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Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA
2009-11-01
Full Text Available.Adenosine-to-inosine (A-to-I) editing has been shown to be an important mechanism that increases protein diversity in the brain of organisms from human to fly. The family of ADAR enzymes converts some adenosines of RNA duplexes to inosines through hydrolytic deamination. The adenosine recognition mechanism is still largely unknown. Here, to investigate it, we analyzed a set of selectively edited substrates with a cluster of edited sites. We used a large set of individual transcripts sequenced by the 454 sequencing technique. On average, we analyzed 570 single transcripts per edited region at four different developmental stages from embryogenesis to adulthood. To our knowledge, this is the first time, large-scale sequencing has been used to determine synchronous editing events. We demonstrate that edited sites are only coupled within specific distances from each other. Furthermore, our results show that the coupled sites of editing are positioned on the same side of a helix, indicating that the three-dimensional structure is key in ADAR enzyme substrate recognition. Finally, we propose that editing by the ADAR enzymes is initiated by their attraction to one principal site in the substrate.
Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA
2009-11-01
Adenosine-to-inosine (A-to-I) editing has been shown to be an important mechanism that increases protein diversity in the brain of organisms from human to fly. The family of ADAR enzymes converts some...Full Text Available
Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA
2009-01-01
Adenosine-to-inosine (A-to-I) editing has been shown to be an important mechanism that increases protein diversity in the brain of organisms from human to fly. The family of ADAR enzymes converts some adenosines of RNA duplexes to inosines through hydrolytic deamination. The adenosine recognition mechanism is still largely unknown. Here, to investigate it, we analyzed a set of selectively edited substrates with a cluster of edited sites. We used a large set of individual transcripts sequenced by the 454 sequencing technique. On average, we analyzed 570 single transcripts per edited region at four different developmental stages from embryogenesis to adulthood. To our knowledge, this is the first time, large-scale sequencing has been used to determine synchronous editing events. We demonstra...
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
Evidence for large diversity in the human transcriptome created by Alu RNA editing
2009-01-01
Adenosine-to-inosine (A-to-I) RNA editing alters the original genomic content of the human transcriptome and is essential for maintenance of normal life in mammals. A-to-I editing in Alu repeats is abundant in the human genome, with many thousands of expressed Alu sequences undergoing editing. Little is known so far about the contribution of Alu editing to transcriptome complexity. Transcripts derived from a single edited Alu sequence can be edited in multiple sites, and thus could theoretically generate a large number of different transcripts. Here we explored whether the combinatorial potential nature of edited Alu sequences is actually fulfilled in the human transcriptome. We analyzed datasets of editing sites and performed an analysis of a detailed transcript set of one edited Alu sequ...
Evidence for large diversity in the human transcriptome created by Alu RNA editing
2009-11-01
Full Text Available.Adenosine-to-inosine (A-to-I) RNA editing alters the original genomic content of the human transcriptome and is essential for maintenance of normal life in mammals. A-to-I editing in Alu repeats is abundant in the human genome, with many thousands of expressed Alu sequences undergoing editing. Little is known so far about the contribution of Alu editing to transcriptome complexity. Transcripts derived from a single edited Alu sequence can be edited in multiple sites, and thus could theoretically generate a large number of different transcripts. Here we explored whether the combinatorial potential nature of edited Alu sequences is actually fulfilled in the human transcriptome. We analyzed datasets of editing sites and performed an analysis of a detailed transcript set of one edited Alu sequence. We found that editing appears at many more sites than detected by earlier genomic screens. To a large extent, editing of different sites within the same transcript is only weakly correlated. Thus, rather than finding a few versions of each transcript, a large number of edited variants arise, resulting in immense transcript diversity that eclipses alternative splicing as mechanism of transcriptome diversity, although with less impact on the proteome.
Widespread cleavage of A-to-I hyperediting substrates
2009-09-01
Full Text Available.A-to-I RNA editing is the conversion of adenosine to inosine in double-stranded cellular and viral RNAs. Recently, abundant hyperediting of human transcripts, affecting thousands of genes, has been reported. Most of these editing sites are confined to intramolecular hairpin double-stranded RNA (dsRNA) structures formed by pairing of neighboring, reversely oriented, primate-specific Alu repeats. The biological implication of this extensive modification is still a mystery. A number of studies have shown that heavily edited transcripts are often retained in the nucleus. A recent study found that the edited region in transcripts of the mouse Slc7a2 gene is post-transcriptionally cleaved upon stress, enabling the release of the mRNA to the cytoplasm, followed by its translation. Here, we aim to test whether this scenario might be relevant for many other hyperedited Alu targets. Bioinformatics analysis of publicly available mRNA and expressed sequence tag data provides evidence showing that neighboring, reversely oriented, Alu elements are often cleaved at both ends of the region harboring the inverted repeats followed by rejoining of the two parts of the transcript on both sides of the inverted repeats, resulting in almost inosine-free mRNA products. Deleted segments vary among transcripts of the same gene and are not flanked by the canonical splicing signal sequences. The tissue distribution of these events seems to correlate with known A-to-I editing patterns, suggesting that it depends on the dsRNA structure being edited. Results are experimentally verified by polymerase chain reaction and cloning data. A database of 566 human and 107 mouse putative cleavage loci is supplied.
Editing modifies the GABA(A) receptor subunit alpha3.
2007-01-01
Adenosine to inosine (A-to-I) pre-mRNA editing by the ADAR enzyme family has the potential to increase the variety of the proteome. This editing by adenosine deamination is essential in mammals for a functional brain. To detect novel substrates for A-to-I editing we have used an experimental method to find selectively edited sites and combined it with bioinformatic techniques that find stem-loop structures suitable for editing. We present here the first verified editing candidate detected by this screening procedure. We show that Gabra-3, which codes for the alpha3 subunit of the GABA(A) receptor, is a substrate for editing by both ADAR1 and ADAR2. Editing of the Gabra-3 mRNA recodes an isoleucine to a methionine. The extent of editing is low at birth but increases with age, reaching close to 100% in the adult brain. We therefore propose that editing of the Gabra-3 mRNA is important for normal brain development.
TaqMan-based, real-time quantitative polymerase chain reaction method for RNA editing analysis
2009-01-01
Abnormal adenosine to inosine (A-to-I) messenger RNA (mRNA) editing has been linked to several disease states afflicting the central nervous system. Here we report an assay to determine RNA editing frequencies at specific sites that is based on quantitative polymerase chain reaction (qPCR) with TaqMan probes. The assay was tested by measuring the frequency of the A-to-I mRNA editing at the Q/R site of the human kainate receptor subunit GluR5 and was compared with two established methods of assessing RNA editing: sequencing of individual clones and restriction analysis. The qPCR assay displayed high sensitivity and reproducibility, demonstrated exceptional discrimination between edited and unedited transcript variants, and proved to have several advantages over the other editing methods. Du...
Determination of editors at the novel A-to-I editing positions
2008-01-01
A-to-I RNA editing modifies a variety of biologically important mRNAs, and is specifically catalyzed by either adenosine deaminase acting on RNA type 1 (ADAR1) or type 2 (ADAR2) in mammals including human. Recently several novel A-to-I editing sites were identified in mRNAs abundantly expressed in mammalian organs by means of computational genomic analysis, but which enzyme catalyzes these editing sites has not been determined. Using RNA interference (RNAi) knockdowns, we found that cytoplasmic fragile X mental retardation protein interacting protein 2 (CYFIP2) mRNA had an ADAR2-mediated editing position and bladder cancer associated protein (BLCAP) mRNA had an ADAR1-mediated editing position. In addition, we found that ADAR2 forms a complex with mRNAs with ADAR2-mediated editing positions...
Adenosine deamination in human transcripts generates novel microRNA binding sites
2009-12-15
Full Text Available.Animals regulate gene expression at multiple levels, contributing to the complexity of the proteome. Among these regulatory events are post-transcriptional gene silencing, mediated by small non-coding RNAs (e.g. microRNAs), and adenosine-to-inosine (A-to-I) editing, generated by adenosine deaminases that act on double-stranded RNA (ADAR). Recent data suggest that these regulatory processes are connected at a fundamental level. A-to-I editing can affect Drosha processing or directly alter the microRNA (miRNA) sequences responsible for mRNA targeting. Here, we analyzed the previously reported adenosine deaminations occurring in human cDNAs, and asked if there was a relationship between A-to-I editing events in the mRNA 3′ untranslated regions (UTRs) and mRNA:miRNA binding. We find significant correlations between A-to-I editing and changes in miRNA complementarities. In all, over 3000 of the 12 723 distinct adenosine deaminations assessed were found to form 7-mer complementarities (known as seed matches) to a subset of human miRNAs. In 200 of the ESTs, we also noted editing within a specific 13 nucleotide motif. Strikingly, deamination of this motif simultaneously creates seed matches to three (otherwise unrelated) miRNAs. Our results suggest the creation of miRNA regulatory sites as a novel function for ADAR activity. Consequently, many miRNA target sites may only be identifiable through examining expressed sequences.
RNA editing: a driving force for adaptive evolution?
2009-10-01
Full Text Available.Genetic variability is considered a key to the evolvability of species. The conversion of an adenosine (A) to inosine (I) in primary RNA transcripts can result in an amino acid change in the encoded protein, a change in secondary structure of the RNA, creation or destruction of a splice consensus site, or otherwise alter RNA fate. Substantial transcriptome and proteome variability is generated by A-to-I RNA editing through site-selective post-transcriptional recoding of single nucleotides. We posit that this epigenetic source of phenotypic variation is an unrecognized mechanism of adaptive evolution. The genetic variation introduced through editing occurs at low evolutionary cost since predominant production of the wild-type protein is retained. This property even allows exploration of sequence space that is inaccessible through mutation, leading to increased phenotypic plasticity and provides an evolutionary advantage for acclimatization as well as long-term adaptation. Furthermore, continuous probing for novel RNA editing sites throughout the transcriptome is an intrinsic property of the editing machinery and represents the molecular basis for increased adaptability. We propose that higher organisms have therefore evolved to systems with increasing RNA editing activity and, as a result, to more complex systems.
A-to-I pre-mRNA editing of the serotonin 2C receptor: Comparisons among inbred mouse strains
2006-01-01
The serotonin receptor 5HT2CR pre-mRNA is subject to adenosine deamination (RNA editing) at five residues located within a 15 nucleotide stretch of the coding region. Such changes of adenosine to inosine (A-to-I) can produce 32 mRNA variants, encoding 24 different protein isoforms, some of which vary in biochemical and pharmacological properties. Because serotonin mediates diverse neurological processes relevant to behavior and because inbred mouse strains vary in their responses to tests of learning and behavior, we have examined the A-to-I editing patterns of the 5HT2CR mRNA in whole brains from eight mouse strains. By sequencing approximately 100 clones from individual mice, we generated detailed information on levels of editing at each site and patterns of editing that identify a total...
2009-05-07
$$bIn 2005, Italy’s National Institute for Nuclear Physics (INFN) introduced a fun new educational initiative called ‘Physics on board’. CERN is now also on board, coordinating the project’s extension to European level and the participation of scientists from Portugal, Spain and France. School children at the Civitavecchia stopover (27/04/09), taking part in one of the ‘Physics on board ‘ activities, the ‘winch’, used to measure the multiplication factor of their own pulling force.‘Physics on board’ is a science outreach project with the aim of stimulating young people’s interest in physics by transforming a sailing yacht into a real-life travelling laboratory, specially designed with secondary-school children in mind. The ‘Adriatica’ is a vessel made famous by the Italian TV show Velisti per Caso, presented by Patrizio Roversi and Syusi Blady on Rai 3. As they sail up and down the Italian coastline, scientists from INFN, some of them CERN users, make frequent stopovers and meet thousands of schoolchildren eager to learn all about modern physics, and at the same time try out fun-filled educational activities on land and at sea. In this, the project’s fourth year, numerous experiments and attractions have been devised on the themes of navigation and physics; for instance, pupils learn that the now commonplace navigational device, the GPS, could not have come into being without Einstein’s general theory of relativity. CALLING ALL PHYSICISTS A resounding success since 2005, this Italian-born project is now being taken to the European level. Any physicists living in Portugal, Spain or France who are interested in taking part can contact the project coordinator, Paola Catapano, at the following address: mailto:Paola.Catapano@cern.ch. Additional information (in Italian only) can be found on the project website: http://web.infn.it/fisicainbarca/
Geac is a registered trademark of Geac Computer Corporation, Ltd. SmartStream and Active Architecture are registered trademarks, and Active Access and Geac Enterprise Solutions are trademarks of Geac Enterprise Solutions, Inc. HP-UX is a registered trademark of Hewlett-Packard Corporation.
Navigating the caArray User Interface ............................................................ 14 Elements in the caArray User Interface ...................................................... 14 caArray Welcome Page Navigation Menu ................................................ 15 User Interface Footer ..................................................................................... 16 My Experiment Workspace .......................................................................... 16 Chapter 3 Navigating and Searching caArray ....................................................19 Browsing the caArray Repository ..................................................................... 19 Searching the caArray Repository .................................................................... 22 Experiment Search Results ........................................................................... 24 caArray 2.0 User?s Guide iv This is a U.S. Government work.
Requesting a User Account ................................................................................ 10 Using caArray Online Help ............................................................................... 13 Navigating the caArray User Interface ............................................................ 13 Elements in the caArray User Interface ...................................................... 14 caArray Welcome Page Navigation Menu ................................................ 15 User Interface Footer ..................................................................................... 16 My Experiment Workspace .......................................................................... 16 Chapter 3 Navigating and Searching caArray ....................................................19 Browsing the caArray Repository ..................................................................... 19 Searching the caArray Repository .................................................................... 22 Experiment Search Results ........................................................................... 24 caArray 2.0 User?s Guide iv This is a U.S. Government work.
axion: Axion - Java Database - News
The Axion news feed is on hiatus, yet Axion is still being actively developed. ... Better late than never, it's the Axion database project's October 2003 ...
A small, fast, SQL and JDBC compliant relational database engine written in and for the Java programming language. [Open source, BSD License]
Widespread cleavage of A-to-I hyperediting substrates
2009-09-01
A-to-I RNA editing is the conversion of adenosine to inosine in double-stranded cellular and viral RNAs. Recently, abundant hyperediting of human transcripts, affecting thousands of genes, has been...Full Text Available
Valinomycin Biosynthetic Gene Cluster in Streptomyces: Conservation, Ecology and Evolution
Many Streptomyces strains are known to produce valinomycin (VLM) antibiotic and the VLM biosynthetic gene cluster (vlm) has been characterized in two independent isolates....Full Text Available
Valinomycin Biosynthetic Gene Cluster in Streptomyces: Conservation, Ecology and Evolution
Full Text Available.Many Streptomyces strains are known to produce valinomycin (VLM) antibiotic and the VLM biosynthetic gene cluster (vlm) has been characterized in two independent isolates. Here we report the phylogenetic relationships of these strains using both parsimony and likelihood methods, and discuss whether the vlm gene cluster shows evidence of horizontal transmission common in natural product biosynthetic genes. Eight Streptomyces strains from around the world were obtained and sequenced for three regions of the two large nonribosomal peptide synthetase genes (vlm1 and vlm2) involved in VLM biosynthesis. The DNA sequences representing the vlm gene cluster are highly conserved among all eight environmental strains. The geographic distribution pattern of these strains and the strict congruence between the trees of the two vlm genes and the housekeeping genes, 16S rDNA and trpB, suggest vertical transmission of the vlm gene cluster in Streptomyces with no evidence of horizontal gene transfer. We also explored the relationship of the sequence of vlm genes to that of the cereulide biosynthetic genes (ces) found in Bacillus cereus and found them highly divergent from each other at DNA level (genetic distance values≥95.6%). It is possible that the vlm gene cluster and the ces gene cluster may share a relatively distant common ancestor but these two gene clusters have since evolved independently.
Introduction ............................................................................................................................... 26 History of Media-Effects Research ............................................................................................. 27 Levels of Theory and Analysis .................................................................................................... 28 Summary .................................................................................................................................... 44 References ................................................................................................................................... 45 Part 2?Tobacco Marketing...................................................................................51 Chapter 3?Key Principles of Tobacco Promotion and Rationales for Regulation .....................53 Introduction ............................................................................................................................... 54 Key Principles of Tobacco Advertising and Promotion.
The plant mitochondrial mat-r gene/nad1 gene complex
1996-12-31
We have completed sequencing segments of the maize mitochondrial (mt) DNA that contains all five of the exons (A-E) of the gene (nad1) for subunit I of the respiratory chain NADH dehydrogenase. Analysis of these sequences indicates that exons B and C are joined by a continuous group II intron, but the remaining exons are associated with partial group II introns and are encoded at widely separated locations in the maize mtDNA molecule. We have shown that mature transcripts of the maize nad1 gene contain 23 edited nucleotides, and that transcripts of maize and soybean mat-r genes contain 15 and 14 edits, respectively. The majority of edits in nad1 transcripts result in amino acid replacements that increase similarity between the maize NAD1 protein and NAD1 proteins of other plant species and of animal species. We found that the intron between exons b and c is not edited. From data obtained using PCR and sequencing we have shown that transcripts containing all possible exon combinations exist in maize mitochondria.
Teachers staying ahead of the game
2009-07-31
$$bEven though the school holidays are in full swing, some 40 high-school teachers have come to CERN to take part in the High School Teachers (HST) programme organised by the CERN Education Group (see box). Far from considering this as a piece of holiday fun, the teachers are getting their hands dirty and putting in some serious hours’ learning. The High School Teachers 2009 at CERN.The 3-week HST programme hosts dozens of teachers from around the world, offering a deeper insight into particle physics through a variety of lectures, visits and workshops. The programme’s ambitious overall aim is to help these teachers to inspire their students to follow careers in science. In the second week, they split up into working groups to evaluate CERN’s existing educational tools or create new ones. "This year, one of the groups is reviewing some of the CERN visits service itineraries," says HST programme manager Mick Storr. "From their perspective as teachers they can give us a valuable insight into the quality of our tools and thus help us improve them. Another group is sifting through the video archives on the CERN website and drawing up a league table of CERN videos highlighting those which provide the most educational benefit." Did you know? When it was launched for the first time in 1998, the HST programme had only 9 participants. Today, 35 to 40 people are selected every year out of more than 100 applications from all corners of the globe: CERN’s Member States, of course, but this year the programme also included teachers from the United States, Chile, Mexico, South Africa, India and, for the first time, Croatia, Japan and Australia. In so doing they’re not only working for CERN and their colleagues, but also and above all fulfilling their mission as teachers by working for the benefit of their students. One participant, Juliana Mitrevski, has shown devotion beyond the call of duty. She’s from Australia, where schools are not on holiday at the moment, and has set up a blog to enable her students to carry on learning even while she’s at CERN: "I record what I do every day on the blog and describe the lectures I’ve attended," she explains. Juliana hopes her light-hearted, avant-garde approach will have the desired effect of triggering her students’ interest: "I’ve included a link to the video of the LHC rap and set up an HST group for my students on Facebook," she says. Beyond the strictly educational and scientific aspects, the participants also appreciate the social side of this international programme. "When you’re working with people from 23 different countries it’s a real cultural melting pot and a great opportunity to compare teaching methods," notes Polish teacher Mazgorzata Karulak. "After three weeks together, the teachers grow very close and it’s sad to think we’ll all be returning home soon," says Terrence Baine, a Canadian teaching in Norway, who is attending the programme for the second time as part of his research for a PhD in Physics Education. "I’ve kept in touch with the good friends I made during last year’s programme and I’m sure it’ll be the same for those attending this year." For more information and the full list of working groups for 2009: http://teachers.web.cern.ch/teachers/ http://education.web.cern.ch/education/Welcome.html http://julianaatcern.blogspot.com/ The educational resources created by the participants can be accessed on-line via the programme website: http://teachers.web.cern.ch/teachers/materials/default.htm
1991-01-01
Schizophrenia is a devasting mental disorder that is the focus of a great deal of research. Some symptoms of the disease, such as auditory hallucinations and delusions, can be ameliorated with drug treatment, whereas other symptoms, such as social withdrawal and cognitive decline, remain uncontrolled. It is possible that these latter symptoms that are often termed ''negative symptoms'' are the result of anatomical and neurochemical abnormalities, whereas those symptoms of the disease such as auditory hallucinations that are termed ''positive symptoms'' may be a result of only neurochemical disorders. The drugs used to treat schizophrenia are designated neuroleptics. The term neuroleptic was chosen to emphasize the similarity of pharmacological profiles of drugs with entirely different chemical structures. Especially prominent features of the effects of neuroleptics include the following: a state of affective indifference; a decrease in locomotor activity; a decrease in excitation, agitation, and aggressiveness; and an antipsychotic action in patients with acute as well as chronic psychoses.
Synthesis and applications of selectively {sup 13}C-labeled RNA
1994-12-01
Spectral overlap is a substantial problem in NMR studies of RNA molecules >30 nucleotides. To overcome this difficulty, we synthesized selectively {sup 13}C-labeled RNAs and adapted several isotope-edited two- and three-dimensional NMR experiments originally developed for protein studies. We optimized protocols for synthesis of multi-gram quantities of CTP, UTp, ATP, and GTP using a combination of synthetic organic and enzymatic methods. Uracil is prepared in 40 to 50% yield from {sup 13}C-cyanide in two steps. Using acetyl- tribenzoyl-ribose and standard chemistry uracil is then attached to the sugar (90% yield). The tribenzoyl-uridine intermediate is converted into uridine or cytidine quantitatively, depending on the deblocking protocol. Labeled purines are synthesized using simple pyrimidine precursors and reacting with {sup 13}C-formic acid (80% yield). Purine nucleosides are then synthesized using uridine phosphorylase and purine nucleoside phosphorylase. The nucleosides were converted to NMPs by treatment with POC1{sub 3} in triethylphosphate. We converted NMPs to NTPs by standard enzymatic methods. Selectively labeled RNAs were synthesized by run-off transcription using {sup 13}C-labeled NTPs. Several different strategies help solve over-lap problems in larger RNAs. Isotope-edited two-dimensional NMR experiments such as {omega}1-1/2 X-filtered NOESY simplify NMR spectra by dividing the normal NOESY spectrum into two subspectra-one involving NOEs from protons bound to {sup 12}C and one from protons bound to {sup 13}C. For example, we labeled A and U residues of a 34-nucleotide pseudoknot, and the {sup 12}C subspectrum of the 1/2 X-filtered NOESY contained NOEs only from G and C residues (along with adenine 2H); the {sup 13}C subspectrum contained NOEs only from A and U residues. Each subspectrum has less overlap than the NOESY of an unlabeled sample; the editing strategy allows each resonance to be identified by residue type (A, C, G, or U).
2009-01-01
Substitutional editing increases genomic plasticity by changing or modifying bases at the RNA level. In this study we sequenced 10 mature chloroplast mRNAs, the chloroplast 16S rRNA and a partial chloroplast 23S rRNA from the dinoflagellate Heterocapsa triquetra, and found multiple types of substitutional editing, with A-to-G editing predominating. A-to-G editing of mRNAs converts two unusual AUA start codons into conventional AUG start codons, but three AUA start codons are not edited, showing that this dinoflagellate chloroplast has three possible start codons: AUG, AUA and UUG. To analyze the editing effects on rRNAs, we computationally predicted the secondary structure of the 16S rRNA based on the E. coli model. There are twenty editing sites in well-conserved regions of the secondary ...
Structural studies on an internal loop from a hairpin ribozyme
1994-12-01
Ribozymes, RNA enzymes, catalyze site-specific RNA cleavage and ligation reactions. We are studying the three-dimensional structure of a hairpin ribozyme derived from the minus strand of tobacco ring spot virus satellite RNA ((-)sTRSV), which has been engineering to specifically cleave the HIV-1 RNA. The minimum structure for the catalytic reaction involves a 50-nucleotide ribozyme and a 14-nucleotide substrate. The proposed secondary structure of the ribozyme-substrate complex consists of four short helices separated by two internal loops. The relatively large size (64-nucleotide) of the ribozyme-substrate complex presents formidable problems in solving the structure using NMR. Therefore we are studying smaller structural subunits of the complex. We are determining the high resolution structure of the symmetric internal loop involving the cleavage site and the flanking helices. One strand of the internal loop was selectively {sup 13}C-labeled at C8 of each purine and C6 of each pyrimidine. By using {sup 13}C-edited two-dimensional NMR, the proton NOESY spectrum was greatly simplified. This allowed unambiguous sequential proton resonance assignments along each strand. Three-dimensional {sup 1}-{sup 13}C HMQC-NOESY was used to further facilitate resonance assignments. We are also enzymatically synthesizing the entire 50-nucleotide ribozyme and will combine it with the {sup 13}C-labeled substrate. Through comparison of the NOE connectivities of the labeled nucleotides from the internal loop alone with those from the entire complex, the differences between the two structures can be elucidated.
2008-10-14
The young sigma Orionis cluster in the Orion Belt is an incomparable site for studying the formation and evolution of high-mass, solar-like, and low-mass stars, brown dwarfs, and substellar objects below the deuterium burning mass limit. The first version of the Mayrit catalogue was a thorough data compilation of cluster members and candidates, which is regularly used by many authors of different disciplines. I show two new applications of the catalogue and advance preliminar results on very wide binarity and the initial mass function from 18 to 0.035 Msol in sigma Orionis. The making-up of a new version of the Mayrit catalogue with additional useful data is in progress.
Staff Rules & Regulations – modification No. 2 to the 11th Edition
2008-08-01
$$bIn June 2008, the Finance Committee and the Council approved the following amendments to the Staff Rules and Regulations:Chapter II, Conditions of Employment and Association, Section 4 (Leave): page 26 has been amended - with effect from 1 July 2008;Chapter III, Working Conditions, Section 1 (Working Hours): pages 30 to 32 have been amended and pages 33 and 34 have been deleted – with effect from 1 July 2008. Modification No. 2 is available from departmental secretariats (paper copies), or from the HR Department’s intranet site. In accordance with the above-mentioned amendments, the deleted parts of Chapter III will appear in the relevant administrative circulars. Until the revision of the latter (currently in process) is completed, the deleted parts of Chapter III continue to apply in accordance with transition measures decided by the Director-General. Please note that modification No. 1, concerning amendments approved by the Council in June 2007 to Annexes A 1 and correction of errata found in R A 5, R A 6, R A 7, R A 9 and R A 10 during the second half of 2007, still remains available from secretariats or the above-mentioned site. An updated index will be posted on the site shortly. HR Department Tel. 78003
Staff Rules & Regulations – modification No. 2 to the 11th Edition
2008-07-24
$$bIn June 2008, the Finance Committee and the Council approved the following amendments to the Staff Rules and Regulations:Chapter II, Conditions of Employment and Association, Section 4 (Leave): page 26 has been amended - with effect from 1 July 2008;Chapter III, Working Conditions, Section 1 (Working Hours): pages 30 to 32 have been amended and pages 33 and 34 have been deleted – with effect from 1 July 2008. Modification No. 2 is available from departmental secretariats (paper copies), or from the HR Department’s intranet site. In accordance with the above-mentioned amendments, the deleted parts of Chapter III will appear in the relevant administrative circulars. Until the revision of the latter (currently in process) is completed, the deleted parts of Chapter III continue to apply in accordance with transition measures decided by the Director-General. Please note that modification No. 1, concerning amendments approved by the Council in June 2007 to Annexes A 1 and correction of errata found in R A 5, R A 6, R A 7, R A 9 and R A 10 during the second half of 2007, still remains available from secretariats or the above-mentioned site. An updated index will be posted on the site shortly. HR Department Tel. 78003
Sampling plans to find faulty waste storage drums
1990-01-01
In environmental surveillance work, one is often faced with the task of determining by a random sample that hazardous waste is stored safely. In many cases such waste is kept in drums which are accumulated at various sites, and some of these sites are thought to have a more deleterious effect on the drums than other sites. In this paper, knowledge'' of the sites is used to develop sampling plans which increase the probability of finding faulty drums. An exchange algorithm to determine the sample sizes is given, and the influence of the prior knowledge'' on these sample sizes is investigated.
SNPs in human miRNA genes affect biogenesis and function
2009-09-01
MicroRNAs (miRNAs) are 21–25-nucleotide-long, noncoding RNAs that are involved in translational regulation. Most miRNAs derive from a two-step sequential processing: the generation of pre-miRNA...Full Text Available
SNPs in human miRNA genes affect biogenesis and function
2009-09-01
Full Text Available.MicroRNAs (miRNAs) are 21–25-nucleotide-long, noncoding RNAs that are involved in translational regulation. Most miRNAs derive from a two-step sequential processing: the generation of pre-miRNA from pri-miRNA by the Drosha/DGCR8 complex in the nucleus, and the generation of mature miRNAs from pre-miRNAs by the Dicer/TRBP complex in the cytoplasm. Sequence variation around the processing sites, and sequence variations in the mature miRNA, especially the seed sequence, may have profound affects on miRNA biogenesis and function. In the context of analyzing the roles of miRNAs in Schizophrenia and Autism, we defined at least 24 human X-linked miRNA variants. Functional assays were developed and performed on these variants. In this study we investigate the affects of single nucleotide polymorphisms (SNPs) on the generation of mature miRNAs and their function, and report that naturally occurring SNPs can impair or enhance miRNA processing as well as alter the sites of processing. Since miRNAs are small functional units, single base changes in both the precursor elements as well as the mature miRNA sequence may drive the evolution of new microRNAs by altering their biological function. Finally, the miRNAs examined in this study are X-linked, suggesting that the mutant alleles could be determinants in the etiology of diseases.
Additional optional software to use with the caCORE SDK is listed in Table 3.3, includ-ing the software name, version, description and URL columns. The included (Incl.) col-umn indicates (with a Yes) if the software is packaged with the SDK.
2009-11-05
Collaborative edition is achieved by distinct sites that work independently on (a copy of) a shared document. Conflicts may arise during this process and must be solved by the collaborative editor. In pure Peer to Peer collaborative editing, no centralization nor locks nor time-stamps are used which make conflict resolution difficult. We propose an algorithm which relies on the notion or semantics dependence and avoids the need of any integration transformation to solve conflicts. Furthermore, it doesn't use any history file recording operations performed since starting the edition process. We show how to define editing operations for semi-structured documents i.e. XML-like trees, that are enriched with informations derived for free from the editing process. Then we define the semantics dependence relation required by the algorithm and we present preliminary results obtained by a prototype implementation.
Regulatory roles of natural antisense transcripts
2009-09-01
Mammalian genomes encode numerous natural antisense transcripts, but the function of these transcripts is not well understood. Functional validation studies indicate that antisense transcripts...Full Text Available
Regulatory roles of natural antisense transcripts
2009-09-01
Full Text Available.Mammalian genomes encode numerous natural antisense transcripts, but the function of these transcripts is not well understood. Functional validation studies indicate that antisense transcripts are not a uniform regulatory RNA group, but instead belong to multiple categories with some common features. Recent evidence indicates that antisense transcripts are frequently functional and use diverse transcriptional and post-transcriptional gene regulatory mechanisms to carry out a wide variety of biological roles.
RNA editing: a driving force for adaptive evolution?
2009-10-01
Genetic variability is considered a key to the evolvability of species. The conversion of an adenosine (A) to inosine (I) in primary RNA transcripts can result in an amino acid change in the...Full Text Available
2009-06-18
$$b The end of a Council week is a good opportunity to bring you up to date with the status of the LHC, and I’m pleased to say that we had a good deal of positive news to report to the delegations today. The bottom line is that we remain on course to restart the LHC safely this year, albeit currently about 2-3 weeks later than we’d hoped at Chamonix. This Council week has seen many important developments for our future. I am particularly pleased that Council approved the Medium Term Plan and budget for 2010 as presented by the management. This is a strong vote of confidence in all of you. The President of Council is reporting on Council business in this issue of the Bulletin, so I will focus on the status of the LHC. A tremendous amount of work has been done to understand fully the splices in the LHC’s superconducting cable and copper stabilizers. One of these splices was the root cause of the incident last September that brought the LHC to a standstill. We’ve learned a great deal since then. It’s mostly good news but there’s also plenty of food for thought. The good news is that all the measurements done so far indicate that we will be ready by September or October to run the LHC safely in the range 4-5 TeV per beam. The food for thought is that the same tests tell us that before we can run safely above 5 TeV, more work is needed. This will be carried out in future shutdown periods. Many of you will have heard, or seen on the LHC web pages, that we’re warming up sector 4-5. This will give us increased confidence that we fully understand the splices. We’re warming up this sector because we have developed a new non-invasive technique for investigating the splices. The sector has been measured at a temperature of 80 K, indicating at least one suspect splice. By warming the sector, the results of the test can be checked at room temperature, allowing us to confirm the reliability of the test at 80 K. If the 80 K measurements are confirmed, any suspect splices in this sector will be repaired. More importantly, validation of the 80K measurements will allow the splice resistance in the last three sectors to be measured at this temperature, thereby avoiding the time needed for re-warming. When these measurements are done, we’ll have to balance energy against time: 4 TeV should require no further repairs, for example, whereas 5 TeV could call for more work. The measurements in these last three sectors will allow us to make that decision, determining the initial operating energy of the LHC in the range 4-5 TeV, and the start date for the first run. The Bulletin will continue to keep you up to date with LHC progress, and if you are interested in a full report, Steve Myers at CERN and Jim Strait at Fermilab will be making detailed presentations on 2 July. Steve’s presentation will be webcast at http://www.cern.ch/webcast. Rolf Heuer
Full Text Available.BackgroundKCNE1 represents the regulatory beta-subunit of the slowly activating delayed rectifier potassium channel (IKs). Variants of KCNE1 have repeatedly been linked to the long-QT syndrome (LQTS), a disorder which predisposes to deafness, ventricular tachyarrhythmia, syncope, and sudden cardiac death.ResultsWe here analyze the evolution of the common Gly38Ser variant (rs1805127), using genomic DNAs, complementary DNAs, and HEK293-expressed variants of altogether 19 mammalian species. The between species comparison reveals that the human-specific Gly38Ser polymorphism evolved under strong positive Darwinian selection, probably in adaptation to specific challenges in the fine-tuning of IKs channels. The involved amino acid exchanges (Asp > Gly, Gly > Ser) are moderately radical and do not induce apparent changes in posttranslational modification. According to population genetic analyses (HapMap phase II) a heterozygote advantage accounts for the maintenance of the Gly38Ser polymorphism in humans. On the other hand, the expression of the 38Ser allele seems to be disadvantageous under certain conditions, as suggested by the sporadic deficiency of 38Ser-coding mRNAs in heterozygote Central Europeans and the depletion of homozygotes 38Ser in the Yoruban sample.ConclusionWe speculate that individual differences in genomic imprinting or genomic recoding might have contributed to conflicting results of recent association studies between Gly38Ser polymorphism and QT phenotype. The findings thus highlight the relevance of mRNA data in future association studies of genotypes and clinical disorders. To the best of our knowledge, they moreover provide first time evidence for a unique pattern; i.e. coincidence of positive Darwinian selection and polymorphism with a sporadically suppressed expression of one allele.
BackgroundKCNE1 represents the regulatory beta-subunit of the slowly activating delayed rectifier potassium channel (IKs). Variants of KCNE1 have repeatedly been linked to the long-QT...Full Text Available
1982-04-01
This edited transcript of a presentation on personnel neutron discusses the accuracy of present dosimetry practices, requirements, calibration, dosemeter types, quality factors, operational problems, and dosimetry for a criticality accident. 32 figs. (ACR)
Peer to Peer Optimistic Collaborative Editing on XML-like trees
2009-01-28
Collaborative editing consists in editing a common document shared by several independent sites. This may give rise to conficts when two different users perform simultaneous uncompatible operations. Centralized systems solve this problem by using locks that prevent some modifications to occur and leave the resolution of confict to users. On the contrary, peer to peer (P2P) editing doesn't allow locks and the optimistic approach uses a Integration Transformation IT that reconciliates the conficting operations and ensures convergence (all copies are identical on each site). Two properties TP1 and TP2, relating the set of allowed operations Op and the transformation IT, have been shown to ensure the correctness of the process. The choice of the set Op is crucial to define an integration operation that satisfies TP1 and TP2. Many existing algorithms don't satisfy these properties and are indeed incorrect i.e. convergence is not guaranteed. No algorithm enjoying both properties is known for strings and little work has been done for XML trees in a pure P2P framework (that doesn't use time-stamps for instance). We focus on editing unranked unordered labeled trees, so-called XML-like trees that are considered for instance in the Harmony pro ject. We show that no transformation satisfying TP1 and TP2 can exist for a first set of operations but we show that TP1 and TP2 hold for a richer set of operations. We show how to combine our appro ach with any convergent editing process on strings (not necessarily based on integration transformation) to get a convergent process.
1970-08-01
This is the 19th Annual Report of the Biology Department.
1996-12-31
Well crystallized Li4Mn5O12 was prepared from LiOAc-Mn(NO3)2 under flowing oxygen. Rietveld refinement with XRD and neutron powder diffraction indicated that Li4Mn5O12 has cubic spinel structure in which the Li ions occupy both the tetrahedral sites 8a and part of the octahedral sites 16d but not the 16c sites, while all the Mn ions occupy the 16d sites of the space group Fd{bar 3}m. The lattice parameter was found to be sensitive to synthesis temperature owing to variation in Mn valence. Sample prepared at 500 C showed better electrode performance: a rechargeable capacity of 135 mAh/g for the cell Li/Li4Mn5O12 at cell voltages 2.5-3.6 V. It is found that Mn oxidation state in Li4Mn5O12 has a strong effect on electrode performance of Li/Li4Mn5O12 cell.
2009-10-01
$$bThe best-selling American author of ‘A Short History of Nearly Everything’, Bill Bryson, visited CERN on 14 September. When asked whether, after this visit, he would rewrite the chapter about CERN, he replied: "Oh yes, absolutely"! Bill Bryson visited CERN on 14 September.When Eureka, the Times’ new monthly science magazine, asked Bill Bryson to contribute an article, he was ‘thrilled’ to visit CERN. "This is a place that I’ve heard about for a long long time," he said. "I’ve had images in my mind and I always wanted to come here and see what it was like. I arrived just at the right time, one of the most exciting times in CERN’s history." One of the first surprises for him was driving through the charming French countryside from the CERN Control Centre and accelerator complex in Prévessin, to the CMS experiment in Cessy, whereas the campus in Meyrin was more in line with what he imagined CERN’s ‘academic-type buildings’ to look like. Bryson’s book ‘A Short History of Nearly Everything’ explains in simple terms the whys, hows and whens of science. The book won him the Aventis Prize for best general science book in 2004. However, it only mentions CERN very briefly. "Everything I wrote about CERN in my book was based on not having ever been here", he explains. "What CERN is doing is tremendously exciting and interesting and is something that even non-scientists ought to be taking an interest in," he enthused. Indeed, one of the things he will explain to the Eureka readers will be why finding the Higgs boson is more important then just ‘interesting’, as there are so many knock-on effects. During the morning’s visits he admitted: "It’s so complicated. I usually write books and have time to research the background. Now I’ve just got notes and scraps of thought from a flying visit to convert into an article. But it’s amazing. You usually only read about these things in the newspapers so to come to visit, to have it become a reality, to be able to talk to the physicists and to begin to understand it, is truly amazing." And by the afternoon, when he visited the Computer Centre, the Antiproton Decelerator and the ALPHA antihydrogen experiment, he was beginning to understand how the different parts of CERN fit together – particularly how the computing aspects support the LHC experiments. "You made me feel terribly welcome here. I could ask any questions I wanted. There isn’t any sort of ‘oh, I don’t want to talk about that.’ It ‘s a very open and honest organization. I think that’s wonderful, really!", he concluded. Rebecca Leam Watch the video of the interview: var flash_video_player=get_video_player_path(); insert_player_for_external('rtmp://flashstream.cern.ch:1935/player&id=foo/MediaArchive/Video/Public/Movies/2009/CERN-MOVIE-2009-092/CERN-MOVIE-2009-092-0753-kbps-640x360-25-fps-audio-64-kbps-44-kHz-stereo', 'mms://mediastream.cern.ch/MediaArchive/Video/Public/Movies/2009/CERN-MOVIE-2009-092/CERN-MOVIE-2009-092-Multirate-200-to-753-kbps-640x360-25-fps.wmv', 'false', 533, 300, 'http://mediaarchive.cern.ch/MediaArchive/Video/Public/Movies/2009/CERN-MOVIE-2009-092/CERN-MOVIE-2009-092-posterframe-640x360-at-0-percent.jpg', '1208151'); ---------------- The second edition of The Times Eureka magazine featuring CERN will be published in the UK on 5 November 2009.
National Ignition Facility (NIF) operations procedures plan
1998-05-06
The purpose of this Operations Procedures Plan is to establish a standard procedure which outlines how NIF Operations procedures will be developed (i.e , written, edited, reviewed, approved, published, revised) and accessed by the NIF Operations staff who must use procedures in order to accomplish their tasks. In addition, this Plan is designed to provide a guide to the NIF Project staff to assist them in planning and writing procedures. Also, resource and scheduling information is provided.
Montreal Axion - Wikipedia, the free encyclopedia
The Montreal Axion are a National Women's Hockey League team located in Montreal, Quebec, Canada. v ? d ? e · Sports teams based in the province of Quebec, ...
Participation in I2 Imaging Product Line and BOD meetings. Release 2.2.1 has been released to production with bug fixes and modifications that were required. A SOW for Rel 2.3-2.4 has been submitted to SAIC Frederick as a Yellow Ticket and has been approved. Rel. 3.0 change requests are being collected and will be submitted by or on March 20, 2007. At that time we will create a document to bid as an RFP.
2010-01-01
The evolution of insecticide resistance is a global constraint to agricultural production. Spinosad is a new, low-environmental-risk insecticide that primarily targets nicotinic acetylcholine receptors...Full Text Available
2010-01-01
Full Text Available.The evolution of insecticide resistance is a global constraint to agricultural production. Spinosad is a new, low-environmental-risk insecticide that primarily targets nicotinic acetylcholine receptors (nAChR) and is effective against a wide range of pest species. However, after only a few years of application, field evolved resistance emerged in the diamondback moth, Plutella xylostella, an important pest of brassica crops worldwide. Spinosad resistance in a Hawaiian population results from a single incompletely recessive and autosomal gene, and here we use AFLP linkage mapping to identify the chromosome controlling resistance in a backcross family. Recombinational mapping with more than 700 backcross progeny positioned a putative spinosad target, nAChR alpha 6 (Pxα6), at the resistance locus, PxSpinR. A mutation within the ninth intron splice junction of Pxα6 results in mis-splicing of transcripts, which produce a predicted protein truncated between the third and fourth transmembrane domains. Additional resistance-associated Pxα6 transcripts that excluded the mutation containing exon were detected, and these were also predicted to produce truncated proteins. Identification of the locus of resistance in this important crop pest will facilitate field monitoring of the spread of resistance and offer insights into the genetic basis of spinosad resistance in other species.
Serving Size for the Milks on Cereal Serving size for the milks on cereal will be handled in the same way as regular food items.
Microsoft Word - Chapter 9 - Administrative.doc
The CC will use ATF reports to determine the number of randomized ineligible protocol violations that have occurred for each SC within a given timeframe.
Mechanism of RNA recoding: New twists in brain protein production
University of Connecticut Health Center scientist, Robert Reenan, has uncovered new rules of RNA recoding--a genetic editing method cells use to expand the number of proteins assembled from a single DNA code. According ...
LHC inauguration, LHCfest only two weeks away!
2008-10-02
$$bThe official ceremony for the inauguration of the LHC with Heads of State and Ministers from CERN’s Member States, to be held on Tuesday 21 October, will be followed by an LHCfest to thank all those who took part in bringing the accelerator to completion. The invitation will be sent in the next few days by internal mail.The event has been made possible by generous donations from a range of companies and organizations. Practical information for CERN personnel involved 1. REGISTRATION will be at the Globe of Science and Innovation - invited members of personnel: follow instructions on your invitation card; - volunteers: you will receive instructions via e-mail. 2. SHUTTLE SERVICE There will be no access to the inauguration site for private vehicles. A shuttle service will be provided from the Globe of Science and Innovation between 7:30 and 11:30 for members of the personnel involved in the organization and thereafter for all invited guests: Shuttle departures for all invited guests after registration and security check as indicated on personal invitation cards; Return shuttles from ceremony location, back to reserved parkings start at 18:00. Regularly updated maps available at: http://www.cern.ch/LHC2008/inauguration/traffic.html LHCfest After the official ceremony, the party will go on at the same location to involve and thank all "Cernois" – physicists, engineers, technicians and administrators – who took part in the LHC adventure and who could not be invited to the Official Inauguration ceremony. Since the maximum capacity of the LHCfest location is limited to about 3000 people, an invitation will be sent in the next few days by internal mail to all members of personnel (blue card) and to members of the other categories (users, retired staff and industrial support) invited by the departments and LHC experiments. PROGRAMME 18:30 Musique municipale de Meyrin and LHC films; 20:00 Address by Director-General Robert Aymar; 20:15 Introduction by Frans Lanting and visual concert "Origins"; 20:30-22:30 Buffet service; 21:30 Concerts by Cernettes and Canettes; 23:30 End of LHCfest. PRACTICAL INFO Therewill be no access to the LHCfest site for private vehicles. Please use the shuttle service from the designated car parks on the Meyrin and Prévessin sites. Shuttle departures will start at 18:30. The last return shuttle to the Meyrin and Prévessin car parks will be at 23:30. … And more Highlights As already indicated in previous Bulletin articles, innovation will be the leitmotiv of the two events. A central highlight of both the LHC inauguration and the LHCfest will be a special visual concert. More info on the LHC2008 website: http://www.cern.ch/lhc2008 ORIGINS Adapted from LIFE: A Journey Through Time ORIGINS is a celebration of the wonder of the cosmos and the glory of life on Earth, as expressed through the imagery of National Geographic resident photographer Frans Lanting and the music of Philip Glass. Specially commissioned by CERN for the ceremony to inaugurate the Large Hadron Collider, ORIGINS is a 20-minute adaptation of the original, one-hour, multimedia production LIFE: A Journey Through Time, featuring Frans Lanting’s photographs and Philip Glass’s music, choreographed by Alexander V. Nichols. Performed by a symphony orchestra with projected images, LIFE interprets the history of life on Earth from its earliest beginnings with the Big Bang to its present diversity. Performed by the Orchestre de la Suisse Romande, conducted by Carolyn Kuan. Concepts and images by Frans Lanting, music by Philip Glass, arranged for orchestra by Michael Riesman, visual choreography by Alexander V. Nichols. Project editing by Christine Eckstrom.
2009-11-01
Mammalian cells repair DNA double-strand breaks (DSBs) via efficient pathways of direct, nonhomologous DNA end joining (NHEJ) and homologous recombination (HR). Prior work has identified a complex of...Full Text Available
2009-11-01
Full Text Available.Mammalian cells repair DNA double-strand breaks (DSBs) via efficient pathways of direct, nonhomologous DNA end joining (NHEJ) and homologous recombination (HR). Prior work has identified a complex of two polypeptides, PSF and p54(nrb), as a stimulatory factor in a reconstituted in vitro NHEJ system. PSF also stimulates early steps of HR in vitro. PSF and p54(nrb) are RNA recognition motif-containing proteins with well-established functions in RNA processing and transport, and their apparent involvement in DSB repair was unexpected. Here we investigate the requirement for p54(nrb) in DSB repair in vivo. Cells treated with siRNA to attenuate p54(nrb) expression exhibited a delay in DSB repair in a γ-H2AX focus assay. Stable knockdown cell lines derived by p54(nrb) miRNA transfection showed a significant increase in ionizing radiation-induced chromosomal aberrations. They also showed increased radiosensitivity in a clonogenic survival assay. Together, results indicate that p54(nrb) contributes to rapid and accurate repair of DSBs in vivo in human cells and that the PSF·p54(nrb) complex may thus be a potential target for radiosensitizer development.
Identification of the chloroplast adenosine-to-inosine tRNA editing enzyme
2009-07-01
Plastids (chloroplasts) of higher plants exhibit two types of conversional RNA editing: cytidine-to-uridine editing in mRNAs and adenosine-to-inosine editing in at least one plastid genome-encoded tRNA,...Full Text Available
Identification of the chloroplast adenosine-to-inosine tRNA editing enzyme
2009-07-01
Full Text Available.Plastids (chloroplasts) of higher plants exhibit two types of conversional RNA editing: cytidine-to-uridine editing in mRNAs and adenosine-to-inosine editing in at least one plastid genome-encoded tRNA, the tRNA-Arg(ACG). The enzymes catalyzing RNA editing reactions in plastids are unknown. Here we report the identification of the A-to-I tRNA editing enzyme from chloroplasts of the model plant Arabidopsis thaliana. The protein (AtTadA) has an unusual structure in that it harbors a large N-terminal domain of >1000 amino acids, which is not required for catalytic activity. The C-terminal region of the protein displays sequence similarity to tadA, the tRNA adenosine deaminase from Escherichia coli. We show that AtTadA is imported into chloroplasts in vivo and demonstrate that the in vitro translated protein triggers A-to-I editing in the anticodon of the plastid tRNA-Arg(ACG). Suppression of AtTadA gene expression in transgenic Arabidopsis plants by RNAi results in reduced A-to-I editing in the chloroplast tRNA-Arg(ACG). The RNAi lines display a mild growth phenotype, presumably due to reduced chloroplast translational efficiency upon limited availability of edited tRNA-Arg(ACG).
INEL BNCT Research Program, Program publications 1992
1993-11-01
This document is a collection of the published reports describing research supporting the Idaho National Engineering Laboratory (INEL) Boron Neutron Capture Therapy (BNCT) Research Program for calendar year 1992. Contributions from the principal investigators about their individual projects are included, specifically, chemistry (pituitary tumor studies, boron drug development including liposomes, lipoproteins, and carboranylalarnine derivatives), pharmacology (murine screenings, toxicity testing, ICP-AES analysis of biological samples), physics (radiation dosimetry software, neutron beam and filter design, neutron beam measurement dosimetry), and radiation biology (small and large animal models tissue studies and efficacy studies). These reports have previously appeared in two books: Progress in Neutron Capture Therapy for Cancer, edited by B. J. Allen, D. E. Moore, B. V. Harrington, Plenum Press, 1992; and Boron Neutron Capture Therapy Toward Clinical Trials of Glioma Patients, edited by D. Gabel and R. Moss, Plenum Press, 1992. Reports have also appeared in four journals: Analytica Chimica Acta, Inorganic Chemistry, Nuclear Science and Engineering, and the Proceedings of the National Academy of Science.
Hydrochemical data base for the Death Valley Region, California and Nevada
1995-02-01
Ground-water chemistry data derived from samples collected within an approximately 100,000-square-kilometer area in the Southern Great Basin have been compiled into a digital data base. The data were compiled from published reports, the U.S. Geological Survey (USGS) National Water Information System (NWIS), and previously unpublished USGS files. The data are contained in two compressed files which self-expand into Lotus (.WK1) files. The first file contains 4,738 records (4.84 megabytes) and represents the basic compilation of all identified analyses. The second file is an edited version of the first and contains 3,733 records (3.84 megabytes). Editing included the removal of duplicate records and the combining of records, when appropriate. The analyses presented are of variable quality and comprehensiveness and include no isotopic data. Of the 3,733 analyses in the edited data base, 58 percent of the major ion concentrations balance to within {+-}10 percent. Most of the remaining records are not sufficiently complete for a balance to be calculated.
1995-09-01
This report is a transcript of an interview with William D. Moss by representatives of the US DOE Office of Human Radiation Experiments. Mr. Moss was selected for this interview because of his work at Los Alamos National Laboratory concerning analytical methods in the chemical determination of plutonium in biological materials. After a brief biographical sketch, Mr. Moss relates his understanding of how occupational exposure limits were determined for the Manhattan Project, how data from those workers who were exposed to plutonium was collected and analyzed, how the experiments were planned and data was gathered from plutonium or polonium injections in man, how problems with analytical procedures compounded health physics aspects of the project, and problems remaining in the interpretation of these data.
1995-09-01
This document is a transcript of an interview of Dr. John Randolph Tottler by representatives of the US DOE Office of Human Radiation Experiments. Dr. Tottler was selected for this interview because of his career with the Atomic Energy Commission Division of Biology and Medicine (DBM), particularly as its director from 1967 to 1972. After a short biographical sketch Dr. Tottler discusses his remembrances on a wide range topics including nucleic acid and leukemia research at Oak Ridge, AEC biochemistry training in South America, DBM`s research focus on radiation effects, early leadership of DBM, relations with the US Public Health Service, controversies on low-level radiation, iodine from fallout, on John Gofman, and Project Plowshare, funding for AEC Research Programs and for international research, testicular irradiation of prisoners in Washington State and Oregon, Plutonium injections, ethics of government radiation research, and opinions of public misperceptions about radiation and cancer.
Good-bye Summer Students 2009!
2009-08-24
$$bIn its 47th edition, the CERN Summer Student programme has welcomed almost 200 young students from around the world. As it proves to do each year, the programme has provided a unique experience for all participants. CERN Summer Students 2009 in the Microcosm garden.During the summer months between June and August, your normal lunchtime routine is inevitably disrupted by the small stampede of students that leaves the Main Auditorium just around midday and starts queuing in Restaurant 1. When this happens, you can’t help but notice that the CERN Summer Students have arrived! With its rich lecture series, inspirational visits and actual work experience, the Summer Student programme provides a real chance to get acquainted with a career in particle physics, engineering and computation. The programme includes a morning lecture series that covers a large variety of topics, from particle physics to engineering, information technology and statistics, and during the afternoon, each student works as a member of one of the experimental teams on a specific supervised project. Discussion sessions complement the morning lectures and each student has the unique chance to descend 100 m underground for a visit to one of the experiments located around the LHC ring. At the end of their stay, students submit brief reports on their assigned projects, and a selected few make short presentations in the Main Auditorium, describing to their colleagues the work that they have been doing at CERN. Needless to say, this is a very important experience for those who are chosen to participate. The majority of the students are entering their final year of undergraduate education and the experience provides them with an excellent insight into what they will pursue after obtaining their degree. "It’s a fantastic way to actually get involved with ongoing scientific research," explains Will Barter, who studies at Cambridge University, "It is very useful for me and for the other students because we are at the point when we need to work out where we are going with our careers and whether we really do want to pursue science." The prospect of learning from and working alongside scientists conducting the world-leading research at CERN attracts students from both Member and many non-Member States. "This year, a total of 174 students have been enrolled from both member States and non-Member States with Summer Student contracts," says Ingrid Schmid, Coordinator of the programme. "The students attending from non-Member states are participating with the help of John Ellis, the Coordinator for non-Member States. Also there are many more Member State and non-Member State students who have come to follow the lectures but are supported financially by their respective universities or other funding agencies." John Ellis reckons that, in addition to students from the 20 Member States, some 40 non-Member States are represented this year. All will take back with them unforgettable memories of a global partnership in science. Along with the official programme organized by the HR Department, Summies (as they are commonly called) never fail to set up an after-work programme of social activities, which includes outings and parties. This year they have also formed a Facebook group to aid with organization and spreading news and they have even designed their own souvenir T-shirt. All information about the programme, its past editions and a link to the application form for future editions can be found here.
Information processing in the brain requires a delicate balance between excitation and inhibition. Glycine receptors (GlyR) are involved in inhibitory mechanisms mainly at a synaptic level, but potential...Full Text Available
Full Text Available.Information processing in the brain requires a delicate balance between excitation and inhibition. Glycine receptors (GlyR) are involved in inhibitory mechanisms mainly at a synaptic level, but potential novel roles for these receptors recently emerged due to the discovery of posttranscriptional processing. GLR transcripts are edited through enzymatic modification of a single nucleotide leading to amino acid substitution within the neurotransmitter binding domain. RNA editing produces gain-of-function receptors well suited for generation and maintenance of tonic inhibition of neuronal excitability. As neuronal activity deprivation in early stages of development or in epileptic tissue is detrimental to neurons and because RNA editing of GlyR is up-regulated in temporal lobe epilepsy patients with a severe course of disease a pathophysiological role of these receptors emerges. This review contains a state-of-the-art discussion of (patho)physiological implications of GlyR RNA editing.
For one weekend, CERN takes a stand at Geneva’s Nuit de la science
2008-07-17
$$bCERN took part in the seventh year of the Nuit de la science on 5-6 July dedicated to the theme of Time. Some 30 000 visitors filed through the 52 stands set up around the Perle du Lac park. The Geneva ‘Musée d’histoire des sciences’, the heart of the event (Copyright MHS - Photo: Philippe Wagneur). Michel Boffard, a CERN guide, makes a simple experiment to show super-conductivity (Photo: Claude Guérin).Two aspects of the LHC were presented in the display. The technical principles on which the machine is based were illustrated using a bell jar, liquid nitrogen and visually striking experiments. Meanwhile, under the heading ‘The Time Machine’, posters and mockups were used to explain the theoretical side of the LHC and its scientific aims. Benefitting from the adjacent photography exhibition, ‘CERN through the lens of Peter Ginter’, the stand attracted a steady stream of interested visitors, who were not put off by the wet weather. In the opinion of the visitors, this educational combination was an enriching experience that shone a welcome light on a discipline often viewed as inaccessible. For one weekend, visitors were able to share the physicists’ dream.
Evidence for large diversity in the human transcriptome created by Alu RNA editing
2009-11-01
Adenosine-to-inosine (A-to-I) RNA editing alters the original genomic content of the human transcriptome and is essential for maintenance of normal life in mammals. A-to-I editing in Alu...Full Text Available
Evidence for ADAR-induced hypermutation of the Drosophila sigma virus (Rhabdoviridae)
Full Text Available.BackgroundADARs are RNA editing enzymes that target double stranded RNA and convert adenosine to inosine, which is read by translation machinery as if it were guanosine. Aside from their role in generating protein diversity in the central nervous system, ADARs have been implicated in the hypermutation of some RNA viruses, although why this hypermutation occurs is not well understood.ResultsHere we describe the hypermutation of adenosines to guanosines in the genome of the sigma virus--a negative sense RNA virus that infects Drosophila melanogaster. The clustering of these mutations and the context in which they occur indicates that they have been caused by ADARs. However, ADAR-editing of viral RNA is either rare or edited viral RNA are rapidly degraded, as we only detected evidence for editing in two of the 104 viral isolates we studied.ConclusionThis is the first evidence for ADARs targeting viruses outside of mammals, and it raises the possibility that ADARs could play a role in the antiviral defences of insects.
Evidence for ADAR-induced hypermutation of the Drosophila sigma virus (Rhabdoviridae)
BackgroundADARs are RNA editing enzymes that target double stranded RNA and convert adenosine to inosine, which is read by translation machinery as if it were guanosine. Aside from...Full Text Available
Dual discoveries in genetic processing improve accuracy of genome information
University of Connecticut Health Center geneticists have made a two-fold discovery in gene recoding that will significantly increase understanding of the information in genome sequences and could prove to be a knowledge ...
Distinct roles for sequences upstream of and downstream from Physarum editing sites
2009-09-01
RNAs in the mitochondria of Physarum polycephalum contain nonencoded nucleotides that are added during RNA synthesis. Essentially all steady-state RNAs are accurately and fully edited,...Full Text Available
Distinct roles for sequences upstream of and downstream from Physarum editing sites
2009-09-01
Full Text Available.RNAs in the mitochondria of Physarum polycephalum contain nonencoded nucleotides that are added during RNA synthesis. Essentially all steady-state RNAs are accurately and fully edited, yet the signals guiding these precise nucleotide insertions are presently unknown. To localize the regions of the template that are required for editing, we constructed a series of chimeric templates that substitute varying amounts of DNA either upstream of or downstream from C insertion sites. Remarkably, all sequences necessary for C addition are contained within ∼9 base pairs on either side of the insertion site. In addition, our data strongly suggest that sequences within this critical region affect different steps in the editing reaction. Template alterations upstream of an editing site influence nucleotide selection and/or insertion, while downstream changes affect editing site recognition and templated extension from the added, unpaired nucleotide. The data presented here provide the first evidence that individual regions of the DNA template play discrete mechanistic roles and represent a crucial initial step toward defining the source of the editing specificity in Physarum mitochondria. In addition, these findings have mechanistic implications regarding the potential involvement of the mitochondrial RNA polymerase in the editing reaction.
2004-03-01
The departmental plans of domestic wastes management are official documents which manage the actions needed to realize the legislative and regulation objectives concerning the domestic wastes and related wastes. A first evaluation has been realized in 1997 for 47 edited plans. In the context of the new wastes policy a new evaluation has been realized by the ADEME in 2002 for 98 plans. It provides the methodology of the study, the analysis of the plans, the sites and management of wastes, economic data, the equipment and investments. (A.L.B.)
Creativity at the Film-Making Club: Let there be light!
2008-10-02
$$bThe Film-Making Club was created in 2005, and already has ten short films to its credit. Spotlight on a club that does more than making movies! Making a film requires solid teamwork and genuine commitment. In addition to shooting, which requires at least five people in key roles—plus the actors!—there is also the work of casting, location work, choice of equipment and techniques, logistics (hardware, costume design etc.) and post-production, which includes film editing and soundtrack.What does it take to make a film? "It involves a marriage of the power of the imagination, the technical constraints and the actors’ performances," explains Quentin King, the current president and founder of the club. "You need a real synthesis of art and technique," he adds. For club member Neal Hartman, "the French word réalisateur really reflects this aspect of the work, where you need to imagine something, then reconceptualise it in terms of its feasibility in order to realise it in the best possible way. Essentially, you have to find a way of transforming a dream into a visual reality." The club members have already realised a few dreams in various forms. In 2007 the club, still in its infancy, organised the CinéGlobe festival, bringing to CERN’s Globe, recently inaugurated as a communication forum, a festival of short films and audiovisual workshops. The festival accepted 1450 entries from 80 countries, representing 100 hours of screen time, which the selection board whittled down to 5 hours. The work of the committee went far beyond that, however: sponsors had to be found, partnerships set up, logistics organised. The result: a thousand visitors flocked to the Globe in just three days. The audiovisual workshops brought together professionals and enthusiasts around short films, spawning further workshops and lectures and incidentally providing "film people" from all around the Lake Geneva area with a valuable networking opportunity. If there was no 2008 edition, this was largely because of a lack of available time to meet all the demands involved. "There was certainly no lack of demand from professionals and the public alike. We had plenty of enquiries about a repeat event," concludes Jacques-Hervé Fichet, the former club president who was behind the project. The club’s motto remains: learn by doing. That’s why, in addition to the films currently in the pipeline, Quentin King and Neal Hartman are, respectively, organising and participating in the "48 Hour Film Project". This event, which in 2007 was held in 55 cities around the world, is refereed by a professional jury. The goal is to advance film-making and promote film-makers with local and international distribution, as a final festival brings together all of the winning entries in each city. The competition comes to Geneva for the first time on 10-12 October 2008. The challenge is to make a complete movie, from script to post-production, in just 48 hours, starting with the allocation of a random movie genre to each team. Not content with organising the event, the club has put together its own team. A few volunteers are still needed! Are you up for a 48-hour sprint? If you want to be a member of our film-making team, learn more about the club, help with the organising of the competition or find the website of the competition, go to http://info-oye.web.cern.ch/info-oye/
Conversion of Morphology of ICD-O-2 to ICD-10
The International Classification of Diseases for Oncology, Third Edition1 (ICD-O-3) was published by the World Health Organization (WHO) in 2000 and is to be used for coding neoplasms diagnosed on or after January 1, 2001 in the United States.
Characterization of bovine miRNAs by sequencing and bioinformatics analysis
Full Text Available.BackgroundMicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules which regulate gene expression by fully or partially binding to their complementary sequences in mRNAs or promoters. A large number of miRNAs and their expression patterns have been reported in human, mouse and rat. However, miRNAs and their expression patterns in live stock species such as beef cattle are not well studied.ResultsWe constructed and sequenced small-RNA libraries to yield a total of 13,541 small-RNA sequences from 11 bovine tissues including brain, subcutaneous fat, muscle, liver, kidney, spleen and thymus. In total, 228 miRNAs including 29 novel miRNA candidates were identified. Of the 199 miRNAs, 101 have been previously reported as bovine miRNAs and the other 98 are bovine orthologs of known miRNAs that have been identified in at least one other mammalian species. Of the 29 novel miRNA candidates, 17 appeared at this point in time to be bovine specific, while the remaining 12 had evidence of evolutionary conservation in other mammalian species. Five miRNAs (miR-23a, -23b, -99a, -125b and -126-5p) were very abundant across the 11 tissues, accounting for 44.3% of all small RNA sequences. The expression analysis of selected miRNAs using qRT-PCR also showed that miR-26a and -99a were highly expressed in all tissues, while miR-122 and miR-133a were predominantly expressed in liver and muscle, respectively.ConclusionThe miRNA expression patterns among 11 tissues from beef cattle revealed that most miRNAs were ubiquitously expressed in all tissues, while only a few miRNAs were tissue specific. Only 60% miRNAs in this study were found to display strand bias, suggesting that there are some key factors for mature miRNA selection other than internal stability. Most bovine miRNAs are highly conserved in other three mammalian species, indicating that these miRNAs may have a role in different species that are potential molecular markers for evolution.
Characterization of bovine miRNAs by sequencing and bioinformatics analysis
BackgroundMicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules which regulate gene expression by fully or partially binding to their complementary sequences in mRNAs...Full Text Available
Cancer Survival Among Adults: U.S. SEER Program, 1988-2001 (low res)
Relative Survival Rate (%) 1-Year 2-Year 3-Year 5-Year 8-Year 10-Year Lip 3,982 100.0 99.6 97.7 96.2 93.5 90.4 88.0 White Female 708 17.8 99.7 96.7 96.4 93.1 90.0 89.9 White Male 3,184 80.0 99.9 98.2 96.4 93.9 90.6 87.7 Black Female 22 0.
2008-08-01
$$bAs all eyes turn to the LHC in the run-up to the big switch-on, online media are providing a keyhole into the deepest corners of CERN. From YouTube to blogs, communicating ideas has never before had the capacity to reach so many people. A wide range of websites comment on CERN.Blogs, YouTube, social networking, podcasting, Twitter, SecondLife, Flickr…. it’s easy to get lost in the ever expanding world of Web 2.0. But it’s also hard to ignore the fact that these web facilities are becoming a central part of everyday life, whether it’s for finding information, sharing interests with friends, keeping up to date with news, or simply for entertainment. CERN’s profile on these sites is also increasing, but as with everything on the Internet there is a huge range in the quality of information available, stretching from officially endorsed sites all the way to the plain ridiculous! This is our guide to some of the best CERN content in the virtual world. (See box for all web addresses). The first stop for any discerning Internet surfer wanting to learn about CERN should surely be the new public website. Launched in December 2007, it’s the official voice of CERN, featuring news, publications, scientific information and details of the run-up to the switch-on of the LHC. However, James Gillies, the Communication Group Leader, has a positive attitude to exploring other online media. "YouTube, for example, allows you to reach audiences that you wouldn’t reach otherwise and allows you to be in touch with them. The fact that we allow people to comment on videos delivers the message that we are very open." CERN’s official channel on YouTube, ‘CERNTV’, has been accessible to the public since the Open Days in April this year. Featuring 42 documentary-style videos and animations, the site has over 600 regular subscribers and the most popular clip ‘CERN in 3 minutes’ has been viewed over 140,000 times. Silvano de Gennaro, from the Communication Group, explains the philosophy behind creating the channel: "The idea really comes from our mandate to inspire the next generation of physicists. We only put up official videos that were produced for the wider public, whether they are aimed at kids or documentary style films. What we don’t want to do is to put very technical videos on there which people find too difficult and then end up looking somewhere else." However, there are some reservations. "With the new web, the global information landscape has changed such that it is no longer possible for CERN to retain full control of information," says Gillies. Certainly, there are many unofficial sites that contain information that is not correct, a good example being the site ‘LHC Countdown’, which claims to know when the LHC will start! There are also security fears on social networking sites that use ‘peer-to-peer’ (P2P) applications designed to share content between interconnected participants across the Internet. They are popular for sharing music, video, software and other data. Examples are: KaZaA, Napster, Gnutella, etc. David Myers, Head of Computer Security, points out that "whilst newspapers have an address and can be sued, contributors to blogs and social networking sites can be anonymous and may have a hidden agenda, so readers need to exercise critical judgement as to the veracity of what they read." He also adds that "P2P file sharing applications violate CERN’s Computing Rules on file services in most configurations (see: http://htt/rp://cern.ch/security/file-sharing/). One reason is because they are known to be targets for viruses and some install spyware - software that can steal confidential information such as bank account transactions. Removing spyware is usually not trivial and often requires re-installation of computers from scratch." These concerns aside, there are some non-official websites that do a good job in letting people know about CERN. One example is the ‘CERN Podcast’ that consists of short audio programmes of discussions between Brian Cox, a UK physicist and science communicator, and various VIPs and celebrities. Aimed at everyone from science-fiction fans to academics, the concepts behind the podcast have been tailored to suit web broadcasting. As Cox explains, "Our idea is not to make a radio programme, but a conversation. It means we do very little editing, have no particular time constraints and let things take their course. There’s an honesty to it that is difficult to get with traditional media." Blogging is yet another phenomenon of Web 2.0, and as with the other online media there is a huge range of both content and quality to be found. Members of the CERN personnel author some of the blogs, often describing their scientific work alongside musings on life at CERN. For example the ‘US LHC blog’ is written by ten Americans working at CERN, with topics ranging from pixel detectors to social events. Other blogs, for example ‘Higgs: into the heart of imagination’ written by Dutch collaborators, take a more creative stance by including video interviews and news posts. The topic is almost inexhaustibly wide. Each site finds its own audience and potentially reaches hundreds of thousands of people. See the box for a list of the sites and blogs we have mentioned here, and feel free to suggest more (Bulletin-Editors@cern.ch)! CERN public website: http://www.cern.ch CERN TV: http://www.youtube.com/cern Podcasts about CERN: http://www.cernpodcast.com Blogs US LHC blog: http://uslhc.us/blogs/ Higgs: into the heart of imagination: http://weblogs.hollanddoc.nl/higgs/ Look here http://cern.ch/security/Recommendations/ for some suggestions as to how to avoid being caught out by Internet scams.
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Axion Project Incubation Status - Apache Incubator
For general project status, see the Axion project website. ... The axion project never moved to the ASF from tigris.org. 2003-12-19: The Apache Incubator ...
Axion - Wikipedia, the free encyclopedia
The axion is a hypothetical elementary particle postulated by Peccei-Quinn theory in 1977 to resolve the strong-CP problem in quantum chromodynamics (QCD). ...
Adenosine deamination in human transcripts generates novel microRNA binding sites
2009-12-15
Animals regulate gene expression at multiple levels, contributing to the complexity of the proteome. Among these regulatory events are post-transcriptional gene silencing, mediated by small non-coding...Full Text Available
Full Text Available.BackgroundMitochondrial DNA sequencing increasingly results in the recognition of genetically divergent, but morphologically cryptic lineages. Species delimitation approaches that rely on multiple lines of evidence in areas of co-occurrence are particularly powerful to infer their specific status. We investigated the species boundaries of two cryptic lineages of the land snail genus Trochulus in a contact zone, using mitochondrial and nuclear DNA marker as well as shell morphometrics.ResultsBoth mitochondrial lineages have a distinct geographical distribution with a small zone of co-occurrence. In the same area, we detected two nuclear genotype clusters, each being highly significantly associated to one mitochondrial lineage. This association however had exceptions: a small number of individuals in the contact zone showed intermediate genotypes (4%) or cytonuclear disequilibrium (12%). Both mitochondrial lineage and nuclear cluster were statistically significant predictors for the shell shape indicating morphological divergence. Nevertheless, the lineage morphospaces largely overlapped (low posterior classification success rate of 69% and 78%, respectively): the two lineages are truly cryptic.ConclusionThe integrative approach using multiple lines of evidence supported the hypothesis that the investigated Trochulus lineages are reproductively isolated species. In the small contact area, however, the lineages hybridise to a limited extent. This detection of a hybrid zone adds an instance to the rare reported cases of hybridisation in land snails.
BackgroundMitochondrial DNA sequencing increasingly results in the recognition of genetically divergent, but morphologically cryptic lineages. Species delimitation approaches that...Full Text Available
A softball event in the Higgs field…
2008-08-01
$$bCERN’s two softball teams, the Quarks and the Leptons, held their annual tournament in the "Higgs field" at the Prévessin site on 19 and 20 July. Here, the Bulletin shines a spotlight on a little known sport in Switzerland. Leptons vs Quarks on the ‘Higgs field’ at the Prévessin site, in 2007.With summer in full swing, the Bulletin takes a look at some of CERN’s clubs. We invite you to discover the Organization from the point of view of the individuals eager to share their passions and achieve the best performances.Softball, a direct descendant of baseball invented in the US, was originally intended to be played indoors but soon took off as an outdoor sport and the women’s version is now an Olympic event. More tactical than baseball, softball - a somewhat misleading term as the ball is not especially soft - requires the active participation of a coach who advises the players during play. The coach’s role is to estimate the amount of a time a player has to reach a base while the ball is being fielded. Games are played between two teams, each comprising ten players, which take it in turns to bat and field. Founded in 1980, the CERN Softball Club today comprises two teams, the Leptons and the Quarks. On 19 and 20 July the Club held its seventh "Bernie Tourney" tournament, named in honour of Bernard Sutton, who founded both the club and the Geneva Softball League. The two teams, who were of course represented in the tournament are made up of both male and female players of all ages. The Leptons team has been going since 1980, while the Quarks team was created 18 years later to welcome an influx of new, inexperienced arrivals. According to the Quarks, the Leptons take the game much too seriously, to which the Leptons reply, a smile on their faces, that the Quarks are too inexperienced to understand… But on the day of the competition, they put aside their rivalry for a friendly barbecue at the "Boson Chalet", a hut built on the "Higgs field" by the Club’s members. For more information on the CERN Softball Club, go to: http://Softball.cern.chContact: Softball.Club@cern.ch
Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection
2009-09-01
Full Text Available.Adenosine deaminases that act on dsRNA (ADARs) are enzymes that target double-stranded regions of RNA converting adenosines into inosines (A-to-I editing) thus contributing to genome complexity and fine regulation of gene expression. It has been described that a member of the ADAR family, ADAR1, can target viruses and affect their replication process. Here we report evidence showing that ADAR1 stimulates human immuno deficiency virus type 1 (HIV-1) replication by using both editing-dependent and editing-independent mechanisms. We show that over-expression of ADAR1 in HIV-1 producer cells increases viral protein accumulation in an editing-independent manner. Moreover, HIV-1 virions generated in the presence of over-expressed ADAR1 but not an editing-inactive ADAR1 mutant are released more efficiently and display enhanced infectivity, as demonstrated by challenge assays performed with T cell lines and primary CD4+ T lymphocytes. Finally, we report that ADAR1 associates with HIV-1 RNAs and edits adenosines in the 5′ untranslated region (UTR) and the Rev and Tat coding sequence. Overall these results suggest that HIV-1 has evolved mechanisms to take advantage of specific RNA editing activity of the host cell and disclose a stimulatory function of ADAR1 in the spread of HIV-1.
Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection
2009-09-01
Adenosine deaminases that act on dsRNA (ADARs) are enzymes that target double-stranded regions of RNA converting adenosines into inosines (A-to-I editing) thus contributing to genome complexity and...Full Text Available
Editing independent effects of ADARs on the miRNA/siRNA pathways
2009-10-21
Full Text Available.Adenosine deaminases acting on RNA (ADARs) are best known for altering the coding sequences of mRNA through RNA editing, as in the GluR-B Q/R site. ADARs have also been shown to affect RNA interference (RNAi) and microRNA processing by deamination of specific adenosines to inosine. Here, we show that ADAR proteins can affect RNA processing independently of their enzymatic activity. We show that ADAR2 can modulate the processing of mir-376a2 independently of catalytic RNA editing activity. In addition, in a Drosophila assay for RNAi deaminase-inactive ADAR1 inhibits RNAi through the siRNA pathway. These results imply that ADAR1 and ADAR2 have biological functions as RNA-binding proteins that extend beyond editing per se and that even genomically encoded ADARs that are catalytically inactive may have such functions.
Editing independent effects of ADARs on the miRNA/siRNA pathways
2009-10-21
Adenosine deaminases acting on RNA (ADARs) are best known for altering the coding sequences of mRNA through RNA editing, as in the GluR-B Q/R site. ADARs have also been shown to affect RNA interference...Full Text Available
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