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Sample records for a-to-i editing detects

  1. Computational detection and functional analysis of human tissue-specific A-to-I RNA editing.

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    Tao He

    Full Text Available A-to-I RNA editing is a widespread post-transcriptional modification event in vertebrates. It could increase transcriptome and proteome diversity through recoding the genomic information and cross-linking other regulatory events, such as those mediated by alternative splicing, RNAi and microRNA (miRNA. Previous studies indicated that RNA editing can occur in a tissue-specific manner in response to the requirements of the local environment. We set out to systematically detect tissue-specific A-to-I RNA editing sites in 43 human tissues using bioinformatics approaches based on the Fisher's exact test and the Benjamini & Hochberg false discovery rate (FDR multiple testing correction. Twenty-three sites in total were identified to be tissue-specific. One of them resulted in an altered amino acid residue which may prevent the phosphorylation of PARP-10 and affect its activity. Eight and two tissue-specific A-to-I RNA editing sites were predicted to destroy putative exonic splicing enhancers (ESEs and exonic splicing silencers (ESSs, respectively. Brain-specific and ovary-specific A-to-I RNA editing sites were further verified by comparing the cDNA sequences with their corresponding genomic templates in multiple cell lines from brain, colon, breast, bone marrow, lymph, liver, ovary and kidney tissue. Our findings help to elucidate the role of A-to-I RNA editing in the regulation of tissue-specific development and function, and the approach utilized here can be broadened to study other types of tissue-specific substitution editing.

  2. A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins

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    Furey Terrence S

    2010-01-01

    Full Text Available Abstract Background Several 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. Results We 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. Conclusions Using 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.

  3. Altered A-to-I RNA Editing in Human Embryogenesis

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    Mandel, Rachel; Ziskind, Anna; Nahor, Irit; Safran, Michal; Osenberg, Sivan; Sherf, Ofra; Rechavi, Gideon; Itskovitz-Eldor, Joseph

    2012-01-01

    Post-transcriptional events play an important role in human development. The question arises as to whether Adenosine to Inosine RNA editing, catalyzed by the ADAR (Adenosine Deaminase acting on RNA) enzymes, differs in human embryogenesis and in adulthood. We tested the editing of various target genes in coding (FLNA, BLCAP, CYFIP2) and non-coding sequences at their Alu elements (BRCA1, CARD11, RBBP9, MDM4, FNACC), as well as the transcriptional levels of the ADAR1 enzymes. This analysis was performed on five fetal and adult human tissues: brain, heart, liver, kidney, and spleen, as well as on human embryonic stem cells (hESCs), which represent the blastocyst stage in early human development. Our results show substantially greater editing activity for most adult tissue samples relative to fetal ones, in six of the eight genes tested. To test the effect of reduced A-to-I RNA editing activity in early human development we used human embryonic stem cells (hESCs) as a model and tried to generate hESC clones that overexpress the ADAR1–p110 isoform. We were unable to achieve overexpression of ADAR1–p110 by either transfection or lentiviral infection, though we easily generated hESC clones that expressed the GFP transgene and overexpressed ADAR1-p110 in 293T cells and in primary human foreskin fibroblast (HFF) cells. Moreover, in contrast to the expected overexpression of ADAR1-p110 protein following its introduction into hESCs, the expression levels of this protein decreased dramatically 24–48 hr post infection. Similar results were obtained when we tried to overexpress ADAR1-p110 in pluripotent embryonal carcinoma cells. This suggests that ADAR1 protein is substantially regulated in undifferentiated pluripotent hESCs. Overall, our data suggest that A-to-I RNA editing plays a critical role during early human development. PMID:22859999

  4. Altered A-to-I RNA editing in human embryogenesis.

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    Ronit Shtrichman

    Full Text Available Post-transcriptional events play an important role in human development. The question arises as to whether Adenosine to Inosine RNA editing, catalyzed by the ADAR (Adenosine Deaminase acting on RNA enzymes, differs in human embryogenesis and in adulthood. We tested the editing of various target genes in coding (FLNA, BLCAP, CYFIP2 and non-coding sequences at their Alu elements (BRCA1, CARD11, RBBP9, MDM4, FNACC, as well as the transcriptional levels of the ADAR1 enzymes. This analysis was performed on five fetal and adult human tissues: brain, heart, liver, kidney, and spleen, as well as on human embryonic stem cells (hESCs, which represent the blastocyst stage in early human development. Our results show substantially greater editing activity for most adult tissue samples relative to fetal ones, in six of the eight genes tested. To test the effect of reduced A-to-I RNA editing activity in early human development we used human embryonic stem cells (hESCs as a model and tried to generate hESC clones that overexpress the ADAR1-p110 isoform. We were unable to achieve overexpression of ADAR1-p110 by either transfection or lentiviral infection, though we easily generated hESC clones that expressed the GFP transgene and overexpressed ADAR1-p110 in 293T cells and in primary human foreskin fibroblast (HFF cells. Moreover, in contrast to the expected overexpression of ADAR1-p110 protein following its introduction into hESCs, the expression levels of this protein decreased dramatically 24-48 hr post infection. Similar results were obtained when we tried to overexpress ADAR1-p110 in pluripotent embryonal carcinoma cells. This suggests that ADAR1 protein is substantially regulated in undifferentiated pluripotent hESCs. Overall, our data suggest that A-to-I RNA editing plays a critical role during early human development.

  5. Small RNA and A-to-I Editing in Autism Spectrum Disorders

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    Eran, Alal

    One in every 88 children is diagnosed with Autism Spectrum Disorders (ASDs), a set of neurodevelopmental conditions characterized by social impairments, communication deficits, and repetitive behavior. ASDs have a substantial genetic component, but the specific cause of most cases remains unknown. Understanding gene-environment interactions underlying ASD is essential for improving early diagnosis and identifying critical targets for intervention and prevention. Towards this goal, we surveyed adenosine-to-inosine (A-to-I) RNA editing in autistic brains. A-to-I editing is an epigenetic mechanism that fine-tunes synaptic function in response to environmental stimuli, shown to modulate complex behavior in animals. We used ultradeep sequencing to quantify A-to-I receding of candidate synaptic genes in postmortem cerebella from individuals with ASD and neurotypical controls. We found unexpectedly wide distributions of human A-to-I editing levels, whose extremes were consistently populated by individuals with ASD. We correlated A-to-I editing with isoform usage, identified clusters of correlated sites, and examined differential editing patterns. Importantly, we found that individuals with ASD commonly use a dysfunctional form of the editing enzyme ADARB1. We next profiled small RNAs thought to regulate A-to-I editing, which originate from one of the most commonly altered loci in ASD, 15q11. Deep targeted sequencing of SNORD115 and SNORD116 transcripts enabled their high-resolution detection in human brains, and revealed a strong gender bias underlying their expression. The consistent 2-fold upregulation of 15q11 small RNAs in male vs. female cerebella could be important in delineating the role of this locus in ASD, a male dominant disorder. Overall, these studies provide an accurate population-level view of small RNA and A-to-I editing in human cerebella, and suggest that A-to-I editing of synaptic genes may be informative for assessing the epigenetic risk for autism

  6. Perturbing A-to-I RNA editing using genetics and homologous recombination.

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    Staber, Cynthia J; Gell, Selena; Jepson, James E C; Reenan, Robert A

    2011-01-01

    Evidence for the chemical conversion of adenosine-to-inosine (A-to-I) in messenger RNA (mRNA) has been detected in numerous metazoans, especially those "most successful" phyla: Arthropoda, Mollusca, and Chordata. The requisite enzymes for A-to-I editing, ADARs (adenosine deaminases acting on RNA) are highly conserved and are present in every higher metazoan genome sequenced to date. The fruit fly, Drosophila melanogaster, represents an ideal model organism for studying A-to-I editing, both in terms of fundamental biochemistry and in relation to determining adaptive downstream effects on physiology and behavior. The Drosophila genome contains a single structural gene for ADAR (dAdar), yet the fruit fly transcriptome has the widest range of conserved and validated ADAR targets in coding mRNAs of any known organism. In addition, many of the genes targeted by dADAR have been genetically identified as playing a role in nervous system function, providing a rich source of material to investigate the biological relevance of this intriguing process. Here, we discuss how recent advances in the use of ends-out homologous recombination (HR) in Drosophila make possible both the precise control of the editing status for defined adenosine residues and the engineering of flies with globally altered RNA editing of the fly transcriptome. These new approaches promise to significantly improve our understanding of how mRNA modification contributes to insect physiology and ethology.

  7. Trans and cis factors affecting A-to-I RNA editing efficiency of a noncoding editing target in C. elegans.

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    Washburn, Michael C; Hundley, Heather A

    2016-05-01

    Adenosine-to-inosine RNA editing by ADARs affects thousands of adenosines in an organism's transcriptome. However, adenosines are not edited at equal levels nor do these editing levels correlate well with ADAR expression levels. Therefore, additional mechanisms are utilized by the cell to dictate the editing efficiency at a given adenosine. To examine cis-and trans-acting factors that regulate A-to-I editing levels specifically in neural cells, we utilized the model organism Caenorhabditis elegans We demonstrate that a double-stranded RNA (dsRNA) binding protein, ADR-1, inhibits editing in neurons, which is largely masked when examining editing levels from whole animals. Furthermore, expression of ADR-1 and mRNA expression of the editing target can act synergistically to regulate editing efficiency. In addition, we identify a dsRNA region within the Y75B8A.83' UTR that acts as acis-regulatory element by enhancing ADR-2 editing efficiency. Together, this work identifies mechanisms that regulate editing efficiency of noncoding A-to-I editing sites, which comprise the largest class of ADAR targets.

  8. A-to-I RNA editing: A new mechanism of genomic information modification

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A-to-I RNA editing, the important event of gene modification, which takes place at post-transcriptional level, was firstly reported in 1991. The molecular mechanism of A-to-I RNA editing involves site-selective deamination of adenosine to inosine in pre-mRNA, which leads to altering translation codons and splicing in nuclear transcripts, thereby functionally distinct proteins can be produced from a single gene. The mammalian editing enzymes ADARs (adenosine deaminases acting on RNA) are widely expressed in brain and other tissues, however, up to date their substrates are mainly found in the central nervous system. It has recently been noticed that imperfect editing of these RNA substrates play critical roles in corresponding diseases, indicating that A-to-I RNA editing may be quite important in physiological or pathophysiological processes. Finding more new substrates of ADARs, especially in peripheral tissues, and performing functional research on new genes will be helpful to elucidate the biological significance of A-to-I RNA editing.

  9. A-to-I RNA editing: the "ADAR" side of human cancer.

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    Galeano, Federica; Tomaselli, Sara; Locatelli, Franco; Gallo, Angela

    2012-05-01

    Carcinogenesis is a complex, multi-stage process depending on both endogenous and exogenous factors. In the past years, DNA mutations provided important clues to the comprehension of the molecular pathways involved in numerous cancers. Recently, post-transcriptional modification events, such as RNA editing, are emerging as new players in several human diseases, including tumours. A-to-I RNA editing changes the nucleotide sequence of target RNAs, introducing A-to-I/G "mutations". Since ADAR enzymes catalyse this nucleotide conversion, their expression/activity is essential and finely regulated in normal cells. This review summarizes the available knowledge on A-to-I RNA editing in the cancer field, giving a new view on how ADARs may play a role in carcinogenesis.

  10. Deciphering the functions and regulation of brain-enriched A-to-I RNA editing.

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    Li, Jin Billy; Church, George M

    2013-11-01

    Adenosine-to-inosine (A-to-I) RNA editing, in which genomically encoded adenosine is changed to inosine in RNA, is catalyzed by adenosine deaminase acting on RNA (ADAR). This fine-tuning mechanism is critical during normal development and diseases, particularly in relation to brain functions. A-to-I RNA editing has also been hypothesized to be a driving force in human brain evolution. A large number of RNA editing sites have recently been identified, mostly as a result of the development of deep sequencing and bioinformatic analyses. Deciphering the functional consequences of RNA editing events is challenging, but emerging genome engineering approaches may expedite new discoveries. To understand how RNA editing is dynamically regulated, it is imperative to construct a spatiotemporal atlas at the species, tissue and cell levels. Future studies will need to identify the cis and trans regulatory factors that drive the selectivity and frequency of RNA editing. We anticipate that recent technological advancements will aid researchers in acquiring a much deeper understanding of the functions and regulation of RNA editing.

  11. Antisense sequencing improves the accuracy and precision of A-to-I editing measurements using the peak height ratio method

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    Rinkevich Frank D

    2012-01-01

    Full Text Available Abstract Background A-to-I RNA editing is found in all phyla of animals and contributes to transcript diversity that may have profound impacts on behavior and physiology. Many transcripts of genes involved in axonal conductance, synaptic transmission and modulation are the targets of A-to-I RNA editing. There are a number of methods to measure the extent of A-to-I RNA editing, but they are generally costly and time consuming. One way to determine the frequency of A-to-I RNA editing is the peak height ratio method, which compares the size of peaks on electropherograms that represent unedited and edited sites. Findings Sequencing of 4 editing sites of the Dα6 nicotinic acetylcholine receptor subunit with an antisense primer (which uses T/C peaks to measure unedited and edited sites, respectively showed very accurate and precise measurements of A-to-I RNA editing. The accuracy and precision were excellent for all editing sites, including those edited with high or low frequencies. The frequency of A-to-I RNA editing was comparable to the editing frequency as measured by clone counting from the same sample. Sequencing these same sites with the sense primer (which uses A/G peaks yielded inaccurate and imprecise measurements. Conclusions We have validated and improved the accuracy and precision of the peak height ratio method to measure the frequency of A-to-I RNA editing, and shown that results are primer specific. Thus, the correct sequencing primer must be utilized for the most dependable data. When compared to other methods used to measure the frequency of A-to-I RNA editing, the major benefits of the peak height ratio are that this method is inexpensive, fast, non-labor intensive and easily adaptable to many laboratory and field settings.

  12. Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition

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    Gal-Mark, Nurit; Shallev, Lea; Sweetat, Sahar; Barak, Michal; Billy Li, Jin; Levanon, Erez Y.; Eisenberg, Eli; Behar, Oded

    2017-01-01

    Adenosine to Inosine (A-to-I) RNA editing is a co- or post-transcriptional mechanism that modifies genomically encoded nucleotides at the RNA level. A-to-I RNA editing is abundant in the brain, and altered editing levels have been reported in various neurological pathologies and following spinal cord injury (SCI). The prevailing concept is that the RNA editing process itself is dysregulated by brain pathologies. Here we analyzed recent RNA-seq data, and found that, except for few mammalian conserved editing sites, editing is significantly higher in neurons than in other cell populations of the brain. We studied A-to-I RNA editing in stab wound injury (SWI) and SCI models and showed that the apparent under-editing observed after injury correlates with an approximately 20% reduction in the relative density of neurons, due to cell death and immune cell infiltration that may account for the observed under-editing. Studies of neuronal and astrocyte cultures and a computational analysis of SCI RNA-seq data further supported the possibility that a reduction in neuronal density is responsible for alterations in the tissue-wide editing patterns upon injury. Thus, our data suggest that the case for a mechanistic linkage between A-to-I RNA editing and brain pathologies should be revisited. PMID:28266523

  13. The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers | Office of Cancer Genomics

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    Adenosine-to-inosine (A-to-I) RNA editing is a widespread post-transcriptional mechanism, but its genomic landscape and clinical relevance in cancer have not been investigated systematically. We characterized the global A-to-I RNA editing profiles of 6,236 patient samples of 17 cancer types from The Cancer Genome Atlas and revealed a striking diversity of altered RNA-editing patterns in tumors relative to normal tissues. We identified an appreciable number of clinically relevant editing events, many of which are in noncoding regions.

  14. Reciprocal regulation of A-to-I RNA editing and the vertebrate nervous system

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    Andrew Charles Penn

    2013-04-01

    Full Text Available The fine control of molecules mediating communication in the nervous system is key to adjusting neuronal responsiveness during development and in maintaining the stability of established networks in the face of altered sensory input. To prevent culmination of pathological recurrent network excitation or debilitating periods of quiescence, adaptive alterations occur in the signalling molecules and ion channels that control membrane excitability and synaptic transmission. However, rather than encoding (and thus ‘hardwiring’ modified gene copies, the nervous systems of metazoa have opted for expanding on post-transcriptional pre-mRNA splicing by altering key encoded amino acids using a conserved mechanism of A-to-I RNA editing: the enzymatic deamination of adenosine resulting in a change in the nucleotide to inosine. Inosine exhibits similar base-pairing properties to guanosine with respect to tRNA codon recognition, replication by polymerases and RNA secondary structure forming capacity. In addition to recoding within the open reading frame, adenosine deamination also occurs with high frequency throughout the non-coding transcriptome, where it affects multiple aspects of RNA metabolism and gene expression. We will describe here the recoding function of key RNA editing targets in the mammalian central nervous system (CNS and their potential to be regulated. We will then discuss how interactions of A-to-I editing with gene expression and alternative splicing could play a wider role in regulating the neuronal transcriptome. Finally, we will highlight the increasing complexity of this multifaceted control hub by summarising new findings from high-throughput studies.

  15. Construction of a guide-RNA for site-directed RNA mutagenesis utilising intracellular A-to-I RNA editing

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    Fukuda, Masatora; Umeno, Hiromitsu; Nose, Kanako; Nishitarumizu, Azusa; Noguchi, Ryoma; Nakagawa, Hiroyuki

    2017-01-01

    As an alternative to DNA mutagenesis, RNA mutagenesis can potentially become a powerful gene-regulation method for fundamental research and applied life sciences. Adenosine-to-inosine (A-to-I) RNA editing alters genetic information at the transcript level and is an important biological process that is commonly conserved in metazoans. Therefore, a versatile RNA-mutagenesis method can be achieved by utilising the intracellular RNA-editing mechanism. Here, we report novel guide RNAs capable of inducing A-to-I mutations by guiding the editing enzyme, human adenosine deaminase acting on RNA (ADAR). These guide RNAs successfully introduced A-to-I mutations into the target-site, which was determined by the reprogrammable antisense region. In ADAR2-over expressing cells, site-directed RNA editing could also be performed by simply introducing the guide RNA. Our guide RNA framework provides basic insights into establishing a generally applicable RNA-mutagenesis method. PMID:28148949

  16. Comparative analysis of A-to-I editing in human and non-human primate brains reveals conserved patterns and context-dependent regulation of RNA editing.

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    O'Neil, Richard T; Wang, Xiaojing; Morabito, Michael V; Emeson, Ronald B

    2017-04-06

    A-to-I RNA editing is an important process for generating molecular diversity in the brain through modification of transcripts encoding several proteins important for neuronal signaling. We investigated the relationships between the extent of editing at multiple substrate transcripts (5HT2C, MGLUR4, CADPS, GLUR2, GLUR4, and GABRA3) in brain tissue obtained from adult humans and rhesus macaques. Several patterns emerged from these studies revealing conservation of editing across primate species. Additionally, variability in the human population allows us to make novel inferences about the co-regulation of editing at different editing sites and even across different brain regions.

  17. Alu Sequences in Undifferentiated Human Embryonic Stem Cells Display High Levels of A-to-I RNA Editing

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    Osenberg, Sivan; Paz Yaacov, Nurit; Safran, Michal; Moshkovitz, Sharon; Shtrichman, Ronit; Sherf, Ofra; Jacob-Hirsch, Jasmine; Keshet, Gilmor; Amariglio, Ninette; Itskovitz-Eldor, Joseph; Rechavi, Gideon

    2010-01-01

    Adenosine to Inosine (A-to-I) RNA editing is a site-specific modification of RNA transcripts, catalyzed by members of the ADAR (Adenosine Deaminase Acting on RNA) protein family. RNA editing occurs in human RNA in thousands of different sites. Some of the sites are located in protein-coding regions but the majority is found in non-coding regions, such as 3′UTRs, 5′UTRs and introns - mainly in Alu elements. While editing is found in all tissues, the highest levels of editing are found in the brain. It was shown that editing levels within protein-coding regions are increased during embryogenesis and after birth and that RNA editing is crucial for organism viability as well as for normal development. In this study we characterized the A-to-I RNA editing phenomenon during neuronal and spontaneous differentiation of human embryonic stem cells (hESCs). We identified high editing levels of Alu repetitive elements in hESCs and demonstrated a global decrease in editing levels of non-coding Alu sites when hESCs are differentiating, particularly into the neural lineage. Using RNA interference, we showed that the elevated editing levels of Alu elements in undifferentiated hESCs are highly dependent on ADAR1. DNA microarray analysis showed that ADAR1 knockdown has a global effect on gene expression in hESCs and leads to a significant increase in RNA expression levels of genes involved in differentiation and development processes, including neurogenesis. Taken together, we speculate that A-to-I editing of Alu sequences plays a role in the regulation of hESC early differentiation decisions. PMID:20574523

  18. Alu sequences in undifferentiated human embryonic stem cells display high levels of A-to-I RNA editing.

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    Sivan Osenberg

    Full Text Available Adenosine to Inosine (A-to-I RNA editing is a site-specific modification of RNA transcripts, catalyzed by members of the ADAR (Adenosine Deaminase Acting on RNA protein family. RNA editing occurs in human RNA in thousands of different sites. Some of the sites are located in protein-coding regions but the majority is found in non-coding regions, such as 3'UTRs, 5'UTRs and introns - mainly in Alu elements. While editing is found in all tissues, the highest levels of editing are found in the brain. It was shown that editing levels within protein-coding regions are increased during embryogenesis and after birth and that RNA editing is crucial for organism viability as well as for normal development. In this study we characterized the A-to-I RNA editing phenomenon during neuronal and spontaneous differentiation of human embryonic stem cells (hESCs. We identified high editing levels of Alu repetitive elements in hESCs and demonstrated a global decrease in editing levels of non-coding Alu sites when hESCs are differentiating, particularly into the neural lineage. Using RNA interference, we showed that the elevated editing levels of Alu elements in undifferentiated hESCs are highly dependent on ADAR1. DNA microarray analysis showed that ADAR1 knockdown has a global effect on gene expression in hESCs and leads to a significant increase in RNA expression levels of genes involved in differentiation and development processes, including neurogenesis. Taken together, we speculate that A-to-I editing of Alu sequences plays a role in the regulation of hESC early differentiation decisions.

  19. Consistent levels of A-to-I RNA editing across individuals in coding sequences and non-conserved Alu repeats

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    Osenberg Sivan

    2010-10-01

    Full Text Available Abstract Background Adenosine to inosine (A-to-I RNA-editing is an essential post-transcriptional mechanism that occurs in numerous sites in the human transcriptome, mainly within Alu repeats. It has been shown to have consistent levels of editing across individuals in a few targets in the human brain and altered in several human pathologies. However, the variability across human individuals of editing levels in other tissues has not been studied so far. Results Here, we analyzed 32 skin samples, looking at A-to-I editing level in three genes within coding sequences and in the Alu repeats of six different genes. We observed highly consistent editing levels across different individuals as well as across tissues, not only in coding targets but, surprisingly, also in the non evolutionary conserved Alu repeats. Conclusions Our findings suggest that A-to-I RNA-editing of Alu elements is a tightly regulated process and, as such, might have been recruited in the course of primate evolution for post-transcriptional regulatory mechanisms.

  20. A-to-I editing of protein coding and noncoding RNAs.

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    Mallela, Arka; Nishikura, Kazuko

    2012-01-01

    Adenosine deaminase acting on RNA (ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA) substrates. Inosine pairs preferentially with cytidine, as opposed to uridine; therefore, ADAR editing alters the sequence and base pairing properties of both protein-coding and non-coding RNA. Editing can directly alter the sequence of protein-coding transcripts and modify splicing, or affect a variety of non-coding targets, including microRNA, small interfering RNA, viral transcripts, and repeat elements such as Alu and LINE. Such editing has a wide range of physiological effects, including modification of targets in the brain and in disease states.

  1. Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats

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    Eisenberg Eli

    2010-07-01

    Full Text Available Abstract Background Alu repeats in the human transcriptome undergo massive adenosine to inosine RNA editing. This process is selective, as editing efficiency varies greatly among different adenosines. Several studies have identified weak sequence motifs characterizing the editing sites, but these alone do not account for the large diversity observed. Results Here we build a dataset of 29,971 editing sites and use it to characterize editing preferences. We focus on structural aspects, studying the double-stranded RNA structure of the Alu repeats, and show the editing frequency of a given site to depend strongly on the micro-structure it resides in. Surprisingly, we find that interior loops, and especially the nucleotides at their edges, are more likely to be edited than helices. In addition, the sequence motifs characterizing editing sites vary with the micro-structure. Finally, we show that thermodynamic stability of the site is important for its editing. Conclusions Analysis of a large dataset of editing events reveals more information on sequence and structural motifs characterizing the A-to-I editing process

  2. Identification of an RNA element for specific coordination of A-to-I RNA editing on HTR2C pre-mRNA.

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    Fukuda, Masatora; Oyama, Yui; Nishitarumizu, Azusa; Omura, Miki; Nose, Kanako; Deshimaru, Masanobu

    2015-10-01

    Adenosine-to-Inosine (A-to-I) RNA editing is an intracellular mechanism in which inosine is specifically substituted against adenosine by the action of adenosine deaminases acting on RNA (ADARs). Serotonin 2C receptor (HTR2C) is encoded through combinatorial A-to-I RNA editing at recoding sites (A - E site) on its pre-mRNA. Although the efficiency of RNA editing at particular sites is known to be critical for modulating the serotonin signaling, the mechanistic details of site-specific editing on HTR2C pre-mRNA are not fully understood. Toward complete understanding of this mechanism, we discovered an RNA element, which coordinates site-specific RNA editing on HTR2C pre-mRNA by an in vitro editing assay and secondary structural analysis of mutant HTR2C RNA fragments. Our results showed that HTR2C pre-mRNA forms a characteristic structure, which was restricted by the internal loop and Watson-Crick base-pair interaction on site E, for intrinsic editing. We suggest that the internal loop would contribute toward adjusting the relative distance and/or geometry between the editing sites and the scaffold for ADAR.

  3. Detecting Single-Nucleotide Substitutions Induced by Genome Editing.

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    Miyaoka, Yuichiro; Chan, Amanda H; Conklin, Bruce R

    2016-08-01

    The detection of genome editing is critical in evaluating genome-editing tools or conditions, but it is not an easy task to detect genome-editing events-especially single-nucleotide substitutions-without a surrogate marker. Here we introduce a procedure that significantly contributes to the advancement of genome-editing technologies. It uses droplet digital polymerase chain reaction (ddPCR) and allele-specific hydrolysis probes to detect single-nucleotide substitutions generated by genome editing (via homology-directed repair, or HDR). HDR events that introduce substitutions using donor DNA are generally infrequent, even with genome-editing tools, and the outcome is only one base pair difference in 3 billion base pairs of the human genome. This task is particularly difficult in induced pluripotent stem (iPS) cells, in which editing events can be very rare. Therefore, the technological advances described here have implications for therapeutic genome editing and experimental approaches to disease modeling with iPS cells.

  4. Using REDItools to Detect RNA Editing Events in NGS Datasets.

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    Picardi, Ernesto; D'Erchia, Anna Maria; Montalvo, Antonio; Pesole, Graziano

    2015-03-09

    RNA editing is a post-transcriptional/co-transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organisms and different cellular locations through evolutionally and biochemically unrelated proteins. RNA editing has a plethora of biological effects including the modulation of alternative splicing and fine-tuning of gene expression. RNA editing events by base substitutions can be detected on a genomic scale by NGS technologies through the REDItools package, an ad hoc suite of Python scripts to study RNA editing using RNA-Seq and DNA-Seq data or RNA-Seq data alone. REDItools implement effective filters to minimize biases due to sequencing errors, mapping errors, and SNPs. The package is freely available at Google Code repository (http://code.google.com/p/reditools/) and released under the MIT license. In the present unit we show three basic protocols corresponding to three main REDItools scripts.

  5. A-to-I RNA编辑事件对外显子剪接增强子潜在影响的生物信息学分析%Investigating the Potential Effects on the Exonic Splicing Enhancers Caused by Human A-to-I RNA Editing with Bioinformatics Skills

    Institute of Scientific and Technical Information of China (English)

    艾鼎伦; 何涛; 何涛涛; 汪莉; 王玉民

    2010-01-01

    目的:研究人A-to-I RNA编辑事件对外显子剪接增强子(ESE)的潜在影响.方法:搜集文献报道的人A-to-I RNA编辑位点,并筛选包含有A-to-I RNA编辑位点的ESE,分析人A-to-I RNA编辑前后单碱基变化对ESE的潜在影响.结果:3640个A-to-I RNA编辑位点可能使其所在的ESE功能发生潜在改变;A-to-I RNA编辑事件对不同类型ESE的潜在影响不同.结论:A-to-I RNA 编辑事件可能潜在影响ESE的功能,对ESE的潜在影响为量的调节,而非质的改变.

  6. The dsRBP and Inactive Editor ADR-1 Utilizes dsRNA Binding to Regulate A-to-I RNA Editing across the C. elegans Transcriptome

    OpenAIRE

    Michael C. Washburn; Boyko Kakaradov; Balaji Sundararaman; Emily Wheeler; Shawn Hoon; Gene W. Yeo; Heather A. Hundley

    2014-01-01

    Inadequate adenosine-to-inosine editing of noncoding regions occurs in disease but is often uncorrelated with ADAR levels, underscoring the need to study deaminase-independent control of editing. C. elegans have two ADAR proteins, ADR-2 and the theoretically catalytically inactive ADR-1. Using high-throughput RNA sequencing of wild-type and adr mutant worms, we expand the repertoire of C. elegans edited transcripts over 5-fold and confirm that ADR-2 is the only active deaminase in vivo. Despi...

  7. Comparative RNA editing in autistic and neurotypical cerebella.

    Science.gov (United States)

    Eran, A; Li, J B; Vatalaro, K; McCarthy, J; Rahimov, F; Collins, C; Markianos, K; Margulies, D M; Brown, E N; Calvo, S E; Kohane, I S; Kunkel, L M

    2013-09-01

    Adenosine-to-inosine (A-to-I) RNA editing is a neurodevelopmentally regulated epigenetic modification shown to modulate complex behavior in animals. Little is known about human A-to-I editing, but it is thought to constitute one of many molecular mechanisms connecting environmental stimuli and behavioral outputs. Thus, comprehensive exploration of A-to-I RNA editing in human brains may shed light on gene-environment interactions underlying complex behavior in health and disease. Synaptic function is a main target of A-to-I editing, which can selectively recode key amino acids in synaptic genes, directly altering synaptic strength and duration in response to environmental signals. Here, we performed a high-resolution survey of synaptic A-to-I RNA editing in a human population, and examined how it varies in autism, a neurodevelopmental disorder in which synaptic abnormalities are a common finding. Using ultra-deep (>1000 × ) sequencing, we quantified the levels of A-to-I editing of 10 synaptic genes in postmortem cerebella from 14 neurotypical and 11 autistic individuals. A high dynamic range of editing levels was detected across individuals and editing sites, from 99.6% to below detection limits. In most sites, the extreme ends of the population editing distributions were individuals with autism. Editing was correlated with isoform usage, clusters of correlated sites were identified, and differential editing patterns examined. Finally, a dysfunctional form of the editing enzyme adenosine deaminase acting on RNA B1 was found more commonly in postmortem cerebella from individuals with autism. These results provide a population-level, high-resolution view of A-to-I RNA editing in human cerebella and suggest that A-to-I editing of synaptic genes may be informative for assessing the epigenetic risk for autism.

  8. Editing modifies the GABA(A) receptor subunit alpha3

    DEFF Research Database (Denmark)

    Ohlson, Johan; Pedersen, Jakob Skou; Haussler, David

    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...

  9. Uncovering RNA editing sites in long non-coding RNAs

    Directory of Open Access Journals (Sweden)

    Ernesto ePicardi

    2014-12-01

    Full Text Available RNA editing is an important co/post-transcriptional molecular process able to modify RNAs by nucleotide insertions/deletions or substitutions. In human, the most common RNA editing event involves the deamination of adenosine (A into inosine (I through the adenosine deaminase acting on RNA (ADAR proteins. Although A-to-I editing can occur in both coding and non coding RNAs, recent findings, based on RNA-seq experiments, have clearly demonstrated that a large fraction of RNA editing events alter non-coding RNAs sequences including untranslated regions of mRNAs (UTRs, introns, long non-coding RNAs (lncRNA and low molecular weight RNAs (tRNA, miRNAs and others. An accurate detection of A-to-I events occurring in non-coding RNAs is of utmost importance to clarify yet unknown functional roles of RNA editing in the context of gene expression regulation and maintenance of cell homeostasis. In the last few years, massive transcriptome sequencing has been employed to identify putative RNA editing changes at genome scale. Despite several efforts, the computational prediction of A-to-I sites in complete eukaryotic genomes is yet a challenging task. We have recently developed a software package, called REDItools, in order to simplify the detection of RNA editing events from deep sequencing data. In the present work, we show the potential of our tools in recovering A-to-I candidates from RNA-Seq experiments as well as guidelines to improve the RNA editing detection in non-coding RNAs, with specific attention to the lncRNAs.

  10. News Editing. Second Edition.

    Science.gov (United States)

    Westley, Bruce H.

    A revision of the first edition of "News Editing," this is a textbook for the newspaper editor. The duties of the editor are detailed, as are those of other newspaper employees. Among the basic editing skills the author includes suggestions for sentence structure, word usage, and vocabulary. Examples are given of editing for objectivity, handling…

  11. Simultaneous detection of valine and lactate using MEGA-PRESS editing in pyogenic brain abscess.

    Science.gov (United States)

    Lange, Thomas; Ko, Cheng-Wen; Lai, Ping-Hong; Dacko, Michael; Tsai, Shang-Yueh; Buechert, Martin

    2016-12-01

    Valine and lactate have been recognized as important metabolic markers to diagnose brain abscess by means of MRS. However, in vivo unambiguous detection and quantification is hampered by macromolecular contamination. In this work, MEGA-PRESS difference editing of valine and lactate is proposed. The method is validated in vitro and applied for quantitative in vivo experiments in one healthy subject and two brain abscess patients. It is demonstrated that with this technique the overlapping lipid signal can be reduced by more than an order of magnitude and thus the robustness of valine and lactate detection in vivo can be enhanced. Quantification of the two abscess MEGA-PRESS spectra yielded valine/lactate concentration ratios of 0.10 and 0.27. These ratios agreed with the concentration ratios determined from concomitantly acquired short-TE PRESS data and were in line with literature values. The quantification accuracy of lactate (as measured with Cramér-Rao lower bounds in LCModel processing) was better for MEGA-PRESS than for short-TE PRESS in all acquired in vivo datasets. The Cramér-Rao lower bounds of valine were only better for MEGA-PRESS in one of the two abscess cases, while in the other case coediting of isoleucine confounded the quantification in the MEGA-PRESS analysis. MEGA-PRESS and short-TE PRESS should be combined for unambiguous quantification of amino acids in abscess measurements. Simultaneous valine/lactate MEGA-PRESS editing might benefit the distinction of brain abscesses from tumors, and further categorization of bacteria with reasonable sensitivity and specificity.

  12. Edit wars in Wikipedia

    CERN Document Server

    Sumi, Róbert; Rung, András; Kornai, András; Kertész, János

    2011-01-01

    We present a new, efficient method for automatically detecting severe conflicts `edit wars' in Wikipedia and evaluate this method on six different language WPs. We discuss how the number of edits, reverts, the length of discussions, the burstiness of edits and reverts deviate in such pages from those following the general workflow, and argue that earlier work has significantly over-estimated the contentiousness of the Wikipedia editing process.

  13. Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis

    DEFF Research Database (Denmark)

    Lonowski, Lindsey A; Narimatsu, Yoshiki; Riaz, Anjum;

    2017-01-01

    This protocol describes methods for increasing and evaluating the efficiency of genome editing based on the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated 9) system, transcription activator-like effector nucleases (TALENs) or zinc-finger nucleases (ZFNs...

  14. Genetic Architectures of Quantitative Variation in RNA Editing Pathways.

    Science.gov (United States)

    Gu, Tongjun; Gatti, Daniel M; Srivastava, Anuj; Snyder, Elizabeth M; Raghupathy, Narayanan; Simecek, Petr; Svenson, Karen L; Dotu, Ivan; Chuang, Jeffrey H; Keller, Mark P; Attie, Alan D; Braun, Robert E; Churchill, Gary A

    2016-02-01

    RNA editing refers to post-transcriptional processes that alter the base sequence of RNA. Recently, hundreds of new RNA editing targets have been reported. However, the mechanisms that determine the specificity and degree of editing are not well understood. We examined quantitative variation of site-specific editing in a genetically diverse multiparent population, Diversity Outbred mice, and mapped polymorphic loci that alter editing ratios globally for C-to-U editing and at specific sites for A-to-I editing. An allelic series in the C-to-U editing enzyme Apobec1 influences the editing efficiency of Apob and 58 additional C-to-U editing targets. We identified 49 A-to-I editing sites with polymorphisms in the edited transcript that alter editing efficiency. In contrast to the shared genetic control of C-to-U editing, most of the variable A-to-I editing sites were determined by local nucleotide polymorphisms in proximity to the editing site in the RNA secondary structure. Our results indicate that RNA editing is a quantitative trait subject to genetic variation and that evolutionary constraints have given rise to distinct genetic architectures in the two canonical types of RNA editing.

  15. Transfer Rate Edited experiment for the selective detection of Chemical Exchange via Saturation Transfer (TRE-CEST).

    Science.gov (United States)

    Friedman, Joshua I; Xia, Ding; Regatte, Ravinder R; Jerschow, Alexej

    2015-07-01

    Chemical Exchange Saturation Transfer (CEST) magnetic resonance experiments have become valuable tools in magnetic resonance for the detection of low concentration solutes with far greater sensitivity than direct detection methods. Accurate measures of rates of chemical exchange provided by CEST are of particular interest to biomedical imaging communities where variations in chemical exchange can be related to subtle variations in biomarker concentration, temperature and pH within tissues using MRI. Despite their name, however, traditional CEST methods are not truly selective for chemical exchange and instead detect all forms of magnetization transfer including through-space NOE. This ambiguity crowds CEST spectra and greatly complicates subsequent data analysis. We have developed a Transfer Rate Edited CEST experiment (TRE-CEST) that uses two different types of solute labeling in order to selectively amplify signals of rapidly exchanging proton species while simultaneously suppressing 'slower' NOE-dominated magnetization transfer processes. This approach is demonstrated in the context of both NMR and MRI, where it is used to detect the labile amide protons of proteins undergoing chemical exchange (at rates⩾30s(-1)) while simultaneously eliminating signals originating from slower (∼5s(-1)) NOE-mediated magnetization transfer processes. TRE-CEST greatly expands the utility of CEST experiments in complex systems, and in-vivo, in particular, where it is expected to improve the quantification of chemical exchange and magnetization transfer rates while enabling new forms of imaging contrast.

  16. In vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI) : [3,4-(CH2)-C-13] glutamate/glutamine tomography in rat brain

    NARCIS (Netherlands)

    Hyder, F; Renken, R; Rothman, DL

    1999-01-01

    A method for in vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI) is described. This method is composed of an echo-planar based acquisition implemented with C-13-H-1 J editing spectroscopy and is intended for high temporal and spatial resolution in vivo spectros

  17. Exploring the RNA editing potential of RNA-Seq data by ExpEdit.

    Science.gov (United States)

    D'Antonio, Mattia; Picardi, Ernesto; Castrignanò, Tiziana; D'Erchia, Anna Maria; Pesole, Graziano

    2015-01-01

    Revealing the impact of A-to-I RNA editing in RNA-Seq experiments is relevant in humans because RNA editing can influence gene expression. In addition, its deregulation has been linked to a variety of human diseases. Exploiting the RNA editing potential in complete RNA-Seq datasets, however, is a challenging task. Indeed, no dedicated software is available, and sometimes deep computational skills and appropriate hardware resources are required. To explore the impact of known RNA editing events in massive transcriptome sequencing experiments, we developed the ExpEdit web service application. In the present work, we provide an overview of ExpEdit as well as methodologies to investigate known RNA editing in human RNA-Seq datasets.

  18. REDIdb: the RNA editing database.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

    2007-01-01

    The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

  19. Cluster editing

    DEFF Research Database (Denmark)

    Böcker, S.; Baumbach, Jan

    2013-01-01

    . The problem has been the inspiration for numerous algorithms in bioinformatics, aiming at clustering entities such as genes, proteins, phenotypes, or patients. In this paper, we review exact and heuristic methods that have been proposed for the Cluster Editing problem, and also applications......The Cluster Editing problem asks to transform a graph into a disjoint union of cliques using a minimum number of edge modifications. Although the problem has been proven NP-complete several times, it has nevertheless attracted much research both from the theoretical and the applied side...

  20. Multilinguals and Wikipedia Editing

    CERN Document Server

    Hale, Scott A

    2013-01-01

    This article analyzes one month of edits to Wikipedia in order to examine the role of users editing multiple language editions (referred to as multilingual users). Such multilingual users may serve an important function in diffusing information across different language editions of the project, and prior work has suggested this could reduce the level of self-focus bias in each edition. This study finds multilingual users are much more active than their single-edition (monolingual) counterparts. They are found in all language editions, but smaller-sized editions with fewer users have a higher percentage of multilingual users than larger-sized editions. About a quarter of multilingual users always edit the same articles in multiple languages, while just over 40% of multilingual users edit different articles in different languages. When non-English users do edit a second language edition, that edition is most frequently English. Nonetheless, several regional and linguistic cross-editing patterns are also present...

  1. In vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI): [3,4-(13)CH(2)]glutamate/glutamine tomography in rat brain.

    Science.gov (United States)

    Hyder, F; Renken, R; Rothman, D L

    1999-12-01

    A method for in vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI) is described. This method is composed of an echo-planar based acquisition implemented with (13)C-(1)H J editing spectroscopy and is intended for high temporal and spatial resolution in vivo spectroscopic imaging of (13)C turnover, from D-[1,6-(13)C]glucose to glutamate and glutamine, in the brain. At a static magnetic field strength of 7 T, both in vitro and in vivo chemical shift imaging data are presented with a spatial resolution of 8 microL (i.e., 1.25 x 1.25 x 5.00 mm(3)) and a maximum spectral bandwidth of 5.2 ppm in (1)H. Chemical shift imaging data acquired every 11 minutes allowed detection of regional [4-(13)CH(2)]glutamate turnover in rat brain. The [4-(13)CH(2)]glutamate turnover curves, which can be converted to tricarboxylic acid cycle fluxes, showed that the tricarboxylic acid cycle flux (V(TCA)) in pure gray and white matter can range from 1.2 +/- 0.2 to 0.5 +/- 0.1 micromol/g/min, respectively, for morphine-anesthetized rats. The mean cortical V(TCA) from 32 voxels of 1.0 +/- 0.3 micromol/g/min (N = 3) is in excellent agreement with previous localized measurements that have demonstrated that V(TCA) can range from 0.9-1.1 micromol/g/min under identical anesthetized conditions. Magn Reson Med 42:997-1003, 1999.

  2. Isotope-edited infrared spectroscopy.

    Science.gov (United States)

    Buchner, Ginka S; Kubelka, Jan

    2012-01-01

    Isotope-edited infrared (IR) spectroscopy is a powerful tool for studying structural and dynamical properties of peptides and proteins with site-specific resolution. Labeling of selected amide carbonyls with (13)C results in detectable sidebands of amide I' vibrations, which provide information about local conformation and/or solvent exposure without structural perturbation to the protein. Incorporation of isotopically labeled amino acids at specific positions is achieved by the chemical synthesis of the studied proteins. We describe the basic procedures for synthesis of (13)C isotopically edited protein samples, experimental IR spectroscopic measurements, and analysis of the site-specific structural changes from the thermal unfolding IR data.

  3. A strategy for developing a hammerhead ribozyme for selective RNA cleavage depending on substitutional RNA editing.

    Science.gov (United States)

    Fukuda, Masatora; Kurihara, Kei; Tanaka, Yasuyoshi; Deshimaru, Masanobu

    2012-09-01

    Substitutional RNA editing plays a crucial role in the regulation of biological processes. Cleavage of target RNA that depends on the specific site of substitutional RNA editing is a useful tool for analyzing and regulating intracellular processes related to RNA editing. Hammerhead ribozymes have been utilized as small catalytic RNAs for cleaving target RNA at a specific site and may be used for RNA-editing-specific RNA cleavage. Here we reveal a design strategy for a hammerhead ribozyme that specifically recognizes adenosine to inosine (A-to-I) and cytosine to uracil (C-to-U) substitutional RNA-editing sites and cleaves target RNA. Because the hammerhead ribozyme cleaves one base upstream of the target-editing site, the base that pairs with the target-editing site was utilized for recognition. RNA-editing-specific ribozymes were designed such that the recognition base paired only with the edited base. These ribozymes showed A-to-I and C-to-U editing-specific cleavage activity against synthetic serotonin receptor 2C and apolipoprotein B mRNA fragments in vitro, respectively. Additionally, the ribozyme designed for recognizing A-to-I RNA editing at the Q/R site on filamin A (FLNA) showed editing-specific cleavage activity against physiologically edited FLNA mRNA extracted from cells. We demonstrated that our strategy is effective for cleaving target RNA in an editing-dependent manner. The data in this study provided an experimental basis for the RNA-editing-dependent degradation of specific target RNA in vivo.

  4. Multiplex editing system

    DEFF Research Database (Denmark)

    2015-01-01

    The present invention relates to a multiplex editing system. The system allows multiple editing of nucleic acid sequences such as genomic sequences, such as knockins of genes of interest in a genome, knockouts of genomic sequences and/or allele replacement. Also provided herein are a method...... for editing nucleic acids and a cell comprising a stably integrated endonuclease....

  5. Oligophrenin-1 (OPHN1, a gene involved in X-linked intellectual disability, undergoes RNA editing and alternative splicing during human brain development.

    Directory of Open Access Journals (Sweden)

    Sabina Barresi

    Full Text Available Oligophrenin-1 (OPHN1 encodes for a Rho-GTPase-activating protein, important for dendritic morphogenesis and synaptic function. Mutations in this gene have been identified in patients with X-linked intellectual disability associated with cerebellar hypoplasia. ADAR enzymes are responsible for A-to-I RNA editing, an essential post-transcriptional RNA modification contributing to transcriptome and proteome diversification. Specifically, ADAR2 activity is essential for brain development and function. Herein, we show that the OPHN1 transcript undergoes post-transcriptional modifications such as A-to-I RNA editing and alternative splicing in human brain and other tissues. We found that OPHN1 editing is detectable already at the 18th week of gestation in human brain with a boost of editing at weeks 20 to 33, concomitantly with OPHN1 expression increase and the appearance of a novel OPHN1 splicing isoform. Our results demonstrate that multiple post-transcriptional events occur on OPHN1, a gene playing an important role in brain function and development.

  6. Oligophrenin-1 (OPHN1), a gene involved in X-linked intellectual disability, undergoes RNA editing and alternative splicing during human brain development.

    Science.gov (United States)

    Barresi, Sabina; Tomaselli, Sara; Athanasiadis, Alekos; Galeano, Federica; Locatelli, Franco; Bertini, Enrico; Zanni, Ginevra; Gallo, Angela

    2014-01-01

    Oligophrenin-1 (OPHN1) encodes for a Rho-GTPase-activating protein, important for dendritic morphogenesis and synaptic function. Mutations in this gene have been identified in patients with X-linked intellectual disability associated with cerebellar hypoplasia. ADAR enzymes are responsible for A-to-I RNA editing, an essential post-transcriptional RNA modification contributing to transcriptome and proteome diversification. Specifically, ADAR2 activity is essential for brain development and function. Herein, we show that the OPHN1 transcript undergoes post-transcriptional modifications such as A-to-I RNA editing and alternative splicing in human brain and other tissues. We found that OPHN1 editing is detectable already at the 18th week of gestation in human brain with a boost of editing at weeks 20 to 33, concomitantly with OPHN1 expression increase and the appearance of a novel OPHN1 splicing isoform. Our results demonstrate that multiple post-transcriptional events occur on OPHN1, a gene playing an important role in brain function and development.

  7. 肿瘤中GLI1RNA编辑的下调及其潜在功能分析%Down-regulation of RNA editing of GLI1 in tumors and analysis of its potential function

    Institute of Scientific and Technical Information of China (English)

    张颖; 胡亚欧; 何涛; 侯小强; 汪莉; 张部昌; 王玉民

    2012-01-01

    Objective To detect the A-to-[ RNA editing in the coding region of cancer associated gene GUI, compare the difference in the editing level between tumor and normal cell lines , and to analyze the potential effect of this editing event in the hope of discovering the role of the RNA editing in the occurrence and progression of cancer . Methods The identification of the A-to-[ RNA editing event and the comparison of the editing level were carried out by comparing the cDNA sequences with their corresponding genomic templates based on PCR , RT-PCR and sequencing methods. The potential functional implications of RNA editing were analyzed by multiple bioinformatics tools . Results An A-to-I RNA editing site mapped to chr 12: 56150891 changed the arginine residue at position 701 of the GUI protein to a glutamine residue, which was detected in the human brain , breast, small intestine tissues and multiple cell lines. Compared with normal controls, the editing level of this site decreased in the hepatoma and breast cancer cell lines . By bioinformatics analysis, this editing event altered amino acid residue and was predicted to destroy putative exonic splicing enhancers ( ESE) and affect putative protein tertiary structure. Conclusion This A-to-I RNA editing event in the coding region of GUI occurs in many diverse human tissues and cell lines. Down^-egulation of RNA editing of GUI in hepatoma and breast cancer cell lines may be associated with the occurrence and progression of cancer .%目的 检测癌相关基因GLI1编码区发生的A-to-I RNA编辑,比较编辑水平在肿瘤与正常细胞系中的差异,并分析编辑事件的潜在影响,以期揭示其与癌症发生发展的关联.方法 通过PCR、RT-PCR及测序的方法检测GLI1编码区DNA和RNA序列上的差异,以此来识别该区域上的A-to-I RNA编辑事件和比较肿瘤与正常细胞系中编辑位点的编辑水平差异.使用多种生物信息学工具分析编辑事

  8. Developing new levels of edit

    Energy Technology Data Exchange (ETDEWEB)

    Prono, J.; DeLanoy, M.; Deupree, R.; Skiby, J.; Thompson, B.

    1998-07-01

    In 1985, the writing and editing group at Los Alamos National Laboratory established four levels of edit for technical reports. When a survey in 1994 showed that both authors and editors felt the levels were not meeting author needs, the authors set about revising them. Their goals were to simplify the editing process, focus editing on improving technical clarity, and ensure that value was added in editing. This paper describes the revision process and product -- three author-based levels of edit.

  9. A distant cis acting intronic element induces site-selective RNA editing

    DEFF Research Database (Denmark)

    Daniel, Chammiran; Venø, Morten Trillingsgaard; Ekdahl, Ylva

    2012-01-01

    Transcripts have been found to be site selectively edited from adenosine-to-inosine (A-to-I) in the mammalian brain, mostly in genes involved in neurotransmission. While A-to-I editing occurs at double-stranded structures, other structural requirements are largely unknown. We have investigated...... shown to be important for A-to-I editing. We demonstrate that the element also can induce editing in related but normally not edited RNA sequences. In human, thousands of genes are edited in duplexes formed by inverted repeats in non-coding regions. It is likely that numerous such duplexes can induce...... the requirements for editing at the I/M site in the Gabra-3 transcript of the GABA(A) receptor. We identify an evolutionarily conserved intronic duplex, 150 nt downstream of the exonic hairpin where the I/M site resides, which is required for its editing. This is the first time a distant RNA structure has been...

  10. Regulation of gene expression in neuronal tissue by RNA interference and editing

    DEFF Research Database (Denmark)

    Venø, Morten Trillingsgaard

    No tissue in the mammalian organism is more complex than the brain. This complexity is in part the result of precise timing and interplay of a large number mechanisms modulating gene expression post-transcriptionally. Fine-tuning mechanisms such as A-to-I editing of RNA transcripts and regulation...... mediated by microRNAs are crucial for the correct function of the mammalian brain. We are addressing A-to-I editing and regulation by microRNAs with spatio-temporal resolution in the embryonic porcine brain by Solexa sequencing of microRNAs and 454 sequencing of edited neuronal messenger RNAs, resulting...... in detailed data of both of these fine-tuning mechanisms in the embryonic development of the pig. Editing levels of transcripts examined are generally seen to increase through development, in agreement with editing of specific microRNA also examined in the Solexa sequencing study. Three studies examining...

  11. Quality text editing

    Directory of Open Access Journals (Sweden)

    Gyöngyi Bujdosó

    2009-10-01

    Full Text Available Text editing is more than the knowledge of word processing techniques. Originally typographers, printers, text editors were the ones qualified to edit texts, which were well structured, legible, easily understandable, clear, and were able to emphasize the coreof the text. Time has changed, and nowadays everyone has access to computers as well as to text editing software and most users believe that having these tools is enough to edit texts. However, text editing requires more skills. Texts appearing either in printed or inelectronic form reveal that most of the users do not realize that they are not qualified to edit and publish their works. Analyzing the ‘text-products’ of the last decade a tendency can clearly be drawn. More and more documents appear, which instead of emphasizingthe subject matter, are lost in the maze of unstructured text slices. Without further thoughts different font types, colors, sizes, strange arrangements of objects, etc. are applied. We present examples with the most common typographic and text editing errors. Our aim is to call the attention to these mistakes and persuadeusers to spend time to educate themselves in text editing. They have to realize that a well-structured text is able to strengthen the effect on the reader, thus the original message will reach the target group.

  12. Learning string edit distance

    CERN Document Server

    Ristad, E S; Ristad, Eric Sven; Yianilos, Peter N.

    1996-01-01

    In many applications, it is necessary to determine the similarity of two strings. A widely-used notion of string similarity is the edit distance: the minimum number of insertions, deletions, and substitutions required to transform one string into the other. In this report, we provide a stochastic model for string edit distance. Our stochastic model allows us to learn a string edit distance function from a corpus of examples. We illustrate the utility of our approach by applying it to the difficult problem of learning the pronunciation of words in conversational speech. In this application, we learn a string edit distance with one fourth the error rate of the untrained Levenshtein distance. Our approach is applicable to any string classification problem that may be solved using a similarity function against a database of labeled prototypes. Keywords: string edit distance, Levenshtein distance, stochastic transduction, syntactic pattern recognition, prototype dictionary, spelling correction, string correction, ...

  13. CRISPR Genome Editing

    Science.gov (United States)

    A research article about a technique for gene editing known as CRISPR-Cas9. The technique has made it much easier and faster for cancer researchers to study mutations and test new therapeutic targets.

  14. Developing new levels of edit

    Energy Technology Data Exchange (ETDEWEB)

    Prono, J.K.

    1997-06-01

    Since 1985, Los Alamos National Laboratory (LANL) staff have had four levels of edit to choose from for technical reports. When a CQI survey showed that both authors and editors felt the levels were not meeting author needs, LANL set about revising them. The goals were to simplify the editing process, focus editing on improving technical clarity, and ensure value added in editing. This paper describes the revision process and product--three author-based levels of edit.

  15. Comprehensive high-resolution analysis of the role of an Arabidopsis gene family in RNA editing.

    Directory of Open Access Journals (Sweden)

    Stéphane Bentolila

    2013-06-01

    Full Text Available In flowering plants, mitochondrial and chloroplast mRNAs are edited by C-to-U base modification. In plant organelles, RNA editing appears to be generally a correcting mechanism that restores the proper function of the encoded product. Members of the Arabidopsis RNA editing-Interacting Protein (RIP family have been recently shown to be essential components of the plant editing machinery. We report the use of a strand- and transcript-specific RNA-seq method (STS-PCRseq to explore the effect of mutation or silencing of every RIP gene on plant organelle editing. We confirm RIP1 to be a major editing factor that controls the editing extent of 75% of the mitochondrial sites and 20% of the plastid C targets of editing. The quantitative nature of RNA sequencing allows the precise determination of overlapping effects of RIP factors on RNA editing. Over 85% of the sites under the influence of RIP3 and RIP8, two moderately important mitochondrial factors, are also controlled by RIP1. Previously uncharacterized RIP family members were found to have only a slight effect on RNA editing. The preferential location of editing sites controlled by RIP7 on some transcripts suggests an RNA metabolism function for this factor other than editing. In addition to a complete characterization of the RIP factors for their effect on RNA editing, our study highlights the potential of RNA-seq for studying plant organelle editing. Unlike previous attempts to use RNA-seq to analyze RNA editing extent, our methodology focuses on sequencing of organelle cDNAs corresponding to known transcripts. As a result, the depth of coverage of each editing site reaches unprecedented values, assuring a reliable measurement of editing extent and the detection of numerous new sites. This strategy can be applied to the study of RNA editing in any organism.

  16. Comprehensive high-resolution analysis of the role of an Arabidopsis gene family in RNA editing.

    Science.gov (United States)

    Bentolila, Stéphane; Oh, Julyun; Hanson, Maureen R; Bukowski, Robert

    2013-06-01

    In flowering plants, mitochondrial and chloroplast mRNAs are edited by C-to-U base modification. In plant organelles, RNA editing appears to be generally a correcting mechanism that restores the proper function of the encoded product. Members of the Arabidopsis RNA editing-Interacting Protein (RIP) family have been recently shown to be essential components of the plant editing machinery. We report the use of a strand- and transcript-specific RNA-seq method (STS-PCRseq) to explore the effect of mutation or silencing of every RIP gene on plant organelle editing. We confirm RIP1 to be a major editing factor that controls the editing extent of 75% of the mitochondrial sites and 20% of the plastid C targets of editing. The quantitative nature of RNA sequencing allows the precise determination of overlapping effects of RIP factors on RNA editing. Over 85% of the sites under the influence of RIP3 and RIP8, two moderately important mitochondrial factors, are also controlled by RIP1. Previously uncharacterized RIP family members were found to have only a slight effect on RNA editing. The preferential location of editing sites controlled by RIP7 on some transcripts suggests an RNA metabolism function for this factor other than editing. In addition to a complete characterization of the RIP factors for their effect on RNA editing, our study highlights the potential of RNA-seq for studying plant organelle editing. Unlike previous attempts to use RNA-seq to analyze RNA editing extent, our methodology focuses on sequencing of organelle cDNAs corresponding to known transcripts. As a result, the depth of coverage of each editing site reaches unprecedented values, assuring a reliable measurement of editing extent and the detection of numerous new sites. This strategy can be applied to the study of RNA editing in any organism.

  17. Editing Audio with Audacity

    Directory of Open Access Journals (Sweden)

    Brandon Walsh

    2016-08-01

    Full Text Available For those interested in audio, basic sound editing skills go a long way. Being able to handle and manipulate the materials can help you take control of your object of study: you can zoom in and extract particular moments to analyze, process the audio, and upload the materials to a server to compliment a blog post on the topic. On a more practical level, these skills could also allow you to record and package recordings of yourself or others for distribution. That guest lecture taking place in your department? Record it and edit it yourself! Doing so is a lightweight way to distribute resources among various institutions, and it also helps make the materials more accessible for readers and listeners with a wide variety of learning needs. In this lesson you will learn how to use Audacity to load, record, edit, mix, and export audio files. Sound editing platforms are often expensive and offer extensive capabilities that can be overwhelming to the first-time user, but Audacity is a free and open source alternative that offers powerful capabilities for sound editing with a low barrier for entry. For this lesson we will work with two audio files: a recording of Bach’s Goldberg Variations available from MusOpen and another recording of your own voice that will be made in the course of the lesson. This tutorial uses Audacity 2.1.2, released January 2016.

  18. Precision genome editing

    DEFF Research Database (Denmark)

    Steentoft, Catharina; Bennett, Eric P; Schjoldager, Katrine Ter-Borch Gram

    2014-01-01

    Precise and stable gene editing in mammalian cell lines has until recently been hampered by the lack of efficient targeting methods. While different gene silencing strategies have had tremendous impact on many biological fields, they have generally not been applied with wide success in the field...... of glycobiology, primarily due to their low efficiencies, with resultant failure to impose substantial phenotypic consequences upon the final glycosylation products. Here, we review novel nuclease-based precision genome editing techniques enabling efficient and stable gene editing, including gene disruption...... by introducing single or double-stranded breaks at a defined genomic sequence. We here compare and contrast the different techniques and summarize their current applications, highlighting cases from the field of glycobiology as well as pointing to future opportunities. The emerging potential of precision gene...

  19. Beginning to edit physics

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, P.W.

    1995-02-01

    A physicist-turned-editor shows you the basics required for copyediting physics papers (physical quantities, symbols, units, scientific notation, the structure of mathematical expressions, the nature of graphs), and points the way to learning enough ``editorial physics`` to begin substantive editing.

  20. The Craft of Editing

    DEFF Research Database (Denmark)

    Moeran, Brian

    To edit is to make a choice, or series of choices. Will I write a rough draft of this essay in longhand, or hammer it out on my computer? If the latter, what font shall I use? Times New Roman, Book Antiqua, or Garamond? Once I get started, what style shall I adopt: realistic, confessional or impr...

  1. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

    DEFF Research Database (Denmark)

    Peng, Zhiyu; Cheng, Yanbing; Tan, Bertrand Chin-Ming

    2012-01-01

    a computational pipeline that carefully controls for false positives while calling RNA editing events from genome and whole-transcriptome data of the same individual. We identified 22,688 RNA editing events in noncoding genes and introns, untranslated regions and coding sequences of protein-coding genes. Most......RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed...... changes (∼93%) converted A to I(G), consistent with known editing mechanisms based on adenosine deaminase acting on RNA (ADAR). We also found evidence of other types of nucleotide changes; however, these were validated at lower rates. We found 44 editing sites in microRNAs (miRNAs), suggesting a potential...

  2. Fan edits and the legacy of The Phantom Edit

    Directory of Open Access Journals (Sweden)

    Joshua Wille

    2014-09-01

    Full Text Available A fan edit can generally be defined as an alternative version of a film or television text created by a fan. It offers a different viewing experience, much as a song remix offers a different listening experience. The contemporary wave of fan edits has emerged during the remix zeitgeist of digital media and at a time when digital video editing technology has become more affordable and popular. The increasing number of alternative versions of films and the works of revisionist Hollywood filmmakers such as George Lucas have contributed to a greater public understanding of cinema as a fluid medium instead of one that exists in a fixed form. The Phantom Edit (2000, a seminal fan edit based on Lucas's Star Wars Episode I: The Phantom Menace (1999, inspired new ranks of fan editors. However, critics have misunderstood fan edits as merely the work of disgruntled fans. In order to provide a critical and historical basis for studies in fan editing as a creative practice, I examine previous interpretations of fan edits in the context of relevant contemporary works, and I use an annotated chronology of The Phantom Edit to trace its influence on subsequent fan editing communities and uncover their relationship with intellectual property disputes.

  3. Understanding Physics, First Edition

    Science.gov (United States)

    Cummings, Karen; Laws, Priscilla W.; Redish, Edward F.; Cooney, Patrick J.

    2004-03-01

    Built on the foundations of Halliday, Resnick, and Walker's Fundamentals of Physics Sixth Edition, this text is designed to work with interactive learning strategies that are increasingly being used in physics instruction (for example, microcomputer-based labs, interactive lectures, etc. ). In doing so, it incorporates new approaches based upon Physics Education Research (PER), aligns with courses that use computer-based laboratory tools, and promotes Activity Based Physics in lectures, labs, and recitations.

  4. Interactive Metro Map Editing.

    Science.gov (United States)

    Wang, Yu-Shuen; Peng, Wan-Yu

    2016-02-01

    Manual editing of a metro map is essential because many aesthetic and readability demands in map generation cannot be achieved by using a fully automatic method. In addition, a metro map should be updated when new metro lines are developed in a city. Considering that manually designing a metro map is time-consuming and requires expert skills, we present an interactive editing system that considers human knowledge and adjusts the layout to make it consistent with user expectations. In other words, only a few stations are controlled and the remaining stations are relocated by our system. Our system supports both curvilinear and octilinear layouts when creating metro maps. It solves an optimization problem, in which even spaces, route straightness, and maximum included angles at junctions are considered to obtain a curvilinear result. The system then rotates each edge to extend either vertically, horizontally, or diagonally while approximating the station positions provided by users to generate an octilinear layout. Experimental results, quantitative and qualitative evaluations, and user studies show that our editing system is easy to use and allows even non-professionals to design a metro map.

  5. Revising and editing for translators

    CERN Document Server

    Mossop, Brian

    2014-01-01

    Revising and Editing for Translators provides guidance and learning materials for translation students learning to edit texts written by others, and professional translators wishing to improve their self-revision ability or learning to revise the work of others. Editing is understood as making corrections and improvements to texts, with particular attention to tailoring them to the given readership. Revising is this same task applied to draft translations. The linguistic work of editors and revisers is related to the professional situations in which they work. Mossop offers in-depth coverage of a wide range of topics, including copyediting, style editing, structural editing, checking for consistency, revising procedures and principles, and translation quality assessment. This third edition provides extended coverage of computer aids for revisers, and of the different degrees of revision suited to different texts. The inclusion of suggested activities and exercises, numerous real-world examples, a proposed gra...

  6. Nanoparticles for Site Specific Genome Editing

    Science.gov (United States)

    McNeer, Nicole Ali

    Triplex-forming peptide nucleic acids (PNAs) can be used to coordinate the recombination of short 50-60 by "donor DNA" fragments into genomic DNA, resulting in site-specific correction of genetic mutations or the introduction of advantageous genetic modifications. Site-specific gene editing in hematopoietic stem and progenitor cells (HSPCs) could result in treatment or cure of inherited disorders of the blood such as beta-thalassemia. Gene editing in HSPCs and differentiated T cells could help combat HIV/AIDs by modifying receptors, such as CCR5, necessary for R5-tropic HIV entry. However, translation of genome modification technologies to clinical practice is limited by challenges in intracellular delivery, especially in difficult-to-transfect hematolymphoid cells. In vivo gene editing could also provide novel treatment for systemic monogenic disorders such as cystic fibrosis, an autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane receptor. Here, we have engineered biodegradable nanoparticles to deliver oligonucleotides for site-specific genome editing of disease-relevant genes in human cells, with high efficiency, low toxicity, and editing of clinically relevant cell types. We designed nanoparticles to edit the human beta-globin and CCR5 genes in hematopoietic cells. We show that poly(lactic-co-glycolic acid) (PLGA) nanoparticles can delivery PNA and donor DNA for site-specific gene modification in human hematopoietic cells in vitro and in vivo in NOD-scid IL2rgammanull mice. Nanoparticles delivered by tail vein localized to hematopoietic compartments in the spleen and bone marrow of humanized mice, resulting in modification of the beta-globin and CCR5 genes. Modification frequencies ranged from 0.005 to 20% of cells depending on the organ and cell type, without detectable toxicity. This project developed highly versatile methods for delivery of therapeutics to hematolymphoid cells and hematopoietic stem cells, and will help to

  7. A co-CRISPR strategy for efficient genome editing in Caenorhabditis elegans.

    Science.gov (United States)

    Kim, Heesun; Ishidate, Takao; Ghanta, Krishna S; Seth, Meetu; Conte, Darryl; Shirayama, Masaki; Mello, Craig C

    2014-08-01

    Genome editing based on CRISPR (clustered regularly interspaced short palindromic repeats)-associated nuclease (Cas9) has been successfully applied in dozens of diverse plant and animal species, including the nematode Caenorhabditis elegans. The rapid life cycle and easy access to the ovary by micro-injection make C. elegans an ideal organism both for applying CRISPR-Cas9 genome editing technology and for optimizing genome-editing protocols. Here we report efficient and straightforward CRISPR-Cas9 genome-editing methods for C. elegans, including a Co-CRISPR strategy that facilitates detection of genome-editing events. We describe methods for detecting homologous recombination (HR) events, including direct screening methods as well as new selection/counterselection strategies. Our findings reveal a surprisingly high frequency of HR-mediated gene conversion, making it possible to rapidly and precisely edit the C. elegans genome both with and without the use of co-inserted marker genes.

  8. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    the previously available DNA binding templates, zinc fingers and meganucleases. Recently, the area experimented a quantum leap because of the introduction of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system (clustered regularly interspaced short palindromic...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  9. Video summarization and semantics editing tools

    Science.gov (United States)

    Xu, Li-Qun; Zhu, Jian; Stentiford, Fred

    2001-01-01

    This paper describes a video summarization and semantics editing tool that is suited for content-based video indexing and retrieval with appropriate human operator assistance. The whole system has been designed with a clear focus on the extraction and exploitation of motion information inherent in the dynamic video scene. The dominant motion information has ben used explicitly for shot boundary detection, camera motion characterization, visual content variations description, and for key frame extraction. Various contributions have been made to ensure that the system works robustly with complex scenes and across different media types. A window-based graphical user interface has been designed to make the task very easy for interactive analysis and editing of semantic events and episode where appropriate.

  10. Residential and Light Commercial HVAC. Teacher Edition and Student Edition. Second Edition.

    Science.gov (United States)

    Stephenson, David

    This package contains teacher and student editions of a residential and light commercial heating, ventilation, and air conditioning (HVAC) course of study. The teacher edition contains information on the following: using the publication; national competencies; competency profile; related academic and workplace skills list; tools, equipment, and…

  11. Introduction to Surgical Technology. Third Edition. Teacher Edition [and] Student Edition.

    Science.gov (United States)

    Bushey, Vicki; Hildebrand, Bob; Hildebrand, Dinah; Johnson, Dave; Sikes, John; Tahah, Ann; Walker, Susan; Zielsdorf, Lani

    These teacher and student editions provide instructional materials for an introduction to surgical technology course. Introductory materials in the teacher edition include information on use, instructional/task analysis, academic and workplace skill classifications and definitions, related academic and workplace skill list, and crosswalk to…

  12. Fundamentals of Welding. Teacher Edition [and] Student Edition [and] Student Workbook. Second Edition.

    Science.gov (United States)

    Fortney, Clarence; Gregory, Mike; New, Larry

    Teacher and student editions and a student workbook for fundamentals of welding comprise the first of six in a series of competency-based instructional materials for welding programs. Introductory pages in the teacher edition are training and competency profile, instructional/task analysis, basic skills icons and classifications, basic skills…

  13. Oxyacetylene Welding and Oxyfuel Cutting. Third Edition. Teacher Edition [and] Student Edition [and] Student Workbook.

    Science.gov (United States)

    Knapp, John; Harper, Eddie

    This Oklahoma curriculum guide, which includes a teacher edition, a student edition, and a student workbook, provides three units for a course on oxyacetylene welding, oxyfuel cutting, and cutting done with alternative fuels such as MAPP, propane, and natural gas. The three units are: "Oxyacetylene Welding"; "Oxyfuel Cutting";…

  14. Human BLCAP transcript: new editing events in normal and cancerous tissues.

    Science.gov (United States)

    Galeano, Federica; Leroy, Anne; Rossetti, Claudia; Gromova, Irina; Gautier, Philippe; Keegan, Liam P; Massimi, Luca; Di Rocco, Concezio; O'Connell, Mary A; Gallo, Angela

    2010-07-01

    Bladder cancer-associated protein (BLCAP) is a highly conserved protein among species, and it is considered a novel candidate tumor suppressor gene originally identified from human bladder carcinoma. However, little is known about the regulation or the function of this protein. Here, we show that the human BLCAP transcript undergoes multiple A-to-I editing events. Some of the new editing events alter the highly conserved amino terminus of the protein creating alternative protein isoforms by changing the genetically coded amino acids. We found that both ADAR1 and ADAR2-editing enzymes cooperate to edit this transcript and that different tissues displayed distinctive ratios of edited and unedited BLCAP transcripts. Moreover, we observed a general decrease in BLCAP-editing level in astrocytomas, bladder cancer and colorectal cancer when compared with the related normal tissues. The newly identified editing events, found to be downregulated in cancers, could be useful for future studies as a diagnostic tool to distinguish malignancies or epigenetic changes in different tumors.

  15. Tools of Radio Astronomy, 5th edition

    Science.gov (United States)

    Wilson, Thomas L.; Rohlfs, Kristian; Huttemeister, Susanne

    2012-12-01

    New 5th corrected edition of the book http://adsabs.harvard.edu/abs/2009tra..book.....W in Russian, translated by O. Verkhodanov and S. Trushkin, editing S.A. Trushkin from Special astrophysical observatory RAS. This edition contains the translation of the 5th Springer edition of 2009 and new additional chapter (wrote by authors) of Solutions of the problems.

  16. Water quality management library. 2. edition

    Energy Technology Data Exchange (ETDEWEB)

    Eckenfelder, W.W.; Malina, J.F.; Patterson, J.W. [eds.

    1998-12-31

    A series of ten books offered in conjunction with Water Quality International, the Biennial Conference and Exposition of the International Association on Water Pollution Research and Control (IAWPRC). Volume 1, Activated Sludge Process, Design and Control, 2nd edition, 1998: Volume 2, Upgrading Wastewater Treatment Plants, 2nd edition, 1998: Volume 3, Toxicity Reduction, 2nd edition, 1998: Volume 4, Municipal Sewage Sludge Management, 2nd edition, 1998: Volume 5, Design and Retrofit of Wastewater Treatment Plants for Biological Nutrient Removal, 1st edition, 1992: Volume 6, Dynamics and Control of the Activated Sludge Process, 2nd edition, 1998: Volume 7: Design of Anaerobic Processes for the Treatment of Industrial and Municipal Wastes, 1st edition, 1992: Volume 8, Groundwater Remediation, 1st edition, 1992: Volume 9, Nonpoint Pollution and Urban Stormwater Management, 1st edition, 1995: Volume 10, Wastewater Reclamation and Reuse, 1st edition, 1998.

  17. Modern Physics, 4th edition

    Science.gov (United States)

    Tipler, Paul A.; Llewellyn, Ralph

    The new edition of the classic text for the intermediate-level modern physics course, revised and updated to take students to the forefront of contemporary research and applications across the full spectrum of science and technology."

  18. Foundations of Mechanics, Second Edition

    OpenAIRE

    1987-01-01

    Preface to the Second Edition. Since the first edition of this book appeared in 1967, there has been a great deal of activity in the field of symplectic geometry and Hamiltonian systems. In addition to the recent textbooks of Arnold, Arnold-Avez, Godbillon, Guillemin-Sternberg, Siegel-Moser, and Souriau, there have been many research articles published. Two good collections are "Symposia Mathematica," vol. XIV, and "Géométrie Symplectique el Physique Mathématique," CNRS, Colloque Intern...

  19. Genome editing in cardiovascular diseases.

    Science.gov (United States)

    Strong, Alanna; Musunuru, Kiran

    2017-01-01

    Genome-editing tools, which include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems, have emerged as an invaluable technology to achieve somatic and germline genomic manipulation in cells and model organisms for multiple applications, including the creation of knockout alleles, introducing desired mutations into genomic DNA, and inserting novel transgenes. Genome editing is being rapidly adopted into all fields of biomedical research, including the cardiovascular field, where it has facilitated a greater understanding of lipid metabolism, electrophysiology, cardiomyopathies, and other cardiovascular disorders, has helped to create a wider variety of cellular and animal models, and has opened the door to a new class of therapies. In this Review, we discuss the applications of genome-editing technology throughout cardiovascular disease research and the prospect of in vivo genome-editing therapies in the future. We also describe some of the existing limitations of genome-editing tools that will need to be addressed if cardiovascular genome editing is to achieve its full scientific and therapeutic potential.

  20. A plant mitochondrial sequence transcribed in transgenic tobacco chloroplasts is not edited

    Energy Technology Data Exchange (ETDEWEB)

    Sutton, C.A.; Hanson, M.R. [Cornell Univ., Ithaca, NY (United States); Zoubenko, O.V.; Maliga, P. [State Univ. of New Jersey, Piscataway, NJ (United States)

    1995-03-01

    RNA editing occurs in two higher-plant organelles, chloroplasts, and mitochondria. Because chloroplasts and mitochondria exhibit some similarity in editing site selection, we investigated whether mitochondrial RNA sequences could be edited in chloroplasts. We produced transgenic tobacco plants that contained chimeric genes in which the second exon of a Petunia hybrida mitochondrial coxII gene was under the control of chloroplast gene regulatory sequences. coxII transcripts accumulated to low or high levels in transgenic chloroplasts containing chimeric genes with the plastid ribosomal protein gene rps16 or the rRNA operon promoter, respectively. Exon 2 of coxII was chosen because it carries seven editing sites and is edited in petunia mitochondria even when located in an abnormal context in an aberrant recombined gene. When editing of the coxII transcripts in transgenic chloroplasts was examined, no RNA editing at any of the usual sites was detected, nor was there any novel editing at any other sites. These results indicate that the RNA editing mechanisms of chloroplasts and mitochondria are not identical but must have at least some organelle-specific components. 33 refs., 5 figs.

  1. Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition.

    Science.gov (United States)

    Madina, Bhaskara R; Kumar, Vikas; Metz, Richard; Mooers, Blaine H M; Bundschuh, Ralf; Cruz-Reyes, Jorge

    2014-07-01

    Mitochondrial mRNAs in kinetoplastids require extensive U-insertion/deletion editing that progresses 3'-to-5' in small blocks, each directed by a guide RNA (gRNA), and exhibits substrate and developmental stage-specificity by unsolved mechanisms. Here, we address compositionally related factors, collectively known as the mitochondrial RNA-binding complex 1 (MRB1) or gRNA-binding complex (GRBC), that contain gRNA, have a dynamic protein composition, and transiently associate with several mitochondrial factors including RNA editing core complexes (RECC) and ribosomes. MRB1 controls editing by still unknown mechanisms. We performed the first next-generation sequencing study of native subcomplexes of MRB1, immunoselected via either RNA helicase 2 (REH2), that binds RNA and associates with unwinding activity, or MRB3010, that affects an early editing step. The particles contain either REH2 or MRB3010 but share the core GAP1 and other proteins detected by RNA photo-crosslinking. Analyses of the first editing blocks indicate an enrichment of several initiating gRNAs in the MRB3010-purified complex. Our data also indicate fast evolution of mRNA 3' ends and strain-specific alternative 3' editing within 3' UTR or C-terminal protein-coding sequence that could impact mitochondrial physiology. Moreover, we found robust specific copurification of edited and pre-edited mRNAs, suggesting that these particles may bind both mRNA and gRNA editing substrates. We propose that multiple subcomplexes of MRB1 with different RNA/protein composition serve as a scaffold for specific assembly of editing substrates and RECC, thereby forming the editing holoenzyme. The MRB3010-subcomplex may promote early editing through its preferential recruitment of initiating gRNAs.

  2. 3D Surface Editing Based on Level-Sets

    Institute of Scientific and Technical Information of China (English)

    Lin Maosong; Zhang Dianhua

    2005-01-01

    A novel method which integrates the topological flexibility of the level-set approach and the simphcity of point-sampled surfaces is proposed. The grid structure resulted from the level-set approach not only offers a wide range of powerful surface editing techniques for the point set surface editing, but also facilitates the topological change with ease. With the aid of point-based resampling,the method updates the surface shape of the point-based geometry quickly without worrying about point connectivity at all. The point set surface can also change its topology properly whenever a collision with other parts of itself is detected. The experiment demonstrates their effectiveness on several scanned objects and scan-converted models. Four examples of surface editing operations: smoothing, tapering, deforming, and Boolean operations, are presented.

  3. Connectivity editing for quadrilateral meshes

    KAUST Repository

    Peng, Chihan

    2011-12-01

    We propose new connectivity editing operations for quadrilateral meshes with the unique ability to explicitly control the location, orientation, type, and number of the irregular vertices (valence not equal to four) in the mesh while preserving sharp edges. We provide theoretical analysis on what editing operations are possible and impossible and introduce three fundamental operations to move and re-orient a pair of irregular vertices. We argue that our editing operations are fundamental, because they only change the quad mesh in the smallest possible region and involve the fewest irregular vertices (i.e., two). The irregular vertex movement operations are supplemented by operations for the splitting, merging, canceling, and aligning of irregular vertices. We explain how the proposed high-level operations are realized through graph-level editing operations such as quad collapses, edge flips, and edge splits. The utility of these mesh editing operations are demonstrated by improving the connectivity of quad meshes generated from state-of-art quadrangulation techniques.

  4. Connectivity editing for quadrilateral meshes

    KAUST Repository

    Peng, Chihan

    2011-12-12

    We propose new connectivity editing operations for quadrilateral meshes with the unique ability to explicitly control the location, orientation, type, and number of the irregular vertices (valence not equal to four) in the mesh while preserving sharp edges. We provide theoretical analysis on what editing operations are possible and impossible and introduce three fundamental operations to move and re-orient a pair of irregular vertices. We argue that our editing operations are fundamental, because they only change the quad mesh in the smallest possible region and involve the fewest irregular vertices (i.e., two). The irregular vertex movement operations are supplemented by operations for the splitting, merging, canceling, and aligning of irregular vertices. We explain how the proposed highlevel operations are realized through graph-level editing operations such as quad collapses, edge flips, and edge splits. The utility of these mesh editing operations are demonstrated by improving the connectivity of quad meshes generated from state-of-art quadrangulation techniques. © 2011 ACM.

  5. CTD writing and editing standards

    Science.gov (United States)

    Caruthers, C. M.

    1991-03-01

    The Computer and Telecommunication Division (CTD) recognizes that the communication of clear, accurate, reasonably complete information is essential to the success of its Laboratory mission. CTD therefore encourages all Division personnel to adhere to the principles of good writing and to the standards for grammar, usage, style, formats, and publication procedures that are described in CTD Writing and Editing Standards. We encourage CTD personnel to read CTD Writing and Editing Standards and to use it continually as a desktop reference. It will help CTD writers to produce better documents consistent with CTD standards in less time. Applying the principles specified in this document on how to write and organize technical information will speed up the editing, review, and revision processes. CTD Writing and Editing Standards complements the Argonne National Laboratory Technical Publications Guide, which serves as the basic Argonne documentation reference on issues concerning DOE orders and guidelines, NRC directives, and other sponsor requirements. However, this Laboratory-wide document does not address matters of grammar or style. Documents recommended in CTD Writing and Editing Standards are usually available for purchase at the Document Distribution Counter (Building 221, Room A-134) or through the mail (by calling extension 2-5405 and ordering copies).

  6. [Genome editing of industrial microorganism].

    Science.gov (United States)

    Zhu, Linjiang; Li, Qi

    2015-03-01

    Genome editing is defined as highly-effective and precise modification of cellular genome in a large scale. In recent years, such genome-editing methods have been rapidly developed in the field of industrial strain improvement. The quickly-updating methods thoroughly change the old mode of inefficient genetic modification, which is "one modification, one selection marker, and one target site". Highly-effective modification mode in genome editing have been developed including simultaneous modification of multiplex genes, highly-effective insertion, replacement, and deletion of target genes in the genome scale, cut-paste of a large DNA fragment. These new tools for microbial genome editing will certainly be applied widely, and increase the efficiency of industrial strain improvement, and promote the revolution of traditional fermentation industry and rapid development of novel industrial biotechnology like production of biofuel and biomaterial. The technological principle of these genome-editing methods and their applications were summarized in this review, which can benefit engineering and construction of industrial microorganism.

  7. Understanding Editing Behaviors in Multilingual Wikipedia.

    Science.gov (United States)

    Kim, Suin; Park, Sungjoon; Hale, Scott A; Kim, Sooyoung; Byun, Jeongmin; Oh, Alice H

    2016-01-01

    Multilingualism is common offline, but we have a more limited understanding of the ways multilingualism is displayed online and the roles that multilinguals play in the spread of content between speakers of different languages. We take a computational approach to studying multilingualism using one of the largest user-generated content platforms, Wikipedia. We study multilingualism by collecting and analyzing a large dataset of the content written by multilingual editors of the English, German, and Spanish editions of Wikipedia. This dataset contains over two million paragraphs edited by over 15,000 multilingual users from July 8 to August 9, 2013. We analyze these multilingual editors in terms of their engagement, interests, and language proficiency in their primary and non-primary (secondary) languages and find that the English edition of Wikipedia displays different dynamics from the Spanish and German editions. Users primarily editing the Spanish and German editions make more complex edits than users who edit these editions as a second language. In contrast, users editing the English edition as a second language make edits that are just as complex as the edits by users who primarily edit the English edition. In this way, English serves a special role bringing together content written by multilinguals from many language editions. Nonetheless, language remains a formidable hurdle to the spread of content: we find evidence for a complexity barrier whereby editors are less likely to edit complex content in a second language. In addition, we find that multilinguals are less engaged and show lower levels of language proficiency in their second languages. We also examine the topical interests of multilingual editors and find that there is no significant difference between primary and non-primary editors in each language.

  8. Understanding Editing Behaviors in Multilingual Wikipedia.

    Directory of Open Access Journals (Sweden)

    Suin Kim

    Full Text Available Multilingualism is common offline, but we have a more limited understanding of the ways multilingualism is displayed online and the roles that multilinguals play in the spread of content between speakers of different languages. We take a computational approach to studying multilingualism using one of the largest user-generated content platforms, Wikipedia. We study multilingualism by collecting and analyzing a large dataset of the content written by multilingual editors of the English, German, and Spanish editions of Wikipedia. This dataset contains over two million paragraphs edited by over 15,000 multilingual users from July 8 to August 9, 2013. We analyze these multilingual editors in terms of their engagement, interests, and language proficiency in their primary and non-primary (secondary languages and find that the English edition of Wikipedia displays different dynamics from the Spanish and German editions. Users primarily editing the Spanish and German editions make more complex edits than users who edit these editions as a second language. In contrast, users editing the English edition as a second language make edits that are just as complex as the edits by users who primarily edit the English edition. In this way, English serves a special role bringing together content written by multilinguals from many language editions. Nonetheless, language remains a formidable hurdle to the spread of content: we find evidence for a complexity barrier whereby editors are less likely to edit complex content in a second language. In addition, we find that multilinguals are less engaged and show lower levels of language proficiency in their second languages. We also examine the topical interests of multilingual editors and find that there is no significant difference between primary and non-primary editors in each language.

  9. Description scheme for video editing work

    Science.gov (United States)

    Ruiloba, Rosa I.; Joly, Philippe

    2001-03-01

    This article presents a Description Scheme (DS) to describe the audio-visual documents from the video editing work point of view. This DS is based on edition techniques used in the video edition domain. The main objective of this DS is to provide a complete, modular and extensible description of the structure of the video documents based on editing process. This VideoEditing DS is generic in the sense that it may be used in a large number of applications such as video document indexing and analysis, description of Edit Decision List and elaboration of editing patterns. It is based on accurate and complete definitions of shots and transition effects required for video document analysis applications. The VideoEditing DS allows three levels of description : analytic, synthetic and semantic. In the DS, the higher (resp. the lower) is the element of description, the more analytic (resp. synthetic) is the information. %Phil This DS allows describing the editing work made by editing boards, using more detailed descriptors of Shots and Transition DSs. These elements are provided to define editing patterns that allow several possible reconstructions of movies depending on, for example, the target audience. A part of the video description made with this DS may be automatically produced by the video to shots segmentation algorithms (analytic DSs ) or by editing software, at the same time the edition work is made. This DS gives an answer to the needs related to the exchange of editing work descriptions between editing softwares. At the same time, the same DS provide an analytic description of editing work which is complementary to existing standards for Edit Decision Lists like SMPTE or AAF.

  10. Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing.

    Science.gov (United States)

    Fukuda, Masatora; Kurihara, Kei; Yamaguchi, Shota; Oyama, Yui; Deshimaru, Masanobu

    2014-03-01

    Adenosine-to-inosine (A-to-I) RNA editing is an endogenous regulatory mechanism involved in various biological processes. Site-specific, editing-state-dependent degradation of target RNA may be a powerful tool both for analyzing the mechanism of RNA editing and for regulating biological processes. Previously, we designed an artificial hammerhead ribozyme (HHR) for selective, site-specific RNA cleavage dependent on the A-to-I RNA editing state. In the present work, we developed an improved strategy for constructing a trans-acting HHR that specifically cleaves target editing sites in the adenosine but not the inosine state. Specificity for unedited sites was achieved by utilizing a sequence encoding the intrinsic cleavage specificity of a natural HHR. We used in vitro selection methods in an HHR library to select for an extended HHR containing a tertiary stabilization motif that facilitates HHR folding into an active conformation. By using this method, we successfully constructed highly active HHRs with unedited-specific cleavage. Moreover, using HHR cleavage followed by direct sequencing, we demonstrated that this ribozyme could cleave serotonin 2C receptor (HTR2C) mRNA extracted from mouse brain, depending on the site-specific editing state. This unedited-specific cleavage also enabled us to analyze the effect of editing state at the E and C sites on editing at other sites by using direct sequencing for the simultaneous quantification of the editing ratio at multiple sites. Our approach has the potential to elucidate the mechanism underlying the interdependencies of different editing states in substrate RNA with multiple editing sites.

  11. Boneless Pose Editing and Animation

    DEFF Research Database (Denmark)

    Bærentzen, Jakob Andreas; Hansen, Kristian Evers; Erleben, Kenny

    2007-01-01

    In this paper, we propose a pose editing and animation method for triangulated surfaces based on a user controlled partitioning of the model into deformable parts and rigid parts which are denoted handles. In our pose editing system, the user can sculpt a set of poses simply by transforming...... the handles for each pose. Using Laplacian editing, the deformable parts are deformed to match the handles. In our animation system the user can constrain one or several handles in order to define a new pose. New poses are interpolated from the examples poses, by solving a small non-linear optimization...... problem in order to obtain the interpolation weights. While the system can be used simply for building poses, it is also an animation system. The user can specify a path for a given constraint and the model is animated correspondingly....

  12. A strategy for developing a hammerhead ribozyme for selective RNA cleavage depending on substitutional RNA editing

    OpenAIRE

    Fukuda, Masatora; Kurihara, Kei; Tanaka, Yasuyoshi; Deshimaru, Masanobu

    2012-01-01

    Engineered site-specific RNA cleavage is widely used for gene regulation, RNA mapping, and synthetic RNA production. Here the authors extend the range of engineered recognition selectivity to include cleavage of sequence motifs containing naturally occurring base modifications. They describe and implement a designer hammerhead ribozyme that cleaves a target sequence 1 nt from a site of adenosine to inosine (A-to-I) or cytosine to uracil (C-to-U) editing in synthetic or physiological mRNA cont...

  13. Gas Metal Arc Welding and Flux-Cored Arc Welding. Third Edition. Teacher Edition [and] Student Edition [and] Student Workbook.

    Science.gov (United States)

    Knapp, John; Harper, Eddie

    This packet, containing a teacher's edition, a student edition, and a student workbook, introduces students to high deposition welding and processes for "shielding" a weld. In addition to general information, the teacher edition consists of introductory pages and teacher pages, as well as unit information that corresponds to the…

  14. Gas Tungsten Arc Welding and Plasma Arc Cutting. Teacher Edition [and] Student Edition [and] Student Workbook. Second Edition.

    Science.gov (United States)

    Harper, Eddie; Knapp, John

    This packet of instructional materials for a gas tungsten arc welding (GTAW) and plasma arc cutting course is comprised of a teacher edition, student edition, and student workbook. The teacher edition consists of introductory pages and teacher pages. Introductory pages include training and competency profile, state duty/task crosswalk,…

  15. [An introduction on the editions of Zhang Gao's Yi shuo (Medical Narrations)].

    Science.gov (United States)

    Wang, Xuguang; Lu, Xiang

    2014-11-01

    Zhang Gao's Yi shuo (Medical Narrations) of the Southern Song Dynasty had 2 kinds of editions: domestic editions and foreign editions. The former includes 1 Song edition, 14 Ming editions, 3 Qing editions and 25 editions after the Republic of China. The latter, mainly 2 classes, the Japanese edition and Korean printing type edition. In the Ming Dynasty, the editions of Yi shuo generated 2 branches: inherited edition and supplementary edition. The inherited editions include Gu Dingfang's edition, Zhang Yaode's edition, Wu Mianxue's edition, Wu Zhongheng's edition, Wang Kentang's edition, editions from Si ku quan shu (Imperial Collection of Four), stereotype edition of the 3th year of Xuantong reign (1911) from Shanghai Civilization Bookstore, edition of the 2(nd) year of Manji of Japan etc. The supplemental editions include Zhang Zili's edition, Shen Fan's edition, Fu Feng'ao's edition, transcript of the late Ming Dynasty preserved in the Library of Peking University, and Korean printing type edition etc.

  16. Medical writing, revising and editing

    DEFF Research Database (Denmark)

    Pilegaard, Morten

    2006-01-01

    The globalization of science makes medical writing, editing and revision a rapidly growing field of linguistic study and practice. Medical science texts are written according to uniform, general guidelines and medical genres have become highly conventionalized in terms of structure and linguistic...... form. Medical editing often takes the form of peer review and mainly addresses issues of contents and overall validity. Medical revision incorporates the checking of the macrostructure and the microstructure of the text, its language and style and its suitability for the target reader or client...

  17. Beginning XML, 5th Edition

    CERN Document Server

    Fawcett, Joe; Quin, Liam R E

    2012-01-01

    A complete update covering the many advances to the XML language The XML language has become the standard for writing documents on the Internet and is constantly improving and evolving. This new edition covers all the many new XML-based technologies that have appeared since the previous edition four years ago, providing you with an up-to-date introductory guide and reference. Packed with real-world code examples, best practices, and in-depth coverage of the most important and relevant topics, this authoritative resource explores both the advantages and disadvantages of XML and addresses the mo

  18. Introducing ZBrush 3rd Edition

    CERN Document Server

    Keller, Eric

    2012-01-01

    Learn ZBrush inside and out with this updated new edition Get totally comfortable sculpting in a digital environment with the latest edition of this bestselling beginner's guide to ZBrush. Fully updated for the newest version of the software, ZBrush 4R3, this book dispels any fears you might have about the difficulty of using ZBrush and soon has you creating realistic, cartoon, and organic models with flair. Learn all the essentials, as you complete fun tutorials on painting, meshes, organic scripting, hard surface sculpting, lighting, rendering, and more. Introduces you to ZBrush, the sculpt

  19. Language Editing at Astronomy & Astrophysics

    Science.gov (United States)

    Adams, J.

    2011-07-01

    In 2002, the A&A Board of Directors voted that all articles must be written in English and decided to improve the overall quality of the language in the articles with the help of a team of language editors. This article reviews the general advantages of editing the English expression and describes both the aims of this effort and its place in the full publication process. This is followed by the Guide to language editing that has been available on the Journal's website for several years now.

  20. Genome editing comes of age.

    Science.gov (United States)

    Kim, Jin-Soo

    2016-09-01

    Genome editing harnesses programmable nucleases to cut and paste genetic information in a targeted manner in living cells and organisms. Here, I review the development of programmable nucleases, including zinc finger nucleases (ZFNs), TAL (transcription-activator-like) effector nucleases (TALENs) and CRISPR (cluster of regularly interspaced palindromic repeats)-Cas9 (CRISPR-associated protein 9) RNA-guided endonucleases (RGENs). I specifically highlight the key advances that set the foundation for the rapid and widespread implementation of CRISPR-Cas9 genome editing approaches that has revolutionized the field.

  1. Delivery technologies for genome editing.

    Science.gov (United States)

    Yin, Hao; Kauffman, Kevin J; Anderson, Daniel G

    2017-03-24

    With the recent development of CRISPR technology, it is becoming increasingly easy to engineer the genome. Genome-editing systems based on CRISPR, as well as transcription activator-like effector nucleases (TALENs) and zinc-finger nucleases (ZFNs), are becoming valuable tools for biomedical research, drug discovery and development, and even gene therapy. However, for each of these systems to effectively enter cells of interest and perform their function, efficient and safe delivery technologies are needed. This Review discusses the principles of biomacromolecule delivery and gene editing, examines recent advances and challenges in non-viral and viral delivery methods, and highlights the status of related clinical trials.

  2. Investigating RNA editing factors from trypanosome mitochondria

    Science.gov (United States)

    Aphasizheva, Inna; Zhang, Liye; Aphasizhev, Ruslan

    2016-01-01

    Mitochondrial U-insertion/deletion mRNA editing is carried out by two principal multiprotein assemblies, enzymatic RNA editing core (RECC) and RNA editing substrate binding (RESC) complexes, and a plethora of auxiliary factors. An integral part of mitochondrial gene expression, editing receives inputs from primary mRNA and gRNA precursor processing pathways, and generates substrates for mRNA polyadenylation and translation. Although nearly all RECC-embedded enzymes have been implicated in specific editing reactions, the majority of proteins that populate the RESC are also essential for generating edited mRNAs. However, lack of recognizable motifs in RESC subunits limits the prowess of bioinformatics in guiding biochemical experiments and elucidating their specific biological functions. In this chapter, we describe a generic workflow for investigating mitochondrial mRNA editing in Trypanosoma brucei and focus on several methods that proved instrumental is assigning definitive functions to editing factors lacking known signature sequences. PMID:27020893

  3. Power Product Equipment Technician: Equipment Systems. Teacher Edition. Student Edition.

    Science.gov (United States)

    Hilley, Robert

    This packet contains teacher and student editions on the topic of equipment systems, intended for the preparation of power product equipment technicians. This publication contains seven units: (1) principles of power transmission; (2) mechanical drive systems; (3) principles of fluid power; (4) hydraulic and pneumatic drive systems; (5) wheel and…

  4. Human Genome Editing and Ethical Considerations.

    Science.gov (United States)

    Krishan, Kewal; Kanchan, Tanuj; Singh, Bahadur

    2016-04-01

    Editing human germline genes may act as boon in some genetic and other disorders. Recent editing of the genome of the human embryo with the CRISPR/Cas9 editing tool generated a debate amongst top scientists of the world for the ethical considerations regarding its effect on the future generations. It needs to be seen as to what transformation human gene editing brings to humankind in the times to come.

  5. Strategies of Qualitative Inquiry. Third Edition

    Science.gov (United States)

    Denzin, Norman K., Ed.; Lincoln, Yvonna S., Ed.

    2007-01-01

    "Strategies of Qualitative Inquiry, Third Edition," the second volume in the paperback version of "The SAGE Handbook of Qualitative Research, 3rd Edition," consists of Part III of the handbook ("Strategies of Inquiry"). "Strategies of Qualitative Inquiry, Third Edition" presents the major tactics--historically, the research methods--that…

  6. Teaching Students to Self-Edit.

    Science.gov (United States)

    Ferris, Dana

    1995-01-01

    Emphasizes the need for students to develop their editing skills. This article suggests that teachers and students should concentrate on major error patterns, and teachers should personalize editing instruction. Attention should also be given to the most frequent and glaring errors. Students who followed this editing approach significantly reduced…

  7. Testing post-editing guidelines

    DEFF Research Database (Denmark)

    Flanagan, Marian; Christensen, Tina Paulsen

    2014-01-01

    There is a growing interest in machine translation (MT) and post-editing (PE). MT has been around for decades, but the use of the technology has grown significantly in the language industry in recent years, while PE is still a relatively new task. Consequently, there are currently no standard PE ...

  8. Veterinary Microbiology, 3rd Edition

    Science.gov (United States)

    Veterinary Microbiology, Third Edition is organized into four sections and begins with an updated and expanded introductory section on infectious disease pathogenesis, diagnosis and clinical management. The second section covers bacterial and fungal pathogens, and the third section describes viral d...

  9. Money and Schools. Fifth Edition

    Science.gov (United States)

    Thompson, David C.; Crampton, Faith E.; Wood, R. Craig

    2012-01-01

    In the new edition of this essential, all-inclusive text, the authors provide more important research for future principals and others enrolled in graduate-level school finance courses. Written in a style that is highly readable, the book offers strong connections to real-world experiences. Readers get both a broad overview of funding concepts and…

  10. Efficient Video Editing for Mobile Applications

    Directory of Open Access Journals (Sweden)

    Ignasi Vegas Pajaro

    2017-01-01

    Full Text Available Recording, storing and sharing video content has become one of the most popular usages of smartphones. This has resulted in demand for video editing apps that the users can use to edit their videos before sharing on various social networks. This study describes a technique to create a video editing application that uses the processing power of both GPU and CPU to process various editing tasks. The results and subsequent discussion shows that using the processing power of both the GPU and CPU in the video editing process makes the application much more time-efficient and responsive as compared to just the CPU-based processing.

  11. Electromagnetic Fields, 2nd Edition

    Science.gov (United States)

    Wangsness, Roald K.

    1986-07-01

    This revised edition provides patient guidance in its clear and organized presentation of problems. It is rich in variety, large in number and provides very careful treatment of relativity. One outstanding feature is the inclusion of simple, standard examples demonstrated in different methods that will allow students to enhance and understand their calculating abilities. There are over 145 worked examples; virtually all of the standard problems are included.

  12. Strategic Leadership Primer (Third Edition)

    Science.gov (United States)

    2010-01-01

    Meinhart, while also acknowledging previous edition contributions from Dr� Lenny Wong, Dr� Craig Bullis , and Colonel (Ret) George Reed� 1 CHAPTER 1...the cyber war� Although the strategies are different between commercial and government entities, at the end of the day both seek competitive...and everyone else—to 140 characters per tweet, and he tweets once or more almost daily�4 400 million people have established accounts on Facebook �5

  13. Editing as a psychological practice.

    Science.gov (United States)

    Beebe, John

    2006-06-01

    The experience of the Jungian analyst in the role of editor of manuscripts by creative colleagues is examined. Historical precedents include Michael Fordham's editorial correspondence with Jung around the latter's synchronicity essay; Jung's handling of manuscripts submitted by Sabina Spielrein to the Jahrbuch für psychoanalytische und psychopathologische Forschungen and various authors to the Zentralblatt für Psychotherapie und ihre Grenzgebiete, and the author's close editing of a paper submitted by Andrew Samuels to the Journal of Analytical Psychology. In addition to mustering an adequate amount of generosity, erudition, and availability, the analytic editor must know how to clarify a psychological argument and to gauge the psychological impact of the written text. Notwithstanding transference/countertransference phenomena that can emerge around issues of competition, envy, and territoriality when author and editor are also fellow-authors working in the same field, the editor needs to be comfortable about serving as the author's selfobject and midwife. From an analytic perspective, although communicating decisions about the best way to put ideas into words can sometimes attract transference to the editor, the more profound transference that analysts experience in the editing situation is toward the text being edited, which helps to motivate donated time spent caring for journal manuscripts.

  14. RNA Editing in Plant Mitochondria

    Science.gov (United States)

    Hiesel, Rudolf; Wissinger, Bernd; Schuster, Wolfgang; Brennicke, Axel

    1989-12-01

    Comparative sequence analysis of genomic and complementary DNA clones from several mitochondrial genes in the higher plant Oenothera revealed nucleotide sequence divergences between the genomic and the messenger RNA-derived sequences. These sequence alterations could be most easily explained by specific post-transcriptional nucleotide modifications. Most of the nucleotide exchanges in coding regions lead to altered codons in the mRNA that specify amino acids better conserved in evolution than those encoded by the genomic DNA. Several instances show that the genomic arginine codon CGG is edited in the mRNA to the tryptophan codon TGG in amino acid positions that are highly conserved as tryptophan in the homologous proteins of other species. This editing suggests that the standard genetic code is used in plant mitochondria and resolves the frequent coincidence of CGG codons and tryptophan in different plant species. The apparently frequent and non-species-specific equivalency of CGG and TGG codons in particular suggests that RNA editing is a common feature of all higher plant mitochondria.

  15. Connectivity editing for quad-dominant meshes

    KAUST Repository

    Peng, Chihan

    2013-08-01

    We propose a connectivity editing framework for quad-dominant meshes. In our framework, the user can edit the mesh connectivity to control the location, type, and number of irregular vertices (with more or fewer than four neighbors) and irregular faces (non-quads). We provide a theoretical analysis of the problem, discuss what edits are possible and impossible, and describe how to implement an editing framework that realizes all possible editing operations. In the results, we show example edits and illustrate the advantages and disadvantages of different strategies for quad-dominant mesh design. © 2013 The Author(s) Computer Graphics Forum © 2013 The Eurographics Association and John Wiley & Sons Ltd.

  16. A potential role for NF1 mRNA editing in the pathogenesis of NF1 tumors

    Energy Technology Data Exchange (ETDEWEB)

    Cappione, A.J.; French, B.L.; Skuse, G.R. [Univ. of Rochester School of Medicine and Dentistry, NY (United States)

    1997-02-01

    Neurofibromatosis type I (NF1) is a common disorder that predisposes to neoplasia in tissues derived from the embryonic neural crest. The NF1 gene encodes a tumor suppressor that most likely acts through the interaction of its GTPase-activating protein (GAP)-related domain (GRD) with the product of the ras protooncogene. We have previously identified a site in the NF1 mRNA, within the first half of the NF1 GRD, which undergoes base-modification editing. Editing at that site changes a C to a U, thereby introducing an in-frame stop codon. NF1 RNA editing has been detected in all cell types studied, to date. In order to investigate the role played by editing in NF1 tumorigenesis, we analyzed RNA from 19 NF1 and 4 non-NF1 tumors. We observed varying levels of NF1 mRNA editing in different tumors, with a higher range of editing levels in more malignant tumors (e.g., neurofibrosarcomas) compared to benign tumors (cutaneous neurofibromas). Plexiform neurofibromas have an intermediate range of levels of NF1 mRNA editing. We also compared tumor and nontumor tissues from several NF1 individuals, to determine the extent of variability present in the constitutional levels of NF1 mRNA editing and to determine whether higher levels are present in tumors. The constitutional levels of NF1 mRNA editing varied slightly but were consistent with the levels observed in non-NF1 individuals. In every case, there was a greater level of NF1 mRNA editing in the tumor than in the nontumor tissue from the same patient. These results suggest that inappropriately high levels of NF1 mRNA editing does play a role in NF1 tumorigenesis and that editing may result in the functional equivalent of biallelic inactivation of the NF1 tumor suppressor. 24 refs., 4 figs., 2 tabs.

  17. Review on Urban Sociology(2nd Edition)

    Institute of Scientific and Technical Information of China (English)

    Liu; Yuting; Li; Caige

    2016-01-01

    Urban Sociology(2nd Edition)Author:Gu Chaolin,Liu Jiayan,et al.Year:2013Publisher:Tsinghua University Press ISBN:9787302337591(446 pages,in Chinese)Urban Sociology is a textbook edited by Gu Chaolin,a wellk now n schola r of u rba n st udies i n Ch i na,a nd published by Tsinghua University Press in 2013.The first edition of this book,

  18. Operational Transformation In Co-Operative Editing

    Directory of Open Access Journals (Sweden)

    Mandeep Kaur

    2015-08-01

    Full Text Available Cooperative Editing Systems in real-time allows a virtual team to view and edit a shared document at the same time. The document shared must be synchronized in order to ensure consistency for all the participants. This paper describes the Operational Transformation the evolution of its techniques its various applications major issues and achievements. In addition this paper will present working of a platform where two users can edit a code programming file at the same time.

  19. Operational Transformation In Co-Operative Editing

    OpenAIRE

    Mandeep Kaur; Manpreet Singh; Harneet Kaur; Simran Kaur

    2015-01-01

    Cooperative Editing Systems in real-time allows a virtual team to view and edit a shared document at the same time. The document shared must be synchronized in order to ensure consistency for all the participants. This paper describes the Operational Transformation the evolution of its techniques its various applications major issues and achievements. In addition this paper will present working of a platform where two users can edit a code programming file at the same time.

  20. Parallel Evolution and Lineage-Specific Expansion of RNA Editing in Ctenophores

    Science.gov (United States)

    Kohn, Andrea B.; Sanford, Rachel S.; Yoshida, Masa-aki; Moroz, Leonid L.

    2015-01-01

    RNA editing is a process of targeted alterations of nucleotides in all types of RNA molecules (e.g., rRNA, tRNA, mRNA, and miRNA). As a result, the transcriptional output differs from its genomic DNA template. RNA editing can be defined both by biochemical mechanisms and by enzymes that perform these reactions. There are high levels of RNA editing detected in the mammalian nervous system, suggesting that nervous systems use this mechanism to increase protein diversity, because the post-transcription modifications lead to new gene products with novel functions. By re-annotating the ctenophore genomes, we found that the number of predicted RNA-editing enzymes is comparable to the numbers in mammals, but much greater than in other non-bilaterian basal metazoans. However, the overall molecular diversity of RNA-editing enzymes in ctenophores is lower, suggesting a possible “compensation” by an expansion of the ADAT1-like subfamily in this lineage. In two genera of ctenophores, Pleurobrachia and Mnemiopsis, there are high levels of expression for RNA-editing enzymes in their aboral organs, the integrative center involved in control of locomotion and geotaxis. This finding supports the hypothesis that RNA editing is correlated with the complexity of tissues and behaviors. Smaller numbers of RNA-editing enzymes in Porifera and Placozoa also correlates with the primary absence of neural and muscular systems in these lineages. In ctenophores, the expansion of the RNA-editing machinery can also provide mechanisms that support the remarkable capacity for regeneration in these animals. In summary, despite their compact genomes, a wide variety of epigenomic mechanisms employed by ctenophores and other non-bilaterian basal metazoans can provide novel insights into the evolutionary origins of biological novelties. PMID:26089435

  1. Digital PCR to assess gene-editing frequencies (GEF-dPCR) mediated by designer nucleases.

    Science.gov (United States)

    Mock, Ulrike; Hauber, Ilona; Fehse, Boris

    2016-03-01

    Genome editing using designer nucleases such as transcription activator-like effector nucleases (TALENs) or clustered regularly interspersed short palindromic repeats (CRISPR)-Cas9 nucleases is an emerging technology in basic and applied research. Whereas the application of editing tools, namely CRISPR-Cas9, has recently become very straightforward, quantification of resulting gene knockout rates still remains a bottleneck. This is particularly true if the product of a targeted gene is not easily detectable. To address this problem, we devised a novel gene-editing frequency digital PCR (GEF-dPCR) technique. GEF-dPCR exploits two differently labeled probes that are placed within one amplicon at the gene-editing target site to simultaneously detect wild-type and nonhomologous end-joining (NHEJ)-affected alleles. Taking advantage of the principle of dPCR, this enables concurrent quantification of edited and wild-type alleles in a given sample. We propose that our method is optimal for the monitoring of gene-edited cells in vivo, e.g., in clinical settings. Here we describe preparation, design of primers and probes, and setup and analysis of GEF-dPCR. The setup of GEF-dPCR requires up to 2 weeks (depending on the starting point); once the dPCR has been established, the protocol for sample analysis takes <1 d.

  2. Fuel Cell Handbook, Fourth Edition

    Energy Technology Data Exchange (ETDEWEB)

    Stauffer, D.B; Hirschenhofer, J.H.; Klett, M.G.; Engleman, R.R.

    1998-11-01

    Robust progress has been made in fuel cell technology since the previous edition of the Fuel Cell Handbook was published in January 1994. This Handbook provides a foundation in fuel cells for persons wanting a better understanding of the technology, its benefits, and the systems issues that influence its application. Trends in technology are discussed, including next-generation concepts that promise ultra high efficiency and low cost, while providing exceptionally clean power plant systems. Section 1 summarizes fuel cell progress since the last edition and includes existing power plant nameplate data. Section 2 addresses the thermodynamics of fuel cells to provide an understanding of fuel cell operation at two levels (basic and advanced). Sections 3 through 6 describe the four major fuel cell types and their performance based on cell operating conditions. The section on polymer electrolyte membrane fuel cells has been added to reflect their emergence as a significant fuel cell technology. Phosphoric acid, molten carbonate, and solid oxide fuel cell technology description sections have been updated from the previous edition. New information indicates that manufacturers have stayed with proven cell designs, focusing instead on advancing the system surrounding the fuel cell to lower life cycle costs. Section 7, Fuel Cell Systems, has been significantly revised to characterize near-term and next-generation fuel cell power plant systems at a conceptual level of detail. Section 8 provides examples of practical fuel cell system calculations. A list of fuel cell URLs is included in the Appendix. A new index assists the reader in locating specific information quickly.

  3. Repfinder: Finding approximately repeated scene elements for image editing

    KAUST Repository

    Cheng, Ming-Ming

    2010-07-26

    Repeated elements are ubiquitous and abundant in both manmade and natural scenes. Editing such images while preserving the repetitions and their relations is nontrivial due to overlap, missing parts, deformation across instances, illumination variation, etc. Manually enforcing such relations is laborious and error-prone. We propose a novel framework where user scribbles are used to guide detection and extraction of such repeated elements. Our detection process, which is based on a novel boundary band method, robustly extracts the repetitions along with their deformations. The algorithm only considers the shape of the elements, and ignores similarity based on color, texture, etc. We then use topological sorting to establish a partial depth ordering of overlapping repeated instances. Missing parts on occluded instances are completed using information from other instances. The extracted repeated instances can then be seamlessly edited and manipulated for a variety of high level tasks that are otherwise difficult to perform. We demonstrate the versatility of our framework on a large set of inputs of varying complexity, showing applications to image rearrangement, edit transfer, deformation propagation, and instance replacement. © 2010 ACM.

  4. APP Snrinn Edition Kicks Off

    Institute of Scientific and Technical Information of China (English)

    Tang Rong

    2012-01-01

    When European textile insiders still take delight in talking about the last apparel sourcing show in September 2011, the debut of APP Spring edition bring people back to the Le Bourget Expo Center, with entire passion. The 7th APP Show, sponsored by China National Textile and Apparel Council (CNTAC), organized by the Sub-Council of Textile Industry, China Council for the Promotion of International Trade (CCPIT TEX), China National Garment Association and Messe Frankfurt French Subsidiary, was on display from Feb 13th to 16th 2012,

  5. Biocommunication and natural genome editing

    Institute of Scientific and Technical Information of China (English)

    Guenther; Witzany

    2010-01-01

    The biocommunicative approach investigates communication processes within and among cells,tissues,organs and organisms as sign-mediated interactions,and nucleotide sequences as code,i.e.language-like text,which follows in parallel three kinds of rules:combinatorial (syntactic),context-sensitive(pragmatic),and contentspecific(semantic).Natural genome editing from a bio-communicative perspective is competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements and the ability to(re-)combine and(re-)regulate them according to context-dependent(i.e.adaptational) purposes of the host organism.

  6. GPU Computing Gems Emerald Edition

    CERN Document Server

    Hwu, Wen-mei W

    2011-01-01

    ".the perfect companion to Programming Massively Parallel Processors by Hwu & Kirk." -Nicolas Pinto, Research Scientist at Harvard & MIT, NVIDIA Fellow 2009-2010 Graphics processing units (GPUs) can do much more than render graphics. Scientists and researchers increasingly look to GPUs to improve the efficiency and performance of computationally-intensive experiments across a range of disciplines. GPU Computing Gems: Emerald Edition brings their techniques to you, showcasing GPU-based solutions including: Black hole simulations with CUDA GPU-accelerated computation and interactive display of

  7. Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity.

    Science.gov (United States)

    Tycko, Josh; Myer, Vic E; Hsu, Patrick D

    2016-08-04

    Advances in the development of delivery, repair, and specificity strategies for the CRISPR-Cas9 genome engineering toolbox are helping researchers understand gene function with unprecedented precision and sensitivity. CRISPR-Cas9 also holds enormous therapeutic potential for the treatment of genetic disorders by directly correcting disease-causing mutations. Although the Cas9 protein has been shown to bind and cleave DNA at off-target sites, the field of Cas9 specificity is rapidly progressing, with marked improvements in guide RNA selection, protein and guide engineering, novel enzymes, and off-target detection methods. We review important challenges and breakthroughs in the field as a comprehensive practical guide to interested users of genome editing technologies, highlighting key tools and strategies for optimizing specificity. The genome editing community should now strive to standardize such methods for measuring and reporting off-target activity, while keeping in mind that the goal for specificity should be continued improvement and vigilance.

  8. RNA Editing and Its Molecular Mechanism in Plant Organelles

    OpenAIRE

    2016-01-01

    RNA editing by cytidine (C) to uridine (U) conversions is widespread in plant mitochondria and chloroplasts. In some plant taxa, “reverse” U-to-C editing also occurs. However, to date, no instance of RNA editing has yet been reported in green algae and the complex thalloid liverworts. RNA editing may have evolved in early land plants 450 million years ago. However, in some plant species, including the liverwort, Marchantia polymorpha, editing may have been lost during evolution. Most RNA edit...

  9. Efficient Communication Protocols for Deciding Edit Distance

    DEFF Research Database (Denmark)

    Jowhari, Hossein

    2012-01-01

    Parsing method of [5,6] in combination with the Karp-Rabin fingerprints. In addition to yielding non-trivial bounds for the edit distance problem, this paper suggest a new conceptual framework and raises new questions regarding the embeddability of edit distance into the Hamming cube which might...

  10. Tax Justice Focus – The Whistleblower edition

    OpenAIRE

    Young, M A; Tax Justice Network

    2015-01-01

    Guest edited by Mary Alice Young of the University of the West of England, this edition is both an exploration of the difficulties confronting people who want to blow the whistle on companies engaged in providing financial services, and an acknowledgment of their personal courage.

  11. Books in Action: The Armed Services Editions.

    Science.gov (United States)

    Cole, John Y., Ed.

    In an effort to reach a wide audience, the Center for the Book in the Library of Congress presents this book in honor of the 40th anniversary celebration of the Armed Services Editions (ASE), the paperback books distributed during World War II. The titles of the essays and their authors are as follows: "The Armed Services Editions: An…

  12. Accounting for Independent Schools. Second Edition.

    Science.gov (United States)

    National Association of Independent Schools, Boston, MA.

    This is a thoroughly revised edition of the 1969 publication, "Accounting for Independent Schools," a guide that attempted to codify basic accounting principles and practices for specific application to independent schools. The focus of the second edition is more on refining practices than on initiating them, and more on extending the managerial…

  13. Non-GMO genetically edited crop plants.

    Science.gov (United States)

    Kanchiswamy, Chidananda Nagamangala; Malnoy, Mickael; Velasco, Riccardo; Kim, Jin-Soo; Viola, Roberto

    2015-09-01

    Direct delivery of purified Cas9 protein with guide RNA into plant cells, as opposed to plasmid-mediated delivery, displays high efficiency and reduced off-target effects. Following regeneration from edited cells, the ensuing plant is also likely to bypass genetically modified organism (GMO) legislation as the genome editing complex is degraded in the recipient cells.

  14. Applications of genome editing in insects

    Science.gov (United States)

    Insect genome editing was first reported 1991 in Drosophila melanogaster but the technology used was not portable to other species. Not until the recent development of facile, engineered DNA endonuclease systems has gene editing become widely available to insect scientists. Most applications in inse...

  15. Caution required for handling genome editing technology.

    Science.gov (United States)

    Araki, Motoko; Nojima, Kumie; Ishii, Tetsuya

    2014-05-01

    Genome-editing technology, although a robust tool for genetic engineering, is creating indistinct regulatory boundaries between naturally occurring and modified organisms. However, researchers must act with caution in research and development to avoid misleading society. Furthermore, appropriate regulations should be proactively discussed and established for handling genome-editing technology.

  16. Profs, Professionals Agree about Students' Editing Skills.

    Science.gov (United States)

    Fee, Frank; Russial, John; Auman Ann

    2003-01-01

    Considers where journalism educators should focus when they design editing curriculum. Examines what professors say is important for students to know about editing. Compares what professors at accredited programs say about necessary skills with what professional copy editors say is important. Concludes that professors and professionals are largely…

  17. Editing Technical Proposals (The Friendly Editor).

    Science.gov (United States)

    Bush, Don

    1994-01-01

    Makes suggestions for editing technical proposals. Discusses the marketeers, the hierarchy of hype, how to save days, managing story boards, expediting a laborious process, teaching engineers to write, writing incrementally, the art group, and the editing task. Argues that the best proposals come from starting to write early. (SR)

  18. A New Perspective on Peer Editing.

    Science.gov (United States)

    Amores, Maria J.

    1997-01-01

    Describes the peer-editing behaviors of eight undergraduate students in a third-year Spanish composition and grammar review course. Data collected over four months through interviews, participant observation, artifact inventories, and questionnaires revealed a strong tendency among informants to define the peer-editing process in social and…

  19. Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases.

    Science.gov (United States)

    Renaud, Jean-Baptiste; Boix, Charlotte; Charpentier, Marine; De Cian, Anne; Cochennec, Julien; Duvernois-Berthet, Evelyne; Perrouault, Loïc; Tesson, Laurent; Edouard, Joanne; Thinard, Reynald; Cherifi, Yacine; Menoret, Séverine; Fontanière, Sandra; de Crozé, Noémie; Fraichard, Alexandre; Sohm, Frédéric; Anegon, Ignacio; Concordet, Jean-Paul; Giovannangeli, Carine

    2016-03-08

    Genome editing has now been reported in many systems using TALEN and CRISPR-Cas9 nucleases. Precise mutations can be introduced during homology-directed repair with donor DNA carrying the wanted sequence edit, but efficiency is usually lower than for gene knockout and optimal strategies have not been extensively investigated. Here, we show that using phosphorothioate-modified oligonucleotides strongly enhances genome editing efficiency of single-stranded oligonucleotide donors in cultured cells. In addition, it provides better design flexibility, allowing insertions more than 100 bp long. Despite previous reports of phosphorothioate-modified oligonucleotide toxicity, clones of edited cells are readily isolated and targeted sequence insertions are achieved in rats and mice with very high frequency, allowing for homozygous loxP site insertion at the mouse ROSA locus in particular. Finally, when detected, imprecise knockin events exhibit indels that are asymmetrically positioned, consistent with genome editing taking place by two steps of single-strand annealing.

  20. Adaptive sampling for mesh spectrum editing

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiang-jun; ZHANG Hong-xin; BAO Hu-jun

    2006-01-01

    A mesh editing framework is presented in this paper, which integrates Free-Form Deformation (FFD) and geometry signal processing. By using simplified model from original mesh, the editing task can be accomplished with a few operations. We take the deformation of the proxy and the position coordinates of the mesh models as geometry signal. Wavelet analysis is employed to separate local detail information gracefully. The crucial innovation of this paper is a new adaptive regular sampling approach for our signal analysis based editing framework. In our approach, an original mesh is resampled and then refined iteratively which reflects optimization of our proposed spectrum preserving energy. As an extension of our spectrum editing scheme,the editing principle is applied to geometry details transferring, which brings satisfying results.

  1. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

    Directory of Open Access Journals (Sweden)

    Masfique Mehedi

    Full Text Available Ebolavirus (EBOV, the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen.

  2. Fuel Cell Handbook, Fifth Edition

    Energy Technology Data Exchange (ETDEWEB)

    Energy and Environmental Solutions

    2000-10-31

    Progress continues in fuel cell technology since the previous edition of the Fuel Cell Handbook was published in November 1998. Uppermost, polymer electrolyte fuel cells, molten carbonate fuel cells, and solid oxide fuel cells have been demonstrated at commercial size in power plants. The previously demonstrated phosphoric acid fuel cells have entered the marketplace with more than 220 power plants delivered. Highlighting this commercial entry, the phosphoric acid power plant fleet has demonstrated 95+% availability and several units have passed 40,000 hours of operation. One unit has operated over 49,000 hours. Early expectations of very low emissions and relatively high efficiencies have been met in power plants with each type of fuel cell. Fuel flexibility has been demonstrated using natural gas, propane, landfill gas, anaerobic digester gas, military logistic fuels, and coal gas, greatly expanding market opportunities. Transportation markets worldwide have shown remarkable interest in fuel cells; nearly every major vehicle manufacturer in the U.S., Europe, and the Far East is supporting development. This Handbook provides a foundation in fuel cells for persons wanting a better understanding of the technology, its benefits, and the systems issues that influence its application. Trends in technology are discussed, including next-generation concepts that promise ultrahigh efficiency and low cost, while providing exceptionally clean power plant systems. Section 1 summarizes fuel cell progress since the last edition and includes existing power plant nameplate data. Section 2 addresses the thermodynamics of fuel cells to provide an understanding of fuel cell operation at two levels (basic and advanced). Sections 3 through 8 describe the six major fuel cell types and their performance based on cell operating conditions. Alkaline and intermediate solid state fuel cells were added to this edition of the Handbook. New information indicates that manufacturers have stayed

  3. BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment.

    Science.gov (United States)

    Boel, Annekatrien; Steyaert, Woutert; De Rocker, Nina; Menten, Björn; Callewaert, Bert; De Paepe, Anne; Coucke, Paul; Willaert, Andy

    2016-07-27

    Targeted mutagenesis by the CRISPR/Cas9 system is currently revolutionizing genetics. The ease of this technique has enabled genome engineering in-vitro and in a range of model organisms and has pushed experimental dimensions to unprecedented proportions. Due to its tremendous progress in terms of speed, read length, throughput and cost, Next-Generation Sequencing (NGS) has been increasingly used for the analysis of CRISPR/Cas9 genome editing experiments. However, the current tools for genome editing assessment lack flexibility and fall short in the analysis of large amounts of NGS data. Therefore, we designed BATCH-GE, an easy-to-use bioinformatics tool for batch analysis of NGS-generated genome editing data, available from https://github.com/WouterSteyaert/BATCH-GE.git. BATCH-GE detects and reports indel mutations and other precise genome editing events and calculates the corresponding mutagenesis efficiencies for a large number of samples in parallel. Furthermore, this new tool provides flexibility by allowing the user to adapt a number of input variables. The performance of BATCH-GE was evaluated in two genome editing experiments, aiming to generate knock-out and knock-in zebrafish mutants. This tool will not only contribute to the evaluation of CRISPR/Cas9-based experiments, but will be of use in any genome editing experiment and has the ability to analyze data from every organism with a sequenced genome.

  4. Image editing with spatiograms transfer.

    Science.gov (United States)

    Papadakis, Nicolas; Bugeau, Aurélie; Caselles, Vicent

    2012-05-01

    Histogram equalization is a well-known method for image contrast enhancement. Nevertheless, as histograms do not include any information on the spatial repartition of colors, their application to local image editing problems remains limited. To cope with this lack of spatial information, spatiograms have been recently proposed for tracking purposes. A spatiogram is an image descriptor that combines a histogram with the mean and the variance of the position of each color. In this paper, we address the problem of local retouching of images by proposing a variational method for spatiogram transfer. More precisely, a reference spatiogram is used to modify the color value of a given region of interest of the processed image. Experiments on shadow removal and inpainting demonstrate the strength of the proposed approach.

  5. AAO Observer - August 2011 Edition

    CERN Document Server

    Brough, Sarah

    2011-01-01

    This edition of the Australian Astronomical Observatory Observer contains articles on the commissioning of the new SAMI instrument giving the first hexabundle galaxy spectra; galaxy parameter variations across and through the 6dFGS Fundamental Plane; an introduction to the new Dragonfly stellar interferometer; an update on the RAdial VElocity (RAVE) survey at half a million spectra; the Magellanic Quasars Survey; the Integrated Photonic Spectrograph's first look at the heart of the Scorpion; using AAOMega to measure the age of the young open cluster IC2602; making MANIFEST fibres for the Giant Magellan Telescope and a Voyage through Filaments of Galaxies. The Observer also contains thoughts on diversity in the astronomy community and reports on the recent Supernovae and their Host Galaxies conference and the 2011 Science Meets Parliament. In addition there are the usual features of the AUSGO Corner, Epping News and Letter from Coona.

  6. Cas9-Guide RNA Directed Genome Editing in Soybean.

    Science.gov (United States)

    Li, Zhongsen; Liu, Zhan-Bin; Xing, Aiqiu; Moon, Bryan P; Koellhoffer, Jessica P; Huang, Lingxia; Ward, R Timothy; Clifton, Elizabeth; Falco, S Carl; Cigan, A Mark

    2015-10-01

    Recently discovered bacteria and archaea adaptive immune system consisting of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) endonuclease has been explored in targeted genome editing in different species. Streptococcus pyogenes Cas9-guide RNA (gRNA) was successfully applied to generate targeted mutagenesis, gene integration, and gene editing in soybean (Glycine max). Two genomic sites, DD20 and DD43 on chromosome 4, were mutagenized with frequencies of 59% and 76%, respectively. Sequencing randomly selected transgenic events confirmed that the genome modifications were specific to the Cas9-gRNA cleavage sites and consisted of small deletions or insertions. Targeted gene integrations through homology-directed recombination were detected by border-specific polymerase chain reaction analysis for both sites at callus stage, and one DD43 homology-directed recombination event was transmitted to T1 generation. T1 progenies of the integration event segregated according to Mendelian laws and clean homozygous T1 plants with the donor gene precisely inserted at the DD43 target site were obtained. The Cas9-gRNA system was also successfully applied to make a directed P178S mutation of acetolactate synthase1 gene through in planta gene editing.

  7. Heritable genome editing with CRISPR/Cas9 induces anosmia in a crop pest moth.

    Science.gov (United States)

    Koutroumpa, Fotini A; Monsempes, Christelle; François, Marie-Christine; de Cian, Anne; Royer, Corinne; Concordet, Jean-Paul; Jacquin-Joly, Emmanuelle

    2016-07-12

    Lepidoptera suffer critical lack of genetic tools and heritable genome edition has been achieved only in a few model species. Here we demonstrate that the CRISPR/Cas9 system is highly efficient for genome editing in a non-model crop pest Lepidoptera, the noctuid moth Spodoptera littoralis. We knocked-out the olfactory receptor co-receptor Orco gene to investigate its function in Lepidoptera olfaction. We find that 89.6% of the injected individuals carried Orco mutations, 70% of which transmitted them to the next generation. CRISPR/Cas9-mediated Orco knockout caused defects in plant odor and sex pheromone olfactory detection in homozygous individuals. Our work genetically defines Orco as an essential OR partner for both host and mate detection in Lepidoptera, and demonstrates that CRISPR/Cas9 is a simple and highly efficient genome editing technique in noctuid pests opening new routes for gene function analysis and the development of novel pest control strategies.

  8. Data Director editor user's manual. [EDIT

    Energy Technology Data Exchange (ETDEWEB)

    McGoldrick, P.

    1977-03-21

    EDIT allows the user to edit or create text, either interactively or in the batch mode. The text may be a source program, program data, or documents. Special provisions permit the creation or editing of APT source-language programs. EDIT processes ASCII files from any accessible Data Director library and outputs files to any such library as specified by the user.

  9. Radar principles for the nonspecialist, 3rd edition

    CERN Document Server

    Toomay, John

    2004-01-01

    Radar Principles for the Non-specialist, Third Edition continues its popular tradition: to distill the very complex technology of radar into its fundamentals, tying them to the laws of nature on one end and to the most modern and complex systems on the other. It starts with electromagnetic propagation, describes a radar of the utmost simplicity, and derives the radar range equation from that simple radar. Once the range equation is available, the book attacks the meaning of each term in it, moving through antennas, detection and tracking, radar cross-section, waveforms andsignal proces

  10. Specification Editing and Discovery Assistant Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The project will prototype a specification editing and discovery tool (SPEEDY) for C/C++ that will assist software developers with modular formal verification tasks...

  11. LabVIEW 8 student edition

    CERN Document Server

    Bishop, Robert H

    2007-01-01

    For courses in Measurement and Instrumentation, Electrical Engineering lab, and Physics and Chemistry lab. This revised printing has been updated to include new LabVIEW 8.2 Student Edition. National Instruments' LabVIEW is the defacto industry standard for test, measurement, and automation software solutions. With the Student Edition of LabVIEW, students can design graphical programming solutions to their classroom problems and laboratory experiments with software that delivers the graphical programming capabilites of the LabVIEW professional version. . The Student Edition is also compatible with all National Instruments data acquisition and instrument control hardware. Note: The LabVIEW Student Edition is available to students, faculty, and staff for personal educational use only. It is not intended for research, institutional, or commercial use. For more information about these licensing options, please visit the National Instruments website at (http:www.ni.com/academic/)

  12. Statistical theory of signal detection

    CERN Document Server

    Helstrom, Carl Wilhelm; Costrell, L; Kandiah, K

    1968-01-01

    Statistical Theory of Signal Detection, Second Edition provides an elementary introduction to the theory of statistical testing of hypotheses that is related to the detection of signals in radar and communications technology. This book presents a comprehensive survey of digital communication systems. Organized into 11 chapters, this edition begins with an overview of the theory of signal detection and the typical detection problem. This text then examines the goals of the detection system, which are defined through an analogy with the testing of statistical hypotheses. Other chapters consider

  13. Looking forward to genetically edited fruit crops.

    Science.gov (United States)

    Nagamangala Kanchiswamy, Chidananda; Sargent, Daniel James; Velasco, Riccardo; Maffei, Massimo E; Malnoy, Mickael

    2015-02-01

    The availability of genome sequences for many fruit crops has redefined the boundaries of genetic engineering and genetically modified (GM) crop plants. However commercialization of GM crops is hindered by numerous regulatory and social hurdles. Here, we focus on recently developed genome-editing tools for fruit crop improvement and their importance from the consumer perspective. Challenges and opportunities for the deployment of new genome-editing tools for fruit plants are also discussed.

  14. Wetland Ecology Principles and Conservation, Second Edition

    OpenAIRE

    Richard Smardon

    2014-01-01

    This is a book review of Wetland Ecology Principles and Conservation, second edition, by Paul Keddy. This review focuses on the book’s content as it relates to wetland sustainability for both science and management. Besides overall comments, comparisons are made with the first edition of the book and then very specific chapter-by-chapter relationships to wetland sustainability are made to illustrate specific applications toward wetland sustainability.

  15. The commercialization of genome-editing technologies.

    Science.gov (United States)

    Brinegar, Katelyn; K Yetisen, Ali; Choi, Sun; Vallillo, Emily; Ruiz-Esparza, Guillermo U; Prabhakar, Anand M; Khademhosseini, Ali; Yun, Seok-Hyun

    2017-01-18

    The emergence of new gene-editing technologies is profoundly transforming human therapeutics, agriculture, and industrial biotechnology. Advances in clustered regularly interspaced short palindromic repeats (CRISPR) have created a fertile environment for mass-scale manufacturing of cost-effective products ranging from basic research to translational medicine. In our analyses, we evaluated the patent landscape of gene-editing technologies and found that in comparison to earlier gene-editing techniques, CRISPR has gained significant traction and this has established dominance. Although most of the gene-editing technologies originated from the industry, CRISPR has been pioneered by academic research institutions. The spinout of CRISPR biotechnology companies from academic institutions demonstrates a shift in entrepreneurship strategies that were previously led by the industry. These academic institutions, and their subsequent companies, are competing to generate comprehensive intellectual property portfolios to rapidly commercialize CRISPR products. Our analysis shows that the emergence of CRISPR has resulted in a fivefold increase in genome-editing bioenterprise investment over the last year. This entrepreneurial movement has spurred a global biotechnology revolution in the realization of novel gene-editing technologies. This global shift in bioenterprise will continue to grow as the demand for personalized medicine, genetically modified crops and environmentally sustainable biofuels increases. However, the monopolization of intellectual property, negative public perception of genetic engineering and ambiguous regulatory policies may limit the growth of these market segments.

  16. Genome editing systems in novel therapies.

    Science.gov (United States)

    Jang, Yoon-Young; Cai, Liuhong; Ye, Zhaohui

    2016-01-01

    Genome editing is the process in which DNA sequences at precise genomic locations are modified. In the past three decades, genome editing by homologous recombination has been successfully performed in mouse for generating genetic models. The low efficiency of this process in human cells, however, had prevented its clinical application until the recent advancements in designer endonuclease technologies. The significantly improved genome editing efficiencies aided by ZFN, TALEN, and CRISPR systems provide unprecedented opportunities not only for biomedical research, but also for developing novel therapies. Applications based on these genome editing tools to disrupt deleterious genes, correct genetic mutations, deliver functional transgenes more effectively or even modify the epigenetic landscape are being actively investigated for gene and cell therapy purposes. Encouraging results have been obtained in limited clinical trials in the past two years. While most of the applications are still in proof-of-principle or preclinical development stages, it is anticipated that the coming years will see increasing clinical success in novel therapies based on the modern genome editing technologies. It should be noted that critical issues still remain before the technologies can be translated into more reliable therapies. These key issues include off-target evaluation, establishing appropriate preclinical models and improving the currently low efficiency of homology-based precise gene replacement. In this review we discuss the preclinical and clinical studies aiming at translating the genome editing technologies as well as the issues that are important for more successful translation.

  17. Genome editing with engineered nucleases in plants.

    Science.gov (United States)

    Osakabe, Yuriko; Osakabe, Keishi

    2015-03-01

    Numerous examples of successful 'genome editing' now exist. Genome editing uses engineered nucleases as powerful tools to target specific DNA sequences to edit genes precisely in the genomes of both model and crop plants, as well as a variety of other organisms. The DNA-binding domains of zinc finger (ZF) proteins were the first to be used as genome editing tools, in the form of designed ZF nucleases (ZFNs). More recently, transcription activator-like effector nucleases (TALENs), as well as the clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) system, which utilizes RNA-DNA interactions, have proved useful. A key step in genome editing is the generation of a double-stranded DNA break that is specific to the target gene. This is achieved by custom-designed endonucleases, which enable site-directed mutagenesis via a non-homologous end-joining (NHEJ) repair pathway and/or gene targeting via homologous recombination (HR) to occur efficiently at specific sites in the genome. This review provides an overview of recent advances in genome editing technologies in plants, and discusses how these can provide insights into current plant molecular biology research and molecular breeding technology.

  18. Approximate Graph Edit Distance in Quadratic Time.

    Science.gov (United States)

    Riesen, Kaspar; Ferrer, Miquel; Bunke, Horst

    2015-09-14

    Graph edit distance is one of the most flexible and general graph matching models available. The major drawback of graph edit distance, however, is its computational complexity that restricts its applicability to graphs of rather small size. Recently the authors of the present paper introduced a general approximation framework for the graph edit distance problem. The basic idea of this specific algorithm is to first compute an optimal assignment of independent local graph structures (including substitutions, deletions, and insertions of nodes and edges). This optimal assignment is complete and consistent with respect to the involved nodes of both graphs and can thus be used to instantly derive an admissible (yet suboptimal) solution for the original graph edit distance problem in O(n3) time. For large scale graphs or graph sets, however, the cubic time complexity may still be too high. Therefore, we propose to use suboptimal algorithms with quadratic rather than cubic time for solving the basic assignment problem. In particular, the present paper introduces five different greedy assignment algorithms in the context of graph edit distance approximation. In an experimental evaluation we show that these methods have great potential for further speeding up the computation of graph edit distance while the approximated distances remain sufficiently accurate for graph based pattern classification.

  19. Precise genome editing by homologous recombination.

    Science.gov (United States)

    Hoshijima, K; Jurynec, M J; Grunwald, D J

    2016-01-01

    Simple and efficient methods are presented for creating precise modifications of the zebrafish genome. Edited alleles are generated by homologous recombination between the host genome and double-stranded DNA (dsDNA) donor molecules, stimulated by the induction of double-strand breaks at targeted loci in the host genome. Because several kilobase-long tracts of sequence can be exchanged, multiple genome modifications can be generated simultaneously at a single locus. Methods are described for creating: (1) alleles with simple sequence changes or in-frame additions, (2) knockin/knockout alleles that express a reporter protein from an endogenous locus, and (3) conditional alleles in which exons are flanked by recombinogenic loxP sites. Significantly, our approach to genome editing allows the incorporation of a linked reporter gene into the donor sequences so that successfully edited alleles can be identified by virtue of expression of the reporter. Factors affecting the efficiency of genome editing are discussed, including the finding that dsDNA products of I-SceI meganuclease enzyme digestion are particularly effective as donor molecules for gene-editing events. Reagents and procedures are described for accomplishing efficient genome editing in the zebrafish.

  20. A single alteration 20 nt 5′ to an editing target inhibits chloroplast RNA editing in vivo

    OpenAIRE

    2001-01-01

    Transcripts of typical dicot plant plastid genes undergo C→U RNA editing at approximately 30 locations, but there is no consensus sequence surrounding the C targets of editing. The cis-acting elements required for editing of the C located at tobacco rpoB editing site II were investigated by introducing translatable chimeric minigenes containing sequence –20 to +6 surrounding the C target of editing. When the –20 to +6 sequence specified by the homologous region pre...

  1. ADAR2-editing activity inhibits glioblastoma growth through the modulation of the CDC14B/Skp2/p21/p27 axis.

    Science.gov (United States)

    Galeano, F; Rossetti, C; Tomaselli, S; Cifaldi, L; Lezzerini, M; Pezzullo, M; Boldrini, R; Massimi, L; Di Rocco, C M; Locatelli, F; Gallo, A

    2013-02-21

    Grade IV astrocytoma or glioblastoma multiforme (GBM) is one of the most aggressive and lethal tumors affecting humans. ADAR2-mediated A-to-I RNA editing, an essential post-transcriptional modification event in brain, is impaired in GBMs and astrocytoma cell lines. However, the role of ADAR2 editing in astrocytomas remains to be defined. Here, we show that ADAR2 editing rescue in astrocytomas prevents tumor growth in vivo and modulates an important cell cycle pathway involving the Skp2/p21/p27 proteins, often altered in glioblastoma. We demonstrate that ADAR2 deaminase activity is essential to inhibit tumor growth. Indeed, we identify the phosphatase CDC14B, which acts upstream of the Skp2/p21/p27 pathway, as a novel and critical ADAR2 target gene involved in glioblastoma growth. Specifically, ADAR2-mediated editing on CDC14B pre-mRNA increases its expression with a consequent reduction of the Skp2 target protein, as shown both in vitro and in vivo. We found that, compared to normal brain, both CDC14B editing and expression are progressively impaired in astrocytomas from grade I to IV, being very low in GBMs. These findings (1) demonstrate that post-transcriptional A-to-I RNA editing might be crucial for glioblastoma pathogenesis, (2) identify ADAR2-editing enzyme as a novel candidate tumor suppressor gene and (3) provide proof of principle that ADAR2 or its substrates may represent a suitable target(s) for possible novel, more effective and less toxic approaches to the treatment of GBMs.

  2. Guided Research in Middle School: Mystery in the Media Center. Second Edition

    Science.gov (United States)

    Harrington, LaDawna

    2011-01-01

    A little imagination, a little drama, a little mystery. Using the guided inquiry model in this updated, second edition, students become detectives at Information Headquarters. They solve a mystery-and enhance their problem-solving and literacy skills. Middle school is a crucial time in the development of problem-solving, critical-thinking, and…

  3. Book Review: New Perspectives on Technical Editing

    Science.gov (United States)

    Murphy, A. J. (Ed.); Sterken, Christiaan

    2012-08-01

    New Perspectives on Technical Editing by Avon J. Murphy (ed.) ISBN : 978-0895033949 (2010) Baywood Publishing Company Inc, Hardcover, 210 pages, 35.5 GBP This book presents a collection of 10 chapters dealing with diverse aspects of technical editing (ie, editorial planning, and analysis and structural changes made to other people's technological documents): research in technical editing, trends and teaching of technical editing, copyediting, and technical journal editing. The role and function of the modern journal and book editor is also dealt with in detail. Each chapter is written by an expert in the field: senior editors, university professors in technical communication, technical writers and linguists. The ever-evolving role of the editor is clearly elucidated in several historical reviews, and in the descriptions of the expectations for the future. A very striking aspect of this book is its extensive collection of bibliographic resources: every chapter lists dozens of very useful references, and the closing chapter, and annotated bibliography, contain many not so well known references, and are most useful. All in all, the book is a treasure trove listing more than 400 references, in addition to numerous webpage URLs embedded in the texts. The book is designed to help the reader to understand current practices and norms in technical editing, and to help to take action in editing as well as in teaching and educating would-be editors. The audience for this book thus includes editors and teachers, but also writers, researchers and students. A deep reading of this book will result in a better understanding of the difference between full technical editing and its much narrower component so well known as copyediting, and will convince any prospective editor that editing should not be undertaken if the people involved do not master the art of precision and accuracy in technical (as well as in human) communication, do not possess the technical know how and computer

  4. Improving Student Revising and Editing Skills through the Use of Peer Editing and Writing Conferencing.

    Science.gov (United States)

    Kolling, Ann

    This report describes instructional strategies that will improve the revising and editing skills of sixth grade students during the writing process. The literature review suggested improved instruction and evaluation through a writer's workshop approach, which would include a positive environment, mini-lessons, teacher modeling, peer editing, and…

  5. Learn Sparse Dictionaries for Edit Propagation.

    Science.gov (United States)

    Xiaowu Chen; Jianwei Li; Dongqing Zou; Qinping Zhao

    2016-04-01

    With the increasing availability of high-resolution images, videos, and 3D models, the demand for scalable large data processing techniques increases. We introduce a method of sparse dictionary learning for edit propagation of large input data. Previous approaches for edit propagation typically employ a global optimization over the whole set of pixels (or vertexes), incurring a prohibitively high memory and time-consumption for large input data. Rather than propagating an edit pixel by pixel, we follow the principle of sparse representation to obtain a representative and compact dictionary and perform edit propagation on the dictionary instead. The sparse dictionary provides an intrinsic basis for input data, and the coding coefficients capture the linear relationship between all pixels and the dictionary atoms. The learned dictionary is then optimized by a novel scheme, which maximizes the Kullback-Leibler divergence between each atom pair to remove redundant atoms. To enable local edit propagation for images or videos with similar appearance, a dictionary learning strategy is proposed by considering range constraint to better account for the global distribution of pixels in their feature space. We show several applications of the sparsity-based edit propagation, including video recoloring, theme editing, and seamless cloning, operating on both color and texture features. Our approach can also be applied to computer graphics tasks, such as 3D surface deformation. We demonstrate that with an atom-to-pixel ratio in the order of 0.01% signifying a significant reduction on memory consumption, our method still maintains a high degree of visual fidelity.

  6. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes

    Science.gov (United States)

    Liang, Zhen; Chen, Kunling; Li, Tingdong; Zhang, Yi; Wang, Yanpeng; Zhao, Qian; Liu, Jinxing; Zhang, Huawei; Liu, Cuimin; Ran, Yidong; Gao, Caixia

    2017-01-01

    Substantial efforts are being made to optimize the CRISPR/Cas9 system for precision crop breeding. The avoidance of transgene integration and reduction of off-target mutations are the most important targets for optimization. Here, we describe an efficient genome editing method for bread wheat using CRISPR/Cas9 ribonucleoproteins (RNPs). Starting from RNP preparation, the whole protocol takes only seven to nine weeks, with four to five independent mutants produced from 100 immature wheat embryos. Deep sequencing reveals that the chance of off-target mutations in wheat cells is much lower in RNP mediated genome editing than in editing with CRISPR/Cas9 DNA. Consistent with this finding, no off-target mutations are detected in the mutant plants. Because no foreign DNA is used in CRISPR/Cas9 RNP mediated genome editing, the mutants obtained are completely transgene free. This method may be widely applicable for producing genome edited crop plants and has a good prospect of being commercialized. PMID:28098143

  7. Designed nucleases for targeted genome editing.

    Science.gov (United States)

    Lee, Junwon; Chung, Jae-Hee; Kim, Ho Min; Kim, Dong-Wook; Kim, Hyongbum

    2016-02-01

    Targeted genome-editing technology using designed nucleases has been evolving rapidly, and its applications are widely expanding in research, medicine and biotechnology. Using this genome-modifying technology, researchers can precisely and efficiently insert, remove or change specific sequences in various cultured cells, micro-organisms, animals and plants. This genome editing is based on the generation of double-strand breaks (DSBs), repair of which modifies the genome through nonhomologous end-joining (NHEJ) or homology-directed repair (HDR). In addition, designed nickase-induced generation of single-strand breaks can also lead to precise genome editing through HDR, albeit at relatively lower efficiencies than that induced by nucleases. Three kinds of designed nucleases have been used for targeted DSB formation: zinc-finger nucleases, transcription activator-like effector nucleases, and RNA-guided engineered nucleases derived from the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) system. A growing number of researchers are using genome-editing technologies, which have become more accessible and affordable since the discovery and adaptation of CRISPR-Cas9. Here, the repair mechanism and outcomes of DSBs are reviewed and the three types of designed nucleases are discussed with the hope that such understanding will facilitate applications to genome editing.

  8. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA.

    Science.gov (United States)

    Zhang, Yi; Liang, Zhen; Zong, Yuan; Wang, Yanpeng; Liu, Jinxing; Chen, Kunling; Qiu, Jin-Long; Gao, Caixia

    2016-08-25

    Editing plant genomes is technically challenging in hard-to-transform plants and usually involves transgenic intermediates, which causes regulatory concerns. Here we report two simple and efficient genome-editing methods in which plants are regenerated from callus cells transiently expressing CRISPR/Cas9 introduced as DNA or RNA. This transient expression-based genome-editing system is highly efficient and specific for producing transgene-free and homozygous wheat mutants in the T0 generation. We demonstrate our protocol to edit genes in hexaploid bread wheat and tetraploid durum wheat, and show that we are able to generate mutants with no detectable transgenes. Our methods may be applicable to other plant species, thus offering the potential to accelerate basic and applied plant genome-engineering research.

  9. BOOK REVIEW: Quantum Gravity: third edition Quantum Gravity: third edition

    Science.gov (United States)

    Rovelli, Carlo

    2012-09-01

    The request by Classical and Quantum Gravity to review the third edition of Claus Kiefer's 'Quantum Gravity' puts me in a slightly awkward position. This is a remarkably good book, which every person working in quantum gravity should have on the shelf. But in my opinion quantum gravity has undergone some dramatic advances in the last few years, of which the book makes no mention. Perhaps the omission only attests to the current vitality of the field, where progress is happening fast, but it is strange for me to review a thoughtful, knowledgeable and comprehensive book on my own field of research, which ignores what I myself consider the most interesting results to date. Kiefer's book is unique as a broad introduction and a reliable overview of quantum gravity. There are numerous books in the field which (often notwithstanding titles) focus on a single approach. There are also countless conference proceedings and article collections aiming to be encyclopaedic, but offering disorganized patchworks. Kiefer's book is a careful and thoughtful presentation of all aspects of the immense problem of quantum gravity. Kiefer is very learned, and brings together three rare qualities: he is pedagogical, he is capable of simplifying matter to the bones and capturing the essential, and he offers a serious and balanced evaluation of views and ideas. In a fractured field based on a major problem that does not yet have a solution, these qualities are precious. I recommend Kiefer's book to my students entering the field: to work in quantum gravity one needs a vast amount of technical knowledge as well as a grasp of different ideas, and Kiefer's book offers this with remarkable clarity. This novel third edition simplifies and improves the presentation of several topics, but also adds very valuable new material on quantum gravity phenomenology, loop quantum cosmology, asymptotic safety, Horava-Lifshitz gravity, analogue gravity, the holographic principle, and more. This is a testament

  10. Quantum Field Theory, Revised Edition

    Science.gov (United States)

    Mandl, F.; Shaw, G.

    1994-01-01

    Quantum Field Theory Revised Edition F. Mandl and G. Shaw, Department of Theoretical Physics, The Schuster Laboratory, The University, Manchester, UK When this book first appeared in 1984, only a handful of W± and Z° bosons had been observed and the experimental investigation of high energy electro-weak interactions was in its infancy. Nowadays, W± bosons and especially Z° bosons can be produced by the thousand and the study of their properties is a precise science. We have revised the text of the later chapters to incorporate these developments and discuss their implications. We have also taken this opportunity to update the references throughout and to make some improvements in the treatment of dimen-sional regularization. Finally, we have corrected some minor errors and are grateful to various people for pointing these out. This book is designed as a short and simple introduction to quantum field theory for students beginning research in theoretical and experimental physics. The three main objectives are to explain the basic physics and formalism of quantum field theory, to make the reader fully proficient in theory calculations using Feynman diagrams, and to introduce the reader to gauge theories, which play such a central role in elementary particle physics. The theory is applied to quantum electrodynamics (QED), where quantum field theory had its early triumphs, and to weak interactions where the standard electro-weak theory has had many impressive successes. The treatment is based on the canonical quantization method, because readers will be familiar with this, because it brings out lucidly the connection between invariance and conservation laws, and because it leads directly to the Feynman diagram techniques which are so important in many branches of physics. In order to help inexperienced research students grasp the meaning of the theory and learn to handle it confidently, the mathematical formalism is developed from first principles, its physical

  11. Gauge Field Theories, 2nd Edition

    Science.gov (United States)

    Frampton, Paul H.

    2000-08-01

    The first edition of Gauge Field Theories, published in 1985, quickly became widely used in universities and other institutions of higher learning around the world. Written by well-known physicist Paul Frampton, the new edition continues to offer a first-rate mathematical treatment of gauge field theories, while thoroughly updating all chapters to keep pace with developments in the field. Frampton emphasizes formalism rather than experiments and provides sufficient detail for readers wishing to do their own calculations or pursue theoretical physics research. Special features of the Second Edition include: * Improved, logical organization of the material on gauge invariance, quantization, and renormalization * Major revision of the chapter on electroweak interactions, incorporating the latest precision data and discovery of the top quark * Discussions of renormalization group and quantum chromodynamics * A completely new chapter on model building

  12. Edit Propagation via Edge-Aware Filtering

    Institute of Scientific and Technical Information of China (English)

    Wei Hu; Zhao Dong; Guo-Dong Yuan

    2012-01-01

    This paper presents a novel framework for efficiently propagating the stroke-based user edits to the regions with similar colors and locations in high resolution images and videos.Our framework is based on the key observation that the edit propagation intrinsically can also be achieved by utilizing recently proposed edge-preserving filters.Therefore,instead of adopting the traditional global optimization which may involve a time-consuming solution,our algorithm propagates edits with the aid of the edge-preserve filters.Such a propagation scheme has low computational complexity and supports multiple kinds of strokes for more flexible user interactions.Further,our method can be easily and efficiently implemented in GPU.The experimental results demonstrate the efficiency and user-friendliness of our approach.

  13. Ethical and regulatory aspects of genome editing.

    Science.gov (United States)

    Kohn, Donald B; Porteus, Matthew H; Scharenberg, Andrew M

    2016-05-26

    Gene editing is a rapidly developing area of biotechnology in which the nucleotide sequence of the genome of living cells is precisely changed. The use of genome-editing technologies to modify various types of blood cells, including hematopoietic stem cells, has emerged as an important field of therapeutic development for hematopoietic disease. Although these technologies offer the potential for generation of transformative therapies for patients suffering from myriad disorders of hematopoiesis, their application for therapeutic modification of primary human cells is still in its infancy. Consequently, development of ethical and regulatory frameworks that ensure their safe and effective use is an increasingly important consideration. Here, we review a number of issues that have the potential to impact the clinical implementation of genome-editing technologies, and suggest paths forward for resolving them such that new therapies can be safely and rapidly translated to the clinic.

  14. Introduction to nuclear science, second edition

    CERN Document Server

    Bryan, Jeff C.

    2013-01-01

    This book was written to provide students who have limited backgrounds in the physical sciences and math with an accessible textbook on nuclear science. Expanding on the foundation of the bestselling first edition, Introduction to Nuclear Science, Second Edition provides a clear and complete introduction to nuclear chemistry and physics, from basic concepts to nuclear power and medical applications. Incorporating suggestions from professors using this book for their courses, the author has created a new text that is approximately 60 percent larger and more comprehensive and flexible than the first.New to This Edition: Thorough review of nuclear forensics, radiology, gamma cameras, and decay through proton or neutron emission More detailed explanations of the necessary mathematics A chapter on dosimetry of radiation fields Expanded discussion of applications, introduced earlier in the text More in-depth coverage of nuclear reactors, including a new chapter examining more reactor types, their safety systems,...

  15. Ranking Highlights in Personal Videos by Analyzing Edited Videos.

    Science.gov (United States)

    Sun, Min; Farhadi, Ali; Chen, Tseng-Hung; Seitz, Steve

    2016-11-01

    We present a fully automatic system for ranking domain-specific highlights in unconstrained personal videos by analyzing online edited videos. A novel latent linear ranking model is proposed to handle noisy training data harvested online. Specifically, given a targeted domain such as "surfing," our system mines the YouTube database to find pairs of raw and their corresponding edited videos. Leveraging the assumption that an edited video is more likely to contain highlights than the trimmed parts of the raw video, we obtain pair-wise ranking constraints to train our model. The learning task is challenging due to the amount of noise and variation in the mined data. Hence, a latent loss function is incorporated to mitigate the issues caused by the noise. We efficiently learn the latent model on a large number of videos (about 870 min in total) using a novel EM-like procedure. Our latent ranking model outperforms its classification counterpart and is fairly competitive compared with a fully supervised ranking system that requires labels from Amazon Mechanical Turk. We further show that a state-of-the-art audio feature mel-frequency cepstral coefficients is inferior to a state-of-the-art visual feature. By combining both audio-visual features, we obtain the best performance in dog activity, surfing, skating, and viral video domains. Finally, we show that impressive highlights can be detected without additional human supervision for seven domains (i.e., skating, surfing, skiing, gymnastics, parkour, dog activity, and viral video) in unconstrained personal videos.

  16. The art of editing RNA structural alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth

    2014-01-01

    Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious, it is re......Manual editing of RNA structural alignments may be considered more art than science, since it still requires an expert biologist to take multiple levels of information into account and be slightly creative when constructing high-quality alignments. Even though the task is rather tedious...

  17. Prince2 2009 edition a pocket guide

    CERN Document Server

    Hedeman, Bert

    2010-01-01

    This Pocket Guide supplies a summary of the PRINCE2 method, to provide a quick introduction as well as a structured overview of the method;Main target Group for this pocket guide is anyone who wants to get to know the method PRINCE2 or a methodical approach for project management. The book is also very useful for members of a project management team on a project using the PRINCE2 method. Furthermore this pocket guide can be used as literature for the preparation of the PRINCE2 2009 Edition Foundation exam;This pocket guide is based on PRINCE2 2009 Edition;This pocket book deals with processes,

  18. Transportation Energy Data Book, Edition 19

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    1999-09-01

    The Transportation Energy Data Book: Edition 19 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (http://www-cta.ornl.gov/data/tedb.htm).

  19. RNA Editing and Drug Discovery for Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Wei-Hsuan Huang

    2013-01-01

    Full Text Available RNA editing is vital to provide the RNA and protein complexity to regulate the gene expression. Correct RNA editing maintains the cell function and organism development. Imbalance of the RNA editing machinery may lead to diseases and cancers. Recently, RNA editing has been recognized as a target for drug discovery although few studies targeting RNA editing for disease and cancer therapy were reported in the field of natural products. Therefore, RNA editing may be a potential target for therapeutic natural products. In this review, we provide a literature overview of the biological functions of RNA editing on gene expression, diseases, cancers, and drugs. The bioinformatics resources of RNA editing were also summarized.

  20. Unravelling the Franklin Mystery, Second Edition with David C. Woodman

    DEFF Research Database (Denmark)

    Burke, Danita Catherine

    2017-01-01

    This is a forthcoming book review of David C. Woodman's second edition of his book "Unravelling the Franklin Mystery."......This is a forthcoming book review of David C. Woodman's second edition of his book "Unravelling the Franklin Mystery."...

  1. Direct Visual Editing of Node Attributes in Graphs

    Directory of Open Access Journals (Sweden)

    Christian Eichner

    2016-10-01

    Full Text Available There are many expressive visualization techniques for analyzing graphs. Yet, there is only little research on how existing visual representations can be employed to support data editing. An increasingly relevant task when working with graphs is the editing of node attributes. We propose an integrated visualize-and-edit approach to editing attribute values via direct interaction with the visual representation. The visualize part is based on node-link diagrams paired with attribute-dependent layouts. The edit part is as easy as moving nodes via drag-and-drop gestures. We present dedicated interaction techniques for editing quantitative as well as qualitative attribute data values. The benefit of our novel integrated approach is that one can directly edit the data while the visualization constantly provides feedback on the implications of the data modifications. Preliminary user feedback indicates that our integrated approach can be a useful complement to standard non-visual editing via external tools.

  2. Measurement and detection of radiation

    CERN Document Server

    Tsoulfanidis, Nicholas

    2011-01-01

    This is an update of the standard textbook for the field of radiation measurement. It includes illustrative examples and new problems. The research and applications of nuclear instrumentation have grown substantially since publication of the previous editions. With the miniaturization of equipment, increased speed of electronic components, and more sophisticated software, radiation detection systems are now more productively used in many disciplines, including nuclear nonproliferation, homeland security, and nuclear medicine. Continuing in the tradition of its bestselling predecessors, "Measurement and Detection of Radiation, Third Edition" illustrates the fundamentals of nuclear interactions and radiation detection with a multitude of examples and problems. It offers a clearly written, accessible introduction to nuclear instrumentation concepts. The following are new to the third edition: a new chapter on the latest applications of radiation detection, covering nuclear medicine, dosimetry, health physics, no...

  3. Human Resources Administration: A School-Based Perspective. Fourth Edition

    Science.gov (United States)

    Smith, Richard

    2009-01-01

    Enhanced and updated, this Fourth Edition of Richard E. Smith's highly successful text examines the growing role of the principal in planning, hiring, staff development, supervision, and other human resource functions. The Fourth Edition includes new sections on ethics, induction, and the role of the mentor teacher. This edition also introduces…

  4. Soil Carbon Sequestration and the Greenhouse Effect (2nd Edition)

    Science.gov (United States)

    This volume is a second edition of the book “Soil Carbon Sequestration and The Greenhouse Effect”. The first edition was published in 2001 as SSSA Special Publ. #57. The present edition is an update of the concepts, processes, properties, practices and the supporting data. All chapters are new co...

  5. Triple-frequency TurboEdit Cycle-slip Processing Method of Weakening Ionospheric Activity

    Directory of Open Access Journals (Sweden)

    HUANG Lingyong

    2015-08-01

    Full Text Available The existing triple-frequency cycle-slip detection method usually can not detect and repair the cycle-slip correctly in the ionospheric activity phase or when the magnetic storm happening. To solve the problem, the triple-frequency TurboEdit method for weakening the ionospheric error is advanced based on the dual-frequency TurboEdit method. Both the triple-frequency geometry-free and ionospheric-free combination and second-order time-difference phase geometry-free combination in this algorithm can whittle the influence of ionospheric error effectively. And then, the triple-frequency data is used to validate this algorithm, the experiment results show that this method can weaken the ionospheric error and realize the no-difference dynamicreal-time cycle-slip detection and correction under ionospheric activity phase.

  6. The Landscape of Qualitative Research. Third Edition

    Science.gov (United States)

    Denzin, Norman K., Ed.; Lincoln, Yvonna, Ed.

    2007-01-01

    This book, the first volume of the paperback versions of the "The SAGE Handbook of Qualitative Research, Third Edition," takes a look at the field from a broadly theoretical perspective, and is composed of the Handbook's Parts I ("Locating the Field"), II ("Major Paradigms and Perspectives"), and VI ("The Future of Qualitative Research"). "The…

  7. Collecting and Interpreting Qualitative Materials. Third Edition

    Science.gov (United States)

    Denzin, Norman K., Ed.; Lincoln, Yvonna, Ed.

    2007-01-01

    This book is the third volume of the paperback versions of "The SAGE Handbook of Qualitative Research, Third Edition." This portion of the handbook considers the tasks of collecting, analyzing, and interpreting empirical materials, and comprises the Handbook's Parts IV ("Methods of Collecting and Analyzing Empirical Materials") and V ("The Art and…

  8. Researching Society and Culture. Third Edition

    Science.gov (United States)

    Seale, Clive, Ed.

    2012-01-01

    Clear, coherent and trusted, this book is the perfect guide to the main social research methods in use today. The much anticipated Third Edition of Clive Seale's bestselling title further expands its coverage to provide an authoritative introduction to all of the social research methods used to analyze qualitative and quantitative data. Written by…

  9. Catalog of Nonresident Training Courses, 1994 Edition

    Science.gov (United States)

    1994-01-01

    Processing ........................................................... 2-7 Endodontics ...The guide for the instructor includes all the command master chief program; Navy ceremonies and the material covered in the Student’s Journal in...Course, PER ORDER QUANTITY RESTRICTION: 5 Student’s Journal SP EDITION: 1993 NAVEDTRA NUMBER: 38202 Command Master Chief Course Student’s NSN: 0502-LP

  10. The Technique of Television Production. Revised Edition.

    Science.gov (United States)

    Millerson, Gerald

    In discussing the technical aspects of television production, this book covers both equipment and techniques used in these areas: camera, lighting, sound, settings, and make-up. Composition of images according to camera movement, placement of subjects, editing, and aural composition are also covered. Steps in the technical planning of a telecast…

  11. Some aspects of RNA repair and editing

    Directory of Open Access Journals (Sweden)

    Kovalchuk M. V.

    2010-11-01

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

  12. CRISPR-Cas9 gene editing

    NARCIS (Netherlands)

    Oude Blenke, Erik; Evers, Martijn J.W.; Mastrobattista, Enrico; Oost, van der John

    2016-01-01

    The CRISPR-Cas9 gene editing system has taken the biomedical science field by storm, initiating rumors about future Nobel Prizes and heating up a fierce patent war, but also making significant scientific impact. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), together with

  13. Notes on the revised standard edition.

    Science.gov (United States)

    Solms, Mark

    2013-02-01

    On the eve of the publication of the Revised Standard Edition of the Complete Psychological Works of Sigmund Freud (24 volumes) and The Complete Neuroscientific Works of Sigmund Freud (4 volumes), the editor of these works describes the policies he followed in succeeding James Strachey, and reflects on the experience of doing so.

  14. Recommended Reference Books in Paperback. Third Edition.

    Science.gov (United States)

    Lang, Jovian P.; O'Gorman, Jack

    Completely revised and updated from the last edition (1992), this annotated, evaluative bibliography presents more than 1,000 outstanding titles chosen for their quality, economy, and availability. Thirty-six chapters describe and judge these affordable paperbacks for libraries with limited budgets. Subject matter includes: general reference, area…

  15. Thermodynamics of Fluids Under Flow Second Edition

    CERN Document Server

    Jou, David; Criado-Sancho, Manuel

    2011-01-01

    This is the second edition of the book “Thermodynamics of Fluids under Flow,” which was published in 2000 and has now been corrected, expanded and updated. This is a companion book to our other title Extended irreversible thermodynamics (D. Jou, J. Casas-Vázquez and G. Lebon, Springer, 4th edition 2010), and of the textbook Understanding non-equilibrium thermodynamics (G. Lebon, D. Jou and J. Casas-Vázquez, Springer, 2008. The present book is more specialized than its counterpart, as it focuses its attention on the non-equilibrium thermodynamics of flowing fluids, incorporating non-trivial thermodynamic contributions of the flow, going beyond local equilibrium theories, i.e., including the effects of internal variables and of external forcing due to the flow. Whereas the book's first edition was much more focused on polymer solutions, with brief glimpses into ideal and real gases, the present edition covers a much wider variety of systems, such as: diluted and concentrated polymer solutions, polymer ble...

  16. Edit propagation using geometric relationship functions

    KAUST Repository

    Guerrero, Paul

    2014-03-01

    We propose a method for propagating edit operations in 2D vector graphics, based on geometric relationship functions. These functions quantify the geometric relationship of a point to a polygon, such as the distance to the boundary or the direction to the closest corner vertex. The level sets of the relationship functions describe points with the same relationship to a polygon. For a given query point, we first determine a set of relationships to local features, construct all level sets for these relationships, and accumulate them. The maxima of the resulting distribution are points with similar geometric relationships. We show extensions to handle mirror symmetries, and discuss the use of relationship functions as local coordinate systems. Our method can be applied, for example, to interactive floorplan editing, and it is especially useful for large layouts, where individual edits would be cumbersome. We demonstrate populating 2D layouts with tens to hundreds of objects by propagating relatively few edit operations. © 2014 ACM 0730-0301/2014/03- ART15 $15.00.

  17. The NMC Horizon Report: 2013 Museum Edition

    Science.gov (United States)

    Johnson, L.; Adams Becker, S.; Freeman, A.

    2013-01-01

    The "NMC Horizon Report: 2013 Museum Edition," is a co-production with the Marcus Institute for Digital Education in the Arts (MIDEA), and examines six emerging technologies for their potential impact on and use in education and interpretation within the museum environment: BYOD (Bring Your Own Device), crowdsourcing, electronic…

  18. International guide to the circus. - 2015 edition

    NARCIS (Netherlands)

    Huey, R.; Albrecht, E.; Belbahri, N.; Brunsdale, M.; Christian, J.; Garcia, J.; Giarola, A.; Jando, D.; Lehmann, R.; Marier, F.; Nieminen, K.; Parkinson, G.; Pierce, R.D.; Revolledo Cárdenas, J.; Rodenhuis, W.; Serena, A.; Schlotfeldt, A.; Shaina, C.; Shrake, P.; Simon, M.; St. Leon, M.; Stone, C.; Cooper, J.; Tamaoki, V.; Winkler, G.

    2015-01-01

    An easy-to-read publication defining 100 key circus terms translated in nine languages. The 2015 edition has been re-created in a smaller "pocket" version, 44 pages in length and weighing 63 grams per book. Additional images have been added to illustrate terms and each book is sold complete with a b

  19. Brief Articles for Latino Parents, 1999 Edition.

    Science.gov (United States)

    ERIC Clearinghouse on Rural Education and Small Schools, Charleston, WV.

    This packet contains six briefs developed specifically for Spanish-speaking Latino parents, and English translations of the briefs. These briefs state what researchers and practitioners have learned about various ways parents can help their children do well in school. Earlier editions of brief articles for parents have been used in various ways by…

  20. ETC 408/508: Technical Editing

    Science.gov (United States)

    Charlton, Michael

    2013-01-01

    The course will focus on the role of the editor in organizational settings, including creating successful writer/editor collaboration. Students will gain practice in editing documents for grammar, syntax, organization, style, emphasis, document design, graphics, and user-centered design. The course will provide an introduction to technology for…

  1. A DESCRIPTIVE INDONESIAN GRAMMAR--PRELIMINARY EDITION.

    Science.gov (United States)

    DYEN, ISIDORE

    THIS PRELIMINARY EDITION COMPRISES A DESCRIPTIVE GRAMMAR OF INDONESIAN (BAHASA INDONESIA), THE OFFICIAL LANGUAGE OF THE REPUBLIC OF INDONESIA. THE THREE SECTIONS--PHONOLOGY, SYNTAX, AND MORPHOLOGY--PRESENT A COMPREHENSIVE LINGUISTIC ANALYSIS OF INDONESIAN, WITH OCCASIONAL CONTRASTIVE REFERENCE TO MALAY, JAVANESE, SUNDANESE, AND SUMATRAN. THIS…

  2. Applied groundwater modeling, 2nd Edition

    Science.gov (United States)

    Anderson, Mary P.; Woessner, William W.; Hunt, Randall J.

    2015-01-01

    This second edition is extensively revised throughout with expanded discussion of modeling fundamentals and coverage of advances in model calibration and uncertainty analysis that are revolutionizing the science of groundwater modeling. The text is intended for undergraduate and graduate level courses in applied groundwater modeling and as a comprehensive reference for environmental consultants and scientists/engineers in industry and governmental agencies.

  3. Science Editing in America: An Overview

    Institute of Scientific and Technical Information of China (English)

    Barbara Gastel

    2003-01-01

    @@ In America, science editing appears to be an increasingly recognized field. In what settings do American science editors work, and what kinds of work do they do ? What is their educational background? What style manuals and other resources do they use? What organizations serve them? What topics and issues do they find of professional interest?

  4. Fundamentals of Physics, Extended 7th Edition

    Science.gov (United States)

    Halliday, David; Resnick, Robert; Walker, Jearl

    2004-05-01

    No other book on the market today can match the 30-year success of Halliday, Resnick and Walker's Fundamentals of Physics! Fundamentals of Physics, 7th Edition and the Extended Version, 7th Edition offer a solid understanding of fundamental physics concepts, helping readers apply this conceptual understanding to quantitative problem solving, in a breezy, easy-to-understand style. A unique combination of authoritative content and stimulating applications. * Numerous improvements in the text, based on feedback from the many users of the sixth edition (both instructors and students) * Several thousand end-of-chapter problems have been rewritten to streamline both the presentations and answers * 'Chapter Puzzlers' open each chapter with an intriguing application or question that is explained or answered in the chapter * Problem-solving tactics are provided to help beginning Physics students solve problems and avoid common error * The first section in every chapter introduces the subject of the chapter by asking and answering, "What is Physics?" as the question pertains to the chapter * Numerous supplements available to aid teachers and students The extended edition provides coverage of developments in Physics in the last 100 years, including: Einstein and Relativity, Bohr and others and Quantum Theory, and the more recent theoretical developments like String Theory.

  5. Ladybugs of South Dakota, 2nd edition

    Science.gov (United States)

    Images of the 80 species of Coccinellidae, commonly known as lady beetles, that occur in South Dakota are presented in taxonomic order. The second edition updates information, including the addition of a species new to South Dakota. Information on each species includes genus-species name, sub-fami...

  6. Psychology's struggle for existence: Second edition, 1913.

    Science.gov (United States)

    Wundt, Wilhelm; Lamiell, James T

    2013-08-01

    Presents an English translation of Wilhelm Wundt's Psychology's struggle for existence: Second edition, 1913, by James T. Lamiell in August, 2012. In his essay, Wundt advised against the impending divorce of psychology from philosophy. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

  7. The agents of natural genome editing

    Institute of Scientific and Technical Information of China (English)

    Guenther Witzany

    2011-01-01

    The DNA serves as a stable information storage medium and every protein which is needed by the cell is produced from this blueprint via an RNA intermediate code. More recently it was found that an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on RNA transcripts. Natural genome editing on one side is the competent agent*driven generation and integration of meaningful DNA nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing on the other side designates the integration of all RNA activities acting on RNA transcripts without altering DNA-encoded genes. If we take the genetic code seriously as a natural code, there must be agents that are competent to act on this code because no natural code codes itself as no natural language speaks itself. As code editing agents,viral and subviral agents have been suggested because there are several indicators that demonstrate viruses competent in both RNA and DNA natural genome editing.

  8. Genome Editing in Sugarcane: Challenges ahead

    Directory of Open Access Journals (Sweden)

    Chakravarthi Mohan

    2016-10-01

    Full Text Available Genome editing opens new and unique opportunities for researchers to enhance crop production. Until 2013, the zinc finger nucleases (ZFNs and transcription activator-like effector nucleases (TALENs were the key tools used for genome editing applications. The advent of RNA-guided engineered nucleases - the type II clustered regularly interspaced short palindromic repeat (CRISPR/Cas9 (CRISPR-associated system from Streptococcus pyogenes holds great potential since it is simple, effective and more versatile than ZFNs and TALENs. CRISPR/Cas9 system has already been successfully employed in several crop plants. Use of these techniques is in its infant stage in sugarcane. Jung and Altpeter (2016 have reported TALEN mediated approach for the first time to reduce lignin content in sugarcane to make it amenable for biofuel production. This is so far the only report describing genome editing in sugarcane. Large genome size, polyploidy, low transformation efficiency, transgene silencing and lack of high throughput screening techniques are certainly great challenges for genome editing in sugarcane which would be discussed in detail in this review.

  9. A Model for Flexibly Editing CSCL Scripts

    Science.gov (United States)

    Sobreira, Pericles; Tchounikine, Pierre

    2012-01-01

    This article presents a model whose primary concern and design rationale is to offer users (teachers) with basic ICT skills an intuitive, easy, and flexible way of editing scripts. The proposal is based on relating an end-user representation as a table and a machine model as a tree. The table-tree model introduces structural expressiveness and…

  10. Teaching Foreign-Language Skills. Second Edition.

    Science.gov (United States)

    Rivers, Wilga M.

    This second edition is a complete reworking of the 1968 text to include later views of language learning and teaching, and theories of linguistics and psychology. The text is intended particularly for use in methods classes in conjunction with observation of experienced foreign language teachers. The early chapters deal with general principles…

  11. Genome Editing in Sugarcane: Challenges Ahead

    Science.gov (United States)

    Mohan, Chakravarthi

    2016-01-01

    Genome editing opens new and unique opportunities for researchers to enhance crop production. Until 2013, the zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) were the key tools used for genome editing applications. The advent of RNA-guided engineered nucleases - the type II clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 (CRISPR-associated) system from Streptococcus pyogenes holds great potential since it is simple, effective and more versatile than ZFNs and TALENs. CRISPR/Cas9 system has already been successfully employed in several crop plants. Use of these techniques is in its infant stage in sugarcane. Jung and Altpeter (2016) have reported TALEN mediated approach for the first time to reduce lignin content in sugarcane to make it amenable for biofuel production. This is so far the only report describing genome editing in sugarcane. Large genome size, polyploidy, low transformation efficiency, transgene silencing and lack of high throughput screening techniques are certainly great challenges for genome editing in sugarcane which would be discussed in detail in this review. PMID:27790238

  12. The NMC Horizon Report: 2014 Library Edition

    NARCIS (Netherlands)

    Johnson, L; Adams Becker, S.; Estrada, V.; Freeman, A.; van den Brekel, Guus

    2014-01-01

    The NMC Horizon Report: 2014 Library Edition, examines key trends, significant challenges, and emerging technologies for their potential impact on academic and research libraries worldwide. While there are many local factors affecting libraries, there are also issues that transcend regional boundari

  13. Does Money Matter in Education? Second Edition

    Science.gov (United States)

    Baker, Bruce D.

    2016-01-01

    This second edition policy brief revisits the long and storied literature on whether money matters in providing a quality education. It includes research released since the original brief in 2012 and covers a handful of additional topics. Increasingly, political rhetoric adheres to the unfounded certainty that money does not make a difference in…

  14. Variable frequency of plastid RNA editing among ferns and repeated loss of uridine-to-cytidine editing from vascular plants.

    Science.gov (United States)

    Guo, Wenhu; Grewe, Felix; Mower, Jeffrey P

    2015-01-01

    The distinct distribution and abundance of C-to-U and U-to-C RNA editing among land plants suggest that these two processes originated and evolve independently, but the paucity of information from several key lineages limits our understanding of their evolution. To examine the evolutionary diversity of RNA editing among ferns, we sequenced the plastid transcriptomes from two early diverging species, Ophioglossum californicum and Psilotum nudum. Using a relaxed automated approach to minimize false negatives combined with manual inspection to eliminate false positives, we identified 297 C-to-U and three U-to-C edit sites in the O. californicum plastid transcriptome but only 27 C-to-U and no U-to-C edit sites in the P. nudum plastid transcriptome. A broader comparison of editing content with the leptosporangiate fern Adiantum capillus-veneris and the hornwort Anthoceros formosae uncovered large variance in the abundance of plastid editing, indicating that the frequency and type of RNA editing is highly labile in ferns. Edit sites that increase protein conservation among species are more abundant and more efficiently edited than silent and non-conservative sites, suggesting that selection maintains functionally important editing. The absence of U-to-C editing from P. nudum plastid transcripts and other vascular plants demonstrates that U-to-C editing loss is a recurrent phenomenon in vascular plant evolution.

  15. Cucumber, melon, pumpkin, and squash: are rules of editing in flowering plants chloroplast genes so well known indeed?

    Science.gov (United States)

    Guzowska-Nowowiejska, Magdalena; Fiedorowicz, Ewa; Plader, Wojciech

    2009-04-01

    The similarities and differences in the chloroplast genes editing patterns of four species from one family (and two genera), which is the first-ever attempt at comparison of such data in closely related species, is discussed. The effective use of the chloroplast genes editing patterns in evolutionary studies, especially in evaluating the kinship between closely related species, is thereby proved. The results indicate that differences in editing patterns between different genera (Cucumis and Cucurbita) exist, and some novel editing sites can be identified even now. However, surprising is the fact of finding editing in the codon for Arg (in flowering plants detected before only in Cuscuta reflexa chloroplast genome, Funk et al.,[Funk H.T., Berg S., Krupinska K., Maier U.G. and Krause K., 2007. Complete DNA sequences of the plastid genomes of two parasitic flowering plants species, Cuscuta reflexa and Cuscuta gronovi. BMC Plant Biol. 7:45, doi: 10.1186/1471-2229-7-45.]), which was believed to have been lost during evolution before the emergence of angiosperms. In addition, the existence of silent editing in plant chloroplasts has been confirmed, and some probable reasons for its presence are pointed out herein.

  16. Cloud Properties of CERES-MODIS Edition 4 and CERES-VIIRS Edition 1

    Science.gov (United States)

    Sun-Mack, Sunny; Minnis, Patrick; Chang, Fu-Lung; Hong, Gang; Arduini, Robert; Chen, Yan; Trepte, Qing; Yost, Chris; Smith, Rita; Brown, Ricky; Chu, Churngwei; Heckert, Elizabeth; Gibson, Sharon; Heck, Patrick W.

    2015-01-01

    The Clouds and Earth's Radiant Energy System (CERES) analyzes MODerate-resolution Imaging Spectroradiometer (MODIS) data and Visible Infrared Imaging Radiometer Suite (VIIRS) to derive cloud properties that are combine with aerosol and CERES broadband flux data to create a multi-parameter data set for climate study. CERES has produced over 15 years of data from Terra and over 13 years of data from Aqua using the CERES-MODIS Edition-2 cloud retrieval algorithm. A recently revised algorithm, CERESMODIS Edition 4, has been developed and is now generating enhanced cloud data for climate research (over 10 years for Terra and 8 years for Aqua). New multispectral retrievals of properties are included along with a multilayer cloud retrieval system. Cloud microphysical properties are reported at 3 wavelengths, 0.65, 1.24, and 2.1 microns to enable better estimates of the vertical profiles of cloud water contents. Cloud properties over snow are retrieved using the 1.24-micron channel. A new CERES-VIIRS cloud retrieval package was developed for the VIIRS spectral complement and is currently producing the CERES-VIIRS Edition 1 cloud dataset. The results from CERES-MODIS Edition 4 and CERES-VIIRS Edition 1 are presented and compared with each other and other datasets, including CALIPSO, CloudSat and the CERES-MODIS Edition-2 results.

  17. Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets

    Directory of Open Access Journals (Sweden)

    Quagliariello Carla

    2008-03-01

    Full Text Available Abstract Background In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogenetically conserved codons and the encoded amino acid residues. Sites undergoing RNA editing evolve at a higher rate than sites not modified by the process. As a result, editing sites strongly affect the evolution of plant mitochondrial genomes, representing an important source of sequence variability and potentially informative characters. To date no clear and convincing evidence has established whether or not editing sites really affect the topology of reconstructed phylogenetic trees. For this reason, we investigated here the effect of RNA editing on the tree building process of twenty different plant mitochondrial gene sequences and by means of computer simulations. Results Based on our simulation study we suggest that the editing ‘noise’ in tree topology inference is mainly manifested at the cDNA level. In particular, editing sites tend to confuse tree topologies when artificial genomic and cDNA sequences are generated shorter than 500 bp and with an editing percentage higher than 5.0%. Similar results have been also obtained with genuine plant mitochondrial genes. In this latter instance, indeed, the topology incongruence increases when the editing percentage goes up from about 3.0 to 14.0%. However, when the average gene length is higher than 1,000 bp (rps3, matR and atp1 no differences in the comparison between inferred genomic and cDNA topologies could be detected. Conclusions Our findings by the here reported in silico and in vivo computer simulation system seem to strongly suggest that editing sites contribute in the generation of misleading phylogenetic trees if the analyzed mitochondrial gene sequence is highly edited (higher than 3.0% and reduced in length (shorter than 500 bp. In the current lack of direct experimental evidence the results

  18. Generation of gene edited birds in one generation using sperm transfection assisted gene editing (STAGE).

    Science.gov (United States)

    Cooper, Caitlin A; Challagulla, Arjun; Jenkins, Kristie A; Wise, Terry G; O'Neil, Terri E; Morris, Kirsten R; Tizard, Mark L; Doran, Timothy J

    2016-11-28

    Generating transgenic and gene edited mammals involves in vitro manipulation of oocytes or single cell embryos. Due to the comparative inaccessibility of avian oocytes and single cell embryos, novel protocols have been developed to produce transgenic and gene edited birds. While these protocols are relatively efficient, they involve two generation intervals before reaching complete somatic and germline expressing transgenic or gene edited birds. Most of this work has been done with chickens, and many protocols require in vitro culturing of primordial germ cells (PGCs). However, for many other bird species no methodology for long term culture of PGCs exists. Developing methodologies to produce germline transgenic or gene edited birds in the first generation would save significant amounts of time and resource. Furthermore, developing protocols that can be readily adapted to a wide variety of avian species would open up new research opportunities. Here we report a method using sperm as a delivery mechanism for gene editing vectors which we call sperm transfection assisted gene editing (STAGE). We have successfully used this method to generate GFP knockout embryos and chickens, as well as generate embryos with mutations in the doublesex and mab-3 related transcription factor 1 (DMRT1) gene using the CRISPR/Cas9 system. The efficiency of the method varies from as low as 0% to as high as 26% with multiple factors such as CRISPR guide efficiency and mRNA stability likely impacting the outcome. This straightforward methodology could simplify gene editing in many bird species including those for which no methodology currently exists.

  19. CRISPR as a strong gene editing tool.

    Science.gov (United States)

    Shen, Shengfu; Loh, Tiing Jen; Shen, Hongling; Zheng, Xuexiu; Shen, Haihong

    2017-01-01

    Clustered regularly-interspaced short palindromic repeats (CRISPR) is a new and effective genetic editing tool. CRISPR was initially found in bacteria to protect it from virus invasions. In the first step, specific DNA strands of virus are identified by guide RNA that is composed of crRNA and tracrRNA. Then RNAse III is required for producing crRNA from pre-crRNA. In The second step, a crRNA:tracrRNA:Cas9 complex guides RNase III to cleave target DNA. After cleavage of DNA by CRISPR-Cas9, DNA can be fixed by Non- Homologous End Joining (NHEJ) and Homology Directed Repair (HDR). Whereas NHEJ is simple and random, HDR is much more complex and accurate. Gene editing by CRISPR is able to be applied to various biological field such as agriculture and treating genetic diseases in human. [BMB Reports 2017; 50(1): 20-24].

  20. Building java programs (3rd edition)

    CERN Document Server

    Reges, Stuart

    2013-01-01

    Building Java Programs: A Back to Basics Approach, Third Edition, introduces novice programmers to basic constructs and common pitfalls by emphasizing the essentials of procedural programming, problem solving, and algorithmic reasoning. By using objects early to solve interesting problems and defining objects later in the course, Building Java Programs develops programming knowledge for a broad audience. NEW! This edition is available with MyProgrammingLab, an innovative online homework and assessment tool. Through the power of practice and immediate personalized feedback, MyProgrammingLab helps students fully grasp the logic, semantics, and syntax of programming. Note: If you are purchasing the standalone text or electronic version, MyProgrammingLab does not come automatically packaged with the text. To purchase MyProgrammingLab, please visit: myprogramminglab.com or you can purchase a package of the physical text + MyProgrammingLab by searching the Pearson Higher Education web site. MyProgrammi...

  1. Post-editing through Speech Recognition

    DEFF Research Database (Denmark)

    Mesa-Lao, Bartolomé

    In the past couple of years automatic speech recognition (ASR) software has quietly created a niche for itself in many situations of our lives. Nowadays it can be found at the other end of customer-support hotlines, it is built into operating systems and it is offered as an alternative text......-input method for smartphones. On another front, given the significant improvements in Machine Translation (MT) quality and the increasing demand for translations, post-editing of MT is becoming a popular practice in the translation industry, since it has been shown to allow for larger volumes of translations...... to be produced saving time and costs. The translation industry is at a deeply transformative point in its evolution and the coming years herald an era of converge where speech technology could make a difference. As post-editing services are becoming a common practice among language service providers and speech...

  2. Transportation Energy Data Book, Edition 18

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy C.

    1998-09-01

    The Transportation Energy Data Book: Edition 18 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. This edition of the Data Book has 11 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 - energy Chapter 3 - emissions; Chapter 4 - transportation and the economy; Chapter 5 - highway vehicles; Chapter 6 - Light vehicles; Chapter 7 - heavy vehicles; Chapter 8 - alternative fuel vehicles; Chapter 9 - fleet vehicles; Chapter 10 - household vehicles; and Chapter 11 - nonhighway modes. The sources used represent the latest available data.

  3. Engineering Delivery Vehicles for Genome Editing.

    Science.gov (United States)

    Nelson, Christopher E; Gersbach, Charles A

    2016-06-07

    The field of genome engineering has created new possibilities for gene therapy, including improved animal models of disease, engineered cell therapies, and in vivo gene repair. The most significant challenge for the clinical translation of genome engineering is the development of safe and effective delivery vehicles. A large body of work has applied genome engineering to genetic modification in vitro, and clinical trials have begun using cells modified by genome editing. Now, promising preclinical work is beginning to apply these tools in vivo. This article summarizes the development of genome engineering platforms, including meganucleases, zinc finger nucleases, TALENs, and CRISPR/Cas9, and their flexibility for precise genetic modifications. The prospects for the development of safe and effective viral and nonviral delivery vehicles for genome editing are reviewed, and promising advances in particular therapeutic applications are discussed.

  4. CERN Video News, 2nd edition

    CERN Multimedia

    2002-01-01

    This week you will be able to watch on the web the second edition of CERN's video news (see Bulletin n°45/2002, p.3). On this news reel: the ATRAP experiment's latest achievements, superconducting cable production for CMS, the CAST experiment and the European digital conferencing project InDiCo. Go to : www.cern.ch/video, or Bulletin web page.

  5. Editing of H2BC NMR spectra.

    Science.gov (United States)

    Nyberg, Nils T; Duus, Jens Ø; Sørensen, Ole W

    2005-12-01

    New versions of the H2BC pulse sequence (Nyberg NT, Duus JØ, Sørensen OW. J. Am. Chem. Soc. 2005; 127: 6154) that edit into two subspectra according to the number of protons attached to 13C nuclei being odd or even are introduced. These sequences can be useful for resolving spectral overlap, which is demonstrated on the molecule prednisolone [(11 beta)-11,17,21-trihydroxypregna-1,4-diene-3,20-dione].

  6. Understanding Physics, First Edition, Study Guide

    Science.gov (United States)

    Cummings, Karen; Laws, Priscilla W.; Redish, Edward F.; Cooney, Patrick J.

    2004-04-01

    Built on the foundations of Halliday, Resnick, and Walker's Fundamentals of Physics Sixth Edition, this text is designed to work with interactive learning strategies that are increasingly being used in physics instruction (for example, microcomputer-based labs, interactive lectures, etc. ). In doing so, it incorporates new approaches based upon Physics Education Research (PER), aligns with courses that use computer-based laboratory tools, and promotes Activity Based Physics in lectures, labs, and recitations.

  7. Genome editing for human gene therapy.

    Science.gov (United States)

    Meissner, Torsten B; Mandal, Pankaj K; Ferreira, Leonardo M R; Rossi, Derrick J; Cowan, Chad A

    2014-01-01

    The rapid advancement of genome-editing techniques holds much promise for the field of human gene therapy. From bacteria to model organisms and human cells, genome editing tools such as zinc-finger nucleases (ZNFs), TALENs, and CRISPR/Cas9 have been successfully used to manipulate the respective genomes with unprecedented precision. With regard to human gene therapy, it is of great interest to test the feasibility of genome editing in primary human hematopoietic cells that could potentially be used to treat a variety of human genetic disorders such as hemoglobinopathies, primary immunodeficiencies, and cancer. In this chapter, we explore the use of the CRISPR/Cas9 system for the efficient ablation of genes in two clinically relevant primary human cell types, CD4+ T cells and CD34+ hematopoietic stem and progenitor cells. By using two guide RNAs directed at a single locus, we achieve highly efficient and predictable deletions that ablate gene function. The use of a Cas9-2A-GFP fusion protein allows FACS-based enrichment of the transfected cells. The ease of designing, constructing, and testing guide RNAs makes this dual guide strategy an attractive approach for the efficient deletion of clinically relevant genes in primary human hematopoietic stem and effector cells and enables the use of CRISPR/Cas9 for gene therapy.

  8. Transportation Energy Data Book: Edition 31

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2012-08-01

    The Transportation Energy Data Book: Edition 31 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  9. Edit Distance to Monotonicity in Sliding Windows

    CERN Document Server

    Chan, Ho-Leung; Lee, Lap-Kei; Pan, Jiangwei; Ting, Hing-Fung; Zhang, Qin

    2011-01-01

    Given a stream of items each associated with a numerical value, its edit distance to monotonicity is the minimum number of items to remove so that the remaining items are non-decreasing with respect to the numerical value. The space complexity of estimating the edit distance to monotonicity of a data stream is becoming well-understood over the past few years. Motivated by applications on network quality monitoring, we extend the study to estimating the edit distance to monotonicity of a sliding window covering the $w$ most recent items in the stream for any $w \\ge 1$. We give a deterministic algorithm which can return an estimate within a factor of $(4+\\eps)$ using $O(\\frac{1}{\\eps^2} \\log^2(\\eps w))$ space. We also extend the study in two directions. First, we consider a stream where each item is associated with a value from a partial ordered set. We give a randomized $(4+\\epsilon)$-approximate algorithm using $O(\\frac{1}{\\epsilon^2} \\log \\epsilon^2 w \\log w)$ space. Second, we consider an out-of-order strea...

  10. Transportation Energy Data Book. Edition 33

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Williams, Susan E. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Boundy, Robert Gary [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-07-01

    The Transportation Energy Data Book: Edition 33 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  11. Transportation Energy Data Book: Edition 34

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Williams, Susan E [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Boundy, Robert Gary [Roltek, Inc., Clinton, TN (United States)

    2015-08-01

    The Transportation Energy Data Book: Edition 34 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  12. Handbook of Adhesion, 2nd Edition

    Science.gov (United States)

    Packham, D. E.

    2005-06-01

    This second edition of the successful Handbook of Adhesion provides concise and authoritative articles covering many aspects of the science and technology associated with adhesion and adhesives. It is intended to fill a gap between the necessarily simplified treatment of the student textbook and the full and thorough treatment of the research monograph and review article. The articles are structured in such a way, with internal cross-referencing and external literature references, that the reader can build up a broader and deeper understanding, as their needs require. This second edition includes many new articles covering developments which have risen in prominence in the intervening years, such as scanning probe techniques, the surface forces apparatus and the relation between adhesion and fractal surfaces. Advances in understanding polymer - polymer interdiffusion are reflected in articles drawing out the implications for adhesive bonding. In addition, articles derived from the earlier edition have been revised and updated where needed. Throughout the book there is a renewed emphasis on environmental implications of the use of adhesives and sealants. The scope of the Handbook, which features nearly 250 articles from over 60 authors, includes the background science - physics, chemistry and material science - and engineering, and also aspects of adhesion relevant to the use of adhesives, including topics such as: Sealants and mastics Paints and coatings Printing and composite materials Welding and autohesion Engineering design The Handbook of Adhesion is intended for scientists and engineers in both academia and industry, requiring an understanding of the various facets of adhesion.

  13. Technology Roadmap: Wind Energy. 2013 edition

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-07-01

    The IEA Wind Power Technology Roadmap 2013 Edition recognises the very significant progress made since the first edition was published in 2009. The technology continues to improve rapidly, and costs of generation from land-based wind installations continue to fall. Wind power is now being deployed in countries with good resources without any dedicated financial incentives. The 2013 Edition targets an increased share (15% to 18%) of global electricity to be provided by wind power in 2050, compared to 12% in the original roadmap of 2009. However, increasing levels of low-cost wind still require predictable, supportive regulatory environments and appropriate market designs. The challenges of integrating higher levels of variable wind power into the grid need to be addressed. For offshore wind, much remains to be done to develop appropriate large-scale systems and to reduce costs. The 2013 Wind Power Roadmap also provides updated analysis on the barriers that exist for the technology and suggests ways to address them, including legal and regulatory recommendations.

  14. Reflectance Transfer for Material Editing and Relighting

    Directory of Open Access Journals (Sweden)

    Adrian Hilton

    2010-10-01

    Full Text Available We present a new approach to diffuse reflectance estimation for dynamic scenes. Non-parametric image statistics are used to transfer reflectance properties from a static example set to a dynamic image sequence. The approach allows diffuse reflectance estimation for surface materials with inhomogeneous appearance, such as those which commonly occur with patterned or textured clothing. Material editing is also possible by transferring edited reflectance properties. Material reflectance properties are initially estimated from static images of the subject under multiple directional illuminations using photometric stereo. The estimated reflectance together with the corresponding image under uniform ambient illumination form a prior set of reference material observations. Material reflectance properties are then estimated for video sequences of a moving person captured under uniform ambient illumination by matching the observed local image statistics to the reference observations. Results demonstrate that the transfer of reflectance properties enables estimation of the dynamic surface normals and subsequent relighting combined with material editing. This approach overcomes limitations of previous work on material transfer and relighting of dynamic scenes which was limited to surfaces with regions of homogeneous reflectance. We evaluate our approach for relighting 3D model sequences reconstructed from multiple view video. Comparison to previous model relighting demonstrates improved reproduction of detailed texture and shape dynamics.

  15. TALEN gene editing takes aim on HIV.

    Science.gov (United States)

    Benjamin, Ronald; Berges, Bradford K; Solis-Leal, Antonio; Igbinedion, Omoyemwen; Strong, Christy L; Schiller, Martin R

    2016-09-01

    Transcription activator-like effector nucleases (TALENs) are one of several types of programmable, engineered nucleases that bind and cleave specific DNA sequences. Cellular machinery repairs the cleaved DNA by introducing indels. In this review, we emphasize the potential, explore progress, and identify challenges in using TALENs as a therapeutic tool to treat HIV infection. TALENs have less off-target editing and can be more effective at tolerating HIV escape mutations than CRISPR/Cas-9. Scientists have explored TALEN-mediated editing of host genes such as viral entry receptors (CCR5 and CXCR4) and a protein involved in proviral integration (LEDGF/p75). Viral targets include the proviral DNA, particularly focused on the long terminal repeats. Major challenges with translating gene therapy from bench to bedside are improving cleavage efficiency and delivery, while minimizing off-target editing, cytotoxicity, and immunogenicity. However, rapid improvements in TALEN technology are enhancing cleavage efficiency and specificity. Therapeutic testing in animal models of HIV infection will help determine whether TALENs are a viable HIV treatment therapy. TALENs or other engineered nucleases could shift the therapeutic paradigm from life-long antiretroviral therapy toward eradication of HIV infection.

  16. Transportation Energy Data Book: Edition 30

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2011-07-01

    The Transportation Energy Data Book: Edition 30 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  17. Transportation Energy Data Book: Edition 21

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    2001-09-13

    The ''Transportation Energy Data Book: Edition 21'' is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (www-cta.ornl.gov/data/tedb.htm). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2--energy; Chapter 3--greenhouse gas emissions; Chapter 4--criteria pollutant emissions; Chapter 5--transportation and the economy; Chapter 6--highway vehicles; Chapter 7--light vehicles; Chapter 8--heavy vehicles; Chapter 9--alternative fuel vehicles; Chapter 10--fleet vehicles; Chapter 11--household vehicles; and Chapter 12--nonhighway modes. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  18. Transportation Energy Data Book: Edition 22

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy C.; Diegel, Susan W.

    2002-12-04

    The Transportation Energy Data Book: Edition 22 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (www.cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 - energy; Chapter 3 - greenhouse gas emissions; Chapter 4 - criteria pollutant emissions; Chapter 5 - transportation and the economy; Chapter 6 - highway vehicles; Chapter 7 - light vehicles; Chapter 8 - heavy vehicles; Chapter 9 - alternative fuel vehicles; Chapter 10 - fleet vehicles; Chapter 11 - household vehicles; and Chapter 12- nonhighway modes. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  19. Transportation Energy Data Book: Edition 27

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2008-06-01

    The Transportation Energy Data Book: Edition 27 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; and Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  20. Transportation Energy Data Book: Edition 28

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2009-06-01

    The Transportation Energy Data Book: Edition 28 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with U.S Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program and the Hydrogen, Fuel Cells, and Infrastructure Technologies Program. Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book are available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; and Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  1. Transportation Energy Data Book: Edition 23

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    2003-10-24

    The ''Transportation Energy Data Book: Edition 23'' is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (www-cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2--energy; Chapter 3--highway vehicles; Chapter 4--light vehicles; Chapter 5--heavy vehicles; Chapter 6--alternative fuel vehicles; Chapter 7--fleet vehicles; Chapter 8--household vehicles; and Chapter 9--nonhighway modes; Chapter 10--transportation and the economy; Chapter 11--greenhouse gas emissions; and Chapter 12--criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  2. Transportation Energy Data Book (Edition 20)

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    2000-10-09

    The ''Transportation Energy Data Book: Edition 20'' is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (www-cta.ornl.gov/data/tedb.htm). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2--energy; Chapter 3--greenhouse gas emissions; Chapter 4--criteria pollutant emissions; Chapter 5--transportation and the economy; Chapter 6--highway vehicles; Chapter 7--light vehicles; Chapter 8--heavy vehicles; Chapter 9--alternative fuel vehicles; Chapter 10--fleet vehicles; Chapter 11--household vehicles; and Chapter 12--nonhighway modes. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  3. Transportation Energy Data Book: Edition 29

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2010-07-01

    The Transportation Energy Data Book: Edition 29 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  4. Transportation Energy Data Book: Edition 32

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL; Boundy, Robert Gary [ORNL

    2013-08-01

    The Transportation Energy Data Book: Edition 32 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 energy; Chapter 3 highway vehicles; Chapter 4 light vehicles; Chapter 5 heavy vehicles; Chapter 6 alternative fuel vehicles; Chapter 7 fleet vehicles; Chapter 8 household vehicles; Chapter 9 nonhighway modes; Chapter 10 transportation and the economy; Chapter 11 greenhouse gas emissions; and Chapter 12 criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the reader s convenience.

  5. Towards GERB Edition 2 TOA fluxes

    Science.gov (United States)

    Ipe, Alessandro; Baudrez, Edward; Clerbaux, Nicolas; Moreels, Johan; Urbain, Manon; Velazquez Blazquez, Almudena

    2016-04-01

    The Geostationary Earth Radiation Budget (GERB) dataset currently covers more than 10 years from 2004 and makes it an unique record for the climate and the numerical weather prediction scientific communities through assimilation in various models and climate studies. Indeed, the geostationary platform of this broadband radiometer flying together with the Spinning Enhanced Visible and InfraRed Imager (SEVIRI) on board of the Meteosat Second Generation (MSG) satellites allows to estimate TOA solar and thermal fluxes every 15 minutes at spatial resolutions upto 10 km (nadir). In this contribution, we will discuss the improvements that were developped for the Edition 1 post-processing. These includes terminator and sunglint modeling through scene identification extrapolation. Moreover, with the experience acquired by generating the Edition 1 dataset as well as through its critical assessment, an improved Edition 2 of the processing is been implemented. This second version aims to fulfill climate data record standards. Such goal will be achieved by improving the scene identification for the selection of solar angular dependency models (ADMs), the solar and thermal narrow-to-broadband conversion schemes, as well as including new thermal ADMs for radiance-to-flux conversion and GERB instrument ageing correction schemes.

  6. Transportation Energy Data Book: Edition 26

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL

    2007-07-01

    The Transportation Energy Data Book: Edition 26 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 - energy; Chapter 3 - highway vehicles; Chapter 4 - light vehicles; Chapter 5 - heavy vehicles; Chapter 6 - alternative fuel vehicles; Chapter 7 - fleet vehicles; Chapter 8 - household vehicles; and Chapter 9- nonhighway modes; Chapter 10 - transportation and the economy; Chapter 11 - greenhouse gas emissions; and Chapter 12 - criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  7. Transportation Energy Data Book: Edition 24

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    2005-03-08

    The ''Transportation Energy Data Book: Edition 24'' is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2--energy; Chapter 3--highway vehicles; Chapter 4--light vehicles; Chapter 5--heavy vehicles; Chapter 6--alternative fuel vehicles; Chapter 7--fleet vehicles; Chapter 8--household vehicles; and Chapter 9--nonhighway modes; Chapter 10--transportation and the economy; Chapter 11--greenhouse gas emissions; and Chapter 12--criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  8. Transportation Energy Data Book: Edition 25

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Stacy Cagle [ORNL; Diegel, Susan W [ORNL

    2006-06-01

    The Transportation Energy Data Book: Edition 25 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Planning, Budget Formulation, and Analysis, under the Energy Efficiency and Renewable Energy (EERE) program in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest editions of the Data Book are available to a larger audience via the Internet (cta.ornl.gov/data). This edition of the Data Book has 12 chapters which focus on various aspects of the transportation industry. Chapter 1 focuses on petroleum; Chapter 2 - energy; Chapter 3 - highway vehicles; Chapter 4 - light vehicles; Chapter 5 - heavy vehicles; Chapter 6 - alternative fuel vehicles; Chapter 7 - fleet vehicles; Chapter 8 - household vehicles; and Chapter 9- nonhighway modes; Chapter 10 - transportation and the economy; Chapter 11 - greenhouse gas emissions; and Chapter 12 - criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and the definition of Census divisions and regions. A glossary of terms and a title index are also included for the readers convenience.

  9. CRISPR/Cas9-Mediated Genome Editing in Soybean Hairy Roots.

    Directory of Open Access Journals (Sweden)

    Yupeng Cai

    Full Text Available As a new technology for gene editing, the CRISPR (clustered regularly interspaced short palindromic repeat/Cas (CRISPR-associated system has been rapidly and widely used for genome engineering in various organisms. In the present study, we successfully applied type II CRISPR/Cas9 system to generate and estimate genome editing in the desired target genes in soybean (Glycine max (L. Merrill.. The single-guide RNA (sgRNA and Cas9 cassettes were assembled on one vector to improve transformation efficiency, and we designed a sgRNA that targeted a transgene (bar and six sgRNAs that targeted different sites of two endogenous soybean genes (GmFEI2 and GmSHR. The targeted DNA mutations were detected in soybean hairy roots. The results demonstrated that this customized CRISPR/Cas9 system shared the same efficiency for both endogenous and exogenous genes in soybean hairy roots. We also performed experiments to detect the potential of CRISPR/Cas9 system to simultaneously edit two endogenous soybean genes using only one customized sgRNA. Overall, generating and detecting the CRISPR/Cas9-mediated genome modifications in target genes of soybean hairy roots could rapidly assess the efficiency of each target loci. The target sites with higher efficiencies can be used for regular soybean transformation. Furthermore, this method provides a powerful tool for root-specific functional genomics studies in soybean.

  10. CRISPR/Cas9-Mediated Genome Editing in Soybean Hairy Roots.

    Science.gov (United States)

    Cai, Yupeng; Chen, Li; Liu, Xiujie; Sun, Shi; Wu, Cunxiang; Jiang, Bingjun; Han, Tianfu; Hou, Wensheng

    2015-01-01

    As a new technology for gene editing, the CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) system has been rapidly and widely used for genome engineering in various organisms. In the present study, we successfully applied type II CRISPR/Cas9 system to generate and estimate genome editing in the desired target genes in soybean (Glycine max (L.) Merrill.). The single-guide RNA (sgRNA) and Cas9 cassettes were assembled on one vector to improve transformation efficiency, and we designed a sgRNA that targeted a transgene (bar) and six sgRNAs that targeted different sites of two endogenous soybean genes (GmFEI2 and GmSHR). The targeted DNA mutations were detected in soybean hairy roots. The results demonstrated that this customized CRISPR/Cas9 system shared the same efficiency for both endogenous and exogenous genes in soybean hairy roots. We also performed experiments to detect the potential of CRISPR/Cas9 system to simultaneously edit two endogenous soybean genes using only one customized sgRNA. Overall, generating and detecting the CRISPR/Cas9-mediated genome modifications in target genes of soybean hairy roots could rapidly assess the efficiency of each target loci. The target sites with higher efficiencies can be used for regular soybean transformation. Furthermore, this method provides a powerful tool for root-specific functional genomics studies in soybean.

  11. A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.

    Directory of Open Access Journals (Sweden)

    Alexander Wait Zaranek

    2010-05-01

    Full Text Available While it is widely held that an organism's genomic information should remain constant, several protein families are known to modify it. Members of the AID/APOBEC protein family can deaminate DNA. Similarly, members of the ADAR family can deaminate RNA. Characterizing the scope of these events is challenging. Here we use large genomic data sets, such as the two billion sequences in the NCBI Trace Archive, to look for clusters of mismatches of the same type, which are a hallmark of editing events caused by APOBEC3 and ADAR. We align 603,249,815 traces from the NCBI trace archive to their reference genomes. In clusters of mismatches of increasing size, at least one systematic sequencing error dominates the results (G-to-A. It is still present in mismatches with 99% accuracy and only vanishes in mismatches at 99.99% accuracy or higher. The error appears to have entered into about 1% of the HapMap, possibly affecting other users that rely on this resource. Further investigation, using stringent quality thresholds, uncovers thousands of mismatch clusters with no apparent defects in their chromatograms. These traces provide the first reported candidates of endogenous DNA editing in human, further elucidating RNA editing in human and mouse and also revealing, for the first time, extensive RNA editing in Xenopus tropicalis. We show that the NCBI Trace Archive provides a valuable resource for the investigation of the phenomena of DNA and RNA editing, as well as setting the stage for a comprehensive mapping of editing events in large-scale genomic datasets.

  12. REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa M R; Verbitskiy, Daniil; Brennicke, Axel; Quagliariello, Carla

    2011-03-01

    RNA editing is a post-transcriptional molecular process whereby the information in a genetic message is modified from that in the corresponding DNA template by means of nucleotide substitutions, insertions and/or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. RNA editing events have been annotated in primary databases as GenBank and at more sophisticated level in the specialized databases REDIdb, dbRES and EdRNA. At present, REDIdb is the only freely available database that focuses on the organellar RNA editing process and annotates each editing modification in its biological context. Here we present an updated and upgraded release of REDIdb with a web-interface refurbished with graphical and computational facilities that improve RNA editing investigations. Details of the REDIdb features and novelties are illustrated and compared to other RNA editing databases. REDIdb is freely queried at http://biologia.unical.it/py_script/REDIdb/.

  13. Edited synoptic cloud reports from ships and land stations over the globe, 1982--1991

    Energy Technology Data Exchange (ETDEWEB)

    Hahn, C.J. [Univ. of Arizona, Tucson, AZ (United States). Dept. of Atmospheric Sciences; Warren, S.G. [Univ. of Washington, Seattle, WA (United States). Dept. of Atmospheric Sciences; London, J. [Univ. of Colorado, Boulder, CO (United States). Dept. of Astrophysical, Planetary and Atmospheric Sciences

    1996-02-01

    Surface synoptic weather reports for the entire globe for the 10-year period from December 1981 through November 1991 have been processed, edited, and rewritten to provide a data set designed for use in cloud analyses. The information in these reports relating to clouds, including the present weather information, was extracted and put through a series of quality control checks. Correctable inconsistencies within reports were edited for consistency, so that the ``edited cloud report`` can be used for cloud analysis. Cases of ``sky obscured`` were interpreted by reference to the present weather code as to whether they indicated fog, rain or snow and were given appropriate cloud type designations. Nimbostratus clouds were also given a special designation. Changes made to an original report are indicated in the edited report so that the original report can be reconstructed if desired. While low cloud amount is normally given directly in the synoptic report, the edited cloud report also includes the amounts, either directly reported or inferred, of middle and high clouds, both the non-overlapped amounts and the ``actual`` amounts. Since illumination from the moon is important for the adequate detection of clouds at night, both the relative lunar illuminance and the solar altitude are given; well as a parameter that indicates whether our recommended illuminance criterion was satisfied. This data set contains 124 million reports from land stations and 15 million reports from ships. Each report is 56 characters in length. The archive consists of 240 files, one file for each month of data for land and ocean separately. With this data set a user can develop a climatology for any particular cloud type or group of types, for any geographical region and any spatial and temporal resolution desired.

  14. Towards a new era in medicine: therapeutic genome editing.

    Science.gov (United States)

    Porteus, Matthew H

    2015-12-22

    Genome editing is the process of precisely modifying the nucleotide sequence of the genome. It has provided a powerful approach to research questions but, with the development of a new set of tools, it is now possible to achieve frequencies of genome editing that are high enough to be useful therapeutically. Genome editing is being developed to treat not only monogenic diseases but also infectious diseases and diseases that have both a genetic and an environmental component.

  15. Gene Editing: A New Tool for Viral Disease.

    Science.gov (United States)

    Kennedy, Edward M; Cullen, Bryan R

    2017-01-14

    The emergence of the CRISPR/Cas system of antiviral adaptive immunity in bacteria as a facile system for gene editing in mammalian cells may well lead to gene editing becoming a novel treatment for a range of human diseases, especially those caused by deleterious germline mutations. Another potential target for gene editing are DNA viruses that cause chronic pathogenic diseases that cannot be cured by using currently available drugs. We review the current state of this field and discuss the potential advantages and problems with using a gene editing approach as a treatment for diseases caused by DNA viruses.

  16. DNA-free genome editing methods for targeted crop improvement.

    Science.gov (United States)

    Kanchiswamy, Chidananda Nagamangala

    2016-07-01

    Evolution of the next-generation clustered, regularly interspaced, short palindromic repeat/Cas9 (CRISPR/Cas9) genome editing tools, ribonucleoprotein (RNA)-guided endonuclease (RGEN) RNPs, is paving the way for developing DNA-free genetically edited crop plants. In this review, I discuss the various methods of RGEN RNPs tool delivery into plant cells and their limitations to adopt this technology to numerous crop plants. Furthermore, focus is given on the importance of developing DNA-free genome edited crop plants, including perennial crop plants. The possible regulation on the DNA-free, next-generation genome-edited crop plants is also highlighted.

  17. Detection of signals in noise

    CERN Document Server

    McDonough, Robert N

    1995-01-01

    The Second Edition is an updated revision to the authors highly successful and widely used introduction to the principles and application of the statistical theory of signal detection. This book emphasizes those theories that have been found to be particularly useful in practice including principles applied to detection problems encountered in digital communications, radar, and sonar.Detection processing based upon the fast Fourier transform

  18. Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases

    Directory of Open Access Journals (Sweden)

    Jean-Baptiste Renaud

    2016-03-01

    Full Text Available Genome editing has now been reported in many systems using TALEN and CRISPR-Cas9 nucleases. Precise mutations can be introduced during homology-directed repair with donor DNA carrying the wanted sequence edit, but efficiency is usually lower than for gene knockout and optimal strategies have not been extensively investigated. Here, we show that using phosphorothioate-modified oligonucleotides strongly enhances genome editing efficiency of single-stranded oligonucleotide donors in cultured cells. In addition, it provides better design flexibility, allowing insertions more than 100 bp long. Despite previous reports of phosphorothioate-modified oligonucleotide toxicity, clones of edited cells are readily isolated and targeted sequence insertions are achieved in rats and mice with very high frequency, allowing for homozygous loxP site insertion at the mouse ROSA locus in particular. Finally, when detected, imprecise knockin events exhibit indels that are asymmetrically positioned, consistent with genome editing taking place by two steps of single-strand annealing.

  19. Special Edition: Environment in Sustainable Development

    Directory of Open Access Journals (Sweden)

    Stephen Morse

    2014-11-01

    Full Text Available When we were invited by the editors of Sustainability to put together a special edition on “Environment in Sustainable Development” our first reaction was to question whether this was really needed. After all, the environment has long been regarded as a central plank in sustainability and there are countless articles and books published on an annual basis that explore the impact of our economic and social activities on our environment. Just what is it that a special edition can achieve? What new angles could we hope to provide? Our initial thinking was to link the special edition to a particular, almost unique, location in time rather than space. We are in the process of recovering, albeit stuttering, from the deepest economic crash experienced by the European and North American economies. The crash has brought some national economies to their knees and, if economic commentators are to be believed, almost destroyed the Euro. Recovery from that crash has been slow and it is arguable whether at the time of writing this has developed much momentum. There is still the skewed perception that prosperity equals economic growth and that economic growth can take place without real (sustainable development or by simply implementing austerity measures and surely without people’s participation. An analogy from National Parks worldwide is when conservation agencies try to enforce protection without local people’s support. All such attempts have either failed or resurrected only once people’s involvement was secured and guaranteed. The unidirectional austerity measures imposed mainly in the countries of southern Europe have destroyed social cohesion leaving deeply wounded societies, while at the same time have also put up for grabs important assets (including natural capital in each of these countries and therefore in jeopardy even their long term recovery.

  20. Beyond Author-Centricity in Scholarly Editing

    Directory of Open Access Journals (Sweden)

    Hans Walter Gabler

    2012-03-01

    Full Text Available Authorship – authority – authorisation – the author – the author’s will – the author’s intention: these form a cluster of notions whose validity for scholarly editing I fundamentally question. Taking measure from a historical survey of the discipline’s principles and practice from their institution under the dominance of stemmatics up to their main present-day ‘author orientation’ (Shillingsburg 1996, I see the need to split the terms ‘author’ and ‘authorship’ into a pragmatic versus a conceptual aspect. What textual scholarship engages with, directly and tangibly, is not authors but texts (and equally not works but texts, materially inscribed in transmissions. In the materiality and artifice of texts, ‘authoriality’ is accessible conceptually only, in a manner analog-ous to the Foucauldian ‘author function’. Under such premises, as well, ‘authority’, ‘authorisation’ and ‘authorial intention’ become recognisable as exogenous to texts, not integral to them. Consequently, I propose to abandon ‘authority’, ‘authorisation’ and ‘authorial intention’ as overriding principles and arbiters in editorial scholarship. Scholarly editing instead should re-situate itself in relation to texts, to textual criticism, to literary criticism and to literary theory alike, and do so by re-focussing the method-ology of its own practice. It should relinquish the external props termed ‘authorised document’, ‘textual authority’, or ‘authorial intention’ hitherto deferred to. Instead, it should revitalise skills fundamental to inherited editorial scholarship, namely those of critically assessing, and of editorially realising, textual validity. To re-embed editorial scholarship in literary criticism and theory, moreover, the interpretative and hermeneutic dimensions of textual criticism and scholarly editing will need to be freshly mapped.

  1. Targeted Genome Regulation and Editing in Plants

    KAUST Repository

    Piatek, Agnieszka

    2016-03-01

    The ability to precisely regulate gene expression patterns and to modify genome sequence in a site-specific manner holds much promise in determining gene function and linking genotype to phenotype. DNA-binding modules have been harnessed to generate customizable and programmable chimeric proteins capable of binding to site-specific DNA sequences and regulating the genome and epigenome. Modular DNA-binding domains from zinc fingers (ZFs) and transcriptional activator-like effectors (TALEs) are amenable to engineering to bind any DNA target sequence of interest. Deciphering the code of TALE repeat binding to DNA has helped to engineer customizable TALE proteins capable of binding to any sequence of interest. Therefore TALE repeats provide a rich resource for bioengineering applications. However, the TALE system is limited by the requirement to re-engineer one or two proteins for each new target sequence. Recently, the clustered regularly interspaced palindromic repeats (CRISPR)/ CRISPR associated 9 (Cas9) has been used as a versatile genome editing tool. This machinery has been also repurposed for targeted transcriptional regulation. Due to the facile engineering, simplicity and precision, the CRISPR/Cas9 system is poised to revolutionize the functional genomics studies across diverse eukaryotic species. In this dissertation I employed transcription activator-like effectors and CRISPR/Cas9 systems for targeted genome regulation and editing and my achievements include: 1) I deciphered and extended the DNA-binding code of Ralstonia TAL effectors providing new opportunities for bioengineering of customizable proteins; 2) I repurposed the CRISPR/Cas9 system for site-specific regulation of genes in plant genome; 3) I harnessed the power of CRISPR/Cas9 gene editing tool to study the function of the serine/arginine-rich (SR) proteins.

  2. Enhancing Student Revising and Editing Skills through Writing Conferences and Peer Editing.

    Science.gov (United States)

    Stemper, Julie

    This report describes instructional strategies to improve the revising and editing skills of sixth grade students during the writing process. The literature review suggested improved instruction and evaluation through a writing workshop approach as a possible solution to the problem of poor revision skills. Within this structure, research also…

  3. Constrained Microaggregation: Adding Constraints for Data Editing

    Directory of Open Access Journals (Sweden)

    Vicenc Torra

    2008-08-01

    Full Text Available Privacy preserving data mining and statistical disclosure control have introduced several methods for data perturbation that can be used for ensuring the privacy of data respondents. Such methods, as rank swapping and microaggregation, perturbate the data introducing some kind of noise. Nevertheless, it is usual that data are edited with care after collection to remove inconsistencies, and such perturbation might cause the introduction of new inconsistencies to them. In this paper we study the development of methods for microaggregation that avoid the introduction of such inconsistencies. That is, methods that ensure the protected data to satisfy a set of given constraints.

  4. European Corporate Law, 2nd edition

    DEFF Research Database (Denmark)

    Werlauff, Erik; Dorresteijn, Adriaan; Monteiro, Tiago Pereira

    a fundamentally similar set of legal characteristics. To its original selection of six representative jurisdictions - Belgium, France, Germany, The Netherlands, Spain, and the United Kingdom - the Second Edition now adds Poland, thus including an Eastern European perspective to supplement those of continental...... to incorporate in a jurisdiction not its own; competition among the legal forms of different Member States; safeguarding of employee involvement in cross-border transactions, especially mergers; simplified company forms adopted in several jurisdictions; creation of new forms of business organisations and step...

  5. PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation

    OpenAIRE

    2013-01-01

    RNA editing is vast in some genetic systems, with up to thousands of targeted C-to-U and U-to-C substitutions in mitochondria and chloroplasts of certain plants. Efficient prognoses of RNA editing in organelle genomes will help to reveal overlooked cases of editing. We present PREPACT 2.0 (http://www.prepact.de) with numerous enhancements of our previously developed Plant RNA Editing Prediction & Analysis Computer Tool. Reference organelle transcriptomes for editing prediction have been exten...

  6. Concepts and tools for gene editing.

    Science.gov (United States)

    Josa, Santiago; Seruggia, Davide; Fernández, Almudena; Montoliu, Lluis

    2016-01-01

    Gene editing is a relatively recent concept in the molecular biology field. Traditional genetic modifications in animals relied on a classical toolbox that, aside from some technical improvements and additions, remained unchanged for many years. Classical methods involved direct delivery of DNA sequences into embryos or the use of embryonic stem cells for those few species (mice and rats) where it was possible to establish them. For livestock, the advent of somatic cell nuclear transfer platforms provided alternative, but technically challenging, approaches for the genetic alteration of loci at will. However, the entire landscape changed with the appearance of different classes of genome editors, from initial zinc finger nucleases, to transcription activator-like effector nucleases and, most recently, with the development of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas). Gene editing is currently achieved by CRISPR-Cas-mediated methods, and this technological advancement has boosted our capacity to generate almost any genetically altered animal that can be envisaged.

  7. Gene Editing, Enhancing and Women's Role.

    Science.gov (United States)

    Simonstein, Frida

    2017-02-02

    A recent article on the front page of The Independent (September 18, 2015) reported that the genetic 'manipulation' of IVF embryos is to start in Britain, using a new revolutionary gene-editing technique, called Crispr/Cas9. About three weeks later (Saturday 10, October 2015), on the front page of the same newspaper, it was reported that the National Health Service (NHS) faces a one billion pound deficit only 3 months into the new year. The hidden connection between these reports is that gene editing could be used to solve issues related to health care allocation. Improving the health of future generations might coincide with public health goals; it might improve the health of individuals and communities, and, if successful, might be seen as a public good. However, enhancing future generations will require In Vitro Fertilisation and Pre-implantation Genetic Diagnosis. Remarkably, the necessary involvement of women in an enhancing scenario has not been discussed by its proponents. The present discourse on moral obligations of future generations, although not referring to women, seems to imply that women might be required, morally, if not legally, to reproduce with IVF. Enhancing future generations will be gendered, unless the artificial womb is developed. These are challenging issues that require a wider perspective, of both women and men. Despite the lack of a unified feminist conclusion in the discussions about the merits and risks of human genome modification, there is an urgent need to clarify the role of women in this scenario.

  8. How Online Access Changed Amateur Video Editing

    Directory of Open Access Journals (Sweden)

    Eugster Benjamin

    2014-12-01

    Full Text Available Digital technology has often been discussed in relation to how it changed either the production or the reception of audiovisual cultures. This paper will consider a combination of both as a crucial part in understanding strategies of inter- and transmedial amateur creativity. Based on an experimental ethnography of the online video subgenre/subculture “YouTubePoop,” the paper will elaborate on the connection between the individual experience and the creation of digital media. The loose collective of independent amateurs behind the YouTubePoop videos makes use of already existing audiovisual material ranging from television shows to videos of other YouTube users. The re-created remixes and mash-ups are characterized by their random selection of original material and their nonsensical humour. Hence, the rapid montage of this heterogeneous content is just as much part of the intensified aesthetic expressiveness as are the applied special effects available in the digital video editing software. Both aspects highlight the strong interdependence of the rapid accessibility of online content and digital technology and the new aesthetic expressions they are fostering. The paper will show how the experience and navigation of digital interfaces (editing software, media players, or homepages affect the design and practice of these video-remixes. This will open the discussion about intertextual strategies of media appropriation to an aesthetic and praxeological analysis of media interaction.

  9. Gene regulation by mRNA editing

    Energy Technology Data Exchange (ETDEWEB)

    Ashkenas, J. [Univ. of Washington, Seattle, WA (United States)

    1997-02-01

    The commonly cited figure of 10{sup 5} genes in the human genome represents a tremendous underestimate of our capacity to generate distinct gene products with unique functions. Our cells possess an impressive collection of tools for altering the products of a single gene to create a variety of proteins. The different gene products may have related but distinct functions, allowing cells of different types or at different developmental stages to fine-tune their patterns of gene expression. These tools may act in the cytoplasm, as when proteins undergo post-translational modifications, or in the nucleus, in the processing of pre-mRNA. Two forms of intranuclear fine-tuning are well established and widely studied: alternative splicing of pre-mRNAs and alternative polyadenylation site selection. In recent years it has become clear that cells possess yet another tool to create RNA sequence diversity, mRNA editing. The term {open_quotes}editing{close_quotes} is applied to posttranscriptional modifications of a purine or pyrimidine, which alter an mRNA sequence as it is read, for example, by ribosomes. Covalent changes to the structure of nucleotide bases are well known to occur on tRNA and rRNA molecules, but such changes in mRNA sequence are novel in that they have the capacity to change specific protein sequences. 43 refs., 1 fig.

  10. Educators Guide to Free Films. Thirty Second Annual Edition.

    Science.gov (United States)

    Horkheimer, Mary Foley, Ed.; Diffor, John C., Ed.

    The 32nd annual edition is a complete, cummulative catalog of 4,779 free films, 828 of which were not listed in the previous edition. A table of contents provides a curricular classification of the materials listed, the body of the guide gives full information on each title by curricular area, a title index provides access to any specific listing…

  11. Recollection Rejection: How Children Edit Their False Memories.

    Science.gov (United States)

    Brainerd, C. J.; Reyna, V. F.

    2002-01-01

    Presents new measure of children's use of an editing operation that suppresses false memories by accessing verbatim traces of true events. Application of the methodology showed that false-memory editing increased dramatically between early and middle childhood. Measure reacted appropriately to experimental manipulations. Developmental reductions…

  12. Foundations of Psychological Testing: A Practical Approach. Second Edition

    Science.gov (United States)

    McIntire, Sandra A.; Miller, Leslie A.

    2006-01-01

    The second edition of "Foundations of Psychological Testing: A Practical Approach" is a text for undergraduate students new to the field of psychological testing. Using a conversational format, the authors aim to prepare students to be informed consumers as test users or test takers. Features new to the second edition include: (1) New Content; (2)…

  13. 76 FR 68740 - Trademark Manual of Examining Procedure, Eighth Edition

    Science.gov (United States)

    2011-11-07

    ...] Trademark Manual of Examining Procedure, Eighth Edition AGENCY: United States Patent and Trademark Office... Manual of Examining Procedure (``TMEP''), and made available an archived copy of the seventh edition, on..., marked to the attention of Editor, Trademark Manual of Examining Procedure, or by hand delivery to...

  14. 75 FR 69921 - Trademark Manual of Examining Procedure, Seventh Edition

    Science.gov (United States)

    2010-11-16

    ... Patent and Trademark Office Trademark Manual of Examining Procedure, Seventh Edition AGENCY: United... Trademark Office (``USPTO'') issued the seventh edition of the Trademark Manual of Examining Procedure... to the attention of Editor, Trademark Manual of Examining Procedure, or by hand delivery to...

  15. Putative impact of RNA editing on drug discovery.

    Science.gov (United States)

    Decher, Niels; Netter, Michael F; Streit, Anne K

    2013-01-01

    Virtually all organisms use RNA editing as a powerful post-transcriptional mechanism to recode genomic information and to increase functional protein diversity. The enzymatic editing of pre-mRNA by ADARs and CDARs is known to change the functional properties of neuronal receptors and ion channels regulating cellular excitability. However, RNA editing is also an important mechanism for genes expressed outside the brain. The fact that RNA editing breaks the 'one gene encodes one protein' hypothesis is daunting for scientists and a probable drawback for drug development, as scientists might search for drugs targeting the 'wrong' protein. This possible difficulty for drug discovery and development became more evident from recent publications, describing that RNA editing events have profound impact on the pharmacology of some common drug targets. These recent studies highlight that RNA editing can cause massive discrepancies between the in vitro and in vivo pharmacology. Here, we review the putative impact of RNA editing on drug discovery, as RNA editing has to be considered before using high-throughput screens, rational drug design or choosing the right model organism for target validation.

  16. Students' Editing Skills and Attitudes toward Word Processing.

    Science.gov (United States)

    Joram, Elana; And Others

    1990-01-01

    Investigates the writing attitudes and text editing skills of students with considerable experience using word-processing systems toward word processing for different phases of the writing process. Finds the students are poor at text editing and typing. Finds that the students prefer paper and pencil for composing first drafts and prefer word…

  17. Qualitative Data Analysis: A Methods Sourcebook. Third Edition

    Science.gov (United States)

    Miles, Matthew B.; Huberman, A. Michael; Saldana, Johnny

    2014-01-01

    The Third Edition of Miles & Huberman's classic research methods text is updated and streamlined by Johnny Saldaña, author of "The Coding Manual for Qualitative Researchers." Several of the data display strategies from previous editions are now presented in re-envisioned and reorganized formats to enhance reader accessibility and…

  18. The Kamusi Project Edit Engine: A Tool for Collaborative Lexicography.

    Science.gov (United States)

    Benjamin, Martin; Biersteker, Ann

    2001-01-01

    Discusses the design and implementation of the Kamusi Project Edit Engine, a Web-based software system uniquely suited to the needs of Swahili collaborative lexicography. Describes the edit engine, including organization of the lexicon and the mechanics by which participants use the system, discusses philosophical issues confronted in the design,…

  19. Dead links, vaporcuts, and creativity in fan edit replication

    Directory of Open Access Journals (Sweden)

    Joshua Wille

    2015-09-01

    Full Text Available In my examination of a Star Wars prequel trilogy fan edit reportedly made by Topher Grace, I introduce the term vaporcut to describe fan edits with reputations that may generate critical discourse but that are not publicly released. I explore the ways some fan editors attempt to recreate intangible projects but inevitably produce variant works that reflect their own creative perspectives.

  20. An Introduction to Music Therapy: Theory and Practice. Third Edition

    Science.gov (United States)

    Davis, William B.; Gfeller, Kate E.; Thaut, Michael H.

    2008-01-01

    "An Introduction to Music Therapy: Theory and Practice, Third Edition," provides a comprehensive overview of the practice of music therapy for the 21st century. It looks at where we have been, where we are today, and where we might be in the future. Combining sound pedagogy with recent research findings, this new edition has been updated and…

  1. Genome editing: intellectual property and product development in plant biotechnology.

    Science.gov (United States)

    Schinkel, Helga; Schillberg, Stefan

    2016-07-01

    Genome editing is a revolutionary technology in molecular biology. While scientists are fascinated with the unlimited possibilities provided by directed and controlled changes in DNA in eukaryotes and have eagerly adopted such tools for their own experiments, an understanding of the intellectual property (IP) implications involved in bringing genome editing-derived products to market is often lacking. Due to the ingenuity of genome editing, the time between new product conception and its actual existence can be relatively short; therefore knowledge about IP of the various genome editing methods is relevant. This point must be regarded in a national framework as patents are instituted nationally. Therefore, when designing scientific work that could lead to a product, it is worthwhile to consider the different methods used for genome editing not only for their scientific merits but also for their compatibility with a speedy and reliable launch into the desired market.

  2. Germline genome-editing research and its socioethical implications.

    Science.gov (United States)

    Ishii, Tetsuya

    2015-08-01

    Genetically modifying eggs, sperm, and zygotes ('germline' modification) can impact on the entire body of the resulting individual and on subsequent generations. With the advent of genome-editing technology, human germline gene modification is no longer theoretical. Owing to increasing concerns about human germline gene modification, a voluntary moratorium on human genome-editing research and/or the clinical application of human germline genome editing has recently been called for. However, whether such research should be suspended or encouraged warrants careful consideration. The present article reviews recent research on mammalian germline genome editing, discusses the importance of public dialogue on the socioethical implications of human germline genome-editing research, and considers the relevant guidelines and legislation in different countries.

  3. THE TEXT OF CAXTON'S SECOND EDITION OF THE CANTERBURY TALES

    Directory of Open Access Journals (Sweden)

    Bordalejo Bárbara

    2005-12-01

    Full Text Available This article describes recent research on the textual relationship between the first and second editions of the Canterbury Tales printed in England by William Caxton and it also explores the textual affiliations of the manuscript source for the corrections in the second edition. Using both computerised and manual methods the variant readings between the first and second editions of the Tales are isolated. Examples of the textual affiliations of the manuscript source of Caxton's second edition are analysed. This article concludes that the manuscript source for the corrections introduced in Caxton's second edition of the Tales was of the same quality as tlie best extant manuscripts and that its readings can help our understanding of the textual tradition and can clarify the text for editors of the Tales.

  4. Biographical introduction, Summary of Contents (manuscript version), Summary of Contents (Latin edition) and Summary of Contents (German edition)

    OpenAIRE

    Aspaas, Per Pippin

    2016-01-01

    This file contains a biographical introduction on Maximilianus (Maximilian) Hell (1720-1792) followed by summaries of contents of all three known versions of his treatise on the Aurora Borealis, the 'Lucis Boreæ Theoria nova' (manuscript version, c. 1770), 'Aurorae Borealis Theoria Nova' (Latin edition, 1776) and 'Neue Theorie des Nordlichtes' (German edition, 1792).

  5. First Season Catfish Farming. A Workbook for Beginning Pond and Cage Culture of Channel Catfish. Teacher Edition and Student Edition.

    Science.gov (United States)

    Oklahoma State Board of Vocational and Technical Education, Stillwater. Curriculum and Instructional Materials Center.

    This workbook, comprised of both the teacher and student editions, presents guidelines useful for first-year catfish farmers in Oklahoma using pond or cage cultures to raise channel catfish. The teacher edition is a set of unit guidelines only. Contents include a list of suggested readings, important addresses with types of information available…

  6. Book review of “The Biomedical Engineering Handbook” fourth edition, edited by Joseph D. Bronzino, Donald R. Peterson

    OpenAIRE

    Koprowski, Robert

    2016-01-01

    This article is a review of the book “The biomedical engineering handbook”, fourth edition: four volume set (ISBN 9781439825334, 254GBP, 5430 pages) edited by Joseph D. Bronzino and Donald R. Peterson published by the CRC Press Taylor & Francis group in 2015. The content of the book and its importance for biomedical engineering have been discussed in this invited review.

  7. High-Content Analysis of CRISPR-Cas9 Gene-Edited Human Embryonic Stem Cells

    Directory of Open Access Journals (Sweden)

    Jared Carlson-Stevermer

    2016-01-01

    Full Text Available CRISPR-Cas9 gene editing of human cells and tissues holds much promise to advance medicine and biology, but standard editing methods require weeks to months of reagent preparation and selection where much or all of the initial edited samples are destroyed during analysis. ArrayEdit, a simple approach utilizing surface-modified multiwell plates containing one-pot transcribed single-guide RNAs, separates thousands of edited cell populations for automated, live, high-content imaging and analysis. The approach lowers the time and cost of gene editing and produces edited human embryonic stem cells at high efficiencies. Edited genes can be expressed in both pluripotent stem cells and differentiated cells. This preclinical platform adds important capabilities to observe editing and selection in situ within complex structures generated by human cells, ultimately enabling optical and other molecular perturbations in the editing workflow that could refine the specificity and versatility of gene editing.

  8. High-Content Analysis of CRISPR-Cas9 Gene-Edited Human Embryonic Stem Cells.

    Science.gov (United States)

    Carlson-Stevermer, Jared; Goedland, Madelyn; Steyer, Benjamin; Movaghar, Arezoo; Lou, Meng; Kohlenberg, Lucille; Prestil, Ryan; Saha, Krishanu

    2016-01-12

    CRISPR-Cas9 gene editing of human cells and tissues holds much promise to advance medicine and biology, but standard editing methods require weeks to months of reagent preparation and selection where much or all of the initial edited samples are destroyed during analysis. ArrayEdit, a simple approach utilizing surface-modified multiwell plates containing one-pot transcribed single-guide RNAs, separates thousands of edited cell populations for automated, live, high-content imaging and analysis. The approach lowers the time and cost of gene editing and produces edited human embryonic stem cells at high efficiencies. Edited genes can be expressed in both pluripotent stem cells and differentiated cells. This preclinical platform adds important capabilities to observe editing and selection in situ within complex structures generated by human cells, ultimately enabling optical and other molecular perturbations in the editing workflow that could refine the specificity and versatility of gene editing.

  9. NEW APPROACHES IN TEXTUAL EDITING. A SELECTION OF ELECTRONIC EDITIONS UNDER ANALYSIS

    Directory of Open Access Journals (Sweden)

    Isabel De la Cruz

    2005-12-01

    Full Text Available In the present article, we make an approach to the world of digital editions available in electronic format. Using as a starting point Professor González Fernández-Corugedo's classification of some of the best web pages related to the topic (available at http://www.uniovi.es/HELL/Hyptxed.html we have examined the design and contents of some sites that deal with texts mainly in Old and Middle English. The readers are offered an outline of what they are expected to find in every page, highlighting their main virtues and shortcomings. As a result of the analysis of al1 these pages we are ready to propose certain steps necessary in the elaboration of a 'good' electronic edition.

  10. Flatland an edition with notes and commentary

    CERN Document Server

    Abbott, Edwin A; Banchoff, Thomas F

    2010-01-01

    Flatland, Edwin Abbott Abbott's story of a two-dimensional universe, as told by one of its inhabitants who is introduced to the mysteries of three-dimensional space, has enjoyed an enduring popularity from the time of its publication in 1884. This fully annotated edition enables the modern-day reader to understand and appreciate the many "dimensions" of this classic satire. Mathematical notes and illustrations enhance the usefulness of Flatland as an elementary introduction to higher-dimensional geometry. Historical notes show connections to late-Victorian England and to classical Greece. Citations from Abbott's other writings as well as the works of Plato and Aristotle serve to interpret the text. Commentary on language and literary style includes numerous definitions of obscure words. An appendix gives a comprehensive account of the life and work of Flatland's remarkable author.

  11. European Code against Cancer 4th Edition

    DEFF Research Database (Denmark)

    Friis, Søren; Kesminiene, Ausrele; Espina, Carolina

    2015-01-01

    of treatment, and initiation according to the time of menopause. Carcinogenicity has also been established for anti-neoplastic agents used in cancer therapy, immunosuppressants, oestrogen-progestogen contraceptives, and tamoxifen. Medical use of ionising radiation, an established carcinogen, can provide major......The 4th edition of the European Code against Cancer recommends limiting - or avoiding when possible - the use of hormone replacement therapy (HRT) because of the increased risk of cancer, nevertheless acknowledging that prescription of HRT may be indicated under certain medical conditions. Current...... evidence shows that HRT, generally prescribed as menopausal hormone therapy, is associated with an increased risk of cancers of the breast, endometrium, and ovary, with the risk pattern depending on factors such as the type of therapy (oestrogen-only or combined oestrogen-progestogen), duration...

  12. The Challenge of Editing Einstein's Scientific Manuscripts

    CERN Document Server

    Sauer, T

    2004-01-01

    Einstein's research manuscripts provide important insights into his exceptional creativity. At the same time, they can present difficulties for a publication in the documentary edition of the Collected Papers of Albert Einstein (CPAE). The problems are illustrated by discussing how some important examples of Einstein's research manuscripts have been included in previous volumes of the CPAE series: his Scratch Notebook from the years 1910-1914, his so-called Zurich Notebook from 1912, documenting his early search for a generally covariant theory of gravitation, and the Einstein-Besso manuscript from 1913, containing calculations of Mercury's perihelion advance on the basis of the Einstein-Grossmann equations. Another category of research notes are "back-of-an-envelope" calculations. A major challenge for future volumes of the CPAE series are Einstein's Berlin and Princeton research manuscripts on a unified field theory. This batch of some 1700 undated manuscript pages presents a formidable challenge also for h...

  13. Astronomical catalog desk reference, 1994 edition

    Science.gov (United States)

    1994-01-01

    The Astronomical Catalog Desk Reference is designed to aid astronomers in locating machine readable catalogs in the Astronomical Data Center (ADC) archives. The key reference components of this document are as follows: A listing of shortened titles for all catalogs available from the ADC (includes the name of the lead author and year of publication), brief descriptions of over 300 astronomical catalogs, an index of ADC catalog numbers by subject keyword, and an index of ADC catalog numbers by author. The heart of this document is the set of brief descriptions generated by the ADC staff. The 1994 edition of the Astronomical Catalog Desk Reference contains descriptions for over one third of the catalogs in the ADC archives. Readers are encouraged to refer to this section for concise summaries of those catalogs and their contents.

  14. Effects of nuclear weapons. Third edition

    Energy Technology Data Exchange (ETDEWEB)

    Glasstone, S.; Dolan, P.J.

    1977-01-01

    Since the last edition of ''The Effects of Nuclear Weapons'' in 1962 much new information has become available concerning nuclear weapon effects. This has come in part from the series of atmospheric tests, including several at very high altitudes, conducted in the Pacific Ocean area in 1962. In addition, laboratory studies, theoretical calculations, and computer simulations have provided a better understanding of the various effects. A new chapter has been added on the electromagnetic pulse. The chapter titles are as follows: general principles of nuclear explosions; descriptions of nuclear explosions; air blast phenomena in air and surface bursts; air blast loading; structural damage from air blast; shock effects of surface and subsurface bursts; thermal radiation and its effects; initial nuclear radiation; residual nuclear radiation and fallout; radio and radar effects; the electromagnetic pulse and its effects; and biological effects. (LTN)

  15. WYLBUR reference manual. [For interactive text editing

    Energy Technology Data Exchange (ETDEWEB)

    Krupp, R.F.; Messina, P.C.; Peavler, J.M.; Schustack, S.; Starai, T.

    1977-04-01

    WYLBUR is a system for manipulating various kinds of text, such as computer programs, manuscripts, letters, forms, articles, or reports. Its on-line interactive text-editing capabilities allow the user to create, change, and correct text, and to search and display it. WYLBUR also has facilities for job submission and retrieval from remote terminals that make it possible for a user to inquire about the status of any job in the system, cancel jobs that are executing or awaiting execution, reroute output, raise job priority, or get information on the backlog of batch jobs. WYLBUR also has excellent recovery capabilities and a fast response time. This manual describes the WYLBUR version currently used at ANL. It is intended primarily as a reference manual; thus, examples of WYLBUR commands are kept to a minimum. (RWR)

  16. The Effects of Nuclear Weapons. Third edition

    Energy Technology Data Exchange (ETDEWEB)

    Glasstone, S; Dolan, P J

    1977-01-01

    Since the last edition of ''The Effects of Nuclear Weapons'' in 1962 much new information has become available concerning nuclear weapon effects. This has come in part from the series of atmospheric tests, including several at very high altitudes, conducted in the Pacific Ocean area in 1962. In addition, laboratory studies, theoretical calculations, and computer simulations have provided a better understanding of the various effects. A new chapter has been added on the electromagnetic pulse. The chapter titles are as follows: general principles of nuclear explosions; descriptions of nuclear explosions; air blast phenomena in air and surface bursts; air blast loading; structural damage from air blast; shock effects of surface and subsurface bursts; thermal radiation and its effects; initial nuclear radiation; residual nuclear radiation and fallout; radio and radar effects; the electromagnetic pulse and its effects; and biological effects. (LTN)

  17. National solar energy education directory. Second edition

    Energy Technology Data Exchange (ETDEWEB)

    Corcoleotes, G; Cronin, S; Kramer, K; O& #x27; Connor, K

    1980-01-01

    The information contained in this directory is derived from responses to a national survey of educational institutions and organizations involved in solar energy educational activities beyond the secondary school level. Phone calls and follow-up mail requests were used to gather additional information when necessary. Every survey instrument was read, coded, and edited before entry into the data base from which this directory was produced. The Directory is organized alphabetically by state. Institutions and organizations within each state are categorized according to type (Colleges and Universities, Junior/Community Colleges, Vocational/Technical Schools, and Other Educational Institutions and Organizations) and listed alphabetically within these categories. Within each institutional listing the amount of information provided will vary according to the completeness of the survey response received from that institution. (MHR)

  18. Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants.

    Science.gov (United States)

    Osakabe, Yuriko; Watanabe, Takahito; Sugano, Shigeo S; Ueta, Risa; Ishihara, Ryosuke; Shinozaki, Kazuo; Osakabe, Keishi

    2016-05-26

    Genome editing using the CRISPR/Cas9 system can be used to modify plant genomes, however, improvements in specificity and applicability are still needed in order for the editing technique to be useful in various plant species. Here, using genome editing mediated by a truncated gRNA (tru-gRNA)/Cas9 combination, we generated new alleles for OST2, a proton pump in Arabidopsis, with no off-target effects. By following expression of Cas9 and the tru-gRNAs, newly generated mutations in CRIPSR/Cas9 transgenic plants were detected with high average mutation rates of up to 32.8% and no off-target effects using constitutive promoter. Reducing nuclear localization signals in Cas9 decreased the mutation rate. In contrast, tru-gRNA Cas9 cassettes driven by meristematic- and reproductive-tissue-specific promoters increased the heritable mutation rate in Arabidopsis, showing that high expression in the germ line can produce bi-allelic mutations. Finally, the new mutant alleles obtained for OST2 exhibited altered stomatal closing in response to environmental conditions. These results suggest further applications in molecular breeding to improve plant function using optimized plant CRISPR/Cas9 systems.

  19. Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants

    Science.gov (United States)

    Osakabe, Yuriko; Watanabe, Takahito; Sugano, Shigeo S; Ueta, Risa; Ishihara, Ryosuke; Shinozaki, Kazuo; Osakabe, Keishi

    2016-01-01

    Genome editing using the CRISPR/Cas9 system can be used to modify plant genomes, however, improvements in specificity and applicability are still needed in order for the editing technique to be useful in various plant species. Here, using genome editing mediated by a truncated gRNA (tru-gRNA)/Cas9 combination, we generated new alleles for OST2, a proton pump in Arabidopsis, with no off-target effects. By following expression of Cas9 and the tru-gRNAs, newly generated mutations in CRIPSR/Cas9 transgenic plants were detected with high average mutation rates of up to 32.8% and no off-target effects using constitutive promoter. Reducing nuclear localization signals in Cas9 decreased the mutation rate. In contrast, tru-gRNA Cas9 cassettes driven by meristematic- and reproductive-tissue-specific promoters increased the heritable mutation rate in Arabidopsis, showing that high expression in the germ line can produce bi-allelic mutations. Finally, the new mutant alleles obtained for OST2 exhibited altered stomatal closing in response to environmental conditions. These results suggest further applications in molecular breeding to improve plant function using optimized plant CRISPR/Cas9 systems. PMID:27226176

  20. Attitudes of second language students towards self-editing their own written texts

    Directory of Open Access Journals (Sweden)

    Daniel Kasule

    2010-05-01

    Full Text Available Recognizing students’ deliberate e!orts to minimize errors in their written texts is valuable in seeing them as responsible active agents in text creation. This paper reports on a brief survey of the attitudes towards self-editing of seventy university students using a questionnaire and class discussion. The context of the study is characterized by its emphasis on evaluating the finished written product. Findings show that students appreciate the role of self-editing in minimizing errors in their texts and that it helps in eventually producing well-written texts. Conceptualizing writing as discourse and therefore as social practice leads to an understanding of writers as socially-situated actors; repositions the student writer as an active agent in text creation; and is central to student-centred pedagogy. We recommend the recognition of self-editing as a vital element in the writing process and that additional error detection mechanisms namely peers, the lecturer, and the computer, increase student autonomy.

  1. TALE: a tale of genome editing.

    Science.gov (United States)

    Zhang, Mingjie; Wang, Feng; Li, Shifei; Wang, Yan; Bai, Yun; Xu, Xueqing

    2014-01-01

    Transcription activator-like effectors (TALEs), first identified in Xanthomonas bacteria, are naturally occurring or artificially designed proteins that modulate gene transcription. These proteins recognize and bind DNA sequences based on a variable numbers of tandem repeats. Each repeat is comprised of a set of ∼ 34 conserved amino acids; within this conserved domain, there are usually two amino acids that distinguish one TALE from another. Interestingly, TALEs have revealed a simple cipher for the one-to-one recognition of proteins for DNA bases. Synthetic TALEs have been used to successfully target genes in a variety of species, including humans. Depending on the type of functional domain that is fused to the TALE of interest, these proteins can have diverse biological effects. For example, after binding DNA, TALEs fused to transcriptional activation domains can function as robust transcription factors (TALE-TFs), while fused to restriction endonucleases (TALENs) can cut DNA. Targeted genome editing, in theory, is capable of modifying any endogenous gene sequence of interest; this can be performed in cells or organisms, and may be applied to clinical gene-based therapies in the future. With current technologies, highly accurate, specific, and reliable gene editing cannot be achieved. Thus, recognition and binding mechanisms governing TALE biology are currently hot research areas. In this review, we summarize the major advances in TALE technology over the past several years with a focus on the interaction between TALEs and DNA, TALE design and construction, potential applications for this technology, and unique characteristics that make TALEs superior to zinc finger endonucleases.

  2. Free Appearance-Editing with Improved Poisson Image Cloning

    Institute of Scientific and Technical Information of China (English)

    Xiao-Hui Bie; Hao-Da Huang; Wen-Cheng Wang

    2011-01-01

    In this paper,we present a new edit tool for the user to conveniently preserve or freely edit the object appearance during seamless image composition.We observe that though Poisson image editing is effective for seamless image composition.Its color bleeding (the color of the target image is propagated into the source image) is not always desired in applications,and it provides no way to allow the user to edit the appearance of the source image.To make it more flexible and practical,we introduce new energy terms to control the appearance change,and integrate them into the Poisson image editing framework.The new energy function could still be realized using efficient sparse linear solvers,and the user can interactively refine the constraints.With the new tool,the user can enjoy not only seamless image composition,but also the flexibility to preserve or manipulate the appearance of the source image at the same time.This provides more potential for creating new images.Experimental results demonstrate the effectiveness of our new edit tool,with similar time cost to the original Poisson image editing.

  3. The clinical applications of genome editing in HIV.

    Science.gov (United States)

    Wang, Cathy X; Cannon, Paula M

    2016-05-26

    HIV/AIDS has long been at the forefront of the development of gene- and cell-based therapies. Although conventional gene therapy approaches typically involve the addition of anti-HIV genes to cells using semirandomly integrating viral vectors, newer genome editing technologies based on engineered nucleases are now allowing more precise genetic manipulations. The possible outcomes of genome editing include gene disruption, which has been most notably applied to the CCR5 coreceptor gene, or the introduction of small mutations or larger whole gene cassette insertions at a targeted locus. Disruption of CCR5 using zinc finger nucleases was the first-in-human application of genome editing and remains the most clinically advanced platform, with 7 completed or ongoing clinical trials in T cells and hematopoietic stem/progenitor cells (HSPCs). Here we review the laboratory and clinical findings of CCR5 editing in T cells and HSPCs for HIV therapy and summarize other promising genome editing approaches for future clinical development. In particular, recent advances in the delivery of genome editing reagents and the demonstration of highly efficient homology-directed editing in both T cells and HSPCs are expected to spur the development of even more sophisticated applications of this technology for HIV therapy.

  4. [The research on the edition of Daquanbencao (Complete Collection of Materia Medica)].

    Science.gov (United States)

    Li, Jian; Zhang, Wei; Zhang, Rui-xian

    2009-07-01

    Zhengleibencao (Classified Materia Medica) had been formed into several kinds of edition systems during its dissemination, among which there was the edition system of Daquanbencao (Complete Collection of Materia Medica). Daquanbencao was originally carved in the Jin dynasty, thereafter it was re-carved in the Yuan, Ming and Qing dynasties so as to form a series of editions such as the edition of Zhenyou in the second year of the Jin dynasty; the edition of the Zongwenshuyuan college in Dade renyan year of the Yuan dynasty; the WANG Qiu's carved edition of Shangyitang hall in the Ming dynasty; the carved edition of Jishanshuyuan, the Jishang mountain college in the Ming dynasty, the reprinted edition of PENG Duan-wu in the Ming dynasty, the supplementary edition of YANG Bi-da in the Qing dynasty;, and the carved edition of KE Feng-shi in the Qing dynasty. Among all the editions, Chongkanjingshizhengleidaquanbencao (Reprinted Classified Daquan Materia Medica from Historical Classics) was the representative one. As a representative of the above editions, the carved edition of WANG took the edition of the Zongwenshuyuan college of the Yuan dynasty as the original edition, but the images picture of materia medica adopted from the edition of Zhenghebencao (Materia Medica of the Zhenghe era).

  5. [From random mutagenesis to precise genome editing: the development and evolution of genome editing techniques in Drosophila].

    Science.gov (United States)

    Su, Fang; Huang, Zongliang; Guo, Yawen; Jiao, Renjie; Zi, Li; Chen, Jianming; Liu, Jiyong

    2016-01-01

    Drosophila melanogaster, an important model organism for studying life science, has contributed more to the research of genetics, developmental biology and biomedicine with the development of genome editing techniques. Drosophila genome-editing techniques have evolved from random mutagenesis to precise genome editing and from simple mutant construction to diverse genome editing methods since the 20th century. Chemical mutagenesis, using Ethyl methanesulfonate (EMS), is an important technique to study gene function in forward genetics, however, the precise knockout of Drosophila genes could not be achieved. The gene targeting technology, based on homologous recombination, has accomplished the precise editing of Drosophila genome for the first time, but with low efficiency. The CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein)-mediated precise genome editing is simple, fast and highly efficient compared with the gene targeting technology in Drosophila. In this review, we focus on Drosophila gene knockout, and summarize the evolution of genome editing techniques in Drosophila, emphasizing the development and applications of gene targeting, zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and CRISPR/Cas9 techniques.

  6. A model for codon position bias in RNA editing

    CERN Document Server

    Liu, T; Liu, Tsunglin; Bundschuh, Ralf

    2005-01-01

    RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias in choosing the positions of the editing sites. In the mitochondrial genes of {\\it Physarum polycephalum}, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose an evolutionary model that explains this bias as the basis of selection at the protein level. The model predicts a distribution of the three positions rather close to the experimental observation in {\\it Physarum}. This suggests that the codon position bias in {\\it Physarum} is mainly a consequence of selection at the protein level.

  7. Review of Methods of Critical Discourse Analysis (second edition)

    Institute of Scientific and Technical Information of China (English)

    邵晓巍

    2014-01-01

    This article, through giving an overview of Methods of Critical Discourse Analysis(second edition), introduces six methodology of doing Critical Discourse Analysis. It is hoped that this article will help those interested in CDA better usher into this field.

  8. Advancing Crop Transformation in the Era of Genome Editing

    Science.gov (United States)

    Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than thirty years of technological advances. Genome editing provides new opportunities to...

  9. Towards social acceptance of plant breeding by genome editing.

    Science.gov (United States)

    Araki, Motoko; Ishii, Tetsuya

    2015-03-01

    Although genome-editing technologies facilitate efficient plant breeding without introducing a transgene, it is creating indistinct boundaries in the regulation of genetically modified organisms (GMOs). Rapid advances in plant breeding by genome-editing require the establishment of a new global policy for the new biotechnology, while filling the gap between process-based and product-based GMO regulations. In this Opinion article we review recent developments in producing major crops using genome-editing, and we propose a regulatory model that takes into account the various methodologies to achieve genetic modifications as well as the resulting types of mutation. Moreover, we discuss the future integration of genome-editing crops into society, specifically a possible response to the 'Right to Know' movement which demands labeling of food that contains genetically engineered ingredients.

  10. Developing Editing Skills in the Beginning Technical Writing Class.

    Science.gov (United States)

    Forbes, Christopher J.

    1986-01-01

    Offers a plan for developing student editing skills in the beginning technical writing class. Suggests guidelines that parallel the revision-oriented heuristics of such scholars as Michael Flanigan and Linda Flower. (FL)

  11. The emerging role of RNA editing in plasticity.

    Science.gov (United States)

    Rosenthal, Joshua J C

    2015-06-01

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

  12. Spatio-temporal regulation of ADAR editing during development in porcine neural tissues

    DEFF Research Database (Denmark)

    Venø, Morten Trillingsgaard; Bramsen, Jesper Bertram; Bendixen, Christian;

    2012-01-01

    Editing by ADAR enzymes is essential for mammalian life. Still, knowledge of the spatio-temporal editing patterns in mammals is limited. By use of 454 amplicon sequencing we examined the editing status of 12 regionally extracted mRNAs from porcine developing brain encompassing a total of 64 putat...... putative ADAR editing sites. In total 24 brain tissues, dissected from up to five regions from embryonic gestation day 23, 42, 60, 80, 100 and 115, were examined for editing....

  13. A combinational CRISPR/Cas9 gene-editing approach can halt HIV replication and prevent viral escape

    Science.gov (United States)

    Lebbink, Robert Jan; de Jong, Dorien C. M.; Wolters, Femke; Kruse, Elisabeth M.; van Ham, Petra M.; Wiertz, Emmanuel J. H. J.; Nijhuis, Monique

    2017-01-01

    HIV presents one of the highest evolutionary rates ever detected and combination antiretroviral therapy is needed to overcome the plasticity of the virus population and control viral replication. Conventional treatments lack the ability to clear the latent reservoir, which remains the major obstacle towards a cure. Novel strategies, such as CRISPR/Cas9 gRNA-based genome-editing, can permanently disrupt the HIV genome. However, HIV genome-editing may accelerate viral escape, questioning the feasibility of the approach. Here, we demonstrate that CRISPR/Cas9 targeting of single HIV loci, only partially inhibits HIV replication and facilitates rapid viral escape at the target site. A combinatorial approach of two strong gRNAs targeting different regions of the HIV genome can completely abrogate viral replication and prevent viral escape. Our data shows that the accelerating effect of gene-editing on viral escape can be overcome and as such gene-editing may provide a future alternative for control of HIV-infection. PMID:28176813

  14. [The Washington summit: orange light for genome editing?].

    Science.gov (United States)

    Jordan, Bertrand

    2016-02-01

    The summit organised in early December 2015 considered in depth the various issues (technical, scientific, societal and ethical) raised by the prospect of genome editing using the extremely effective CRISPR system. Germline editing (for therapeutic or "enhancement" purposes) was stated to be irresponsible under current conditions, but the possibility that this could be considered in the future was not excluded; a mechanism for monitoring progress and possibly revising recommendations was proposed.

  15. Towards a critical edition of Fibonacci’s Liber Abaci

    Directory of Open Access Journals (Sweden)

    Giuseppe Germano

    2013-11-01

    Full Text Available A group of research working at the University of Naples Federico II aim to achieve the goal to offer a modern scientific and widely accessible edition of Fibonacci’s treatise. With a linguistic-philological, an historical-mathematical and a computer approach it has pointed out the value and the need for a multidisciplinary research in order to achieve the goal of making this edition adequately available to the scientific community.

  16. SECONDARY RECEPTOR EDITING IN THE GENERATION OF AUTOIMMUNITY

    Science.gov (United States)

    Eisenberg, Robert A.

    2012-01-01

    Receptor editing is the process that replaces the heavy chain or light chain variable region genes in a B-cell immunoglobulin receptor that is already productively rearranged. It is a major mechanism in the bone marrow for maintaining B-cell tolerance to autoantigens. We propose that a pathological autoimmune process can use receptor editing to induce the de novo creation and activation of B cells with autoreactive receptors in the peripheral immune system. PMID:22349618

  17. Genome Editing for the Generation of Immunodeficient Pigs

    OpenAIRE

    Nestle-Nguyen, Denise

    2015-01-01

    Genome editing comprises the use of customizable engineered nucleases for the genetic modification of cells. Two commonly used systems are transcription activator-like effector nucleases (TALEN) and the CRISPR/Cas system. During this study, genome editing tools were applied for the modification of three genes (JAK3, RAG1, RAG2) playing crucial roles in the immune system, with the aim of generating immunodeficient pigs. Unter dem Begriff “Genome Editing” versteht man die Verwendung von modi...

  18. Molecular Biology of the Cell, Sixth Edition; ISBN: 9780815344643; and Molecular Biology of the Cell, Sixth Edition, The Problems Book; ISBN 9780815344537

    Directory of Open Access Journals (Sweden)

    Stephen Bustin

    2015-11-01

    Full Text Available The latest edition maintains the excellence and appeal of the previous editions. Its clear text and outstanding illustrations, together with the complementary problems book make this an essential companion for students and lecturers alike.

  19. Genome Editing: A New Approach to Human Therapeutics.

    Science.gov (United States)

    Porteus, Matthew

    2016-01-01

    The ability to manipulate the genome with precise spatial and nucleotide resolution (genome editing) has been a powerful research tool. In the past decade, the tools and expertise for using genome editing in human somatic cells and pluripotent cells have increased to such an extent that the approach is now being developed widely as a strategy to treat human disease. The fundamental process depends on creating a site-specific DNA double-strand break (DSB) in the genome and then allowing the cell's endogenous DSB repair machinery to fix the break such that precise nucleotide changes are made to the DNA sequence. With the development and discovery of several different nuclease platforms and increasing knowledge of the parameters affecting different genome editing outcomes, genome editing frequencies now reach therapeutic relevance for a wide variety of diseases. Moreover, there is a series of complementary approaches to assessing the safety and toxicity of any genome editing process, irrespective of the underlying nuclease used. Finally, the development of genome editing has raised the issue of whether it should be used to engineer the human germline. Although such an approach could clearly prevent the birth of people with devastating and destructive genetic diseases, questions remain about whether human society is morally responsible enough to use this tool.

  20. Fundamentals of Physics, 6th Edition Enhanced Problems Version

    Science.gov (United States)

    Halliday, David; Resnick, Robert; Walker, Jearl

    2002-04-01

    No other text on the market today can match the success of Halliday, Resnick and Walker's Fundamentals of Physics. This text continues to outperform the competition year after year, and the new edition will be no exception. Intended for Calculus-based Physics courses, the 6th edition of this extraordinary text is a major redesign of the best-selling 5th edition, which still maintains many of the elements that led to its enormous success. Jearl Walker adds his unique style to this edition with the addition of new problems designed to capture, and keep, students' attention. Nearly all changes are based on suggestions from instructors and students using the 5th edition, from reviewer comments, and from research done on the process of learning. The primary goal of this text is to provide students with a solid understanding of fundamental physics concepts, and to help them apply this conceptual understanding to quantitative problem solving. The principal goal of Halliday-Resnick-Walker is to provide instructors with a tool by which they can teach students how to effectively read scientific material and successfully reason through scientific questions. To sharpen this tool, the Enhanced Problems Version of the sixth edition of Fundamentals of Physics contains over 1000 new, high-quality problems that require thought and reasoning rather than simplistic plugging of data into formulas.

  1. A robust TALENs system for highly efficient mammalian genome editing.

    Science.gov (United States)

    Feng, Yuanxi; Zhang, Siliang; Huang, Xin

    2014-01-10

    Recently, transcription activator-like effector nucleases (TALENs) have emerged as a highly effective tool for genomic editing. A pair of TALENs binds to two DNA recognition sites separated by a spacer sequence, and the dimerized FokI nucleases at the C terminal then cleave DNA in the spacer. Because of its modular design and capacity to precisely target almost any desired genomic locus, TALEN is a technology that can revolutionize the entire biomedical research field. Currently, for genomic editing in cultured cells, two plasmids encoding a pair of TALENs are co-transfected, followed by limited dilution to isolate cell colonies with the intended genomic manipulation. However, uncertain transfection efficiency becomes a bottleneck, especially in hard-to-transfect cells, reducing the overall efficiency of genome editing. We have developed a robust TALENs system in which each TALEN plasmid also encodes a fluorescence protein. Thus, cells transfected with both TALEN plasmids, a prerequisite for genomic editing, can be isolated by fluorescence-activated cell sorting. Our improved TALENs system can be applied to all cultured cells to achieve highly efficient genomic editing. Furthermore, an optimized procedure for genomic editing using TALENs is also presented. We expect our system to be widely adopted by the scientific community.

  2. Statistical optimisation techniques in fatigue signal editing problem

    Energy Technology Data Exchange (ETDEWEB)

    Nopiah, Z. M.; Osman, M. H. [Fundamental Engineering Studies Unit Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM (Malaysia); Baharin, N.; Abdullah, S. [Department of Mechanical and Materials Engineering Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM (Malaysia)

    2015-02-03

    Success in fatigue signal editing is determined by the level of length reduction without compromising statistical constraints. A great reduction rate can be achieved by removing small amplitude cycles from the recorded signal. The long recorded signal sometimes renders the cycle-to-cycle editing process daunting. This has encouraged researchers to focus on the segment-based approach. This paper discusses joint application of the Running Damage Extraction (RDE) technique and single constrained Genetic Algorithm (GA) in fatigue signal editing optimisation.. In the first section, the RDE technique is used to restructure and summarise the fatigue strain. This technique combines the overlapping window and fatigue strain-life models. It is designed to identify and isolate the fatigue events that exist in the variable amplitude strain data into different segments whereby the retention of statistical parameters and the vibration energy are considered. In the second section, the fatigue data editing problem is formulated as a constrained single optimisation problem that can be solved using GA method. The GA produces the shortest edited fatigue signal by selecting appropriate segments from a pool of labelling segments. Challenges arise due to constraints on the segment selection by deviation level over three signal properties, namely cumulative fatigue damage, root mean square and kurtosis values. Experimental results over several case studies show that the idea of solving fatigue signal editing within a framework of optimisation is effective and automatic, and that the GA is robust for constrained segment selection.

  3. KEIMS utility manual (edition 1.0)

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yeun Seung; Eom, Young Sam; Choi, Jin Yeup; Nam, Ji Hwa [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1996-06-01

    Since 1987 when KAERI had started Yonggwang 3 and 4 NSSS system design project, KAERI has carried out so many NSSS system design projects such as Ulchin 3 and 4, Wolsong 2, 3 and 4 and Yonggwang 5 and 6 with fixed members that necessity of increasing productivity has been raised. To improve design work efficiency, it was considered that computerization of workflow which took so much man-power and business time. As result of investigation of design workflow to reduce man-power loss. It was suggested that DDA (Document Distribution for Agreement) workflow, design document stored in DDCD (Document Distribution and Control Center), IOC (Interoffice Correspondence) document, Letter, PM Memo should be preferentially computerized. On the basis of these computerization requirements, MEDIS (Modular Engineering Document Imaging System) was selected. Prototype had been implemented during 1995.9 -1995.12, and from 1996.1 KEIMS (KAERI Engineering Information Management System) has been operated. This MEDIS system utility manual was composed of several technical memos which has been described on customization of MEDIS fit to KEIMS, program development for system check, and information control of database. Further edition would be released as utility technical memo added. (Author) .new.

  4. Transportation energy data book: Edition 13

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.; Strang, S.G.

    1993-03-01

    The Transportation Energy Data Book: Edition 13 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. Each of the major transportation modes -- highway, air, water, rail, pipeline -- is treated in separate chapters or sections. Chapter 1 compares US transportation data with data from seven other countries. Aggregate energy use and energy supply data for all modes are presented in Chapter 2. The highway mode, which accounts for over three-fourths of total transportation energy consumption, is dealt with in Chapter 3. Topics in this chapter include automobiles, trucks, buses, fleet automobiles, federal standards, fuel economies, and vehicle emission data. Household travel behavior characteristics are displayed in Chapter 4. Chapter 5 contains information on alternative fuels and alternatively-fueled vehicles. The last chapter, Chapter 6, covers each of the nonhighway modes: air, water, pipeline, and rail, respectively.

  5. Transportation energy data book: Edition 12

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.; Morris, M.D.

    1992-03-01

    The Transportation Energy Data Book: Edition 12 is a statistical compendium prepared and published by Oak Ridge National Laboratory under contract with the Office of Transportation Technologies in the Department of Energy. Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. Each of the major transportation modes--highway, air, water, rail, pipeline--is treated in separate chapters or sections. Chapter 1 compares US transportation data with data from seven other countries. Aggregate energy use and energy supply data for all modes are presented in Chapter 2. The highway mode, which accounts for over three-fourths of total transportation energy consumption, is dealt with in Chapter 3. Topics in this chapter include automobiles, trucks, buses, fleet automobiles, federal standards, fuel economies, and vehicle emission data. Household travel behavior characteristics are displayed in Chapter 4. Chapter 5 contains information on alternative fuels and alternatively-fueled vehicles. The last chapter, Chapter 6, covers each of the nonhighway modes: air, water, pipeline, and rail, respectively.

  6. Transportation energy data book: edition 16

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C. [Lockheed Martin Energy Systems, Inc., Oak Ridge, TN (United States); McFarlin, D.N. [Tennessee Univ., Knoxville, TN (United States)

    1996-07-01

    The Transportation Energy Data Book: Edition 16 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. Each of the major transportation modes is treated in separate chapters or sections. Chapter 1 compares U.S. transportation data with data from other countries. Aggregate energy use and energy supply data for all modes are presented in Chapter 2. The highway mode, which accounts for over three-fourths of total transportation energy consumption, is dealt with in Chapter 3. Topics in this chapter include automobiles, trucks, buses, fleet vehicles, federal standards, fuel economies, and high- occupancy vehicle lane data. Household travel behavior characteristics are displayed in Chapter 4. Chapter 5 contains information on alternative fuels and alternative fuel vehicles. Chapter 6 covers the major nonhighway modes: air, water, and rail. The last chapter, Chapter 7, presents data on environmental issues relating to transportation.

  7. Transportation energy data book: Edition 15

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.

    1995-05-01

    The Transportation Energy Data Book: Edition 15 is a statistical compendium. Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. Purpose of this document is to present relevant statistical data in the form of tables and graphs. Each of the major transportation modes is treated in separate chapters or sections. Chapter I compares US transportation data with data from other countries. Aggregate energy use and energy supply data for all modes are presented in Chapter 2. The highway mode, which accounts for over three-fourths of total transportation energy consumption, is dealt with in Chapter 3. Topics in this chapter include automobiles, trucks, buses, fleet vehicles, federal standards, fuel economies, and high-occupancy vehicle lane data. Household travel behavior characteristics are displayed in Chapter 4. Chapter 5 contains information on alternative fuels and alternative fuel vehicles. Chapter 6 covers the major nonhighway modes: air, water, and rail. The last chapter, Chapter 7, presents data environmental issues relating to transportation.

  8. Transportation energy data book: Edition 13

    Energy Technology Data Exchange (ETDEWEB)

    Davis, S.C.; Strang, S.G.

    1993-03-01

    The Transportation Energy Data Book: Edition 13 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of Transportation Technologies in the Department of Energy (DOE). Designed for use as a desk-top reference, the data book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. Each of the major transportation modes - highway, air, water, rail, pipeline - is treated in separate chapters or sections. Chapter 1 compares US transportation data with data from seven other countries. Aggregate energy use and energy supply data for all modes are presented in Chapter 2. The highway mode, which accounts for over three-fourths of total transportation energy consumption, is dealt with in Chapter 3. Topics in this chapter include automobiles, trucks, buses, fleet automobiles, federal standards, fuel economies, and vehicle emission data. Household travel behavior characteristics are displayed in Chapter 4. Chapter 5 contains information on alternative fuels and alternatively-fueled vehicles. The last chapter, Chapter 6, covers each of the nonhighway modes: air, water, pipeline, and rail, respectively.

  9. Gene Editing for Treatment of Neurological Infections.

    Science.gov (United States)

    White, Martyn K; Kaminski, Rafal; Wollebo, Hassen; Hu, Wenhui; Malcolm, Thomas; Khalili, Kamel

    2016-07-01

    The study of neurological infections by viruses defines the field of neurovirology, which has emerged in the last 30 years and was founded upon the discovery of a number of viruses capable of infecting the human nervous system. Studies have focused on the molecular and biological basis of viral neurological diseases with the aim of revealing new therapeutic options. The first studies of neurovirological infections can be traced back to the discovery that some viruses have an affinity for the nervous system with research into rabies by Louis Pasteur and others in the 1880s. Today, the immense public health impact of neurovirological infections is illustrated by diseases such as neuroAIDS, progressive multifocal leukoencephalopathy, and viral encephalitis. Recent research has seen the development of powerful new techniques for gene editing that promise revolutionary opportunities for the development of novel therapeutic options. In particular, clustered regulatory interspaced short palindromic repeat-associated 9 system provides an effective, highly specific and versatile tool for targeting DNA viruses that are beginning to allow the development of such new approaches. In this short review, we discuss these recent developments, how they pertain to neurological infections, and future prospects.

  10. Labview advanced programming techniques, second edition

    CERN Document Server

    Bitter, Rick; Nawrocki, Matt

    2006-01-01

    Whether seeking deeper knowledge of LabVIEW®'s capabilities or striving to build enhanced VIs, professionals know they will find everything they need in LabVIEW: Advanced Programming Techniques. Now accompanied by LabVIEW 2011, this classic second edition, focusing on LabVIEW 8.0, delves deeply into the classic features that continue to make LabVIEW one of the most popular and widely used graphical programming environments across the engineering community. The authors review the front panel controls, the Standard State Machine template, drivers, the instrument I/O assistant, error handling functions, hyperthreading, and Express VIs. It covers the introduction of the Shared Variables function in LabVIEW 8.0 and explores the LabVIEW project view. The chapter on ActiveX includes discussion of the Microsoft™ .NET® framework and new examples of programming in LabVIEW using .NET. Numerous illustrations and step-by-step explanations provide hands-on guidance. Reviewing LabVIEW 8.0 and accompanied by the latest s...

  11. Comparative biomechanics: life's physical world (second edition)

    CERN Document Server

    Vogel, Steven

    2013-01-01

    Why do you switch from walking to running at a specific speed? Why do tall trees rarely blow over in high winds? And why does a spore ejected into air at seventy miles per hour travel only a fraction of an inch? Comparative Biomechanics is the first and only textbook that takes a comprehensive look at the mechanical aspects of life--covering animals and plants, structure and movement, and solids and fluids. An ideal entry point into the ways living creatures interact with their immediate physical world, this revised and updated edition examines how the forms and activities of animals and plants reflect the materials available to nature, considers rules for fluid flow and structural design, and explores how organisms contend with environmental forces. Drawing on physics and mechanical engineering, Steven Vogel looks at how animals swim and fly, modes of terrestrial locomotion, organism responses to winds and water currents, circulatory and suspension-feeding systems, and the relationship between size and mech...

  12. Antiviral Defenses in Plants through Genome Editing

    Science.gov (United States)

    Romay, Gustavo; Bragard, Claude

    2017-01-01

    Plant–virus interactions based-studies have contributed to increase our understanding on plant resistance mechanisms, providing new tools for crop improvement. In the last two decades, RNA interference, a post-transcriptional gene silencing approach, has been used to induce antiviral defenses in plants with the help of genetic engineering technologies. More recently, the new genome editing systems (GES) are revolutionizing the scope of tools available to confer virus resistance in plants. The most explored GES are zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats/Cas9 endonuclease. GES are engineered to target and introduce mutations, which can be deleterious, via double-strand breaks at specific DNA sequences by the error-prone non-homologous recombination end-joining pathway. Although GES have been engineered to target DNA, recent discoveries of GES targeting ssRNA molecules, including virus genomes, pave the way for further studies programming plant defense against RNA viruses. Most of plant virus species have an RNA genome and at least 784 species have positive ssRNA. Here, we provide a summary of the latest progress in plant antiviral defenses mediated by GES. In addition, we also discuss briefly the GES perspectives in light of the rebooted debate on genetic modified organisms (GMOs) and the current regulatory frame for agricultural products involving the use of such engineering technologies. PMID:28167937

  13. Biomass Energy Data Book: Edition 2

    Energy Technology Data Exchange (ETDEWEB)

    Wright, Lynn L [ORNL; Boundy, Robert Gary [ORNL; Badger, Philip C [ORNL; Perlack, Robert D [ORNL; Davis, Stacy Cagle [ORNL

    2009-12-01

    The Biomass Energy Data Book is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Biomass Program in the Energy Efficiency and Renewable Energy (EERE) program of the Department of Energy (DOE). Designed for use as a convenient reference, the book represents an assembly and display of statistics and information that characterize the biomass industry, from the production of biomass feedstocks to their end use, including discussions on sustainability. This is the second edition of the Biomass Energy Data Book which is only available online in electronic format. There are five main sections to this book. The first section is an introduction which provides an overview of biomass resources and consumption. Following the introduction to biomass, is a section on biofuels which covers ethanol, biodiesel and bio-oil. The biopower section focuses on the use of biomass for electrical power generation and heating. The fourth section is on the developing area of biorefineries, and the fifth section covers feedstocks that are produced and used in the biomass industry. The sources used represent the latest available data. There are also four appendices which include frequently needed conversion factors, a table of selected biomass feedstock characteristics, assumptions for selected tables and figures, and discussions on sustainability. A glossary of terms and a list of acronyms are also included for the reader's convenience.

  14. Biomass Energy Data Book: Edition 4

    Energy Technology Data Exchange (ETDEWEB)

    Boundy, Robert Gary [ORNL; Diegel, Susan W [ORNL; Wright, Lynn L [ORNL; Davis, Stacy Cagle [ORNL

    2011-12-01

    The Biomass Energy Data Book is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Biomass Program in the Energy Efficiency and Renewable Energy (EERE) program of the Department of Energy (DOE). Designed for use as a convenient reference, the book represents an assembly and display of statistics and information that characterize the biomass industry, from the production of biomass feedstocks to their end use, including discussions on sustainability. This is the fourth edition of the Biomass Energy Data Book which is only available online in electronic format. There are five main sections to this book. The first section is an introduction which provides an overview of biomass resources and consumption. Following the introduction to biomass, is a section on biofuels which covers ethanol, biodiesel and bio-oil. The biopower section focuses on the use of biomass for electrical power generation and heating. The fourth section is on the developing area of biorefineries, and the fifth section covers feedstocks that are produced and used in the biomass industry. The sources used represent the latest available data. There are also two appendices which include frequently needed conversion factors, a table of selected biomass feedstock characteristics, and discussions on sustainability. A glossary of terms and a list of acronyms are also included for the reader's convenience.

  15. Biomass Energy Data Book: Edition 1

    Energy Technology Data Exchange (ETDEWEB)

    Wright, Lynn L [ORNL; Boundy, Robert Gary [ORNL; Perlack, Robert D [ORNL; Davis, Stacy Cagle [ORNL; Saulsbury, Bo [ORNL

    2006-09-01

    The Biomass Energy Data Book is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Office of the Biomass Program and the Office of Planning, Budget and Analysis in the Department of Energy's Energy Efficiency and Renewable Energy (EERE) program. Designed for use as a desk-top reference, the book represents an assembly and display of statistics and information that characterize the biomass industry, from the production of biomass feedstocks to their end use. This is the first edition of the Biomass Energy Data Book and is currently only available online in electronic format. There are five main sections to this book. The first section is an introduction which provides an overview of biomass resources and consumption. Following the introduction to biomass is a section on biofuels which covers ethanol, biodiesel and BioOil. The biopower section focuses on the use of biomass for electrical power generation and heating. The fourth section is about the developing area of biorefineries, and the fifth section covers feedstocks that are produced and used in the biomass industry. The sources used represent the latest available data. There are also three appendices which include measures of conversions, biomass characteristics and assumptions for selected tables and figures. A glossary of terms and a list of acronyms are also included for the reader's convenience.

  16. Biomass Energy Data Book: Edition 3

    Energy Technology Data Exchange (ETDEWEB)

    Boundy, Robert Gary [ORNL; Davis, Stacy Cagle [ORNL

    2010-12-01

    The Biomass Energy Data Book is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Biomass Program in the Energy Efficiency and Renewable Energy (EERE) program of the Department of Energy (DOE). Designed for use as a convenient reference, the book represents an assembly and display of statistics and information that characterize the biomass industry, from the production of biomass feedstocks to their end use, including discussions on sustainability. This is the third edition of the Biomass Energy Data Book which is only available online in electronic format. There are five main sections to this book. The first section is an introduction which provides an overview of biomass resources and consumption. Following the introduction to biomass, is a section on biofuels which covers ethanol, biodiesel and bio-oil. The biopower section focuses on the use of biomass for electrical power generation and heating. The fourth section is on the developing area of biorefineries, and the fifth section covers feedstocks that are produced and used in the biomass industry. The sources used represent the latest available data. There are also four appendices which include frequently needed conversion factors, a table of selected biomass feedstock characteristics, and discussions on sustainability. A glossary of terms and a list of acronyms are also included for the reader's convenience.

  17. The sun and space weather Second Edition

    CERN Document Server

    Hanslmeier, Arnold

    2007-01-01

    This second edition is a great enhancement of literature which will help the reader get deeper into the specific topics. There are new sections included such as space weather data sources and examples, new satellite missions, and the latest results. At the end a comprehensive index is given which will allow the reader to quickly find his topics of interest. The Sun and Space weather are two rapidly evolving topics. The importance of the Sun for the Earth, life on Earth, climate and weather processes was recognized long ago by the ancients. Now, for the first time there is a continuous surveillance of solar activity at nearly all wavelengths. These data can be used to improve our understanding of the complex Sun-Earth interaction. The first chapters of the book deal with the Sun as a star and its activity phenomena as well as its activity cycle in order to understand the complex physics of the Sun-Earth system. The reader will see that there are many phenomena but still no definite explanations and models exis...

  18. Current status of genome editing in vector mosquitoes: A review.

    Science.gov (United States)

    Reegan, Appadurai Daniel; Ceasar, Stanislaus Antony; Paulraj, Michael Gabriel; Ignacimuthu, Savarimuthu; Al-Dhabi, Naif Abdullah

    2017-01-16

    Mosquitoes pose a major threat to human health as they spread many deadly diseases like malaria, dengue, chikungunya, filariasis, Japanese encephalitis and Zika. Identification and use of novel molecular tools are essential to combat the spread of vector borne diseases. Genome editing tools have been used for the precise alterations of the gene of interest for producing the desirable trait in mosquitoes. Deletion of functional genes or insertion of toxic genes in vector mosquitoes will produce either knock-out or knock-in mutants that will check the spread of vector-borne diseases. Presently, three types of genome editing tools viz., zinc finger nuclease (ZFN), transcription activator-like effector nucleases (TALEN) and clustered regulatory interspaced short palindromic repeats (CRISPR) and CRISPR associated protein 9 (Cas9) are widely used for the editing of the genomes of diverse organisms. These tools are also applied in vector mosquitoes to control the spread of vector-borne diseases. A few studies have been carried out on genome editing to control the diseases spread by vector mosquitoes and more studies need to be performed with the utilization of more recently invented tools like CRISPR/Cas9 to combat the spread of deadly diseases by vector mosquitoes. The high specificity and flexibility of CRISPR/Cas9 system may offer possibilities for novel genome editing for the control of important diseases spread by vector mosquitoes. In this review, we present the current status of genome editing research on vector mosquitoes and also discuss the future applications of vector mosquito genome editing to control the spread of vectorborne diseases.

  19. Physics and engineering of radiation detection

    CERN Document Server

    Ahmed, Syed Naeem

    2015-01-01

    Physics and Engineering of Radiation Detection presents an overview of the physics of radiation detection and its applications. It covers the origins and properties of different kinds of ionizing radiation, their detection and measurement, and the procedures used to protect people and the environment from their potentially harmful effects. The second edition is fully revised and provides the latest developments in detector technology and analyses software. Also, more material related to measurements in particle physics and a complete solutions manual have been added.

  20. Novel AIDS therapies based on gene editing.

    Science.gov (United States)

    Khalili, Kamel; White, Martyn K; Jacobson, Jeffrey M

    2017-02-16

    HIV/AIDS remains a major public health issue. In 2014, it was estimated that 36.9 million people are living with HIV worldwide, including 2.6 million children. Since the advent of combination antiretroviral therapy (cART), in the 1990s, treatment has been so successful that in many parts of the world, HIV has become a chronic condition in which progression to AIDS has become increasingly rare. However, while people with HIV can expect to live a normal life span with cART, lifelong medication is required and cardiovascular, renal, liver, and neurologic diseases are still possible, which continues to prompt research for a cure for HIV. Infected reservoir cells, such as CD4+ T cells and myeloid cells, allow persistence of HIV as an integrated DNA provirus and serve as a potential source for the re-emergence of virus. Attempts to eradicate HIV from these cells have focused mainly on the so-called "shock and kill" approach, where cellular reactivation is induced so as to trigger the purging of virus-producing cells by cytolysis or immune attack. This approach has several limitations and its usefulness in clinical applications remains to be assessed. Recent advances in gene-editing technology have allowed the use of this approach for inactivating integrated proviral DNA in the genome of latently infected cells or knocking out HIV receptors. Here, we review this strategy and its potential to eliminate the latent HIV reservoir resulting in a sterile cure of AIDS.

  1. Trait stacking via targeted genome editing.

    Science.gov (United States)

    Ainley, William M; Sastry-Dent, Lakshmi; Welter, Mary E; Murray, Michael G; Zeitler, Bryan; Amora, Rainier; Corbin, David R; Miles, Rebecca R; Arnold, Nicole L; Strange, Tonya L; Simpson, Matthew A; Cao, Zehui; Carroll, Carley; Pawelczak, Katherine S; Blue, Ryan; West, Kim; Rowland, Lynn M; Perkins, Douglas; Samuel, Pon; Dewes, Cristie M; Shen, Liu; Sriram, Shreedharan; Evans, Steven L; Rebar, Edward J; Zhang, Lei; Gregory, Phillip D; Urnov, Fyodor D; Webb, Steven R; Petolino, Joseph F

    2013-12-01

    Modern agriculture demands crops carrying multiple traits. The current paradigm of randomly integrating and sorting independently segregating transgenes creates severe downstream breeding challenges. A versatile, generally applicable solution is hereby provided: the combination of high-efficiency targeted genome editing driven by engineered zinc finger nucleases (ZFNs) with modular 'trait landing pads' (TLPs) that allow 'mix-and-match', on-demand transgene integration and trait stacking in crop plants. We illustrate the utility of nuclease-driven TLP technology by applying it to the stacking of herbicide resistance traits. We first integrated into the maize genome an herbicide resistance gene, pat, flanked with a TLP (ZFN target sites and sequences homologous to incoming DNA) using WHISKERS™-mediated transformation of embryogenic suspension cultures. We established a method for targeted transgene integration based on microparticle bombardment of immature embryos and used it to deliver a second trait precisely into the TLP via cotransformation with a donor DNA containing a second herbicide resistance gene, aad1, flanked by sequences homologous to the integrated TLP along with a corresponding ZFN expression construct. Remarkably, up to 5% of the embryo-derived transgenic events integrated the aad1 transgene precisely at the TLP, that is, directly adjacent to the pat transgene. Importantly and consistent with the juxtaposition achieved via nuclease-driven TLP technology, both herbicide resistance traits cosegregated in subsequent generations, thereby demonstrating linkage of the two independently transformed transgenes. Because ZFN-mediated targeted transgene integration is becoming applicable across an increasing number of crop species, this work exemplifies a simple, facile and rapid approach to trait stacking.

  2. Next-Generation Sequencing and Genome Editing in Plant Virology.

    Science.gov (United States)

    Hadidi, Ahmed; Flores, Ricardo; Candresse, Thierry; Barba, Marina

    2016-01-01

    Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21-24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology.

  3. Next-Generation Sequencing and Genome Editing in Plant Virology

    Science.gov (United States)

    Hadidi, Ahmed; Flores, Ricardo; Candresse, Thierry; Barba, Marina

    2016-01-01

    Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21–24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology. PMID:27617007

  4. Next-Generation Sequencing and Genome Editing in Plant Virology

    Directory of Open Access Journals (Sweden)

    Ahmed Hadidi

    2016-08-01

    Full Text Available Next-generation sequencing (NGS has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21-24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus; beet curly top virus and beet severe curly top virus (curtovirus; and bean yellow dwarf virus (mastrevirus. The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus and cucumber vein yellowing virus (ipomovirus, family, Potyviridae by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology.Keywords: Next-generation sequencing, NGS, plant virology, plant viruses, viroids, resistance to plant viruses by CRISPR-Cas9

  5. A Digital PCR-Based Method for Efficient and Highly Specific Screening of Genome Edited Cells.

    Directory of Open Access Journals (Sweden)

    Scott D Findlay

    Full Text Available The rapid adoption of gene editing tools such as CRISPRs and TALENs for research and eventually therapeutics necessitates assays that can rapidly detect and quantitate the desired alterations. Currently, the most commonly used assay employs "mismatch nucleases" T7E1 or "Surveyor" that recognize and cleave heteroduplexed DNA amplicons containing mismatched base-pairs. However, this assay is prone to false positives due to cancer-associated mutations and/or SNPs and requires large amounts of starting material. Here we describe a powerful alternative wherein droplet digital PCR (ddPCR can be used to decipher homozygous from heterozygous mutations with superior levels of both precision and sensitivity. We use this assay to detect knockout inducing alterations to stem cell associated proteins, NODAL and SFRP1, generated using either TALENs or an "all-in-one" CRISPR/Cas plasmid that we have modified for one-step cloning and blue/white screening of transformants. Moreover, we highlight how ddPCR can be used to assess the efficiency of varying TALEN-based strategies. Collectively, this work highlights how ddPCR-based screening can be paired with CRISPR and TALEN technologies to enable sensitive, specific, and streamlined approaches to gene editing and validation.

  6. Geminivirus-Mediated Genome Editing in Potato (Solanum tuberosum L.) Using Sequence-Specific Nucleases.

    Science.gov (United States)

    Butler, Nathaniel M; Baltes, Nicholas J; Voytas, Daniel F; Douches, David S

    2016-01-01

    Genome editing using sequence-specific nucleases (SSNs) is rapidly being developed for genetic engineering in crop species. The utilization of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated systems (CRISPR/Cas) for inducing double-strand breaks facilitates targeting of virtually any sequence for modification. Targeted mutagenesis via non-homologous end-joining (NHEJ) has been demonstrated extensively as being the preferred DNA repair pathway in plants. However, gene targeting via homologous recombination (HR) remains more elusive but could be a powerful tool for directed DNA repair. To overcome barriers associated with gene targeting, a geminivirus replicon (GVR) was used to deliver SSNs targeting the potato ACETOLACTATE SYNTHASE1 (ALS1) gene and repair templates designed to incorporate herbicide-inhibiting point mutations within the ALS1 locus. Transformed events modified with GVRs held point mutations that were capable of supporting a reduced herbicide susceptibility phenotype, while events transformed with conventional T-DNAs held no detectable mutations and were similar to wild-type. Regeneration of transformed events improved detection of point mutations that supported a stronger reduced herbicide susceptibility phenotype. These results demonstrate the use of geminiviruses for delivering genome editing reagents in plant species, and a novel approach to gene targeting in a vegetatively propagated species.

  7. Geminivirus-mediated genome editing in potato (Solanum tuberosum L. using sequence-specific nucleases

    Directory of Open Access Journals (Sweden)

    Nathaniel M Butler

    2016-07-01

    Full Text Available Genome editing using sequence-specific nucleases (SSNs is rapidly being developed for genetic engineering in crop species. The utilization of zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs and CRISPR/Cas (clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated systems (Cas for inducing double-strand breaks facilitates targeting of virtually any sequence for modification. Targeted mutagenesis via nonhomologous end-joining has been demonstrated extensively as being the preferred DNA repair pathway in plants. However, gene targeting via homologous recombination remains more elusive but could be a powerful tool for directed DNA repair. To overcome barriers associated with gene targeting, a geminivirus replicon (GVR was used to deliver SSNs targeting the potato ACETOLACTATE SYNTHASE1 (ALS1 gene and repair templates designed to incorporate herbicide-inhibiting point mutations within the ALS1 locus. Transformed events modified with GVRs held both point mutations that were capable of supporting a reduced herbicide susceptibility phenotype, while events transformed with conventional T-DNAs held no detectable mutations and were similar to wild-type. Regeneration of transformed events improved detection of point mutations that supported a stronger reduced herbicide susceptibility phenotype. These results demonstrate the use of geminiviruses for delivering genome editing reagents in plant species, and an approach to gene targeting in a vegetatively propagated species.

  8. A Digital PCR-Based Method for Efficient and Highly Specific Screening of Genome Edited Cells

    Science.gov (United States)

    Berman, Jennifer R.; Postovit, Lynne-Marie

    2016-01-01

    The rapid adoption of gene editing tools such as CRISPRs and TALENs for research and eventually therapeutics necessitates assays that can rapidly detect and quantitate the desired alterations. Currently, the most commonly used assay employs “mismatch nucleases” T7E1 or “Surveyor” that recognize and cleave heteroduplexed DNA amplicons containing mismatched base-pairs. However, this assay is prone to false positives due to cancer-associated mutations and/or SNPs and requires large amounts of starting material. Here we describe a powerful alternative wherein droplet digital PCR (ddPCR) can be used to decipher homozygous from heterozygous mutations with superior levels of both precision and sensitivity. We use this assay to detect knockout inducing alterations to stem cell associated proteins, NODAL and SFRP1, generated using either TALENs or an “all-in-one” CRISPR/Cas plasmid that we have modified for one-step cloning and blue/white screening of transformants. Moreover, we highlight how ddPCR can be used to assess the efficiency of varying TALEN-based strategies. Collectively, this work highlights how ddPCR-based screening can be paired with CRISPR and TALEN technologies to enable sensitive, specific, and streamlined approaches to gene editing and validation. PMID:27089539

  9. Oligonucleotide-directed mutagenesis for precision gene editing.

    Science.gov (United States)

    Sauer, Noel J; Mozoruk, Jerry; Miller, Ryan B; Warburg, Zachary J; Walker, Keith A; Beetham, Peter R; Schöpke, Christian R; Gocal, Greg F W

    2016-02-01

    Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide-directed mutagenesis (ODM), one of the many tools of Cibus' Rapid Trait Development System (RTDS(™) ) technology, offers a rapid, precise and non-transgenic breeding alternative for trait improvement in agriculture to address this urgent need. This review explores the application of ODM as a precision genome editing technology, with emphasis on using oligonucleotides to make targeted edits in plasmid, episomal and chromosomal DNA of bacterial, fungal, mammalian and plant systems. The process of employing ODM by way of RTDS technology has been improved in many ways by utilizing a fluorescence conversion system wherein a blue fluorescent protein (BFP) can be changed to a green fluorescent protein (GFP) by editing a single nucleotide of the BFP gene (CAC→TAC; H66 to Y66). For example, dependent on oligonucleotide length, applying oligonucleotide-mediated technology to target the BFP transgene in Arabidopsis thaliana protoplasts resulted in up to 0.05% precisely edited GFP loci. Here, the development of traits in commercially relevant plant varieties to improve crop performance by genome editing technologies such as ODM, and by extension RTDS, is reviewed.

  10. Unified Compression-Based Acceleration of Edit-Distance Computation

    CERN Document Server

    Hermelin, Danny; Landau, Shir; Weimann, Oren

    2010-01-01

    The edit distance problem is a classical fundamental problem in computer science in general, and in combinatorial pattern matching in particular. The standard dynamic programming solution for this problem computes the edit-distance between a pair of strings of total length O(N) in O(N^2) time. To this date, this quadratic upper-bound has never been substantially improved for general strings. However, there are known techniques for breaking this bound in case the strings are known to compress well under a particular compression scheme. The basic idea is to first compress the strings, and then to compute the edit distance between the compressed strings. As it turns out, practically all known o(N^2) edit-distance algorithms work, in some sense, under the same paradigm described above. It is therefore natural to ask whether there is a single edit-distance algorithm that works for strings which are compressed under any compression scheme. A rephrasing of this question is to ask whether a single algorithm can explo...

  11. Image editing with Adobe Photoshop 6.0.

    Science.gov (United States)

    Caruso, Ronald D; Postel, Gregory C

    2002-01-01

    The authors introduce Photoshop 6.0 for radiologists and demonstrate basic techniques of editing gray-scale cross-sectional images intended for publication and for incorporation into computerized presentations. For basic editing of gray-scale cross-sectional images, the Tools palette and the History/Actions palette pair should be displayed. The History palette may be used to undo a step or series of steps. The Actions palette is a menu of user-defined macros that save time by automating an action or series of actions. Converting an image to 8-bit gray scale is the first editing function. Cropping is the next action. Both decrease file size. Use of the smallest file size necessary for the purpose at hand is recommended. Final file size for gray-scale cross-sectional neuroradiologic images (8-bit, single-layer TIFF [tagged image file format] at 300 pixels per inch) intended for publication varies from about 700 Kbytes to 3 Mbytes. Final file size for incorporation into computerized presentations is about 10-100 Kbytes (8-bit, single-layer, gray-scale, high-quality JPEG [Joint Photographic Experts Group]), depending on source and intended use. Editing and annotating images before they are inserted into presentation software is highly recommended, both for convenience and flexibility. Radiologists should find that image editing can be carried out very rapidly once the basic steps are learned and automated.

  12. Refinements to the Boolean approach to automatic data editing

    Energy Technology Data Exchange (ETDEWEB)

    Liepins, G.E.

    1980-09-01

    Automatic data editing consists of three components: identification of erroneous records, identification of most likely erroneous fields within an erroneous record (fields to impute), and assignment of acceptable values to failing records. Moreover the types of data considered naturally fall into three categories: coded (categorical) data, continuous data, and mixed data (both coded and continuous). For the case of coded data, a natural way to approach automatic data is commonly referred to as the Boolean approach, first developed by Fellegi and Holt. For the fields to impute problem, central to the operation of the Fellegi-Holt approach is the explicit recognition of certain implied edits; Fellegi and Holt orginally required a complete set of edits, and their algorithm to generate this complete set has occasionally had the distinct disadvantage of failing to converge within reasonable time. The primary results of this paper is an algorithm that significantly prunes the Fellegi-Holt edit generation process, yet, nonetheless, generates a sufficient collection of implied edits adequate for the solution of the fields to impute problem. 3 figures.

  13. ME-CAGEBIRDr,X-CPMG-HSQMBC. A phase sensitive, multiplicity edited long range HSQC with absorptive line shapes

    Science.gov (United States)

    Koskela, Harri; Kilpeläinen, Ilkka; Heikkinen, Sami

    2016-11-01

    ME-CAGEBIRDr,X-CPMG-HSMBC pulse sequence is a phase sensitive, carbon multiplicity edited 2D-experiment for detecting heteronuclear correlations originating from long-range 1H, 13C-couplings, nJCH. The presented method allows measurement of nJCH-values as well as is capable of separating different carbon types in subspectra (13C/13CH2 and 13CH/13CH3) with minimal amount of cross talk i.e. cross peaks from wrong carbon multiplicity. Pure lineshapes and clean subspectra are achieved by utilizing CPMG in polarization transfer period, CRISIS-approach in multiplicity editing period and zero-quantum filtration. The obtained spectral properties together with simple setup of the experiment make ME-CAGEBIRDr,X-CPMG-HSMBC a useful addition into synthetic organic chemistry oriented NMR-tool collection.

  14. Measurement and detection of radiation

    CERN Document Server

    Tsoulfanidis, Nicholas

    2015-01-01

    This fourth edition reflects recent major developments that have occurred in radiation detector materials, systems, and applications. It continues to provide the most practical and up-to-date introduction to radiation detector technology, proper measurement techniques, and analysis of results for engineers and scientists using radiation sources. New chapters emphasize the expanded use of radiation detection systems in nuclear non-proliferation, homeland security, and nuclear medicine. The book also discusses the correct ways to perform measurements following current health physics procedures.

  15. Space Science Reference Guide, 2nd Edition

    Science.gov (United States)

    Dotson, Renee (Editor)

    2003-01-01

    This Edition contains the following reports: GRACE: Gravity Recovery and Climate Experiment; Impact Craters in the Solar System; 1997 Apparition of Comet Hale-Bopp Historical Comet Observations; Baby Stars in Orion Solve Solar System Mystery; The Center of the Galaxy; The First Rock in the Solar System; Fun Times with Cosmic Rays; The Gamma-Ray Burst Next Door; The Genesis Mission: An Overview; The Genesis Solar Wind Sample Return Mission; How to Build a Supermassive Black Hole; Journey to the Center of a Neutron Star; Kepler's Laws of Planetary Motion; The Kuiper Belt and Oort Cloud ; Mapping the Baby Universe; More Hidden Black Hole Dangers; A Polarized Universe; Presolar Grains of Star Dust: Astronomy Studied with Microscopes; Ring Around the Black Hole; Searching Antarctic Ice for Meteorites; The Sun; Astrobiology: The Search for Life in the Universe; Europa and Titan: Oceans in the Outer Solar System?; Rules for Identifying Ancient Life; Inspire ; Remote Sensing; What is the Electromagnetic Spectrum? What is Infrared? How was the Infrared Discovered?; Brief History of Gyroscopes ; Genesis Discovery Mission: Science Canister Processing at JSC; Genesis Solar-Wind Sample Return Mission: The Materials ; ICESat: Ice, Cloud, and Land Elevation Satellite ICESat: Ice, Cloud, and Land; Elevation Satellite ICESat: Ice, Cloud, and Land Elevation Satellite ICESat: Ice, Cloud, and Land Elevation Satellite ICESat: Ice, Cloud, and Land Elevation Satellite Measuring Temperature Reading; The Optical Telescope ; Space Instruments General Considerations; Damage by Impact: The Case at Meteor Crater, Arizona; Mercury Unveiled; New Data, New Ideas, and Lively Debate about Mercury; Origin of the Earth and Moon; Space Weather: The Invisible Foe; Uranus, Neptune, and the Mountains of the Moon; Dirty Ice on Mars; For a Cup of Water on Mars; Life on Mars?; The Martian Interior; Meteorites from Mars, Rocks from Canada; Organic Compounds in Martian Meteorites May be Terrestrial

  16. Advances in therapeutic CRISPR/Cas9 genome editing.

    Science.gov (United States)

    Savić, Nataša; Schwank, Gerald

    2016-02-01

    Targeted nucleases are widely used as tools for genome editing. Two years ago the clustered regularly interspaced short palindromic repeat (CRISPR)-associated Cas9 nuclease was used for the first time, and since then has largely revolutionized the field. The tremendous success of the CRISPR/Cas9 genome editing tool is powered by the ease design principle of the guide RNA that targets Cas9 to the desired DNA locus, and by the high specificity and efficiency of CRISPR/Cas9-generated DNA breaks. Several studies recently used CRISPR/Cas9 to successfully modulate disease-causing alleles in vivo in animal models and ex vivo in somatic and induced pluripotent stem cells, raising hope for therapeutic genome editing in the clinics. In this review, we will summarize and discuss such preclinical CRISPR/Cas9 gene therapy reports.

  17. Gene Editing: Powerful New Tools for Nephrology Research and Therapy.

    Science.gov (United States)

    Miyagi, Ayano; Lu, Aiwu; Humphreys, Benjamin D

    2016-10-01

    Biologic research is experiencing a transformation brought about by the ability of programmable nucleases to manipulate the genome. In the recently developed CRISPR/Cas system, short RNA sequences guide the endonuclease Cas9 to any location in the genome, causing a DNA double-strand break (DSB). Repair of DSBs allows the introduction of targeted genetic manipulations with high precision. Cas9-mediated gene editing is simple, scalable, and rapid, and it can be applied to virtually any organism. Here, we summarize the development of modern gene editing techniques and the biology of DSB repair on which these techniques are based. We discuss technical points in applying this technology and review its use in model organisms. Finally, we describe prospects for the use of gene editing to treat human genetic diseases. This technology offers tremendous promise for equipping the nephrology research community to better model and ultimately, treat kidney diseases.

  18. Control of gene editing by manipulation of DNA repair mechanisms.

    Science.gov (United States)

    Danner, Eric; Bashir, Sanum; Yumlu, Saniye; Wurst, Wolfgang; Wefers, Benedikt; Kühn, Ralf

    2017-04-03

    DNA double-strand breaks (DSBs) are produced intentionally by RNA-guided nucleases to achieve genome editing through DSB repair. These breaks are repaired by one of two main repair pathways, classic non-homologous end joining (c-NHEJ) and homology-directed repair (HDR), the latter being restricted to the S/G2 phases of the cell cycle and notably less frequent. Precise genome editing applications rely on HDR, with the abundant c-NHEJ formed mutations presenting a barrier to achieving high rates of precise sequence modifications. Here, we give an overview of HDR- and c-NHEJ-mediated DSB repair in gene editing and summarize the current efforts to promote HDR over c-NHEJ.

  19. Rome m: The functional gastrointestinal disorders, third edition, 2006

    Institute of Scientific and Technical Information of China (English)

    Randa Mostafa

    2008-01-01

    Functional gastrointestinal disorders (FGIDs) represent a common and important class of disorders within gastroenterology. Rome I, the first edition was published in 1994, with symptom-based diagnostic criteria for FGIDs. These criteria began to change the diagnostic approach to FGIDs, and no longer considered "diagnoses of exclusion" but rather "diagnoses of inclusion". Rome n, the second edition published in 2000, resulted from the continual process of analyzing new scientific and clinical evidence in the study of FGIDs. Rome n, diagnostic criteria for irritable bowel syndrome (IBS), was extended with a focus on the frequency of symptoms occurring twelve weeks (not necessarily consecutive weeks) within twelve months. ROME m, the third edition, conservative one, was published in September 2006, with changes made only where there is good evidence to do so. Some of the differences between Rome n and Rome m criteria are highlighted in this issue.

  20. Genome-editing tools for stem cell biology.

    Science.gov (United States)

    Vasileva, E A; Shuvalov, O U; Garabadgiu, A V; Melino, G; Barlev, N A

    2015-07-23

    Human pluripotent stem cells provide a versatile platform for regenerative studies, drug testing and disease modeling. That the expression of only four transcription factors, Oct4, Klf4, Sox2 and c-Myc (OKSM), is sufficient for generation of induced pluripotent stem cells (iPSCs) from differentiated somatic cells has revolutionized the field and also highlighted the importance of OKSM as targets for genome editing. A number of novel genome-editing systems have been developed recently. In this review, we focus on successful applications of several such systems for generation of iPSCs. In particular, we discuss genome-editing systems based on zinc-finger fusion proteins (ZFs), transcription activator-like effectors (TALEs) and an RNA-guided DNA-specific nuclease, Cas9, derived from the bacterial defense system against viruses that utilizes clustered regularly interspaced short palindromic repeats (CRISPR).

  1. Harnessing CRISPR-Cas systems for bacterial genome editing.

    Science.gov (United States)

    Selle, Kurt; Barrangou, Rodolphe

    2015-04-01

    Manipulation of genomic sequences facilitates the identification and characterization of key genetic determinants in the investigation of biological processes. Genome editing via clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) constitutes a next-generation method for programmable and high-throughput functional genomics. CRISPR-Cas systems are readily reprogrammed to induce sequence-specific DNA breaks at target loci, resulting in fixed mutations via host-dependent DNA repair mechanisms. Although bacterial genome editing is a relatively unexplored and underrepresented application of CRISPR-Cas systems, recent studies provide valuable insights for the widespread future implementation of this technology. This review summarizes recent progress in bacterial genome editing and identifies fundamental genetic and phenotypic outcomes of CRISPR targeting in bacteria, in the context of tool development, genome homeostasis, and DNA repair.

  2. Some neurolinguistic implications of prearticulatory editing in production.

    Science.gov (United States)

    Garnsey, S M; Dell, G S

    1984-09-01

    This paper argues that a complete model of language production must include a prearticulatory editing component. The function of this component is to monitor planned speech for deviations from the speaker's intention and repair any deviations that are found. It is claimed that adding such an editing component onto a production model fundamentally changes any account of aphasic symptoms using that model. As a case in point it is shown that E. M. Saffran's (1982, British Journal of Psychology, 73, 317-337) argument that agrammatic Broca's aphasia involves a deficit at the functional level of M. F. Garrett's (1975, in G. H. Bower (Ed.). The psychology of learning and motivation, New York: Academic Press) production model is no longer sound when prearticulatory editing processes are considered.

  3. HMMEditor: a visual editing tool for profile hidden Markov model

    Directory of Open Access Journals (Sweden)

    Cheng Jianlin

    2008-03-01

    Full Text Available Abstract Background Profile Hidden Markov Model (HMM is a powerful statistical model to represent a family of DNA, RNA, and protein sequences. Profile HMM has been widely used in bioinformatics research such as sequence alignment, gene structure prediction, motif identification, protein structure prediction, and biological database search. However, few comprehensive, visual editing tools for profile HMM are publicly available. Results We develop a visual editor for profile Hidden Markov Models (HMMEditor. HMMEditor can visualize the profile HMM architecture, transition probabilities, and emission probabilities. Moreover, it provides functions to edit and save HMM and parameters. Furthermore, HMMEditor allows users to align a sequence against the profile HMM and to visualize the corresponding Viterbi path. Conclusion HMMEditor provides a set of unique functions to visualize and edit a profile HMM. It is a useful tool for biological sequence analysis and modeling. Both HMMEditor software and web service are freely available.

  4. Simple Genome Editing of Rodent Intact Embryos by Electroporation.

    Directory of Open Access Journals (Sweden)

    Takehito Kaneko

    Full Text Available The clustered regularly interspaced short palindromic repeat (CRISPR/CRISPR-associated (Cas system is a powerful tool for genome editing in animals. Recently, new technology has been developed to genetically modify animals without using highly skilled techniques, such as pronuclear microinjection of endonucleases. Technique for animal knockout system by electroporation (TAKE method is a simple and effective technology that produces knockout rats by introducing endonuclease mRNAs into intact embryos using electroporation. Using TAKE method and CRISPR/Cas system, the present study successfully produced knockout and knock-in mice and rats. The mice and rats derived from embryos electroporated with Cas9 mRNA, gRNA and single-stranded oligodeoxynucleotide (ssODN comprised the edited targeted gene as a knockout (67% of mice and 88% of rats or knock-in (both 33%. The TAKE method could be widely used as a powerful tool to produce genetically modified animals by genome editing.

  5. Editing Newton in Geneva and Rome: The Annotated Edition of the Principia by Calandrini, Le Seur and Jacquier.

    Science.gov (United States)

    Guicciardini, Niccolò

    2015-07-01

    This contribution examines the circumstances of composition of the annotated edition of Newton's Principia that was printed in Geneva in 1739-1742, which ran to several editions and was still in print in Britain in the mid-nineteenth century. This edition was the work of the Genevan Professor of Mathematics, Jean Louis Calandrini, and of two Minim friars based in Rome, Thomas Le Seur and François Jacquier. The study of the context in which this edition was conceived sheds light on the early reception of Newtonianism in Geneva and Rome. By taking into consideration the careers of Calandrini, Le Seur and Jacquier, as authors, lecturers and leading characters of Genevan and Roman cultural life, I will show that their involvement in the enterprise of annotating Newton's Principia answered specific needs of Genevan and Roman culture. The publication and reception of the Genevan annotated edition has also a broader European dimension. Both Calandrini and Jacquier were in touch with the French république des lettres, most notably with Clairaut and Du Châtelet, and with the Bernoulli family in Basel. Therefore, this study is also relevant for the understanding of the dissemination of Newton's ideas in Europe.

  6. Efficient and allele-specific genome editing of disease loci in human iPSCs.

    Science.gov (United States)

    Smith, Cory; Abalde-Atristain, Leire; He, Chaoxia; Brodsky, Brett R; Braunstein, Evan M; Chaudhari, Pooja; Jang, Yoon-Young; Cheng, Linzhao; Ye, Zhaohui

    2015-03-01

    Efficient and precise genome editing is crucial for realizing the full research and therapeutic potential of human induced pluripotent stem cells (iPSCs). Engineered nucleases including CRISPR/Cas9 and transcription activator like effector nucleases (TALENs) provide powerful tools for enhancing gene-targeting efficiency. In this study, we investigated the relative efficiencies of CRISPR/Cas9 and TALENs in human iPSC lines for inducing both homologous donor-based precise genome editing and nonhomologous end joining (NHEJ)-mediated gene disruption. Significantly higher frequencies of NHEJ-mediated insertions/deletions were detected at several endogenous loci using CRISPR/Cas9 than using TALENs, especially at nonexpressed targets in iPSCs. In contrast, comparable efficiencies of inducing homologous donor-based genome editing were observed at disease-associated loci in iPSCs. In addition, we investigated the specificity of guide RNAs used in the CRISPR/Cas9 system in targeting disease-associated point mutations in patient-specific iPSCs. Using myeloproliferative neoplasm patient-derived iPSCs that carry an acquired JAK2-V617F point mutation and α1-antitrypsin (AAT) deficiency patient-derived iPSCs that carry an inherited Z-AAT point mutation, we demonstrate that Cas9 can specifically target either the mutant or the wild-type allele with little disruption at the other allele differing by a single nucleotide. Overall, our results demonstrate the advantages of the CRISPR/Cas9 system in allele-specific genome targeting and in NHEJ-mediated gene disruption.

  7. MindEdit: A P300-based text editor for mobile devices.

    Science.gov (United States)

    Elsawy, Amr S; Eldawlatly, Seif; Taher, Mohamed; Aly, Gamal M

    2017-01-01

    Practical application of Brain-Computer Interfaces (BCIs) requires that the whole BCI system be portable. The mobility of BCI systems involves two aspects: making the electroencephalography (EEG) recording devices portable, and developing software applications with low computational complexity to be able to run on low computational-power devices such as tablets and smartphones. This paper addresses the development of MindEdit; a P300-based text editor for Android-based devices. Given the limited resources of mobile devices and their limited computational power, a novel ensemble classifier is utilized that uses Principal Component Analysis (PCA) features to identify P300 evoked potentials from EEG recordings. PCA computations in the proposed method are channel-based as opposed to concatenating all channels as in traditional feature extraction methods; thus, this method has less computational complexity compared to traditional P300 detection methods. The performance of the method is demonstrated on data recorded from MindEdit on an Android tablet using the Emotiv wireless neuroheadset. Results demonstrate the capability of the introduced PCA ensemble classifier to classify P300 data with maximum average accuracy of 78.37±16.09% for cross-validation data and 77.5±19.69% for online test data using only 10 trials per symbol and a 33-character training dataset. Our analysis indicates that the introduced method outperforms traditional feature extraction methods. For a faster operation of MindEdit, a variable number of trials scheme is introduced that resulted in an online average accuracy of 64.17±19.6% and a maximum bitrate of 6.25bit/min. These results demonstrate the efficacy of using the developed BCI application with mobile devices.

  8. Efficient Mitochondrial Genome Editing by CRISPR/Cas9

    Directory of Open Access Journals (Sweden)

    Areum Jo

    2015-01-01

    Full Text Available The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9 system has been widely used for nuclear DNA editing to generate mutations or correct specific disease alleles. Despite its flexible application, it has not been determined if CRISPR/Cas9, originally identified as a bacterial defense system against virus, can be targeted to mitochondria for mtDNA editing. Here, we show that regular FLAG-Cas9 can localize to mitochondria to edit mitochondrial DNA with sgRNAs targeting specific loci of the mitochondrial genome. Expression of FLAG-Cas9 together with gRNA targeting Cox1 and Cox3 leads to cleavage of the specific mtDNA loci. In addition, we observed disruption of mitochondrial protein homeostasis following mtDNA truncation or cleavage by CRISPR/Cas9. To overcome nonspecific distribution of FLAG-Cas9, we also created a mitochondria-targeted Cas9 (mitoCas9. This new version of Cas9 localizes only to mitochondria; together with expression of gRNA targeting mtDNA, there is specific cleavage of mtDNA. MitoCas9-induced reduction of mtDNA and its transcription leads to mitochondrial membrane potential disruption and cell growth inhibition. This mitoCas9 could be applied to edit mtDNA together with gRNA expression vectors without affecting genomic DNA. In this brief study, we demonstrate that mtDNA editing is possible using CRISPR/Cas9. Moreover, our development of mitoCas9 with specific localization to the mitochondria should facilitate its application for mitochondrial genome editing.

  9. Explanatory Supplement to the Astronomical Almanac (3rd Edition)

    Science.gov (United States)

    Urban, Sean E.; Seidelmann, P. K.

    2014-01-01

    Publications and software from the the Astronomical Applications Department of the US Naval Observatory (USNO) are used throughout the world, not only in the Department of Defense for safe navigation, but by many people including other navigators, astronomers, aerospace engineers, and geodesists. Products such as The Nautical Almanac, The Astronomical Almanac, and the Multiyear Interactive Computer Almanac (MICA) are regarded as international standards. To maintain credibility, it is imperative that the methodologies employed and the data used are well documented. "The Explanatory Supplement to the Astronomical Almanac" (hereafter, "The ES") is a major source of such documentation. It is a comprehensive reference book on positional astronomy, covering the theories and algorithms used to produce The Astronomical Almanac, an annual publication produced jointly by the Nautical Almanac Office of USNO and Her Majesty's Nautical Almanac Office (HMNAO). The first edition of The ES appeared in 1961, and the second followed in 1992. Several major changes have taken place in fundamental astronomy since the second edition was published. Advances in radio observations allowed the celestial reference frame to be tied to extragalactic radio sources, thus the International Celestial Reference System replaced the FK5 system. The success of ESA's Hipparcos satellite dramatically altered observational astrometry. Improvements in Earth orientation observations lead to new precession and nutation theories. Additionally, a new positional paradigm, no longer tied to the ecliptic and equinox, was accepted. Largely because of these changes, staff at USNO and HMNAO decided the time was right for the next edition of The ES. The third edition is now available; it is a complete revision of the 1992 book. Along with subjects covered in the previous two editions, the book also contains descriptions of the major advancements in positional astronomy over the last 20 years, some of which are

  10. The Third Edition of the Inka Brodzka-Wald Award

    Directory of Open Access Journals (Sweden)

    Jolanta Sujecka

    2016-12-01

    Full Text Available The Third Edition of the Inka Brodzka-Wald Award On 16 June 2015, the Academy for the Development of Philanthropy in Poland and the Adam Mickiewicz Literary Society announced the winners of the third edition of the Inka Brodzka-Wald Award for doctoral dissertations in the humanities. The competition was open for theses which concerned present issues and were defended in 2014.   Komunikat o rozstrzygnięciu trzeciej edycji Nagrody im. Inki Brodzkiej-Wald za rok 2014.

  11. Editing at the crossroad of innate and adaptive immunity.

    Science.gov (United States)

    Turelli, Priscilla; Trono, Didier

    2005-02-18

    Genetic information can be altered through the enzymatic modification of nucleotide sequences. This process, known as editing, was originally identified in the mitochondrial RNA of trypanosomes and later found to condition events as diverse as neurotransmission and lipid metabolism in mammals. Recent evidence reveals that editing enzymes may fulfill one of their most essential roles in the defense against infectious agents: first, as the mediators of antibody diversification, a step crucial for building adaptive immunity, and second, as potent intracellular poisons for the replication of viruses. Exciting questions are raised, which take us to the depth of the intimate relations between vertebrates and the microbial underworld.

  12. Atmel AVR Microcontroller Primer Programming and Interfacing, Second Edition

    CERN Document Server

    Barrett, Steven F

    2012-01-01

    This textbook provides practicing scientists and engineers a primer on the Atmel AVR microcontroller. In this second edition we highlight the popular ATmega164 microcontroller and other pin-for-pin controllers in the family with a complement of flash memory up to 128 kbytes. The second edition also adds a chapter on embedded system design fundamentals and provides extended examples on two different autonomous robots. Our approach is to provide the fundamental skills to quickly get up and operating with this internationally popular microcontroller. We cover the main subsystems aboard the ATmega

  13. Close Reading and Slow Programming — Computer Code as Digital Scholarly Edition

    NARCIS (Netherlands)

    van Zundert, Joris J.

    2016-01-01

    Currently most digital scholarly editions are representational digital documentary editions, largely along the lines described by Elena Pierazzo (2015). Alternative theoretical perspectives take less document centric and more process analytical oriented approaches. Textual scholars have, for instanc

  14. Fast and sensitive detection of indels induced by precise gene targeting

    DEFF Research Database (Denmark)

    Yang, Zhang; Steentoft, Catharina; Hauge, Camilla

    2015-01-01

    The nuclease-based gene editing tools are rapidly transforming capabilities for altering the genome of cells and organisms with great precision and in high throughput studies. A major limitation in application of precise gene editing lies in lack of sensitive and fast methods to detect...... and characterize the induced DNA changes. Precise gene editing induces double-stranded DNA breaks that are repaired by error-prone non-homologous end joining leading to introduction of insertions and deletions (indels) at the target site. These indels are often small and difficult and laborious to detect...

  15. Digital Critical Editing, Digital Text Analysis, and Charles R. Maturin’s Melmoth the Wanderer

    OpenAIRE

    Murtagh, Shane

    2015-01-01

    This thesis considers why critical editions have not established themselves in the digital medium to the same extent as documentary editions and offers some potential ways to remedy this. The written thesis is accompanied by a digital critical edition of Charles R. Maturin’s Melmoth the Wanderer, which acts as an example of and case study for the arguments set forth in the written thesis. This edition can be accessed at app.melmoththewanderer.com or at https://pacific-harbor-29...

  16. Endonuclease mediated genome editing in drug discovery and development: promises and challenges.

    Science.gov (United States)

    Prabhu, Vidya; Xu, Han

    Site specific genome editing has been gradually employed in drug discovery and development process over the past few decades. Recent development of CRISPR technology has significantly accelerated the incorporation of genome editing in the bench side to bedside process. In this review, we summarize examples of applications of genome editing in the drug discovery and development process. We also discuss current hurdles and solutions of genome editing.

  17. Application Progress of CRISPR/Cas9 System for Gene Editing in Tumor Research

    OpenAIRE

    Liu, Chao; Li, Zhiwei; Zhang, Yanqiao

    2015-01-01

    TCRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated nuclease 9) gene editing system is a new type of gene editing technology developed based on the immune mechanism of archaea resisting the invasion of exogenous nucleic acid. Compared with traditional gene editing system, CRISPR/Cas9 system is more efficient, easier operating, and less cytotoxic. Currently, CRISPR/Cas9 gene editing technology has been applied to many aspects of cancer research, including r...

  18. Substantive Editing as a Form of Plagiarism among Postgraduate Students in Australia

    Science.gov (United States)

    Lines, Lisa

    2016-01-01

    In university plagiarism policies, and in the research into plagiarism, one form of collusion remains virtually unacknowledged: substantive editing performed by editors. While almost all Australian universities allow postgraduate students to have their thesis professionally edited, "substantive" editing is prohibited. This article…

  19. Financial Accounting for Local and State School Systems: 2014 Edition. NCES 2015-347

    Science.gov (United States)

    Allison, Gregory S.

    2015-01-01

    The 2014 edition of "Financial Accounting for Local and State School Systems" updates the 2009 (see ED505993) and 2003 editions of the handbook. The 2003 edition was the work of the NCES National Forum on Education Statistics, Core Finance Data Task Force. That task force systematically rewrote nearly the entire text, incorporating new…

  20. Genes (including RNA editing information) - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RMG Genes... (including RNA editing information) Data detail Data name Genes (including RNA editing information...ase Site Policy | Contact Us Genes (including RNA editing information) - RMG | LSDB Archive ...

  1. 203 SINGLE-STEP GENE EDITING OF 3 XENOANTIGENS IN PORCINE FIBROBLASTS USING PROGRAMMABLE NUCLEASES.

    Science.gov (United States)

    Perota, A; Lagutina, I; Quadalti, C; Duchi, R; Turini, P; Crotti, G; Colleoni, S; Conchon, S; Concordet, J-P; Lazzari, G; Soulillou, J-P; Galli, C

    2016-01-01

    Programmable nucleases (ZFN, Tal Effector Nucleases, and CRISPR) opened a new era for mammal genome editing, in particular for the pigs used for xenotransplantation. Multiple gene editing events are required both for knockout (KO) of xenoantigens and for targeted integration of human protective genes (Perota et al. 2016 J. Genet. Genomics 43, 233-23). The objective of the present work was to edit selected pig lines to KO the enzymes coding for the most relevant xenoantigens (i.e. GGTA1, CMAH, and B4GalNT2), combining Talens and CRISPR/Cas9 technologies to magnetic beads selection (Li et al. 2013 Xenotransplantation 22, 20-31). Primary porcine adult fibroblasts were transfected using Nucleofector (V-024 program). In a single reaction 2×10(6) fibroblasts were co-transfected using 2 different sets of TALENS (4μg/set) specific for CMAH (Conchon et al., 2013) and GGTA1 (Perota et al., 2015) genes together with B4GalNT2-specific CRISPR/Cas9 expression vector (2μg; pX330-B4GalNT2; Estrada et al., 2015). Eight days post-transfection (DPT), Gal-/- cells were selected initially using biotin-conjugated IB4 lectin (Sigma, St. Louis, MO, USA) and magnetic beads (Dynabeads M-280, Thermo Fisher Scientific, Waltham, MA, USA). The selected cells were then plated on 150-mm Petri dishes (200 cells/dish) and cultured for 10 days. Selected colonies were expanded for PCR analysis and cryopreserved for somatic cell nuclear transfer (SCNT). All colonies were analysed by PCR for CMAH gene and their resulting products were digested with HindIII (HindIII-RFLP). Colonies that lost wild-type HindIII as a consequence of Talens effected deletion were PCR characterised for GGTA1, selecting those that had detectable Indels after gel electrophoresis and finally analysed by PCR for B4GalNT2. All PCR products were validated by sequencing for all the 3 genes of interest (TopoTA, Thermo Fisher Scientific). Selected colonies were used as nuclear donors for SCNT (Lagutina et al., 2006). Eight DPT we

  2. BOOK REVIEW: Experimental Stochatics (2nd edition)

    Science.gov (United States)

    Wiberg, P.

    2004-05-01

    for teachers of computational stochastic methods, is the main contribution of this electronic monograph. However, both the book and software suffer from several severe problems. Firstly, I feel that the structure of the text is weak. Probably this is partly the result of the text from the CD-ROM being put into a book format, but the short paragraphs and poorly structured sentences destroy the reading experience. Secondly, although the software is functional, I believe that, like me, many users will be disappointed by the quality of the user interface and the visualizations. The opportunities to interact with the simulations are limited. Thirdly, the presentation is slightly old fashioned and lacking in pedagogical structure. For example, flow charts and Pascal programs are used to present algorithms. To conclude, I am surprised that this electronic monograph warranted a second edition in this form. Teachers may find the examples useful as a starting point, but students and researchers are advised to look elsewhere. JG was supported by KBN grant no 2 P03A 020 24.

  3. Progress With Developing Use of Gene Editing To Cure Chronic Infection With Hepatitis B Virus.

    Science.gov (United States)

    Ely, Abdullah; Moyo, Buhle; Arbuthnot, Patrick

    2016-04-01

    Chronic infection with hepatitis B virus (HBV) occurs in approximately 6% of the world's population. Carriers of the virus are at risk for life-threatening complications, and developing curative treatment remains a priority. The main shortcoming of licensed therapies is that they do not affect viral covalently closed circular DNA (cccDNA), a stable intermediate of replication. Harnessing gene editing to mutate cccDNA provides the means to inactivate HBV gene expression permanently. Reports have described use of engineered zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR-associated (Cas) nucleases. Although inhibition of viral replication has been demonstrated, reliably detecting mutations in cccDNA has been difficult. Also, the dearth of murine models that mimic cccDNA formation has hampered analysis in vivo. To reach a stage of clinical use, efficient delivery of the editors to HBV-infected hepatocytes and limiting unintended off-target effects will be important. Investigating therapeutic efficacy in combination with other treatment strategies, such as immunotherapies, may be useful to augment antiviral effects. Advancing gene editing as a mode of treating HBV infection is now at an interesting stage and significant progress is likely to be made in the immediate future.

  4. Targeted genome editing of sweet orange using Cas9/sgRNA.

    Directory of Open Access Journals (Sweden)

    Hongge Jia

    Full Text Available Genetic modification, including plant breeding, has been widely used to improve crop yield and quality, as well as to increase disease resistance. Targeted genome engineering is expected to contribute significantly to future varietal improvement, and genome editing technologies using zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9/single guide RNA (sgRNA have already been successfully used to genetically modify plants. However, to date, there has been no reported use of any of the current genome editing approaches in sweet orange, an important fruit crop. In this study, we first developed a novel tool, Xcc-facilitated agroinfiltration, for enhancing transient protein expression in sweet orange leaves. We then successfully employed Xcc-facilitated agroinfiltration to deliver Cas9, along with a synthetic sgRNA targeting the CsPDS gene, into sweet orange. DNA sequencing confirmed that the CsPDS gene was mutated at the target site in treated sweet orange leaves. The mutation rate using the Cas9/sgRNA system was approximately 3.2 to 3.9%. Off-target mutagenesis was not detected for CsPDS-related DNA sequences in our study. This is the first report of targeted genome modification in citrus using the Cas9/sgRNA system-a system that holds significant promise for the study of citrus gene function and for targeted genetic modification.

  5. Targeted genome editing of sweet orange using Cas9/sgRNA.

    Science.gov (United States)

    Jia, Hongge; Wang, Nian

    2014-01-01

    Genetic modification, including plant breeding, has been widely used to improve crop yield and quality, as well as to increase disease resistance. Targeted genome engineering is expected to contribute significantly to future varietal improvement, and genome editing technologies using zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9/single guide RNA (sgRNA) have already been successfully used to genetically modify plants. However, to date, there has been no reported use of any of the current genome editing approaches in sweet orange, an important fruit crop. In this study, we first developed a novel tool, Xcc-facilitated agroinfiltration, for enhancing transient protein expression in sweet orange leaves. We then successfully employed Xcc-facilitated agroinfiltration to deliver Cas9, along with a synthetic sgRNA targeting the CsPDS gene, into sweet orange. DNA sequencing confirmed that the CsPDS gene was mutated at the target site in treated sweet orange leaves. The mutation rate using the Cas9/sgRNA system was approximately 3.2 to 3.9%. Off-target mutagenesis was not detected for CsPDS-related DNA sequences in our study. This is the first report of targeted genome modification in citrus using the Cas9/sgRNA system-a system that holds significant promise for the study of citrus gene function and for targeted genetic modification.

  6. Standards of specialized diabetes care. Edited by Dedov II, Shestakova MV (6th edition

    Directory of Open Access Journals (Sweden)

    Ivan Ivanovich Dedov

    2013-06-01

    Full Text Available Dear Colleagues!We are glad to present the 6th Edition of Standards of Diabetes Care. These evidence-based guidelines were designed to standardize and facilitate diabetes care in all regions of the Russian Federation. The Standards are updated on the regular basis to incorporate new data and relevant recommendations from national and international clinical societies, including World Health Organization Guidelines (WHO, 2011, International Diabetes Federation (IDF, 2011, American Diabetes Association (ADA, 2013, American Association of Clinical Endocrinologists (AACE, 2009, International Society for Pediatric and Adolescent Diabetes (ISPAD, 2009 and Russian Association of Endocrinologists (RAE, 2011, 2012. Current edition of the “Standards” also integrates results of completed randomized clinical trials (ADVANCE, ACCORD, VADT, UKPDS, etc., as well as findings from the national studies of diabetes mellitus (DM, conducted in close partnership with a number of Russian hospitals.Latest data indicates that prevalence of DM increased during the last decade more than two-fold, reaching some 371 million patients by 2013. According to the current estimation by the International Diabetes Federation, every tenth inhabitant of the planet will be suffering from DM by 2030. These observations resulted in the UN Resolution 61/225 passed on 20.12.2006 that encouraged all Member States “to develop national policies for the prevention, treatment and care of diabetes”.Like many other countries, Russian Federation experiences a sharp rise in the prevalence of DM. According to Russian State Diabetes Register, there are at least 3.799 million patients with DM in this country. However, the epidemiological survey conducted by the Federal Endocrinology Research Centre during 2002-2010 suggests that actual prevalence is 3 to 4 times greater than the officially recognized and, by this estimate, amounts to 9-10 million persons, comprising 7% of the

  7. 45 CFR 73.735-705 - Writing and editing.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Writing and editing. 73.735-705 Section 73.735-705 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION STANDARDS OF CONDUCT... not be expressed or implied in the material itself or advertising or promotional material,...

  8. Australian Alps: Kosciuszko, Alpine and Namadgi National Parks (Second Edition

    Directory of Open Access Journals (Sweden)

    Nicole Porter

    2017-02-01

    Full Text Available Reviewed: Australian Alps: Kosciuszko, Alpine and Namadgi National Parks (Second Edition By Deidre Slattery. Clayton South, Australia: CSIRO Publishing, 2015. xvii + 302 pp. AU$ 45.00, US$ 35.95. ISBN 978-1-486-30171-3.

  9. Competencies for Librarians Serving Children in Public Libraries. Revised Edition.

    Science.gov (United States)

    Journal of Youth Services in Libraries, 2001

    2001-01-01

    This revised edition of competencies for librarians serving children in public libraries was developed by the American Library Association. Highlights include knowledge of client group; administrative and management skills; communication skills; materials and collection development; skills in developing library programs, advocacy, public…

  10. Coping with Downsizing as a Writing and Editing Group.

    Science.gov (United States)

    Steve, Mike; Bigelow, Tom

    1993-01-01

    Maintains that writers and editors are likely candidates for downsizing within an organization. Notes that centralization-decentralization factors are valuable in addressing downsizing, as is knowledge of corporate management's point of view toward its investment in writing and editing. Offers five self-assessment scenarios to help prepare for the…

  11. Genome editing: The efficient tool CRISPR–Cpf1

    KAUST Repository

    Mahfouz, Magdy M.

    2017-03-01

    The novel features of the CRISPR–Cpf1 RNA-guided endonuclease system facilitate precise and efficient genome engineering. Application of CRISPR–Cpf1 in plants shows promise for robust gene editing and regulation, opening exciting possibilities for targeted trait improvement in crops.

  12. Optimization of genome editing through CRISPR-Cas9 engineering.

    Science.gov (United States)

    Zhang, Jian-Hua; Adikaram, Poorni; Pandey, Mritunjay; Genis, Allison; Simonds, William F

    2016-04-01

    CRISPR (Clustered Regularly-Interspaced Short Palindromic Repeats)-Cas9 (CRISPR associated protein 9) has rapidly become the most promising genome editing tool with great potential to revolutionize medicine. Through guidance of a 20 nucleotide RNA (gRNA), CRISPR-Cas9 finds and cuts target protospacer DNA precisely 3 base pairs upstream of a PAM (Protospacer Adjacent Motif). The broken DNA ends are repaired by either NHEJ (Non-Homologous End Joining) resulting in small indels, or by HDR (Homology Directed Repair) for precise gene or nucleotide replacement. Theoretically, CRISPR-Cas9 could be used to modify any genomic sequences, thereby providing a simple, easy, and cost effective means of genome wide gene editing. However, the off-target activity of CRISPR-Cas9 that cuts DNA sites with imperfect matches with gRNA have been of significant concern because clinical applications require 100% accuracy. Additionally, CRISPR-Cas9 has unpredictable efficiency among different DNA target sites and the PAM requirements greatly restrict its genome editing frequency. A large number of efforts have been made to address these impeding issues, but much more is needed to fully realize the medical potential of CRISPR-Cas9. In this article, we summarize the existing problems and current advances of the CRISPR-Cas9 technology and provide perspectives for the ultimate perfection of Cas9-mediated genome editing.

  13. Educators Guide to Free Films. Thirty-Sixth Edition.

    Science.gov (United States)

    Horkheimer, Mary Foley, Comp.; Diffor, John C., Comp.

    This edition lists more than 4000 films available free of cost throughout the United States generally, with those available in Australia and Canada indicated separately. Listings are organized according to curriculum categories. Each listing includes title, description of the contents, date of release, size, whether sound or silent, running time,…

  14. Baishideng's century goal: Editing and publishing high-quality articles

    Institute of Scientific and Technical Information of China (English)

    Lian-Sheng Ma

    2009-01-01

    Baishideng's goal over the next few years is to edit and publish high-quality articles through the open-access model, to maximize the benefits to members of the editorial board, authors and readers, as well as achieving social and economic benefits.

  15. Brief Intervention for School Problems: Outcome Informed Strategies, Second Edition

    Science.gov (United States)

    Murphy, John J.; Duncan, Barry L.

    2007-01-01

    Now in a revised and updated second edition, this highly practical guide provides innovative strategies for resolving academic and behavioral difficulties by enlisting the strengths and resources of students, parents, and teachers. Extensive new case material illustrates the authors' creative approach to building solutions and "busting problems"…

  16. Analysis of individual differences in radiosensitivity using genome editing.

    Science.gov (United States)

    Matsuura, S; Royba, E; Akutsu, S N; Yanagihara, H; Ochiai, H; Kudo, Y; Tashiro, S; Miyamoto, T

    2016-06-01

    Current standards for radiological protection of the public have been uniformly established. However, individual differences in radiosensitivity are suggested to exist in human populations, which could be caused by nucleotide variants of DNA repair genes. In order to verify if such genetic variants are responsible for individual differences in radiosensitivity, they could be introduced into cultured human cells for evaluation. This strategy would make it possible to analyse the effect of candidate nucleotide variants on individual radiosensitivity, independent of the diverse genetic background. However, efficient gene targeting in cultured human cells is difficult due to the low frequency of homologous recombination (HR) repair. The development of artificial nucleases has enabled efficient HR-mediated genome editing to be performed in cultured human cells. A novel genome editing strategy, 'transcription activator-like effector nuclease (TALEN)-mediated two-step single base pair editing', has been developed, and this was used to introduce a nucleotide variant associated with a chromosomal instability syndrome bi-allelically into cultured human cells to demonstrate that it is the causative mutation. It is proposed that this editing technique will be useful to investigate individual radiosensitivity.

  17. Calibrated hot deck imputation for numerical data under edit restrictions

    NARCIS (Netherlands)

    de Waal, A.G.; Coutinho, Wieger; Shlomo, Natalie

    2017-01-01

    We develop a non-parametric imputation method for item non-response based on the well-known hot-deck approach. The proposed imputation method is developed for imputing numerical data that ensure that all record-level edit rules are satisfied and previously estimated or known totals are exactly prese

  18. The Copyright Book: A Practical Guide. Fourth Edition.

    Science.gov (United States)

    Strong, William S.

    In response to important changes in copyright law as the United States accommodates itself to the Berne Convention and develops means to take account of new technologies, this guide puts these changes in a form and context that will make sense to persons who are concerned about their rights under the law. New material in the fourth edition of this…

  19. Using Technology with Classroom Instruction that Works. Second Edition

    Science.gov (United States)

    Kuhn, Matt; Hubbell, Elizabeth R.; Pitler, Howard

    2012-01-01

    If you've upgraded to the second edition of the landmark book "Classroom Instruction That Works," you need this companion guide to help you use technology to support research-based instruction. The authors follow the revised Instructional Planning Guide that makes it easier for you to know when to emphasize each of the instructional strategies,…

  20. AAV Vectorization of DSB-mediated Gene Editing Technologies.

    Science.gov (United States)

    Moser, Rachel J; Hirsch, Matthew L

    2016-01-01

    Recent work both at the bench and the bedside demonstrate zinc-finger nucleases (ZFNs), CRISPR/Cas9, and other programmable site-specific endonuclease technologies are being successfully utilized within and alongside AAV vectors to induce therapeutically relevant levels of directed gene editing within the human chromosome. Studies from past decades acknowledge that AAV vector genomes are enhanced substrates for homology-directed repair in the presence or absence of targeted DNA damage within the host genome. Additionally, AAV vectors are currently the most efficient format for in vivo gene delivery with no vector related complications in >100 clinical trials for diverse diseases. At the same time, advancements in the design of custom-engineered site-specific endonucleases and the utilization of elucidated endonuclease formats have resulted in efficient and facile genetic engineering for basic science and for clinical therapies. AAV vectors and gene editing technologies are an obvious marriage, using AAV for the delivery of repair substrate and/or a gene encoding a designer endonuclease; however, while efficient delivery and enhanced gene targeting by vector genomes are advantageous, other attributes of AAV vectors are less desirable for gene editing technologies. This review summarizes the various roles that AAV vectors play in gene editing technologies and provides insight into its trending applications for the treatment of genetic diseases.

  1. Targeted genome editing in human repopulating haematopoietic stem cells

    NARCIS (Netherlands)

    P. Genovese (Pietro); G. Schiroli (Giulia); G. Escobar (Giulia); T. Di Tomaso (Tiziano); C. Firrito (Claudia); A. Calabria (Andrea); D. Moi (Davide); R. Mazzieri (Roberta); C. Bonini (Chiara); M.V. Holmes (Michael); P.D. Gregory (Philip); M. van der Burg (Mirjam); B. Gentner (Bernhard); E. Montini (Eugenio); A. Lombardo (Angelo); L. Naldini (Luigi)

    2014-01-01

    textabstractTargeted genome editing by artificial nucleases has brought the goal of site-specific transgene integration and gene correction within the reach of gene therapy. However, its application to long-term repopulating haematopoietic stem cells (HSCs) has remained elusive. Here we show that po

  2. CRISPR/Cas9 based genome editing of Penicillium chrysogenum

    NARCIS (Netherlands)

    Pohl, Carsten; Kiel, Jan A K W; Driessen, Arnold J M; Bovenberg, Roel A L; Nygård, Yvonne

    2016-01-01

    CRISPR/Cas9 based systems have emerged as versatile platforms for precision genome editing in a wide range of organisms. Here we have developed powerful CRISPR/Cas9 tools for marker-based and marker-free genome modifications in Penicillium chrysogenum, a model filamentous fungus and industrially rel

  3. How to Be a Brilliant English Teacher. Second Edition

    Science.gov (United States)

    Wright, Trevor

    2012-01-01

    Now in its second edition, Trevor Wright's hugely popular "How to be a Brilliant English Teacher" is packed with practical advice drawn from his extensive and successful experience as an English teacher, examiner and teacher trainer. This accessible and readable guide offers sound theoretical principles with exciting practical suggestions for the…

  4. What! I Have To Give a Speech? 2nd Edition.

    Science.gov (United States)

    Snyder, Kenneth; Murphy, Thomas J.

    Noting that fear of public speaking is shared by people of all types, the second edition of this book offers practical, easy-to-follow strategies for confident and effective public speaking. The book discusses the following aspects of public speaking: what to talk about; how to research a topic; how to organize a speech; how to keep an audience…

  5. Therapeutic Uses of Music with Older Adults. Second Edition

    Science.gov (United States)

    Clair, Alicia Ann; Memmott, Jenny

    2008-01-01

    In this comprehensively updated second edition, written by Alicia Ann Clair and Jenny Memmott the extraordinary benefits of music therapy for older adults are detailed. "Therapeutic Uses of Music with Older Adults" not only examines these benefits but also clarifies the reasons that music is beneficial. This important book shows both informal and…

  6. Multicultural Education: Issues and Perspectives. 6th Edition

    Science.gov (United States)

    Banks, James A.; Banks, Cherry A. McGee

    2006-01-01

    Today's classrooms are more diverse than ever before. In order to reach these students, educators must be aware of the issues facing their various cultural, racial, ethnic, and language groups. Focusing on the pertinent issues in multicultural education, this new edition raises these critical issues and facilitates meaningful discussion. It has…

  7. Dental Hygiene Program Clinic Manual, Fall 1997. Fourth Edition.

    Science.gov (United States)

    Errico, Mary; Cama, Christine; Pastoriza-Maldonado, Alida

    This is the fourth edition of the Clinic Manual for the Dental Hygiene Program at Eugenio Maria de Hostos Community College in the Bronx (New York). It contains general information, grading procedures, performance guides, and clinical forms related to the program. Section 1 provides an introduction to clinic philosophy, policies, goals and…

  8. 75 FR 42786 - Accounting Guide for LSC Recipients (2010 Edition)

    Science.gov (United States)

    2010-07-22

    ... provisions. The Accounting Guide for LSC Recipients (2010 edition) can be located by accessing LSC's Web site... provisions easier to understand. Comments Received to Proposed Revisions to Accounting Guide Following the... recommending a reference in 2-2.6 to the provision on accounting for attorneys' fees, now set forth in 45...

  9. Illustrated glossary of process equipment. Chinese/English/French edition

    Energy Technology Data Exchange (ETDEWEB)

    Paruit, B.

    1984-01-01

    Here is a volume of process equipment and terms in standard Mandarin Chinese, English, and French. As with the English/French/Spanish edition, each page illustrates a particular piece of equipment, with captions identifying the key components. Glossaries at the end of each major section include the Romanized pronunciation of the Chinese.

  10. Research in Special Education: Designs, Methods, and Applications. Second Edition

    Science.gov (United States)

    Rumrill, Phillip D., Jr.; Cook, Bryan G.; Wiley, Andrew L.

    2011-01-01

    The goal of this second edition is to provide a comprehensive overview of the philosophical, ethical, methodological, and analytical fundamentals of social science and educational research, as well as specify aspects of special education research that distinguish it from scientific inquiry in other fields of education and human services. Foremost…

  11. On optimal comparability editing with applications to molecular diagnostics

    NARCIS (Netherlands)

    Boecker, S.; Briesemeister, S.; Klau, G.W.

    2009-01-01

    BACKGROUND: The COMPARABILITY EDITING problem appears in the context of hierarchical disease classification based on noisy data. We are given a directed graph G representing hierarchical relationships between patient subgroups. The task is to identify the minimum number of edge insertions or deletio

  12. ACSM's Health/Fitness Facility Standards and Guidelines. Second Edition.

    Science.gov (United States)

    Peterson, James A., Ed; Tharrett, Stephen J., Ed.

    The American College of Sports Medicine (ACSM) sets the industry standard for certifying professionals involved in health and fitness and their clinical applications. This 5-part publication provides a revised edition of six standards representing the industry's consensus on design and operation of a safe and high-quality health/fitness facility.…

  13. Schools and Society: A Sociological Approach to Education, Third Edition

    Science.gov (United States)

    Ballantine, Jeanne H., Ed.; Spade, Joan Z., Ed.

    2007-01-01

    This third edition, now published by Pine Forge Press, features original readings and article excerpts by leaders in the area of Sociology of Education. With a wide array of theoretical perspectives, a broad range of respected sources, and inclusion of both classic and contemporary studies, this comprehensive, integrated text addresses key issues…

  14. RADON REDUCTION TECHNIQUES FOR DETACHED HOUSES, TECHNICAL GUIDANCE (SECOND EDITION)

    Science.gov (United States)

    This document is intended for use by State officials, radon mitigation contractors, building contractors, concerned homeowners, and other persons as an aid in the selection, design, and operation of radon reduction measurements for houses. It is the second edition of EPA's techn...

  15. Fundamentals of Physics, Student Study Guide, Extended 7th Edition

    Science.gov (United States)

    Halliday, David; Resnick, Robert; Walker, Jearl

    2004-06-01

    No other book on the market today can match the 30-year success of Halliday, Resnick and Walker's Fundamentals of Physics! Fundamentals of Physics, 7th Edition and the Extended Version, 7th Edition offer a solid understanding of fundamental physics concepts, helping readers apply this conceptual understanding to quantitative problem solving, in a breezy, easy-to-understand style. A unique combination of authoritative content and stimulating applications. * Numerous improvements in the text, based on feedback from the many users of the sixth edition (both instructors and students) * Several thousand end-of-chapter problems have been rewritten to streamline both the presentations and answers * 'Chapter Puzzlers' open each chapter with an intriguing application or question that is explained or answered in the chapter * Problem-solving tactics are provided to help beginning Physics students solve problems and avoid common error * The first section in every chapter introduces the subject of the chapter by asking and answering, "What is Physics?" as the question pertains to the chapter * Numerous supplements available to aid teachers and students The extended edition provides coverage of developments in Physics in the last 100 years, including: Einstein and Relativity, Bohr and others and Quantum Theory, and the more recent theoretical developments like String Theory.

  16. Journal Editing and Ethical Research Practice: Perspectives of Journal Editors

    Science.gov (United States)

    Randell-Moon, Holly; Anderson, Nicole; Bretag, Tracey; Burke, Anthony; Grieshaber, Sue; Lambert, Anthony; Saltmarsh, David; Yelland, Nicola

    2011-01-01

    This article offers perspectives from academics with recent journal editing experience on a range of ethical issues and dilemmas that regularly pose challenges for those in editorial roles. Each contributing author has provided commentary and reflection on a select topic that was identified in the research literature concerning academic publishing…

  17. Who's Who in Space: The International Space Year Edition.

    Science.gov (United States)

    Martin, Ron

    1993-01-01

    Reviews the reference book "Who's Who in Space: The International Space Year Edition" and provides a lesson plan for grades five and six to teach library media skills. Objectives, instructional roles, activity and procedures, evaluation, and follow-up are described. (EAM)

  18. The Bacterial Origins of the CRISPR Genome-Editing Revolution.

    Science.gov (United States)

    Sontheimer, Erik J; Barrangou, Rodolphe

    2015-07-01

    Like most of the tools that enable modern life science research, the recent genome-editing revolution has its biological roots in the world of bacteria and archaea. Clustered, regularly interspaced, short palindromic repeats (CRISPR) loci are found in the genomes of many bacteria and most archaea, and underlie an adaptive immune system that protects the host cell against invasive nucleic acids such as viral genomes. In recent years, engineered versions of these systems have enabled efficient DNA targeting in living cells from dozens of species (including humans and other eukaryotes), and the exploitation of the resulting endogenous DNA repair pathways has provided a route to fast, easy, and affordable genome editing. In only three years after RNA-guided DNA cleavage was first harnessed, the ability to edit genomes via simple, user-defined RNA sequences has already revolutionized nearly all areas of biological science. CRISPR-based technologies are now poised to similarly revolutionize many facets of clinical medicine, and even promise to advance the long-term goal of directly editing genomic sequences of patients with inherited disease. In this review, we describe the biological and mechanistic basis for these remarkable immune systems, and how their engineered derivatives are revolutionizing basic and clinical research.

  19. Genome-editing Technologies for Gene and Cell Therapy.

    Science.gov (United States)

    Maeder, Morgan L; Gersbach, Charles A

    2016-03-01

    Gene therapy has historically been defined as the addition of new genes to human cells. However, the recent advent of genome-editing technologies has enabled a new paradigm in which the sequence of the human genome can be precisely manipulated to achieve a therapeutic effect. This includes the correction of mutations that cause disease, the addition of therapeutic genes to specific sites in the genome, and the removal of deleterious genes or genome sequences. This review presents the mechanisms of different genome-editing strategies and describes each of the common nuclease-based platforms, including zinc finger nucleases, transcription activator-like effector nucleases (TALENs), meganucleases, and the CRISPR/Cas9 system. We then summarize the progress made in applying genome editing to various areas of gene and cell therapy, including antiviral strategies, immunotherapies, and the treatment of monogenic hereditary disorders. The current challenges and future prospects for genome editing as a transformative technology for gene and cell therapy are also discussed.

  20. Genome-Editing Technologies for Enhancing Plant Disease Resistance

    Science.gov (United States)

    Andolfo, Giuseppe; Iovieno, Paolo; Frusciante, Luigi; Ercolano, Maria R.

    2016-01-01

    One of the greatest challenges for agricultural science in the 21st century is to improve yield stability through the progressive development of superior cultivars. The increasing numbers of infectious plant diseases that are caused by plant-pathogens make it ever more necessary to develop new strategies for plant disease resistance breeding. Targeted genome engineering allows the introduction of precise modifications directly into a commercial variety, offering a viable alternative to traditional breeding methods. Genome editing is a powerful tool for modifying crucial players in the plant immunity system. In this work, we propose and discuss genome-editing strategies and targets for improving resistance to phytopathogens. First of all, we present the opportunities to rewrite the effector-target sequence for avoiding effector-target molecular interaction and also to modify effector-target promoters for increasing the expression of target genes involved in the resistance process. In addition, we describe potential approaches for obtaining synthetic R-genes through genome-editing technologies (GETs). Finally, we illustrate a genome editing flowchart to modify the pathogen recognition sites and engineer an R-gene that mounts resistance to some phylogenetically divergent pathogens. GETs potentially mark the beginning of a new era, in which synthetic biology affords a basis for obtaining a reinforced plant defense system. Nowadays it is conceivable that by modulating the function of the major plant immunity players, we will be able to improve crop performance for a sustainable agriculture. PMID:27990151

  1. Consumer acceptance of food crops developed by genome editing.

    Science.gov (United States)

    Ishii, Tetsuya; Araki, Motoko

    2016-07-01

    One of the major problems regarding consumer acceptance of genetically modified organisms (GMOs) is the possibility that their transgenes could have adverse effects on the environment and/or human health. Genome editing, represented by the CRISPR/Cas9 system, can efficiently achieve transgene-free gene modifications and is anticipated to generate a wide spectrum of plants. However, the public attitude against GMOs suggests that people will initially be unlikely to accept these plants. We herein explored the bottlenecks of consumer acceptance of transgene-free food crops developed by genome editing and made some recommendations. People should not pursue a zero-risk bias regarding such crops. Developers are encouraged to produce cultivars with a trait that would satisfy consumer needs. Moreover, they should carefully investigate off-target mutations in resultant plants and initially refrain from agricultural use of multiplex genome editing for better risk-benefit communication. The government must consider their regulatory status and establish appropriate regulations if necessary. The government also should foster communication between the public and developers. If people are informed of the benefits of genome editing-mediated plant breeding and trust in the relevant regulations, and if careful risk-benefit communication and sincere considerations for the right to know approach are guaranteed, then such transgene-free crops could gradually be integrated into society.

  2. Pediatric Dentistry: A Clinical Approach, 3rd Edition

    DEFF Research Database (Denmark)

    Pediatric Dentistry: A Clinical Approach, Third Edition provides a uniquely clear, comprehensive, and clinical approach to the dental treatment of children and adolescents. •Offers systematic coverage of all clinical, scientific and social topics relating to pediatric dentistry •Thoroughly revised...

  3. [Genome Editing Tools and their Application in Experimental Ophthalmology].

    Science.gov (United States)

    Yanik, M; Wende, W; Stieger, K

    2017-01-23

    New genome editing tools in molecular biology are revolutionising precise genome surgery and have greatly influenced experimental ophthalmology too. Aside from the commonly used nuclease-based platforms, such as the zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN), CRISPR/Cas systems, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes, perform very efficiently in site-specific DNA cleavage within living cells. DNA double strand breaks (DSB) are repaired through two different conserved repair pathways: NHEJ (non-homologous end joining) and HDR (homology directed repair). By using the correct DNA templates, these repair pathways can be used to knock out defective genes or to repair mutations. Genome editing technology lays the ground for new strategies in basic science, biotechnology, and biomedical science, as well as clinical studies with genome editing. Therapeutic gene editing strategies are now concentrating on diseases in the retina, due to the comparatively easy accessibility of the eye and with local application in vivo.

  4. Fluency Training a Writing Skill: Editing for Concision

    Science.gov (United States)

    Dermer, Marshall L.; Lopez, Shannon L.; Messling, Paul A., III

    2009-01-01

    The goal of this study was to design and evaluate fluency-based training units to help students eliminate inconcision. Participants first completed a 1.5-hr lesson on writing concisely and then a 5-min test during which they edited sentences containing inconcise text from the training units. Subsequently, participants were randomly assigned to an…

  5. Outdoor Biology Instructional Strategies Trial Edition. Set III.

    Science.gov (United States)

    Fairwell, Kay, Ed.; And Others

    The predominant focus of the 24 Outdoor Biology Instructional Strategies (OBIS) Trial Edition Set III activities is on animal behavior, and the adaptations and diversity of both plants and animals. Night time activities, games, investigation, experimentation, and crafts are used to study ants, birds, clams, water snails, water striders, spiders,…

  6. Diagnosis of bone and joint disorders. Second edition

    Energy Technology Data Exchange (ETDEWEB)

    Resnick, D.; Niwayama, G.

    1987-01-01

    This book features descriptions of the anatomy, histology, radiography, radiology, biomechanics, and pathology of individual joints. It includes fresh new perspectives and contemporary coverage on important areas of musculoskeletal imaging not covered in the 1981 edition: iatrogenic, endocrine, infections, and oncologic disorders.

  7. Fostering Teacher Candidates' Reflective Practice through Video Editing

    Science.gov (United States)

    Trent, Margaret; Gurvitch, Rachel

    2015-01-01

    Recently, interest in using video to promote the reflective practice in preservice teacher education has increased. Video recordings of teaching incidents inspire the reflective practice in preservice teachers by allowing them to analyze instruction and view teaching in an objective light. As an extension of video recording, video editing has…

  8. Genome-editing Technologies for Gene and Cell Therapy

    Science.gov (United States)

    Maeder, Morgan L; Gersbach, Charles A

    2016-01-01

    Gene therapy has historically been defined as the addition of new genes to human cells. However, the recent advent of genome-editing technologies has enabled a new paradigm in which the sequence of the human genome can be precisely manipulated to achieve a therapeutic effect. This includes the correction of mutations that cause disease, the addition of therapeutic genes to specific sites in the genome, and the removal of deleterious genes or genome sequences. This review presents the mechanisms of different genome-editing strategies and describes each of the common nuclease-based platforms, including zinc finger nucleases, transcription activator-like effector nucleases (TALENs), meganucleases, and the CRISPR/Cas9 system. We then summarize the progress made in applying genome editing to various areas of gene and cell therapy, including antiviral strategies, immunotherapies, and the treatment of monogenic hereditary disorders. The current challenges and future prospects for genome editing as a transformative technology for gene and cell therapy are also discussed. PMID:26755333

  9. Interactive Translation Prediction versus Conventional Post-editing in Practice

    DEFF Research Database (Denmark)

    Sanchis-Trilles, German; Alabau, Vicent; Buck, Christian;

    2014-01-01

    We conducted a field trial in computer-assisted professional translation to compare Interactive Translation Prediction (ITP) against conventional post- editing (PE) of machine translation (MT) output. In contrast to the conventional PE set-up, where an MT system first produces a static translatio...

  10. The Literature Review: Six Steps to Success. Second Edition

    Science.gov (United States)

    Machi, Lawrence A.; McEvoy, Brenda T.

    2012-01-01

    This new edition of the best-selling book offers graduate students in education and the social sciences a road map to developing and writing an effective literature review for a research project, thesis, or dissertation. Organized around a proven six-step model and incorporating technology into all of the steps, the book provides examples,…

  11. Introduction to Approaches in Music Therapy. Second Edition

    Science.gov (United States)

    Darrow, Alice Ann, Ed.

    2008-01-01

    The second edition of "Introduction to Approaches in Music Therapy" includes a new introductory chapter that addresses historical perspectives on the approaches, a rationale for the categorization of approaches, and discussion on professional issues related to the use of these approaches. Each of the chapters addressing approaches includes updated…

  12. Weeding the Library Media Center Collections. Second Edition.

    Science.gov (United States)

    Buckingham, Betty Jo; And Others

    This second edition of guidelines for weeding school library media collections is addressed especially to elementary and secondary school library media centers and to community college and vocational school library resource centers in Iowa. This publication is designed for those who want weeding of all formats of materials and equipment (not just…

  13. Weeding Library Collections: Library Weeding Methods. Fourth Edition.

    Science.gov (United States)

    Slote, Stanly J.

    Weeding is one of the best ways to make long-term improvements to library collections, but it is also a difficult and sometimes painful task. In the tradition of previous editions, this book guides librarians in the process of methodical and efficient weeding. The book shows how to identify core collections versus the weedable items. The approach…

  14. The GMAT Exposed: Tricks from 20 GMATs. 2nd Edition.

    Science.gov (United States)

    White, David M.

    This book discusses tricks for answering questions on the Graduate Management Admission Test (GMAT). The tricks are based on an analysis of 20 editions of the GMAT which have been made public pursuant to New York's Truth in Testing Law. Sample GMAT questions published by the Graduate Management Admission Council are referenced to exemplify the…

  15. Utilization-Focused Evaluation: The New Century Text. Edition 3.

    Science.gov (United States)

    Patton, Michael Quinn

    This new edition offers an evaluation text that ranges from identifying the primary users of an evaluation to focusing the evaluation, making methods decisions, analyzing data, and presenting findings. Both practical and theoretical, the book tells how to conduct program evaluations and why they should be conducted in the manner prescribed. Each…

  16. Grants for Elementary & Secondary Education. 2012 Digital Edition

    Science.gov (United States)

    Foundation Center, 2011

    2011-01-01

    This publication is only available as a downloadable file. See who's giving and getting grants in your field. Strengthen your search for funds with the Foundation Center's digital edition of "Grants for Elementary & Secondary Education." This new "Grant Guide" reveals the scope of current foundation giving in the field. You'll find descriptions of…

  17. A Short History of the Movies. Second Edition.

    Science.gov (United States)

    Mast, Gerald

    This second edition of "A Short History of the Movies" includes expanded information and judgments about some of the "old masters" of film; an updated discussion of the "new masters"; and new sections on Japanese, Indian, and Czech cinema. In general, this history reveals significant trends in film history. American films are the primary focus,…

  18. [The meaning of the sixth edition of "Organon der Heilkunst"].

    Science.gov (United States)

    Schmidt, Josef M

    2002-01-01

    Like any artist, the paractitioner of the healing art should exactly know his tools, i.e. his medicines and the directions for their application. In addition, he should be able to rely on their genuineness. Regarding the tool "Organon", considerable uncertainty has been expressed by some physicians about the authenticity of Hahnemann's instructions for preparing and applying Q-potencies, as described in the sixth edition of the Organon of Medicine published by Richard Haehl in 1921. Since 1992, however, the first text-critical edition of the sixth edition of the Organonis available. Unlike Haehl's edition this one is exclusively based on Hahnemann's original manuscript and precisely transcribing all its handwriting, vouches for its authenticity. Hence there is no reason left to ignore Hahnemanns instructions concerning Q-potencies. This paper presents the history of the reception of Q-potencies as well as their prerequisites and evolution up to Hahnemann's final modifications of his earlier directions. As it turns out, these late instructions of Hahnemann do not mean complete change of all his previous opinions. Rather they are the logical completion of a course followed by him for ten years already. Q-potencies were Hahnemann's solution of the following therapeutic dilemma: on the one side physicians are inclined to repeat the dose of a high potency as often as possible in order to accelerate the process of healing; on the other side they should refrain from repeating the dose to avoid violent aggravations of the state of the patient.

  19. Review of traffic conflicts technique studies. Third edition.

    NARCIS (Netherlands)

    Kraay, J.H.

    1983-01-01

    A review of literature concerning traffic conflicts technique studies is presented. The 204 references arranged, alphabetically by authors' names are given with abstracts. The procedure used in comping this survey is outlined. Third revised edition, with 103 new publications since 1979.

  20. Grants for Libraries & Information Services. 2012 Digital Edition

    Science.gov (United States)

    Foundation Center, 2011

    2011-01-01

    This publication is only available as a downloadable file. See who's giving and getting grants in your field. Strengthen your search for funds with the Foundation Center's digital edition of "Grants for Libraries & Information Services." This new "Grant Guide" reveals the scope of current foundation giving in the field. You'll find descriptions of…

  1. Air Pollution Manual, Part 1--Evaluation. Second Edition.

    Science.gov (United States)

    Giever, Paul M., Ed.

    Due to the great increase in technical knowledge and improvement in procedures, this second edition has been prepared to update existing information. Air pollution legislation is reviewed. Sources of air pollution are examined extensively. They are treated in terms of natural sources, man-made sources, metropolitan regional emissions, emission…

  2. Genome editing for crop improvement: Challenges and opportunities.

    Science.gov (United States)

    Abdallah, Naglaa A; Prakash, Channapatna S; McHughen, Alan G

    2015-01-01

    Genome or gene editing includes several new techniques to help scientists precisely modify genome sequences. The techniques also enables us to alter the regulation of gene expression patterns in a pre-determined region and facilitates novel insights into the functional genomics of an organism. Emergence of genome editing has brought considerable excitement especially among agricultural scientists because of its simplicity, precision and power as it offers new opportunities to develop improved crop varieties with clear-cut addition of valuable traits or removal of undesirable traits. Research is underway to improve crop varieties with higher yields, strengthen stress tolerance, disease and pest resistance, decrease input costs, and increase nutritional value. Genome editing encompasses a wide variety of tools using either a site-specific recombinase (SSR) or a site-specific nuclease (SSN) system. Both systems require recognition of a known sequence. The SSN system generates single or double strand DNA breaks and activates endogenous DNA repair pathways. SSR technology, such as Cre/loxP and Flp/FRT mediated systems, are able to knockdown or knock-in genes in the genome of eukaryotes, depending on the orientation of the specific sites (loxP, FLP, etc.) flanking the target site. There are 4 main classes of SSN developed to cleave genomic sequences, mega-nucleases (homing endonuclease), zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and the CRISPR/Cas nuclease system (clustered regularly interspaced short palindromic repeat/CRISPR-associated protein). The recombinase mediated genome engineering depends on recombinase (sub-) family and target-site and induces high frequencies of homologous recombination. Improving crops with gene editing provides a range of options: by altering only a few nucleotides from billions found in the genomes of living cells, altering the full allele or by inserting a new gene in a targeted region of

  3. Gene editing for cell engineering: trends and applications.

    Science.gov (United States)

    Gupta, Sanjeev K; Shukla, Pratyoosh

    2016-08-18

    Gene editing with all its own advantages in molecular biology applications has made easy manipulation of various production hosts with the discovery and implementation of modern gene editing tools such as Crispr (Clustered regularly interspaced short palindromic repeats), TALENs (Transcription activator-like effector nucleases) and ZFNs (Zinc finger nucleases). With the advent of these modern tools, it is now possible to manipulate the genome of industrial production hosts such as yeast and mammalian cells which allows developing a potential and cost effective recombinant therapeutic protein. These tools also allow single editing to multiple genes for knocking-in or knocking-out of a host genome quickly in an efficient manner. A recent study on "multiplexed" gene editing revolutionized the knock-out and knock-in events of yeast and CHO, mammalian cells genome for metabolic engineering as well as high, stable, and consistent expression of a transgene encoding complex therapeutic protein such as monoclonal antibody. The gene of interest can either be integrated or deleted at single or multiple loci depending on the strategy and production requirement. This review will give a gist of all the modern tools with a brief description and advances in genetic manipulation using three major tools being implemented for the modification of such hosts with the emphasis on the use of Crispr-Cas9 for the "multiplexing gene-editing approach" for genetic manipulation of yeast and CHO mammalian hosts that ultimately leads to a fast track product development with consistent, improved product yield, quality, and thus affordability for a population at large.

  4. [CRISPR/Cas9-based genome editing systems and the analysis of targeted genome mutations in plants].

    Science.gov (United States)

    Xingliang, Ma; Yaoguang, Liu

    2016-02-01

    Targeted genomic editing technologies use programmable DNA nucleases to cleave genomic target sites, thus inducing targeted mutations in the genomes. The newly prevailed clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system that consists of the Cas9 nuclease and single guide RNA (sgRNA) has the advantages of simplicity and high efficiency as compared to other programmable DNA nuclease systems such as zinc finger nucleases (ZFNs) and transcription activator like effector nucleases (TALENs). Currently, a number of cases have been reported on the application of the CRISPR/Cas9 genomic editing technology in plants. In this review, we summarize the strategies for preparing the Cas9 and sgRNA expression constructs, the transformation method for obtaining targeted mutations, the efficiency and features of the resulting mutations and the methods for detecting or genotyping of the mutation sites. We also discuss the existing problems and perspectives of CRISPR/Cas9-based genomic editing in plants.

  5. Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing.

    Science.gov (United States)

    Wu, Dong-Dong; Ye, Ling-Qun; Li, Yan; Sun, Yan-Bo; Shao, Yi; Chen, Chunyan; Zhu, Zhu; Zhong, Li; Wang, Lu; Irwin, David M; Zhang, Yong E; Zhang, Ya-Ping

    2015-08-01

    Next-generation RNA sequencing has been successfully used for identification of transcript assembly, evaluation of gene expression levels, and detection of post-transcriptional modifications. Despite these large-scale studies, additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome. Here, we provide a total of 6.5 billion RNA-seq reads from different subregions of the human brain. A significant correlation was observed between the levels of alternative splicing and RNA editing, which might be explained by a competition between the molecular machineries responsible for the splicing and editing of RNA. Young human protein-coding genes demonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans. We also found that a significantly greater number of young human protein-coding genes are expressed in the putamen, a tissue that was also observed to have the highest level of RNA-editing activity. The putamen, which previously received little attention, plays an important role in cognitive ability, and our data suggest a potential contribution of the putamen to human evolution.

  6. BOOK REVIEW: A First Course in General Relativity (Second Edition) A First Course in General Relativity (Second Edition)

    Science.gov (United States)

    Poisson, Eric

    2010-05-01

    A few years ago, in my review of Sean Carroll's book in Classical and Quantum Gravity [1], I wrote that while the 1970s was the decade of Weinberg [2] and Misner, Thorne and Wheeler [3], and while the eighties was the decade of Schutz [4] and Wald [5], the 2000s was clearly the decade of Hartle [6] and Carroll [7]. In my opinion, these books continue to stand out in the surprisingly dense crowd of introductory textbooks on general relativity. At the dawn of this new decade I look forward to see what fresh pedagogical insights will be produced next, and who will be revealed as the winners of the 2010s. It is, of course, much too early to tell, but Schutz is back, and he will set the standard just as he did back in 1985. This is the long-awaited second edition of his `First Course', a short, accessible, and very successful introduction to general relativity. The changes from the first edition are modest: Schutz wisely refrained from bloating the text with new topics, and limited himself to updating his discussion of gravitational-wave sources and detectors, neutron-star and black-hole astrophysics, and suggestions for further reading. Most importantly, he completely rewrote the chapter on cosmology, a topic that has evolved enormously since the first edition. The book begins in chapter 1 with a beautiful review of special relativity that emphasizes spacetime geometry and stays away from an algebraic approach based on the Lorentz transformation, which appears only later in the chapter. This is followed up in chapters 2 and 3 with an introduction to vector and tensor analysis in flat spacetime. The point of view is modern (tensors are defined as linear mapping of vectors and one-forms into real numbers) but the presentation is very accessible and avoids an overload of mathematical fine print. In chapter 4 the book introduces the spacetime description of fluids; it is here that the energy-momentum tensor makes its first appearance. The move to curved spacetime is

  7. ELECTRONIC PROFESSIONAL EDITIONS IN THE SYSTEM OF SCIENTIFIC PERIODICALS: STATE AND PROSPECTS

    Directory of Open Access Journals (Sweden)

    Nataliia M. Kropocheva

    2014-02-01

    Full Text Available The article highlights relevant current problems concerning the formation, present state and prospects of the development of the native electronic professional editions on pedagogy. The historical overview of the development of the electronic books in the world and in Ukraine in general, and also including the professional editions was made. It was conducted the analysis of national and international legal framework for existing electronic editions, as well as researched the structure and software of the native electronic professional editions on pedagogy. Based on the results, it was formulated the conclusions and developed some suggestions for the improvement of electronic editions.

  8. Coming 5th Edition of the API Standard 618: major changes compared to the API 618, 4th edition

    NARCIS (Netherlands)

    Pyle, A.; Eijk, A.; Elferink, H.

    2003-01-01

    This paper will present the highlights of changes that will be found in the 5th Edition of API 618, which is expected to be published in late 2003 or early 2004. Approximately every 5 years the API Standards are revised in such a way that the latest field experiences and proven designs are included

  9. What Video Games Have to Teach Us about Learning and Literacy. Second Edition: Revised and Updated Edition

    Science.gov (United States)

    Gee, James Paul

    2007-01-01

    The author begins his classic book with "I want to talk about video games--yes, even violent video games--and say some positive things about them." With this simple but explosive statement, one of America's most well-respected educators looks seriously at the good that can come from playing video games. In this revised edition, new games like…

  10. Validation of the fifth edition BI-RADS ultrasound lexicon with comparison of fourth and fifth edition diagnostic performance using video clips

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Jung Hyun; Kim, Min Jung; Lee, Hye Sun [Yonsei University College of Medicine, Seoul (Korea, Republic of); Kim, Sung Hun [Dept. of Radiology, Seoul St. Mary' s Hospital, The Catholic University of Korea, Seoul(Korea, Republic of); Youk, Ji Hyun [Dept. of Radiology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Jeong, Sun Hye [Dept. of Radiology, Soonchunhyang University Bucheon Hospital, Bucheon (Korea, Republic of); Kim, You Me [Dept. of Radiology, Dankook University Hospital, Dankook University College of Medicine, Cheonan (Korea, Republic of)

    2016-08-15

    The aim of this study was to evaluate the positive predictive value (PPV) and the diagnostic performance of the ultrasonographic descriptors in the fifth edition of BI-RADS, comparing with the fourth edition using video clips. From September 2013 to July 2014, 80 breast masses in 74 women (mean age, 47.5±10.7 years) from five institutions of the Korean Society of Breast Imaging were included. Two radiologists individually reviewed the static and video images and analyzed the images according to the fourth and fifth edition of BI-RADS. The PPV of each descriptor was calculated and diagnostic performances between the fourth and fifth editions were compared. Of the 80 breast masses, 51 (63.8%) were benign and 29 (36.2%) were malignant. Suspicious ultrasonographic features such as irregular shape, non-parallel orientation, angular or spiculated margins, and combined posterior features showed higher PPV in both editions (all P<0.05). No significant differences were found in the diagnostic performances between the two editions (all P>0.05). The area under the receiver operating characteristics curve was higher in the fourth edition (0.708 to 0.690), without significance (P=0.416). The fifth edition of the BI-RADS ultrasound lexicon showed comparable performance to the fourth edition and can be useful in the differential diagnosis of breast masses using ultrasonography.

  11. Books authored/co-authored and edited/co-edited by members of staff of the Department of Medieval/Medieval and Renaissance Archaeology, Aarhus University, 1971-2014

    DEFF Research Database (Denmark)

    Roesdahl, Else

    2015-01-01

    Chronologically organized list of books authored/co-authored and edited/co-edited by members of staff of the Department of Medieval and Renaissance Archaeology, Aarhus University, 1971-2014......Chronologically organized list of books authored/co-authored and edited/co-edited by members of staff of the Department of Medieval and Renaissance Archaeology, Aarhus University, 1971-2014...

  12. Changes in the APA "Publication Manual": How the New Fifth Edition Will Affect Research Reporting in the Social Sciences.

    Science.gov (United States)

    Daniel, Larry G.

    The American Psychological Association (APA) has recently published the fifth edition of its "Publication Manual." This paper provides a brief overview of how this edition differs from previous editions and summarizes features of the new edition that will be likely to have an impact on social science research over the next several years.…

  13. 200 years Organon of Medicine - A comparative review of its six editions (1810-1842).

    Science.gov (United States)

    Schmidt, Josef M

    2010-10-01

    In 2010 the 200th anniversary of the Organon is celebrated by the homeopathic community. Samuel Hahnemann's Organon of Rational Therapeutics, published in 1810, however, marks neither the beginning of homeopathy nor the endpoint of its development. On the one hand, its contents are based on terms and concepts developed and published by Hahnemann during the preceding two decades. On the other hand, the five revised editions of the Organon that followed in the next three decades contain major changes of theory and conceptions. Hahnemann's basic idea, running through all the stages of the foundation, elaboration, and defence of his doctrine, may be detected by a comparative review of his works from a historical and philosophical perspective.

  14. UNCERTAIN TRAINING DATA EDITION FOR AUTOMATIC OBJECT-BASED CHANGE MAP EXTRACTION

    Directory of Open Access Journals (Sweden)

    S. Hajahmadi

    2013-09-01

    Full Text Available Due to the rapid transformation of the societies, and the consequent growth of the cities, it is necessary to study these changes in order to achieve better control and management of urban areas and assist the decision-makers. Change detection involves the ability to quantify temporal effects using multi-temporal data sets. The available maps of the under study area is one of the most important sources for this reason. Although old data bases and maps are a great resource, it is more than likely that the training data extracted from them might contain errors, which affects the procedure of the classification; and as a result the process of the training sample editing is an essential matter. Due to the urban nature of the area studied and the problems caused in the pixel base methods, object-based classification is applied. To reach this, the image is segmented into 4 scale levels using a multi-resolution segmentation procedure. After obtaining the segments in required levels, training samples are extracted automatically using the existing old map. Due to the old nature of the map, these samples are uncertain containing wrong data. To handle this issue, an editing process is proposed according to K-nearest neighbour and k-means algorithms. Next, the image is classified in a multi-resolution object-based manner and the effects of training sample refinement are evaluated. As a final step this classified image is compared with the existing map and the changed areas are detected.

  15. Tracking Amendments to Legislation and Other Political Texts with a Novel Minimum-Edit-Distance Algorithm: DocuToads

    DEFF Research Database (Denmark)

    Hermansson, Henrik Alf Jonas; Cross, James

    2015-01-01

    Political scientists often nd themselves tracking amendments to political texts. As different actors weigh in, texts change as they are drafted and redrafted, reflecting political preferences and power. This study provides a novel solution to the problem of detecting amendments to political text......) and substantive amount of amendments made between version of texts. To illustrate the usefulness and eciency of the approach we replicate two existing studies from the field of legislative studies. Our results demonstrate that minimum edit distance methods can produce superior measures of text amendments to hand...

  16. Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology.

    Science.gov (United States)

    Alagoz, Yagiz; Gurkok, Tugba; Zhang, Baohong; Unver, Turgay

    2016-08-03

    Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease system is a powerful RNA-guided genome editing tool. CRISPR/Cas9 has been well studied in model plant species for targeted genome editing. However, few studies have been reported on plant species without whole genome sequence information. Currently, no study has been performed to manipulate metabolic pathways using CRISPR/Cas9. In this study, the type II CRISPR/SpCas9 system was used to knock out, via nonhomologous end-joining genome repair, the 4'OMT2 in opium poppy (Papaver somniferum L.), a gene which regulates the biosythesis of benzylisoquinoline alkaloids (BIAs). For sgRNA transcription, viral-based TRV and synthetic binary plasmids were designed and delivered into plant cells with a Cas9 encoding-synthetic vector by Agrobacterium-mediated transformation. InDels formed by CRISPR/Cas9 were detected by sequence analysis. Our results showed that the biosynthesis of BIAs (e.g. morphine, thebaine) was significantly reduced in the transgenic plants suggesting that 4'OMT2 was efficiently knocked-out by our CRISPR-Cas9 genome editing approach. In addition, a novel uncharacterized alkaloid was observed only in CRISPR/Cas9 edited plants. Thus, the applicabilitiy of the CRISPR/Cas9 system was demonstrated for the first time for medicinal aromatic plants by sgRNAs transcribed from both synthetic and viral vectors to regulate BIA metabolism and biosynthesis.

  17. The New Edition of Chopin’s Correspondence

    Directory of Open Access Journals (Sweden)

    Helman-Bednarczyk Zofia

    2016-12-01

    Full Text Available Some of Fryderyk Chopin’s letters were published individually or in groups already in the 2nd half of the 19th century. With the passage of time, more letters from and to Chopin were printed in monographs dedicated to his life and work. The first editions of Chopin’s collected letters come from the 1st half of the 20th century (by Scharlitt and von Guttry in Germany, Henryk Opieński – in Poland. B.E. Sydow’s Fryderyk Chopin’s Correspondence of 1955 continues to be used as the basic source edition by Chopin biographers. It has many strong points, but has become largely outdated.

  18. Genome Editing and Its Applications in Model Organisms.

    Science.gov (United States)

    Ma, Dongyuan; Liu, Feng

    2015-12-01

    Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas), has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine.

  19. [One hundred years of Freud editions in The Netherlands].

    Science.gov (United States)

    Greven, Elsbeth

    2009-01-01

    The history of Dutch editions of Freud is discussed from a publisher's point of view. The author focuses on the main publishers involved in presenting Freud's work to the Dutch public: S. C. van Doesburgh, De Wereldbibliotheek, De Bezige Bij and Uitgeverij Boom. She describes their role, together with their networks of translators, editors and psychoanalysts, in the production, perception and reception of Freud's work--and hence in the development of psychoanalysis in The Netherlands--as well as their approaches to translation, publishing strategies and use of paratextual resources. Three main stages can be identified: 1. 1912 to World War I (Freud was introduced), 2. World War I to 1950 (Freud was popularised), and 3. 1960 to 1990 (Freud was canonised, but also criticised). A fourth stage, the historicisation of Freud, began in 2006 with a new, scholarly edition of his Werken, arranged in chronological order.

  20. Three editions of the Star Catalogue of Tycho Brahe

    CERN Document Server

    Verbunt, Frank

    2010-01-01

    Tycho Brahe completed his catalogue with the positions and magnitudes of 1004 fixed stars in 1598. This catalogue circulated in manuscript form. Brahe edited a shorter version with 777 stars, printed in 1602, and Kepler edited the full catalogue of 1004 stars, printed in 1627. We provide machine-readable versions of the three versions of the catalogue, describe the differences between them and briefly discuss their accuracy on the basis of comparison with modern data from the Hipparcos Catalogue. We also compare our results with earlier analyses by Dreyer (1916) and Rawlins (1993), finding good overall agreement. The magnitudes given by Brahe correlate well with modern values, his longitudes and latitudes have error distributions with widths of about 2 arcmin, with excess numbers of stars with larger errors (as compared to Gaussian distributions), in particular for the faintest stars. Errors in positions larger than 10 arcmin, which comprise about 15 per cent of the entries, are likely due to computing or cop...

  1. Using Apollo to browse and edit genome annotations.

    Science.gov (United States)

    Misra, Sima; Harris, Nomi

    2006-01-01

    An annotation is any feature that can be tied to genomic sequence, such as an exon, transcript, promoter, or transposable element. As biological knowledge increases, annotations of different types need to be added and modified, and links to other sources of information need to be incorporated, to allow biologists to easily access all of the available sequence analysis data and design appropriate experiments. The Apollo genome browser and editor offers biologists these capabilities. Apollo can display many different types of computational evidence, such as alignments and similarities based on BLAST searches (UNITS 3.3 & 3.4), and enables biologists to utilize computational evidence to create and edit gene models and other genomic features, e.g., using experimental evidence to refine exon-intron structures predicted by gene prediction algorithms. This protocol describes simple ways to browse genome annotation data, as well as techniques for editing annotations and loading data from different sources.

  2. The EDIT school trains future experts in detector technologies

    CERN Multimedia

    CERN Bulletin

    2011-01-01

    The Excellence in Detectors and Instrumentation Technologies (EDIT) School has just taken place for the first time. The enthusiastic feedback from the organizers and the participants shows how the School’s format is just the right formula for today’s young researchers specializing in experimental physics. To mark the importance of the event, Rolf Heuer dedicated the School to Georges Charpak.   Rolf Heuer and Pier Oddone visit Building 154, which hosted some of the EDIT School laboratory activities. Like many other branches of science, today’s particle physics relies on very complex instruments to provide the performance that unresolved questions require. When we say ‘particle physics’ we actually mean a whole lot of different specializations that young researchers choose to pursue when they are at university. “In the present situation, it might very well happen that an experimental particle physicist at the end of his/her studies has ne...

  3. From hacking the human genome to editing organs.

    Science.gov (United States)

    Tobita, Takamasa; Guzman-Lepe, Jorge; Collin de l'Hortet, Alexandra

    2015-01-01

    In the recent decades, human genome engineering has been one of the major interesting research subjects, essentially because it raises new possibilities for personalized medicine and biotechnologies. With the development of engineered nucleases such as the Zinc Finger Nucleases (ZFNs), the Transcription activator-like effector nucleases (TALENs) and more recently the Clustered Regularly Interspaced short Palindromic Repeats (CRISPR), the field of human genome edition has evolved very rapidly. Every new genetic tool is broadening the scope of applications on human tissues, even before we can completely master each of these tools. In this review, we will present the recent advances regarding human genome edition tools, we will discuss the numerous implications they have in research and medicine, and we will mention the limits and concerns about such technologies.

  4. TALEN-mediated genome editing: prospects and perspectives.

    Science.gov (United States)

    Wright, David A; Li, Ting; Yang, Bing; Spalding, Martin H

    2014-08-15

    Genome editing is the practice of making predetermined and precise changes to a genome by controlling the location of DNA DSBs (double-strand breaks) and manipulating the cell's repair mechanisms. This technology results from harnessing natural processes that have taken decades and multiple lines of inquiry to understand. Through many false starts and iterative technology advances, the goal of genome editing is just now falling under the control of human hands as a routine and broadly applicable method. The present review attempts to define the technique and capture the discovery process while following its evolution from meganucleases and zinc finger nucleases to the current state of the art: TALEN (transcription-activator-like effector nuclease) technology. We also discuss factors that influence success, technical challenges and future prospects of this quickly evolving area of study and application.

  5. TALEN-mediated genome editing: prospects and perspectives

    Energy Technology Data Exchange (ETDEWEB)

    Wright, DA; Li, T; Yang, B; Spalding, MH

    2014-08-15

    Genome editing is the practice of making predetermined and precise changes to a genome by controlling the location of DNA DSBs (double-strand breaks) and manipulating the cell's repair mechanisms. This technology results from harnessing natural processes that have taken decades and multiple lines of inquiry to understand. Through many false starts and iterative technology advances, the goal of genome editing is just now falling under the control of human hands as a routine and broadly applicable method. The present review attempts to define the technique and capture the discovery process while following its evolution from meganucleases and zinc finger nucleases to the current state of the art: TALEN (transcription-activator-like effector nuclease) technology. We also discuss factors that influence success, technical challenges, and future prospects of this quickly evolving area of study and application.

  6. Genome Editing in Human Cells Using CRISPR/Cas Nucleases.

    Science.gov (United States)

    Wyvekens, Nicolas; Tsai, Shengdar Q; Joung, J Keith

    2015-10-01

    The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has been broadly adopted for highly efficient genome editing in a variety of model organisms and human cell types. Unlike previous genome editing technologies such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), CRISPR/Cas technology does not require complex protein engineering and can be utilized by any researcher proficient in basic molecular biology and cell culture techniques. This unit describes protocols for design and cloning of vectors expressing single or multiplex gRNAs, for transient transfection of human cell lines, and for quantitation of mutation frequencies by T7 endonuclease I assay. These protocols also include guidance for using two improvements that increase the specificity of CRISPR/Cas nucleases: truncated gRNAs and dimeric RNA-guided FokI nucleases.

  7. Genome Editing and Its Applications in Model Organisms

    Directory of Open Access Journals (Sweden)

    Dongyuan Ma

    2015-12-01

    Full Text Available Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, and the clustered regularly-interspaced short palindromic repeat (CRISPR/CRISPR-associated (Cas, has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine.

  8. GENOME EDITING IN HUMAN CELLS USING CRISPR/CAS NUCLEASES

    Science.gov (United States)

    Wyvekens, Nicolas; Tsai, Shengdar; Joung, J. Keith

    2016-01-01

    The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has been broadly adopted for highly efficient genome editing in a variety of model organisms and human cell types. Unlike previous genome editing technologies such as Zinc Finger Nucleases (ZFNs) and Transcription Activator-Like Effector Nucleases (TALENs), the CRISPR/Cas technology does not require complex protein engineering and can be utilized by any researcher proficient in basic molecular biology and cell culture techniques. Here we describe protocols for design and cloning of vectors expressing single or multiplex gRNAs, for transient transfection of human cell lines, and for quantitation of mutation frequencies by T7 Endonuclease I assay. These protocols also include guidance for using two improvements that increase the specificity of CRISPR/Cas nucleases: truncated gRNAs and dimeric RNA-guided FokI nucleases. PMID:26423589

  9. Exploring the Secrets of the Aurora Second Edition

    CERN Document Server

    Akasofu, Syun-Ichi

    2007-01-01

    This new edition of Exploring the Secrets of the Aurora is based on the author's own experiences as a scientist. It describes the history of progress made in auroral science and magnetospheric physics by providing examples of ideas, controversies, struggles, acceptance, and success. Although no general methodologies are mentioned, the hope is that the reader will learn about the history of progress in auroral science and examples of dealing with the many controversies. This book aims to help young scientific researchers learn how to persevere during periods of controversy and struggles for acceptance. In this second edition, by utilizing multiple examples, Akasofu is successful in demonstrating the importance and usefulness of Synthesis. "Probably the book's most valuable contribution to the history of space physics is precisely the narration of the discovery of substorms.---The book has special features.---Akasofu's coverage of the history of pre-space age solar-terrestrial relations is the most comprehensiv...

  10. Concise review: Human cell engineering: cellular reprogramming and genome editing.

    Science.gov (United States)

    Mali, Prashant; Cheng, Linzhao

    2012-01-01

    Cell engineering is defined here as the collective ability to both reset and edit the genome of a mammalian cell. Until recently, this had been extremely challenging to achieve as nontransformed human cells are significantly refractory to both these processes. The recent success in reprogramming somatic cells into induced pluripotent stem cells that are self-renewable in culture, coupled with our increasing ability to effect precise and predesigned genomic editing, now readily permits cellular changes at both the genetic and epigenetic levels. These dual capabilities also make possible the generation of genetically matched, disease-free stem cells from patients for regenerative medicine. The objective of this review is to summarize the key enabling developments on these two rapidly evolving research fronts in human cell engineering, highlight unresolved issues, and outline potential future research directions.

  11. A TALE nuclease architecture for efficient genome editing.

    Science.gov (United States)

    Miller, Jeffrey C; Tan, Siyuan; Qiao, Guijuan; Barlow, Kyle A; Wang, Jianbin; Xia, Danny F; Meng, Xiangdong; Paschon, David E; Leung, Elo; Hinkley, Sarah J; Dulay, Gladys P; Hua, Kevin L; Ankoudinova, Irina; Cost, Gregory J; Urnov, Fyodor D; Zhang, H Steve; Holmes, Michael C; Zhang, Lei; Gregory, Philip D; Rebar, Edward J

    2011-02-01

    Nucleases that cleave unique genomic sequences in living cells can be used for targeted gene editing and mutagenesis. Here we develop a strategy for generating such reagents based on transcription activator-like effector (TALE) proteins from Xanthomonas. We identify TALE truncation variants that efficiently cleave DNA when linked to the catalytic domain of FokI and use these nucleases to generate discrete edits or small deletions within endogenous human NTF3 and CCR5 genes at efficiencies of up to 25%. We further show that designed TALEs can regulate endogenous mammalian genes. These studies demonstrate the effective application of designed TALE transcription factors and nucleases for the targeted regulation and modification of endogenous genes.

  12. APOBEC3A is implicated in a novel class of G-to-A mRNA editing in WT1 transcripts.

    Directory of Open Access Journals (Sweden)

    Ahmadreza Niavarani

    Full Text Available Classic deamination mRNA changes, including cytidine to uridine (C-to-U and adenosine to inosine (A-to-I, are important exceptions to the central dogma and lead to significant alterations in gene transcripts and products. Although there are a few reports of non-classic mRNA alterations, as yet there is no molecular explanation for these alternative changes. Wilms Tumor 1 (WT1 mutations and variants are implicated in several diseases, including Wilms tumor and acute myeloid leukemia (AML. We observed two alternative G-to-A changes, namely c.1303G>A and c.1586G>A in cDNA clones and found them to be recurrent in a series of 21 umbilical cord blood mononuclear cell (CBMC samples studied. Two less conserved U-to-C changes were also observed. These alternative changes were found to be significantly higher in non-progenitor as compared to progenitor CBMCs, while they were found to be absent in a series of AML samples studied, indicating they are targeted, cell type-specific mRNA editing modifications. Since APOBEC/ADAR family members are implicated in RNA/DNA editing, we screened them by RNA-interference (RNAi for WT1-mRNA changes and observed near complete reversal of WT1 c.1303G>A alteration upon APOBEC3A (A3A knockdown. The role of A3A in mediating this change was confirmed by A3A overexpression in Fujioka cells, which led to a significant increase in WT1 c.1303G>A mRNA editing. Non-progenitor CBMCs showed correspondingly higher levels of A3A-mRNA and protein as compared to the progenitor ones. To our knowledge, this is the first report of mRNA modifying activity for an APOBEC3 protein and implicates A3A in a novel G-to-A form of editing. These findings open the way to further investigations into the mechanisms of other potential mRNA changes, which will help to redefine the RNA editing paradigm in both health and disease.

  13. Validation of the fifth edition BI-RADS ultrasound lexicon with comparison of fourth and fifth edition diagnostic performance using video clips

    Directory of Open Access Journals (Sweden)

    Jung Hyun Yoon

    2016-10-01

    Full Text Available Purpose The aim of this study was to evaluate the positive predictive value (PPV and the diagnostic performance of the ultrasonographic descriptors in the fifth edition of BI-RADS, comparing with the fourth edition using video clips. Methods From September 2013 to July 2014, 80 breast masses in 74 women (mean age, 47.5±10.7 years from five institutions of the Korean Society of Breast Imaging were included. Two radiologists individually reviewed the static and video images and analyzed the images according to the fourth and fifth edition of BI-RADS. The PPV of each descriptor was calculated and diagnostic performances between the fourth and fifth editions were compared. Results Of the 80 breast masses, 51 (63.8% were benign and 29 (36.2% were malignant. Suspicious ultrasonographic features such as irregular shape, non-parallel orientation, angular or spiculated margins, and combined posterior features showed higher PPV in both editions (all P0.05. The area under the receiver operating characteristics curve was higher in the fourth edition (0.708 to 0.690, without significance (P=0.416. Conclusion The fifth edition of the BI-RADS ultrasound lexicon showed comparable performance to the fourth edition and can be useful in the differential diagnosis of breast masses using ultrasonography.

  14. The expression of apoB mRNA editing factors is not the sole determinant for the induction of editing in differentiating Caco-2 cells

    Energy Technology Data Exchange (ETDEWEB)

    Galloway, Chad A. [Department of Biochemistry and Biophysics, University of Rochester School of Medicine, 601 Elmwood Ave., Rochester, NY 14642 (United States); Smith, Harold C., E-mail: harold.smith@rochester.edu [Department of Biochemistry and Biophysics, University of Rochester School of Medicine, 601 Elmwood Ave., Rochester, NY 14642 (United States)

    2010-01-01

    Apolipoprotein B mRNA is edited at cytidine 6666 in the enterocytes lining the small intestine of all mammals; converting a CAA codon to a UAA stop codon. The conversion is {approx}80% efficient in this tissue and leads to the expression of the truncated protein, ApoB48, essential for secretion of dietary lipid as chylomicrons. Caco-2 cell raft cultures have been used as an in vitro model for the induction of editing activity during human small intestinal cell differentiation. This induction of apoB mRNA editing has been ascribed to the expression of APOBEC-1. In agreement our data demonstrated differentiation-dependent induction of expression of the editing enzyme APOBEC-1 and in addition we show alternative splicing of the essential auxiliary factor ACF. However, transfection of these editing factors in undifferentiated proliferating Caco-2 cells was not sufficient to induce robust apoB mRNA editing activity. Only differentiation of Caco-2 cells could induce more physiological like levels of apoB mRNA editing. The data suggested that additional regulatory mechanism(s) were induced by differentiation that controlled the functional activity of editing factors.

  15. Syntax Editing for Mark 4-A System Performance Test Software

    Science.gov (United States)

    Jacobson, G. N.

    1983-01-01

    This article describes the syntax editing concepts used by the Operations Sustaining Engineering Section in implementing System Performance Test software for the Mark 4-A era. The processing functions are discussed, as well as the necessary data structures and table generation macros used in implementing those functions. In addition, the procedural and software interfaces which have been developed for users of the syntax editor are described, including the forms required for establishing directive and parameter characteristics.

  16. Genome Editing and Its Applications in Model Organisms

    OpenAIRE

    Dongyuan Ma; Feng Liu

    2015-01-01

    Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas), has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, subs...

  17. Improvement of Synthetic Biology Tools for DNA Editing

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda

    with the development and improvement of DNA editing strategies,compatible with other DNA assembly methodologies, genome engineering and,eventually, automation processes. Expanding and optimizing the synbio toolkit has important applications in pathway optimization for metabolic engineering, design and characterization...... of gene circuits, synthesis of whole genomes and natural product discovery. In line with this, it is also described in this thesis how discovery of new cytochromes P450 (CYPs) from marine bacteria could benefit industrial processes....

  18. Editing of EIA coded, numerically controlled, machine tool tapes

    Science.gov (United States)

    Weiner, J. M.

    1975-01-01

    Editing of numerically controlled (N/C) machine tool tapes (8-level paper tape) using an interactive graphic display processor is described. A rapid technique required for correcting production errors in N/C tapes was developed using the interactive text editor on the IMLAC PDS-ID graphic display system and two special programs resident on disk. The correction technique and special programs for processing N/C tapes coded to EIA specifications are discussed.

  19. Life Coaching: A Cognitive-behavioural Approach Second Edition

    OpenAIRE

    Neenan, Michael; Dryden, Windy

    2013-01-01

    The new edition, retains the key features of the first which successfully showed how to tackle self-defeating thinking and replace it with a problem-solving outlook and provided clear and helpful advice on dealing with troublesome emotions, overcoming procrastination, becoming assertive, and tackling poor time management. In addition it now offers a brand new chapter on the emerging topic of resilience as well as updates throughout.

  20. Data Analysis A Model Comparison Approach, Second Edition

    CERN Document Server

    Judd, Charles M; Ryan, Carey S

    2008-01-01

    This completely rewritten classic text features many new examples, insights and topics including mediational, categorical, and multilevel models. Substantially reorganized, this edition provides a briefer, more streamlined examination of data analysis. Noted for its model-comparison approach and unified framework based on the general linear model, the book provides readers with a greater understanding of a variety of statistical procedures. This consistent framework, including consistent vocabulary and notation, is used throughout to develop fewer but more powerful model building techniques. T

  1. Newer Gene Editing Technologies toward HIV Gene Therapy

    OpenAIRE

    2013-01-01

    Despite the great success of highly active antiretroviral therapy (HAART) in ameliorating the course of HIV infection, alternative therapeutic approaches are being pursued because of practical problems associated with life-long therapy. The eradication of HIV in the so-called “Berlin patient” who received a bone marrow transplant from a CCR5-negative donor has rekindled interest in genome engineering strategies to achieve the same effect. Precise gene editing within the cells is now a realist...

  2. CRISPR-mediated genome editing of Plasmodium falciparum malaria parasites.

    Science.gov (United States)

    Lee, Marcus Cs; Fidock, David A

    2014-01-01

    The development of the CRISPR-Cas system is revolutionizing genome editing in a variety of organisms. The system has now been used to manipulate the genome of Plasmodium falciparum, the most lethal malaria-causing species. The ability to generate gene deletions or nucleotide substitutions rapidly and economically promises to accelerate the analysis of novel drug targets and to help elucidate the function of specific genes or gene families, while complementing genome-wide association studies.

  3. CRISPR-mediated genome editing of Plasmodium falciparum malaria parasites

    OpenAIRE

    Lee, Marcus CS; David A Fidock

    2014-01-01

    The development of the CRISPR-Cas system is revolutionizing genome editing in a variety of organisms. The system has now been used to manipulate the genome of Plasmodium falciparum, the most lethal malaria-causing species. The ability to generate gene deletions or nucleotide substitutions rapidly and economically promises to accelerate the analysis of novel drug targets and to help elucidate the function of specific genes or gene families, while complementing genome-wide association studies.

  4. The application of genome editing in studying hearing loss.

    Science.gov (United States)

    Zou, Bing; Mittal, Rahul; Grati, M'hamed; Lu, Zhongmin; Shu, Yilai; Tao, Yong; Feng, Youg; Xie, Dinghua; Kong, Weijia; Yang, Shiming; Chen, Zheng-Yi; Liu, Xuezhong

    2015-09-01

    Targeted genome editing mediated by clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) technology has emerged as one of the most powerful tools to study gene functions, and with potential to treat genetic disorders. Hearing loss is one of the most common sensory disorders, affecting approximately 1 in 500 newborns with no treatment. Mutations of inner ear genes contribute to the largest portion of genetic deafness. The simplicity and robustness of CRISPR/Cas9-directed genome editing in human cells and model organisms such as zebrafish, mice and primates make it a promising technology in hearing research. With CRISPR/Cas9 technology, functions of inner ear genes can be studied efficiently by the disruption of normal gene alleles through non-homologous-end-joining (NHEJ) mechanism. For genetic hearing loss, CRISPR/Cas9 has potential to repair gene mutations by homology-directed-repair (HDR) or to disrupt dominant mutations by NHEJ, which could restore hearing. Our recent work has shown CRISPR/Cas9-mediated genome editing can be efficiently performed in the mammalian inner ear in vivo. Thus, application of CRISPR/Cas9 in hearing research will open up new avenues for understanding the pathology of genetic hearing loss and provide new routes in the development of treatment to restore hearing. In this review, we describe major methodologies currently used for genome editing. We will highlight applications of these technologies in studies of genetic disorders and discuss issues pertaining to applications of CRISPR/Cas9 in auditory systems implicated in genetic hearing loss.

  5. John Cleland's The Dictionary of Love: An XML Edition

    OpenAIRE

    Davis, Emily Katherine

    2007-01-01

    Conducting and disseminating humanities research is fast becoming a highly technological endeavor. The variety of multimedia options for presenting information changes the questions we ask and the answers we find as well as the problems we encounter and the solutions we devise. The following essays provide an account of creating a digital edition of John Cleland's The Dictionary of Love using XML. The project utilizes traditional literary research methods while working toward an untraditio...

  6. Materials Science and Engineering: An Introduction, 7th Edition

    Science.gov (United States)

    Callister, William D., Jr.

    2006-01-01

    Now in its seventh edition, this accessible book provides readers with clear and concise discussions of key concepts while also incorporating familiar terminology. The author treats the important properties of the three primary types of materials (metals, ceramics, and polymers) and composites, as well as the relationships that exist between the structural elements of materials and their properties. Throughout, the emphasis is placed on mechanical behavior and failure, including techniques that are employed to improve performance.

  7. A robust TALENs system for highly efficient mammalian genome editing

    OpenAIRE

    Feng, Yuanxi; Zhang, Siliang; Huang, Xin

    2014-01-01

    Recently, transcription activator–like effector nucleases (TALENs) have emerged as a highly effective tool for genomic editing. A pair of TALENs binds to two DNA recognition sites separated by a spacer sequence, and the dimerized FokI nucleases at the C terminal then cleave DNA in the spacer. Because of its modular design and capacity to precisely target almost any desired genomic locus, TALEN is a technology that can revolutionize the entire biomedical research field. Currently, for genomic ...

  8. FLASH Assembly of TALENs Enables High-Throughput Genome Editing

    OpenAIRE

    Reyon, Deepak; Tsai, Shengdar Q.; Khayter, Cyd; Foden, Jennifer A.; Sander, Jeffry D.; Joung, J. Keith

    2012-01-01

    Engineered transcription activator-like effector nucleases (TALENs) have shown promise as facile and broadly applicable genome editing tools. However, no publicly available high-throughput method for constructing TALENs has been published and large-scale assessments of the success rate and targeting range of the technology remain lacking. Here we describe the Fast Ligation-based Automatable Solid-phase High-throughput (FLASH) platform, a rapid and cost-effective method we developed to enable ...

  9. Estimation and detection information trade-off for x-ray system optimization

    Science.gov (United States)

    Cushing, Johnathan B.; Clarkson, Eric W.; Mandava, Sagar; Bilgin, Ali

    2016-05-01

    X-ray Computed Tomography (CT) systems perform complex imaging tasks to detect and estimate system parameters, such as a baggage imaging system performing threat detection and generating reconstructions. This leads to a desire to optimize both the detection and estimation performance of a system, but most metrics only focus on one of these aspects. When making design choices there is a need for a concise metric which considers both detection and estimation information parameters, and then provides the user with the collection of possible optimal outcomes. In this paper a graphical analysis of Estimation and Detection Information Trade-off (EDIT) will be explored. EDIT produces curves which allow for a decision to be made for system optimization based on design constraints and costs associated with estimation and detection. EDIT analyzes the system in the estimation information and detection information space where the user is free to pick their own method of calculating these measures. The user of EDIT can choose any desired figure of merit for detection information and estimation information then the EDIT curves will provide the collection of optimal outcomes. The paper will first look at two methods of creating EDIT curves. These curves can be calculated using a wide variety of systems and finding the optimal system by maximizing a figure of merit. EDIT could also be found as an upper bound of the information from a collection of system. These two methods allow for the user to choose a method of calculation which best fits the constraints of their actual system.

  10. RNA Editing Sites Exist in Protein-coding Genes in the Chloroplast Genome of Cycas taitungensis

    Institute of Scientific and Technical Information of China (English)

    Haiyan Chen; Likun Deng; Yuan Jiang; Ping Lu; Jianing Yu

    2011-01-01

    RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations.In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes,especially in seed plants.Using prediction and experimental determination,we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis.A total of 85 editing sites were identified in 25 transcripts.Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution.The editing in the first and third codon position disappeared quicker than that in the second codon position,ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids.These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction.Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas,most likely due to slower evolution speed.

  11. A comparison of the first and second editions of the Dictionary of Literary Slovene

    Directory of Open Access Journals (Sweden)

    Simon Krek

    2014-12-01

    Full Text Available The paper investigates the differences between the first and second editions of the Dictionary of Literary Slovene (SSKJ. The analysis is two-fold: first, a detailed comparison of headword lists of both editions is conducted, followed by the comparison of 2,500 entries from both editions, consisting of a hundred entries for each letter. The analysis shows that the spelling and pronunciation changes to the entries in the second edition were made without the approval of any relevant language authority. Also, the changes introduced are random and inconsistent, and are affecting the consistency of lexicographic description of the first edition, especially on the grammatical level. Furthermore, the editorial decision to make identifying the source of lexicographic information (i.e. the first edition of SSKJ or the Dictionary of New Words of the Slovenian language impossible, raises doubts about lexicographic credibility of the second edition as a description of contemporary Slovene. From the lexicographic perspective, it would have been more appropriate to leave the first edition unchanged and the Dictionary of New Words of the Slovenian language as a separate publication. In addition, the second edition of SSKJ is not freely available online, and neither of the editions is freely available in the form of a dictionary database for natural language processing and other uses.

  12. Loss of matK RNA editing in seed plant chloroplasts

    Directory of Open Access Journals (Sweden)

    Maier Uwe G

    2009-08-01

    Full Text Available Abstract Background RNA editing in chloroplasts of angiosperms proceeds by C-to-U conversions at specific sites. Nuclear-encoded factors are required for the recognition of cis-elements located immediately upstream of editing sites. The ensemble of editing sites in a chloroplast genome differs widely between species, and editing sites are thought to evolve rapidly. However, large-scale analyses of the evolution of individual editing sites have not yet been undertaken. Results Here, we analyzed the evolution of two chloroplast editing sites, matK-2 and matK-3, for which DNA sequences from thousands of angiosperm species are available. Both sites are found in most major taxa, including deep-branching families such as the nymphaeaceae. However, 36 isolated taxa scattered across the entire tree lack a C at one of the two matK editing sites. Tests of several exemplary species from this in silico analysis of matK processing unexpectedly revealed that one of the two sites remain unedited in almost half of all species examined. A comparison of sequences between editors and non-editors showed that specific nucleotides co-evolve with the C at the matK editing sites, suggesting that these nucleotides are critical for editing-site recognition. Conclusion (i Both matK editing sites were present in the common ancestor of all angiosperms and have been independently lost multiple times during angiosperm evolution. (ii The editing activities corresponding to matK-2 and matK-3 are unstable. (iii A small number of third-codon positions in the vicinity of editing sites are selectively constrained independent of the presence of the editing site, most likely because of interacting RNA-binding proteins.

  13. CERES BiDirectional Scans (BDS) data in HDF (CER_BDS_TRMM-PFM_Edition1)

    Science.gov (United States)

    Wielicki, Bruce A. (Principal Investigator)

    Each BiDirectional Scans (BDS) data product contains twenty-four hours of Level-1b data for each CERES scanner instrument mounted on each spacecraft. The BDS includes samples taken in normal and short Earth scan elevation profiles in both fixed and rotating azimuth scan modes (including space, internal calibration, and solar calibration views). The BDS contains Level-0 raw (unconverted) science and instrument data as well as the geolocated converted science and instrument data. The BDS contains additional data not found in the Level-0 input file, including converted satellite position and velocity data, celestial data, converted digital status data, and parameters used in the radiance count conversion equations. The following CERES BDS data sets are currently available: CER_BDS_TRMM-PFM_Edition1 CER_BDS_Terra-FM1_Edition1 CER_BDS_Terra-FM2_Edition1 CER_BDS_Terra-FM1_Edition2 CER_BDS_Terra-FM2_Edition2 CER_BDS_Aqua-FM3_Edition1 CER_BDS_Aqua-FM4_Edition1 CER_BDS_Aqua-FM3_Edition2 CER_BDS_Aqua-FM4_Edition2 CER_BDS_Aqua-FM3_Edition1-CV CER_BDS_Aqua-FM4_Edition1-CV CER_BDS_Terra-FM1_Edition1-CV CER_BDS_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1997-12-27; Stop_Date=2000-12-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Temporal_Resolution=1 day; Temporal_Resolution_Range=Daily - < Weekly].

  14. Newer Gene Editing Technologies toward HIV Gene Therapy

    Directory of Open Access Journals (Sweden)

    Premlata Shankar

    2013-11-01

    Full Text Available Despite the great success of highly active antiretroviral therapy (HAART in ameliorating the course of HIV infection, alternative therapeutic approaches are being pursued because of practical problems associated with life-long therapy. The eradication of HIV in the so-called “Berlin patient” who received a bone marrow transplant from a CCR5-negative donor has rekindled interest in genome engineering strategies to achieve the same effect. Precise gene editing within the cells is now a realistic possibility with recent advances in understanding the DNA repair mechanisms, DNA interaction with transcription factors and bacterial defense mechanisms. Within the past few years, four novel technologies have emerged that can be engineered for recognition of specific DNA target sequences to enable site-specific gene editing: Homing Endonuclease, ZFN, TALEN, and CRISPR/Cas9 system. The most recent CRISPR/Cas9 system uses a short stretch of complementary RNA bound to Cas9 nuclease to recognize and cleave target DNA, as opposed to the previous technologies that use DNA binding motifs of either zinc finger proteins or transcription activator-like effector molecules fused to an endonuclease to mediate sequence-specific DNA cleavage. Unlike RNA interference, which requires the continued presence of effector moieties to maintain gene silencing, the newer technologies allow permanent disruption of the targeted gene after a single treatment. Here, we review the applications, limitations and future prospects of novel gene-editing strategies for use as HIV therapy.

  15. Ancient sedimentary environments and their subsurface diagnosis, third edition

    Energy Technology Data Exchange (ETDEWEB)

    Selley, R.C.

    1985-01-01

    All the worlds coal, most of its petroleum, and many ore deposits occur within sedimentary rocks (sandstones, limestones and shales). The distribution of these minerals is closely related to the sedimentary environment of the host rock. For example, an oil field trapped in an old beach sand will be elongated parallel to the basin margin, while a bed of coal within an abandoned river channel will trend into the basin. This book shows how to diagnose the depositional environments of sedimentary rocks and indicates how this knowledge may be applied to the search for petroleum, coal and sedimentary ore deposits. The first edition of this book appeared in 1970. It was primarily concerned with the interpretation of sedimentary environments from outcrop, from an aesthetic stance, with no thought of vulgar commercial application. The second edition (1977) reflected the author's experience in the oil industry and included sections on the use of geophysical well logs in subsurface facies analysis. In recent years the field that is loosely termed seismic stratigraphy developed, where sedimentary concepts are applied to the interpretation of seismic data. Today seismic surveys may delineate channels, deltas, reefs, submarine fans, and other deposits. The thrid edition contains sections on the seismic characteristics of the various sedimentary facies, and the sections on metalliferous sedimentary deposits and recent environments have been expanded.

  16. The Role of Gene Editing in Neurodegenerative Diseases.

    Science.gov (United States)

    Fan, Hueng-Chuen; Chi, Ching-Shiang; Lee, Yih-Jing; Tsai, Jeng-Dau; Lin, Shinn-Zong; Harn, Horng-Jyh

    2017-03-03

    Neurodegenerative diseases (NDs), at least including Alzheimer's, Huntington's, and Parkinson's diseases, have become the most dreaded maladies because of no precise diagnostic tools or definite treatments for these debilitating diseases. The increased prevalence and a substantial impact on the social-economic and medical care of NDs propel governments to develop policies to counteract the impact. Although the etiologies of NDs are still unknown, growing evidence suggests that genetic, cellular and circuit alternations may cause the generation of abnormal misfolded proteins, which uncontrolledly accumulate to damage eventually overwhelms the protein-disposal mechanisms of these neurons, leading to a common pathological feature of NDs. If the functions and the connectivity can be restored, alterations and accumulated damages may improve. The gene-editing tools, including Zincfinger nucleases, Transcription activator-like effector nucleases, and Clustered regularly interspaced short palindromic repeats associated nucleases have emerged as a novel tool not only for generating specific ND animal models for interrogating the mechanisms and screening potential drugs against NDs, but also for the editing sequence-specific genes to help patients with NDs to regain the functions and connectivity. This review introduces the clinical manifestations of three distinct NDs and the applications of the gene-editing technology on these debilitating diseases.

  17. Newer gene editing technologies toward HIV gene therapy.

    Science.gov (United States)

    Manjunath, N; Yi, Guohua; Dang, Ying; Shankar, Premlata

    2013-11-14

    Despite the great success of highly active antiretroviral therapy (HAART) in ameliorating the course of HIV infection, alternative therapeutic approaches are being pursued because of practical problems associated with life-long therapy. The eradication of HIV in the so-called "Berlin patient" who received a bone marrow transplant from a CCR5-negative donor has rekindled interest in genome engineering strategies to achieve the same effect. Precise gene editing within the cells is now a realistic possibility with recent advances in understanding the DNA repair mechanisms, DNA interaction with transcription factors and bacterial defense mechanisms. Within the past few years, four novel technologies have emerged that can be engineered for recognition of specific DNA target sequences to enable site-specific gene editing: Homing Endonuclease, ZFN, TALEN, and CRISPR/Cas9 system. The most recent CRISPR/Cas9 system uses a short stretch of complementary RNA bound to Cas9 nuclease to recognize and cleave target DNA, as opposed to the previous technologies that use DNA binding motifs of either zinc finger proteins or transcription activator-like effector molecules fused to an endonuclease to mediate sequence-specific DNA cleavage. Unlike RNA interference, which requires the continued presence of effector moieties to maintain gene silencing, the newer technologies allow permanent disruption of the targeted gene after a single treatment. Here, we review the applications, limitations and future prospects of novel gene-editing strategies for use as HIV therapy.

  18. Editing CCR5: a novel approach to HIV gene therapy.

    Science.gov (United States)

    Cornu, Tatjana I; Mussolino, Claudio; Bloom, Kristie; Cathomen, Toni

    2015-01-01

    Acquired immunodeficiency syndrome (AIDS) is a life-threatening disorder caused by infection of individuals with the human immunodeficiency virus (HIV). Entry of HIV-1 into target cells depends on the presence of two surface proteins on the cell membrane: CD4, which serves as the main receptor, and either CCR5 or CXCR4 as a co-receptor. A limited number of people harbor a genomic 32-bp deletion in the CCR5 gene (CCR5∆32), leading to expression of a truncated gene product that provides resistance to HIV-1 infection in individuals homozygous for this mutation. Moreover, allogeneic hematopoietic stem cell (HSC) transplantation with CCR5∆32 donor cells seems to confer HIV-1 resistance to the recipient as well. However, since Δ32 donors are scarce and allogeneic HSC transplantation is not exempt from risks, the development of gene editing tools to knockout CCR5 in the genome of autologous cells is highly warranted. Targeted gene editing can be accomplished with designer nucleases, which essentially are engineered restriction enzymes that can be designed to cleave DNA at specific sites. During repair of these breaks, the cellular repair pathway often introduces small mutations at the break site, which makes it possible to disrupt the ability of the targeted locus to express a functional protein, in this case CCR5. Here, we review the current promise and limitations of CCR5 gene editing with engineered nucleases, including factors affecting the efficiency of gene disruption and potential off-target effects.

  19. Research progress of genome editing and derivative technologies in plants.

    Science.gov (United States)

    Qiwei, Shan; Caixia, Gao

    2015-10-01

    Genome editing technologies using engineered nucleases have been widely used in many model organisms. Genome editing with sequence-specific nuclease (SSN) creates DNA double-strand breaks (DSBs) in the genomic target sites that are primarily repaired by the non-homologous end joining (NHEJ) or homologous recombination (HR) pathways, which can be employed to achieve targeted genome modifications such as gene mutations, insertions, replacements or chromosome rearrangements. There are three major SSNs─zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) system. In contrast to ZFN and TALEN, which require substantial protein engineering to each DNA target, the CRISPR/Cas9 system requires only a change in the guide RNA. For this reason, the CRISPR/Cas9 system is a simple, inexpensive and versatile tool for genome engineering. Furthermore, a modified version of the CRISPR/Cas9 system has been developed to recruit heterologous domains that can regulate endogenous gene expression, such as activation, depression and epigenetic regulation. In this review, we summarize the development and applications of genome editing technologies for basic research and biotechnology, as well as highlight challenges and future directions, with particular emphasis on plants.

  20. Advancing Crop Transformation in the Era of Genome Editing.

    Science.gov (United States)

    Altpeter, Fredy; Springer, Nathan M; Bartley, Laura E; Blechl, Ann E; Brutnell, Thomas P; Citovsky, Vitaly; Conrad, Liza J; Gelvin, Stanton B; Jackson, David P; Kausch, Albert P; Lemaux, Peggy G; Medford, June I; Orozco-Cárdenas, Martha L; Tricoli, David M; Van Eck, Joyce; Voytas, Daniel F; Walbot, Virginia; Wang, Kan; Zhang, Zhanyuan J; Stewart, C Neal

    2016-07-01

    Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized.