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Full Text Available.BackgroundSeveral bioinformatic approaches have previously been used to find novel sites of ADAR mediated A-to-I RNA editing in human. These studies have discovered thousands of genes that are hyper-edited in their non-coding intronic regions, especially in alu retrotransposable elements, but very few substrates that are site-selectively edited in coding regions. Known RNA edited substrates suggest, however, that site selective A-to-I editing is particularly important for normal brain development in mammals.ResultsWe have compiled a screen that enables the identification of new sites of site-selective editing, primarily in coding sequences. To avoid hyper-edited repeat regions, we applied our screen to the alu-free mouse genome. Focusing on the mouse also facilitated better experimental verification. To identify candidate sites of RNA editing, we first performed an explorative screen based on RNA structure and genomic sequence conservation. We further evaluated the results of the explorative screen by determining which transcripts were enriched for A-G mismatches between the genomic template and the expressed sequence since the editing product, inosine (I), is read as guanosine (G) by the translational machinery. For expressed sequences, we only considered coding regions to focus entirely on re-coding events. Lastly, we refined the results from the explorative screen using a novel scoring scheme based on characteristics for known A-to-I edited sites. The extent of editing in the final candidate genes was verified using total RNA from mouse brain and 454 sequencing.ConclusionsUsing this method, we identified and confirmed efficient editing at one site in the Gabra3 gene. Editing was also verified at several other novel sites within candidates predicted to be edited. Five of these sites are situated in genes coding for the neuron-specific RNA binding proteins HuB and HuD.
BackgroundSeveral bioinformatic approaches have previously been used to find novel sites of ADAR mediated A-to-I RNA editing in human. These studies have discovered thousands of...Full Text Available
http://www.ojs.unisa.edu.au/index.php/IJEI/article/view/477
I am very pleased to welcome readers to Volume 5(2) of the International Journal for Educational Integrity. Before introducing the current issue, I would like to begin with a couple of announcements. The 4th Asia-Pacific Conference on Educational Integrity: Creating an Inclusive Approach will be held at the University of Wollongong, in New South Wales, Australia, from 28-30 September. The conference is built around a stimulating, discussion-centred format on a range of topics from plagiarism to values in teaching and learning, and the broader educational context. Presentation proposals and registrations are still being accepted. For full details, please go the conference website: http://www.uow.edu.au/conferences/4APCEI_2009/home.html Shortly after 4APCEI, the Center for Academic Integrity will hold its Annual Conference. Creating a culture of integrity: Research and best practices will be held at Washington University in St Louis, Missouri, USA, from 16-18 October. Proposals relating to current trends in academic integrity, data on the success rates of various approaches to academic integrity initiatives, innovative new approaches and models of best practices are invited. For full details, please go the conference website: http://www.academicintegrity.org/conferences/2009_Conference/index.php This edition of the IJEI includes two full papers and four reviews of recently published books on issues relating to educational integrity. Brian Martin opens the journal with an expansive essay which elaborates on the little explored topic of ‘academic patronage’. Martin defines academic patronage as the bias and discrimination that occurs through decisions made, processes used, assistance given to individuals and personal interactions in academia. After providing careful descriptions of the various forms of academic patronage, Martin uses the example of honours thesis examining to illustrate some of the tensions inherent in a practice with “considerable potential for patronage”. While acknowledging the value of mentoring, such as supporting research students, and providing training, advice, references and job opportunities, Martin makes the case that academic patronage has the potential to undermine the meritocratic foundation of academia. In the second paper of this issue, Malcolm Rees and Lisa Emerson share a revised version of their presentation from the 3rd International Plagiarism Conference at Northumbria University in June 2008. Based on structured interviews with nine staff members at Massey University in New Zealand, Rees and Emerson extend the research on electronic detection of plagiarism by exploring the impact that the text-matching software program, Turnitin, has had on assessment practice. They asked staff if their use of Turnitin in traditional text-based assessments had resulted in alternative assessment approaches to reduce incidences of plagiarism, and to encourage students to work effectively with secondary source material. Although the authors found that seven of the nine staff members surveyed had not changed their assessment practices, two cases of innovative practice were identified and are showcased in the paper. The last 12 months has seen the publication of some truly outstanding books on academic integrity, and the second part of the current issue provides reviews of four of these texts. I was fortunate to be given a sneak preview of Cheating in School: What we know and what we can do (Stephen F. Davis, Patrick F. Drinan and Tricia Bertram Gallant) due to be released in August this year by Wiley-Blackwell. Julianne East from La Trobe University in Melbourne reviews Rebecca Moore Howard’s and Amy Robillard’s Pluralizing plagiarism: Identities, Contexts, Pedagogies, published by Boynton/Cook last year; Ursula McGowan from the University of Adelaide, South Australia, reviews Pedagogy, not policing: Positive approaches to academic integrity at the university (Tyra Twomey, Holly White and Ken Sagendorf), published earlier this year by the Graduate School Press at Syracuse University; and Ruth Walker from the University of Wollongong, New South Wales, reviews Caroline Eisner’s and Martha Vicinus’ edited collection Originality, Imitation and Plagiarism: Teaching Writing in the Digital Age (2008). These books, all published in the U.S., provide diverse perspectives on the multi-faceted topic of academic integrity. What brings them together is the clear commitment from each of the authors to move away from a simplistic and/or punitive focus on student plagiarism to examine the broader educational context. Academic integrity is the commitment to five fundamental values: honesty, trust, fairness, respect and responsibility (Center for Academic Integrity 2009). This view of integrity as a “clustering of values beyond honesty” (Davis, Drinan & Bertram Gallant, 2009, forthcoming, p. 26), involves much more than a commitment from students not to cheat. The Center for Academic Integrity (CAI) makes explicit that academic integrity is multi-dimensional and is enabled by all those in the educational enterprise, from students to parents, instructors and administrators. It is for this reason that the CAI’s counterpart and sponsor of this journal, the Asia Pacific Forum on Educational Integrity (APFEI), prefaces ‘integrity’ with ‘educational’ rather than ‘academic’. From the first conference in 2003, we have attempted to encapsulate the complex aspects and numerous stakeholders of integrity across the various educational sectors, with a clear intention not to limit the topic to universities (Bretag & Green, 2009, under review). It is evident from the books reviewed in this issue that the field of academic/educational integrity is attracting researchers with a sophisticated understanding of the issues that go well beyond student plagiarism, writing practices or even research ethics. Tracey Bretag, Editor IJEI References Bretag, T. & Green, M. (2009, under review). Determining outcomes for academic misconduct: Is it more important to be consistent or fair? Paper submitted for review to the 4th Asia-Pacific Conference on Educational Integrity: Creating an Inclusive Approach, University of Wollongong, 28-30 September 2009. Center for Academic Integrity (2009). Retrieved May 28, 2009 from http://www.academicintegrity.org/index.php Davis, S. F., Drinan, P. F. & Bertram Gallant, T. (2009, forthcoming). Cheating in school: What we know and what we can do. MA, USA: Wiley Blackwell, Malden. Publisher: International Journal for Educational Integrity Format: application/x-pdf Coverage: Language: Source: International Journal for Educational Integrity; Vol 5, No 1 (2009) Rights: Authors retain the copyright for their work, while granting the journal the exclusive right of first publication.
http://hdl.handle.net/2440/1819
Copyright © 2003 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of AmericaReceived for publication December 29, 2002. Two novel solid-state 13C nuclear magnetic resonance (NMR) spectroscopic techniques, PSRE (proton spin relaxation editing) and RESTORE [Restoration of Spectra via TCH and T1H (T One Rho H) Editing], were used to provide detailed chemical characterization of the organic matter from six Australian sewage sludges. These methods were used to probe the submicrometer heterogeneity of sludge organic matter, and identify and quantify spatially distinct components. Analysis of the T1H relaxation behavior of the sludges indicated that each sludge contained two types of organic domains. Carbon-13 PSRE NMR subspectra were generated to determine the chemical nature of these domains. The rapidly relaxing component of each sludge was rich in protein and alkyl carbon, and was identified as dead bacterial material. The slowly relaxing component of each sludge was rich in carbohydrate and lignin structures, and was identified as partly degraded plant material. The bacterial domains were shown, using the RESTORE technique, to also have characteristically rapid T1H relaxation rates. This rapid T1H relaxation was identified as the main cause of underrepresentation of these domains in standard 13C cross polarization (CP) NMR spectra of sludges. The heterogeneous nature of sewage sludge organic matter has implications for land application of sewage sludge, since the two components are likely to have different capacities for sorbing organic and inorganic toxicants present in sewage sludge, and will decompose at different rates.Ronald J. Smernik, Ian W. Oliver and Graham Merrington Publisher: American Society of Agronomy Contributor: School of Earth and Environmental Sciences Other identifier: Journal of Environmental Quality, 2003; 32 (4):1523-1533; 0047-2425; 0020030527 Language: en_US Source: http://jeq.scijournals.org/cgi/content/abstract/32/4/1523
http://hdl.handle.net/10536/DRO/DU:30019490
Objectives: Individual clinical interviews are typically viewed as the “gold standard” when diagnosing major depressive disorder (MDD) and when examining the validity of self-rated questionnaires. However, this approach may be problematic with older people, who are known to underreport depressive symptomatology. This study examined the effect of including an informant interview on prevalence estimations of MDD in an aged-care sample. Design: The results of an individual clinical interview for MDD were compared with those obtained when an informant interview was incorporated into the assessment. Results from each diagnostic approach were compared with scores on a self-rated depression instrument. Setting: Low-level aged-care residential facilities in Melbourne (equivalent to “residential homes,” “homes for the elderly,” or “assisted living facilities” in other countries). Participants: One hundred and sixty-eight aged-care residents (mean age: 84.68 years; SD: 6.16 years) with normal cognitive functioning. Measurements: Individual clinical interviews were conducted using the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition Axis I Disorders. This interview was modified for use with staff informants. Self-reported depression was measured using the Geriatric Depression Scale-15 (GDS-15). Results: The estimated point prevalence of MDD rose from 16% to 22% by including an informant clinical interview in the diagnostic procedure. Overall, 27% of depressed residents failed to disclose symptoms in the clinical interview. The concordance of the GDS-15 with a diagnosis of MDD was substantially lower when an informant source was included in the diagnostic procedure. Conclusion: Individual interviews and self-report questionnaires may be insufficient to detect depression among older adults. This study supports the use of an informant interview as an adjunct when diagnosing MDD among cognitively intact aged-care residents. Publisher: American Association for Geriatric Psychiatry Relation: isMemberOf: School of Psychology collection Coverage: 2009-05-01 Language: eng Rights: 2009, American Association for Geriatric Psychiatry
http://espace.library.uq.edu.au/view/UQ:141044
Chlamydial infection is responsible for a wide spectrum of diseases of the eye, genitourinary tract, and lung. This group of organisms is also implicated in the pathogenesis of coronary artery disease as well as arthritis. Since cross-species infection is widely reported (though probably underestimated), it is an advantage to have a rapid and reliable method to detect all forms of chlamydiae in patient samples. We have identified a 160/163-bp DNA fragment in Chlamydia which is highly conserved in all chlamydial species. A polymerase chain reaction method based on this sequence has been developed to detect, in clinical samples, chlamydiae which have been shown to be positive by fluorescent-staining immunoassay; this method can be utilized in combination with restriction endonuclease cleavage to identify individual chlamydial species. Thus we have developed a sensitive and rapid detection method and have used it on samples from patients with respiratory and genital infections. (C) 1999 Editions scientifiques et medicales Elsevier SAS. Publisher: Elsevier Contributor: M Hofnung Coverage: 1999-01-01T00:00:00Z
2006-10-01
Z-DNA binding protein 1 (ZBP1) belongs to a family of proteins that contain the Zα domain, which binds specifically to left-handed Z-DNA and Z-RNA. Like all vertebrate proteins in the Zα...Full Text Available
2006-10-01
Full Text Available.Z-DNA binding protein 1 (ZBP1) belongs to a family of proteins that contain the Zα domain, which binds specifically to left-handed Z-DNA and Z-RNA. Like all vertebrate proteins in the Zα family, it contains two Zα-like domains and is highly inducible by immunostimulation. Using circular dichroism spectroscopy and electrophoretic mobility shift assays we show that both Zα domains can bind Z-DNA independently and that substrate binding is greatly enhanced when both domains are linked. Full length ZBP1 and a prominent splice variant lacking the first Zα domain (ΔZα) showed strikingly different subcellular localizations. While the full length protein showed a finely punctate cytoplasmatic distribution, ZBP1ΔZα accumulated in large cytoplasmic granules. Mutation of residues important for Z-DNA binding in the first Zα domain resulted in a distribution comparable to that of ZBP1ΔZα. The ZBP1ΔZα granules are distinct from stress granules (SGs) and processing bodies but dynamically interacted with these. Polysome stabilization led to the disassembly of ZBP1ΔZα granules, indicating that mRNA are integral components. Heat shock and arsenite exposure had opposing effects on ZBP1 isoforms: while ZBP1ΔZα granules disassembled, full length ZBP1 accumulated in SGs. Our data link ZBP1 to mRNA sorting and metabolism and indicate distinct roles for ZBP1 isoforms.
Volatile organic compound (VOC) retardation in ground water
1996-05-01
This project studies the mechanisms that cause the retardation of Volatile Organic Compounds (VOC) in ground water. Laboratory column and diffusion experiments were run in an effort to determine the contribution of each mechanism to the retarded flow of the VOCs. Retardation factors (Rf), distribution coefficients (Kd) and diffusion coefficients (Dd) were determined for four VOCs commonly found in ground water. Comparison of two separate column experiments at different velocities shows that retardation is independent of flow velocity. The results from the diffusion experiment are presently being analyzed.
Visualization of scalar topology for structural enhancement
1998-09-22
Scalar fields arise in every scientific application. Existing scalar visualization techniques require that the user infer the global scalar structure from what is frequently an insufficient display of information. We present a visualization technique which numerically detects the structure at all scales, removing from the user the responsibility of extracting information implicit in the data, and presenting the structure explicitly for analysis. We further demonstrate how scalar topology detection proves useful for correct visualization and image processing applications such as image co-registration, isocontouring, and mesh compression.
User`s manual for the master equipment list: Phase 1
1997-05-12
This manual is intended to provide a user with enough detailed instruction to guide them through the Master Equipment List Phase 1 (MEL Phase 1) application system operations. The MEL Phase 1 application is a database system that stores Equipment Identification Number (EIN) information to support equipment tracking in the 200E and 200W Tank Farms for the Tank Waste Remediation System Division. The MEL Phase 1 application supports both the user application and administrative control functions. The user application functions include: viewing by Folder, reporting, performing queries, and editing specific data. The administrative control functions include: maintaining valid user identifications, passwords, privileges, defining drop-down lists, and review of the change log relating to EIN data entries, additions, deletions, and editing. The scope of this User`s Manual is to discuss these functions and is intended to guide users and answer questions regarding the MEL Phase 1 application.
Two dimensional NMR of liquids and oriented molecules
1987-02-01
Chapter 1 discusses the quantum mechanical formalism used for describing the interaction between magnetic dipoles that dictates the appearance of a spectrum. The NMR characteristics of liquids and liquid crystals are stressed. Chapter 2 reviews the theory of multiple quantum and two dimensional NMR. Properties of typical spectra and phase cycling procedures are discussed. Chapter 3 describes a specific application of heteronuclear double quantum coherence to the removal of inhomogeneous broadening in liquids. Pulse sequences have been devised which cancel out any contribution from this inhomogeneity to the final spectrum. An interpretation of various pulse sequences for the case of /sup 13/C and /sup 1/H is given, together with methods of spectral editing by removal or retention of the homo- or heteronuclear J coupling. The technique is applied to a demonstration of high resolution in both frequency and spatial dimensions with a surface coil. In Chapter 4, multiple quantum filtered 2-D spectroscopy is demonstrated as an effective means of studying randomly deuterated molecules dissolved in a nematic liquid crystal. Magnitudes of dipole coupling constants have been determined for benzene and hexane, and their signs and assignments found from high order multiple quantum spectra. For the first time, a realistic impression of the conformation of hexane can be estimated from these results. Chapter 5 is a technical description of the MDB DCHIB-DR11W parallel interface which has been set up to transfer data between the Data General Nova 820 minicomputer, interfaced to the 360 MHz spectrometer, and the Vax 11/730. It covers operation of the boards, physical specifications and installation, and programs for testing and running the interface.
The ionization fraction gradient across the Horsehead edge: An archetype for molecular clouds
2009-02-17
The ionization fraction plays a key role in the chemistry and dynamics of molecular clouds. We study the H13CO+, DCO+ and HOC+ line emission towards the Horsehead, from the shielded core to the UV irradiated cloud edge, i.e., the Photodissociation Region (PDR), as a template to investigate the ionization fraction gradient in molecular clouds. We analyze a PdBI map of the H13CO+ J=1-0 line, complemented with IRAM-30m H13CO+ and DCO+ higher-J line maps and new HOC+ and CO+ observations. We compare self-consistently the observed spatial distribution and line intensities with detailed depth-dependent predictions of a PDR model coupled with a nonlocal radiative transfer calculation. The chemical network includes deuterated species, 13C fractionation reactions and HCO+/HOC+ isomerization reactions. The role of neutral and charged PAHs in the cloud chemistry and ionization balance is investigated. The detection of HOC+ reactive ion towards the Horsehead PDR proves the high ionization fraction of the outer UV irradiated regions, where we derive a low [HCO+]/[HOC+]~75-200 abundance ratio. In the absence of PAHs, we reproduce the observations with gas-phase metal abundances, [Fe+Mg+...], lower than 4x10(-9) (with respect to H) and a cosmic-rays ionization rate of zeta=(5+/-3)x10(-17) s(-1). The inclusion of PAHs modifies the ionization fraction gradient and increases the required metal abundance. The ionization fraction in the Horsehead edge follows a steep gradient, with a scale length of ~0.05 pc (or ~25''), from [e-]~10(-4) (or n_e ~ 1-5 cm(-3)) in the PDR to a few times ~10(-9) in the core. PAH^- anions play a role in the charge balance of the cold and neutral gas if substantial amounts of free PAHs are present ([PAH] >10(-8)).
The XMM-Newton Wide-Field Survey in the COSMOS Field. The point-like X-ray source catalogue
2009-01-19
The COSMOS survey is a multiwavelength survey aimed to study the evolution of galaxies, AGN and the large scale structure. The XMM-COSMOS is a deep X-ray survey over the full 2 deg2 of the COSMOS area. It consists of 55 XMM-Newton pointings for a total exposure of ~1.5 Ms with an average vignetting corrected depth of 40 ks across the field of view and a sky coverage of 2.13 deg2. We present the catalogue of point-like X-ray sources detected with the EPIC CCD cameras, the logN-logS relations and the X-ray colour-colour diagrams. The analysis was performed in the 0.5-2 keV, 2-10 keV and 5-10 keV energy bands. The completeness of the catalogue as well as logN-logS have been calibrated using Monte Carlo simulations. The catalogs contains a total of 1887 unique sources detected in at least one band. The survey, that shows unprecedented homogeneity, has a flux limit of ~1.7x10-15 erg cm-2 s-1, ~9.3x10-15 erg cm-2 s-1 and ~1.3x10-14 erg cm-2 s-1 over 90% of the area (1.92 deg2) in the 0.5-2 keV, 2-10 keV and 5-10 keV energy band, respectively. Thanks to the rather homogeneous exposure over a large area, the derived logN-logS relations are very well determined over the flux range sampled by XMM-COSMOS. These relations have been compared with XRB synthesis models, which reproduce the observations with an agreement of ~10% in the 5-10 keV and 2-10 keV band, while in the 0.5-2 keV band the agreement is of the order of ~20%. The hard X-ray colors confirmed that the majority of the extragalactic sources, in a bright subsample, are actually Type I or Type II AGN. About 20% of the sources have X-ray luminosity typical of AGN (L_X >1042 erg/s) although they do not show any clear signature of nuclear activity in the optical spectrum.
2008-10-20
We present the current status of the QUIJOTE (Q-U-I JOint TEnerife) CMB Experiment, a new instrument which will start operations early 2009 at Teide Observatory, with the aim of characterizing the polarization of the CMB and other processes of galactic and extragalactic emission in the frequency range 10-30 GHz and at large angular scales. QUIJOTE will be a valuable complement at low frequencies for the PLANCK mission, and will have the required sensitivity to detect a primordial gravitational-wave component if the tensor-to-scalar ratio is larger than r=0.05.
The Potential Regulation of L1 Mobility by RNA Interference
2006-01-01
The hypothesis that RNA interference constrains L1 mobility seems inherently reasonable: L1 mobility can be dangerous and L1 RNA, the presumed target of RNAi, serves as a critical retrotransposition...Full Text Available
The Potential Regulation of L1 Mobility by RNA Interference
2006-01-01
Full Text Available.The hypothesis that RNA interference constrains L1 mobility seems inherently reasonable: L1 mobility can be dangerous and L1 RNA, the presumed target of RNAi, serves as a critical retrotransposition intermediate. Despite its plausibility, proof for this hypothesis has been difficult to obtain. Studies attempting to link the L1 retrotransposition frequency to alterations in RNAi activity have been hampered by the long times required to measure retrotransposition frequency, the pleiotropic and toxic effects of altering RNAi over similar time periods, and the possibility that other cellular machinery may contribute to the regulation of L1s. Another problem is that the commonly used L1 reporter cassette may serve as a substrate for RNAi. Here we review the L1-RNAi hypothesis and describe a genetic assay with a modified reporter cassette that detects approximately 4 times more L1 insertions than the conventional retrotransposition assay.
Summaries of FY 1992 research in nuclear physics
1993-07-01
This report summarizes the research projects supported by the Division of Nuclear Physics in the Office of High Energy and Nuclear Physics during FY 1992. This Division is a component of the Office of Energy Research and provides about 85% of the funding for nuclear physics research in the United States. The objectives of the Nuclear Physics Program are two-fold: (1) to understand the interactions and structures of atomic nuclei and nuclear matter and the fundamental forces of nature as manifested in nuclear matter and (2) to foster application of this knowledge to other sciences and technical disciplines. These summaries are intended to provide a convenient guide for those interested in the research supported by the Division of Nuclear Physics. We remind the readers that this compilation is just an overview of the Nuclear Physics Program. What we attempt to portray correctly is the breadth of the program and level of activity in the field of nuclear physics research as well as the new capabilities and directions that continually alter the public face of the nuclear sciences. We hope that the limitations of space, constraints of fon-nat, and rigors of editing have not extinguished the excitement of the science as it was originally portrayed.
Results from DROXO. II. - [Ne II] and X-ray emission from Rho Ophiuchi young stellar objects
2009-06-26
The infrared [Ne II] and [Ne III] fine structure lines at 12.81um and 15.55um are predicted to trace the circumstellar disk gas subject to X-ray heating and ionization. We investigate the origin of these lines by comparing observations with models of X-ray irradiated disks and by searching for empirical correlations between the line luminosities and stellar and circumstellar parameters. We measure neon line fluxes and X-ray luminosities for 28 young stellar objects in the Rho Ophiuchi star formation region for which good quality infrared spectra and X-ray data have been obtained, the former with the Spitzer IRS and the latter with the Deep Rho Ophiuchi XMM-Newton Observation. We detect the [Ne II] and the [Ne III] lines in 10 and 1 cases, respectively. Line luminosities show no correlation with X-ray emission. The luminosity of the [Ne II] line for one star, and that of both the [Ne II] and [Ne III] lines for a second star, match the predictions of published models of X-ray irradiated disks; for the remaining 8 objects the [Ne II] emission is 1-3 dex higher than predicted on the basis of their L_X. Class I objects show significantly stronger [Ne II] lines than Class II and Class III ones. A correlation is moreover found between the [Ne II] line emission and the disk mass accretion rates. This might point toward a role of accretion-generated UV emission in the generation of the line or to other mechanisms related to mass inflows from circumstellar disks and envelopes and/or to the associated mass outflows (winds and jets). We conclude that the X-ray luminosity is not the only parameter that determines the [Ne II] emission. Explaining the strong [Ne II] emission of Class I objects likely requires the inclusion in the models of additional physical components such as the envelope, inflows, and outflows.
Refining and end use study of coal liquids I - pilot plant studies
1995-12-31
The Office of Fossil Energy, Pittsburgh Energy Technology Center is examining the ways in which coal liquids may best be integrated into the refinery of the 2000-2015 time frame and what performance and emission properties will prevail among the slate of fuels produced. The study consists of a Basic Program administered by Bechtel Group, Inc. to build a linear programming refinery model and provide processing and fuel properties data through subcontractors Southwest Research Institute, Amoco Oil R&D, and M.W. Kellogg Company. The model will be used in an Option 1 to devise a slate of test fuels meeting advanced specifications, which will be produced and tested for physical ASTM-type properties, engine performance, and vehicle emissions. Three coal liquids will be included: a direct liquid from bituminous coal, another from subbituminous, and a Fischer-Tropsch indirect liquefaction product. This paper reports the work to date on fractions of the first direct liquid including naphtha hydrotreating, heavy distillate hydrotreating, FCC of the heavy distillate hydrotreater products. Also reported are the first stages of work on the indirect liquefaction wax including feed preparation and FCC tests of blends with petroleum FCC feed.
RNA editing of a miRNA precursor
2004-08-01
Micro RNAs comprise a large family of small, functional RNAs with important roles in the regulation of protein coding genes in animals and plants. Here we show that human and mouse miRNA22 precursor...Full Text Available
RNA editing of a miRNA precursor
2004-08-01
Full Text Available.Micro RNAs comprise a large family of small, functional RNAs with important roles in the regulation of protein coding genes in animals and plants. Here we show that human and mouse miRNA22 precursor molecules are subject to posttranscriptional modification by A-to-I RNA editing in vivo. The observed editing events are predicted to have significant implications for the biogenesis and function of miRNA22 and might point toward a more general role for RNA editing in the regulation of miRNA gene expression.
1997-04-29
The glutamate receptor subunit B (GluR-B) pre-mRNA is edited at two adenosine residues, resulting in amino acid changes that alter the electrophysiologic properties of the glutamate receptor. Previous...Full Text Available
1997-04-29
Full Text Available.The glutamate receptor subunit B (GluR-B) pre-mRNA is edited at two adenosine residues, resulting in amino acid changes that alter the electrophysiologic properties of the glutamate receptor. Previous studies showed that these amino acid changes are due to adenosine to inosine conversions in two codons resulting from adenosine deamination. Here, we describe the purification and characterization of an activity from human HeLa cells that efficiently and accurately edits GluR-B pre-mRNA at both of these sites. The purified activity contains a human homolog of the recently reported rat RED1 (rRED1) protein, a member of the family of double-stranded RNA-dependent deaminase proteins. Recombinant human RED1 (hRED1), but not recombinant dsRAD, another member of the family, efficiently edits both the Q/R and R/G sites of GluR-B RNA. We conclude that the GluR-B editing activity present in HeLa cell extracts and the recombinant hRED1 protein are indistinguishable.
Proliferation-dependent and cell cycle–regulated transcription of mouse pericentric heterochromatin
2007-11-05
Pericentric heterochromatin transcription has been implicated in Schizosaccharomyces pombe heterochromatin assembly and maintenance. However, in mammalian systems, evidence for such...Full Text Available
Proliferation-dependent and cell cycle–regulated transcription of mouse pericentric heterochromatin
2007-11-05
Full Text Available.Pericentric heterochromatin transcription has been implicated in Schizosaccharomyces pombe heterochromatin assembly and maintenance. However, in mammalian systems, evidence for such transcription is inconsistent. We identify two populations of RNA polymerase II–dependent mouse γ satellite repeat sequence–derived transcripts from pericentric heterochromatin that accumulate at different times during the cell cycle. A small RNA species was synthesized exclusively during mitosis and rapidly eliminated during mitotic exit. A more abundant population of large, heterogeneous transcripts was induced late in G1 phase and their synthesis decreased during mid S phase, which is coincident with pericentric heterochromatin replication. In cells that lack the Suv39h1,2 methyltransferases responsible for H3K9 trimethylation, transcription occurs from more sites but is still cell cycle regulated. Transcription is not detected in quiescent cells and induction during G1 phase is sensitive to serum deprivation or the cyclin-dependent kinase inhibitor roscovatine. We demonstrate that mammalian pericentric heterochromatin transcription is linked to cellular proliferation. Our data also provide an explanation for inconsistencies in the detection of such transcripts in different systems.
Probing Cold Dark Matter Cusps by Gravitational Lensing
2006-12-28
I elaborate on my prediction that an indirect detection of cold dark matter (CDM) may be possible by observing the gravitational lensing effects of the CDM cusp caustics at cosmological distances. Cusps in the distribution of CDM are plentiful once density perturbations enter the nonlinear regime of structure formation. Caustic ring model of galactic halo formation provides a well defined density profile and geometry near the cusps of the caustic rings. I calculate the gravitational lensing effects of the cusps in this model. As a pointlike background source passes behind a cusp of a cosmological foreground halo, the magnification in its image may be detected by present instruments. Depending on the strength of detected effect and the time scale of brightness change, it may even be possible to discriminate between the CDM candidates: axions and weakly interacting massive particles.
1998-12-31
Seismic stratigraphy represents an attractive framework for interpretation of 3-D data. This presentation is an introduction to a set of primitives that will enable guided interpretation of seismic signals in the framework of seismic stratigraphy. A method capable of automatic detection of terminations is proposed. The new procedure can be run on the entire seismic volume or it may be restricted to a limited time interval and detects terminations in an unguided manner without prior interpretation. The density of terminations can be computed. The procedure may alternatively be guided by pre-existing interpretation, e.g. detecting terminations onto an interpreted horizon. In such a case, the density of terminations will be a new surface attribute. 6 refs., 3 figs.
1987-06-01
Using digital subtraction radiography, the author detects an 0.1% change in areal density in a phantom. Areal density is the product rho x, where rho is the material density and x is the material thickness. Therefore, it is possible to detect an 0.1% difference in either density or thickness in unknown samples. A special x-ray television camera detects the areal density change on the phantom. In a difference image, formed by subtracting the 128-television-frame averages of the phantom image from the phantom-and-step image, the step is resolved with a 1-mm spatial resolution. Surprisingly, crossed 2-..mu..m-diam tungsten wires that overlie the phantom are also detected. This procedure takes a few seconds. The performance of any digital imaging x-ray system will improve by using the averaging and digital subtraction techniques. 8 refs., 6 figs.
1995-12-31
The objectives of this program are to (a) develop a process for converting natural gas to methyl chloride via an oxyhydrochlorination route using highly selective, stable catalysts in a fixed-bed, (b) design a reactor capable of removing the large amount of heat generated in the process so as to control the reaction, (c) develop a recovery system capable of removing the methyl chloride from the product stream and (d) determine the economics and commercial viability of the process. The general approach has been as follows: (a) design and build a laboratory scale reactor, (b) define and synthesize suitable OHC catalysts for evaluation, (c) select first generation OHC catalyst for Process Development Unit (PDU) trials, (d) design, construct and startup PDU, (e) evaluate packed bed reactor design, (f) optimize process, in particular, product recovery operations, (g) determine economics of process, (h) complete preliminary engineering design for Phase II and (i) make scale-up decision and formulate business plan for Phase II. Conclusions regarding process development and catalyst development are presented.
Mapping genes to human chromosome 19
1996-05-01
For this project, 22 Expressed Sequence Tags (ESTs) were fine mapped to regions of human chromosome 19. An EST is a short DNA sequence that occurs once in the genome and corresponds to a single expressed gene. {sup 32}P-radiolabeled probes were made by polymerase chain reaction for each EST and hybridized to filters containing a chromosome 19-specific cosmid library. The location of the ESTs on the chromosome was determined by the location of the ordered cosmid to which the EST hybridized. Of the 22 ESTs that were sublocalized, 6 correspond to known genes, and 16 correspond to anonymous genes. These localized ESTs may serve as potential candidates for disease genes, as well as markers for future physical mapping.
Manufacturing high-efficiency, high damage threshold diffraction gratings with lift-off processing
1996-05-01
High-efficiency, high damage threshold diffraction gratings fabricated out of multilayers of dielectric materials are needed for the application of chirped-pulse amplification (CPA) in the Petawatt Laser Project. The underlying multilayers are deposited onto a flat substrate by standard e-beam evaporation. The grating structures themselves, however, can either be etched into a plane layer or deposited between a photoresist grating mask which is subsequently lifted off. The latter procedure, although more easily applied to large apertures, requires high-aspect ratio, vertical sidewall photoresist grating masks with, preferably, an overhanging structure to facilitate liftoff. By varying factors in each processing step, sample gratings were fabricated and then characterized. Using a high-contrast profile photoresist (AZ7710), we have been able to create grating masks with both vertical sidewalls and high-aspect ratios (>4.5). We have also had some encouraging preliminary results in making overhanging structures by including a pre-development hlorobenzene soak in the processing steps. Once these samples are deposited with an oxide and the grating masks lifted off to create the final grating, a more definitive processing method can be developed based on the results.
Magnetic field regulation control system analysis
1996-05-01
This study comprises (1) an analytical characterization of the Cameca ion microscope`s magnetic field regulation circuitry and (2) comparisons between the analytical predictions and the measured performance of the control system. It is the first step in a project to achieve routine field regulation better than 10ppm. The control loop was decomposed into functional subcircuits and simulated in SPICE to determine DC, AC, and transient response. Transfer functions were extracted from SPICE, simplified, and analyzed in MATLAB. Both SPICE and MATLAB simulations were calculated for step inputs, and these results were compared to actual measurements. Magnetic field fluctuations were measured at high mass resolving power. The frequency spectrum of the fluctuations was analyzed by FFT. Difficulties encountered and implications for future work are discussed.
2009-03-01
Studies of the transcriptional output of the human and mouse genomes have revealed that there are many more transcripts produced than can be accounted for by predicted protein-coding genes. Using a...Full Text Available
2009-03-01
Full Text Available.Studies of the transcriptional output of the human and mouse genomes have revealed that there are many more transcripts produced than can be accounted for by predicted protein-coding genes. Using a custom microarray, we have identified 184 non-coding RNAs that exhibit more than twofold up- or down-regulation upon differentiation of C2C12 myoblasts into myotubes. Here, we focus on the Men ε/β locus, which is up-regulated 3.3-fold during differentiation. Two non-coding RNA isoforms are produced from a single RNA polymerase II promoter, differing in the location of their 3′ ends. Men ε is a 3.2-kb polyadenylated RNA, whereas Men β is an ∼20-kb transcript containing a genomically encoded poly(A)-rich tract at its 3′-end. The 3′-end of Men β is generated by RNase P cleavage. The Men ε/β transcripts are localized to nuclear paraspeckles and directly interact with NONO. Knockdown of MEN ε/β expression results in the disruption of nuclear paraspeckles. Furthermore, the formation of paraspeckles, after release from transcriptional inhibition by DRB treatment, was suppressed in MEN ε/β-depleted cells. Our findings indicate that the MEN ε/β non-coding RNAs are essential structural/organizational components of paraspeckles.
Intronic Alus Influence Alternative Splicing
2008-09-01
Full Text Available.Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the human transcriptome. Most of the editing sites are located in the primate-specific retrotransposed element called Alu. A large fraction of Alus are found in intronic sequences, implying extensive Alu-Alu dsRNA formation in mRNA precursors. Yet, the effect of these intronic Alus on splicing of the flanking exons is largely unknown. Here, we show that more Alus flank alternatively spliced exons than constitutively spliced ones; this is especially notable for those exons that have changed their mode of splicing from constitutive to alternative during human evolution. This implies that Alu insertions may change the mode of splicing of the flanking exons. Indeed, we demonstrate experimentally that two Alu elements that were inserted into an intron in opposite orientation undergo base-pairing, as evident by RNA editing, and affect the splicing patterns of a downstream exon, shifting it from constitutive to alternative. Our results indicate the importance of intronic Alus in influencing the splicing of flanking exons, further emphasizing the role of Alus in shaping of the human transcriptome.
Intronic Alus Influence Alternative Splicing
2008-09-01
Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the...Full Text Available
Integrated Baseline System (IBS) Version 2.0: Utilities Guide
1994-03-01
The Integrated Baseline System (IBS) is an emergency management planning and analysis tool being developed under the direction of the US Army Nuclear and Chemical Agency. This Utilities Guide explains how you can use the IBS utility programs to manage and manipulate various kinds of IBS data. These programs include utilities for creating, editing, and displaying maps and other data that are referenced to geographic location. The intended audience for this document are chiefly data managers but also system managers and some emergency management planners and analysts.
2007-12-01
We and other investigators have demonstrated up-regulation of the expression of the RNA-editing gene 150-kDa adenosine deaminase that acts on RNA (ADAR1) in systemic lupus erythematosus (SLE) T cells...Full Text Available
2007-12-01
Full Text Available.We and other investigators have demonstrated up-regulation of the expression of the RNA-editing gene 150-kDa adenosine deaminase that acts on RNA (ADAR1) in systemic lupus erythematosus (SLE) T cells and B cells, peripheral blood mononuclear cells (PBMC), natural killer (NK) cells. The presence of a small proportion of activated T cells is the hallmark of SLE. Therefore, it was hypothesized that 150-kDa ADAR1 gene expression is induced by the physiological activation of T cells. To examine this hypothesis, normal T cells were activated by anti-CD3-ε plus anti-CD28 for various time periods from 0 to 48 hr. The expression of 110-kDa and 150-kDa ADAR1, and interleukin (IL)-2 and β-actin gene transcripts was analysed. An approximately fourfold increase in 150-kDa ADAR1 gene expression was observed in activated T cells. ADAR2 gene transcripts are substrates for ADAR1 and ADAR2 enzymes. Therefore, we assessed the role of the 150-kDa ADAR enzyme in editing of ADAR2 gene transcripts. In activated T cells, site-selective editing of the −2 site was observed. Previous studies indicate that this site is predominantly edited by ADAR1. In addition to this, novel editing sites at base positions −56, −48, −45, −28, −19, −15, +46 and +69 were identified in activated T cells. On the basis of these results, it is proposed that 150-kDa ADAR1 gene expression is selectively induced in T cells by anti-CD3-ε and anti-CD28 stimulation and that it may play a role in site-selective editing of gene transcripts and in altering the functions of several gene products of T cells during activation and proliferation.
Gravitational waves astronomy: the ultimate test for Einstein's General Relativity
2010-04-09
It is well known that Einstein's General Relativity (GR) achieved a great success and overcame lots of experimental tests. On the other hand, GR also showed some shortcomings and flaws which today advise theorists to ask if it is the definitive theory of gravity. In this review we show that, if advanced projects on the detection of Gravitational Waves (GWs) will improve their sensitivity, allowing to perform a GWs astronomy, understanding if Einstein's GR is the correct and definitive theory of gravity will be possible. For this goal, accurate angular and frequency dependent response functions of interferometers for GWs arising from various Theories of Gravity, i.e. GR and Extended Theories of Gravity will have to be used. This review is founded on the Essay which won an Honorable Mention at the the 2009 Gravity Research Foundation Awards.
Galaxy bulges and their black holes: a requirement for the quenching of star formation
2008-04-28
One of the central features of the last 8 to 10 billion years of cosmic history has been the emergence of a well-populated red sequence of non-star-forming galaxies. A number of models of galaxy formation and evolution have been devised to attempt to explain this behavior. Most current models require feedback from supermassive black holes (AGN feedback) to quench star formation in galaxies in the centers of their dark matter halos (central galaxies). Such models make the strong prediction that all quenched central galaxies must have a large supermassive black hole (and, by association, a prominent bulge component). I show using data from the Sloan Digital Sky Survey that the observations are consistent with this prediction. Over 99.5% of red sequence galaxies with stellar masses in excess of 10^{10} M_{\sun} have a prominent bulge component (as defined by having a Sersic index n above 1.5). Those very rare red sequence central galaxies with little or no bulge (n<1.5) usually have detectable star formation or AGN activity; the fraction of truly quenched bulgeless central galaxies is <0.1% of the total red sequence population. I conclude that a bulge, and by implication a supermassive black hole, is an absolute requirement for full quenching of star formation in central galaxies. This is in agreement with the most basic prediction of the AGN feedback paradigm.
Formation, evolution and multiplicity of brown dwarfs and giant exoplanets
2008-10-14
This proceeding summarises the talk of the awardee of the Spanish Astronomical Society award to the the best Spanish thesis in Astronomy and Astrophysics in the two-year period 2006-2007. The thesis required a tremendous observational effort and covered many different topics related to brown dwarfs and exoplanets, such as the study of the mass function in the substellar domain of the young sigma Orionis cluster down to a few Jupiter masses, the relation between the cluster stellar and substellar populations, the accretion discs in cluster brown dwarfs, the frequency of very low-mass companions to nearby young stars at intermediate and wide separations, or the detectability of Earth-like planets in habitable zones around ultracool (L- and T-type) dwarfs in the solar neighbourhood.
Far-Infrared detection of H2D+ toward Sgr B2
2007-01-19
We report on the first far-IR detection of H2D+, using the Infrared Space Observatory, in the line of sight toward Sgr B2 in the galactic center. The transition at 126.853 um connecting the ground level of o-H2D+, 1_1,1 with the the 2_1,2 level at 113 K, is observed in absorption against the continuum emission of the cold dust of the source. The line is broad, with a total absorption covering 350 km s^-1, i.e., similar to that observed in the fundamental transitions of H2O, OH and CH at ~179, 119 and 149 um respectively. For the physical conditions of the different absorbing clouds the H2D+ column density ranges from 2 to 5x10^13 cm^-2, i.e., near an order of magnitude below the upper limits obtained from ground based submillimeter telescopes. The derived H2D+ abundance is of a few 10^-10, which agrees with chemical models predictions for a gas at a kinetic temperature of ~20K.
Far-IR detection of neutral atomic oxygen toward the Horsehead Nebula
2009-06-04
We present the first detection of neutral atomic oxygen (3P_1-3P_2 fine structure line at ~63um) toward the Horsehead photodissociation region (PDR). The cloud has been mapped with the Spitzer Space Telescope at far-IR (FIR) wavelengths using MIPS in the Spectral Energy Distribution (SED) mode. The [OI]63um line peaks at the illuminated edge of the cloud at AV~0.1-0.5 (inwards the gas becomes too cold and outwards the gas density drops). The luminosity carried by the [OI]63um line represents a significant fraction of the total FIR dust luminosity (I_63/I_FIR~4x10^-3). We analyze the dust continuum emission and the nonlocal OI excitation and radiative transfer in detail. The observations are reproduced with a gas density of n_H~10^4 cm^-3 and gas and dust temperatures of T_k~100 K and T_d~30 K. We conclude that the determination of the OI 3P_J level populations and emergent line intensities at such ``low'' densities is a complex non-LTE problem. FIR radiative pumping, [OI]63um subthermal emission, [OI]145um suprathermal and even maser emission can occur and decrease the resulting [OI]63/145 intensity ratio. The Herschel Space Observatory, observing from ~57 to 672um, will allow us to exploit the diagnostic power of FIR fine structure lines with unprecedented resolution and sensitivity.
FY-93 noncontacting acoustic ultrasonic signature analysis development
1994-04-01
A noncontacting, long-standoff inspection system with proven capabilities in container fill identification has been under development at the Idaho National Engineering Laboratory. The system detects subtle change in container vibration characteristics caused by differences in the physical properties of the fill materials. A container is inspected by acoustically inducting it to vibrate and sensing the vibrational response with a laser vibrometer. A standoff distance of several meters is feasible. In previous work the system proved to be a reliable means of distinguishing between munitions with a variety of chemical fills. During FY-93, the system was modified to improve performance and simplify operation. Other FY-93 accomplishments include progress in modeling the vibrational characteristics of containers and refinements to the statistical classification algorithms. Progress was also made in identifying other applications for this technology.
Epigenetic Principles and Mechanisms Underlying Nervous System Functions in Health and Disease
2008-12-11
Full Text Available.Epigenetics and epigenomic medicine encompass a new science of brain and behavior that are already providing unique insights into the mechanisms underlying brain development, evolution, neuronal and network plasticity and homeostasis, senescence, the etiology of diverse neurological diseases and neural regenerative processes. Epigenetic mechanisms include DNA methylation, histone modifications, nucleosome repositioning, higher-order chromatin remodeling, non-coding RNAs, and RNA and DNA editing. RNA is centrally involved in directing these processes, implying that the transcriptional state of the cell is the primary determinant of epigenetic memory. This transcriptional state can be modified by internal and external cues affecting gene expression and post-transcriptional processing, but also by RNA and DNA editing through activity-dependent intracellular transport and modulation of RNAs and RNA regulatory supercomplexes, and through trans-neuronal and systemic trafficking of functional RNA subclasses. These integrated processes promote dynamic reorganization of nuclear architecture and the genomic landscape to modulate functional gene and neural networks with complex temporal and spatial trajectories. Epigenetics represents the long sought after molecular interface mediating gene-environmental interactions during critical periods throughout the lifecycle. The discipline of environmental epigenomics has begun to identify combinatorial profiles of environmental stressors modulating the latency, initiation and progression of specific neurological disorders, and more selective disease biomarkers and graded molecular responses to emerging therapeutic interventions. Pharmacoepigenomic therapies will promote accelerated recovery of impaired and seemingly irrevocably lost cognitive, behavioral, sensorimotor functions through epigenetic reprogramming of endogenous regional neural stem cell fate decisions, targeted tissue remodeling and restoration of neural network integrity, plasticity and connectivity.
Epigenetic Principles and Mechanisms Underlying Nervous System Functions in Health and Disease
2008-12-11
Epigenetics and epigenomic medicine encompass a new science of brain and behavior that are already providing unique insights into the mechanisms underlying brain development, evolution, neuronal...Full Text Available
Effect of pretreating of host oil on coprocessing
1995-12-31
The principal objective of this research was to determine if coprocessing performance (i.e., coal conversion and oil yield) could be significantly improved by pretreating the heavy resid prior to reacting it with coal. For this purpose, two petroleum vacuum resids (1000{degrees}F+), one from the Amoco Co. and another from the Citgo Co., were used as such and after they had been pretreated by catalytic hydrogenation and hydrocracking reactions. The pretreatments were aimed at improving the host oil by; (1) converting any aromatic structures in the petroleum to hydroaromatic compounds capable of donating hydrogen, (2) cracking the heavy oil to lower molecular weight material that might serve as a better solvent, (3) reducing the coking propensity of the heavy oil through the hydrogenation of polynuclear aromatic compounds, and (4) removing metals and heteroatoms that might poison a coprocessing catalyst. Highly dispersed catalysts, including fine particle Fe- and Mo-based, and dicobalt octacarbonyl, Co{sub 2}(CO){sub 8}, were used in this study. The untreated and pretreated resids were extensively characterized in order to determine chemical changes brought about by the pretreatments. The modified heavy oils were then coprocessed with an Illinois No. 6 coal as well as with a Wyodak coal, and compared to coprocessing with untreated resids under the same hydroliquefaction conditions. The amount of oil derived from coal was estimated by measuring the level of phenolic oxygen (derived mainly from coal) present in the oil products. Results are presented and discussed.
2003-07-01
Hepatitis delta virus (HDV) produces two essential forms of the sole viral protein from the same open reading frame by using host RNA editing activity at the amber/W site in the antigenomic RNA. The...Full Text Available
2003-07-01
Full Text Available.Hepatitis delta virus (HDV) produces two essential forms of the sole viral protein from the same open reading frame by using host RNA editing activity at the amber/W site in the antigenomic RNA. The roles of these two forms, HDAg-S and HDAg-L, are opposed. HDAg-S is required for viral RNA replication, whereas HDAg-L, which is produced as a result of editing, inhibits viral RNA replication and is required for virion packaging. Both the rate and amount of editing are important because excessive editing will inhibit viral RNA replication, whereas insufficient editing will reduce virus secretion. Here we show that for HDV genotype III, which is associated with severe HDV disease, HDAg-L strongly inhibits editing of a nonreplicating genotype III reporter RNA, while HDAg-S inhibits only when expressed at much higher levels. The different inhibitory efficiencies are due to RNA structural elements located ca. 25 bp 3′ of the editing site in the double-hairpin RNA structure required for editing at the amber/W site in HDV genotype III RNA. These results are consistent with regulation of amber/W editing in HDV genotype III by a negative-feedback mechanism due to differential interactions between structural elements in the HDV genotype III RNA and the two forms of HDAg.
Development of acoustic flow instruments for solid/gas pipe flows
1986-05-01
Two nonintrusive acoustic flow sensing techniques are reported. One technique, passive in nature, simply measures the bandpassed acoustic noise level produced by particle/particle and particle/wall collisions. The noise levels, given in true RMS voltages or in autocorrelations, show a linear relationship to particle velocity but increase with solid concentration. Therefore, the passive technique requires calibration and a separate measure of solid concentration before it can be used to monitor the particle velocity. The second technique is based on the active cross-correlation principle. It measures particle velocity directly by correlating flow-related signatures at two sensing stations. The velocity data obtained by this technique are compared with measurements by a radioactive-particle time-of-flight (TOF) method. A multiplier of 1.53 is required to bring the acoustic data into agreement with the radioactive TOF result. The difference may originate from the difference in flow fields where particles are detected. The radioactive method senses particles mainly in the turbulent region and essentially measures average particle velocity across the pipe, while the acoustic technique detects particles near the pipe wall, and so measures the particle velocity in the viscous sublayer. Both techniques were tested in flows of limestone and air and 1-mm glass beads and air at the Argonne National Laboratory Solid/Gas Test Facility (SGFTF). The test matrix covered solid velocities of 20 to 30 m/s in a 2-in. pipe and solid-to-gas loading ratios of 6 to 22. 37 refs., 19 figs., 4 tabs.
Developing a computational model of human hand kinetics using AVS
1996-05-01
As part of an ongoing effort to develop a finite element model of the human hand at the Institute for Scientific Computing Research (ISCR), this project extended existing computational tools for analyzing and visualizing hand kinetics. These tools employ a commercial, scientific visualization package called AVS. FORTRAN and C code, originally written by David Giurintano of the Gillis W. Long Hansen`s Disease Center, was ported to a different computing platform, debugged, and documented. Usability features were added and the code was made more modular and readable. When the code is used to visualize bone movement and tendon paths for the thumb, graphical output is consistent with expected results. However, numerical values for forces and moments at the thumb joints do not yet appear to be accurate enough to be included in ISCR`s finite element model. Future work includes debugging the parts of the code that calculate forces and moments and verifying the correctness of these values.
Current tools for the identification of miRNA genes and their targets
2009-05-01
The discovery of microRNAs (miRNAs), almost 10 years ago, changed dramatically our perspective on eukaryotic gene expression regulation. However, the broad and important functions of these regulators...Full Text Available
Current tools for the identification of miRNA genes and their targets
2009-05-01
Full Text Available.The discovery of microRNAs (miRNAs), almost 10 years ago, changed dramatically our perspective on eukaryotic gene expression regulation. However, the broad and important functions of these regulators are only now becoming apparent. The expansion of our catalogue of miRNA genes and the identification of the genes they regulate owe much to the development of sophisticated computational tools that have helped either to focus or interpret experimental assays. In this article, we review the methods for miRNA gene finding and target identification that have been proposed in the last few years. We identify some problems that current approaches have not yet been able to overcome and we offer some perspectives on the next generation of computational methods.
Conserved alternative and antisense transcripts at the programmed cell death 2 locus
Full Text Available.BackgroundThe programmed cell death 2 (Pdcd2) gene on mouse chromosome 17 was evaluated as a member of a highly conserved synteny, a candidate for an imprinted locus, and a candidate for the Hybrid sterility 1 (Hst1) gene.ResultsNew mouse transcripts were identified at this locus: an alternative Pdcd2 mRNA skipping the last two coding exons and two classes of antisense RNAs. One class of the antisense RNA overlaps the alternative exon and the other the entire Pdcd2 gene. The antisense RNAs are alternative transcripts of the neighboring TATA-binding protein gene (Tbp) that are located mainly in the cell nucleus. Analogous alternative PDCD2 forms truncating the C-terminal domain were also detected in human and chicken. Alternative transcripts of the chicken PDCD2 and TBP genes also overlap. No correlation in the transcription of the alternative and overlapping mRNAs was detected. Allelic sequencing and transcription studies did not reveal any support for the candidacy of Pdcd2 for Hst1. No correlated expression of Pdcd2 with the other two genes of the highly conserved synteny was observed. Pdcd2, Chd1, and four other genes from this region were not imprinted in the embryo.ConclusionThe conservation of alternative transcription of the Pdcd2 gene in mouse, human and chicken suggests the biological importance of such truncated protein. The biological function of the alternative PDCD2 is likely to be opposite to that of the constitutive form. The ratio of the constitutive and alternative Pdcd2 mRNAs differs in the tissues, suggesting a developmental role.The identified Tbp-alternative Pdcd2-antisense transcripts may interfere with the transcription of the Pdcd2 gene, as they are transcribed at a comparable level. The conservation of the Pdcd2/Tbp sense-antisense overlap in the mouse and chicken points out its biological relevance. Our results also suggest that some cDNAs in databases labeled as noncoding are incomplete alternative cDNAs of neighboring protein-coding genes.
Conserved alternative and antisense transcripts at the programmed cell death 2 locus
BackgroundThe programmed cell death 2 (Pdcd2) gene on mouse chromosome 17 was evaluated as a member of a highly conserved synteny, a candidate for an imprinted locus,...Full Text Available
Clustered and Triggered Star Formation in W5: Observations with Spitzer
2008-08-26
We present images and initial results from our extensive Spitzer Space Telescope imaging survey of the W5 H II region with the Infrared Array Camera (IRAC) and Multiband Imaging Photometer for Spitzer (MIPS). We detect dense clusters of stars, centered on the O stars: HD 18326, BD +60 586, HD 17505 and HD 17520. At 24 microns substantial extended emission is visible, presumably from heated dust grains that survive in the strongly ionizing environment of the H {\sc ii} region. With photometry of more than 18000 point sources, we analyze the clustering properties of objects classified as young stars by their IR spectral energy distributions (a total of 2064 sources) across the region using a minimal-spanning-tree algorithm. We find ~40--70% of infrared excess sources belong to clusters with >10 members. We find that within the evacuated cavities of the H II regions that make up W5, the ratio of Class II to Class I sources is ~7 times higher than for objects coincident with molecular gas as traced by 12CO emission and near-IR extinction maps. We attribute this contrast to an age difference between the two locations, and postulate that at least two distinct generations of star formation are visible across W5. Our preliminary analysis shows that triggering is a plausible mechanism to explain the multiple generations of star formation in W5, and merits further investigation.
Carbon Stars in the Hamburg/ESO Survey: Abundances
2006-03-21
We have carried out a detailed abundance analysis for a sample of 16 carbon stars found among candidate extremely metal-poor (EMP) stars from the Hamburg/ESO Survey. We find that the Fe-metallicities for the cooler C-stars (Teff ~ 5100K) have been underestimated by a factor of ~10 by the standard HES survey tools. The results presented here provided crucial supporting data used by Cohen et al (2006) to derive the frequency of C-stars among EMP stars. C-enhancement in these EMP C-stars appears to be independent of Fe-metallicity and approximately constant at ~1/5 the solar C/H. The mostly low C12/C13 ratios (~4) and the high N abundances in many of these stars suggest that material which has been through proton burning via the CN cycle comprises most of the stellar envelope. C-enhancement is associated with strong enrichment of heavy nuclei beyond the Fe-peak for 12 of the 16 stars. The remaining C-stars from the HES, which tend to be the most Fe-metal poor, show no evidence for enhancement of the heavy elements. Very high enhancements of lead are detected in some of the C-stars with highly enhanced Ba. (We show that) the s-process is responsible for the enhancement of the heavy elements for the majority of the C-stars in our sample. We suggest that both the s-process rich and Ba-normal C-stars result from phenomena associated with mass transfer in binary systems. This leads directly to the progression from C-stars to CH stars and then to Ba stars as the Fe-metallicity increases. (abridged and slightly edited to shorten)
CERN Scientific Book Fair 2008
2008-10-02
$$b The CERN Bookshop and CERN Library invite you to attend the 2008 CERN Book Fair 2008, a three-day scientific book festival offering you the opportunity to meet key publishers and electronic book suppliers and to browse and purchase books at significant discounts. Some ten companies will be participating and will bring with them a selection of titles in physics, technology, mathematics, engineering and popular science. There will also be a number of tie-in events intended to give you an insight into the writing and publishing process from authors within our own community. Come along and meet the authors, discuss your book ideas with the publishers’ representatives or simply browse the books on offer. The Fair will take place in Building 500 in the area near the Main Auditorium, and special presentations (as detailed below) will be held in rooms nearby or in the Library. Participating publishers and book traders include: Cambridge University Press, Durnell Marketing, Elsevier, EPFL Press – PPUR, Imperial College Press, Oxford University Press, Princeton University Press, Springer, World Scientific. Fair opening times: Wednesday 8 October 10:00 – 18:00 Thursday 9 October 9:00 – 18:00 Friday 10 October 9:00 – 18:00 Further information: http://bookfair2008.web.cern.ch/Bookfair2008/ Schedule of book presentations by the authors: Wednesday 8 October 16:30 - "Escape from Leipzig" by Harald Fritzsch, World Scientific, 2008. Room C, Bldg. 61-1-007. Thursday 9 October 16:30 - "Cosmic Anger: Abdus Salam, the First Muslim Nobel Scientist" by Gordon Fraser, Oxford University Press, 2008. Library (Bldg. 52 1st floor). Friday 10 October 10:30 - "Particle Detection with Drift Chambers", 2nd ed., by Walter Blum, Werner Riegler and Luigi Rolandi, Springer, 2008. Library (Bldg. 52 1st floor). 11:30 - An advance presentation of two forthcoming books edited or written by Herwig Schopper:-"LEP: The Lord of the Collider Rings at CERN 1980-2000: The Making,Operation and Legacy of the World's Largest Scientific Instrument", Springer.-"Elementary Particles", the first in a series of handbooks on elementary particles to appear as vol. I/21A of "Landolt Börnstein", Springer. Library (Bldg. 52 1st floor).16:00 - Lucio Rossi introduces the first volume of the new series "Reviews of Accelerator Science and Technology", ed. by Alex Chao and Weiren Chou, World Scientific, 2008. Room C, Bldg. 61-1-007. 17:00 - "Engines of Discovery: a Century of Particle Accelerators", by Andrew Sessler and Edmund Wilson, World Scientific, 2007. Room C, Bldg. 61-1-007.
Behavior of iodine in the dissolution of spent nuclear fuels
1997-08-01
The results of laboratory-scale experiments concerning the behavior of iodine in the dissolution of spent nuclear fuels, which were carried out at the Japan Atomic Energy Research Institute, are summarized. Based on previous and new experimental results, the difference in quantity of residual iodine in the fuel solution between laboratory-scale experiments and reprocessing plants is discussed, Iodine in spent fuels is converted to the following four states: (1) oxidation into I{sub 2} by nitric acid, (2) oxidation into I{sub 2} by nitrous acid generated in the dissolution, (3) formation of a colloid of insoluble iodides such as AgI and PdI{sub 2}, and (4) deposition on insoluble residue. Nitrous acid controls the amount of colloid formed. As a result, up to 10% of iodine in spent fuels is retained in the fuel solution, up to 3% is deposited on insoluble residue, and the balance volatilizes to the off-gas, Contrary to earlier belief, when the dissolution is carried out in 3 to 4 M HNO{sub 3} at 100{degrees}C, the main iodine species in a fuel solution is a colloid, not iodate, Immediately after its formation, the colloid is unstable and decomposes partially in the hot nitric acid solution through the following reaction: AgI(s) + 2HNO{sub 3}(aq) = {1/2}I{sub 2}(aq) + AgNO{sub 3}(aq) + NO{sub 2}(g) + H{sub 2}O(1). For high concentrations of gaseous iodine, I{sub 2}(g), and NO{sub 2}, this reaction is reversed towards formation of the colloid (AgI). Since these concentrations are high near the liquid surface of a plant-scale dissolver, there is a possibility that the colloid is formed there through this reversal, Simulations performed in laboratory-scale experiments demonstrated this reversal, This phenomenon can be one reason the quantity of residual iodine in spent fuels is higher in reprocessing plants than in laboratory-scale experiments. 17 refs., 5 figs., 3 tabs.
Beam vectoring trigger for E910
1996-05-01
Experiment 910 (e910) is a proton-gold nucleus collision experiment planned to run at the Alternating Gradient Synchrotron at Brookhaven National Laboratory. A gold foil target will be bombarded with high energy protons in an attempt to experimentally verify the existence of the H-dibaryon, a six quark particle permitted by the Standard Model. Strange particle production will also be measured to further understand nucleus-nucleus interactions, where enhanced strange particle production may signal a phase transition in the quark-gluon plasma. My work has been to create a {open_quotes}look up table{close_quotes} for use in the trigger to discriminate between interacting and non-interacting protons. In its final form, this look up table will be a file resident on a CAMAC crate as part of the online data acquisition system, and will contain predicted trajectory data for non-interacting protons of various initial positions and momenta. The table will be created by several programs I have written that work in conjunction with the software simulator eosgx.
Automated Editing of Radio Interferometer Data with Pieflag
2006-03-09
Editing of radio interferometer data, a process commonly known as ``flagging'', can be laborious and time-consuming. One quickly tends to flag more data than actually required, sacrificing sensitivity and image fidelity in the process. I describe a program, Pieflag, which can analyse radio interferometer data to filter out measurements which are likely to be affected by interference. Pieflag uses two algorithms to allow for data sets which are either dominated by receiver noise or by source structure. Together, the algorithms detect essentially all affected data whilst the amount of data which is not affected by interference but falsely marked as such is kept to a minimum. The sections marked by Pieflag are very similar to what would be deemed affected by the observer in a visual inspection of the data. Pieflag displays its results concisely and allows the user to add and remove flags interactively. It is written in Python, is easy to install and use, and has a variety of options to adjust its algorithms to a particular observing situation. I describe how Pieflag works and illustrate its effect using data from typical observations.
Assessment of fiber optic sensors and other advanced sensing technologies for nuclear power plants
1996-03-01
As a result of problems such as calibration drift in nuclear plant pressure sensors and the recent oil loss syndrome in some models of Rosemount pressure transmitters, the nuclear industry has become interested in fiber optic pressure sensors. Fiber optic sensing technologies have been considered for the development of advanced instrumentation and control (I&C) systems for the next generation of reactors and in older plants which are retrofitted with new I&C systems. This paper presents the results of a six-month Phase I study to establish the state-of-the-art in fiber optic pressure sensing. This study involved a literature review, contact with experts in the field, an industrial survey, a site visit to a fiber optic sensor manufacturer, and laboratory testing of a fiber optic pressure sensor. The laboratory work involved both static and dynamic performance tests. This initial Phase I study has recently been granted a two-year extension by the U.S. Nuclear Regulatory Commission (NRC). The next phase will evaluate fiber optic pressure sensors in specific nuclear plant applications in addition to other advanced methods for monitoring critical nuclear plant equipment.
2010-06-01
RNA editing is a post-transcriptional modification of pre-mRNA that results in increased diversity in transcriptomes and proteomes. It occurs in a wide variety of eukaryotic organisms and in some viruses....Full Text Available
2010-06-01
Full Text Available.RNA editing is a post-transcriptional modification of pre-mRNA that results in increased diversity in transcriptomes and proteomes. It occurs in a wide variety of eukaryotic organisms and in some viruses. One of the most common forms of pre-mRNA editing is A-to-I editing, in which adenosine is deaminated to inosine, which is read as guanosine during translation. This phenomenon has been observed in numerous transcripts, including the mammalian 5-HT2C receptor, which can be edited at five distinct sites. Methods used to date to quantify 5-HT2C receptor editing are labor-intensive, expensive and provide limited information regarding the relative abundance of 5-HT2C receptor editing variants. Here, we present a novel, ultra high-throughput method to quantify 5-HT2C receptor editing, compare it to a more conventional method, and use it to assess the effect of a range of genetic and pharmacologic manipulations on 5-HT2C editing. We conclude that this new method is powerful and economical, and we provide evidence that alterations in 5-HT2C editing appear to be a result of regional changes in brain activity, rather than a mechanism to normalize 5-HT2C signaling.
2009-03-27
SummaryNEAT1 RNA, a highly abundant 4 kb ncRNA, is retained in nuclei in ~10–20 large foci that we show is completely coincident with paraspeckles, nuclear domains implicated...Full Text Available
2009-03-27
Full Text Available.SummaryNEAT1 RNA, a highly abundant 4 kb ncRNA, is retained in nuclei in ~10–20 large foci that we show is completely coincident with paraspeckles, nuclear domains implicated in mRNA nuclear retention. Depletion of NEAT1 RNA via RNAi eradicates paraspeckles, suggesting it controls sequestration of the paraspeckle proteins, PSP1 and p54, factors linked to A-I editing. Unlike over-expression of PSP1, NEAT1 over-expression increases paraspeckle number, and paraspeckles emanate exclusively from the NEAT1 transcription site. The PSP-1 RNA binding domain is required for its co-localization with NEAT1 RNA in paraspeckles, and biochemical analyses supports that NEAT1 RNA binds with paraspeckle proteins. Unlike other nuclear retained RNAs, NEAT1 RNA is not A-I edited, consistent with a structural role in paraspeckles. Collectively results demonstrate that NEAT1 functions as an essential structural determinant of paraspeckles, providing a precedent for a ncRNA as the foundation of a nuclear domain.
Alu Recombination-Mediated Structural Deletions in the Chimpanzee Genome
2007-10-01
With more than 1.2 million copies, Alu elements are one of the most important sources of structural variation in primate genomes. Here, we compare the chimpanzee and human genomes to...Full Text Available
Alu Recombination-Mediated Structural Deletions in the Chimpanzee Genome
2007-10-01
Full Text Available.With more than 1.2 million copies, Alu elements are one of the most important sources of structural variation in primate genomes. Here, we compare the chimpanzee and human genomes to determine the extent of Alu recombination-mediated deletion (ARMD) in the chimpanzee genome since the divergence of the chimpanzee and human lineages (∼6 million y ago). Combining computational data analysis and experimental verification, we have identified 663 chimpanzee lineage-specific deletions (involving a total of ∼771 kb of genomic sequence) attributable to this process. The ARMD events essentially counteract the genomic expansion caused by chimpanzee-specific Alu inserts. The RefSeq databases indicate that 13 exons in six genes, annotated as either demonstrably or putatively functional in the human genome, and 299 intronic regions have been deleted through ARMDs in the chimpanzee lineage. Therefore, our data suggest that this process may contribute to the genomic and phenotypic diversity between chimpanzees and humans. In addition, we found four independent ARMD events at orthologous loci in the gorilla or orangutan genomes. This suggests that human orthologs of loci at which ARMD events have already occurred in other nonhuman primate genomes may be “at-risk” motifs for future deletions, which may subsequently contribute to human lineage-specific genetic rearrangements and disorders.
2008-07-01
Full Text Available.Embryonic poly(A) binding protein (EPAB), expressed in oocytes and early embryos, binds and stabilizes maternal mRNAs, and mediates initiation of their translation. We identified an alternatively spliced form of Epab lacking exon 10 (c.Ex10del) and investigated the regulation of Epab mRNA alternative splicing as a model for alternative splicing in oocytes and early preimplantation embryos. Specifically, we evaluated the following mechanisms: imprinting; RNA editing and exonic splicing enhancers (ESEs). Sequence analysis led to the identification of two single nucleotide polymorphisms (SNPs): one was detected in exon 9 (rs55858A/G), and served as a marker for the parental origin of the alternatively spliced form, and the other was found in exon 10 (rs56574G/C), and co-segregated with the exon 9 SNP. We found that the presence of rs56574G in exon 10 led to the formation of an ESE, leading to efficient exclusion of exon 10. Real-time RT–PCR results revealed a 5-fold increase in the expression of the c.Ex10del alternative splicing variant in animals carrying rs56574G/G in exon 10 compared with rs56574C/C at the same locus. Our findings suggest that SNPs may alter the ratio between alternative splicing variants of oocyte-specific proteins. The role that these subtle differences play in determining individual reproductive outcome remains to be determined.
2008-07-01
Embryonic poly(A) binding protein (EPAB), expressed in oocytes and early embryos, binds and stabilizes maternal mRNAs, and mediates initiation of their translation. We identified an alternatively spliced...Full Text Available
2007-09-01
We describe a rapid, high-throughput method to scan for new RNA editing sites. This method is adapted from high-resolution melting (HRM) analysis of amplicons, a technique used in clinical research...Full Text Available
2007-09-01
Full Text Available.We describe a rapid, high-throughput method to scan for new RNA editing sites. This method is adapted from high-resolution melting (HRM) analysis of amplicons, a technique used in clinical research to detect mutations in genomes. The assay was validated by the discovery of six new editing sites in different chloroplast transcripts of Arabidopsis thaliana. A screen of a collection of mutants uncovered a mutant defective for editing of one of the newly discovered sites. We successfully adapted the technique to quantify editing of partially edited sites in different individuals or different tissues. This new method will be easily applicable to RNA from any organism and should greatly accelerate the study of the role of RNA editing in physiological processes as diverse as plant development or human health.
A near-infrared/optical/X-ray survey in the centre of sigma Orionis
2007-05-08
Because of the intense brightness of the OB-type multiple star system sigma Ori, the low-mass stellar and substellar populations close to the centre of the very young sigma Orionis cluster is poorly know. I present an IJHKs survey in the cluster centre, able to detect from the massive early-type stars down to cluster members below the deuterium burning mass limit. The near-infrared and optical data have been complemented with X-ray imaging. Ten objects have been found for the first time to display high-energy emission. Previously known stars with clear spectroscopic youth indicators and/or X-ray emission define a clear sequence in the I vs. I-Ks diagram. I have found six new candidate cluster members that follow this sequence. One of them, in the magnitude interval of the brown dwarfs in the cluster, displays X-ray emission and a very red J-Ks colour, indicative of a disc. Other three low-mass stars have excesses in the Ks band as well. The frequency of X-ray emitters in the area is 80+/-20 %. The spatial density of stars is very high, of up to 1.6+/-0.1 arcmin-2. There is no indication of lower abundance of substellar objects in the cluster centre. Finally, I also report two cluster stars with X-ray emission located at only 8000-11000 AU to sigma Ori AB, two sources with peculiar colours and an object with X-ray emission and near-infrared magnitudes similar to those of previously-known substellar objects in the cluster.
A fine pair of gifts for St Valentine’s Day
2008-02-14
$$bLike briefly separated twin sisters, ATLAS’s small wheels were once again united at the experiment’s surface building at Point 1 on St Valentine’s Day. The lowering of the small wheels into the tunnel will mark the end of the installation of detector components for the experiment. In a delicate operation, the small wheels were slowly and painstakingly transported one after the other on a lorry towing a double trailer from Building 191 to the ATLAS experiment surface building at Point 1. Each measuring 10 metres in diameter and weighing almost 140 tonnes, the small wheels will allow the muon tracks to be reconstructed with an extreme precision of 10 microns. The two small wheels of the ATLAS muon spectrometer will be the last detector components to be installed in the cavern. The first made its final journey on 8 February and the second on 14 February, ready to be lowered into the cavern. At the time this edition of the Bulletin went to press, this latter operation had not yet been completed. Modest in scale compared with the large 25 m diameter muon spectrometer wheels (see Bulletin Nos. 41 and 42, 2007), the small wheels still have a diameter of 10 m and each weigh 140 tonnes. Unlike the large wheels, whose assembly was completed in the cavern, they have been assembled at the surface in Building 191 on the Meyrin site. In view of their scale, transporting them has been a delicate operation. Like a giant slow-moving tortoise, a lorry pulling two trailers transported the first small wheel to Point 1 on 8 February. Less than a week later, the lorry was back to fetch the second one for St Valentine’s Day. "We are delighted and relieved to have completed this operation on schedule", says Ariella Cattai, the physicist in charge of the small wheel project. "The assembly of these modules represented a real challenge. We had to put together the various scattered parts - and coordinate the different teams to do that - in record time." Like some outsize jigsaw puzzle, ATLAS’s small wheels took a year to assemble. They comprise thousands of components from all over the world (Bulgaria, Serbia, the Czech Republic, Pakistan, Russia, Israel, USA, and Japan, etc.), which have been assembled with millimetre precision. "We are very proud of having put together these detectors, which will be located in the forward position in the area closest to the beam’s axis," explains George Mikenberg, who is in charge of the muon spectrometer project. "They will allow the muon tracks to be reconstructed with extreme precision down to 10 microns". Sandwiched between the calorimeter and the two end-caps of the torroid magnet, the small wheels are the muon detectors closest to the interaction point in the small-angle region. They will be located in a highly radioactive area. They consist of three of the four types of muon chambers used in the ATLAS experiment, trigger chambers (TGCs) and two types of precision chamber (CSCs and MDTs). They each consist of two disks placed one against the other and slotted together with a central cylindrical component. One of them is shielding which will absorb particles other than the muons. The other acts as the support for the detection chambers. These two wheels complete ATLAS’s highly sophisticated muon spectrometer, whose purpose is to detect the eagerly awaited disintegration of the Higgs boson into two muon pairs.
A Left Handed RNA Double Helix Bound by the Zα Domain of the RNA Editing Enzyme ADAR1
2007-04-01
SummaryThe A-form RNA double helix can be transformed to a left handed helix, called Z-RNA. Currently, little is known about the detailed structural features of Z-RNA or its involvement...Full Text Available
A Left Handed RNA Double Helix Bound by the Zα Domain of the RNA Editing Enzyme ADAR1
2007-04-01
Full Text Available.SummaryThe A-form RNA double helix can be transformed to a left handed helix, called Z-RNA. Currently, little is known about the detailed structural features of Z-RNA or its involvement in cellular processes. The discovery that certain interferon response proteins have domains that can stabilize Z-RNA as well as Z-DNA opens the way for the study of Z-RNA. Here we present the 2.25 Å crystal structure of the Zα domain of the RNA editing enzyme ADAR1 (double stranded RNA adenosine deaminase) complexed to a dUr(CG)3 duplex RNA. The Z-RNA helix is associated with a unique solvent pattern which distinguishes it from the otherwise similar conformation of Z-DNA. Based on the structure we propose a model suggesting how differences in solvation lead to two types of Z-RNA structures. The interaction of Zα with Z-RNA demonstrates how the interferon-induced isoform of ADAR1 could be targeted towards selected dsRNAs containing purine-pyrimidine repeats, possibly of viral origin.
A Cytidine Deaminase Edits C to U in Transfer RNAs in Archaea
2009-05-01
Full Text Available.All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri harbors 30 (out of 34) tRNA genes with cytidine at position 8. Here, we demonstrate C-to-U editing at this location in the tRNA’s tertiary core, and present the crystal structure of a tRNA-specific cytidine deaminase, CDAT8, which has the cytidine deaminase domain linked to a tRNA-binding THUMP domain. CDAT8 is specific for C deamination at position 8, requires only the acceptor stem hairpin for activity, and belongs to a unique family within the “cytidine deaminase–like” superfamily. The presence of this C-to-U editing enzyme guarantees the proper folding and functionality of all M. kandleri tRNAs.
A Cytidine Deaminase Edits C to U in Transfer RNAs in Archaea
2009-05-01
All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri...Full Text Available
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