Structure of the Tetrahymena thermophila telomerase RNA helix II template boundary element

Telomere addition by telomerase requires an internal templating sequence located in the RNA subunit of telomerase. The correct boundary definition of this template sequence is essential for the proper addition of the nucleotide repeats. Incorporation of incorrect telomeric repeats onto the ends of chromosomes has been shown to induce chromosomal instability in ciliate, yeast and human cells. A 5′ template boundary defining element (TBE) has been identified in human, yeast and ciliate telomerase RNAs. Here, we report the solution structure of the TBE element (helix II) from Tetrahymena thermophila telomerase RNA. Our results indicate that helix II and its capping pentaloop form a well-defined structure including unpaired, stacked adenine nucleotides in the stem and an unusual syn adenine nucleotide in the loop. A comparison of the T.thermophila helix II pentaloop with a pentaloop of the same sequence found in the 23S rRNA of the Haloarcula marismortui ribosome suggests possible RNA and/or protein interactions for the helix II loop within the Tetrahymena telomerase holoenzyme

Variation in prey delivered to common Black-Hawk (Buteogallus anthracinus) nests in Arizona drainage basins

Understanding how raptor diets vary across local and regional scales can be important when human actions have the potential to alter prey abundances. We combined data on prey delivered to 16 Common Black-Hawk (Buteogallus anthracinus) nests in three tributaries of the Verde River, Arizona, in 2008 and 2009 with similar data reported previously (1994) for three other Arizona drainage basins to better understand variation in diet composition within and across drainage basins. Within the three drainage basins studied in 2008 and 2009, nests clustered into two groups: those along Fossil Creek, where fish and amphibians were common, and those in Wet Beaver and Oak Creek drainage basins, where reptiles and nonnative crayfish were more abundant. When data from all six drainage basins were combined, drainage basins again clustered into two groups, with prey deliveries in one cluster dominated by fish and amphibians and in the other cluster by reptiles. These results confirm the opportunistic nature of prey use by Common Black-Hawks and highlight the variation in diet that can occur both within and among drainage basins. Management targeting the eradication of nonnative crayfish or the reintroduction of native amphibians and fish could alter prey availability for this raptor species

Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA

Telomerase extends the 3′-ends of linear chromosomes by adding conserved telomeric DNA repeats and is essential for cell proliferation and genomic stability. Telomerases from all organisms contain a telomerase reverse transcriptase and a telomerase RNA (TER), which together provide the minimal functional elements for catalytic activity in vitro. The RNA component of many functional ribonucleoproteins contains modified nucleotides, including conserved pseudouridines (Ψs) that can have subtle effects on structure and activity. We have identified potential Ψ modification sites in human TER. Two of the predicted Ψs are located in the loop of the essential P6.1 hairpin from the CR4-CR5 domain that is critical for telomerase catalytic activity. We investigated the effect of P6.1 pseudouridylation on its solution NMR structure, thermodynamic stability of folding and telomerase activation in vitro. The pseudouridylated P6.1 has a significantly different loop structure and increase in stability compared to the unmodified P6.1. The extent of loop nucleotide interaction with adjacent residues more closely parallels the extent of loop nucleotide evolutionary sequence conservation in the Ψ-modified P6.1 structure. Pseudouridine-modification of P6.1 slightly attenuates telomerase activity but slightly increases processivity in vitro. Our results suggest that Ψs could have a subtle influence on human telomerase activity via impact on TER–TERT or TER–TER interactions

Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA

Formation of a pseudoknot in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the pseudoknot (PK) is in equilibrium with an extended hairpin (HP) structure. We use molecular simulations of a coarse-grained model, which reproduces most of the salient features of the experimental melting profiles of PK and HP, to show that crowding enhances the stability of PK relative to HP in the wild type and in a mutant associated with dyskeratosis congenita. In monodisperse suspensions, small crowding particles increase the stability of compact structures to a greater extent than larger crowders. If the sizes of crowders in a binary mixture are smaller than the unfolded RNA, the increase in melting temperature due to the two components is additive. In a ternary mixture of crowders that are larger than the unfolded RNA, which mimics the composition of ribosome, large enzyme complexes and proteins in E. coli, the marginal increase in stability is entirely determined by the smallest component. We predict that crowding can restore partially telomerase activity in mutants, which dramatically decrease the PK stability.Comment: File "JACS_MAIN_archive_PDF_from_DOC.pdf" (PDF created from DOC) contains the main text of the paper File JACS_SI_archive.tex + 7 figures are the supplementary inf

FUSE: Lightweight Guaranteed Distributed Failure Notification

FUSE is a lightweight failure notification service for building distributed systems. Distributed systems built with FUSE are guaranteed that failure notifications never fail. Whenever a failure notification is triggered, all live members of the FUSE group will hear a notification within a bounded period of time, irrespective of node or communication failures. In contrast to previous work on failure detection, the responsibility for deciding that afailure has occurred is shared between the FUSE service and the distributed application. This allows applications to implement their own definitions of failure. Our experience building a scalable distributed event delivery system on an overlay network has convinced us of the usefulness of this service. Our results demonstrate that the network costs of each FUSE group can be small; in particular, our overlay network implementation requires no additional liveness-verifying ping traffic beyond that already needed to maintain the overlay, making the steady state network load independent of the number of active FUSE groups

Einstein's quantum theory of the monatomic ideal gas: non-statistical arguments for a new statistics

In this article, we analyze the third of three papers, in which Einstein presented his quantum theory of the ideal gas of 1924-1925. Although it failed to attract the attention of Einstein's contemporaries and although also today very few commentators refer to it, we argue for its significance in the context of Einstein's quantum researches. It contains an attempt to extend and exhaust the characterization of the monatomic ideal gas without appealing to combinatorics. Its ambiguities illustrate Einstein's confusion with his initial success in extending Bose's results and in realizing the consequences of what later became to be called Bose-Einstein statistics. We discuss Einstein's motivation for writing a non-combinatorial paper, partly in response to criticism by his friend Ehrenfest, and we paraphrase its content. Its arguments are based on Einstein's belief in the complete analogy between the thermodynamics of light quanta and of material particles and invoke considerations of adiabatic transformations as well as of dimensional analysis. These techniques were well-known to Einstein from earlier work on Wien's displacement law, Planck's radiation theory, and the specific heat of solids. We also investigate the possible role of Ehrenfest in the gestation of the theory.Comment: 57 pp

Experimental determination of the transient transport and of fluctuations relevant to transport in ASDEX

Particle transport was studied in ASDEZ with modulated puffing of the discharge gas and of impurities. The energy transport is investigated by numerical simulation of the heat pulse after the swatooth crash. Small scale density fluctuations are investigated in the confinement region with far infrared scattering and reflectometry and in the edge plasma with langmuir probes and Ha diagnostic. In addition to a diffuse component of the particle transport, a strong inward drift is observed in all discharges. In ohmic discharges the transport coefficients decrease and saturate like 1/TE with increasing density. They are smaller in deuterium that in hydrogen. In the improved ohmic confinement (IOC)regime mainly D in the outer region is reduced. D increases proportionally to the heating power in L-mode discharges. The improvement of particle confinement in the H-mode is explained by a increase of the inward drift at the edge rather than a decrease of D. The impurity diffusion coefficient is independent of the impurity mass and charge. In ohmic discharges, it varies with ne like the bulk diffusion coefficient, is independent of B or increases weakly with B and increases with Ip. In L-mode discharges, Dimp increases linearly with the heating power. The electron thermal condustivity determined by heat pulse propagation exceeds the stationary value by a factor of 3-4, assuming merely diffusive heat transport. Convection does not significantly reduce this factor. however, non-diagonal terms

Research priorities for liver glycogen storage disease:An international priority setting partnership with the James Lind Alliance

The international liver glycogen storage disease (GSD) priority setting partnership (IGSDPSP) was established to identify the top research priorities in this area. The multiphase methodology followed the principles of the James Lind Alliance (JLA) guidebook. An international scoping survey in seven languages was distributed to patients, carers, and healthcare professionals to gather uncertainties, which were consolidated into summary questions. The existing literature was reviewed to ensure that the summary questions had not yet been answered. A second survey asked responders to prioritize these summary questions. A final shortlist of 22 questions was discussed during an international multi-stakeholder workshop, and a consensus was reached on the top 11 priorities using an adapted nominal group technique.In the first survey, a total of 1388 questions were identified from 763 responders from 58 countries. These original uncertainties were refined into 72 summary questions for a second prioritization survey. In total 562 responders from 58 countries answered the second survey. From the second survey, the top 10 for patients, carers and healthcare professionals was identified and this shortlist of 22 questions was taken to the final workshop. During the final workshop, participants identified the worldwide top 11 research priorities for liver GSD. In addition, a top three research priorities per liver GSD subtype was identified.This unique priority setting partnership is the first international, multilingual priority setting partnership focusing on ultra-rare diseases. This process provides a valuable resource for researchers and funding agencies to foster interdisciplinary and transnational research projects with a clear benefit for patients

Single-Molecule Analysis of the Human Telomerase RNA·Dyskerin Interaction and the Effect of Dyskeratosis Congenita Mutations†

It has been proposed that human telomerase RNA (hTR) interacts with dyskerin, prior to assembly of the telomerase holoenzyme. The direct interaction of dyskerin and hTR has not been demonstrated and is an experimentally challenging research problem because of difficulties in expressing and purifying dyskerin in quantities that are useful for biophysical analysis. By orthogonally labeling dyskerin and hTR, we have been able to employ single-molecule two-color coincidence detection (TCCD) to observe directly the formation of a dyskerin·hTR complex. By systematic deletion of hTR subdomains, we have gained insights into the RNA sites required for interaction with dyskerin. We then investigated mutated forms of hTR and dyskerin that are associated with dyskeratosis congenita (DC), on the basis of clinical genetics studies, for their effects on the dyskerin·hTR interaction. Dyskerin mutations associated with X-linked DC resulted in significant impairment of the dyskerin·hTR interaction, whereas mutations in hTR associated with autosomal dominant (AD) DC did not affect the interaction. We propose that disruption of the dyskerin·hTR interaction may contribute to X-linked DC