovery, RNAi has become a powerful biological technique for gene function studies and drug discovery. The very first requirement of applying RNAi is to design functional small interfering RNA (siRNA that can uniquely induce the degradation of the targeted mRNA. It has been shown that many functional synthetic siRNAs share some common characteristics, such as GC content limitation and free energy preferences at both terminals, etc. Results Our three-phase algorithm was developed to design siRNA on a whole-genome scale based on those identified characteristics of functional siRNA. When this algorithm was applied to design short hairpin RNA (shRNA, the validated success rate of shRNAs was over 70%, which was almost double the rate reported for TRC library. This indicates that the designs of siRNA and shRNA may share the same concerns. Further analysis of the shRNA dataset of 444 designs reveals that the high free energy states of the two terminals have the largest positive impact on the shRNA efficacy. Enforcing these energy characteristics of both terminals can further improve the shRNA design success rate to 83.1%. We also found that functional shRNAs have less probability for their 3' terminals to be involved in mRNA secondary structure formation. Conclusion Functional shRNAs prefer high free energy states at both terminals. High free energy states of the two terminals were found to be the largest positive impact factor on shRNA efficacy. In addition, the accessibility of the 3' terminal is another key factor to shRNA efficacy.

  19. Decay law and time dilatation

    CERN Document Server

    Giacosa, Francesco


    We study the decay law for a moving unstable particle. The usual time-dilatation formula states that the decay width for an unstable state moving with a momentum $p$ and mass $M$ is $\\tilde{\\Gamma}_{p}=\\Gamma M/\\sqrt{p^{2}+M^{2}}$ with $\\Gamma$ being the decay width in the rest frame. In agreement with previous studies, we show that in the context of QM as well as QFT this equation is \\textit{not} correct provided that the quantum measurement is performed in a reference frame in which the unstable particle has momentum $p$ (note, a momentum eigenstate is \\textit{not} a velocity eigenstate in QM). We then give, to our knowledge for the first time, an analytic expression of an improved formula and we show that the deviation from $\\tilde{\\Gamma}_{p}$ has a maximum for $p/M=\\sqrt{2/3},$ but is typically \\textit{very} small. Then, the result can be easily generalized to a momentum wave packet. As a next step, we show that care is needed when one makes a boost of an unstable state with zero momentum/velocity: namel...

  20. LHCb: Rare Decays at LHCb

    CERN Multimedia

    Teodorescu, E


    The decay modes $B_d\\to K^*\\gamma$ and $B_s \\to \\phi \\gamma$ are promising laboratories for the search of New Physics effects, their properties being particularly sensitive to the presence of new heavy particles that may propagate virtually within the one-loop process involved in penguin diagrams. The penguin $B_s \\to \\phi \\gamma$ decay has been observed by Belle with rather poor precision, $\\mathcal{B}$($B_s \\to \\phi \\gamma$) = 57$^{+22}_{-19}$ x 10$^{-6}$, therefore, additional measurements are expected for this channel. With a data sample corresponding to an integrated luminosity of ~36 pb$^{-1}$ collected in 2010, a clear and promising signal has been observed for the $B_d\\to K^*\\gamma$. The mass resolution is dominated by the electromagnetic calorimeter energy resolution (ECAL is inter-calibrated at the ~2% level). A first hint of the $B_s \\to \\Phi \\gamma$  decay has also been observed. Given this preliminary results and the theory predictions, we expect that, with the data we will record in 2011, th...

  1. LHCb: Radiative Decays at LHCb

    CERN Multimedia

    Teodorescu, E


    The decay modes $B_d\\to K^*\\gamma$ and $B_s \\to \\phi \\gamma$ are promising laboratories for the search of New Physics effects, their properties being particularly sensitive to the presence of new heavy particles that may propagate virtually within the one-loop process involved in penguin diagrams. The penguin $B_s \\to \\phi \\gamma$ decay has been observed by Belle with rather poor precision, $\\mathcal{B}$($B_s \\to \\phi \\gamma$) = 57$^{+22}_{-19}$ x 10$^{-6}$, therefore, additional measurements are expected for this channel. With a data sample corresponding to an integrated luminosity of ~36 pb$^{-1}$ collected in 2010, a clear and promising signal has been observed for the $B_d\\to K^*\\gamma$. The mass resolution is dominated by the electromagnetic calorimeter energy resolution (ECAL is inter-calibrated at the ~2% level). A first hint of the $B_s \\to \\Phi \\gamma$  decay has also been observed. Given this preliminary results and the theory predictions, we expect that, with the data we will record in 2011, th...

  2. Energy Landscape of Cellular Networks (United States)

    Wang, Jin


    Cellular Networks are in general quite robust and perform their biological functions against the environmental perturbations. Progresses have been made from experimental global screenings, topological and engineering studies. However, there are so far few studies of why the network should be robust and perform biological functions from global physical perspectives. In this work, we will explore the global properties of the network from physical perspectives. The aim of this work is to develop a conceptual framework and quantitative physical methods to study the global nature of the cellular network. The main conclusion of this presentation is that we uncovered the underlying energy landscape for several small cellular networks such as MAPK signal transduction network and gene regulatory networks, from the experimentally measured or inferred inherent chemical reaction rates. The underlying dynamics of these networks can show bi-stable as well as oscillatory behavior. The global shapes of the energy landscapes of the underlying cellular networks we have studied are robust against perturbations of the kinetic rates and environmental disturbances through noise. We derived a quantitative criterion for robustness of the network function from the underlying landscape. It provides a natural explanation of the robustness and stability of the network for performing biological functions. We believe the robust landscape is a global universal property for cellular networks. We believe the robust landscape is a quantitative realization of Darwinian principle of natural selection at the cellular network level. It may provide a novel algorithm for optimizing the network connections, which is crucial for the cellular network design and synthetic biology. Our approach is general and can be applied to other cellular networks.

  3. Constraints on hadronically decaying dark matter

    Energy Technology Data Exchange (ETDEWEB)

    Garny, Mathias [Technische Univ. Muenchen, Garching (Germany). Physik-Department; Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Ibarra, Alejandro [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Tran, David [Technische Univ. Muenchen, Garching (Germany). Physik-Department; Minnesota Univ., Minneapolis, MN (United States). School of Physics and Astronomy


    We present general constraints on dark matter stability in hadronic decay channels derived from measurements of cosmic-ray antiprotons.We analyze various hadronic decay modes in a model-independent manner by examining the lowest-order decays allowed by gauge and Lorentz invariance for scalar and fermionic dark matter particles and present the corresponding lower bounds on the partial decay lifetimes in those channels. We also investigate the complementarity between hadronic and gamma-ray constraints derived from searches for monochromatic lines in the sky, which can be produced at the quantum level if the dark matter decays into quark-antiquark pairs at leading order.

  4. Latest results in rare decays at LHCb

    CERN Document Server

    Kreps, Michal


    Recent results from the LHCb experiment on decays governed by $b \\rightarrow s\\mu^+\\mu^-$ or $b\\rightarrow s\\gamma$ transitions are reviewed. The updated isospin asymmetry in $B \\rightarrow K^{(*)} \\mu^+\\mu^-$ decay are in good agreement with the Standard Model. Results of the angular analysis of $B \\rightarrow K\\mu^+ \\mu^-$ decay help to exclude large cancellation between left- and right-handed couplings in the $B^0_s \\rightarrow \\mu^+\\mu^-$ decay. Finally using the decay $B^+ \\rightarrow K^+\\pi^-\\pi^+\\gamma$, nonzero photon polarization is observed for the first time in $b\\rightarrow s\\gamma$ transitions.

  5. Leptonic decays of the Ds meson (United States)

    ALEPH Collaboration; Heister, A.; Schael, S.; Barate, R.; De Bonis, I.; Decamp, D.; Goy, C.; Lees, J.-P.; Merle, E.; Minard, M.-N.; Pietrzyk, B.; Boix, G.; Bravo, S.; Casado, M. P.; Chmeissani, M.; Crespo, J. M.; Fernandez, E.; Fernandez-Bosman, M.; Garrido, Ll.; Graugés, E.; Martinez, M.; Merino, G.; Miquel, R.; Mir, Ll. M.; Pacheco, A.; Ruiz, H.; Colaleo, A.; Creanza, D.; de Palma, M.; Iaselli, G.; Maggi, G.; Maggi, M.; Nuzzo, S.; Ranieri, A.; Raso, G.; Ruggieri, F.; Selvaggi, G.; Silvestris, L.; Tempesta, P.; Tricomi, A.; Zito, G.; Huang, X.; Lin, J.; Ouyang, Q.; Wang, T.; Xie, Y.; Xu, R.; Xue, S.; Zhang, J.; Zhang, L.; Zhao, W.; Abbaneo, D.; Azzurri, P.; Buchmüller, O.; Cattaneo, M.; Cerutti, F.; Clerbaux, B.; Drevermann, H.; Forty, R. W.; Frank, M.; Gianotti, F.; Greening, T. C.; Hansen, J. B.; Harvey, J.; Hutchcroft, D. E.; Janot, P.; Jost, B.; Kado, M.; Mato, P.; Moutoussi, A.; Ranjard, F.; Rolandi, L.; Schlatter, D.; Schneider, O.; Sguazzoni, G.; Tejessy, W.; Teubert, F.; Valassi, A.; Videau, I.; Ward, J.; Badaud, F.; Falvard, A.; Gay, P.; Henrard, P.; Jousset, J.; Michel, B.; Monteil, S.; Montret, J.-C.; Pallin, D.; Perret, P.; Hansen, J. D.; Hansen, J. R.; Hansen, P. H.; Nilsson, B. S.; Wäänänen, A.; Kyriakis, A.; Markou, C.; Simopoulou, E.; Vayaki, A.; Zachariadou, K.; Blondel, A.; Bonneaud, G.; Brient, J.-C.; Rougé, A.; Rumpf, M.; Swynghedauw, M.; Verderi, M.; Videau, H.; Ciulli, V.; Focardi, E.; Parrini, G.; Antonelli, A.; Antonelli, M.; Bencivenni, G.; Bologna, G.; Bossi, F.; Campana, P.; Capon, G.; Chiarella, V.; Laurelli, P.; Mannocchi, G.; Murtas, F.; Murtas, G. P.; Passalacqua, L.; Pepe-Altarelli, M.; Spagnolo, P.; Halley, A.; Lynch, J. G.; Negus, P.; O'Shea, V.; Raine, C.; Thompson, A. S.; Wasserbaech, S.; Cavanaugh, R.; Dhamotharan, S.; Geweniger, C.; Hanke, P.; Hansper, G.; Hepp, V.; Kluge, E. E.; Putzer, A.; Sommer, J.; Stenzel, H.; Tittel, K.; Werner, S.; Wunsch, M.; Beuselinck, R.; Binnie, D. M.; Cameron, W.; Dornan, P. J.; Girone, M.; Marinelli, N.; Sedgbeer, J. K.; Thompson, J. C.; Ghete, V. M.; Girtler, P.; Kneringer, E.; Kuhn, D.; Rudolph, G.; Bouhova-Thacker, E.; Bowdery, C. K.; Finch, A. J.; Foster, F.; Hughes, G.; Jones, R. W. L.; Pearson, M. R.; Robertson, N. A.; Jakobs, K.; Kleinknecht, K.; Quast, G.; Renk, B.; Sander, H.-G.; Wachsmuth, H.; Zeitnitz, C.; Bonissent, A.; Carr, J.; Coyle, P.; Leroy, O.; Payre, P.; Rousseau, D.; Talby, M.; Ragusa, F.; David, A.; Dietl, H.; Ganis, G.; Hüttmann, K.; Lütjens, G.; Mannert, C.; Männer, W.; Moser, H.-G.; Settles, R.; Wiedenmann, W.; Wolf, G.; Boucrot, J.; Callot, O.; Davier, M.; Duflot, L.; Grivaz, J.-F.; Heusse, Ph.; Jacholkowska, A.; Lefrançois, J.; Veillet, J.-J.; Yuan, C.; Bagliesi, G.; Boccali, T.; Foà, L.; Giammanco, A.; Giassi, A.; Ligabue, F.; Messineo, A.; Palla, F.; Sanguinetti, G.; Sciabà, A.; Tenchini, R.; Venturi, A.; Verdini, P. G.; Blair, G. A.; Cowan, G.; Green, M. G.; Medcalf, T.; Misiejuk, A.; Strong, J. A.; Teixeira-Dias, P.; von Wimmersperg-Toeller, J. H.; Clifft, R. W.; Edgecock, T. R.; Norton, P. R.; Tomalin, I. R.; Bloch-Devaux, B.; Colas, P.; Emery, S.; Kozanecki, W.; Lançon, E.; Lemaire, M.-C.; Locci, E.; Perez, P.; Rander, J.; Renardy, J.-F.; Roussarie, A.; Schuller, J.-P.; Schwindling, J.; Trabelsi, A.; Vallage, B.; Konstantinidis, N.; Litke, A. M.; Taylor, G.; Booth, C. N.; Cartwright, S.; Combley, F.; Lehto, M.; Thompson, L. F.; Affholderbach, K.; Böhrer, A.; Brandt, S.; Grupen, C.; Ngac, A.; Prange, G.; Sieler, U.; Giannini, G.; He, H.; Putz, J.; Rothberg, J.; Armstrong, S. R.; Berkelman, K.; Cranmer, K.; Ferguson, D. P. S.; Gao, Y.; González, S.; Hayes, O. J.; Hu, H.; Jin, S.; Kile, J.; McNamara, P. A.; Nielsen, J.; Pan, Y. B.; von Wimmersperg-Toeller, J. H.; Wiedenmann, W.; Wu, J.; Wu, Sau Lan; Wu, X.; Zobernig, G.; Dissertori, G.


    The purely leptonic decays Ds-->τν and Ds-->μν are studied in a sample of four million hadronic /Z decays collected with the ALEPH detector at the LEP e+e- collider from 1991 to 1995. The branching fractions are extracted from a combination of two analyses, one optimized to select Ds-->τν decays with /τ-->eνν¯ or /μνν¯, and the other optimized for Ds-->μν decays. The results are used to evaluate the Ds decay constant, within the Standard Model: fDs=[285+/-19(stat)+/-40(syst)] MeV.

  6. Three-body charmless B decays workshop

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Haim, E.; Chauveau, J.; Hartfiel, B.; Ocariz, J. [Laboratoire de Physique Nucleaire et de Hautes Energies (LPNHE), 75 - Paris (France); Charles, J. [LPT, 13 - Marseille (France)


    The purpose of this workshop was multifarious: -) to present and discuss the current experimental perspectives based on the full expected statistics from B-factories by 2008, -) to share and further develop analysis methods, -) to present and discuss the theoretical work on the subject, -) to discuss the future of B-factories, and -) to establish a work plan until 2009. The contributions have focused on 3 body charmless B decays and mostly 3 body hadronic charmless B decays, they have also dealt with semileptonic decays, radiative decays, charm and charmonium decays, and scattering processes. This document gathers the slides of the presentations.

  7. Mathematical Modeling of Cellular Metabolism. (United States)

    Berndt, Nikolaus; Holzhütter, Hermann-Georg


    Cellular metabolism basically consists of the conversion of chemical compounds taken up from the extracellular environment into energy (conserved in energy-rich bonds of organic phosphates) and a wide array of organic molecules serving as catalysts (enzymes), information carriers (nucleic acids), and building blocks for cellular structures such as membranes or ribosomes. Metabolic modeling aims at the construction of mathematical representations of the cellular metabolism that can be used to calculate the concentration of cellular molecules and the rates of their mutual chemical interconversion in response to varying external conditions as, for example, hormonal stimuli or supply of essential nutrients. Based on such calculations, it is possible to quantify complex cellular functions as cellular growth, detoxification of drugs and xenobiotic compounds or synthesis of exported molecules. Depending on the specific questions to metabolism addressed, the methodological expertise of the researcher, and available experimental information, different conceptual frameworks have been established, allowing the usage of computational methods to condense experimental information from various layers of organization into (self-) consistent models. Here, we briefly outline the main conceptual frameworks that are currently exploited in metabolism research.

  8. Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins

    Directory of Open Access Journals (Sweden)

    Rebecca Bish


    Full Text Available DDX6 (p54/RCK is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58 of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2 and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2. We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6’s multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6’s interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions

  9. Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins. (United States)

    Bish, Rebecca; Cuevas-Polo, Nerea; Cheng, Zhe; Hambardzumyan, Dolores; Munschauer, Mathias; Landthaler, Markus; Vogel, Christine


    DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58) of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2) and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2). We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6's multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6's interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions-many of which are likely

  10. Modulation of microRNA-mRNA Target Pairs by Human Papillomavirus 16 Oncoproteins

    Directory of Open Access Journals (Sweden)

    Mallory E. Harden


    Full Text Available The E6 and E7 proteins are the major oncogenic drivers encoded by high-risk human papillomaviruses (HPVs. While many aspects of the transforming activities of these proteins have been extensively studied, there are fewer studies that have investigated how HPV E6/E7 expression affects the expression of cellular noncoding RNAs. The goal of our study was to investigate HPV16 E6/E7 modulation of cellular microRNA (miR levels and to determine the potential consequences for cellular gene expression. We performed deep sequencing of small and large cellular RNAs in primary undifferentiated cultures of human foreskin keratinocytes (HFKs with stable expression of HPV16 E6/E7 or a control vector. After integration of the two data sets, we identified 51 differentially expressed cellular miRs associated with the modulation of 1,456 potential target mRNAs in HPV16 E6/E7-expressing HFKs. We discovered that the degree of differential miR expression in HFKs expressing HPV16 E6/E7 was not necessarily predictive of the number of corresponding mRNA targets or the potential impact on gene expression. Additional analyses of the identified miR-mRNA pairs suggest modulation of specific biological activities and biochemical pathways. Overall, our study supports the model that perturbation of cellular miR expression by HPV16 E6/E7 importantly contributes to the rewiring of cellular regulatory circuits by the high-risk HPV E6 and E7 proteins that contribute to oncogenic transformation.

  11. The La protein functions redundantly with tRNA modification enzymes to ensure tRNA structural stability. (United States)

    Copela, Laura A; Chakshusmathi, Ghadiyaram; Sherrer, R Lynn; Wolin, Sandra L


    Although the La protein stabilizes nascent pre-tRNAs from nucleases, influences the pathway of pre-tRNA maturation, and assists correct folding of certain pre-tRNAs, it is dispensable for growth in both budding and fission yeast. Here we show that the Saccharomyces cerevisiae La shares functional redundancy with both tRNA modification enzymes and other proteins that contact tRNAs during their biogenesis. La is important for growth in the presence of mutations in either the arginyl tRNA synthetase or the tRNA modification enzyme Trm1p. In addition, two pseudouridine synthases, PUS3 and PUS4, are important for growth in strains carrying a mutation in tRNA(Arg)(CCG) and are essential when La is deleted in these strains. Depletion of Pus3p results in accumulation of the aminoacylated mutant tRNA(Arg)(CCG) in nuclei, while depletion of Pus4p results in decreased stability of the mutant tRNA. Interestingly, the degradation of mutant unstable forms of tRNA(Arg)(CCG) does not require the Trf4p poly(A) polymerase, suggesting that yeast cells possess multiple pathways for tRNA decay. These data demonstrate that La functions redundantly with both tRNA modifications and proteins that associate with tRNAs to achieve tRNA structural stability and efficient biogenesis.

  12. RNA Secondary Structure Modulates FMRP’s Bi-Functional Role in the MicroRNA Pathway

    Directory of Open Access Journals (Sweden)

    Phillip Kenny


    Full Text Available MicroRNAs act by post-transcriptionally regulating the gene expression of 30%–60% of mammalian genomes. MicroRNAs are key regulators in all cellular processes, though the mechanism by which the cell activates or represses microRNA-mediated translational regulation is poorly understood. In this review, we discuss the RNA binding protein Fragile X Mental Retardation Protein (FMRP and its role in microRNA-mediated translational regulation. Historically, FMRP is known to function as a translational suppressor. However, emerging data suggests that FMRP has both an agonistic and antagonistic role in regulating microRNA-mediated translational suppression. This bi-functional role is dependent on FMRP’s interaction with the RNA helicase Moloney leukemia virus 10 (MOV10, which modifies the structural landscape of bound mRNA, therefore facilitating or inhibiting its association with the RNA-Induced Silencing Complex.

  13. In vitro and in vivo characterization of microRNA-targeted alphavirus replicon and helper RNAs. (United States)

    Kamrud, Kurt I; Coffield, V McNeil; Owens, Gary; Goodman, Christin; Alterson, Kim; Custer, Max; Murphy, Michael A; Lewis, Whitney; Timberlake, Sarah; Wansley, Elizabeth K; Berglund, Peter; Smith, Jonathan


    Alphavirus-based replicon vector systems (family Togaviridae) have been developed as expression vectors with demonstrated potential in vaccine development against both infectious diseases and cancer. The single-cycle nature of virus-like replicon particles (VRP), generated by supplying the structural proteins from separate replicable helper RNAs, is an attractive safety component of these systems. MicroRNAs (miRNAs) have emerged as important cellular RNA regulation elements. Recently, miRNAs have been employed as a mechanism to attenuate or restrict cellular tropism of replication-competent viruses, such as oncolytic adenoviruses, vesicular stomatitis virus, and picornaviruses as well as nonreplicating lentiviral and adenoviral vectors. Here, we describe the incorporation of miRNA-specific target sequences into replicable alphavirus helper RNAs that are used in trans to provide the structural proteins required for VRP production. VRP were found to be efficiently produced using miRNA-targeted helper RNAs if miRNA-specific inhibitors were introduced into cells during VRP production. In the absence of such inhibitors, cellular miRNAs were capable of downregulating helper RNA replication in vitro. When miRNA targets were incorporated into a replicon RNA, cellular miRNAs were capable of downregulating replicon RNA replication upon delivery of VRP into animals, demonstrating activity in vivo. These data provide the first example of miRNA-specific repression of alphavirus replicon and helper RNA replication and demonstrate the feasibility of miRNA targeting of expression vector helper functions that are provided in trans.

  14. Cellular Viscosity in Prokaryotes and Thermal Stability of Low Molecular Weight Biomolecules. (United States)

    Cuecas, Alba; Cruces, Jorge; Galisteo-López, Juan F; Peng, Xiaojun; Gonzalez, Juan M


    Some low molecular weight biomolecules, i.e., NAD(P)H, are unstable at high temperatures. The use of these biomolecules by thermophilic microorganisms has been scarcely analyzed. Herein, NADH stability has been studied at different temperatures and viscosities. NADH decay increased at increasing temperatures. At increasing viscosities, NADH decay rates decreased. Thus, maintaining relatively high cellular viscosity in cells could result in increased stability of low molecular weight biomolecules (i.e., NADH) at high temperatures, unlike what was previously deduced from studies in diluted water solutions. Cellular viscosity was determined using a fluorescent molecular rotor in various prokaryotes covering the range from 10 to 100°C. Some mesophiles showed the capability of changing cellular viscosity depending on growth temperature. Thermophiles and extreme thermophiles presented a relatively high cellular viscosity, suggesting this strategy as a reasonable mechanism to thrive under these high temperatures. Results substantiate the capability of thermophiles and extreme thermophiles (growth range 50-80°C) to stabilize and use generally considered unstable, universal low molecular weight biomolecules. In addition, this study represents a first report, to our knowledge, on cellular viscosity measurements in prokaryotes and it shows the dependency of prokaryotic cellular viscosity on species and growth temperature.

  15. Spermine Condenses DNA, but Not RNA Duplexes

    Energy Technology Data Exchange (ETDEWEB)

    Katz, Andrea M.; Tolokh, Igor S.; Pabit, Suzette A.; Baker, Nathan; Onufriev, Alexey V.; Pollack, Lois


    Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA, and some RNAs such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA, but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA and compare our findings with predictions of molecular dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence, containing a mixture of 14 GC pairs and 11 AU pairs, resists condensation relative to DNA of an equivalent sequence or to 25 base pair poly(rA):poly(rU) RNA. Comparison of wide-angle x-ray scattering profiles with simulation suggests that spermine is sequestered deep within the major groove of mixed sequence RNA, preventing condensation by limiting opportunities to bridge to other molecules as well as stabilizing the RNA by locking it into a particular conformation. In contrast, for DNA, simulations suggest that spermine binds external to the duplex, offering opportunities for intermolecular interaction. The goal of this study is to explain how RNA can remain soluble, and available for interaction with other molecules in the cell, despite the presence of spermine at concentrations high enough to precipitate DNA.

  16. Competition between radiative and strong force decay (United States)

    Tabor, Samuel


    For nuclear states unbound to neutron decay, radiative emission is often assumed to not dominate over neutron decay mediated by the far stronger strong interaction, except for very low neutron energies and high angular momentum barriers. Recent experimental investigations of 19O and 27 Mg populated in heavy-ion fusion-evaporation reactions have revealed predominantly gamma decays from a number of states unbound to neutron decay by up to 2 MeV. In most cases the angular momentum barrier is not sufficient to inhibit neutron decay enough to allow E-M decay with widths of up to an eV or so to win. Other inhibitions to particle decay, including low spectroscopic factors, will be discussed. Supported in part by NSF Grant No. 1401574.

  17. Examining CP Symmetry in Strange Baryon Decays

    CERN Document Server

    Luk, K B


    Non-conservation of CP symmetry can manisfest itself in non-leptonic hyperon decays as a difference in the decay parameter between the strange-baryon decay and its charge conjugate. By comparing the decay distribution in the $\\Lambda$ helicity frame for the decay sequence $\\Xi^{-} \\to \\Lambda \\pi^{-}$, $\\Lambda \\to p \\pi^{-}$ with that of $\\bar{\\Xi}^{+}$ decay, E756 at Fermilab did not observe any CP-odd effect at the $10^{-2}$ level. The status of a follow-up experiment, HyperCP (FNAL E871), to search for CP violation in charged $\\Xi-\\Lambda$ decay with a sensitivity of $10^{-4}$ is also presented.

  18. Re-inspection of small RNA sequence datasets reveals several novel human miRNA genes.

    Directory of Open Access Journals (Sweden)

    Thomas Birkballe Hansen

    Full Text Available BACKGROUND: miRNAs are key players in gene expression regulation. To fully understand the complex nature of cellular differentiation or initiation and progression of disease, it is important to assess the expression patterns of as many miRNAs as possible. Thereby, identifying novel miRNAs is an essential prerequisite to make possible a comprehensive and coherent understanding of cellular biology. METHODOLOGY/PRINCIPAL FINDINGS: Based on two extensive, but previously published, small RNA sequence datasets from human embryonic stem cells and human embroid bodies, respectively [1], we identified 112 novel miRNA-like structures and were able to validate miRNA processing in 12 out of 17 investigated cases. Several miRNA candidates were furthermore substantiated by including additional available small RNA datasets, thereby demonstrating the power of combining datasets to identify miRNAs that otherwise may be assigned as experimental noise. CONCLUSIONS/SIGNIFICANCE: Our analysis highlights that existing datasets are not yet exhaustedly studied and continuous re-analysis of the available data is important to uncover all features of small RNA sequencing.

  19. Messenger RNA Turnover Processes in Escherichia coli, Bacillus subtilis, and Emerging Studies in Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    Kelsi L. Anderson


    Full Text Available The regulation of mRNA turnover is a recently appreciated phenomenon by which bacteria modulate gene expression. This review outlines the mechanisms by which three major classes of bacterial trans-acting factors, ribonucleases (RNases, RNA binding proteins, and small noncoding RNAs (sRNA, regulate the transcript stability and protein production of target genes. Because the mechanisms of RNA decay and maturation are best characterized in Escherichia coli, the majority of this review will focus on how these factors modulate mRNA stability in this organism. However, we also address the effects of RNases, RNA binding proteins, sRNAs on mRNA turnover, and gene expression in Bacillus subtilis, which has served as a model for studying RNA processing in gram-positive organisms. We conclude by discussing emerging studies on the role modulating mRNA stability has on gene expression in the important human pathogen Staphylococcus aureus.

  20. Hierarchical Cellular Structures in High-Capacity Cellular Communication Systems

    CERN Document Server

    Jain, R K; Agrawal, N K


    In the prevailing cellular environment, it is important to provide the resources for the fluctuating traffic demand exactly in the place and at the time where and when they are needed. In this paper, we explored the ability of hierarchical cellular structures with inter layer reuse to increase the capacity of mobile communication network by applying total frequency hopping (T-FH) and adaptive frequency allocation (AFA) as a strategy to reuse the macro and micro cell resources without frequency planning in indoor pico cells [11]. The practical aspects for designing macro- micro cellular overlays in the existing big urban areas are also explained [4]. Femto cells are inducted in macro / micro / pico cells hierarchical structure to achieve the required QoS cost effectively.

  1. Combinatorics of RNA-RNA interaction

    DEFF Research Database (Denmark)

    Li, Thomas J X; Reidys, Christian


    RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...

  2. Aminoacyl-tRNA Synthetase Complexes in Evolution

    Directory of Open Access Journals (Sweden)

    Svitlana Havrylenko


    Full Text Available Aminoacyl-tRNA synthetases are essential enzymes for interpreting the genetic code. They are responsible for the proper pairing of codons on mRNA with amino acids. In addition to this canonical, translational function, they are also involved in the control of many cellular pathways essential for the maintenance of cellular homeostasis. Association of several of these enzymes within supramolecular assemblies is a key feature of organization of the translation apparatus in eukaryotes. It could be a means to control their oscillation between translational functions, when associated within a multi-aminoacyl-tRNA synthetase complex (MARS, and nontranslational functions, after dissociation from the MARS and association with other partners. In this review, we summarize the composition of the different MARS described from archaea to mammals, the mode of assembly of these complexes, and their roles in maintenance of cellular homeostasis.

  3. Comment on "Length-dependent translation of messenger RNA by ribosomes"

    CERN Document Server

    Zhang, Yunxin


    In recent paper [Phys. Rev. E {\\bf 83}, 042903 (2011)], a simple model for the translation of messenger RNA by ribosomes is provided, and the expression of translational ratio of protein is given. In this comments, varied methods to get this ratio are addressed. Depending on a different method, we find that, roughly speaking, this translational ratio decays exponentially with mRNA length in prokaryotic cell, and reciprocally with mRNA length in eukaryotic cells.

  4. SUPERKILLER Complex Components Are Required for the RNA Exosome-Mediated Control of Cuticular Wax Biosynthesis in Arabidopsis Inflorescence Stems. (United States)

    Zhao, Lifang; Kunst, Ljerka


    ECERIFERUM7 (CER7)/AtRRP45B core subunit of the exosome, the main cellular 3'-to-5' exoribonuclease, is a positive regulator of cuticular wax biosynthesis in Arabidopsis (Arabidopsis thaliana) inflorescence stems. CER7-dependent exosome activity determines stem wax load by controlling transcript levels of the wax-related gene CER3 Characterization of the second-site suppressors of the cer7 mutant revealed that small interfering RNAs (siRNAs) are direct effectors of CER3 expression. To explore the relationship between the exosome and posttranscriptional gene silencing (PTGS) in regulating CER3 transcript levels, we investigated two additional suppressor mutants, wax restorer1 (war1) and war7. We show that WAR1 and WAR7 encode Arabidopsis SUPERKILLER3 (AtSKI3) and AtSKI2, respectively, components of the SKI complex that associates with the exosome during cytoplasmic 3'-to-5' RNA degradation, and that CER7-dependent regulation of wax biosynthesis also requires participation of AtSKI8. Our study further reveals that it is the impairment of the exosome-mediated 3'-5' decay of CER3 transcript in the cer7 mutant that triggers extensive production of siRNAs and efficient PTGS of CER3. This identifies PTGS as a general mechanism for eliminating highly abundant endogenous transcripts that is activated when 3'-to-5' mRNA turnover by the exosome is disrupted. Diminished efficiency of PTGS in ski mutants compared with cer7, as evidenced by lower accumulation of CER3-related siRNAs, suggests that reduced amounts of CER3 transcript are available for siRNA synthesis, possibly because CER3 mRNA that does not interact with SKI is degraded by 5'-to-3' XRN4 exoribonuclease.

  5. Classifying cellular automata using grossone (United States)

    D'Alotto, Louis


    This paper proposes an application of the Infinite Unit Axiom and grossone, introduced by Yaroslav Sergeyev (see [7] - [12]), to the development and classification of one and two-dimensional cellular automata. By the application of grossone, new and more precise nonarchimedean metrics on the space of definition for one and two-dimensional cellular automata are established. These new metrics allow us to do computations with infinitesimals. Hence configurations in the domain space of cellular automata can be infinitesimally close (but not equal). That is, they can agree at infinitely many places. Using the new metrics, open disks are defined and the number of points in each disk computed. The forward dynamics of a cellular automaton map are also studied by defined sets. It is also shown that using the Infinite Unit Axiom, the number of configurations that follow a given configuration, under the forward iterations of cellular automaton maps, can now be computed and hence a classification scheme developed based on this computation.

  6. Prognosis of Different Cellular Generations

    Directory of Open Access Journals (Sweden)

    Preetish Ranjan


    Full Text Available Technological advancement in mobile telephony from 1G to 3G, 4G and 5G has a very axiomatic fact that made an entire world a global village. The cellular system employs a different design approach and technology that most commercial radio and television system use. In the cellular system, the service area is divided into cells and a transmitter is designed to serve an individual cell. The system seeks to make efficient use of available channels by using low-power transmitters to allow frequency reuse at a smaller distance. Maximizing the number of times each channel can be reused in a given geographical area is the key to an efficient cellular system design. During the past three decades, the world has seen significant changes in telecommunications industry. There have been some remarkable aspects to the rapid growth in wireless communications, as seen by the large expansion in mobile systems. This paper focuses on “Past, Present & Future of Cellular Telephony” and some light has been thrown upon the technologies of the cellular systems, namely 1G, 2G, 2.5G, 3G and future generations like 4G and 5G systems as well.

  7. Systemic RNA Interference Deficiency-1 (SID-1) Extracellular Domain Selectively Binds Long Double-stranded RNA and Is Required for RNA Transport by SID-1. (United States)

    Li, Weiqiang; Koutmou, Kristin S; Leahy, Daniel J; Li, Min


    During systemic RNA interference (RNAi) in Caenorhabditis elegans, RNA spreads across different cells and tissues in a process that requires the systemic RNA interference deficient-1 (sid-1) gene, which encodes an integral membrane protein. SID-1 acts cell-autonomously and is required for cellular import of interfering RNAs. Heterologous expression of SID-1 in Drosophila Schneider 2 cells enables passive uptake of dsRNA and subsequent soaking RNAi. Previous studies have suggested that SID-1 may serve as an RNA channel, but its precise molecular role remains unclear. To test the hypothesis that SID-1 mediates a direct biochemical recognition of RNA molecule and subsequent permeation, we expressed the extracellular domain (ECD) of SID-1 and purified it to near homogeneity. Recombinant purified SID-1 ECD selectively binds dsRNA but not dsDNA in a length-dependent and sequence-independent manner. Genetic missense mutations in SID-1 ECD causal for deficient systemic RNAi resulted in significant reduction in its affinity for dsRNA. Furthermore, full-length proteins with these mutations decrease SID-1-mediated RNA transport efficiency, providing evidence that dsRNA binding to SID-1 ECD is related to RNA transport. To examine the functional similarity of mammalian homologs of SID-1 (SIDT1 and SIDT2), we expressed and purified mouse SIDT1 and SIDT2 ECDs. We show that they bind long dsRNA in vitro, supportive of dsRNA recognition. In summary, our study illustrates the functional importance of SID-1 ECD as a dsRNA binding domain that contributes to RNA transport.


    Energy Technology Data Exchange (ETDEWEB)



    In his review of radionuclides for dating purposes, Roth noted that there were a large number of nuclides, normally considered ''stable'' but which are radioactive with a very long half-life. Roth suggested that I review the data on the half-life values of these long-lived nuclides for a discussion session at the next meeting. These half-life values for long-lived nuclides include those due to various decay modes, {alpha}-decay, {beta}-decay, electron capture decay, {beta}{beta}-decay and spontaneous fission decay. This report is preliminary but will provide a quick overview of the extensive table of data on the recommendations from that review.

  9. JENDL FP decay data file 2000

    Energy Technology Data Exchange (ETDEWEB)

    Katakura, Jun-ichi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Yoshida, Tadashi [Musashi Inst. of Tech., Tokyo (Japan); Oyamatsu, Kazuhiro [Aichi Shukutoku Univ., Nagakute, Aichi (Japan); Tachibana, Takahiro [Waseda Univ., Tokyo (Japan)


    A decay data file of fission product (FP) nuclides has been developed for the use in nuclear technology field as one of special purpose files of JENDL (Japanese Evaluated Nuclear Data Library) in the format of ENDF/B and it is called JENDL FP Decay Data File 2000. The file includes the decay data for 1229 fission product nuclides: 142 stable and 1087 unstable nuclides. The data included for a nuclide are decay modes, their Q values and branching ratios, average decay energy values of beta-rays, gamma-rays and alpha-particles and their spectral data. The primary source of the decay data is ENSDF (Evaluated Nuclear Structure Data File), which is the internationally recognized data file of nuclear structure properties. The data in ENSDF, however, cover only measured ones. The data of the short-lived nuclides needed for the application fields such as decay heat prediction are often incomplete or not measured because of their short half-lives. For such nuclides a theoretical model calculation is applied to derive the needed data such as average decay energies and spectral data. The data in JENDL FP Decay Data File 2000 have been tested by summation calculation comparing its results with measured data of decay heat values and aggregate fission product spectra of various fissioning nuclei. The comparison showed good agreement between the calculated results and the measured values. (author)

  10. Rare beauty and charm decays at LHCb

    Directory of Open Access Journals (Sweden)

    Albrecht Johannes


    Full Text Available Rare heavy flavor decays are an ideal place to search for the effects of potential new particles that modify the decay rates or the Lorentz structure of the decay vertices. The LHCb experiment, a dedicated heavy flavour experiment at the LHC at CERN. It has recorded the worlds largest sample of heavy meson and lepton decays. The status of the rare decay analyses with 1 fb−1 of √s = 7 TeV and 1.1 fb−1 of √s = 8 TeV of pp–collisions collected by the LHCb experiment in 2011 and 2012 is reviewed. The worlds most precise measurements of the angular structure of B0 → K*0μ+μ− and B+ → K+μ+μ− decays is discussed, as well as the isospin asymmetry measurement in B → K(*μ+μ− decays. The first evidence for the very rare decay Bs0 → µ+µ− is presented together with the most stringent upper exclusion limits on the branching fraction of decays of B0, D0 and Ks0 mesons into two muons. This note finishes with the discussion of searches for lepton number and lepton flavor violating τ decays.

  11. Determination of the Turbulent Decay Exponent (United States)

    Perot, J.; Zusi, Chris


    All theories concerning the decay of isotropic turbulence agree that the turbulent kinetic energy has a power law dependence on time. However, there is significant disagreement about what the value of the exponent should be for this power law. The primary theories, proposed by researchers such as Batchelor, Townsend, and Kolmogorov, have the decay exponent at values of 1, 6/5, 10/7, 3/2, 2, and 5/2. The debate over the decay exponent has remained unresolved for many decades because the decay exponent is an extremely sensitive quantity. Experiments have decay times which are too short to be able to accurately differentiate between the various theoretical possibilities, and all prior numerical simulations of decaying turbulence impose the decay rate a priori via the choice of initial conditions. In this work, direct numerical simulation is used to achieve very long decay times, and the initial turbulence is generated by the Navier-Stokes equations and is not imposed. The initial turbulence is created by the stirring action of the flow past 768 small randomly placed cubes. Stirring occurs at 1/30th of the simulation domain size so that the low wavenumber and large scale behavior of the turbulent spectrum which dictates the decay rate is generated by the fluid and is not imposed. It is shown that in all 16 simulations the decay exponent closely matches the theoretical predictions of Saffman at both high and low Reynolds numbers. Perot, AIP Advances 1, 022104 (2011).

  12. Vacuum Decay via Lorentzian Wormholes (United States)

    Rosales, J. L.

    We speculate about the space-time description due to the presence of Lorentzian worm-holes (handles in space-time joining two distant regions or other universes) in quantum gravity. The semiclassical rate of production of these Lorentzian wormholes in Reissner-Nordström space-times is calculated as a result of the spontaneous decay of vacuum due to a real tunneling configuration. In the magnetic case it only depends on the value of the field theoretical fine structure constant. We predict that the quantum probability corresponding to the nucleation of such geodesically complete space-times should be acutally negligible in our physical Universe.

  13. Experiments on double beta decay

    Energy Technology Data Exchange (ETDEWEB)

    Busto, J. [Neuchatel Univ. (Switzerland). Inst. de Physique


    The Double Beta Decay, and especially ({beta}{beta}){sub 0{nu}} mode, is an excellent test of Standard Model as well as of neutrino physics. From experimental point of view, a very large number of different techniques are or have been used increasing the sensitivity of this experiments quite a lot (the factor of 10{sup 4} in the last 20 years). In future, in spite of several difficulties, the sensitivity would be increased further, keeping the interest of this very important process. (author) 4 figs., 5 tabs., 21 refs.

  14. Gravitational effects on inflaton decay

    Energy Technology Data Exchange (ETDEWEB)

    Ema, Yohei; Jinno, Ryusuke; Mukaida, Kyohei [Department of Physics, University of Tokyo,Tokyo 113-0033 (Japan); Nakayama, Kazunori [Department of Physics, University of Tokyo,Tokyo 113-0033 (Japan); Kavli IPMU, TODIAS, University of Tokyo,Kashiwa 277-8583 (Japan)


    We point out that the inflaton inevitably couples to all non-conformally coupled matters gravitationally through an oscillation in the Hubble parameter or the cosmic scale factor. It leads to particle production during the inflaton oscillation regime, which is most efficient just after inflation. Moreover, the analysis is extended to the model with non-minimal inflaton couplings to gravity, in which the Hubble parameter oscillates more violently. We apply our results to the graviton production by the inflaton: gravitons are also produced just after inflation, but the non-minimal coupling does not induce inflaton decay into the graviton pair.

  15. Gravitational Effects on Inflaton Decay

    CERN Document Server

    Ema, Yohei; Mukaida, Kyohei; Nakayama, Kazunori


    We point out that the inflaton inevitably couples to all non-conformally coupled matters gravitationally through an oscillation in the Hubble parameter or the cosmic scale factor. It leads to particle production during the inflaton oscillation regime, which is most efficient just after inflation. Moreover, the analysis is extended to the model with non-minimal inflaton couplings to gravity, in which the Hubble parameter oscillates more violently. We apply our results to the graviton production by the inflaton: gravitons are also produced just after inflation, but the non-minimal coupling does not induce inflaton decay into the graviton pair.

  16. Semiclassical calculation of decay rates

    CERN Document Server

    Bessa, A; Fraga, E S


    Several relevant aspects of quantum-field processes can be well described by semiclassical methods. In particular, the knowledge of non-trivial classical solutions of the field equations, and the thermal and quantum fluctuations around them, provide non-perturbative information about the theory. In this work, we discuss the calculation of the one-loop effective action from the semiclasssical viewpoint. We intend to use this formalism to obtain an accurate expression for the decay rate of non-static metastable states.

  17. Neutrinoless double beta decay experiments

    CERN Document Server

    Zuber, K


    The study of neutrinoless double beta decay is of outmost importance for neutrino physics. It is considered to be the gold plated channel to probe the fundamental character of neutrinos and to determine the neutrino mass. From the experimental point about nine different isotopes are explored for the search. After a general introduction follows a short discussion on nuclear matrix element calculations and supportive measurements. The current experimental status of double beta searches is presented followed by a short discussion of the ideas and proposals for large scale experiments.

  18. Radiative Ke3 decays revisited

    CERN Document Server

    Gasser, J; Paver, N; Verbeni, M


    Motivated by recent experimental results and ongoing measurements, we review the chiral perturbation theory prediction for radiative Ke3 decays (neutral kaons). Special emphasis is given on the stability of the inner bremsstrahlung-dominated relative branching ratio vs. the Ke3 form factors, and on the separation of the structure dependent amplitude in differential distributions over the phase space. For the structure dependent terms, an assessment of the order p^6 corrections is given. In particular, a full next-to-leading order calculation of the axial component is performed. The experimental analysis of the photon energy spectrum is discussed, and other potentially useful distributions are introduced.

  19. Tau decays into K* mesons (United States)

    Albrecht, H.; Hamacher, T.; Hofmann, R. P.; Kirchhoff, T.; Mankel, R.; Nau, A.; Nowak, S.; Schröder, H.; Schulz, H. D.; Walter, M.; Wurth, R.; Hast, C.; Kapitza, H.; Kolanoski, H.; Kosche, A.; Lange, A.; Lindner, A.; Schieber, M.; Siegmund, T.; Spaan, B.; Thurn, H.; Töpfer, D.; Wegener, D.; Eckstein, P.; Schubert, K. R.; Schwierz, R.; Waldi, R.; Reim, K.; Wegener, H.; Eckmann, R.; Kuipers, H.; Mai, O.; Mundt, R.; Oest, T.; Reiner, R.; Schmidt-Parzefall, W.; Stiewe, J.; Werner, S.; Ehret, K.; Hofmann, W.; Hüpper, A.; Knöpfle, K. T.; Spengler, J.; Krieger, P.; Macfarlane, D. B.; Saull, P. R. B.; Tzamariudaki, K.; van de Water, R. G.; Yoon, T.-S.; Frankl, C.; Reßing, D.; Schmidtler, M.; Schneider, M.; Weseler, S.; Kernel, G.; Križan, P.; Križnič, E.; Podobnik, T.; Živko, T.; Balagura, V.; Belyaev, I.; Schechelnitsky, S.; Danilov, M.; Doutskoy, A.; Gershtein, Yu.; Golutvin, A.; Korolko, I.; Kostina, G.; Litvintsev, D.; Lubimov, V.; Pakhlov, P.; Semenov, S.; Snizhko, A.; Tichomirov, I.; Zaitsev, Yu.


    Using the ARGUS detector at the storage ring DORIS II we have measured τ decays into three charged mesons containing K * mesons. Exploiting the good particle identification capabilities of the detector we have determined the following branching ratios:Brleft( {tau ^ - to overline {K^{*0} } π ^ - v_tau } right) = left( {0.25 ± 0.10 ± 0.05} right)% , B r (τ-→ K *0 K - v τ)= (0.20±0.05±0.04)%, and B r (τ-→ K *- X 0 v τ) =(1.15±0.15-0.18 +0.13)%.

  20. Role of highly conserved pyrimidine-rich sequences in the 3' untranslated region of the GAP-43 mRNA in mRNA stability and RNA-protein interactions. (United States)

    Kohn, D T; Tsai, K C; Cansino, V V; Neve, R L; Perrone-Bizzozero, N I


    We have shown previously that the mRNA for the growth-associated protein GAP-43 is selectively stabilized during neuronal differentiation. In this study, we explored the role of its highly conserved 3' untranslated region (3'UTR) in mRNA stability and RNA-protein interactions. The 3'UTRs of the rat and chicken GAP-43 mRNAs show 78% sequence identity, which is equivalent to the conservation of their coding regions. In rat PC12 cells stably transfected with the full-length rat or chicken GAP-43 cDNAs, the transgene mRNAs decayed with same half-life of about 3 h. The GAP-43 3'UTR also caused the rabbit beta-globin mRNA to decay with a half-life of 4 h, indicating that the major determinants for GAP-43 mRNA stability are localized in its highly conserved 3'UTR. Three brain cytosolic RNA-binding proteins (molecular mass 40, 65 and 95 kDa) were found to interact with both the rat and chicken GAP-43 mRNAs. These RNA-protein interactions were specific and involved pyrimidine-rich sequences in the 3'UTR. Like the GAP-43 mRNA, the activity of these proteins was enriched in brain and increased during development. We propose that highly conserved pyrimidine-rich sequences in the 3'UTR of this mRNA regulate GAP-43 gene expression via interactions with specific RNA-binding proteins.