283 research outputs found

    Litigation and special education :

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

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    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

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    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

    Banse, K. and S.A. Piontkovsky (eds.). The mesoscale structure of the epipelagic ecosystem of the open Northern Arabian Sea

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    Book review: BANSE, K. and S.A. PIONTKOVSKY (eds.). – 2006. The mesoscale structure of the epipelagic ecosystem of the open Northern Arabian Sea. Universities Press, Hyderabad, India. 237 pp. ISBN 81 7371 496 7This book presents an extensive body of information obtained mainly from the thirtieth cruise of the R/V Professor Bodyanitsky to the Arabian Sea, carried out in 1990. It is part of a series published by the Universities Press, India, with the support of the Indian Academy of Sciences in Bangalore, whose aim is to narrow the English-Russian language gap concerning scientific literature on low-latitude oceansPeer reviewe

    Equilibrium between radiation and matter for classical relativistic multiperiodic systems. II. Study of radiative equilibrium with Rayleigh-Jeans radiation

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    We continue the study of the problem of equilibrium between radiation and classical relativistic systems begun previously Phys. Rev. D 27 1254 (1983). We consider the emission and absorption of energy by a relativistic pointlike particle immersed in a Rayleigh-Jeans radiation field. The particle is acted upon by a force which, if alone, would produce a multiply periodic motion. It is shown that radiative balance at each frequency holds. A discussion is given of the results reported in both papers

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

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    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

    The Telomerase Database

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    Telomerase is a ribonucleoprotein enzyme that extends DNA at the chromosome ends in most eukaryotes. Since 1985, telomerase has been studied intensively and components of the telomerase complex have been identified from over 160 eukaryotic species. In the last two decades, there has been a growing interest in studying telomerase owing to its vital role in chromosome stability and cellular immortality. To keep up with the remarkable explosion of knowledge about telomerase, we compiled information related to telomerase in an exhaustive database called the Telomerase Database (http://telomerase.asu.edu/). The Telomerase Database provides comprehensive information about (i) sequences of the RNA and protein subunits of telomerase, (ii) sequence alignments based on the phylogenetic relationship and structure, (iii) secondary structures of the RNA component and tertiary structures of various subunits of telomerase, (iv) mutations of telomerase components found in human patients and (v) active researchers who contributed to the wealth of current knowledge on telomerase. The information is hierarchically organized by the components, i.e. the telomerase reverse transcriptase (TERT), telomerase RNA (TR) and other telomerase-associated proteins. The Telomerase Database is a useful resource especially for researchers who are interested in investigating the structure, function, evolution and medical relevance of the telomerase enzyme

    How mammalian predation contributes to tropical tree community structure

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    The recruitment of seedlings from seeds is the key demographic transition for rain forest trees. Though tropical forest mammals are known to consume many seeds, their effects on tree community structure remain little known. To evaluate their effects, we monitored 8000 seeds of 24 tree species using exclosure cages that were selectively permeable to three size-classes of mammals for up to 4.4 years. Small and medium-bodied mammals removed many more seeds than did large mammals, and they alone generated beta diversity and negative density dependence, whereas all mammals reduced diversity and shaped local species composition. Thus, small and medium-bodied mammals more strongly contributed to community structure and promoted species coexistence than did large mammals. Given that seedling recruitment is seed-limited for most species, alterations to the composition of the community of mammalian seed predators is expected to have long-term consequences for tree community structure in tropical forests

    A strong conditional mutualism limits and enhances seed dispersal and germination of a tropical palm

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    Seed predation and seed dispersal can have strong effects on early life history stages of plants. These processes have often been studied as individual effects, but the degree to which their relative importance co-varies with seed predator abundance and how this influences seed germination rates is poorly understood. Therefore, we used a combination of observations and field experiments to determine the degree to which germination rates of the palm Astrocaryum mexicanum varied with abundance of a small mammal seed predator/disperser, Heteromysdesmarestianus, in a lowland tropical forest. Patterns of abundance of the two species were strongly related; density of H. desmarestianus was low in sites with low density of A. mexicanum and vice versa. Rates of predation and dispersal of A. mexicanum seeds depended on abundance of H. desmarestianus; sites with high densities of H. desmarestianus had the highest rates of seed predation and lowest rates of seed germination, but a greater total number of seeds were dispersed and there was greater density of seedlings, saplings, and adults of A. mexicanum in these sites. When abundance of H. desmarestianus was experimentally reduced, rates of seed predation decreased, but so did dispersal of A. mexicanum seeds. Critically, rates of germination of dispersed seeds were 5 times greater than undispersed seeds. The results suggest that the relationship between A. mexicanum and H. desmarestianus is a conditional mutualism that results in a strong local effect on the abundance of each species. However, the magnitude and direction of these effects are determined by the relative strength of opposing, but related, mechanisms. A. mexicanum nuts provide H. desmarestianus with a critical food resource, and while seed predation on A. mexicanum nuts by H. desmarestianus is very intense, A. mexicanum ultimately benefits because of the relatively high germination rates of its seeds that are dispersed by H. desmarestianus
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