shift based editing: Topics by Science.gov

Sample records for shift based editing

Gene Editing and Gene-Based Therapeutics for Cardiomyopathies.

PubMed

Ohiri, Joyce C; McNally, Elizabeth M

2018-04-01

With an increasing understanding of genetic defects leading to cardiomyopathy, focus is shifting to correcting these underlying genetic defects. One approach involves treating mutant RNA through antisense oligonucleotides; the first drug has received regulatory approval to treat specific mutations associated with Duchenne muscular dystrophy. Gene editing is being evaluated in the preclinical setting. For inherited cardiomyopathies, genetic correction strategies require tight specificity for the mutant allele. Gene-editing methods are being tested to create deletions that may be useful to restore protein expression by through the bypass of mutations that restore protein production. Site-specific gene editing, which is required to correct many point mutations, is a less efficient process than inducing deletions. Copyright © 2017 Elsevier Inc. All rights reserved.
Implementation of 3 T Lactate-Edited 3D 1H MR Spectroscopic Imaging with Flyback Echo-Planar Readout for Gliomas Patients

PubMed Central

Chen, Albert P.; Zierhut, Matthew L.; Ozturk-Isik, Esin; Vigneron, Daniel B.; Nelson, Sarah J.

2010-01-01

The purpose of this study was to implement a new lactate-edited 3D 1H magnetic resonance spectroscopic imaging (MRSI) sequence at 3 T and demonstrate the feasibility of using this sequence for measuring lactate in patients with gliomas. A 3D PRESS MRSI sequence incorporating shortened, high bandwidth 180° pulses, new dual BASING lactate-editing pulses, high bandwidth very selective suppression (VSS) pulses and a flyback echo-planar readout was implemented at 3 T. Over-prescription factor of PRESS voxels was optimized using phantom to minimize chemical shift artifacts. The lactate-edited flyback sequence was compared with lactate-edited MRSI using conventional elliptical k-space sampling in a phantom and volunteers, and then applied to patients with gliomas. The results demonstrated the feasibility of detecting lactate within a short scan time of 9.5 min in both phantoms and patients. Over-prescription of voxels gave less chemical shift artifacts allowing detection of lactate on the majority of the selected volume. The normalized SNR of brain metabolites using the flyback encoding were comparable to the SNR of brain metabolites using conventional phase encoding MRSI. The specialized lactate-edited 3D MRSI sequence was able to detect lactate in brain tumor patients at 3 T. The implementation of this technique means that brain lactate can be evaluated in a routine clinical setting to study its potential as a marker for prognosis and response to therapy. PMID:20652745
Combining Fourier phase encoding and broadband inversion toward J-edited spectra

NASA Astrophysics Data System (ADS)

Lin, Yulan; Guan, Quanshuai; Su, Jianwei; Chen, Zhong

2018-06-01

Nuclear magnetic resonance (NMR) spectra are often utilized for gathering accurate information relevant to molecular structures and composition assignments. In this study, we develop a homonuclear encoding approach based on imparting a discrete phase modulation of the targeted cross peaks, and combine it with a pure shift experiments (PSYCHE) based J-modulated scheme, providing simple 2D J-edited spectra for accurate measurement of scalar coupling networks. Chemical shifts and J coupling constants of protons coupled to the specific protons are demonstrated along the F2 and F1 dimensions, respectively. Polychromatic pulses by Fourier phase encoding were performed to simultaneously detect several coupling networks. Proton-proton scalar couplings are chosen by a polychromatic pulse and a PSYCHE element. Axis peaks and unwanted couplings are complete eradicated by incorporating a selective COSY block as a preparation period. The theoretical principles and the signal processing procedure are laid out, and experimental observations are rationalized on the basis of theoretical analyses.
The Art of Problem Posing. 3rd Edition

ERIC Educational Resources Information Center

Brown, Stephen I.; Walter, Marion I.

2005-01-01

The new edition of this classic book describes and provides a myriad of examples of the relationships between problem posing and problem solving, and explores the educational potential of integrating these two activities in classrooms at all levels. "The Art of Problem Posing, Third Edition" encourages readers to shift their thinking…
The commercialization of genome-editing technologies.

PubMed

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

2017-11-01

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.
The Second Dimension--Crosscutting Concepts

ERIC Educational Resources Information Center

Duschl, Richard A.

2012-01-01

The recently published National Research Council (NRC) report "A Framework for K-12 Science Education: Practices, Crosscutting Concepts, and Core Ideas" (NRC 2011) offers a thoughtful research-based agenda that helps guide teachers in making the shift to a doing-led agenda in K-12 science education. In the December 2011 editions of the NSTA…
Recent advances in the use of ZFN-mediated gene editing for human gene therapy.

PubMed

Chandrasegaran, Srinivasan

2017-01-01

Targeted genome editing with programmable nucleases has revolutionized biomedical research. The ability to make site-specific modifications to the human genome, has invoked a paradigm shift in gene therapy. Using gene editing technologies, the sequence in the human genome can now be precisely engineered to achieve a therapeutic effect. Zinc finger nucleases (ZFNs) were the first programmable nucleases designed to target and cleave custom sites. This article summarizes the advances in the use of ZFN-mediated gene editing for human gene therapy and discusses the challenges associated with translating this gene editing technology into clinical use.
Using Score Equating and Measurement Invariance to Examine the Flynn Effect in the Wechsler Adult Intelligence Scale.

PubMed

Benson, Nicholas; Beaujean, A Alexander; Taub, Gordon E

2015-01-01

The Flynn effect (FE; i.e., increase in mean IQ scores over time) is commonly viewed as reflecting population shifts in intelligence, despite the fact that most FE studies have not investigated the assumption of score comparability. Consequently, the extent to which these mean differences in IQ scores reflect population shifts in cognitive abilities versus changes in the instruments used to measure these abilities is unclear. In this study, we used modern psychometric tools to examine the FE. First, we equated raw scores for each common subtest to be on the same scale across instruments. This enabled the combination of scores from all three instruments into one of 13 age groups before converting raw scores into Z scores. Second, using age-based standardized scores for standardization samples, we examined measurement invariance across the second (revised), third, and fourth editions of the Wechsler Adult Intelligence Scale. Results indicate that while scores were equivalent across the third and fourth editions, they were not equivalent across the second and third editions. Results suggest that there is some evidence for an increase in intelligence, but also call into question many published FE findings as presuming the instruments' scores are invariant when this assumption is not warranted.
Shaping the Global Civil Society: An Interview with Michael Peters

ERIC Educational Resources Information Center

Heraud, Richard; Tesar, Marek

2017-01-01

Professor Michael A. Peters has worked in an era of transformation that has taken him from a labour-intensive paper-based form of production to the computerised reproduction of thought, and the current shift in the publishing landscape from a reader-subscription to an author-pays model. Most of what he has learned in publishing and editing he has…
A review of American psychiatry through its diagnoses: the history and development of the Diagnostic and Statistical Manual of Mental Disorders.

PubMed

Fischer, Bernard A

2012-12-01

The history of the Diagnostic and Statistical Manual of Mental Disorders (DSM) reflects the larger history of American psychiatry. As the field anticipates DSM-5, it is useful to take stock of this history and consider not only how diagnosis impacts our understanding of mental illness but also how contemporary thought influences diagnosis. Before the DSM, the field was disjointed. The publication of the first American diagnostic manual, the precursor of the DSM, mirrored society's interest in organized record keeping and prevention rather than treatment of mental illness. The first and second editions of DSM brought a common language to diagnosis and were largely the work of outpatient and academic psychiatrists rather than those based in large state hospitals. The third edition of the DSM saw the shift in American psychiatry's leadership from the eminent clinician to the researcher, whereas the fourth edition reflected the rise of "evidence-based medicine." DSM-5 will likewise represent the current status of the field-not only with regard to science but also reflecting the place of American psychiatry in medicine today.
The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection

PubMed Central

Kong, Yimeng; Pan, Bohu; Chen, Longxian; Wang, Hongbing; Hao, Pei; Li, Xuan

2016-01-01

The hydrolytic deamination of adenosine to inosine (A-to-I editing) in precursor mRNA induces variable gene products at the post-transcription level. How and to what extent A-to-I RNA editing diversifies transcriptome is not fully characterized in the evolution, and very little is known about the selective constraints that drive the evolution of RNA editing events. Here we present a study on A-to-I RNA editing, by generating a global profile of A-to-I editing for a phylogeny of seven Drosophila species, a model system spanning an evolutionary timeframe of approximately 45 million years. Of totally 9281 editing events identified, 5150 (55.5%) are located in the coding sequences (CDS) of 2734 genes. Phylogenetic analysis places these genes into 1,526 homologous families, about 5% of total gene families in the fly lineages. Based on conservation of the editing sites, the editing events in CDS are categorized into three distinct types, representing events on singleton genes (type I), and events not conserved (type II) or conserved (type III) within multi-gene families. While both type I and II events are subject to purifying selection, notably type III events are positively selected, and highly enriched in the components and functions of the nervous system. The tissue profiles are documented for three editing types, and their critical roles are further implicated by their shifting patterns during holometabolous development and in post-mating response. In conclusion, three A-to-I RNA editing types are found to have distinct evolutionary dynamics. It appears that nervous system functions are mainly tested to determine if an A-to-I editing is beneficial for an organism. The coding plasticity enabled by A-to-I editing creates a new class of binary variations, which is a superior alternative to maintain heterozygosity of expressed genes in a diploid mating system. PMID:27467689
Paradigm shifts and the development of the diagnostic and statistical manual of mental disorders: past experiences and future aspirations.

PubMed

First, Michael B

2010-11-01

Work is currently under way on the Diagnostic and Statistical Manual of Mental Disorders (DSM), Fifth Edition, due to be published by the American Psychiatric Association in 2013. Dissatisfaction with the current categorical descriptive approach has led to aspirations for a paradigm shift for DSM-5. A historical review of past revisions of the DSM was performed. Efforts undertaken before the start of the DSM-5 development process to conduct a state-of-the science review and set a research agenda were examined to determine if results supported a paradigm shift for DSM-5. Proposals to supplement DSM-5 categorical diagnosis with dimensional assessments are reviewed and critiqued. DSM revisions have alternated between paradigm shifts (the first edition of the DSM in 1952 and DSM-III in 1980) and incremental improvements (DSM-II in 1968, DSM-III-R in 1987, and DSM-IV in 1994). The results of the review of the DSM-5 research planning initiatives suggest that despite the scientific advances that have occurred since the descriptive approach was first introduced in 1980, the field lacks a sufficiently deep understanding of mental disorders to justify abandoning the descriptive approach in favour of a more etiologically based alternative. Proposals to add severity and cross-cutting dimensions throughout DSM-5 are neither paradigm shifting, given that simpler versions of such dimensions are already a component of DSM-IV, nor likely to be used by busy clinicians without evidence that they improve clinical outcomes. Despite initial aspirations that DSM would undergo a paradigm shift with this revision, DSM-5 will continue to adopt a descriptive categorical approach, albeit with a greatly expanded dimensional component.
Adenosine-to-Inosine Editing of MicroRNA-487b Alters Target Gene Selection After Ischemia and Promotes Neovascularization.

PubMed

van der Kwast, Reginald V C T; van Ingen, Eva; Parma, Laura; Peters, Hendrika A B; Quax, Paul H A; Nossent, A Yaël

2018-02-02

Adenosine-to-inosine editing of microRNAs has the potential to cause a shift in target site selection. 2'-O-ribose-methylation of adenosine residues, however, has been shown to inhibit adenosine-to-inosine editing. To investigate whether angiomiR miR487b is subject to adenosine-to-inosine editing or 2'-O-ribose-methylation during neovascularization. Complementary DNA was prepared from C57BL/6-mice subjected to hindlimb ischemia. Using Sanger sequencing and endonuclease digestion, we identified and validated adenosine-to-inosine editing of the miR487b seed sequence. In the gastrocnemius muscle, pri-miR487b editing increased from 6.7±0.4% before to 11.7±1.6% ( P =0.02) 1 day after ischemia. Edited pri-miR487b is processed into a novel microRNA, edited miR487b, which is also upregulated after ischemia. We confirmed editing of miR487b in multiple human primary vascular cell types. Short interfering RNA-mediated knockdown demonstrated that editing is adenosine deaminase acting on RNA 1 and 2 dependent. Using reverse-transcription at low dNTP concentrations followed by quantitative-PCR, we found that the same adenosine residue is methylated in mice and human primary cells. In the murine gastrocnemius, the estimated methylation fraction increased from 32.8±14% before to 53.6±12% 1 day after ischemia. Short interfering RNA knockdown confirmed that methylation is fibrillarin dependent. Although we could not confirm that methylation directly inhibits editing, we do show that adenosine deaminase acting on RNA 1 and 2 and fibrillarin negatively influence each other's expression. Using multiple luciferase reporter gene assays, we could demonstrate that editing results in a complete switch of target site selection. In human primary cells, we confirmed the shift in miR487b targeting after editing, resulting in a edited miR487b targetome that is enriched for multiple proangiogenic pathways. Furthermore, overexpression of edited miR487b, but not wild-type miR487b, stimulates angiogenesis in both in vitro and ex vivo assays. MiR487b is edited in the seed sequence in mice and humans, resulting in a novel, proangiogenic microRNA with a unique targetome. The rate of miR487b editing, as well as 2'-O-ribose-methylation, is increased in murine muscle tissue during postischemic neovascularization. Our findings suggest miR487b editing plays an intricate role in postischemic neovascularization. © 2017 American Heart Association, Inc.
RNA editing makes mistakes in plant mitochondria: editing loses sense in transcripts of a rps19 pseudogene and in creating stop codons in coxI and rps3 mRNAs of Oenothera.

PubMed Central

Schuster, W; Brennicke, A

1991-01-01

An intact gene for the ribosomal protein S19 (rps19) is absent from Oenothera mitochondria. The conserved rps19 reading frame found in the mitochondrial genome is interrupted by a termination codon. This rps19 pseudogene is cotranscribed with the downstream rps3 gene and is edited on both sides of the translational stop. Editing, however, changes the amino acid sequence at positions that were well conserved before editing. Other strange editings create translational stops in open reading frames coding for functional proteins. In coxI and rps3 mRNAs CGA codons are edited to UGA stop codons only five and three codons, respectively, downstream to the initiation codon. These aberrant editings in essential open reading frames and in the rps19 pseudogene appear to have been shifted to these positions from other editing sites. These observations suggest a requirement for a continuous evolutionary constraint on the editing specificities in plant mitochondria. Images PMID:1762921
Automatic frequency and phase alignment of in vivo J-difference-edited MR spectra by frequency domain correlation.

PubMed

Wiegers, Evita C; Philips, Bart W J; Heerschap, Arend; van der Graaf, Marinette

2017-12-01

J-difference editing is often used to select resonances of compounds with coupled spins in 1 H-MR spectra. Accurate phase and frequency alignment prior to subtracting J-difference-edited MR spectra is important to avoid artefactual contributions to the edited resonance. In-vivo J-difference-edited MR spectra were aligned by maximizing the normalized scalar product between two spectra (i.e., the correlation over a spectral region). The performance of our correlation method was compared with alignment by spectral registration and by alignment of the highest point in two spectra. The correlation method was tested at different SNR levels and for a broad range of phase and frequency shifts. In-vivo application of the proposed correlation method showed reduced subtraction errors and increased fit reliability in difference spectra as compared with conventional peak alignment. The correlation method and the spectral registration method generally performed equally well. However, better alignment using the correlation method was obtained for spectra with a low SNR (down to ~2) and for relatively large frequency shifts. Our correlation method for simultaneously phase and frequency alignment is able to correct both small and large phase and frequency drifts and also performs well at low SNR levels.
Il Fasciculo di Medicina of 1493: medical culture through the eyes of the artist.

PubMed

DiMaio, Salvatore; Discepola, Federico; Del Maestro, Rolando F

2006-01-01

THE FASCICULUS MEDICINA, printed in 1491, is considered the first illustrated medical book. The Latin essays and illustrations in this volume provide insight into the medical knowledge of Western Europe and, in the Italian edition published in 1493, glimpses into the medical culture of the late 15th century. We outline the scientific and social environments into which the Fasciculus Medicinae of 1491 was introduced and the transition that occurred with the publication of the 1493 Italian edition. The artist of the 1493 Fasciculo witnessed a paradigm shift occurring. In four woodcuts, the artist captured four themes: the relevance of knowledge-based medicine, the emergence of laboratory medicine, the Hippocratic lessons of patient observation, and the emerging revolution in anatomy.
Small molecules enhance CRISPR genome editing in pluripotent stem cells.

PubMed

Yu, Chen; Liu, Yanxia; Ma, Tianhua; Liu, Kai; Xu, Shaohua; Zhang, Yu; Liu, Honglei; La Russa, Marie; Xie, Min; Ding, Sheng; Qi, Lei S

2015-02-05

The bacterial CRISPR-Cas9 system has emerged as an effective tool for sequence-specific gene knockout through non-homologous end joining (NHEJ), but it remains inefficient for precise editing of genome sequences. Here we develop a reporter-based screening approach for high-throughput identification of chemical compounds that can modulate precise genome editing through homology-directed repair (HDR). Using our screening method, we have identified small molecules that can enhance CRISPR-mediated HDR efficiency, 3-fold for large fragment insertions and 9-fold for point mutations. Interestingly, we have also observed that a small molecule that inhibits HDR can enhance frame shift insertion and deletion (indel) mutations mediated by NHEJ. The identified small molecules function robustly in diverse cell types with minimal toxicity. The use of small molecules provides a simple and effective strategy to enhance precise genome engineering applications and facilitates the study of DNA repair mechanisms in mammalian cells. Copyright © 2015 Elsevier Inc. All rights reserved.
pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning.

PubMed

Wilcox, Jennifer L; Bevilacqua, Philip C

2013-10-22

Shifting of pKa's in RNA is important for many biological processes; however, the driving forces responsible for shifting are not well understood. Herein, we determine how structural environments surrounding protonated bases affect pKa shifting in double-stranded RNA (dsRNA). Using (31)P NMR, we determined the pKa of the adenine in an A(+)·C base pair in various sequence and structural environments. We found a significant dependence of pKa on the base pairing strength of nearest neighbors and the location of a nearby bulge. Increasing nearest neighbor base pairing strength shifted the pKa of the adenine in an A(+)·C base pair higher by an additional 1.6 pKa units, from 6.5 to 8.1, which is well above neutrality. The addition of a bulge two base pairs away from a protonated A(+)·C base pair shifted the pKa by only ~0.5 units less than a perfectly base paired hairpin; however, positioning the bulge just one base pair away from the A(+)·C base pair prohibited formation of the protonated base pair as well as several flanking base pairs. Comparison of data collected at 25 °C and 100 mM KCl to biological temperature and Mg(2+) concentration revealed only slight pKa changes, suggesting that similar sequence contexts in biological systems have the potential to be protonated at biological pH. We present a general model to aid in the determination of the roles protonated bases may play in various dsRNA-mediated processes including ADAR editing, miRNA processing, programmed ribosomal frameshifting, and general acid-base catalysis in ribozymes.
Framing effects in choices between multioutcome life-expectancy lotteries.

PubMed

Bernstein, L M; Chapman, G B; Elstein, A S

1999-01-01

To explore framing or editing effects and a method to debias framing in a clinical context. Clinical scenarios using multioutcome life-expectancy lotteries of equal value required choices between two supplementary drugs that either prolonged or shortened life from the 20-year beneficial effect of a baseline drug. The effects of these supplementary drugs were presented in two conditions, using a between-subjects design. In segregated editing (n = 116) the effects were presented separately from the effects of the baseline drug. In integrated editing (n = 100), effects of supplementary and baseline drugs were combined in the lottery presentation. Each subject responded to 30 problems. To explore one method of debiasing, another 100 subjects made choices after viewing both segregated and integrated editings of 20 problems (dual framing). Statistically significant preference reversals between segregated and integrated editing of pure lotteries occurred only when one framing placed outcomes in the gain domain, and the other framing placed them in the loss domain. When both editings resulted in gain-domain outcomes only, there was no framing effect. There was a related relationship of framing-effect shifts from losses to gains in mixed-lottery-choice problems. Responses to the dual framing condition did not consistently coincide with responses to either single framing. In some situations, dual framing eliminated or lessened framing effects. The results support two components of prospect theory, coding outcomes as gains or losses from a reference point, and an s-shaped utility function (concave in gain, convex in loss domains). Presenting both alternative editings of a complex situation prior to choice more fully informs the decision maker and may help to reduce framing effects. Given the extent to which preferences shift in response to alternative presentations, it is unclear which choice represents the subject's "true preferences."
Reevaluating American Grand Strategy in an Era of Retrenchment

DTIC Science & Technology

2012-06-01

institutions.30 The United States 23 Bruce D. Jones, Shepard Forman, and Richard Gowan, ed., Cooperating...13. 25 Teresa Whitfield, “New Arrangements for Peace Negotiation” in Cooperating For Peace and Security, edited by Bruce D. Jones, Shepard Forman...Shifting Strategic Environment” in Cooperating For Peace and Security, edited by Bruce D. Jones, Shepard Forman, and Richard Gowan (New York, NY

Clinical application of the five-factor model.

PubMed

Widiger, Thomas A; Presnall, Jennifer Ruth

2013-12-01

The Five-Factor Model (FFM) has become the predominant dimensional model of general personality structure. The purpose of this paper is to suggest a clinical application. A substantial body of research indicates that the personality disorders included within the American Psychiatric Association's (APA) Diagnostic and Statistical Manual of Mental Disorders (DSM) can be understood as extreme and/or maladaptive variants of the FFM (the acronym "DSM" refers to any particular edition of the APA DSM). In addition, the current proposal for the forthcoming fifth edition of the DSM (i.e., DSM-5) is shifting closely toward an FFM dimensional trait model of personality disorder. Advantages of this shifting conceptualization are discussed, including treatment planning. © 2012 Wiley Periodicals, Inc.
Unraveling the meaning of chemical shifts in protein NMR.

PubMed

Berjanskii, Mark V; Wishart, David S

2017-11-01

Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.
A new strategy for in vivo spectral editing. Application to GABA editing using selective homonuclear polarization transfer spectroscopy

NASA Astrophysics Data System (ADS)

Shen, Jun; Yang, Jehoon; Choi, In-Young; Li, Shizhe Steve; Chen, Zhengguang

2004-10-01

A novel single-shot in vivo spectral editing method is proposed in which the signal to be detected, is regenerated anew from the thermal equilibrium magnetization of a source to which it is J-coupled. The thermal equilibrium magnetization of the signal to be detected together with those of overlapping signals are suppressed by single-shot gradient dephasing prior to the signal regeneration process. Application of this new strategy to in vivo GABA editing using selective homonuclear polarization transfer allows complete suppression of overlapping creatine and glutathione while detecting the GABA-4 methylene resonance at 3.02 ppm with an editing yield similar to that of conventional editing methods. The NAA methyl group at 2.02 ppm was simultaneously detected and can be used as an internal navigator echo for correcting the zero order phase and frequency shifts and as an internal reference for concentration. This new method has been demonstrated for robust in vivo GABA editing in the rat brain and for study of GABA synthesis after acute vigabatrin administration.
Brief Report: An Exploratory Study Comparing Diagnostic Outcomes for Autism Spectrum Disorders under DSM-IV-TR with the Proposed DSM-5 Revision

ERIC Educational Resources Information Center

Gibbs, Vicki; Aldridge, Fiona; Chandler, Felicity; Witzlsperger, Ellen; Smith, Karen

2012-01-01

The proposed revision for Autism spectrum disorders (ASDs) in the Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition (DSM-5) represents a shift from the Diagnostic and Statistical Manual of Mental Disorders-Fourth Edition, Text Revision (DSM-IV-TR). As the proposed DSM-5 criteria require a higher minimum number of symptoms to be…
In vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI): [3,4-(13)CH(2)]glutamate/glutamine tomography in rat brain.

PubMed

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. Copyright 1999 Wiley-Liss, Inc.
The shift-invariant discrete wavelet transform and application to speech waveform analysis.

PubMed

Enders, Jörg; Geng, Weihua; Li, Peijun; Frazier, Michael W; Scholl, David J

2005-04-01

The discrete wavelet transform may be used as a signal-processing tool for visualization and analysis of nonstationary, time-sampled waveforms. The highly desirable property of shift invariance can be obtained at the cost of a moderate increase in computational complexity, and accepting a least-squares inverse (pseudoinverse) in place of a true inverse. A new algorithm for the pseudoinverse of the shift-invariant transform that is easier to implement in array-oriented scripting languages than existing algorithms is presented together with self-contained proofs. Representing only one of the many and varied potential applications, a recorded speech waveform illustrates the benefits of shift invariance with pseudoinvertibility. Visualization shows the glottal modulation of vowel formants and frication noise, revealing secondary glottal pulses and other waveform irregularities. Additionally, performing sound waveform editing operations (i.e., cutting and pasting sections) on the shift-invariant wavelet representation automatically produces quiet, click-free section boundaries in the resulting sound. The capabilities of this wavelet-domain editing technique are demonstrated by changing the rate of a recorded spoken word. Individual pitch periods are repeated to obtain a half-speed result, and alternate individual pitch periods are removed to obtain a double-speed result. The original pitch and formant frequencies are preserved. In informal listening tests, the results are clear and understandable.
The shift-invariant discrete wavelet transform and application to speech waveform analysis

NASA Astrophysics Data System (ADS)

Enders, Jörg; Geng, Weihua; Li, Peijun; Frazier, Michael W.; Scholl, David J.

2005-04-01

The discrete wavelet transform may be used as a signal-processing tool for visualization and analysis of nonstationary, time-sampled waveforms. The highly desirable property of shift invariance can be obtained at the cost of a moderate increase in computational complexity, and accepting a least-squares inverse (pseudoinverse) in place of a true inverse. A new algorithm for the pseudoinverse of the shift-invariant transform that is easier to implement in array-oriented scripting languages than existing algorithms is presented together with self-contained proofs. Representing only one of the many and varied potential applications, a recorded speech waveform illustrates the benefits of shift invariance with pseudoinvertibility. Visualization shows the glottal modulation of vowel formants and frication noise, revealing secondary glottal pulses and other waveform irregularities. Additionally, performing sound waveform editing operations (i.e., cutting and pasting sections) on the shift-invariant wavelet representation automatically produces quiet, click-free section boundaries in the resulting sound. The capabilities of this wavelet-domain editing technique are demonstrated by changing the rate of a recorded spoken word. Individual pitch periods are repeated to obtain a half-speed result, and alternate individual pitch periods are removed to obtain a double-speed result. The original pitch and formant frequencies are preserved. In informal listening tests, the results are clear and understandable. .
Conformational and chemical selection by a trans-acting editing domain

PubMed Central

Danhart, Eric M.; Bakhtina, Marina; Cantara, William A.; Kuzmishin, Alexandra B.; Ma, Xiao; Sanford, Brianne L.; Vargas-Rodriguez, Oscar; Košutić, Marija; Goto, Yuki; Suga, Hiroaki; Nakanishi, Kotaro; Micura, Ronald; Musier-Forsyth, Karin

2017-01-01

Molecular sieves ensure proper pairing of tRNAs and amino acids during aminoacyl-tRNA biosynthesis, thereby avoiding detrimental effects of mistranslation on cell growth and viability. Mischarging errors are often corrected through the activity of specialized editing domains present in some aminoacyl-tRNA synthetases or via single-domain trans-editing proteins. ProXp-ala is a ubiquitous trans-editing enzyme that edits Ala-tRNAPro, the product of Ala mischarging by prolyl-tRNA synthetase, although the structural basis for discrimination between correctly charged Pro-tRNAPro and mischarged Ala-tRNAAla is unclear. Deacylation assays using substrate analogs reveal that size discrimination is only one component of selectivity. We used NMR spectroscopy and sequence conservation to guide extensive site-directed mutagenesis of Caulobacter crescentus ProXp-ala, along with binding and deacylation assays to map specificity determinants. Chemical shift perturbations induced by an uncharged tRNAPro acceptor stem mimic, microhelixPro, or a nonhydrolyzable mischarged Ala-microhelixPro substrate analog identified residues important for binding and deacylation. Backbone 15N NMR relaxation experiments revealed dynamics for a helix flanking the substrate binding site in free ProXp-ala, likely reflecting sampling of open and closed conformations. Dynamics persist on binding to the uncharged microhelix, but are attenuated when the stably mischarged analog is bound. Computational docking and molecular dynamics simulations provide structural context for these findings and predict a role for the substrate primary α-amine group in substrate recognition. Overall, our results illuminate strategies used by a trans-editing domain to ensure acceptance of only mischarged Ala-tRNAPro, including conformational selection by a dynamic helix, size-based exclusion, and optimal positioning of substrate chemical groups. PMID:28768811
Identifying the Machine Translation Error Types with the Greatest Impact on Post-editing Effort

PubMed Central

Daems, Joke; Vandepitte, Sonia; Hartsuiker, Robert J.; Macken, Lieve

2017-01-01

Translation Environment Tools make translators’ work easier by providing them with term lists, translation memories and machine translation output. Ideally, such tools automatically predict whether it is more effortful to post-edit than to translate from scratch, and determine whether or not to provide translators with machine translation output. Current machine translation quality estimation systems heavily rely on automatic metrics, even though they do not accurately capture actual post-editing effort. In addition, these systems do not take translator experience into account, even though novices’ translation processes are different from those of professional translators. In this paper, we report on the impact of machine translation errors on various types of post-editing effort indicators, for professional translators as well as student translators. We compare the impact of MT quality on a product effort indicator (HTER) with that on various process effort indicators. The translation and post-editing process of student translators and professional translators was logged with a combination of keystroke logging and eye-tracking, and the MT output was analyzed with a fine-grained translation quality assessment approach. We find that most post-editing effort indicators (product as well as process) are influenced by machine translation quality, but that different error types affect different post-editing effort indicators, confirming that a more fine-grained MT quality analysis is needed to correctly estimate actual post-editing effort. Coherence, meaning shifts, and structural issues are shown to be good indicators of post-editing effort. The additional impact of experience on these interactions between MT quality and post-editing effort is smaller than expected. PMID:28824482
Identifying the Machine Translation Error Types with the Greatest Impact on Post-editing Effort.

PubMed

Daems, Joke; Vandepitte, Sonia; Hartsuiker, Robert J; Macken, Lieve

2017-01-01

Translation Environment Tools make translators' work easier by providing them with term lists, translation memories and machine translation output. Ideally, such tools automatically predict whether it is more effortful to post-edit than to translate from scratch, and determine whether or not to provide translators with machine translation output. Current machine translation quality estimation systems heavily rely on automatic metrics, even though they do not accurately capture actual post-editing effort. In addition, these systems do not take translator experience into account, even though novices' translation processes are different from those of professional translators. In this paper, we report on the impact of machine translation errors on various types of post-editing effort indicators, for professional translators as well as student translators. We compare the impact of MT quality on a product effort indicator (HTER) with that on various process effort indicators. The translation and post-editing process of student translators and professional translators was logged with a combination of keystroke logging and eye-tracking, and the MT output was analyzed with a fine-grained translation quality assessment approach. We find that most post-editing effort indicators (product as well as process) are influenced by machine translation quality, but that different error types affect different post-editing effort indicators, confirming that a more fine-grained MT quality analysis is needed to correctly estimate actual post-editing effort. Coherence, meaning shifts, and structural issues are shown to be good indicators of post-editing effort. The additional impact of experience on these interactions between MT quality and post-editing effort is smaller than expected.
A long antisense RNA in plant chloroplasts.

PubMed

Georg, J; Honsel, A; Voss, B; Rennenberg, H; Hess, W R

2010-05-01

Based on computational prediction of RNA secondary structures, a long antisense RNA (asRNA) was found in chloroplasts of Arabidopsis, Nicotiana tabacum and poplar, which occurs in two to three major transcripts. Mapping of primary 5' ends, northern hybridizations and quantitative real-time reverse transcription polymerase chain reaction (qPCR) experiments demonstrated that these transcripts originate from a promoter that is typical for the plastid-encoded RNA polymerase and are over their full length in antisense orientation to the gene ndhB and therefore were designated asRNA_ndhB. The asRNA_ndhB transcripts predominantly accumulate in young leaves and at physiological growth temperatures. Two nucleotide positions in the mRNA that are subject to C-to-U RNA editing and which were previously found to be sensitive to elevated temperatures are covered by asRNA_ndhB. Nevertheless, the correlation between the accumulation of asRNA_ndhB and RNA editing appeared weak in a temperature shift experiment. With asRNA_ndhB, we describe the first asRNA of plant chloroplasts that covers RNA editing sites, as well as a group II intron splice acceptor site, and that is under developmental control, raising the possibility that long asRNAs could be involved in RNA maturation or the control of RNA stability.
Breast-feeding, bottle-feeding and Dr. Spock: the shifting context of choice.

PubMed

Knaak, Stephanie

2005-05-01

In today's environment, breast-feeding represents both a medical gold standard for infant feeding and a moral gold standard for mothering. The morally charged character of this discourse makes the notion of choice in infant feeding particularly problematic and fraught with difficulty. From an historical content analysis of selected editions from 1946 to 1998 of Dr. Spock's famous child-care manual, this paper explicates the process through which the breast versus bottle discourse has shifted over the last half-century, and how these shifts have shaped the context of choice within which mothers must make their infant-feeding decisions.
Genome Editing Tools in Plants

PubMed Central

Mohanta, Tapan Kumar; Bashir, Tufail; Hashem, Abeer; Bae, Hanhong

2017-01-01

Genome editing tools have the potential to change the genomic architecture of a genome at precise locations, with desired accuracy. These tools have been efficiently used for trait discovery and for the generation of plants with high crop yields and resistance to biotic and abiotic stresses. Due to complex genomic architecture, it is challenging to edit all of the genes/genomes using a particular genome editing tool. Therefore, to overcome this challenging task, several genome editing tools have been developed to facilitate efficient genome editing. Some of the major genome editing tools used to edit plant genomes are: Homologous recombination (HR), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), pentatricopeptide repeat proteins (PPRs), the CRISPR/Cas9 system, RNA interference (RNAi), cisgenesis, and intragenesis. In addition, site-directed sequence editing and oligonucleotide-directed mutagenesis have the potential to edit the genome at the single-nucleotide level. Recently, adenine base editors (ABEs) have been developed to mutate A-T base pairs to G-C base pairs. ABEs use deoxyadeninedeaminase (TadA) with catalytically impaired Cas9 nickase to mutate A-T base pairs to G-C base pairs. PMID:29257124
BE-PLUS: a new base editing tool with broadened editing window and enhanced fidelity.

PubMed

Jiang, Wen; Feng, Songjie; Huang, Shisheng; Yu, Wenxia; Li, Guanglei; Yang, Guang; Liu, Yajing; Zhang, Yu; Zhang, Lei; Hou, Yu; Chen, Jia; Chen, Jieping; Huang, Xingxu

2018-06-06

Base editor (BE), containing a cytidine deaminase and catalytically defective Cas9, has been widely used to perform base editing. However, the narrow editing window of BE limits its utility. Here, we developed a new editing technology named as base editor for programming larger C to U (T) scope (BE-PLUS) by fusing 10 copies of GCN4 peptide to nCas9(D10A) for recruiting scFv-APOBEC-UGI-GB1 to the target sites. The new system achieves base editing with a broadened window, resulting in an increased genome-targeting scope. Interestingly, the new system yielded much fewer unwanted indels and non-C-to-T conversions. We also demonstrated its potential use in gene disruption across the whole genome through induction of stop codons (iSTOP). Taken together, the BE-PLUS system offers a new editing tool with increased editing window and enhanced fidelity.
Residential Construction Trends in America's Metropolitan Regions: 2010 and 2009 Editions

EPA Pesticide Factsheets

These two reports examine residential building permits in the 50 largest U.S. metropolitan regions at the county or jurisdictional level to determine whether there has been a shift toward redevelopment and which regions have seen the most change.
Statistical Physics Approaches to RNA Editing

NASA Astrophysics Data System (ADS)

Bundschuh, Ralf

2012-02-01

The central dogma of molecular Biology states that DNA is transcribed base by base into RNA which is in turn translated into proteins. However, some organisms edit their RNA before translation by inserting, deleting, or substituting individual or short stretches of bases. In many instances the mechanisms by which an organism recognizes the positions at which to edit or by which it performs the actual editing are unknown. One model system that stands out by its very high rate of on average one out of 25 bases being edited are the Myxomycetes, a class of slime molds. In this talk we will show how the computational methods and concepts from statistical Physics can be used to analyze DNA and protein sequence data to predict editing sites in these slime molds and to guide experiments that identified previously unknown types of editing as well as the complete set of editing events in the slime mold Physarum polycephalum.
Changing genetic information through RNA editing

NASA Technical Reports Server (NTRS)

Maas, S.; Rich, A.

2000-01-01

RNA editing, the post-transcriptional alteration of a gene-encoded sequence, is a widespread phenomenon in eukaryotes. As a consequence of RNA editing, functionally distinct proteins can be produced from a single gene. The molecular mechanisms involved include single or multiple base insertions or deletions as well as base substitutions. In mammals, one type of substitutional RNA editing, characterized by site-specific base-modification, was shown to modulate important physiological processes. The underlying reaction mechanism of substitutional RNA editing involves hydrolytic deamination of cytosine or adenosine bases to uracil or inosine, respectively. Protein factors have been characterized that are able to induce RNA editing in vitro. A supergene family of RNA-dependent deaminases has emerged with the recent addition of adenosine deaminases specific for tRNA. Here we review the developments that have substantially increased our understanding of base-modification RNA editing over the past few years, with an emphasis on mechanistic differences, evolutionary aspects and the first insights into the regulation of editing activity.
A different approach to multiplicity-edited heteronuclear single quantum correlation spectroscopy

NASA Astrophysics Data System (ADS)

Sakhaii, Peyman; Bermel, Wolfgang

2015-10-01

A new experiment for recording multiplicity-edited HSQC spectra is presented. In standard multiplicity-edited HSQC experiments, the amplitude of CH2 signals is negative compared to those of CH and CH3 groups. We propose to reverse the sign of 13C frequencies of CH2 groups in t1 as criteria for editing. Basically, a modified [BIRD]r,x element (Bilinear Rotation Pulses and Delays) is inserted in a standard HSQC pulse sequence with States-TPPI frequency detection in t1 for this purpose. The modified BIRD element was designed in such a way as to pass or stop the evolution of the heteronuclear 1JHC coupling. This is achieved by adding a 180° proton RF pulse in each of the 1/2J periods. Depending on their position the evolution is switched on or off. Usually, the BIRD- element is applied on real and imaginary increments of a HSQC experiment to achieve the editing between multiplicities. Here, we restrict the application of the modified BIRD element to either real or imaginary increments of the HSQC. With this new scheme for editing, changing the frequency and/or amplitude of the CH2 signals becomes available. Reversing the chemical shift axis for CH2 signals simplifies overcrowded frequency regions and thus avoids accidental signal cancellation in conventional edited HSQC experiments. The practical implementation is demonstrated on the protein Lysozyme. Advantages and limitations of the idea are discussed.
Educating Students with Mild Disabilities: Strategies and Methods. Second Edition.

ERIC Educational Resources Information Center

Meyen, Edward L., Ed.; Vergason, Glenn A., Ed.; Whelan, Richard J., Ed.

This book addresses inclusive environments and the shifting of instruction of children with disabilities to the general classroom teacher. The major themes are behavior management, curriculum, and instructional strategies. Individual chapters include: (1) "Discipline in Special Education and General Education Settings" (Deborah Deutsch…
Dramatic Enhancement of Genome Editing by CRISPR/Cas9 Through Improved Guide RNA Design

PubMed Central

Farboud, Behnom; Meyer, Barbara J.

2015-01-01

Success with genome editing by the RNA-programmed nuclease Cas9 has been limited by the inability to predict effective guide RNAs and DNA target sites. Not all guide RNAs have been successful, and even those that were, varied widely in their efficacy. Here we describe and validate a strategy for Caenorhabditis elegans that reliably achieved a high frequency of genome editing for all targets tested in vivo. The key innovation was to design guide RNAs with a GG motif at the 3′ end of their target-specific sequences. All guides designed using this simple principle induced a high frequency of targeted mutagenesis via nonhomologous end joining (NHEJ) and a high frequency of precise DNA integration from exogenous DNA templates via homology-directed repair (HDR). Related guide RNAs having the GG motif shifted by only three nucleotides showed severely reduced or no genome editing. We also combined the 3′ GG guide improvement with a co-CRISPR/co-conversion approach. For this co-conversion scheme, animals were only screened for genome editing at designated targets if they exhibited a dominant phenotype caused by Cas9-dependent editing of an unrelated target. Combining the two strategies further enhanced the ease of mutant recovery, thereby providing a powerful means to obtain desired genetic changes in an otherwise unaltered genome. PMID:25695951

Automated search of control points in surface-based morphometry.

PubMed

Canna, Antonietta; Russo, Andrea G; Ponticorvo, Sara; Manara, Renzo; Pepino, Alessandro; Sansone, Mario; Di Salle, Francesco; Esposito, Fabrizio

2018-04-16

Cortical surface-based morphometry is based on a semi-automated analysis of structural MRI images. In FreeSurfer, a widespread tool for surface-based analyses, a visual check of gray-white matter borders is followed by the manual placement of control points to drive the topological correction (editing) of segmented data. A novel algorithm combining radial sampling and machine learning is presented for the automated control point search (ACPS). Four data sets with 3 T MRI structural images were used for ACPS validation, including raw data acquired twice in 36 healthy subjects and both raw and FreeSurfer preprocessed data of 125 healthy subjects from public databases. The unedited data from a subgroup of subjects were submitted to manual control point search and editing. The ACPS algorithm was trained on manual control points and tested on new (unseen) unedited data. Cortical thickness (CT) and fractal dimensionality (FD) were estimated in three data sets by reconstructing surfaces from both unedited and edited data, and the effects of editing were compared between manual and automated editing and versus no editing. The ACPS-based editing improved the surface reconstructions similarly to manual editing. Compared to no editing, ACPS-based and manual editing significantly reduced CT and FD in consistent regions across different data sets. Despite the extra processing of control point driven reconstructions, CT and FD estimates were highly reproducible in almost all cortical regions, albeit some problematic regions (e.g. entorhinal cortex) may benefit from different editing. The use of control points improves the surface reconstruction and the ACPS algorithm can automate their search reducing the burden of manual editing. Copyright © 2018 Elsevier Inc. All rights reserved.
Community, Educational, and Social Impact Perspectives.

ERIC Educational Resources Information Center

Schoeny, Donna Hager, Ed.; Decker, Larry E., Ed.

This volume consists of edited versions of 17 papers and reaction papers that were commissioned to examine the community, educational, and social impact of community education. Various topics pertaining to the impact of community education are examined, including educational programs of students, school closings and shifting populations, the…
Temperature-dependent sex-reversal by a transformer-2 gene-edited mutation in the spotted wing drosophila, Drosophila suzukii.

PubMed

Li, Jianwei; Handler, Alfred M

2017-09-28

Female to male sex reversal was achieved in an emerging agricultural insect pest, Drosophila suzukii, by creating a temperature-sensitive point mutation in the sex-determination gene, transformer-2 (tra-2), using CRISPR/Cas9 (clustered regularly interspaced palindromic repeats/CRISPR-associated) homology-directed repair gene-editing. Ds-tra-2 ts2 mutants developed as normal fertile XX and XY adults at permissive temperatures below 20 °C, but at higher restrictive temperatures (26 to 29 °C) chromosomal XX females developed as sterile intersexuals with a predominant male phenotype, while XY males developed with normal morphology, but were sterile. The temperature-dependent function of the Ds-TRA-2 ts2 protein was also evident by the up- and down-regulation of female-specific Ds-Yolk protein 1 (Ds-Yp1) gene expression by temperature shifts during adulthood. This study confirmed the temperature-dependent function of a gene-edited mutation and provides a new method for the more general creation of conditional mutations for functional genomic analysis in insects, and other organisms. Furthermore, it provides a temperature-dependent system for creating sterile male populations useful for enhancing the efficacy of biologically-based programs, such as the sterile insect technique (SIT), to control D. suzukii and other insect pest species of agricultural and medical importance.
Wikis and Collaborative Inquiry

ERIC Educational Resources Information Center

Lamb, Annette; Johnson, Larry

2009-01-01

Wikis are simply Web sites that provide easy-to-use tools for creating, editing, and sharing digital documents, images, and media files. Multiple participants can enter, submit, manage, and update a single Web workspace creating a community of authors and editors. Wiki projects help young people shift from being "consumers" of the Internet to…
How do clinicians actually use the Diagnostic and Statistical Manual of Mental Disorders in clinical practice and why we need to know more.

PubMed

First, Michael B; Bhat, Venkat; Adler, David; Dixon, Lisa; Goldman, Beth; Koh, Steve; Levine, Bruce; Oslin, David; Siris, Sam

2014-12-01

The clinical use of the Diagnostic and Statistical Manual of Mental Disorders (DSM) is explicitly stated as a goal for both the DSM Fourth Edition and DSM Fifth Edition (DSM-5) revisions. Many uses assume a relatively faithful application of the DSM diagnostic definitions. However, studies demonstrate significant discrepancies between clinical psychiatric diagnoses with those made using structured interviews suggesting that clinicians do not systematically apply the diagnostic criteria. The limited information regarding how clinicians actually use the DSM raises important questions: a) How can the clinical use be improved without first having a baseline assessment? b) How can potentially significant shifts in practice patterns based on wording changes be assessed without knowing the extent to which the criteria are used as written? Given the American Psychiatric Association's plans for interim revisions to the DSM-5, the value of a detailed exploration of its actual use in clinical practice remains a significant ongoing concern and deserves further study including a number of survey and in vivo studies.
'For the benefit of the people': the Dutch translation of the Fasciculus medicinae, Antwerp 1512.

PubMed

Coppens, Christian

2009-01-01

The article deals with the Dutch translation of the Fasciculus medicinae based on the Latin edition, Venice 1495, with the famous woodcuts created in 1494 for the Italian translation of the original Latin edition of 1491. The woodcuts are compared with the Venetian model. New features in the Antwerp edition include the Skeleton and the Zodiac Man, bot originally based on German models. The text also deals with other woodcuts in the Low Countries based on these Venetian illustrations. The Appendices provide a short title catalog of all the editions and translations based on the Venetian edition and a stemma.
Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes.

PubMed

Hess, Gaelen T; Tycko, Josh; Yao, David; Bassik, Michael C

2017-10-05

The past several years have seen an explosion in development of applications for the CRISPR-Cas9 system, from efficient genome editing, to high-throughput screening, to recruitment of a range of DNA and chromatin-modifying enzymes. While homology-directed repair (HDR) coupled with Cas9 nuclease cleavage has been used with great success to repair and re-write genomes, recently developed base-editing systems present a useful orthogonal strategy to engineer nucleotide substitutions. Base editing relies on recruitment of cytidine deaminases to introduce changes (rather than double-stranded breaks and donor templates) and offers potential improvements in efficiency while limiting damage and simplifying the delivery of editing machinery. At the same time, these systems enable novel mutagenesis strategies to introduce sequence diversity for engineering and discovery. Here, we review the different base-editing platforms, including their deaminase recruitment strategies and editing outcomes, and compare them to other CRISPR genome-editing technologies. Additionally, we discuss how these systems have been applied in therapeutic, engineering, and research settings. Lastly, we explore future directions of this emerging technology. Copyright © 2017 Elsevier Inc. All rights reserved.
IntellEditS: intelligent learning-based editor of segmentations.

PubMed

Harrison, Adam P; Birkbeck, Neil; Sofka, Michal

2013-01-01

Automatic segmentation techniques, despite demonstrating excellent overall accuracy, can often produce inaccuracies in local regions. As a result, correcting segmentations remains an important task that is often laborious, especially when done manually for 3D datasets. This work presents a powerful tool called Intelligent Learning-Based Editor of Segmentations (IntellEditS) that minimizes user effort and further improves segmentation accuracy. The tool partners interactive learning with an energy-minimization approach to editing. Based on interactive user input, a discriminative classifier is trained and applied to the edited 3D region to produce soft voxel labeling. The labels are integrated into a novel energy functional along with the existing segmentation and image data. Unlike the state of the art, IntellEditS is designed to correct segmentation results represented not only as masks but also as meshes. In addition, IntellEditS accepts intuitive boundary-based user interactions. The versatility and performance of IntellEditS are demonstrated on both MRI and CT datasets consisting of varied anatomical structures and resolutions.
Mitochondrial tRNA 5'-editing in Dictyostelium discoideum and Polysphondylium pallidum.

PubMed

Abad, Maria G; Long, Yicheng; Kinchen, R Dimitri; Schindel, Elinor T; Gray, Michael W; Jackman, Jane E

2014-05-30

Mitochondrial tRNA (mt-tRNA) 5'-editing was first described more than 20 years ago; however, the first candidates for 5'-editing enzymes were only recently identified in a eukaryotic microbe (protist), the slime mold Dictyostelium discoideum. In this organism, eight of 18 mt-tRNAs are predicted to be edited based on the presence of genomically encoded mismatched nucleotides in their aminoacyl-acceptor stem sequences. Here, we demonstrate that mt-tRNA 5'-editing occurs at all predicted sites in D. discoideum as evidenced by changes in the sequences of isolated mt-tRNAs compared with the expected sequences encoded by the mitochondrial genome. We also identify two previously unpredicted editing events in which G-U base pairs are edited in the absence of any other genomically encoded mismatches. A comparison of 5'-editing in D. discoideum with 5'-editing in another slime mold, Polysphondylium pallidum, suggests organism-specific idiosyncrasies in the treatment of U-G/G-U pairs. In vitro activities of putative D. discoideum editing enzymes are consistent with the observed editing reactions and suggest an overall lack of tRNA substrate specificity exhibited by the repair component of the editing enzyme. Although the presence of terminal mismatches in mt-tRNA sequences is highly predictive of the occurrence of mt-tRNA 5'-editing, the variability in treatment of U-G/G-U base pairs observed here indicates that direct experimental evidence of 5'-editing must be obtained to understand the complete spectrum of mt-tRNA editing events in any species. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
Rodent models in neuroscience research: is it a rat race?

PubMed Central

2016-01-01

ABSTRACT Rodents (especially Mus musculus and Rattus norvegicus) have been the most widely used models in biomedical research for many years. A notable shift has taken place over the last two decades, with mice taking a more and more prominent role in biomedical science compared to rats. This shift was primarily instigated by the availability of a much larger genetic toolbox for mice, particularly embryonic-stem-cell-based targeting technology for gene disruption. With the recent emergence of tools for altering the rat genome, notably genome-editing technologies, the technological gap between the two organisms is closing, and it is becoming more important to consider the physiological, anatomical, biochemical and pharmacological differences between rats and mice when choosing the right model system for a specific biological question. The aim of this short review and accompanying poster is to highlight some of the most important differences, and to discuss their impact on studies of human diseases, with a special focus on neuropsychiatric disorders. PMID:27736744
Twenty Years of Diagnosis and the DSM.

ERIC Educational Resources Information Center

Seligman, Linda

1999-01-01

The process of diagnosing mental disorders and the use of the Diagnostic and Statistical Manual of Mental Disorders (DSM) have been increasingly important for counselors. This article provides information on the hallmarks of this shift. Reviews and discusses the changes form the third and fourth editions of the DSM. Offers predictions as to future…
Design and Drawing for Production. Syllabus. Field Test Edition II.

ERIC Educational Resources Information Center

New York State Education Dept., Albany.

This syllabus, which replaces the New York State Education Department publication "Mechanical Drawing and Design," is intended for use in teaching a high school course in design and drawing for production. The materials included in the guide reflect a shift away from the conventional methods of teaching design and drawing to a greater…
Project Approach: Teaching. Second Edition.

ERIC Educational Resources Information Center

Ho, Rose

The primary objective of the action research chronicled (in English and Chinese) in this book was to shift the teaching method used by preschool teachers in Hong Kong from a teacher-directed mode by training them to use the Project Approach. The secondary objective was to measure children's achievement while using the Project Approach, focusing on…
The SEA of the Future: Leveraging Performance Management to Support School Improvement. Volume 1

ERIC Educational Resources Information Center

Gross, Betheny, Ed.; Jochim, Ashley, Ed.

2013-01-01

"The SEA of the Future" is an education publication series examining how state education agencies can shift from a compliance to a performance-oriented organization through strategic planning and performance management tools to meet growing demands to support education reform while improving productivity. This inaugural edition of…
Update on Research and Leadership. Vol. 21, No. 1. Fall 2009

ERIC Educational Resources Information Center

Bragg, Debra D., Ed.; Taylor, Jason L., Ed.

2009-01-01

This edition features current research, practice, and policy related to the Joyce Foundation's Shifting Gears initiative beginning with an interview with Whitney Smith, Manager of the Employment Program at the Joyce Foundation. Julie Strawn, Center for Law and Social Policy, presents a national perspective of basic skills reform efforts similar to…
Contemporary Literacies and Technologies in English Language Arts Teacher Education: Shift Happens!

ERIC Educational Resources Information Center

George, Marshall; Pope, Carol; Reid, Louann

2015-01-01

Three leaders of the National Council of Teachers of English (NCTE) Conference on English Education (CEE) reflect on the changes that have occurred in English language arts teacher education in the past 15 years since the first edition of "Contemporary Issues in Technology and Teacher Education" ("CITE Journal") was published.…
Revising the personality disorder diagnostic criteria for the Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition (DSM-V): consider the later life context.

PubMed

Balsis, Steve; Segal, Daniel L; Donahue, Cailin

2009-10-01

The categorical measurement approach implemented by the Diagnostic and Statistical Manual of Mental Disorders-Fourth Edition (DSM-IV) personality disorder (PD) diagnostic system is theoretically and pragmatically limited. As a result, many prominent psychologists now advocate for a shift away from this approach in favor of more conceptually sound dimensional measurement. This shift is expected to improve the psychometric properties of the personality disorder (PD) diagnostic system and make it more useful for clinicians and researchers. The current article suggests that despite the probable benefits of such a change, several limitations will remain if the new diagnostic system does not closely consider the context of later life. A failure to address the unique challenges associated with the assessment of personality in older adults likely will result in the continued limited validity, reliability, and utility of the Diagnostic and Statistical Manual of Mental Disorders (DSM) system for this growing population. This article discusses these limitations and their possible implications. (c) 2009 APA, all rights reserved.
REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results.

PubMed

Wu, Shuangyang; Liu, Wanfei; Aljohi, Hasan Awad; Alromaih, Sarah A; Alanazi, Ibrahim O; Lin, Qiang; Yu, Jun; Hu, Songnian

2018-05-01

RNA editing is a post-transcriptional or cotranscriptional process that changes the sequence of the precursor transcript by substitutions, insertions, or deletions. Almost all of the land plants undergo RNA editing in organelles (plastids and mitochondria). Although several software tools have been developed to identify RNA editing events, there has been a great challenge to distinguish true RNA editing events from genome variation, sequencing errors, and other factors. Here we introduce REDO, a comprehensive application tool for identifying RNA editing events in plant organelles based on variant call format files from RNA-sequencing data. REDO is a suite of Perl scripts that illustrate a bunch of attributes of RNA editing events in figures and tables. REDO can also detect RNA editing events in multiple samples simultaneously and identify the significant differential proportion of RNA editing loci. Comparing with similar tools, such as REDItools, REDO runs faster with higher accuracy, and more specificity at the cost of slightly lower sensitivity. Moreover, REDO annotates each RNA editing site in RNAs, whereas REDItools reports only possible RNA editing sites in genome, which need additional steps to obtain RNA editing profiles for RNAs. Overall, REDO can identify potential RNA editing sites easily and provide several functions such as detailed annotations, statistics, figures, and significantly differential proportion of RNA editing sites among different samples.
PlenoPatch: Patch-Based Plenoptic Image Manipulation.

PubMed

Zhang, Fang-Lue; Wang, Jue; Shechtman, Eli; Zhou, Zi-Ye; Shi, Jia-Xin; Hu, Shi-Min

2017-05-01

Patch-based image synthesis methods have been successfully applied for various editing tasks on still images, videos and stereo pairs. In this work we extend patch-based synthesis to plenoptic images captured by consumer-level lenselet-based devices for interactive, efficient light field editing. In our method the light field is represented as a set of images captured from different viewpoints. We decompose the central view into different depth layers, and present it to the user for specifying the editing goals. Given an editing task, our method performs patch-based image synthesis on all affected layers of the central view, and then propagates the edits to all other views. Interaction is done through a conventional 2D image editing user interface that is familiar to novice users. Our method correctly handles object boundary occlusion with semi-transparency, thus can generate more realistic results than previous methods. We demonstrate compelling results on a wide range of applications such as hole-filling, object reshuffling and resizing, changing object depth, light field upscaling and parallax magnification.
Gene editing tools: state-of-the-art and the road ahead for the model and non-model fishes.

PubMed

Barman, Hirak Kumar; Rasal, Kiran Dashrath; Chakrapani, Vemulawada; Ninawe, A S; Vengayil, Doyil T; Asrafuzzaman, Syed; Sundaray, Jitendra K; Jayasankar, Pallipuram

2017-10-01

Advancements in the DNA sequencing technologies and computational biology have revolutionized genome/transcriptome sequencing of non-model fishes at an affordable cost. This has led to a paradigm shift with regard to our heightened understandings of structure-functional relationships of genes at a global level, from model animals/fishes to non-model large animals/fishes. Whole genome/transcriptome sequencing technologies were supplemented with the series of discoveries in gene editing tools, which are being used to modify genes at pre-determined positions using programmable nucleases to explore their respective in vivo functions. For a long time, targeted gene disruption experiments were mostly restricted to embryonic stem cells, advances in gene editing technologies such as zinc finger nuclease, transcriptional activator-like effector nucleases and CRISPR (clustered regulatory interspaced short palindromic repeats)/CRISPR-associated nucleases have facilitated targeted genetic modifications beyond stem cells to a wide range of somatic cell lines across species from laboratory animals to farmed animals/fishes. In this review, we discuss use of different gene editing tools and the strategic implications in fish species for basic and applied biology research.

The neuropsychology of obsessive-compulsive personality disorder: a new analysis.

PubMed

Fineberg, Naomi A; Day, Grace A; de Koenigswarter, Nica; Reghunandanan, Samar; Kolli, Sangeetha; Jefferies-Sewell, Kiri; Hranov, Georgi; Laws, Keith R

2015-10-01

Obsessive compulsive personality disorder (OCPD) is characterized by perfectionism, need for control, and cognitive rigidity. Currently, little neuropsychological data exist on this condition, though emerging evidence does suggest that disorders marked by compulsivity, including obsessive-compulsive disorder (OCD), are associated with impairment in cognitive flexibility and executive planning on neurocognitive tasks. The current study investigated the neurocognitive profile in a nonclinical community-based sample of people fulfilling diagnostic criteria for OCPD in the absence of major psychiatric comorbidity. Twenty-one nonclinical subjects who fulfilled Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) criteria for OCPD were compared with 15 healthy controls on selected clinical and neurocognitive tasks. OCPD was measured using the Compulsive Personality Assessment Scale (CPAS). Participants completed tests from the Cambridge Automated Neuropsychological Test Battery including tests of set shifting (Intra-Extra Dimensional [IED] Set Shifting) executive planning (Stockings of Cambridge [SOC]), and decision making (Cambridge Gamble Task [CGT]). The OCPD group made significantly more IED-ED shift errors and total shift errors, and also showed longer mean initial thinking time on the SOC at moderate levels of difficulty. No differences emerged on the CGT. Nonclinical cases of OCPD showed significant cognitive inflexibility coupled with executive planning deficits, whereas decision-making remained intact. This profile of impairment overlaps with that of OCD and implies that common neuropsychological changes affect individuals with these disorders.
2015 Edition Health Information Technology (Health IT) Certification Criteria, 2015 Edition Base Electronic Health Record (EHR) Definition, and ONC Health IT Certification Program Modifications. Final rule.

PubMed

2015-10-16

This final rule finalizes a new edition of certification criteria (the 2015 Edition health IT certification criteria or "2015 Edition'') and a new 2015 Edition Base Electronic Health Record (EHR) definition, while also modifying the ONC Health IT Certification Program to make it open and accessible to more types of health IT and health IT that supports various care and practice settings. The 2015 Edition establishes the capabilities and specifies the related standards and implementation specifications that Certified Electronic Health Record Technology (CEHRT) would need to include to, at a minimum, support the achievement of meaningful use by eligible professionals (EPs), eligible hospitals, and critical access hospitals (CAHs) under the Medicare and Medicaid EHR Incentive Programs (EHR Incentive Programs) when such edition is required for use under these programs.
Detecting Single-Nucleotide Substitutions Induced by Genome Editing.

PubMed

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. © 2016 Cold Spring Harbor Laboratory Press.
Fundamentals of Welding. Teacher Edition [and] Student Edition [and] Student Workbook. Second Edition.

ERIC Educational Resources Information Center

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…
The Principal as Instructional Leader: A Handbook for Supervisors. 2nd Edition

ERIC Educational Resources Information Center

Zepeda, Sally J.

2007-01-01

Very few people would disagree that the work of the principal is multifaceted, hectic, and fraught with uncertainties, and given the ongoing press for accountability, the very work of the principal as instructional leader is shifting to ensure "results." There are myriad day-to-day activities that take principals away from the important work of…
Whatever Happened to the Silent Scientific Revolution?--Research, Theory and Practice in Distance Education.

ERIC Educational Resources Information Center

Morgan, Alistair

The point of departure for this article is the title of a book edited by David Fetterman, "Qualitative Approaches to Educational Evaluation--The Silent Scientific Revolution." This article addresses the question of how the shift to a qualitative, phenomenological approach has impinged on research and evaluation in distance education.…
Computer-Based Practice in Editing.

ERIC Educational Resources Information Center

Cronnell, Bruce

One goal of computer-based instruction in writing is to help students to edit their compositions, particularly those compositions written on a word processor. This can be accomplished by a complete editing program that would contain the full set of mechanics rules--capitalization, punctuation, spelling, usage--appropriate for the grade level of…
A non-inheritable maternal Cas9-based multiple-gene editing system in mice.

PubMed

Sakurai, Takayuki; Kamiyoshi, Akiko; Kawate, Hisaka; Mori, Chie; Watanabe, Satoshi; Tanaka, Megumu; Uetake, Ryuichi; Sato, Masahiro; Shindo, Takayuki

2016-01-28

The CRISPR/Cas9 system is capable of editing multiple genes through one-step zygote injection. The preexisting method is largely based on the co-injection of Cas9 DNA (or mRNA) and guide RNAs (gRNAs); however, it is unclear how many genes can be simultaneously edited by this method, and a reliable means to generate transgenic (Tg) animals with multiple gene editing has yet to be developed. Here, we employed non-inheritable maternal Cas9 (maCas9) protein derived from Tg mice with systemic Cas9 overexpression (Cas9 mice). The maCas9 protein in zygotes derived from mating or in vitro fertilization of Tg/+ oocytes and +/+ sperm could successfully edit the target genome. The efficiency of such maCas9-based genome editing was comparable to that of zygote microinjection-based genome editing widely used at present. Furthermore, we demonstrated a novel approach to create "Cas9 transgene-free" gene-modified mice using non-Tg (+/+) zygotes carrying maCas9. The maCas9 protein in mouse zygotes edited nine target loci simultaneously after injection with nine different gRNAs alone. Cas9 mouse-derived zygotes have the potential to facilitate the creation of genetically modified animals carrying the Cas9 transgene, enabling repeatable genome engineering and the production of Cas9 transgene-free mice.
Plate tectonics in the classification of personality disorder: shifting to a dimensional model.

PubMed

Widiger, Thomas A; Trull, Timothy J

2007-01-01

The diagnostic categories of the American Psychiatric Association's Diagnostic and Statistical Manual of Mental Disorders were developed in the spirit of a traditional medical model that considers mental disorders to be qualitatively distinct conditions (see, e.g., American Psychiatric Association, 2000). Work is now beginning on the fifth edition of this influential diagnostic manual. It is perhaps time to consider a fundamental shift in how psychopathology is conceptualized and diagnosed. More specifically, it may be time to consider a shift to a dimensional classification of personality disorder that would help address the failures of the existing diagnostic categories as well as contribute to an integration of the psychiatric diagnostic manual with psychology's research on general personality structure. (c) 2007 APA, all rights reserved
[Preface for genome editing special issue].

PubMed

Gu, Feng; Gao, Caixia

2017-10-25

Genome editing technology, as an innovative biotechnology, has been widely used for editing the genome from model organisms, animals, plants and microbes. CRISPR/Cas9-based genome editing technology shows its great value and potential in the dissection of functional genomics, improved breeding and genetic disease treatment. In the present special issue, the principle and application of genome editing techniques has been summarized. The advantages and disadvantages of the current genome editing technology and future prospects would also be highlighted.
Genetic Architectures of Quantitative Variation in RNA Editing Pathways

PubMed Central

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.

2016-01-01

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. PMID:26614740
Where Children Live: Solutions for Serving Young Children and Their Families. Advances in Applied Developmental Psychology, Volume 17.

ERIC Educational Resources Information Center

Roberts, Richard N., Ed.; Magrab, Phyllis R., Ed.

The changing nature of communities necessitates a comprehensive theoretical model for effective delivery of child and family services. This edited volume provides a context for and examples of an emerging paradigm shift in human services toward one in which services for families with young children are provided in their communities. Section 1 of…
Historical Development of Newton's Laws of Motion and Suggestions for Teaching Content

ERIC Educational Resources Information Center

Chang, Wheijen; Bell, Beverley; Jones, Allister

2014-01-01

A review of the history of Newton's Laws of Motion illustrates that the historical development gradually shifted away from intuitive experiences and daily life conventions towards a scientific regulated perspective. Three stages of the historical development are discussed, i.e. prior to the Principia, the 3rd (last) edition of the Principia,…
[The application of CRISPR/Cas9 genome editing technology in cancer research].

PubMed

Wang, Da-yong; Ma, Ning; Hui, Yang; Gao, Xu

2016-01-01

The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease) genome editing technology has become more and more popular in gene editing because of its simple design and easy operation. Using the CRISPR/Cas9 system, researchers can perform site-directed genome modification at the base level. Moreover, it has been widely used in genome editing in multiple species and related cancer research. In this review, we summarize the application of the CRISPR/Cas9 system in cancer research based on the latest research progresses as well as our understanding of cancer research and genome editing techniques.
High-throughput detection and screening of plants modified by gene editing using quantitative real-time polymerase chain reaction.

PubMed

Peng, Cheng; Wang, Hua; Xu, Xiaoli; Wang, Xiaofu; Chen, Xiaoyun; Wei, Wei; Lai, Yongmin; Liu, Guoquan; Godwin, Ian Douglas; Li, Jieqin; Zhang, Ling; Xu, Junfeng

2018-05-15

Gene editing techniques are becoming powerful tools for modifying target genes in organisms. Although several methods have been developed to detect gene-edited organisms, these techniques are time and labour intensive. Meanwhile, few studies have investigated high-throughput detection and screening strategies for plants modified by gene editing. In this study, we developed a simple, sensitive and high-throughput quantitative real-time (qPCR)-based method. The qPCR-based method exploits two differently labelled probes that are placed within one amplicon at the gene editing target site to simultaneously detect the wild-type and a gene-edited mutant. We showed that the qPCR-based method can accurately distinguish CRISPR/Cas9-induced mutants from the wild-type in several different plant species, such as Oryza sativa, Arabidopsis thaliana, Sorghum bicolor, and Zea mays. Moreover, the method can subsequently determine the mutation type by direct sequencing of the qPCR products of mutations due to gene editing. The qPCR-based method is also sufficiently sensitive to distinguish between heterozygous and homozygous mutations in T 0 transgenic plants. In a 384-well plate format, the method enabled the simultaneous analysis of up to 128 samples in three replicates without handling the post-polymerase chain reaction (PCR) products. Thus, we propose that our method is an ideal choice for screening plants modified by gene editing from many candidates in T 0 transgenic plants, which will be widely used in the area of plant gene editing. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.
Utilizing tagged paramagnetic shift reagents to monitor protein dynamics by NMR.

PubMed

Ye, Libin; Van Eps, Ned; Li, Xiang; Ernst, Oliver P; Prosser, R Scott

2017-11-01

Calmodulin is a ubiquitous calcium sensor protein, known to serve as a critical interaction hub with a wide range of signaling partners. While the holo form of calmodulin (CaM-4Ca 2+ ) has a well-defined ground state structure, it has been shown to undergo exchange, on a millisecond timescale, to a conformation resembling that of the peptide bound state. Tagged paramagnetic relaxation agents have been previously used to identify long-range dipolar interactions through relaxation effects on nuclear spins of interest. In the case of calmodulin, this lead to the determination of the relative orientation of the N- and C-terminal domains and the presence of a weakly populated peptide bound like state. Here, we make use of pseudocontact shifts from a tagged paramagnetic shift reagent which allows us to define minor states both in 13 C and 15 N NMR spectra and through 13 C- and 15 N-edited 1 H-CPMG relaxation dispersion measurements. This is validated by pulsed EPR (DEER) spectroscopy which reveals an ensemble consisting of a compact peptide-bound like conformer, an intermediate peptide-bound like conformer, and a (dumbbell-like) extended ground state conformer of CaM-4Ca 2+ , where addition of the MLCK peptide increases the population of the peptide-bound conformers. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.
Curriculum Based Assessment: A Primer. 3rd Edition

ERIC Educational Resources Information Center

Hargis, Charles H.

2004-01-01

The use of curriculum based assessment (CBA) to ensure learning disabled and low achieving students adequate educational opportunity remains the focus in this direct and comprehensive third edition. The additions to this edition are in the way of providing detail and explanation in the context of current and emerging issues in educational…
RNA editing: trypanosomes rewrite the genetic code.

PubMed

Stuart, K

1998-01-01

The understanding of how genetic information is stored and expressed has advanced considerably since the "central dogma" asserted that genetic information flows from the nucleotide sequence of DNA to that of messenger RNA (mRNA) which in turn specifies the amino acid sequence of a protein. It was found that genetic information can be stored as RNA (e.g. in RNA viruses) and can flow from RNA to DNA by reverse transcriptase enzyme activity. In addition, some genes contain introns, nucleotide sequences that are removed from their RNA (by RNA splicing) and thus are not represented in the resultant protein. Furthermore, alternative splicing was found to produce variant proteins from a single gene. More recently, the study of trypanosome parasites revealed an unexpected and indeed counter-intuitive genetic complexity. Genetic information for a single protein can be dispersed among several (DNA) genes in these organisms. One of these genes specifies an encrypted precursor mRNA that is converted to a functional mRNA by a process called RNA editing that inserts and deletes uridylate nucleotides. The sequence of the edited mRNA is specified by multiple small RNAs, named guide RNAs, (gRNAs) each of which is encoded in a separate gene. Thus, edited mRNA sequences are assembled from multiple genes by the transfer of information from one type of RNA to another. The existence of editing was surprising but has stimulated the discovery of other types of RNA editing. The Stuart laboratory has been exploring RNA editing in trypanosomes from the time of its discovery. They found dramatic differences between the mitochondrial gene sequences and those of the corresponding mRNAs, which indicated editing by the insertion and deletion of uridylates. Some editing was modest; simply eliminating shifts in sequence register of minimally extending the protein coding sequence. However, editing of many mRNAs was startingly extensive. The RNA sequence was essentially entirely remodeled with its sequence more the result of editing than the gene sequence. The identities of genes for such extensively edited RNA were not recognizable from the DNA sequence but they were readily identifiable from the edited mRNA sequence. Thus, despite the complex and extensive editing the resultant mRNA sequence is precise. Characterization of partially edited RNAs indicated that editing proceeds in the direction opposite to that used to specify the protein which reflects the use of the gRNAs. The numerous gRNAs that are used for editing are encoded in the DNA molecules whose role was previously a mystery. Using information gained in our earlier studies, the Stuart group developed an in vitro system that reproduces the fundamental process of editing in order to resolve the mechanism by which it occurs. They determined that editing entails a series of enzymatic steps rather than the mechanism used in RNA splicing. They also showed that chimeric gRNA-mRNA molecules are aberrant by-products of editing rather than intermediates in the process as had been proposed. Additional studies are exploring precisely how the number of added and deleted uridylates is specified by the gRNA. The Stuart laboratory showed that editing is performed by an aggregation of enzymes that catalyze the separate steps of editing. It also developed a method to purify this multimolecule complex that contains several, perhaps tens of, proteins. This will allow the study of its composition and the functions of its component parts. Indeed, the gene for one component has been identified and its detailed characterization begun. These studies are developing tools to explore related processes. An early finding in the lab was that the various mRNAs are differentially edited during the life cycle of the parasite. The pattern of this editing indicates that editing serves to regulate the alternation between two modes of energy generation. This regulation is coordinated with other events that are occurring during the life c
RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.

PubMed

Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

2016-01-01

RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software - 'RED' (RNA Editing sites Detector) - for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector.
RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters

PubMed Central

Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

2016-01-01

RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software − ‘RED’ (RNA Editing sites Detector) − for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector. PMID:26930599

A Subdivision-Based Representation for Vector Image Editing.

PubMed

Liao, Zicheng; Hoppe, Hugues; Forsyth, David; Yu, Yizhou

2012-11-01

Vector graphics has been employed in a wide variety of applications due to its scalability and editability. Editability is a high priority for artists and designers who wish to produce vector-based graphical content with user interaction. In this paper, we introduce a new vector image representation based on piecewise smooth subdivision surfaces, which is a simple, unified and flexible framework that supports a variety of operations, including shape editing, color editing, image stylization, and vector image processing. These operations effectively create novel vector graphics by reusing and altering existing image vectorization results. Because image vectorization yields an abstraction of the original raster image, controlling the level of detail of this abstraction is highly desirable. To this end, we design a feature-oriented vector image pyramid that offers multiple levels of abstraction simultaneously. Our new vector image representation can be rasterized efficiently using GPU-accelerated subdivision. Experiments indicate that our vector image representation achieves high visual quality and better supports editing operations than existing representations.
"Diagnostic shift" from eating disorder not otherwise specified to bulimia nervosa using DSM-5 criteria: a clinical comparison with DSM-IV bulimia.

PubMed

MacDonald, Danielle E; McFarlane, Traci L; Olmsted, Marion P

2014-01-01

In the 5th edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5), the diagnostic threshold for binging and compensation in bulimia nervosa (BN) decreased from twice to once weekly for 3 months. This study investigates the validity of this change by examining whether BN patients and those whose diagnoses "shift" to BN with DSM-5 are similar in their psychological functioning. EDNOS patients whose symptoms met DSM-5 BN criteria (n=25) were compared to DSM-IV BN patients (n=146) on clinically relevant variables. No differences were found on: BMI; weight-based self-evaluation; perfectionism; depression and anxiety symptoms; or readiness for change. Differences were found on one Eating Disorder Inventory subscale (i.e., bulimia), with the BN group reporting higher scores, consistent with group definitions. These findings support the modified criteria, suggesting that psychopathology both directly and indirectly related to eating disorders is comparable between those with once weekly versus more frequent bulimic episodes. © 2013.
Diesel Technology: Safety Skills. Teacher Edition [and] Student Edition. Second Edition.

ERIC Educational Resources Information Center

Kellum, Mary

Teacher and student editions of this document are one in a series of competency-based instructional materials for diesel technology programs. The series aligns with the medium/heavy diesel duty truck task list used by the National Institute for Automotive Service Excellence in the certification of medium/heavy duty truck technicians. Introductory…
Human Resources Administration: A School-Based Perspective. Fourth Edition

ERIC Educational Resources Information Center

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…
Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity

PubMed Central

Komor, Alexis C.; Zhao, Kevin T.; Packer, Michael S.; Gaudelli, Nicole M.; Waterbury, Amanda L.; Koblan, Luke W.; Kim, Y. Bill; Badran, Ahmed H.; Liu, David R.

2017-01-01

We recently developed base editing, the programmable conversion of target C:G base pairs to T:A without inducing double-stranded DNA breaks (DSBs) or requiring homology-directed repair using engineered fusions of Cas9 variants and cytidine deaminases. Over the past year, the third-generation base editor (BE3) and related technologies have been successfully used by many researchers in a wide range of organisms. The product distribution of base editing—the frequency with which the target C:G is converted to mixtures of undesired by-products, along with the desired T:A product—varies in a target site–dependent manner. We characterize determinants of base editing outcomes in human cells and establish that the formation of undesired products is dependent on uracil N-glycosylase (UNG) and is more likely to occur at target sites containing only a single C within the base editing activity window. We engineered CDA1-BE3 and AID-BE3, which use cytidine deaminase homologs that increase base editing efficiency for some sequences. On the basis of these observations, we engineered fourth-generation base editors (BE4 and SaBE4) that increase the efficiency of C:G to T:A base editing by approximately 50%, while halving the frequency of undesired by-products compared to BE3. Fusing BE3, BE4, SaBE3, or SaBE4 to Gam, a bacteriophage Mu protein that binds DSBs greatly reduces indel formation during base editing, in most cases to below 1.5%, and further improves product purity. BE4, SaBE4, BE4-Gam, and SaBE4-Gam represent the state of the art in C:G-to-T:A base editing, and we recommend their use in future efforts. PMID:28875174
A to I editing in disease is not fake news.

PubMed

Bajad, Prajakta; Jantsch, Michael F; Keegan, Liam; O'Connell, Mary

2017-09-02

Adenosine deaminases acting on RNA (ADARs) are zinc-containing enzymes that deaminate adenosine bases to inosines within dsRNA regions in transcripts. In short, structured dsRNA hairpins individual adenosine bases may be targeted specifically and edited with up to one hundred percent efficiency, leading to the production of alternative protein variants. However, the majority of editing events occur within longer stretches of dsRNA formed by pairing of repetitive sequences. Here, many different adenosine bases are potential targets but editing efficiency is usually much lower. Recent work shows that ADAR-mediated RNA editing is also required to prevent aberrant activation of antiviral innate immune sensors that detect viral dsRNA in the cytoplasm. Missense mutations in the ADAR1 RNA editing enzyme cause a fatal auto-inflammatory disease, Aicardi-Goutières syndrome (AGS) in affected children. In addition RNA editing by ADARs has been observed to increase in many cancers and also can contribute to vascular disease. Thus the role of RNA editing in the progression of various diseases can no longer be ignored. The ability of ADARs to alter the sequence of RNAs has also been used to artificially target model RNAs in vitro and in cells for RNA editing. Potentially this approach may be used to repair genetic defects and to alter genetic information at the RNA level. In this review we focus on the role of ADARs in disease development and progression and on their potential use to artificially modify RNAs in a targeted manner.
Genome Editing in the Cricket, Gryllus bimaculatus.

PubMed

Watanabe, Takahito; Noji, Sumihare; Mito, Taro

2017-01-01

Hemimetabolous, or incompletely metamorphosing, insects are phylogenetically basal and include many beneficial and deleterious species. The cricket, Gryllus bimaculatus, is an emerging model for hemimetabolous insects, based on the success of RNA interference (RNAi)-based gene-functional analyses and transgenic technology. Taking advantage of genome editing technologies in this species would greatly promote functional genomics studies. Genome editing has proven to be an effective method for site-specific genome manipulation in various species. Here, we describe a protocol for genome editing including gene knockout and gene knockin in G. bimaculatus for functional genomics studies.
Modeling the thermal unfolding 2DIR spectra of a β-hairpin peptide based on the implicit solvent MD simulation.

PubMed

Wu, Tianmin; Yang, Lijiang; Zhang, Ruiting; Shao, Qiang; Zhuang, Wei

2013-07-25

We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a β-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GB(OBC) implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide's conformational change and related IR spectra across its thermal unfolding transition.
Quadrature-Quadrature Phase Shift Keying.

DTIC Science & Technology

1986-09-01

SECURITY CLASSIFICATION OF -IS PAfr All other editions are obsolete ’r- Ac P..N -N- %.. .. V . .. b . h S Debabrata Saha 1986 All Rights Reserved...1.2/T T~,pe of AISA Q -PSK AMSK 0 Y(IitIo ?6 orthogonal Four -level F, J." 𔃻 1i 1/ 2 H13.4 a H P6 E 44 3.5 Modulator Demodulator and Synchronization
Electronic Warfare and Radar Systems Engineering Handbook. 4th Edition

DTIC Science & Technology

2013-10-01

and Maintainability R&M Reliability and Maintainability RAT Ram Air Turbine RBOC Rapid Blooming Offboard Chaff RCP or RHCP Right-hand Circular...Doppler shifted return (see Figure 10). Reflections off rotating jet engine compressor blades, aircraft propellers, ram air turbine (RAT...Doppler techniques, in order to precisely predict aircraft ground speed and direction of motion. Wind influences are taken into account, such that
Can Threatened Languages Be Saved? Reversing Language Shift, Revisited: A 21st Century Perspective. Multilingual Matters 116.

ERIC Educational Resources Information Center

Fishman, Joshua A., Ed.

This edited volume considers the contemporary position of 18 threatened languages. Two important questions are examined in every case: (a) what is the current demographic and functional status of a threatened language? and (b) what is the best way to understand its future prospects? The view presented in this volume is that there are ways to save…
Next Generation Satellite Communications: Automated Doppler Shift Compensation of PSK-31 Via Software-Defined Radio

DTIC Science & Technology

2014-05-09

Interfaces Configuration – Wired Network Connections before Editing Move the cursor to the end of the line that ends with “eth0 inet dhcp ” and type...X”. This will delete text one character back from the cursor. Delete the word “ dhcp ”. Once this is done, type “a” to begin inserting text and add
Accurate identification of RNA editing sites from primitive sequence with deep neural networks.

PubMed

Ouyang, Zhangyi; Liu, Feng; Zhao, Chenghui; Ren, Chao; An, Gaole; Mei, Chuan; Bo, Xiaochen; Shu, Wenjie

2018-04-16

RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, time-consuming identification process. Moreover, these methods have limited generalizability and applicability in species with insufficient genomic annotations or in conditions of limited prior knowledge. We developed DeepRed, a deep learning-based method that identifies RNA editing from primitive RNA sequences without prior-knowledge-based filtering steps or genomic annotations. DeepRed achieved 98.1% and 97.9% area under the curve (AUC) in training and test sets, respectively. We further validated DeepRed using experimentally verified U87 cell RNA-seq data, achieving 97.9% positive predictive value (PPV). We demonstrated that DeepRed offers better prediction accuracy and computational efficiency than current methods with large-scale, mass RNA-seq data. We used DeepRed to assess the impact of multiple factors on editing identification with RNA-seq data from the Association of Biomolecular Resource Facilities and Sequencing Quality Control projects. We explored developmental RNA editing pattern changes during human early embryogenesis and evolutionary patterns in Drosophila species and the primate lineage using DeepRed. Our work illustrates DeepRed's state-of-the-art performance; it may decipher the hidden principles behind RNA editing, making editing detection convenient and effective.
Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

USDA-ARS?s Scientific Manuscript database

CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...
50 CFR Appendix D to Part 404 - Boundary Coordinates for Papaha

Code of Federal Regulations, 2012 CFR

2012-10-01

..., 2008 edition; 19019, 2008 edition; 19022, 2008 edition. These charts are based on World Geodetic System...′.87 Table D-4—Inner Boundary Around Gardner Pinnacles, French Frigate Shoals, and Necker Island Point...
50 CFR Appendix D to Part 404 - Boundary Coordinates for Papaha

Code of Federal Regulations, 2014 CFR

2014-10-01

..., 2008 edition; 19019, 2008 edition; 19022, 2008 edition. These charts are based on World Geodetic System...′.87 Table D-4—Inner Boundary Around Gardner Pinnacles, French Frigate Shoals, and Necker Island Point...
50 CFR Appendix D to Part 404 - Boundary Coordinates for Papaha

Code of Federal Regulations, 2011 CFR

2011-10-01

..., 2008 edition; 19019, 2008 edition; 19022, 2008 edition. These charts are based on World Geodetic System...′.87 Table D-4—Inner Boundary Around Gardner Pinnacles, French Frigate Shoals, and Necker Island Point...
50 CFR Appendix D to Part 404 - Boundary Coordinates for Papaha

Code of Federal Regulations, 2013 CFR

2013-10-01

..., 2008 edition; 19019, 2008 edition; 19022, 2008 edition. These charts are based on World Geodetic System...′.87 Table D-4—Inner Boundary Around Gardner Pinnacles, French Frigate Shoals, and Necker Island Point...
Discriminative Prediction of A-To-I RNA Editing Events from DNA Sequence

PubMed Central

Sun, Jiangming; Singh, Pratibha; Bagge, Annika; Valtat, Bérengère; Vikman, Petter; Spégel, Peter; Mulder, Hindrik

2016-01-01

RNA editing is a post-transcriptional alteration of RNA sequences that, via insertions, deletions or base substitutions, can affect protein structure as well as RNA and protein expression. Recently, it has been suggested that RNA editing may be more frequent than previously thought. A great impediment, however, to a deeper understanding of this process is the paramount sequencing effort that needs to be undertaken to identify RNA editing events. Here, we describe an in silico approach, based on machine learning, that ameliorates this problem. Using 41 nucleotide long DNA sequences, we show that novel A-to-I RNA editing events can be predicted from known A-to-I RNA editing events intra- and interspecies. The validity of the proposed method was verified in an independent experimental dataset. Using our approach, 203 202 putative A-to-I RNA editing events were predicted in the whole human genome. Out of these, 9% were previously reported. The remaining sites require further validation, e.g., by targeted deep sequencing. In conclusion, the approach described here is a useful tool to identify potential A-to-I RNA editing events without the requirement of extensive RNA sequencing. PMID:27764195
A genome-editing strategy to treat β-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition.

PubMed

Traxler, Elizabeth A; Yao, Yu; Wang, Yong-Dong; Woodard, Kaitly J; Kurita, Ryo; Nakamura, Yukio; Hughes, Jim R; Hardison, Ross C; Blobel, Gerd A; Li, Chunliang; Weiss, Mitchell J

2016-09-01

Disorders resulting from mutations in the hemoglobin subunit beta gene (HBB; which encodes β-globin), mainly sickle cell disease (SCD) and β-thalassemia, become symptomatic postnatally as fetal γ-globin expression from two paralogous genes, hemoglobin subunit gamma 1 (HBG1) and HBG2, decreases and adult β-globin expression increases, thereby shifting red blood cell (RBC) hemoglobin from the fetal (referred to as HbF or α2γ2) to adult (referred to as HbA or α2β2) form. These disorders are alleviated when postnatal expression of fetal γ-globin is maintained. For example, in hereditary persistence of fetal hemoglobin (HPFH), a benign genetic condition, mutations attenuate γ-globin-to-β-globin switching, causing high-level HbF expression throughout life. Co-inheritance of HPFH with β-thalassemia- or SCD-associated gene mutations alleviates their clinical manifestations. Here we performed CRISPR-Cas9-mediated genome editing of human blood progenitors to mutate a 13-nt sequence that is present in the promoters of the HBG1 and HBG2 genes, thereby recapitulating a naturally occurring HPFH-associated mutation. Edited progenitors produced RBCs with increased HbF levels that were sufficient to inhibit the pathological hypoxia-induced RBC morphology found in SCD. Our findings identify a potential DNA target for genome-editing-mediated therapy of β-hemoglobinopathies.

The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate

PubMed Central

Mooers, Blaine H.M.; Singh, Amritanshu

2011-01-01

Guide RNAs bind antiparallel to their target pre-mRNAs to form editing substrates in reaction cycles that insert or delete uridylates (Us) in most mitochondrial transcripts of trypanosomes. The 5′ end of each guide RNA has an anchor sequence that binds to the pre-mRNA by base-pair complementarity. The template sequence in the middle of the guide RNA directs the editing reactions. The 3′ ends of most guide RNAs have ∼15 contiguous Us that bind to the purine-rich unedited pre-mRNA upstream of the editing site. The resulting U-helix is rich in G·U wobble base pairs. To gain insights into the structure of the U-helix, we crystallized 8 bp of the U-helix in one editing substrate for the A6 mRNA of Trypanosoma brucei. The fragment provides three samples of the 5′-AGA-3′/5′-UUU-3′ base-pair triple. The fusion of two identical U-helices head-to-head promoted crystallization. We obtained X-ray diffraction data with a resolution limit of 1.37 Å. The U-helix had low and high twist angles before and after each G·U wobble base pair; this variation was partly due to shearing of the wobble base pairs as revealed in comparisons with a crystal structure of a 16-nt RNA with all Watson–Crick base pairs. Both crystal structures had wider major grooves at the junction between the poly(U) and polypurine tracts. This junction mimics the junction between the template helix and the U-helix in RNA-editing substrates and may be a site of major groove invasion by RNA editing proteins. PMID:21878548
Bethesda 2014: improving on a paradigm shift.

PubMed

Wilbur, D C; Nayar, R

2015-12-01

The third iteration of the Bethesda System terminology manual was recently published. This update included changes in the reporting of benign endometrial cells, and guidance for special adequacy situations and for cases in which low grade squamous intraepithelial lesions are accompanied by some cells suggesting that a high grade lesion might also be present. In addition, the manual was increased in size to include more illustrations with special studies and comparisons to histology, a greatly increased reference list, and a new chapter devoted to the modern practice of risk-based management. The third edition of the Bethesda manual is meant to serve as a primary reference for the practice of gynecologic cytology designed to provide a uniform system of reporting Worldwide for clinical, teaching, and research purposes. © 2015 John Wiley & Sons Ltd.
Cognitive ability influences on written expression: Evidence for developmental and sex-based differences in school-age children.

PubMed

Hajovsky, Daniel B; Villeneuve, Ethan F; Reynolds, Matthew R; Niileksela, Christopher R; Mason, Benjamin A; Shudak, Nicholas J

2018-04-01

Some studies have demonstrated that the Cattell-Horn-Carroll (CHC) cognitive abilities influence writing; however, little research has investigated whether CHC cognitive abilities influence writing the same way for males and females across grades. We used multiple group structural equation models to investigate whether CHC cognitive ability influences on written expression differed between grades or sex using the Kaufman Assessment Battery for Children, Second Edition and the Kaufman Tests of Educational Achievement, Second Edition co-normed standardization sample data (N=2117). After testing for consistent measurement of cognitive abilities across grades and sex, we tested whether the cognitive ability influences on written expression were moderated by grade level or sex. An important developmental shift was observed equally across sex groups: Learning Efficiency (Gl) influences decreased whereas Crystallized Ability (Gc) influences increased after fourth grade. Further, Short-Term Memory (Gsm) and Retrieval Fluency (Gr) influences on written expression depended on sex at grades 1-4, with larger Gr influences for females and larger Gsm influences for males. We internally replicated our main findings using two different cognitive explanatory models, adding further support for the developmental and sex-based differential cognitive ability influences on writing. Explanatory cognitive models of writing need to incorporate development, and possibly, sex to provide an expanded understanding of writing development and guard against potential generalizability issues characteristic of special population (i.e., male-female) studies. Copyright © 2017 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.
C-to-U editing and site-directed RNA editing for the correction of genetic mutations.

PubMed

Vu, Luyen Thi; Tsukahara, Toshifumi

2017-07-24

Cytidine to uridine (C-to-U) editing is one type of substitutional RNA editing. It occurs in both mammals and plants. The molecular mechanism of C-to-U editing involves the hydrolytic deamination of a cytosine to a uracil base. C-to-U editing is mediated by RNA-specific cytidine deaminases and several complementation factors, which have not been completely identified. Here, we review recent findings related to the regulation and enzymatic basis of C-to-U RNA editing. More importantly, when C-to-U editing occurs in coding regions, it has the power to reprogram genetic information on the RNA level, therefore it has great potential for applications in transcript repair (diseases related to thymidine to cytidine (T>C) or adenosine to guanosine (A>G) point mutations). If it is possible to manipulate or mimic C-to-U editing, T>C or A>G genetic mutation-related diseases could be treated. Enzymatic and non-enzymatic site-directed RNA editing are two different approaches for mimicking C-to-U editing. For enzymatic site-directed RNA editing, C-to-U editing has not yet been successfully performed, and in theory, adenosine to inosine (A-to-I) editing involves the same strategy as C-to-U editing. Therefore, in this review, for applications in transcript repair, we will provide a detailed overview of enzymatic site-directed RNA editing, with a focus on A-to-I editing and non-enzymatic site-directed C-to-U editing.
A Generic Approach for Pen-Based User Interface Development

NASA Astrophysics Data System (ADS)

Macé, Sébastien; Anquetil, Éric

Pen-based interaction is an intuitive way to realize hand drawn structured documents, but few applications take advantage of it. Indeed, the interpretation of the user hand drawn strokes in the context of document is a complex problem. In this paper, we propose a new generic approach to develop such systems based on three independent components. The first one is a set of graphical and editing functions adapted to pen interaction. The second one is a rule-based formalism that models structured document composition and the corresponding interpretation process. The last one is a hand drawn stroke analyzer that is able to interpret strokes progressively, directly while the user is drawing. We highlight in particular the human-computer interaction induced from this progressive interpretation process. Thanks to this generic approach, three pen-based system prototypes have already been developed, for musical score editing, for graph editing, and for UML class diagram editing
Tracking Color Shift in Ballpoint Pen Ink Using Photoshop Assisted Spectroscopy: A Nondestructive Technique Developed to Rehouse a Nobel Laureate's Manuscript

PubMed Central

Wright, Kristi; Herro, Holly

2016-01-01

Many historically and culturally significant documents from the mid-to-late twentieth century were written in ballpoint pen inks, which contain light-sensitive dyes that present problems for collection custodians and paper conservators. The conservation staff at the National Library of Medicine (NLM), National Institutes of Health, conducted a multiphase project on the chemistry and aging of ballpoint pen ink that culminated in the development of a new method to detect aging of ballpoint pen ink while examining a variety of storage environments. NLM staff determined that ballpoint pen ink color shift can be detected noninvasively using image editing software. Instructions are provided on how to detect color shift in digitized materials using a technique developed specifically for this project—Photoshop Assisted Spectroscopy.1 The study results offer collection custodians storage options for historic documents containing ballpoint pen ink. PMID:27587904
Abundant off-target edits from site-directed RNA editing can be reduced by nuclear localization of the editing enzyme.

PubMed

Vallecillo-Viejo, Isabel C; Liscovitch-Brauer, Noa; Montiel-Gonzalez, Maria Fernanda; Eisenberg, Eli; Rosenthal, Joshua J C

2018-01-02

Site-directed RNA editing (SDRE) is a general strategy for making targeted base changes in RNA molecules. Although the approach is relatively new, several groups, including our own, have been working on its development. The basic strategy has been to couple the catalytic domain of an adenosine (A) to inosine (I) RNA editing enzyme to a guide RNA that is used for targeting. Although highly efficient on-target editing has been reported, off-target events have not been rigorously quantified. In this report we target premature termination codons (PTCs) in messages encoding both a fluorescent reporter protein and the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein transiently transfected into human epithelial cells. We demonstrate that while on-target editing is efficient, off-target editing is extensive, both within the targeted message and across the entire transcriptome of the transfected cells. By redirecting the editing enzymes from the cytoplasm to the nucleus, off-target editing is reduced without compromising the on-target editing efficiency. The addition of the E488Q mutation to the editing enzymes, a common strategy for increasing on-target editing efficiency, causes a tremendous increase in off-target editing. These results underscore the need to reduce promiscuity in current approaches to SDRE.
A hammerhead ribozyme substrate and reporter for in vitro kinetoplastid RNA editing.

PubMed Central

Wang, Bingbing; Salavati, Reza; Heidmann, Stefan; Stuart, Kenneth

2002-01-01

Current in vitro assays for RNA editing in kinetoplastids directly examine the products generated by incubation of pre-mRNA substrate with guide RNA (gRNA) and mitochondrial (mt) extract. RNA editing substrates that are modeled on hammerhead ribozymes were designed with catalytic cores that contained or lacked additional uridylates (Us). They proved to be sensitive reporters of editing activity when used for in vitro assays. A deletion editing substrate that is based on A6 pre-mRNA had no ribozyme activity, but its incubation with gRNA and mt extract resulted in its deletion editing and production of a catalytically active ribozyme. Hammerhead ribozymes are thus sensitive tools to assay in vitro RNA editing. PMID:11991648
Spectrally edited 2D 13Csbnd 13C NMR spectra without diagonal ridge for characterizing 13C-enriched low-temperature carbon materials

NASA Astrophysics Data System (ADS)

Johnson, Robert L.; Anderson, Jason M.; Shanks, Brent H.; Fang, Xiaowen; Hong, Mei; Schmidt-Rohr, Klaus

2013-09-01

Two robust combinations of spectral editing techniques with 2D 13Csbnd 13C NMR have been developed for characterizing the aromatic components of 13C-enriched low-temperature carbon materials. One method (exchange with protonated and nonprotonated spectral editing, EXPANSE) selects cross peaks of protonated and nearby nonprotonated carbons, while the other technique, dipolar-dephased double-quantum/single-quantum (DQ/SQ) NMR, selects signals of bonded nonprotonated carbons. Both spectra are free of a diagonal ridge, which has many advantages: Cross peaks on the diagonal or of small intensity can be detected, and residual spinning sidebands or truncation artifacts associated with the diagonal ridge are avoided. In the DQ/SQ experiment, dipolar dephasing of the double-quantum coherence removes protonated-carbon signals; this approach also eliminates the need for high-power proton decoupling. The initial magnetization is generated with minimal fluctuation by combining direct polarization, cross polarization, and equilibration by 13C spin diffusion. The dipolar dephased DQ/SQ spectrum shows signals from all linkages between aromatic rings, including a distinctive peak from polycondensed aromatics. In EXPANSE NMR, signals of protonated carbons are selected in the first spectral dimension by short cross polarization combined with dipolar dephasing difference. This removes ambiguities of peak assignment to overlapping signals of nonprotonated and protonated aromatic carbons, e.g. near 125 ppm. Spin diffusion is enhanced by dipolar-assisted rotational resonance. Before detection, Csbnd H dipolar dephasing by gated decoupling is applied, which selects signals of nonprotonated carbons. Thus, only cross peaks due to magnetization originating from protonated C and ending on nearby nonprotonated C are retained. Combined with the chemical shifts deduced from the cross-peak position, this double spectral editing defines the bonding environment of aromatic, COO, and Cdbnd O carbons, which is particularly useful for identifying furan and arene rings. The Cdbnd O carbons, whose chemical shifts vary strongly (between 212 and 165 ppm) and systematically depend on their two bonding partners, show particularly informative cross peaks, given that one bonding partner is defined by the other frequency coordinate of the cross peak. The new techniques and the information content of the resulting spectra are validated on sulfuric-acid treated low-temperature carbon materials and on products of the Maillard reaction. The crucial need for spectral editing for correct peak assignment is demonstrated in an example.
Scalable and Versatile Genome Editing Using Linear DNAs with Microhomology to Cas9 Sites in Caenorhabditis elegans

PubMed Central

Paix, Alexandre; Wang, Yuemeng; Smith, Harold E.; Lee, Chih-Yung S.; Calidas, Deepika; Lu, Tu; Smith, Jarrett; Schmidt, Helen; Krause, Michael W.; Seydoux, Geraldine

2014-01-01

Homology-directed repair (HDR) of double-strand DNA breaks is a promising method for genome editing, but is thought to be less efficient than error-prone nonhomologous end joining in most cell types. We have investigated HDR of double-strand breaks induced by CRISPR-associated protein 9 (Cas9) in Caenorhabditis elegans. We find that HDR is very robust in the C. elegans germline. Linear repair templates with short (∼30–60 bases) homology arms support the integration of base and gene-sized edits with high efficiency, bypassing the need for selection. Based on these findings, we developed a systematic method to mutate, tag, or delete any gene in the C. elegans genome without the use of co-integrated markers or long homology arms. We generated 23 unique edits at 11 genes, including premature stops, whole-gene deletions, and protein fusions to antigenic peptides and GFP. Whole-genome sequencing of five edited strains revealed the presence of passenger variants, but no mutations at predicted off-target sites. The method is scalable for multi-gene editing projects and could be applied to other animals with an accessible germline. PMID:25249454
Genome editing of Ralstonia eutropha using an electroporation-based CRISPR-Cas9 technique.

PubMed

Xiong, Bin; Li, Zhongkang; Liu, Li; Zhao, Dongdong; Zhang, Xueli; Bi, Changhao

2018-01-01

Ralstonia eutropha is an important bacterium for the study of polyhydroxyalkanoates (PHAs) synthesis and CO 2 fixation, which makes it a potential strain for industrial PHA production and attractive host for CO 2 conversion. Although the bacterium is not recalcitrant to genetic manipulation, current methods for genome editing based on group II introns or single crossover integration of a suicide plasmid are inefficient and time-consuming, which limits the genetic engineering of this organism. Thus, developing an efficient and convenient method for R. eutropha genome editing is imperative. An efficient genome editing method for R. eutropha was developed using an electroporation-based CRISPR-Cas9 technique. In our study, the electroporation efficiency of R. eutropha was found to be limited by its restriction-modification (RM) systems. By searching the putative RM systems in R. eutropha H16 using REBASE database and comparing with that in E. coli MG1655, five putative restriction endonuclease genes which are related to the RM systems in R. eutropha were predicated and disrupted. It was found that deletion of H16_A0006 and H16_A0008 - 9 increased the electroporation efficiency 1658 and 4 times, respectively. Fructose was found to reduce the leaky expression of the arabinose-inducible pBAD promoter, which was used to optimize the expression of cas9 , enabling genome editing via homologous recombination based on CRISPR-Cas9 in R. eutropha . A total of five genes were edited with efficiencies ranging from 78.3 to 100%. The CRISPR-Cpf1 system and the non-homologous end joining mechanism were also investigated, but failed to yield edited strains. We present the first genome editing method for R. eutropha using an electroporation-based CRISPR-Cas9 approach, which significantly increased the efficiency and decreased time to manipulate this facultative chemolithoautotrophic microbe. The novel technique will facilitate more advanced researches and applications of R. eutropha for PHA production and CO 2 conversion.
Joint Confirmatory Factor Analysis of the Woodcock-Johnson Tests of Cognitive Abilities, Third Edition, and the Stanford-Binet Intelligence Scales, Fifth Edition, with a Preschool Population

ERIC Educational Resources Information Center

Chang, Mei; Paulson, Sharon E.; Finch, W. Holmes; Mcintosh, David E.; Rothlisberg, Barbara A.

2014-01-01

This study examined the underlying constructs measured by the Woodcock-Johnson Tests of Cognitive Abilities, Third Edition (WJ-III COG) and the Stanford-Binet Intelligence Scales, Fifth Edition (SB5), based on the Cattell-Horn-Carrol (CHC) theory of cognitive abilities. This study reports the results of the first joint confirmatory factor analysis…
Education-Stratified Base-Rate Information on Discrepancy Scores Within and Between the Wechsler Adult Intelligence Scale-Third Edition and the Wechsler Memory Scale-Third Edition

ERIC Educational Resources Information Center

Dori, Galit A.; Chelune, Gordon J.

2004-01-01

The Wechsler Adult Intelligence Scale--Third Edition (WAIS-III; D. Wechsler, 1997a) and the Wechsler Memory Scale--Third Edition (WMS-III; D. Wechsler, 1997b) are 2 of the most frequently used measures in psychology and neuropsychology. To facilitate the diagnostic use of these measures in the clinical decision-making process, this article…
The clinical applications of genome editing in HIV.

PubMed

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. © 2016 by The American Society of Hematology.
Alu elements shape the primate transcriptome by cis-regulation of RNA editing

PubMed Central

2014-01-01

Background RNA editing by adenosine to inosine deamination is a widespread phenomenon, particularly frequent in the human transcriptome, largely due to the presence of inverted Alu repeats and their ability to form double-stranded structures – a requisite for ADAR editing. While several hundred thousand editing sites have been identified within these primate-specific repeats, the function of Alu-editing has yet to be elucidated. Results We show that inverted Alu repeats, expressed in the primate brain, can induce site-selective editing in cis on sites located several hundred nucleotides from the Alu elements. Furthermore, a computational analysis, based on available RNA-seq data, finds that site-selective editing occurs significantly closer to edited Alu elements than expected. These targets are poorly edited upon deletion of the editing inducers, as well as in homologous transcripts from organisms lacking Alus. Sequences surrounding sites near edited Alus in UTRs, have been subjected to a lesser extent of evolutionary selection than those far from edited Alus, indicating that their editing generally depends on cis-acting Alus. Interestingly, we find an enrichment of primate-specific editing within encoded sequence or the UTRs of zinc finger-containing transcription factors. Conclusions We propose a model whereby primate-specific editing is induced by adjacent Alu elements that function as recruitment elements for the ADAR editing enzymes. The enrichment of site-selective editing with potentially functional consequences on the expression of transcription factors indicates that editing contributes more profoundly to the transcriptomic regulation and repertoire in primates than previously thought. PMID:24485196
Towards social acceptance of plant breeding by genome editing.

PubMed

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. Copyright © 2015 Elsevier Ltd. All rights reserved.
[CRISPR/Cas system for genome editing in pluripotent stem cells].

PubMed

Vasil'eva, E A; Melino, D; Barlev, N A

2015-01-01

Genome editing systems based on site-specific nucleases became very popular for genome editing in modern bioengineering. Human pluripotent stem cells provide a unique platform for genes function study, disease modeling, and drugs testing. Consequently, technology for fast, accurate and well controlled genome manipulation is required. CRISPR/Cas (clustered regularly interspaced short palindromic repeat/CRISPR-associated) system could be employed for these purposes. This system is based on site-specific programmable nuclease Cas9. Numerous advantages of the CRISPR/Cas system and its successful application to human stem cells provide wide opportunities for genome therapy and regeneration medicine. In this publication, we describe and compare the main genome editing systems based on site-specific programmable nucleases and discuss opportunities and perspectives of the CRISPR/Cas system for application to pluripotent stem cells.
Complete 13C NMR chemical shifts assignment for cholesterol crystals by combined CP-MAS spectral editing and ab initio GIPAW calculations with dispersion forces.

PubMed

Küçükbenli, Emine; Sonkar, Kanchan; Sinha, Neeraj; de Gironcoli, Stefano

2012-04-12

We report here the first fully ab initio determination of (13)C NMR spectra for several crystal structures of cholesterol, observed in various biomaterials. We combine Gauge-Including Projector Augmented Waves (GIPAW) calculations at relaxed structures, fully including dispersion forces, with Magic Angle Spinning Solid State NMR experiments and spectral editing to achieve a detailed interpretation of the complex NMR spectra of cholesterol crystals. By introducing an environment-dependent secondary referencing scheme in our calculations, not only do we reproduce the characteristic spectral features of the different crystalline polymorphs, thus clearly discriminating among them, but also closely represent the spectrum in the region of several highly overlapping peaks. This, in combination with spectral editing, allows us to provide a complete peak assignment for monohydrate (ChM) and low-temperature anhydrous (ChAl) crystal polymorphs. Our results show that the synergy between ab initio calculations and refined experimental techniques can be exploited for an accurate and efficient NMR crystallography of complex systems of great interest for biomaterial studies. The method is general in nature and can be applied for studies of various complex biomaterials.
Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation

PubMed Central

Tang, Weixin; Hu, Johnny H.; Liu, David R.

2017-01-01

Programmable sequence-specific genome editing agents such as CRISPR-Cas9 have greatly advanced our ability to manipulate the human genome. Although canonical forms of genome-editing agents and programmable transcriptional regulators are constitutively active, precise temporal and spatial control over genome editing and transcriptional regulation activities would enable the more selective and potentially safer use of these powerful technologies. Here, by incorporating ligand-responsive self-cleaving catalytic RNAs (aptazymes) into guide RNAs, we developed a set of aptazyme-embedded guide RNAs that enable small molecule-controlled nuclease-mediated genome editing and small molecule-controlled base editing, as well as small molecule-dependent transcriptional activation in mammalian cells. PMID:28656978
On the evaluation of segmentation editing tools

PubMed Central

Heckel, Frank; Moltz, Jan H.; Meine, Hans; Geisler, Benjamin; Kießling, Andreas; D’Anastasi, Melvin; dos Santos, Daniel Pinto; Theruvath, Ashok Joseph; Hahn, Horst K.

2014-01-01

Abstract. Efficient segmentation editing tools are important components in the segmentation process, as no automatic methods exist that always generate sufficient results. Evaluating segmentation editing algorithms is challenging, because their quality depends on the user’s subjective impression. So far, no established methods for an objective, comprehensive evaluation of such tools exist and, particularly, intermediate segmentation results are not taken into account. We discuss the evaluation of editing algorithms in the context of tumor segmentation in computed tomography. We propose a rating scheme to qualitatively measure the accuracy and efficiency of editing tools in user studies. In order to objectively summarize the overall quality, we propose two scores based on the subjective rating and the quantified segmentation quality over time. Finally, a simulation-based evaluation approach is discussed, which allows a more reproducible evaluation without the need for human input. This automated evaluation complements user studies, allowing a more convincing evaluation, particularly during development, where frequent user studies are not possible. The proposed methods have been used to evaluate two dedicated editing algorithms on 131 representative tumor segmentations. We show how the comparison of editing algorithms benefits from the proposed methods. Our results also show the correlation of the suggested quality score with the qualitative ratings. PMID:26158063

Therapeutic gene editing: delivery and regulatory perspectives.

PubMed

Shim, Gayong; Kim, Dongyoon; Park, Gyu Thae; Jin, Hyerim; Suh, Soo-Kyung; Oh, Yu-Kyoung

2017-06-01

Gene-editing technology is an emerging therapeutic modality for manipulating the eukaryotic genome by using target-sequence-specific engineered nucleases. Because of the exceptional advantages that gene-editing technology offers in facilitating the accurate correction of sequences in a genome, gene editing-based therapy is being aggressively developed as a next-generation therapeutic approach to treat a wide range of diseases. However, strategies for precise engineering and delivery of gene-editing nucleases, including zinc finger nucleases, transcription activator-like effector nuclease, and CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats-associated nuclease Cas9), present major obstacles to the development of gene-editing therapies, as with other gene-targeting therapeutics. Currently, viral and non-viral vectors are being studied for the delivery of these nucleases into cells in the form of DNA, mRNA, or proteins. Clinical trials are already ongoing, and in vivo studies are actively investigating the applicability of CRISPR/Cas9 techniques. However, the concept of correcting the genome poses major concerns from a regulatory perspective, especially in terms of safety. This review addresses current research trends and delivery strategies for gene editing-based therapeutics in non-clinical and clinical settings and considers the associated regulatory issues.
Therapeutic gene editing: delivery and regulatory perspectives

PubMed Central

Shim, Gayong; Kim, Dongyoon; Park, Gyu Thae; Jin, Hyerim; Suh, Soo-Kyung; Oh, Yu-Kyoung

2017-01-01

Gene-editing technology is an emerging therapeutic modality for manipulating the eukaryotic genome by using target-sequence-specific engineered nucleases. Because of the exceptional advantages that gene-editing technology offers in facilitating the accurate correction of sequences in a genome, gene editing-based therapy is being aggressively developed as a next-generation therapeutic approach to treat a wide range of diseases. However, strategies for precise engineering and delivery of gene-editing nucleases, including zinc finger nucleases, transcription activator-like effector nuclease, and CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats-associated nuclease Cas9), present major obstacles to the development of gene-editing therapies, as with other gene-targeting therapeutics. Currently, viral and non-viral vectors are being studied for the delivery of these nucleases into cells in the form of DNA, mRNA, or proteins. Clinical trials are already ongoing, and in vivo studies are actively investigating the applicability of CRISPR/Cas9 techniques. However, the concept of correcting the genome poses major concerns from a regulatory perspective, especially in terms of safety. This review addresses current research trends and delivery strategies for gene editing-based therapeutics in non-clinical and clinical settings and considers the associated regulatory issues. PMID:28392568
50 CFR Appendix C to Part 404 - Boundary Coordinated for Papaha

Code of Federal Regulations, 2012 CFR

2012-10-01

..., 2008 edition; 19019, 2008 edition; 19022, 2008 edition. These charts are based on World Geodetic System... 26°51′.13 173°33′.69 76 26°50′.75 173°30′.87 Table C-3—Gardner Pinnacles, French Frigate Shoals, and...
50 CFR Appendix C to Part 404 - Boundary Coordinated for Papaha

Code of Federal Regulations, 2014 CFR

2014-10-01

..., 2008 edition; 19019, 2008 edition; 19022, 2008 edition. These charts are based on World Geodetic System... 26°51′.13 173°33′.69 76 26°50′.75 173°30′.87 Table C-3—Gardner Pinnacles, French Frigate Shoals, and...
Infusion Nursing: An Evidence-Based Approach - Third edition Alexander Mary Infusion Nursing: An Evidence-Based Approach - Third edition 625pp Elsevier 9781416064107 1416064109 [Formula: see text].

PubMed

2010-11-03

This book considers all aspects of infusion therapy and provides a solid evidence base. Its 30 chapters are well organised into six sections covering physiological considerations, infusion therapies and nursing practice.
A novel technique based on in vitro oocyte injection to improve CRISPR/Cas9 gene editing in zebrafish

PubMed Central

Xie, Shao-Lin; Bian, Wan-Ping; Wang, Chao; Junaid, Muhammad; Zou, Ji-Xing; Pei, De-Sheng

2016-01-01

Contemporary improvements in the type II clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system offer a convenient way for genome editing in zebrafish. However, the low efficiencies of genome editing and germline transmission require a time-intensive and laborious screening work. Here, we reported a method based on in vitro oocyte storage by injecting oocytes in advance and incubating them in oocyte storage medium to significantly improve the efficiencies of genome editing and germline transmission by in vitro fertilization (IVF) in zebrafish. Compared to conventional methods, the prior micro-injection of zebrafish oocytes improved the efficiency of genome editing, especially for the sgRNAs with low targeting efficiency. Due to high throughputs, simplicity and flexible design, this novel strategy will provide an efficient alternative to increase the speed of generating heritable mutants in zebrafish by using CRISPR/Cas9 system. PMID:27680290
A trace display and editing program for data from fluorescence based sequencing machines.

PubMed

Gleeson, T; Hillier, L

1991-12-11

'Ted' (Trace editor) is a graphical editor for sequence and trace data from automated fluorescence sequencing machines. It provides facilities for viewing sequence and trace data (in top or bottom strand orientation), for editing the base sequence, for automated or manual trimming of the head (vector) and tail (uncertain data) from the sequence, for vertical and horizontal trace scaling, for keeping a history of sequence editing, and for output of the edited sequence. Ted has been used extensively in the C.elegans genome sequencing project, both as a stand-alone program and integrated into the Staden sequence assembly package, and has greatly aided in the efficiency and accuracy of sequence editing. It runs in the X windows environment on Sun workstations and is available from the authors. Ted currently supports sequence and trace data from the ABI 373A and Pharmacia A.L.F. sequencers.
Human cancer tissues exhibit reduced A-to-I editing of miRNAs coupled with elevated editing of their targets

PubMed Central

Pinto, Yishay; Buchumenski, Ilana

2018-01-01

Abstract A-to-I RNA editing is an important post-transcriptional modification, known to be altered in tumors. It targets dozens of sites within miRNAs, some of which impact miRNA biogenesis and function, as well as many miRNA recognition sites. However, the full extent of the effect of editing on regulation by miRNAs and its behavior in human cancers is still unknown. Here we systematically characterized miRNA editing in 10 593 human samples across 32 cancer types and normal controls. We find that the majority of previously reported sites show little to no evidence for editing in this dataset, compile a list of 58 reliable miRNA editing sites, and study them across normal and cancer samples. Edited miRNA versions tend to suppress expression of known oncogenes, and, consistently, we observe a clear global tendency for hypo-editing in tumors, in strike contrast to the behavior for mRNA editing, allowing an accurate classification of normal/tumor samples based on their miRNA editing profile. In many cancers this profile correlates with patients' survival. Finally, thousands of miRNA binding sites are differentially edited in cancer. Our study thus establishes the important effect of RNA editing on miRNA-regulation in the tumor cell, with prospects for diagnostic and prognostic applications. PMID:29165639
[Genome-editing: focus on the off-target effects].

PubMed

He, Xiubin; Gu, Feng

2017-10-25

Breakthroughs of genome-editing in recent years have paved the way to develop new therapeutic strategies. These genome-editing tools mainly include Zinc-finger nucleases (ZFNs), Transcription activator-like effector nucleases (TALENs), and clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas-based RNA-guided DNA endonucleases. However, off-target effects are still the major issue in genome editing, and limit the application in gene therapy. Here, we summarized the cause and compared different detection methods of off-targets.
Data-Base Software For Tracking Technological Developments

NASA Technical Reports Server (NTRS)

Aliberti, James A.; Wright, Simon; Monteith, Steve K.

1996-01-01

Technology Tracking System (TechTracS) computer program developed for use in storing and retrieving information on technology and related patent information developed under auspices of NASA Headquarters and NASA's field centers. Contents of data base include multiple scanned still images and quick-time movies as well as text. TechTracS includes word-processing, report-editing, chart-and-graph-editing, and search-editing subprograms. Extensive keyword searching capabilities enable rapid location of technologies, innovators, and companies. System performs routine functions automatically and serves multiple users.
Genome editing systems in novel therapies.

PubMed

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.
The Role of Edited Collections in Composition Studies.

ERIC Educational Resources Information Center

Micciche, Laura

2001-01-01

Describes general characteristics of edited collections and then offers a brief history of the genre in composition studies based in part on the existing data in CompPile, an online and ongoing bibliography. Explores several explanations for the proliferation of edited collections in the field. Makes note of what these explanations can say about…
Handbook of Research in Education Finance and Policy, 2nd Edition

ERIC Educational Resources Information Center

Ladd, Helen F., Ed.; Goertz, Margaret E., Ed.

2015-01-01

Sponsored by the Association for Education Finance and Policy (AEFP), the second edition of this groundbreaking handbook assembles in one place the existing research-based knowledge in education finance and policy, with particular attention to elementary and secondary education. Chapters from the first edition have been fully updated and revised…
The Kamusi Project Edit Engine: A Tool for Collaborative Lexicography.

ERIC Educational Resources Information Center

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,…
Civil Technology Applications. Teacher Edition [and] Student Edition.

ERIC Educational Resources Information Center

Schertz, Karen

Teacher and student editions of Civil Technology Applications are one in a series of competency-based instructional materials for drafting and civil technology programs. It includes the technical content and tasks necessary for a student to be employed as a drafter or civil technician in a civil engineering firm. Introductory pages in the teacher…
Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs.

PubMed

Jenko, Janez; Gorjanc, Gregor; Cleveland, Matthew A; Varshney, Rajeev K; Whitelaw, C Bruce A; Woolliams, John A; Hickey, John M

2015-07-02

Genome editing (GE) is a method that enables specific nucleotides in the genome of an individual to be changed. To date, use of GE in livestock has focussed on simple traits that are controlled by a few quantitative trait nucleotides (QTN) with large effects. The aim of this study was to evaluate the potential of GE to improve quantitative traits that are controlled by many QTN, referred to here as promotion of alleles by genome editing (PAGE). Multiple scenarios were simulated to test alternative PAGE strategies for a quantitative trait. They differed in (i) the number of edits per sire (0 to 100), (ii) the number of edits per generation (0 to 500), and (iii) the extent of use of PAGE (i.e. editing all sires or only a proportion of them). The base line scenario involved selecting individuals on true breeding values (i.e., genomic selection only (GS only)-genomic selection with perfect accuracy) for several generations. Alternative scenarios complemented this base line scenario with PAGE (GS + PAGE). The effect of different PAGE strategies was quantified by comparing response to selection, changes in allele frequencies, the number of distinct QTN edited, the sum of absolute effects of the edited QTN per generation, and inbreeding. Response to selection after 20 generations was between 1.08 and 4.12 times higher with GS + PAGE than with GS only. Increases in response to selection were larger with more edits per sire and more sires edited. When the total resources for PAGE were limited, editing a few sires for many QTN resulted in greater response to selection and inbreeding compared to editing many sires for a few QTN. Between the scenarios GS only and GS + PAGE, there was little difference in the average change in QTN allele frequencies, but there was a major difference for the QTN with the largest effects. The sum of the effects of the edited QTN decreased across generations. This study showed that PAGE has great potential for application in livestock breeding programs, but inbreeding needs to be managed.
REDIdb: the RNA editing database.

PubMed

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.
Examining End-Of-Chapter Problems Across Editions of an Introductory Calculus-Based Physics Textbook

NASA Astrophysics Data System (ADS)

Xiao, Bin

End-Of-Chapter (EOC) problems have been part of many physics education studies. Typically, only problems "localized" as relevant to a single chapter were used. This work examines how well this type of problem represents all EOC problems and whether EOC problems found in leading textbooks have changed over the past several decades. To investigate whether EOC problems have connections between chapters, I solved all problems of the E&M; chapters of the most recent edition of a popular introductory level calculus-based textbook and coded the equations used to solve each problem. These results were compared to the first edition of the same text. Also, several relevant problem features were coded for those problems and results were compared for sample chapters across all editions. My findings include two parts. The result of equation usage shows that problems in the E&M; chapters do use equations from both other E&M; chapters and non-E&M; chapters. This out-of-chapter usage increased from the first edition to the last edition. Information about the knowledge structure of E&M; chapters was also revealed. The results of the problem feature study show that most EOC problems have common features but there was an increase of diversity in some of the problem features across editions.
PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.

PubMed

Lee, Woonghee; Kim, Jin Hae; Westler, William M; Markley, John L

2011-06-15

PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY ((13)C-edited and/or (15)N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/.
Comprehensive protocols for CRISPR/Cas9-based gene editing in human pluripotent stem cells

PubMed Central

Santos, David P.; Kiskinis, Evangelos; Eggan, Kevin; Merkle, Florian T.

2016-01-01

Application of the CRISPR/Cas9 system to edit the genomes of human pluripotent stem cells (hPSCs) has the potential to revolutionize hPSC-based disease modeling, drug screening, and transplantation therapy. Here, we aim to provide a single resource to enable groups, even those with limited experience with hPSC culture or the CRISPR/Cas9 system, to successfully perform genome editing. The methods are presented in detail and are supported by a theoretical framework to allow for the incorporation of inevitable improvements in the rapidly evolving gene-editing field. We describe protocols to generate hPSC lines with gene-specific knock-outs, small targeted mutations, or knock-in reporters. PMID:27532820

Precision genome editing using CRISPR-Cas9 and linear repair templates in C. elegans.

PubMed

Paix, Alexandre; Folkmann, Andrew; Seydoux, Geraldine

2017-05-15

The ability to introduce targeted edits in the genome of model organisms is revolutionizing the field of genetics. State-of-the-art methods for precision genome editing use RNA-guided endonucleases to create double-strand breaks (DSBs) and DNA templates containing the edits to repair the DSBs. Following this strategy, we have developed a protocol to create precise edits in the C. elegans genome. The protocol takes advantage of two innovations to improve editing efficiency: direct injection of CRISPR-Cas9 ribonucleoprotein complexes and use of linear DNAs with short homology arms as repair templates. The protocol requires no cloning or selection, and can be used to generate base and gene-size edits in just 4days. Point mutations, insertions, deletions and gene replacements can all be created using the same experimental pipeline. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
Non-viral delivery of genome-editing nucleases for gene therapy.

PubMed

Wang, M; Glass, Z A; Xu, Q

2017-03-01

Manipulating the genetic makeup of mammalian cells using programmable nuclease-based genome-editing technology has recently evolved into a powerful avenue that holds great potential for treating genetic disorders. There are four types of genome-editing nucleases, including meganucleases, zinc finger nucleases, transcription activator-like effector nucleases and clustered, regularly interspaced, short palindromic repeat-associated nucleases such as Cas9. These nucleases have been harnessed to introduce precise and specific changes of the genome sequence at virtually any genome locus of interest. The therapeutic relevance of these genome-editing technologies, however, is challenged by the safe and efficient delivery of nuclease into targeted cells. Herein, we summarize recent advances that have been made on non-viral delivery of genome-editing nucleases. In particular, we focus on non-viral delivery of Cas9/sgRNA ribonucleoproteins for genome editing. In addition, the future direction for developing non-viral delivery of programmable nucleases for genome editing is discussed.
The use of delay in multitrack production

NASA Astrophysics Data System (ADS)

Case, Alexander U.

2003-04-01

Delay, inevitable whenever sound propagates through space, is too often the bane of the acoustician's practice. An audible echo generally relegates a music performance hall-no matter how beautiful it otherwise might sound-to the lowest status. Multitrack music production on the other hand, with its aggressive use of overdubbing, editing, and signal processing, is not bound by those rules of time and space which determine the sound of a hall. In the recording studio, where music is synthesized for playback over loudspeakers, the delay is employed as a powerful, multipurpose tool. It is not avoided. It is in fact embraced. Echoes are used on purpose, strategically, to enhance the loudspeaker listening experience. Moreover, the humble delay is the basis for many nonecho effects. Flanging, chorus, and pitch shifting are delay-based effects regularly used in audio engineering practice. This paper discusses some of the more common delay-based effects, reviewing their technical structure, the psychoacoustic motivation behind them, and the musical value they create.
An iterative method for airway segmentation using multiscale leakage detection

NASA Astrophysics Data System (ADS)

Nadeem, Syed Ahmed; Jin, Dakai; Hoffman, Eric A.; Saha, Punam K.

2017-02-01

There are growing applications of quantitative computed tomography for assessment of pulmonary diseases by characterizing lung parenchyma as well as the bronchial tree. Many large multi-center studies incorporating lung imaging as a study component are interested in phenotypes relating airway branching patterns, wall-thickness, and other morphological measures. To our knowledge, there are no fully automated airway tree segmentation methods, free of the need for user review. Even when there are failures in a small fraction of segmentation results, the airway tree masks must be manually reviewed for all results which is laborious considering that several thousands of image data sets are evaluated in large studies. In this paper, we present a CT-based novel airway tree segmentation algorithm using iterative multi-scale leakage detection, freezing, and active seed detection. The method is fully automated requiring no manual inputs or post-segmentation editing. It uses simple intensity based connectivity and a new leakage detection algorithm to iteratively grow an airway tree starting from an initial seed inside the trachea. It begins with a conservative threshold and then, iteratively shifts toward generous values. The method was applied on chest CT scans of ten non-smoking subjects at total lung capacity and ten at functional residual capacity. Airway segmentation results were compared to an expert's manually edited segmentations. Branch level accuracy of the new segmentation method was examined along five standardized segmental airway paths (RB1, RB4, RB10, LB1, LB10) and two generations beyond these branches. The method successfully detected all branches up to two generations beyond these segmental bronchi with no visual leakages.
Education-stratified base-rate information on discrepancy scores within and between the Wechsler Adult Intelligence Scale--Third Edition and the Wechsler Memory Scale--Third Edition.

PubMed

Dori, Galit A; Chelune, Gordon J

2004-06-01

The Wechsler Adult Intelligence Scale--Third Edition (WAIS-III; D. Wechsler, 1997a) and the Wechsler Memory Scale--Third Edition (WMS-III; D. Wechsler, 1997b) are 2 of the most frequently used measures in psychology and neuropsychology. To facilitate the diagnostic use of these measures in the clinical decision-making process, this article provides information on education-stratified, directional prevalence rates (i.e., base rates) of discrepancy scores between the major index scores for the WAIS-III, the WMS-III, and between the WAIS-III and WMS-III. To illustrate how such base-rate data can be clinically used, this article reviews the relative risk (i.e., odds ratio) of empirically defined "rare" cognitive deficits in 2 of the clinical samples presented in the WAIS-III--WMS-III Technical Manual (The Psychological Corporation, 1997). ((c) 2004 APA, all rights reserved)
An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species

PubMed Central

Hung, Li-Yuan; Chen, Yen-Ju; Mai, Te-Lun; Chen, Chia-Ying; Yang, Min-Yu; Chiang, Tai-Wei; Wang, Yi-Da

2018-01-01

Abstract Adenosine-to-inosine (A-to-I) editing is widespread across the kingdom Metazoa. However, for the lack of comprehensive analysis in nonmodel animals, the evolutionary history of A-to-I editing remains largely unexplored. Here, we detect high-confidence editing sites using clustering and conservation strategies based on RNA sequencing data alone, without using single-nucleotide polymorphism information or genome sequencing data from the same sample. We thereby unveil the first evolutionary landscape of A-to-I editing maps across 20 metazoan species (from worm to human), providing unprecedented evidence on how the editing mechanism gradually expands its territory and increases its influence along the history of evolution. Our result revealed that highly clustered and conserved editing sites tended to have a higher editing level and a higher magnitude of the ADAR motif. The ratio of the frequencies of nonsynonymous editing to that of synonymous editing remarkably increased with increasing the conservation level of A-to-I editing. These results thus suggest potentially functional benefit of highly clustered and conserved editing sites. In addition, spatiotemporal dynamics analyses reveal a conserved enrichment of editing and ADAR expression in the central nervous system throughout more than 300 Myr of divergent evolution in complex animals and the comparability of editing patterns between invertebrates and between vertebrates during development. This study provides evolutionary and dynamic aspects of A-to-I editome across metazoan species, expanding this important but understudied class of nongenomically encoded events for comprehensive characterization. PMID:29294013
Special-effect edit detection using VideoTrails: a comparison with existing techniques

NASA Astrophysics Data System (ADS)

Kobla, Vikrant; DeMenthon, Daniel; Doermann, David S.

1998-12-01

Video segmentation plays an integral role in many multimedia applications, such as digital libraries, content management systems, and various other video browsing, indexing, and retrieval systems. Many algorithms for segmentation of video have appeared within the past few years. Most of these algorithms perform well on cuts, but yield poor performance on gradual transitions or special effects edits. A complete video segmentation system must also achieve good performance on special effect edit detection. In this paper, we discuss the performance of our Video Trails-based algorithms, with other existing special effect edit-detection algorithms within the literature. Results from experiments testing for the ability to detect edits from TV programs, ranging from commercials to news magazine programs, including diverse special effect edits, which we have introduced.
High-efficiency CRISPR/Cas9 multiplex gene editing using the glycine tRNA-processing system-based strategy in maize.

PubMed

Qi, Weiwei; Zhu, Tong; Tian, Zhongrui; Li, Chaobin; Zhang, Wei; Song, Rentao

2016-08-11

CRISPR/Cas9 genome editing strategy has been applied to a variety of species and the tRNA-processing system has been used to compact multiple gRNAs into one synthetic gene for manipulating multiple genes in rice. We optimized and introduced the multiplex gene editing strategy based on the tRNA-processing system into maize. Maize glycine-tRNA was selected to design multiple tRNA-gRNA units for the simultaneous production of numerous gRNAs under the control of one maize U6 promoter. We designed three gRNAs for simplex editing and three multiple tRNA-gRNA units for multiplex editing. The results indicate that this system not only increased the number of targeted sites but also enhanced mutagenesis efficiency in maize. Additionally, we propose an advanced sequence selection of gRNA spacers for relatively more efficient and accurate chromosomal fragment deletion, which is important for complete abolishment of gene function especially long non-coding RNAs (lncRNAs). Our results also indicated that up to four tRNA-gRNA units in one expression cassette design can still work in maize. The examples reported here demonstrate the utility of the tRNA-processing system-based strategy as an efficient multiplex genome editing tool to enhance maize genetic research and breeding.
CRISPR/Cas9-Advancing Orthopoxvirus Genome Editing for Vaccine and Vector Development.

PubMed

Okoli, Arinze; Okeke, Malachy I; Tryland, Morten; Moens, Ugo

2018-01-22

The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (Cas9) technology is revolutionizing genome editing approaches. Its high efficiency, specificity, versatility, flexibility, simplicity and low cost have made the CRISPR/Cas9 system preferable to other guided site-specific nuclease-based systems such as TALENs (Transcription Activator-like Effector Nucleases) and ZFNs (Zinc Finger Nucleases) in genome editing of viruses. CRISPR/Cas9 is presently being applied in constructing viral mutants, preventing virus infections, eradicating proviral DNA, and inhibiting viral replication in infected cells. The successful adaptation of CRISPR/Cas9 to editing the genome of Vaccinia virus paves the way for its application in editing other vaccine/vector-relevant orthopoxvirus (OPXV) strains. Thus, CRISPR/Cas9 can be used to resolve some of the major hindrances to the development of OPXV-based recombinant vaccines and vectors, including sub-optimal immunogenicity; transgene and genome instability; reversion of attenuation; potential of spread of transgenes to wildtype strains and close contacts, which are important biosafety and risk assessment considerations. In this article, we review the published literature on the application of CRISPR/Cas9 in virus genome editing and discuss the potentials of CRISPR/Cas9 in advancing OPXV-based recombinant vaccines and vectors. We also discuss the application of CRISPR/Cas9 in combating viruses of clinical relevance, the limitations of CRISPR/Cas9 and the current strategies to overcome them.
The dynamic nature of conflict in Wikipedia

NASA Astrophysics Data System (ADS)

Gandica, Y.; Sampaio dos Aidos, F.; Carvalho, J.

2014-10-01

The voluntary process of Wikipedia edition provides an environment in which the outcome is clearly a collective product of interactions involving a large number of people. We propose a simple agent-based model, developed from real data, to reproduce the collaborative process of Wikipedia edition. With a small number of simple ingredients, our model mimics several interesting features of real human behaviour, namely in the context of edit wars. We show that the level of conflict is determined by a tolerance parameter, which measures the editors' capability to accept different opinions and to change their own opinion. We propose to measure conflict with a parameter based on mutual reverts, which increases only in contentious situations. Using this parameter, we find a distribution for the inter-peace periods that is heavy tailed. The effects of wiki-robots in the conflict levels and in the edition patterns are also studied. Our findings are compared with previous parameters used to measure conflicts in edit wars.
Multiplexed precision genome editing with trackable genomic barcodes in yeast.

PubMed

Roy, Kevin R; Smith, Justin D; Vonesch, Sibylle C; Lin, Gen; Tu, Chelsea Szu; Lederer, Alex R; Chu, Angela; Suresh, Sundari; Nguyen, Michelle; Horecka, Joe; Tripathi, Ashutosh; Burnett, Wallace T; Morgan, Maddison A; Schulz, Julia; Orsley, Kevin M; Wei, Wu; Aiyar, Raeka S; Davis, Ronald W; Bankaitis, Vytas A; Haber, James E; Salit, Marc L; St Onge, Robert P; Steinmetz, Lars M

2018-07-01

Our understanding of how genotype controls phenotype is limited by the scale at which we can precisely alter the genome and assess the phenotypic consequences of each perturbation. Here we describe a CRISPR-Cas9-based method for multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) in Saccharomyces cerevisiae. MAGESTIC uses array-synthesized guide-donor oligos for plasmid-based high-throughput editing and features genomic barcode integration to prevent plasmid barcode loss and to enable robust phenotyping. We demonstrate that editing efficiency can be increased more than fivefold by recruiting donor DNA to the site of breaks using the LexA-Fkh1p fusion protein. We performed saturation editing of the essential gene SEC14 and identified amino acids critical for chemical inhibition of lipid signaling. We also constructed thousands of natural genetic variants, characterized guide mismatch tolerance at the genome scale, and ascertained that cryptic Pol III termination elements substantially reduce guide efficacy. MAGESTIC will be broadly useful to uncover the genetic basis of phenotypes in yeast.
In trans paired nicking triggers seamless genome editing without double-stranded DNA cutting.

PubMed

Chen, Xiaoyu; Janssen, Josephine M; Liu, Jin; Maggio, Ignazio; 't Jong, Anke E J; Mikkers, Harald M M; Gonçalves, Manuel A F V

2017-09-22

Precise genome editing involves homologous recombination between donor DNA and chromosomal sequences subjected to double-stranded DNA breaks made by programmable nucleases. Ideally, genome editing should be efficient, specific, and accurate. However, besides constituting potential translocation-initiating lesions, double-stranded DNA breaks (targeted or otherwise) are mostly repaired through unpredictable and mutagenic non-homologous recombination processes. Here, we report that the coordinated formation of paired single-stranded DNA breaks, or nicks, at donor plasmids and chromosomal target sites by RNA-guided nucleases based on CRISPR-Cas9 components, triggers seamless homology-directed gene targeting of large genetic payloads in human cells, including pluripotent stem cells. Importantly, in addition to significantly reducing the mutagenicity of the genome modification procedure, this in trans paired nicking strategy achieves multiplexed, single-step, gene targeting, and yields higher frequencies of accurately edited cells when compared to the standard double-stranded DNA break-dependent approach.CRISPR-Cas9-based gene editing involves double-strand breaks at target sequences, which are often repaired by mutagenic non-homologous end-joining. Here the authors use Cas9 nickases to generate coordinated single-strand breaks in donor and target DNA for precise homology-directed gene editing.
Curriculum-Based Assessment: A Primer. 4th Edition

ERIC Educational Resources Information Center

Hargis, Charles H.

2013-01-01

Thoroughly updated and expanded, this fourth edition focuses on the use of curriculum-based assessment to ensure learning disabled and low achieving students adequate educational opportunities. The text explores ways of providing detail and explanation in the context of current and emerging issues in educational assessment and standards. The point…
Comprehensive Protocols for CRISPR/Cas9-based Gene Editing in Human Pluripotent Stem Cells.

PubMed

Santos, David P; Kiskinis, Evangelos; Eggan, Kevin; Merkle, Florian T

2016-08-17

Genome editing of human pluripotent stem cells (hPSCs) with the CRISPR/Cas9 system has the potential to revolutionize hPSC-based disease modeling, drug screening, and transplantation therapy. Here, we aim to provide a single resource to enable groups, even those with limited experience with hPSC culture or the CRISPR/Cas9 system, to successfully perform genome editing. The methods are presented in detail and are supported by a theoretical framework to allow for the incorporation of inevitable improvements in the rapidly evolving gene-editing field. We describe protocols to generate hPSC lines with gene-specific knock-outs, small targeted mutations, or knock-in reporters. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.
A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes.

PubMed

Bazak, Lily; Haviv, Ami; Barak, Michal; Jacob-Hirsch, Jasmine; Deng, Patricia; Zhang, Rui; Isaacs, Farren J; Rechavi, Gideon; Li, Jin Billy; Eisenberg, Eli; Levanon, Erez Y

2014-03-01

RNA molecules transmit the information encoded in the genome and generally reflect its content. Adenosine-to-inosine (A-to-I) RNA editing by ADAR proteins converts a genomically encoded adenosine into inosine. It is known that most RNA editing in human takes place in the primate-specific Alu sequences, but the extent of this phenomenon and its effect on transcriptome diversity are not yet clear. Here, we analyzed large-scale RNA-seq data and detected ∼1.6 million editing sites. As detection sensitivity increases with sequencing coverage, we performed ultradeep sequencing of selected Alu sequences and showed that the scope of editing is much larger than anticipated. We found that virtually all adenosines within Alu repeats that form double-stranded RNA undergo A-to-I editing, although most sites exhibit editing at only low levels (<1%). Moreover, using high coverage sequencing, we observed editing of transcripts resulting from residual antisense expression, doubling the number of edited sites in the human genome. Based on bioinformatic analyses and deep targeted sequencing, we estimate that there are over 100 million human Alu RNA editing sites, located in the majority of human genes. These findings set the stage for exploring how this primate-specific massive diversification of the transcriptome is utilized.
Adeno-associated virus inverted terminal repeats stimulate gene editing.

PubMed

Hirsch, M L

2015-02-01

Advancements in genome editing have relied on technologies to specifically damage DNA which, in turn, stimulates DNA repair including homologous recombination (HR). As off-target concerns complicate the therapeutic translation of site-specific DNA endonucleases, an alternative strategy to stimulate gene editing based on fragile DNA was investigated. To do this, an episomal gene-editing reporter was generated by a disruptive insertion of the adeno-associated virus (AAV) inverted terminal repeat (ITR) into the egfp gene. Compared with a non-structured DNA control sequence, the ITR induced DNA damage as evidenced by increased gamma-H2AX and Mre11 foci formation. As local DNA damage stimulates HR, ITR-mediated gene editing was investigated using DNA oligonucleotides as repair substrates. The AAV ITR stimulated gene editing >1000-fold in a replication-independent manner and was not biased by the polarity of the repair oligonucleotide. Analysis of additional human DNA sequences demonstrated stimulation of gene editing to varying degrees. In particular, inverted yet not direct, Alu repeats induced gene editing, suggesting a role for DNA structure in the repair event. Collectively, the results demonstrate that inverted DNA repeats stimulate gene editing via double-strand break repair in an episomal context and allude to efficient gene editing of the human chromosome using fragile DNA sequences.
Gene Editing: Regulatory and Translation to Clinic.

PubMed

Ando, Dale; Meyer, Kathleen

2017-10-01

The clinical application and regulatory strategy of genome editing for ex vivo cell therapy is derived from the intersection of two fields of study: viral vector gene therapy trials; and clinical trials with ex vivo purification and engraftment of CD34 + hematopoietic stem cells, T cells, and tumor cell vaccines. This article covers the regulatory and translational preclinical activities needed for a genome editing clinical trial modifying hematopoietic stem cells and the genesis of this current strategy based on previous clinical trials using genome-edited T cells. The SB-728 zinc finger nuclease platform is discussed because this is the most clinically advanced genome editing technology. Copyright © 2017 Elsevier Inc. All rights reserved.
Progress of CRISPR-Cas Based Genome Editing in Photosynthetic Microbes.

PubMed

Naduthodi, Mihris Ibnu Saleem; Barbosa, Maria J; van der Oost, John

2018-02-03

The carbon footprint caused by unsustainable development and its environmental and economic impact has become a major concern in the past few decades. Photosynthetic microbes such as microalgae and cyanobacteria are capable of accumulating value-added compounds from carbon dioxide, and have been regarded as environmentally friendly alternatives to reduce the usage of fossil fuels, thereby contributing to reducing the carbon footprint. This light-driven generation of green chemicals and biofuels has triggered the research for metabolic engineering of these photosynthetic microbes. CRISPR-Cas systems are successfully implemented across a wide range of prokaryotic and eukaryotic species for efficient genome editing. However, the inception of this genome editing tool in microalgal and cyanobacterial species took off rather slowly due to various complications. In this review, we elaborate on the established CRISPR-Cas based genome editing in various microalgal and cyanobacterial species. The complications associated with CRISPR-Cas based genome editing in these species are addressed along with possible strategies to overcome these issues. It is anticipated that in the near future this will result in improving and expanding the microalgal and cyanobacterial genome engineering toolbox. © 2018 The Authors. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.
Genome editing: the breakthrough technology for inherited retinal disease?

PubMed

Smith, Andrew J; Carter, Stephen P; Kennedy, Breandán N

2017-10-01

Genetic alterations resulting in a dysfunctional retinal pigment epithelium and/or degenerating photoreceptors cause impaired vision. These juxtaposed cells in the retina of the posterior eye are crucial for the visual cycle or phototransduction. Deficits in these biochemical processes perturb neural processing of images capturing the external environment. Notably, there is a distinct lack of clinically approved pharmacological, cell- or gene-based therapies for inherited retinal disease. Gene editing technologies are rapidly advancing as a realistic therapeutic option. Areas covered: Recent discovery of endonuclease-mediated gene editing technologies has culminated in a surge of investigations into their therapeutic potential. In this review, the authors discuss gene editing technologies and their applicability in treating inherited retinal diseases, the limitations of the technology and the research obstacles to overcome before editing a patient's genome becomes a viable treatment option. Expert opinion: The ability to strategically edit a patient's genome constitutes a treatment revolution. However, concerns remain over the safety and efficacy of either transplanting iPSC-derived retinal cells following ex vivo gene editing, or with direct gene editing in vivo. Ultimately, further refinements to improve efficacy and safety profiles are paramount for gene editing to emerge as a widely available treatment option.
Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease

PubMed Central

Khermesh, Khen; D'Erchia, Anna Maria; Barak, Michal; Annese, Anita; Wachtel, Chaim; Levanon, Erez Y.; Picardi, Ernesto; Eisenberg, Eli

2016-01-01

Adenosine to inosine (A-to-I) RNA editing, catalyzed by the ADAR enzyme family, acts on dsRNA structures within pre-mRNA molecules. Editing of the coding part of the mRNA may lead to recoding, amino acid substitution in the resulting protein, possibly modifying its biochemical and biophysical properties. Altered RNA editing patterns have been observed in various neurological pathologies. Here, we present a comprehensive study of recoding by RNA editing in Alzheimer's disease (AD), the most common cause of irreversible dementia. We have used a targeted resequencing approach supplemented by a microfluidic-based high-throughput PCR coupled with next-generation sequencing to accurately quantify A-to-I RNA editing levels in a preselected set of target sites, mostly located within the coding sequence of synaptic genes. Overall, editing levels decreased in AD patients’ brain tissues, mainly in the hippocampus and to a lesser degree in the temporal and frontal lobes. Differential RNA editing levels were observed in 35 target sites within 22 genes. These results may shed light on a possible association between the neurodegenerative processes typical for AD and deficient RNA editing. PMID:26655226

Primordial germ cell-mediated transgenesis and genome editing in birds.

PubMed

Han, Jae Yong; Park, Young Hyun

2018-01-01

Transgenesis and genome editing in birds are based on a unique germline transmission system using primordial germ cells (PGCs), which is quite different from the mammalian transgenic and genome editing system. PGCs are progenitor cells of gametes that can deliver genetic information to the next generation. Since avian PGCs were first discovered in nineteenth century, there have been numerous efforts to reveal their origin, specification, and unique migration pattern, and to improve germline transmission efficiency. Recent advances in the isolation and in vitro culture of avian PGCs with genetic manipulation and genome editing tools enable the development of valuable avian models that were unavailable before. However, many challenges remain in the production of transgenic and genome-edited birds, including the precise control of germline transmission, introduction of exogenous genes, and genome editing in PGCs. Therefore, establishing reliable germline-competent PGCs and applying precise genome editing systems are critical current issues in the production of avian models. Here, we introduce a historical overview of avian PGCs and their application, including improved techniques and methodologies in the production of transgenic and genome-edited birds, and we discuss the future potential applications of transgenic and genome-edited birds to provide opportunities and benefits for humans.
Differential effects of film on preschool children's behaviour dependent on editing pace.

PubMed

Kostyrka-Allchorne, Katarzyna; Cooper, Nicholas R; Gossmann, Anna Maria; Barber, Katy J; Simpson, Andrew

2017-05-01

Evidence on how the pace of television and film editing affects children's behaviour and attention is inconclusive. We examined whether a fast-paced film affected how preschool-aged children interacted with toys. The study comprised 70 children (36 girls) aged two to four-and-a-half years who attended preschools in Essex, United Kingdom. The children were paired up and tested with either a fast- or a slow-paced film of a narrator reading a children's story. The fast-paced version had 102 camera cuts and 16 still images, and the slow-paced version had 22 camera cuts and four still images. Each dyad took part in two video-recorded free-play sessions, before and after they watched one of the specially edited four-minute films. The number of toys the children played with before and after the film sessions was recorded. Before they watched the films, the children's behaviour did not differ between the groups. However, after watching the film, the children in the fast-paced group shifted their attention between toys more frequently than the children who watched the slow-paced film. Even a brief exposure to differently paced films had an immediate effect on how the children interacted with their toys. ©2017 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.
[Textual research on circulation of the Ming edition of Li Heng's Xiu zhen fang (Pocket Formulary)].

PubMed

Yang, Jinping; Liu, Peng; Lu, Mingjing; Lu, Xing; Li, Shaolin; Jin, Xiumei

2015-03-01

Xiu zhen fang (Pocket Formulary) is a recipe book of the Ming Dynasty, inspired and managed by Zhu Su, compiled by Li Heng of liangyisuo (good physician house) in Zhou wangfu (Zhou's royal palace). The book was compiled and published twice during the reigns of the Hongwu and Yongle Emperors of the Ming Dynasty. Because of its high practicability, there were some editions in circulation, and the book was published several times only in the Ming Dynasty. At present, the earliest extanteditionwas the little character version of Yongle, and the version in the 4(th) year of Zhengde Emperor of the Ming Dynasty was a reprinting edition based on the Yongle edition, sharingthe same edition system. Most of the editions appeared after the reign of Zhengtong Emperor of the Ming Dynasty, titled by "kui ben (head version)" and "da quan (complete edition)" were the editionspublished in the local bookshops, which had rather distinct differences from the Yongle edition system not only in the its format but also in its contents.
Gene editing in clinical isolates of Candida parapsilosis using CRISPR/Cas9.

PubMed

Lombardi, Lisa; Turner, Siobhán A; Zhao, Fang; Butler, Geraldine

2017-08-14

Candida parapsilosis is one of the most common causes of candidiasis, particularly in the very young and the very old. Studies of gene function are limited by the lack of a sexual cycle, the diploid genome, and a paucity of molecular tools. We describe here the development of a plasmid-based CRISPR-Cas9 system for gene editing in C. parapsilosis. A major advantage of the system is that it can be used in any genetic background, which we showed by editing genes in 20 different isolates. Gene editing is carried out in a single transformation step. The CAS9 gene is expressed only when the plasmid is present, and it can be removed easily from transformed strains. There is theoretically no limit to the number of genes that can be edited in any strain. Gene editing is increased by homology-directed repair in the presence of a repair template. Editing by non-homologous end joining (NHEJ) also occurs in some genetic backgrounds. Finally, we used the system to introduce unique tags at edited sites.
Large-scale prediction of ADAR-mediated effective human A-to-I RNA editing.

PubMed

Yao, Li; Wang, Heming; Song, Yuanyuan; Dai, Zhen; Yu, Hao; Yin, Ming; Wang, Dongxu; Yang, Xin; Wang, Jinlin; Wang, Tiedong; Cao, Nan; Zhu, Jimin; Shen, Xizhong; Song, Guangqi; Zhao, Yicheng

2017-08-10

Adenosine-to-inosine (A-to-I) editing by adenosine deaminase acting on the RNA (ADAR) proteins is one of the most frequent modifications during post- and co-transcription. To facilitate the assignment of biological functions to specific editing sites, we designed an automatic online platform to annotate A-to-I RNA editing sites in pre-mRNA splicing signals, microRNAs (miRNAs) and miRNA target untranslated regions (3' UTRs) from human (Homo sapiens) high-throughput sequencing data and predict their effects based on large-scale bioinformatic analysis. After analysing plenty of previously reported RNA editing events and human normal tissues RNA high-seq data, >60 000 potentially effective RNA editing events on functional genes were found. The RNA Editing Plus platform is available for free at https://www.rnaeditplus.org/, and we believe our platform governing multiple optimized methods will improve further studies of A-to-I-induced editing post-transcriptional regulation. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Comparison of Insertional RNA Editing in Myxomycetes

PubMed Central

Chen, Cai; Frankhouser, David; Bundschuh, Ralf

2012-01-01

RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or structural RNA are inserted, deleted, or substituted. A high level of RNA editing has been observed in the mitochondrial genome of Physarum polycephalum. The most frequent editing type in Physarum is the insertion of individual Cs. RNA editing is extremely accurate in Physarum; however, little is known about its mechanism. Here, we demonstrate how analyzing two organisms from the Myxomycetes, namely Physarum polycephalum and Didymium iridis, allows us to test hypotheses about the editing mechanism that can not be tested from a single organism alone. First, we show that using the recently determined full transcriptome information of Physarum dramatically improves the accuracy of computational editing site prediction in Didymium. We use this approach to predict genes in the mitochondrial genome of Didymium and identify six new edited genes as well as one new gene that appears unedited. Next we investigate sequence conservation in the vicinity of editing sites between the two organisms in order to identify sites that harbor the information for the location of editing sites based on increased conservation. Our results imply that the information contained within only nine or ten nucleotides on either side of the editing site (a distance previously suggested through experiments) is not enough to locate the editing sites. Finally, we show that the codon position bias in C insertional RNA editing of these two organisms is correlated with the selection pressure on the respective genes thereby directly testing an evolutionary theory on the origin of this codon bias. Beyond revealing interesting properties of insertional RNA editing in Myxomycetes, our work suggests possible approaches to be used when finding sequence motifs for any biological process fails. PMID:22383871
Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences

PubMed Central

2013-01-01

Background Adenosine-to-inosine (A-to-I) RNA editing is recognized as a cellular mechanism for generating both RNA and protein diversity. Inosine base pairs with cytidine during reverse transcription and therefore appears as guanosine during sequencing of cDNA. Current approaches of RNA editing identification largely depend on the comparison between transcriptomes and genomic DNA (gDNA) sequencing datasets from the same individuals, and it has been challenging to identify editing candidates from transcriptomes in the absence of gDNA information. Results We have developed a new strategy to accurately predict constitutive RNA editing sites from publicly available human RNA-seq datasets in the absence of relevant genomic sequences. Our approach establishes new parameters to increase the ability to map mismatches and to minimize sequencing/mapping errors and unreported genome variations. We identified 695 novel constitutive A-to-I editing sites that appear in clusters (named “editing boxes”) in multiple samples and which exhibit spatial and dynamic regulation across human tissues. Some of these editing boxes are enriched in non-repetitive regions lacking inverted repeat structures and contain an extremely high conversion frequency of As to Is. We validated a number of editing boxes in multiple human cell lines and confirmed that ADAR1 is responsible for the observed promiscuous editing events in non-repetitive regions, further expanding our knowledge of the catalytic substrate of A-to-I RNA editing by ADAR enzymes. Conclusions The approach we present here provides a novel way of identifying A-to-I RNA editing events by analyzing only RNA-seq datasets. This method has allowed us to gain new insights into RNA editing and should also aid in the identification of more constitutive A-to-I editing sites from additional transcriptomes. PMID:23537002
Energy- and Intensity-Modulated Electron Beam for Breast Cancer Treatment

DTIC Science & Technology

1999-10-01

calculations," in Teletherapy: Present and Future, Ed. By T.R. Mackie and J.R. Palta (Advanced Medical Publishing, Madison WI) Mackie TR, Reckwerdt PJ...edited by T. R. Mackie and J. R. Palta from 10% to 20% (or a 5-20 mm shift in the isodose lines) (Advanced Medical Publishing, Madison, WI, 1996). to...Ayyangar K, Palta J R, Sweet J W and Suntharalingam N 1993 Experimental verification of a three-dimensional dose calculation algorithm using a specially
Concept-Based Curriculum and Instruction for the Thinking Classroom. Second Edition (Revised Edition). Concept-Based Curriculum and Instruction Series

ERIC Educational Resources Information Center

Erickson, H. Lynn; Lanning, Lois A.; French, Rachel

2017-01-01

Knowing the facts is not enough. If we want students to develop intellectually, creatively problem-solve, and grapple with complexity, the key is in "conceptual understanding." A Concept-Based curriculum recaptures students' innate curiosity about the world and provides the thrilling feeling of engaging one's mind. This updated edition…
Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing.

PubMed

Miyaoka, Yuichiro; Berman, Jennifer R; Cooper, Samantha B; Mayerl, Steven J; Chan, Amanda H; Zhang, Bin; Karlin-Neumann, George A; Conklin, Bruce R

2016-03-31

Precise genome-editing relies on the repair of sequence-specific nuclease-induced DNA nicking or double-strand breaks (DSBs) by homology-directed repair (HDR). However, nonhomologous end-joining (NHEJ), an error-prone repair, acts concurrently, reducing the rate of high-fidelity edits. The identification of genome-editing conditions that favor HDR over NHEJ has been hindered by the lack of a simple method to measure HDR and NHEJ directly and simultaneously at endogenous loci. To overcome this challenge, we developed a novel, rapid, digital PCR-based assay that can simultaneously detect one HDR or NHEJ event out of 1,000 copies of the genome. Using this assay, we systematically monitored genome-editing outcomes of CRISPR-associated protein 9 (Cas9), Cas9 nickases, catalytically dead Cas9 fused to FokI, and transcription activator-like effector nuclease at three disease-associated endogenous gene loci in HEK293T cells, HeLa cells, and human induced pluripotent stem cells. Although it is widely thought that NHEJ generally occurs more often than HDR, we found that more HDR than NHEJ was induced under multiple conditions. Surprisingly, the HDR/NHEJ ratios were highly dependent on gene locus, nuclease platform, and cell type. The new assay system, and our findings based on it, will enable mechanistic studies of genome-editing and help improve genome-editing technology.
Editable Supercapacitors with Customizable Stretchability Based on Mechanically Strengthened Ultralong MnO2 Nanowire Composite.

PubMed

Lv, Zhisheng; Luo, Yifei; Tang, Yuxin; Wei, Jiaqi; Zhu, Zhiqiang; Zhou, Xinran; Li, Wenlong; Zeng, Yi; Zhang, Wei; Zhang, Yanyan; Qi, Dianpeng; Pan, Shaowu; Loh, Xian Jun; Chen, Xiaodong

2018-01-01

Although some progress has been made on stretchable supercapacitors, traditional stretchable supercapacitors fabricated by predesigning structured electrodes for device assembling still lack the device-level editability and programmability. To adapt to wearable electronics with arbitrary configurations, it is highly desirable to develop editable supercapacitors that can be directly transferred into desirable shapes and stretchability. In this work, editable supercapacitors for customizable shapes and stretchability using electrodes based on mechanically strengthened ultralong MnO 2 nanowire composites are developed. A supercapacitor edited with honeycomb-like structure shows a specific capacitance of 227.2 mF cm -2 and can be stretched up to 500% without degradation of electrochemical performance, which is superior to most of the state-of-the-art stretchable supercapacitors. In addition, it maintains nearly 98% of the initial capacitance after 10 000 stretch-and-release cycles under 400% tensile strain. As a representative of concept for system integration, the editable supercapacitors are integrated with a strain sensor, and the system exhibits a stable sensing performance even under arm swing. Being highly stretchable, easily programmable, as well as connectable in series and parallel, an editable supercapacitor with customizable stretchability is promising to produce stylish energy storage devices to power various portable, stretchable, and wearable devices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Fundamentals of Physics, 6th Edition Enhanced Problems Version

NASA Astrophysics Data System (ADS)

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.
Automatically Detecting Likely Edits in Clinical Notes Created Using Automatic Speech Recognition

PubMed Central

Lybarger, Kevin; Ostendorf, Mari; Yetisgen, Meliha

2017-01-01

The use of automatic speech recognition (ASR) to create clinical notes has the potential to reduce costs associated with note creation for electronic medical records, but at current system accuracy levels, post-editing by practitioners is needed to ensure note quality. Aiming to reduce the time required to edit ASR transcripts, this paper investigates novel methods for automatic detection of edit regions within the transcripts, including both putative ASR errors but also regions that are targets for cleanup or rephrasing. We create detection models using logistic regression and conditional random field models, exploring a variety of text-based features that consider the structure of clinical notes and exploit the medical context. Different medical text resources are used to improve feature extraction. Experimental results on a large corpus of practitioner-edited clinical notes show that 67% of sentence-level edits and 45% of word-level edits can be detected with a false detection rate of 15%. PMID:29854187
Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies.

PubMed

Wang, Gang; Yang, Luhan; Grishin, Dennis; Rios, Xavier; Ye, Lillian Y; Hu, Yong; Li, Kai; Zhang, Donghui; Church, George M; Pu, William T

2017-01-01

Genome editing of human induced pluripotent stem cells (hiPSCs) offers unprecedented opportunities for in vitro disease modeling and personalized cell replacement therapy. The introduction of Cas9-directed genome editing has expanded adoption of this approach. However, marker-free genome editing using standard protocols remains inefficient, yielding desired targeted alleles at a rate of ∼1-5%. We developed a protocol based on a doxycycline-inducible Cas9 transgene carried on a piggyBac transposon to enable robust and highly efficient Cas9-directed genome editing, so that a parental line can be expeditiously engineered to harbor many separate mutations. Treatment with doxycycline and transfection with guide RNA (gRNA), donor DNA and piggyBac transposase resulted in efficient, targeted genome editing and concurrent scarless transgene excision. Using this approach, in 7 weeks it is possible to efficiently obtain genome-edited clones with minimal off-target mutagenesis and with indel mutation frequencies of 40-50% and homology-directed repair (HDR) frequencies of 10-20%.
HN(α/β-COCA-J) Experiment for Measurement of 1JC‧Cα Couplings from Two-Dimensional [15N, 1H] Correlation Spectrum

NASA Astrophysics Data System (ADS)

Permi, Perttu; Sorsa, Tia; Kilpeläinen, Ilkka; Annila, Arto

1999-11-01

Anew method for measurement of one-bond 13C‧-13Cα scalar and dipolar couplings from a two-dimensional [15N, 1H] correlation spectrum is presented. The experiment is based on multiple-quantum coherence, which is created between nitrogen and carbonyl carbon for simultaneous evolution of 15N chemical shift and coupling between 13C‧ and 13Cα. Optional subspectral editing is provided by the spin-state-selective filters. The residual dipolar dipolar contribution to the 13C‧-13Cα coupling can be measured from these simplified [15N, 1H]-HSQC-like spectra. In this way, without explicit knowledge of carbon assignments, conformational changes of proteins dissolved in dilute liquid crystals can be probed conveniently, e.g., in structure activity relationship by NMR studies. The method is demonstrated with human cardiac troponin C.
Jodocus Lommius's Little Golden Book and the history of diagnostic semeiology.

PubMed

Duffin, Jacalyn

2006-07-01

This paper traces the nature and fortunes of Lommius' Medicinal Observations of 1560, its relationship to ancient authors, its two-and-a-half centuries of fame, and its fall. Originating as an accessible manual of diagnosis for municipal authorities, it emphasized the observable aspects of illness and downplayed the role of humors and hidden causes. As a result, it both heralded and served the trend to symptom-based nosology. Eventually, as disease concepts shifted from symptoms to organs, Lommius was eclipsed by the next epistemic fashion: positivistic organicism. The multiple editions of this work invite us to reconsider the sustained influence of ancient writers, including Celsus, in medical pedagogy and semeiology, as well as the timing and location of the development of nosological concepts of disease. Class considerations and the proclivities of twentieth-century scholarship contributed to the obscurity of this book in our time.
The position of DNA cleavage by TALENs and cell synchronization influences the frequency of gene editing directed by single-stranded oligonucleotides.

PubMed

Rivera-Torres, Natalia; Strouse, Bryan; Bialk, Pawel; Niamat, Rohina A; Kmiec, Eric B

2014-01-01

With recent technological advances that enable DNA cleavage at specific sites in the human genome, it may now be possible to reverse inborn errors, thereby correcting a mutation, at levels that could have an impact in a clinical setting. We have been developing gene editing, using single-stranded DNA oligonucleotides (ssODNs), as a tool to direct site specific single base changes. Successful application of this technique has been demonstrated in many systems ranging from bacteria to human (ES and somatic) cells. While the frequency of gene editing can vary widely, it is often at a level that does not enable clinical application. As such, a number of stimulatory factors such as double-stranded breaks are known to elevate the frequency significantly. The majority of these results have been discovered using a validated HCT116 mammalian cell model system where credible genetic and biochemical readouts are available. Here, we couple TAL-Effector Nucleases (TALENs) that execute specific ds DNA breaks with ssODNs, designed specifically to repair a missense mutation, in an integrated single copy eGFP gene. We find that proximal cleavage, relative to the mutant base, is key for enabling high frequencies of editing. A directionality of correction is also observed with TALEN activity upstream from the target base being more effective in promoting gene editing than activity downstream. We also find that cells progressing through S phase are more amenable to combinatorial gene editing activity. Thus, we identify novel aspects of gene editing that will help in the design of more effective protocols for genome modification and gene therapy in natural genes.
TALEN-Mediated Homologous Recombination Produces Site-Directed DNA Base Change and Herbicide-Resistant Rice.

PubMed

Li, Ting; Liu, Bo; Chen, Chih Ying; Yang, Bing

2016-05-20

Over the last decades, much endeavor has been made to advance genome editing technology due to its promising role in both basic and synthetic biology. The breakthrough has been made in recent years with the advent of sequence-specific endonucleases, especially zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPRs) guided nucleases (e.g., Cas9). In higher eukaryotic organisms, site-directed mutagenesis usually can be achieved through non-homologous end-joining (NHEJ) repair to the DNA double-strand breaks (DSBs) caused by the exogenously applied nucleases. However, site-specific gene replacement or genuine genome editing through homologous recombination (HR) repair to DSBs remains a challenge. As a proof of concept gene replacement through TALEN-based HR in rice (Oryza sativa), we successfully produced double point mutations in rice acetolactate synthase gene (OsALS) and generated herbicide resistant rice lines by using TALENs and donor DNA carrying the desired mutations. After ballistic delivery into rice calli of TALEN construct and donor DNA, nine HR events with different genotypes of OsALS were obtained in T0 generation at the efficiency of 1.4%-6.3% from three experiments. The HR-mediated gene edits were heritable to the progeny of T1 generation. The edited T1 plants were as morphologically normal as the control plants while displayed strong herbicide resistance. The results demonstrate the feasibility of TALEN-mediated genome editing in rice and provide useful information for further genome editing by other nuclease-based genome editing platforms. Copyright © 2016 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.
GenomeVx: simple web-based creation of editable circular chromosome maps.

PubMed

Conant, Gavin C; Wolfe, Kenneth H

2008-03-15

We describe GenomeVx, a web-based tool for making editable, publication-quality, maps of mitochondrial and chloroplast genomes and of large plasmids. These maps show the location of genes and chromosomal features as well as a position scale. The program takes as input either raw feature positions or GenBank records. In the latter case, features are automatically extracted and colored, an example of which is given. Output is in the Adobe Portable Document Format (PDF) and can be edited by programs such as Adobe Illustrator. GenomeVx is available at http://wolfe.gen.tcd.ie/GenomeVx
Comprehension Instruction: Research-Based Best Practices. Solving Problems in the Teaching of Literacy. Second Edition

ERIC Educational Resources Information Center

Block, Cathy Collins, Ed.; Parris, Sheri R., Ed.

2008-01-01

Now in a substantially revised and updated second edition, this comprehensive professional resource and text is based on cutting-edge research. In each chapter, leading scholars provide an overview of a particular aspect of comprehension, offer best-practice instructional guidelines and policy recommendations, present key research questions still…

Using Augmented Reality to Support a Software Editing Course for College Students

ERIC Educational Resources Information Center

Wang, Y.-H.

2017-01-01

This study aimed to explore whether integrating augmented reality (AR) techniques could support a software editing course and to examine the different learning effects for students using online-based and AR-based blended learning strategies. The researcher adopted a comparative research approach with a total of 103 college students participating…
Orthogonal-blendshape-based editing system for facial motion capture data.

PubMed

Li, Qing; Deng, Zhigang

2008-01-01

The authors present a novel data-driven 3D facial motion capture data editing system using automated construction of an orthogonal blendshape face model and constrained weight propagation, aiming to bridge the popular facial motion capture technique and blendshape approach. In this work, a 3D facial-motion-capture-editing problem is transformed to a blendshape-animation-editing problem. Given a collected facial motion capture data set, we construct a truncated PCA space spanned by the greatest retained eigenvectors and a corresponding blendshape face model for each anatomical region of the human face. As such, modifying blendshape weights (PCA coefficients) is equivalent to editing their corresponding motion capture sequence. In addition, a constrained weight propagation technique allows animators to balance automation and flexible controls.
CRISPR/Cas9—Advancing Orthopoxvirus Genome Editing for Vaccine and Vector Development

PubMed Central

Okoli, Arinze; Okeke, Malachy I.; Tryland, Morten; Moens, Ugo

2018-01-01

The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (Cas9) technology is revolutionizing genome editing approaches. Its high efficiency, specificity, versatility, flexibility, simplicity and low cost have made the CRISPR/Cas9 system preferable to other guided site-specific nuclease-based systems such as TALENs (Transcription Activator-like Effector Nucleases) and ZFNs (Zinc Finger Nucleases) in genome editing of viruses. CRISPR/Cas9 is presently being applied in constructing viral mutants, preventing virus infections, eradicating proviral DNA, and inhibiting viral replication in infected cells. The successful adaptation of CRISPR/Cas9 to editing the genome of Vaccinia virus paves the way for its application in editing other vaccine/vector-relevant orthopoxvirus (OPXV) strains. Thus, CRISPR/Cas9 can be used to resolve some of the major hindrances to the development of OPXV-based recombinant vaccines and vectors, including sub-optimal immunogenicity; transgene and genome instability; reversion of attenuation; potential of spread of transgenes to wildtype strains and close contacts, which are important biosafety and risk assessment considerations. In this article, we review the published literature on the application of CRISPR/Cas9 in virus genome editing and discuss the potentials of CRISPR/Cas9 in advancing OPXV-based recombinant vaccines and vectors. We also discuss the application of CRISPR/Cas9 in combating viruses of clinical relevance, the limitations of CRISPR/Cas9 and the current strategies to overcome them. PMID:29361752
Evaluation of the 7(th) edition of the UICC-AJCC tumor, node, metastasis classification for esophageal cancer in a Chinese cohort.

PubMed

Huang, Yan; Guo, Weigang; Shi, Shiming; He, Jian

2016-07-01

To assess and evaluate the prognostic value of the 7(th) edition of the Union for International Cancer Control-American Joint Committee on Cancer (UICC-AJCC) tumor, node, metastasis (TNM) staging system for Chinese patients with esophageal cancer in comparison with the 6(th) edition. A retrospective review was performed on 766 consecutive esophageal cancer patients treated with esophagectomy between 2008 and 2012. Patients were staged according to the 6(th) and 7(th) editions for esophageal cancer respectively. Survival was calculated by the Kaplan-Meier method, and multivariate analysis was performed using Cox regression model. Overall 3-year survival rate was 59.5%. There were significant differences in 3-year survival rates among T stages both according to the 6(th) edition and the 7(th) edition (P<0.001). According to the 7(th) edition, the 3-year survival rates of N0 (75.4%), N1 (65.2%), N2 (39.7%) and N3 (27.3%) patients were significant differences (P<0.001). Kaplan-Meier curve revealed a good discriminatory ability from stage I to IV, except for stage IB, IIA and IIB in the 7(th) edition staging system. Based on the 7(th) edition, the degree of differentiation, tumor length and tumor location were not independent prognostic factors on multivariate analysis. The multivariate analyses suggested that pT-, pN-, pTNM-category were all the independent prognostic factors based on the 6(th) and 7(th) edition staging system. The 7(th) edition of AJCC TNM staging system of esophageal cancer should discriminate pT2-3N0M0 (stage IB, IIA and IIB) better when considering the esophageal squamous cell cancer patients. Therefore, to improve and optimize the AJCC TNM classification for Chinese patients with esophageal cancer, more considerations about the value of tumor grade and tumor location in pT2-3N0M0 esophageal squamous cell cancer should be taken in the next new TNM staging system.
Evidence-Based Practice for Nurses and Healthcare Professionals (Third edition) Barker Janet Linsley Paul Kane Ros Evidence-Based Practice for Nurses and Healthcare Professionals (Third edition) 240pp £22.99 Sage 9781473925038 1473925037 [Formula: see text].

PubMed

2016-11-16

This book provides a complete primer on the subject of evidence-based practice in health care. As an introductory single textbook, it is especially useful for nurses undertaking academic study, or who are new to the subject.
Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L.

PubMed Central

Wang, Mengxing; Liu, Hui; Ge, Lingqiao; Xing, Guangwei; Wang, Meng; Weining, Song; Nie, Xiaojun

2016-01-01

RNA editing is an important way to convert cytidine (C) to uridine (U) at specific sites within RNA molecules at a post-transcriptional level in the chloroplasts of higher plants. Although it has been systematically studied in many plants, little is known about RNA editing in the wheat D genome donor Aegilops tauschii L. Here, we investigated the chloroplast RNA editing of Ae. tauschii and compared it with other wheat relatives to trace the evolution of wheat. Through bioinformatics prediction, a total of 34 C-to-U editing sites were identified, 17 of which were validated using RT-PCR product sequencing. Furthermore, 60 sites were found by the RNA-Seq read mapping approach, 24 of which agreed with the prediction and six were validated experimentally. The editing sites were biased toward tCn or nCa trinucleotides and 5′-pyrimidines, which were consistent with the flanking bases of editing sites of other seed plants. Furthermore, the editing events could result in the alteration of the secondary structures and topologies of the corresponding proteins, suggesting that RNA editing might impact the function of target genes. Finally, comparative analysis found some evolutionarily conserved editing sites in wheat and two species-specific sites were also obtained. This study is the first to report on RNA editing in Aegilops tauschii L, which not only sheds light on the evolution of wheat from the point of view of RNA editing, but also lays a foundation for further studies to identify the mechanisms of C-to-U alterations. PMID:28042823
Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum

PubMed Central

Li, Yong

2017-01-01

RNA editing is a rare post-transcriptional event that provides cells with an additional level of gene expression regulation. It has been implicated in various processes including adaptation, viral defence and RNA interference; however, its potential role as a mechanism in acclimatization has just recently been recognised. Here, we show that RNA editing occurs in 1.6% of all nuclear-encoded genes of Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. All base-substitution edit types were present, and statistically significant motifs were associated with three edit types. Strikingly, a subset of genes exhibited condition-specific editing patterns in response to different stressors that resulted in significant increases of non-synonymous changes. We posit that this previously unrecognised mechanism extends this organism’s capability to respond to stress beyond what is encoded by the genome. This in turn may provide further acclimatization capacity to these organisms, and by extension, their coral hosts. PMID:28245292
The structure of myristoylated Mason-Pfizer monkey virus matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in its membrane binding.

PubMed

Prchal, Jan; Srb, Pavel; Hunter, Eric; Ruml, Tomáš; Hrabal, Richard

2012-10-26

We determined the solution structure of myristoylated Mason-Pfizer monkey virus matrix protein by NMR spectroscopy. The myristoyl group is buried inside the protein and causes a slight reorientation of the helices. This reorientation leads to the creation of a binding site for phosphatidylinositols. The interaction between the matrix protein and phosphatidylinositols carrying C(8) fatty acid chains was monitored by observation of concentration-dependent chemical shift changes of the affected amino acid residues, a saturation transfer difference experiment and changes in (31)P chemical shifts. No differences in the binding mode or affinity were observed with differently phosphorylated phosphatidylinositols. The structure of the matrix protein-phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P(2)] complex was then calculated with HADDOCK software based on the intermolecular nuclear Overhauser enhancement contacts between the ligand and the matrix protein obtained from a (13)C-filtered/(13)C-edited nuclear Overhauser enhancement spectroscopy experiment. PI(4,5)P(2) binding was not strong enough for triggering of the myristoyl-switch. The structural changes of the myristoylated matrix protein were also found to result in a drop in the oligomerization capacity of the protein. Copyright © 2012. Published by Elsevier Ltd.
Topological leakage detection and freeze-and-grow propagation for improved CT-based airway segmentation

NASA Astrophysics Data System (ADS)

Nadeem, Syed Ahmed; Hoffman, Eric A.; Sieren, Jered P.; Saha, Punam K.

2018-03-01

Numerous large multi-center studies are incorporating the use of computed tomography (CT)-based characterization of the lung parenchyma and bronchial tree to understand chronic obstructive pulmonary disease status and progression. To the best of our knowledge, there are no fully automated airway tree segmentation methods, free of the need for user review. A failure in even a fraction of segmentation results necessitates manual revision of all segmentation masks which is laborious considering the thousands of image data sets evaluated in large studies. In this paper, we present a novel CT-based airway tree segmentation algorithm using topological leakage detection and freeze-and-grow propagation. The method is fully automated requiring no manual inputs or post-segmentation editing. It uses simple intensity-based connectivity and a freeze-and-grow propagation algorithm to iteratively grow the airway tree starting from an initial seed inside the trachea. It begins with a conservative parameter and then, gradually shifts toward more generous parameter values. The method was applied on chest CT scans of fifteen subjects at total lung capacity. Airway segmentation results were qualitatively assessed and performed comparably to established airway segmentation method with no major visual leakages.
European Guidelines for Quality Assurance in Cervical Cancer Screening. Second edition--summary document.

PubMed

Arbyn, M; Anttila, A; Jordan, J; Ronco, G; Schenck, U; Segnan, N; Wiener, H; Herbert, A; von Karsa, L

2010-03-01

European Guidelines for Quality Assurance in Cervical Cancer Screening have been initiated in the Europe Against Cancer Programme. The first edition established the principles of organised population-based screening and stimulated numerous pilot projects. The second multidisciplinary edition was published in 2008 and comprises approximately 250 pages divided into seven chapters prepared by 48 authors and contributors. Considerable attention has been devoted to organised, population-based programme policies which minimise adverse effects and maximise benefits of screening. It is hoped that this expanded guidelines edition will have a greater impact on countries in which screening programmes are still lacking and in which opportunistic screening has been preferred in the past. Other methodological aspects such as future prospects of human papillomavirus testing and vaccination in cervical cancer control have also been examined in the second edition; recommendations for integration of the latter technologies into European guidelines are currently under development in a related project supported by the European Union Health Programme. An overview of the fundamental points and principles that should support any quality-assured screening programme and key performance indicators are presented here in a summary document of the second guidelines edition in order to make these principles and standards known to a wider scientific community.
Clinical Applications of Genome Editing to HIV Cure.

PubMed

Wang, Cathy X; Cannon, Paula M

2016-12-01

Despite significant advances in HIV drug treatment regimens, which grant near-normal life expectancies to infected individuals who have good virological control, HIV infection itself remains incurable. In recent years, novel gene- and cell-based therapies have gained increasing attention due to their potential to provide a functional or even sterilizing cure for HIV infection with a one-shot treatment. A functional cure would keep the infection in check and prevent progression to AIDS, while a sterilizing cure would eradicate all HIV viruses from the patient. Genome editing is the most precise form of gene therapy, able to achieve permanent genetic disruption, modification, or insertion at a predesignated genetic locus. The most well-studied candidate for anti-HIV genome editing is CCR5, an essential coreceptor for the majority of HIV strains, and the lack of which confers HIV resistance in naturally occurring homozygous individuals. Genetic disruption of CCR5 to treat HIV has undergone clinical testing, with seven completed or ongoing trials in T cells and hematopoietic stem and progenitor cells, and has shown promising safety and potential efficacy profiles. Here we summarize clinical findings of CCR5 editing for HIV therapy, as well as other genome editing-based approaches under pre-clinical development. The anticipated development of more sophisticated genome editing technologies should continue to benefit HIV cure efforts.
Countermeasures that work : seventh edition : traffic tech.

DOT National Transportation Integrated Search

2013-04-01

The National Highway Traffic Safety Administration has published the seventh edition of Countermeasures That Work. The guide is a basic reference to assist State Highway Safety Offices (SHSOs) in selecting effective, evidence-based countermeasures fo...
Accelerated Genome Engineering through Multiplexing

PubMed Central

Zhao, Huimin

2015-01-01

Throughout the biological sciences, the past fifteen years have seen a push towards the analysis and engineering of biological systems at the organism level. Given the complexity of even the simplest organisms, though, to elicit a phenotype of interest often requires genotypic manipulation of several loci. By traditional means, sequential editing of genomic targets requires a significant investment of time and labor, as the desired editing event typically occurs at a very low frequency against an overwhelming unedited background. In recent years, the development of a suite of new techniques has greatly increased editing efficiency, opening up the possibility for multiple editing events to occur in parallel. Termed as multiplexed genome engineering, this approach to genome editing has greatly expanded the scope of possible genome manipulations in diverse hosts, ranging from bacteria to human cells. The enabling technologies for multiplexed genome engineering include oligonucleotide-based and nuclease-based methodologies, and their application has led to the great breadth of successful examples described in this review. While many technical challenges remain, there also exists a multiplicity of opportunities in this rapidly expanding field. PMID:26394307
Guidelines for health technology assessment in Thailand (second edition)--the development process.

PubMed

Chaikledkaew, Usa; Kittrongsiri, Kankamon

2014-05-01

The first Thai-specific HTA guidelines were completed in 2008 with the aim of ensuring that all HTA data was accurate, of high quality, and relevant for making decisions pertaining to healthcare resource allocation. Based on a quality assessment of 89 economic evaluation studies in the Thai context published in international academic journals between 1982 and 2012, the analysis revealed a significant increase in quality of data sources and result reporting in studies published after the dissemination of the first Thai HTA guidelines. As the first Thai HTA guidelines were developed in 2008, a number of areas for improvement have been identified. Therefore, the objective of this chapter is to describe the development process of this second edition of HTA guidelines for Thailand which builds on the success of the first edition, while attempting to address some of the identified limitations of the first edition and reflect the changes that the health care and policy contexts have undergone in the intervening years. It is hoped that this second edition will continue to build on these successes so that policy decision making becomes increasingly evidence-based.
CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum

PubMed Central

Jiang, Yu; Qian, Fenghui; Yang, Junjie; Liu, Yingmiao; Dong, Feng; Xu, Chongmao; Sun, Bingbing; Chen, Biao; Xu, Xiaoshu; Li, Yan; Wang, Renxiao; Yang, Sheng

2017-01-01

Corynebacterium glutamicum is an important industrial metabolite producer that is difficult to genetically engineer. Although the Streptococcus pyogenes (Sp) CRISPR-Cas9 system has been adapted for genome editing of multiple bacteria, it cannot be introduced into C. glutamicum. Here we report a Francisella novicida (Fn) CRISPR-Cpf1-based genome-editing method for C. glutamicum. CRISPR-Cpf1, combined with single-stranded DNA (ssDNA) recombineering, precisely introduces small changes into the bacterial genome at efficiencies of 86–100%. Large gene deletions and insertions are also obtained using an all-in-one plasmid consisting of FnCpf1, CRISPR RNA, and homologous arms. The two CRISPR-Cpf1-assisted systems enable N iterative rounds of genome editing in 3N+4 or 3N+2 days. A proof-of-concept, codon saturation mutagenesis at G149 of γ-glutamyl kinase relieves L-proline inhibition using Cpf1-assisted ssDNA recombineering. Thus, CRISPR-Cpf1-based genome editing provides a highly efficient tool for genetic engineering of Corynebacterium and other bacteria that cannot utilize the Sp CRISPR-Cas9 system. PMID:28469274
Genome editing in the mushroom-forming basidiomycete Coprinopsis cinerea, optimized by a high-throughput transformation system.

PubMed

Sugano, Shigeo S; Suzuki, Hiroko; Shimokita, Eisuke; Chiba, Hirofumi; Noji, Sumihare; Osakabe, Yuriko; Osakabe, Keishi

2017-04-28

Mushroom-forming basidiomycetes produce a wide range of metabolites and have great value not only as food but also as an important global natural resource. Here, we demonstrate CRISPR/Cas9-based genome editing in the model species Coprinopsis cinerea. Using a high-throughput reporter assay with cryopreserved protoplasts, we identified a novel promoter, CcDED1 pro , with seven times stronger activity in this assay than the conventional promoter GPD2. To develop highly efficient genome editing using CRISPR/Cas9 in C. cinerea, we used the CcDED1 pro to express Cas9 and a U6-snRNA promoter from C. cinerea to express gRNA. Finally, CRISPR/Cas9-mediated GFP mutagenesis was performed in a stable GFP expression line. Individual genome-edited lines were isolated, and loss of GFP function was detected in hyphae and fruiting body primordia. This novel method of high-throughput CRISPR/Cas9-based genome editing using cryopreserved protoplasts should be a powerful tool in the study of edible mushrooms.
Effects of armodafinil on simulated driving and alertness in shift work disorder.

PubMed

Drake, Christopher; Gumenyuk, Valentina; Roth, Thomas; Howard, Ryan

2014-12-01

Forty-one percent of shift workers report dozing while driving. This study tested whether armodafinil improves driving simulator performance in subjects with shift work disorder (SWD). A primary outcome was performance late in the shift when workers are typically driving home. Randomized, double-blind, crossover. During each 12-h test session (21:30-09:30), subjects were kept awake except for multiple sleep latency testing (MSLT: 01:30, 03:30, 05:30, and 07:30). Subjective sleepiness (Karolinska Sleepiness Scale, KSS), driving performance, and cognitive performance (digit symbol substitution test and creativity on the Remote Associates Test, RAT) were evaluated during the night shift and commute home times. Hospital-based sleep research laboratory. Twenty night workers (age: 42.7 ± 8.7 y, 17 F) with excessive sleepiness (≥ 10 on the Epworth Sleepiness Scale), meeting International Classification of Sleep Disorders, Second Edition (ICSD-2) criteria for SWD, and having no other medical conditions. Armodafinil (150 mg) or placebo at (23:45 h) on counterbalanced nights separated by 7-14 days. Primary endpoints were driving simulator performance (standard deviation of lateral position (SDLP) and off-road deviations) with four sessions starting 3.25 h after drug administration, objective sleepiness (MSLT; 1.75 to 7.75 h post-drug), and creativity (5 h post-drug). Significant effects of drug were observed for each driving measure (P < 0.05). Armodafinil significantly improved SDLP for simulator sessions at 05:30, 07:30, and 09:30, and off-road deviations at 7 h, 15 min and 9 h, 15 min post-drug (P < 0.05). Armodafinil also improved objective sleepiness from 3.7 ± 0.6 min to 9.7 ± 5.2 min (P < 0.001) and RAT score from 8.75 ± 4.9 to 11.25 ± 6.0 (P < 0.005). Armodafinil 150 mg early in the night shift improves driving simulator performance in SWD. Effects on sleepiness, cognition, and driving were found up to 9.5 h post-ingestion, during the critical time when many night workers are driving home. © 2014 Associated Professional Sleep Societies, LLC.
Baculovirus-based genome editing in primary cells.

PubMed

Mansouri, Maysam; Ehsaei, Zahra; Taylor, Verdon; Berger, Philipp

2017-03-01

Genome editing in eukaryotes became easier in the last years with the development of nucleases that induce double strand breaks in DNA at user-defined sites. CRISPR/Cas9-based genome editing is currently one of the most powerful strategies. In the easiest case, a nuclease (e.g. Cas9) and a target defining guide RNA (gRNA) are transferred into a target cell. Non-homologous end joining (NHEJ) repair of the DNA break following Cas9 cleavage can lead to inactivation of the target gene. Specific repair or insertion of DNA with Homology Directed Repair (HDR) needs the simultaneous delivery of a repair template. Recombinant Lentivirus or Adenovirus genomes have enough capacity for a nuclease coding sequence and the gRNA but are usually too small to also carry large targeting constructs. We recently showed that a baculovirus-based multigene expression system (MultiPrime) can be used for genome editing in primary cells since it possesses the necessary capacity to carry the nuclease and gRNA expression constructs and the HDR targeting sequences. Here we present new Acceptor plasmids for MultiPrime that allow simplified cloning of baculoviruses for genome editing and we show their functionality in primary cells with limited life span and induced pluripotent stem cells (iPS). Copyright © 2017 Elsevier Inc. All rights reserved.
CRISPR editing in biological and biomedical investigation.

PubMed

Huang, Jiaojiao; Wang, Yanfang; Zhao, Jianguo

2018-05-01

Recently, clustered regularly interspaced short palindromic repeats (CRISPR) based genomic editing technologies have armed researchers with powerful new tools to biological and biomedical investigations. To further improve and expand its functionality, natural, and engineered CRISPR associated nine proteins (Cas9s) have been investigated, various CRISPR delivery strategies have been tested and optimized, and multiple schemes have been developed to ensure precise mammalian genome editing. Benefiting from those in-depth understanding and further development of CRISPR, versatile CRISPR-based platforms for genome editing have been rapidly developed to advance investigations in biology and biomedicine. In biological research area, CRISPR has been widely adopted in both fundamental and applied research fields, such as accurate base editing, transcriptional regulation, and genome-wide screening. In biomedical research area, CRISPR has also shown its extensive applicability in the establishment of animal models for genetic disorders especially those large animals and non-human primates models, and gene therapy to combat virus infectious diseases, to correct monogenic disorders in vivo or in pluripotent cells. In this prospect article, after highlighting recent developments of CRISPR systems, we outline different applications and current limitations of CRISPR use in biological and biomedical investigation. Finally, we provide a perspective for future development and potential risks of this multifunctional technology. © 2017 Wiley Periodicals, Inc.
Single-Step qPCR and dPCR Detection of Diverse CRISPR-Cas9 Gene Editing Events In Vivo.

PubMed

Falabella, Micol; Sun, Linqing; Barr, Justin; Pena, Andressa Z; Kershaw, Erin E; Gingras, Sebastien; Goncharova, Elena A; Kaufman, Brett A

2017-10-05

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based technology is currently the most flexible means to create targeted mutations by recombination or indel mutations by nonhomologous end joining. During mouse transgenesis, recombinant and indel alleles are often pursued simultaneously. Multiple alleles can be formed in each animal to create significant genetic complexity that complicates the CRISPR-Cas9 approach and analysis. Currently, there are no rapid methods to measure the extent of on-site editing with broad mutation sensitivity. In this study, we demonstrate the allelic diversity arising from targeted CRISPR editing in founder mice. Using this DNA sample collection, we validated specific quantitative and digital PCR methods (qPCR and dPCR, respectively) for measuring the frequency of on-target editing in founder mice. We found that locked nucleic acid (LNA) probes combined with an internal reference probe (Drop-Off Assay) provide accurate measurements of editing rates. The Drop-Off LNA Assay also detected on-target CRISPR-Cas9 gene editing in blastocysts with a sensitivity comparable to PCR-clone sequencing. Lastly, we demonstrate that the allele-specific LNA probes used in qPCR competitor assays can accurately detect recombinant mutations in founder mice. In summary, we show that LNA-based qPCR and dPCR assays provide a rapid method for quantifying the extent of on-target genome editing in vivo , testing RNA guides, and detecting recombinant mutations. Copyright © 2017 Falabella et al.

Making the Grade: Online Education in the United States, 2006. Midwestern Edition

ERIC Educational Resources Information Center

Allen, I. Elaine; Seaman, Jeff

2007-01-01

"Making the Grade: Online Education in the United States, 2006--Midwestern Edition" is based on data collected for the fourth annual report on the state of online education in U.S. Higher Education. Supported by the Alfred P. Sloan Foundation and based on responses from over 500 Midwestern colleges and universities, this year's study,…
Taking the Lead: New Roles for Teachers and School-Based Coaches, 2nd Edition

ERIC Educational Resources Information Center

Killion, Joellen; Harrison, Cindy

2017-01-01

"Taking the Lead" outlines 10 practical and powerful roles for school-based coaches responsible for helping teachers increase their capacity to serve all students. The second edition is a rich update to Killion and Harrison's essential resource and includes dozens of online tools that support deep exploration and implementation of the…
Un-Standardizing Curriculum: Multicultural Teaching in the Standards-Based Classroom. Second Edition. Multicultural Education Series

ERIC Educational Resources Information Center

Sleeter, Christine E.; Carmona, Judith Flores

2016-01-01

In this second edition of her bestseller, Christine Sleeter and new coauthor Judith Flores Carmona show how educators can learn to teach rich, academically rigorous, multicultural curricula within a standards-based environment. The authors have meticulously updated each chapter to address current changes in education policy and practice. New…
Changes for the new AMA Guides to impairment ratings, 6th Edition: implications and applications for physician disability evaluations.

PubMed

Rondinelli, Robert D

2009-07-01

U.S. Disability Systems share a common procedural approach to the determination of disability for purposes of compensation. The structural and anatomical consequences of the injury or disease are defined and measured according to medical impairment, which is used to estimate the individual's loss in terms of their capacity to perform activities of daily living (ADLs) and, presumptively, their losses in terms of vocational and non-vocational pursuits and quality of life. The physician is traditionally empowered to rate the severity of impairment in terms of a percentage loss to the "whole person" and according to criteria specific to each disability system. Often, the impairment percentage so derived, then is directly translated into a monetary sum for purposes of compensating these losses. The AMA periodically publishes and updates a physician impairment rating guide (the AMA Guides). The 6th Edition, published in 2008, incorporates the definitions and terminology of the ICF and provides a simple means of assessment of ADLs as part of the rating process. It also has shifted the ratings criteria towards a diagnosis-based approach, ostensibly to improve inter-rater consistency and reliability. Further work is needed to refine and validate ADL-based functional assessment tools applicable to medical impairment ratings, and to demonstrate the levels of consistency and reliability of the new rating method. Of equal importance, operational standardization across systems is also needed to enable common criteria and metrics to be developed and applied when determining the non-medical aspects of disability according to vocational and non-vocational pursuits and quality of life. Impairment ratings cannot be optimally designed to serve as the singular determinant of, nor be held solely accountable for, the disability awards.
Self-organizing maps for learning the edit costs in graph matching.

PubMed

Neuhaus, Michel; Bunke, Horst

2005-06-01

Although graph matching and graph edit distance computation have become areas of intensive research recently, the automatic inference of the cost of edit operations has remained an open problem. In the present paper, we address the issue of learning graph edit distance cost functions for numerically labeled graphs from a corpus of sample graphs. We propose a system of self-organizing maps (SOMs) that represent the distance measuring spaces of node and edge labels. Our learning process is based on the concept of self-organization. It adapts the edit costs in such a way that the similarity of graphs from the same class is increased, whereas the similarity of graphs from different classes decreases. The learning procedure is demonstrated on two different applications involving line drawing graphs and graphs representing diatoms, respectively.
Modern Genome Editing Technologies in Huntington's Disease Research.

PubMed

Malankhanova, Tuyana B; Malakhova, Anastasia A; Medvedev, Sergey P; Zakian, Suren M

2017-01-01

The development of new revolutionary technologies for directed gene editing has made it possible to thoroughly model and study NgAgo human diseases at the cellular and molecular levels. Gene editing tools like ZFN, TALEN, CRISPR-based systems, NgAgo and SGN can introduce different modifications. In gene sequences and regulate gene expression in different types of cells including induced pluripotent stem cells (iPSCs). These tools can be successfully used for Huntington's disease (HD) modeling, for example, to generate isogenic cell lines bearing different numbers of CAG repeats or to correct the mutation causing the disease. This review presents common genome editing technologies and summarizes the progress made in using them in HD and other hereditary diseases. Furthermore, we will discuss prospects and limitations of genome editing in understanding HD pathology.
GraDit: graph-based data repair algorithm for multiple data edits rule violations

NASA Astrophysics Data System (ADS)

Ode Zuhayeni Madjida, Wa; Gusti Bagus Baskara Nugraha, I.

2018-03-01

Constraint-based data cleaning captures data violation to a set of rule called data quality rules. The rules consist of integrity constraint and data edits. Structurally, they are similar, where the rule contain left hand side and right hand side. Previous research proposed a data repair algorithm for integrity constraint violation. The algorithm uses undirected hypergraph as rule violation representation. Nevertheless, this algorithm can not be applied for data edits because of different rule characteristics. This study proposed GraDit, a repair algorithm for data edits rule. First, we use bipartite-directed hypergraph as model representation of overall defined rules. These representation is used for getting interaction between violation rules and clean rules. On the other hand, we proposed undirected graph as violation representation. Our experimental study showed that algorithm with undirected graph as violation representation model gave better data quality than algorithm with undirected hypergraph as representation model.
Recent Progress in Genome Editing Approaches for Inherited Cardiovascular Diseases.

PubMed

Kaur, Balpreet; Perea-Gil, Isaac; Karakikes, Ioannis

2018-06-02

This review describes the recent progress in nuclease-based therapeutic applications for inherited heart diseases in vitro, highlights the development of the most recent genome editing technologies and discusses the associated challenges for clinical translation. Inherited cardiovascular disorders are passed from generation to generation. Over the past decade, considerable progress has been made in understanding the genetic basis of inherited heart diseases. The timely emergence of genome editing technologies using engineered programmable nucleases has revolutionized the basic research of inherited cardiovascular diseases and holds great promise for the development of targeted therapies. The genome editing toolbox is rapidly expanding, and new tools have been recently added that significantly expand the capabilities of engineered nucleases. Newer classes of versatile engineered nucleases, such as the "base editors," have been recently developed, offering the potential for efficient and precise therapeutic manipulation of the human genome.
Detection of canonical A-to-G editing events at 3′ UTRs and microRNA target sites in human lungs using next-generation sequencing

PubMed Central

Soundararajan, Ramani; Stearns, Timothy M.; Griswold, Anthony J.; Mehta, Arpit; Czachor, Alexander; Fukumoto, Jutaro; Lockey, Richard F.; King, Benjamin L.; Kolliputi, Narasaiah

2015-01-01

RNA editing is a post-transcriptional modification of RNA. The majority of these changes result from adenosine deaminase acting on RNA (ADARs) catalyzing the conversion of adenosine residues to inosine in double-stranded RNAs (dsRNAs). Massively parallel sequencing has enabled the identification of RNA editing sites in human transcriptomes. In this study, we sequenced DNA and RNA from human lungs and identified RNA editing sites with high confidence via a computational pipeline utilizing stringent analysis thresholds. We identified a total of 3,447 editing sites that overlapped in three human lung samples, and with 50% of these sites having canonical A-to-G base changes. Approximately 27% of the edited sites overlapped with Alu repeats, and showed A-to-G clustering (>3 clusters in 100 bp). The majority of edited sites mapped to either 3′ untranslated regions (UTRs) or introns close to splice sites; whereas, only few sites were in exons resulting in non-synonymous amino acid changes. Interestingly, we identified 652 A-to-G editing events in the 3′ UTR of 205 target genes that mapped to 932 potential miRNA target binding sites. Several of these miRNA edited sites were validated in silico. Additionally, we validated several A-to-G edited sites by Sanger sequencing. Altogether, our study suggests a role for RNA editing in miRNA-mediated gene regulation and splicing in human lungs. In this study, we have generated a RNA editome of human lung tissue that can be compared with other RNA editomes across different lung tissues to delineate a role for RNA editing in normal and diseased states. PMID:26486088
Detection of canonical A-to-G editing events at 3' UTRs and microRNA target sites in human lungs using next-generation sequencing.

PubMed

Soundararajan, Ramani; Stearns, Timothy M; Griswold, Anthony L; Mehta, Arpit; Czachor, Alexander; Fukumoto, Jutaro; Lockey, Richard F; King, Benjamin L; Kolliputi, Narasaiah

2015-11-03

RNA editing is a post-transcriptional modification of RNA. The majority of these changes result from adenosine deaminase acting on RNA (ADARs) catalyzing the conversion of adenosine residues to inosine in double-stranded RNAs (dsRNAs). Massively parallel sequencing has enabled the identification of RNA editing sites in human transcriptomes. In this study, we sequenced DNA and RNA from human lungs and identified RNA editing sites with high confidence via a computational pipeline utilizing stringent analysis thresholds. We identified a total of 3,447 editing sites that overlapped in three human lung samples, and with 50% of these sites having canonical A-to-G base changes. Approximately 27% of the edited sites overlapped with Alu repeats, and showed A-to-G clustering (>3 clusters in 100 bp). The majority of edited sites mapped to either 3' untranslated regions (UTRs) or introns close to splice sites; whereas, only few sites were in exons resulting in non-synonymous amino acid changes. Interestingly, we identified 652 A-to-G editing events in the 3' UTR of 205 target genes that mapped to 932 potential miRNA target binding sites. Several of these miRNA edited sites were validated in silico. Additionally, we validated several A-to-G edited sites by Sanger sequencing. Altogether, our study suggests a role for RNA editing in miRNA-mediated gene regulation and splicing in human lungs. In this study, we have generated a RNA editome of human lung tissue that can be compared with other RNA editomes across different lung tissues to delineate a role for RNA editing in normal and diseased states.
[Comparison of the compilation features of Science of Meridians and Acupoints among different editions].

PubMed

Chen, Xiaojun

The compilation features of Jingluo Shuxue Xue ( Science of Meridians and Acupoints ) among different editions were summarized and analyzed. Jingluo Xue ( Science of Meridians ) and Shuxue Xue ( Science of Acupoints ) published by Shanghai Scientific and Technical Publishers in 1984 are the pioneer as the textbook for the education of acupuncture discipline for the bachelor degree, but there is the big controversy for the editions in 1996. These two books were combined as one, titled Science of Meridians and Acupoints , 2013 edition, published by China Press of Traditional Chinese Medicine. It is concise and coherent in content and is regarded as the milestone in the history of textbook compilation. This book was re-edited in 2007 without major changes in content. The one in 2009 was revised a lot on the basis of the original several editions, published by Shanghai Scientific and Technical Publishers. But unfortunately, it did not bring the big impacts in China. The edition in 2012, published by China Press of Traditional Chinese Medicine had made the innovations besides integrating the achievements of the previous editions, characterized as preciseness and conciseness. By contrast, the edition in 2012, published by People's Medical Publishing House was accomplished by simple modification on the basis of the editions in 2003 and in 2007, without great innovation. Regarding the on-going publication of the textbooks in "the 13th five-year plan", it is viewed that the new edition of textbook should maintain the general framework of "the 12th five-year plan", based on which, a few questions should be revised appropriately. Additionally, "less words, more illustration" should be the basic principle for the revision of the new edition.
RNA Editome in Rhesus Macaque Shaped by Purifying Selection

PubMed Central

Yang, Xin-Zhuang; Tan, Bertrand Chin-Ming; Fang, Huaying; Liu, Chu-Jun; Shi, Mingming; Ye, Zhi-Qiang; Zhang, Yong E.; Deng, Minghua; Zhang, Xiuqin; Li, Chuan-Yun

2014-01-01

Understanding of the RNA editing process has been broadened considerably by the next generation sequencing technology; however, several issues regarding this regulatory step remain unresolved – the strategies to accurately delineate the editome, the mechanism by which its profile is maintained, and its evolutionary and functional relevance. Here we report an accurate and quantitative profile of the RNA editome for rhesus macaque, a close relative of human. By combining genome and transcriptome sequencing of multiple tissues from the same animal, we identified 31,250 editing sites, of which 99.8% are A-to-G transitions. We verified 96.6% of editing sites in coding regions and 97.5% of randomly selected sites in non-coding regions, as well as the corresponding levels of editing by multiple independent means, demonstrating the feasibility of our experimental paradigm. Several lines of evidence supported the notion that the adenosine deamination is associated with the macaque editome – A-to-G editing sites were flanked by sequences with the attributes of ADAR substrates, and both the sequence context and the expression profile of ADARs are relevant factors in determining the quantitative variance of RNA editing across different sites and tissue types. In support of the functional relevance of some of these editing sites, substitution valley of decreased divergence was detected around the editing site, suggesting the evolutionary constraint in maintaining some of these editing substrates with their double-stranded structure. These findings thus complement the “continuous probing” model that postulates tinkering-based origination of a small proportion of functional editing sites. In conclusion, the macaque editome reported here highlights RNA editing as a widespread functional regulation in primate evolution, and provides an informative framework for further understanding RNA editing in human. PMID:24722121
CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum.

PubMed

Pohl, C; Kiel, J A K W; Driessen, A J M; Bovenberg, R A L; Nygård, Y

2016-07-15

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 relevant cell factory. The developed CRISPR/Cas9 toolbox is highly flexible and allows editing of new targets with minimal cloning efforts. The Cas9 protein and the sgRNA can be either delivered during transformation, as preassembled CRISPR-Cas9 ribonucleoproteins (RNPs) or expressed from an AMA1 based plasmid within the cell. The direct delivery of the Cas9 protein with in vitro synthesized sgRNA to the cells allows for a transient method for genome engineering that may rapidly be applicable for other filamentous fungi. The expression of Cas9 from an AMA1 based vector was shown to be highly efficient for marker-free gene deletions.
Therapeutic Genome Editing: Prospects and Challenges

PubMed Central

Cox, David Benjamin Turitz; Platt, Randall Jeffrey; Zhang, Feng

2015-01-01

Recent advances in the development of genome editing technologies based on programmable nucleases have significantly improved our ability to make precise changes in the genomes of eukaryotic cells. Genome editing is already broadening our ability to elucidate the contribution of genetics to disease by facilitating the creation of more accurate cellular and animal models of pathological processes. A particularly tantalizing application of programmable nucleases is the potential to directly correct genetic mutations in affected tissues and cells to treat diseases that are refractory to traditional therapies. Here we discuss current progress towards developing programmable nuclease-based therapies as well as future prospects and challenges. PMID:25654603
One small edit for humans, one giant edit for humankind? Points and questions to consider for a responsible way forward for gene editing in humans.

PubMed

Howard, Heidi C; van El, Carla G; Forzano, Francesca; Radojkovic, Dragica; Rial-Sebbag, Emmanuelle; de Wert, Guido; Borry, Pascal; Cornel, Martina C

2018-01-01

Gene editing, which allows for specific location(s) in the genome to be targeted and altered by deleting, adding or substituting nucleotides, is currently the subject of important academic and policy discussions. With the advent of efficient tools, such as CRISPR-Cas9, the plausibility of using gene editing safely in humans for either somatic or germ line gene editing is being considered seriously. Beyond safety issues, somatic gene editing in humans does raise ethical, legal and social issues (ELSI), however, it is suggested to be less challenging to existing ethical and legal frameworks; indeed somatic gene editing is already applied in (pre-) clinical trials. In contrast, the notion of altering the germ line or embryo such that alterations could be heritable in humans raises a large number of ELSI; it is currently debated whether it should even be allowed in the context of basic research. Even greater ELSI debates address the potential use of germ line or embryo gene editing for clinical purposes, which, at the moment is not being conducted and is prohibited in several jurisdictions. In the context of these ongoing debates surrounding gene editing, we present herein guidance to further discussion and investigation by highlighting three crucial areas that merit the most attention, time and resources at this stage in the responsible development and use of gene editing technologies: (1) conducting careful scientific research and disseminating results to build a solid evidence base; (2) conducting ethical, legal and social issues research; and (3) conducting meaningful stakeholder engagement, education and dialogue.
The AJCC 8th Edition Staging System for Soft Tissue Sarcoma of the Extremities or Trunk: A Cohort Study of the SEER Database.

PubMed

Cates, Justin M M

2018-02-01

Background: The AJCC recently published the 8th edition of its cancer staging system. Significant changes were made to the staging algorithm for soft tissue sarcoma (STS) of the extremities or trunk, including the addition of 2 additional T (size) classifications in lieu of tumor depth and grouping lymph node metastasis (LNM) with distant metastasis as stage IV disease. Whether these changes improve staging system performance is questionable. Patients and Methods: This retrospective cohort analysis of 21,396 adult patients with STS of the extremity or trunk in the SEER database compares the AJCC 8th edition staging system with the 7th edition and a newly proposed staging algorithm using a variety of statistical techniques. The effect of tumor size on disease-specific survival was assessed by flexible, nonlinear Cox proportional hazard regression using restricted cubic splines and fractional polynomials. Results: The slope of covariate-adjusted log hazards for sarcoma-specific survival decreases for tumors >8 cm in greatest dimension, limiting prognostic information contributed by the new T4 classification in the AJCC 8th edition. Anatomic depth independently provides significant prognostic information. LNM is not equivalent to distant, non-nodal metastasis. Based on these findings, an alternative staging system is proposed and demonstrated to outperform both AJCC staging schemes. The analyses presented also disclose no evidence of improved clinical performance of the 8th edition compared with the previous edition. Conclusions: The AJCC 8th edition staging system for STS is no better than the previous 7th edition. Instead, a proposed staging system based on histologic grade, tumor size, and anatomic depth shows significantly higher predictive accuracy, with higher model concordance than either AJCC staging system. Changes to existing staging systems should improve the performance of prognostic models. Until such improvements are documented, AJCC committees should refrain from modifying established staging schemes. Copyright © 2018 by the National Comprehensive Cancer Network.
Comparing esthetic smile perceptions among laypersons with and without orthodontic treatment experience and dentists

PubMed Central

An, Seong-Mu; Choi, Sun-Young; Chung, Young-Wook; Jang, Tae-Ho

2014-01-01

Objective The purpose of this study was to examine whether orthodontic treatment experience affects the individual's perception of smile esthetics and to evaluate differences among orthodontically treated laypersons, non-treated laypersons, and dentists by using computerized image alterations. Methods A photograph of a woman's smile was digitally altered using a software image editing program. The alterations involved gingival margin height, crown width and length, incisal plane canting, and dental midline of the maxillary anterior teeth. Three groups of raters (orthodontically treated laypersons, non-treated laypersons, and dentists) evaluated the original and altered images using a visual analog scale. Results The threshold for detecting changes in maxillary central incisor gingival margin height among laypersons was 1.5 mm; the threshold of dentists, who were more perceptive, was 1.0 mm. For maxillary lateral incisor crown width and height, the threshold of all three groups was 3.0 mm. Canting of the incisal plane was perceived when the canting was 3.0 mm among non-treated laypersons, 2.0 mm among treated laypersons, and 1.0 mm among dentists. Non-treated laypersons could not perceive dental midline shifts; however, treated laypersons and dentists perceived them when the shift was ≥ 3.0 mm. Conclusions Laypersons with and without orthodontic treatment experience and dentists have different perceptions of smile esthetics. Orthodontically treated laypersons were more critical than non-treated laypersons regarding incisal plane canting and dental midline shifts. Based on these findings, it is suggested that orthodontic treatment experience improved the esthetic perceptions of laypersons. PMID:25473645
Detecting duplicate biological entities using Shortest Path Edit Distance.

PubMed

Rudniy, Alex; Song, Min; Geller, James

2010-01-01

Duplicate entity detection in biological data is an important research task. In this paper, we propose a novel and context-sensitive Shortest Path Edit Distance (SPED) extending and supplementing our previous work on Markov Random Field-based Edit Distance (MRFED). SPED transforms the edit distance computational problem to the calculation of the shortest path among two selected vertices of a graph. We produce several modifications of SPED by applying Levenshtein, arithmetic mean, histogram difference and TFIDF techniques to solve subtasks. We compare SPED performance to other well-known distance algorithms for biological entity matching. The experimental results show that SPED produces competitive outcomes.
[Interpretation of update on The AJCC Esophageal Cancer Staging System, Eighth Edition].

PubMed

Yuan, Y; Chen, L Q

2017-02-01

The recently published AJCC Esophageal Cancer Staging System, 8(th) Edition will be implemented on Januray 1, 2018, which was developed by Worldwide Esophageal Cancer Collaboration based on 22 654 esophageal cancer patients from 33 worldwide centers. The definition of T, N, M, G stage and regional lymph nodes were optimized in the 8(th) edition. And the new "2 cm" principle has simplified the definition for the cancer of esophagogastric junction. In addition to pathologic staging, the 8(th) edition also provided clinical staging and pathologic staging after neoadjuvant therapy, making the new esophageal cancer staging system more practicable and reasonable.
On Improving CRISPR for Editing Plant Genes: Ribozyme-Mediated Guide RNA Production and Fluorescence-Based Technology for Isolating Transgene-Free Mutants Generated by CRISPR.

PubMed

He, Yubing; Wang, Rongchen; Dai, Xinhua; Zhao, Yunde

2017-01-01

CRISPR/Cas9-mediated genome editing technology has been used to successfully edit numerous genes in various organisms including plants. There are still two major challenges in using CRISPR/Cas9 technology for gene editing in plants. First, there are very limited choices of promoters that are suitable for in vivo production of single-guide RNAs (sgRNAs), which is complementary to the target sequence and which guides Cas9 to generate double-strand breaks at the target site. It is especially difficult to produce sgRNA molecules with temporal and spatial precision. Second, there is a lack of efficient methods for identifying plants that (1) contain heritable and stable mutations generated by CRISPR/Cas9, and (2) no longer harbor the CRISPR/Cas9 construct and other transgenes. In this chapter, we describe the development of a ribozyme-based strategy that enables the production of sgRNA molecules from any chosen promoter. More importantly, the ribozyme-based technology makes it feasible to produce sgRNAs with temporal and spatial precision, greatly expanding the scope and applications of CRISPR/Cas9 technology. We also developed a fluorescence-based technology that allows us to efficiently and reliably isolate Cas9-free stable Arabidopsis mutants. Thus, we provide effective protocols to overcome two important obstacles in using CRISPR/Cas9 for editing genes in plants. © 2017 Elsevier Inc. All rights reserved.

Genome Editing of Monkey.

PubMed

Liu, Zhen; Cai, Yijun; Sun, Qiang

2017-01-01

Gene-modified monkey models would be particularly valuable in biomedical and neuroscience research. Virus-based transgenic and programmable nucleases-based site-specific gene editing methods (TALEN, CRISPR-cas9) enable the generation of gene-modified monkeys with gain or loss of function of specific genes. Here, we describe the generation of transgenic and knock-out (KO) monkeys with high efficiency by lentivirus and programmable nucleases.
Governance Health Check. Diagnosing Effective Governance for FE Colleges. Second Edition. [and] Diagnosing Effective Governance for Land-Based Colleges. Second Edition.

ERIC Educational Resources Information Center

Learning and Skills Development Agency, London (England).

These two documents are designed to assist governing bodies of England's further education (FE) and land-based colleges self-assess their performance and identify ways of improving their performance. Each document contains a "healthcheck" that requires approximately 30 minutes to complete and that was developed in response to informative…
[Advances in CRISPR-Cas-mediated genome editing system in plants].

PubMed

Wang, Chun; Wang, Kejian

2017-10-25

Targeted genome editing technology is an important tool to study the function of genes and to modify organisms at the genetic level. Recently, CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) system has emerged as an efficient tool for specific genome editing in animals and plants. CRISPR-Cas system uses CRISPR-associated endonuclease and a guide RNA to generate double-strand breaks at the target DNA site, subsequently leading to genetic modifications. CRISPR-Cas system has received widespread attention for manipulating the genomes with simple, easy and high specificity. This review summarizes recent advances of diverse applications of the CRISPR-Cas toolkit in plant research and crop breeding, including expanding the range of genome editing, precise editing of a target base, and efficient DNA-free genome editing technology. This review also discusses the potential challenges and application prospect in the future, and provides a useful reference for researchers who are interested in this field.
Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs.

PubMed

Gonen, Serap; Jenko, Janez; Gorjanc, Gregor; Mileham, Alan J; Whitelaw, C Bruce A; Hickey, John M

2017-01-04

This paper uses simulation to explore how gene drives can increase genetic gain in livestock breeding programs. Gene drives are naturally occurring phenomena that cause a mutation on one chromosome to copy itself onto its homologous chromosome. We simulated nine different breeding and editing scenarios with a common overall structure. Each scenario began with 21 generations of selection, followed by 20 generations of selection based on true breeding values where the breeder used selection alone, selection in combination with genome editing, or selection with genome editing and gene drives. In the scenarios that used gene drives, we varied the probability of successfully incorporating the gene drive. For each scenario, we evaluated genetic gain, genetic variance [Formula: see text], rate of change in inbreeding ([Formula: see text]), number of distinct quantitative trait nucleotides (QTN) edited, rate of increase in favourable allele frequencies of edited QTN and the time to fix favourable alleles. Gene drives enhanced the benefits of genome editing in seven ways: (1) they amplified the increase in genetic gain brought about by genome editing; (2) they amplified the rate of increase in the frequency of favourable alleles and reduced the time it took to fix them; (3) they enabled more rapid targeting of QTN with lesser effect for genome editing; (4) they distributed fixed editing resources across a larger number of distinct QTN across generations; (5) they focussed editing on a smaller number of QTN within a given generation; (6) they reduced the level of inbreeding when editing a subset of the sires; and (7) they increased the efficiency of converting genetic variation into genetic gain. Genome editing in livestock breeding results in short-, medium- and long-term increases in genetic gain. The increase in genetic gain occurs because editing increases the frequency of favourable alleles in the population. Gene drives accelerate the increase in allele frequency caused by editing, which results in even higher genetic gain over a shorter period of time with no impact on inbreeding.
Non-Doppler shift related experimental shock wave measurements using velocity interferometer systems for any reflector.

PubMed

Forsman, A C; Kyrala, G A

2001-05-01

Velocity interferometer system for any reflectors (VISARs), are becoming increasingly popular in the measurement of shock waves in solids and liquids. VISAR techniques are used in measurements of transit time, speed of shock waves in flight in transparent media [L. C. Chhabildas and J. L. Wise, in Proceedings of the 4th APS Topical Conference on Shock Waves in Condensed Matter, Spokane, Washington, 1985, edited by Y. M. Gupta (Plenum, New York, 1986); P. M. Celliers et al., Appl. Phys. Lett. 73, 1320 (1998)], and in measurements of particle velocity. However, in cases where shock compression or release may change the index of refraction n+ik of the material being studied, the VISAR technique must be applied with care. Changes in n and k introduce phase shifts into the VISAR results that are not associated with changes in velocity. This paper presents a derivation of the theoretical output of a line VISAR that includes the effects of changing n and k and an experimental observation of a non-Doppler shift related effect.
Hierarchy effect on electronic structure and core-to-valence transitions in bone tissue: perspectives in medical nanodiagnostics of mineralized bone

NASA Astrophysics Data System (ADS)

Samoilenko, Dmitrii O.; Avrunin, Alexander S.; Pavlychev, Andrey A.

2017-06-01

Electronic structure and core-to-valence transitions in bone tissue are examined in the framework of the morphological 3DSL model that takes into account (i) structural and functional organization of the skeleton in the normal and pathological conditions and (ii) peculiarities of electron wave propagation in a three-dimensional superlattice of "black-nanocrystallites-in-muddy-waters". Our focus is on the HAP-to-bone red shifts of core-to-valence transitions near Ca and P 2p and O 1s edges in single-crystal hydroxyapatite (HAP) Ca10(PO4)6(OH)2. The origin of the HAP-to-bone shift is discussed and the extended comparative analysis of the experimental data is performed. The detected spectral shift is assigned with the effect of hierarchical organization of bone tissue. This hierarchy effect on the core-to-valence transition energies is regarded as a promising tool for medical imaging and perspective pathway for nanodiagnostics of mineralized bone. Contribution to the Topical Issue "Dynamics of Systems at the Nanoscale", edited by Andrey Solov'yov and Andrei Korol.
Research & Technology Report Goddard Space Flight Center

NASA Technical Reports Server (NTRS)

Soffen, Gerald A. (Editor); Truszkowski, Walter (Editor); Ottenstein, Howard (Editor); Frost, Kenneth (Editor); Maran, Stephen (Editor); Walter, Lou (Editor); Brown, Mitch (Editor)

1995-01-01

The main theme of this edition of the annual Research and Technology Report is Mission Operations and Data Systems. Shifting from centralized to distributed mission operations, and from human interactive operations to highly automated operations is reported. The following aspects are addressed: Mission planning and operations; TDRSS, Positioning Systems, and orbit determination; hardware and software associated with Ground System and Networks; data processing and analysis; and World Wide Web. Flight projects are described along with the achievements in space sciences and earth sciences. Spacecraft subsystems, cryogenic developments, and new tools and capabilities are also discussed.
Microwave and Infrared Absorption Properties of Atmospheric Species with Special Emphasis on Line Widths and Shifts.

DTIC Science & Technology

1985-07-01

studied pressure-broadening of the 110.8 GHz line of ozone (6 1 5 6 0 6) for the foreign gases N2 and 02. Considering a temper- ature range from 200...nitrogen and oxygen as tje perturbing gases . Calculations using * conventional Anderson theory or quantum Fourier transform theory2 are shown to be...one gases in the region from 0 to 10,000 cm-’. Emphasis on this edition has been on the addition of numerous millimeter and submillimeter transitions
Addressing the Challenges of Pathogen Evolution on the World's Arable Crops.

PubMed

Burdon, Jeremy J; Zhan, Jiasui; Barrett, Luke G; Papaïx, Julien; Thrall, Peter H

2016-10-01

Advances in genomic and molecular technologies coupled with an increasing understanding of the fine structure of many resistance and infectivity genes, have opened up a new era of hope in controlling the many plant pathogens that continue to be a major source of loss in arable crops. Some new approaches are under consideration including the use of nonhost resistance and the targeting of critical developmental constraints. However, the major thrust of these genomic and molecular approaches is to enhance the identification of resistance genes, to increase their ease of manipulation through marker and gene editing technologies and to lock a range of resistance genes together in simply manipulable resistance gene cassettes. All these approaches essentially continue a strategy that assumes the ability to construct genetic-based resistance barriers that are insurmountable to target pathogens. Here we show how the recent advances in knowledge and marker technologies can be used to generate more durable disease resistance strategies that are based on broad evolutionary principles aimed at presenting pathogens with a shifting, landscape of fluctuating directional selection.
Regulation of Gene Editing Activity Directed by Single-Stranded Oligonucleotides and CRISPR/Cas9 Systems

PubMed Central

Bialk, Pawel; Rivera-Torres, Natalia; Strouse, Bryan; Kmiec, Eric B.

2015-01-01

Single-stranded DNA oligonucleotides (ssODNs) can direct the repair of a single base mutation in human genes. While the regulation of this gene editing reaction has been partially elucidated, the low frequency with which repair occurs has hampered development toward clinical application. In this work a CRISPR/Cas9 complex is employed to induce double strand DNA breakage at specific sites surrounding the nucleotide designated for exchange. The result is a significant elevation in ssODN-directed gene repair, validated by a phenotypic readout. By analysing reaction parameters, we have uncovered restrictions on gene editing activity involving CRISPR/Cas9 complexes. First, ssODNs that hybridize to the non-transcribed strand direct a higher level of gene repair than those that hybridize to the transcribed strand. Second, cleavage must be proximal to the targeted mutant base to enable higher levels of gene editing. Third, DNA cleavage enables a higher level of gene editing activity as compared to single-stranded DNA nicks, created by modified Cas9 (Nickases). Fourth, we calculated the hybridization potential and free energy levels of ssODNs that are complementary to the guide RNA sequences of CRISPRs used in this study. We find a correlation between free energy potential and the capacity of single-stranded oligonucleotides to inhibit specific DNA cleavage activity, thereby indirectly reducing gene editing activity. Our data provide novel information that might be taken into consideration in the design and usage of CRISPR/Cas9 systems with ssODNs for gene editing. PMID:26053390
Regulation of Gene Editing Activity Directed by Single-Stranded Oligonucleotides and CRISPR/Cas9 Systems.

PubMed

Bialk, Pawel; Rivera-Torres, Natalia; Strouse, Bryan; Kmiec, Eric B

2015-01-01

Single-stranded DNA oligonucleotides (ssODNs) can direct the repair of a single base mutation in human genes. While the regulation of this gene editing reaction has been partially elucidated, the low frequency with which repair occurs has hampered development toward clinical application. In this work a CRISPR/Cas9 complex is employed to induce double strand DNA breakage at specific sites surrounding the nucleotide designated for exchange. The result is a significant elevation in ssODN-directed gene repair, validated by a phenotypic readout. By analysing reaction parameters, we have uncovered restrictions on gene editing activity involving CRISPR/Cas9 complexes. First, ssODNs that hybridize to the non-transcribed strand direct a higher level of gene repair than those that hybridize to the transcribed strand. Second, cleavage must be proximal to the targeted mutant base to enable higher levels of gene editing. Third, DNA cleavage enables a higher level of gene editing activity as compared to single-stranded DNA nicks, created by modified Cas9 (Nickases). Fourth, we calculated the hybridization potential and free energy levels of ssODNs that are complementary to the guide RNA sequences of CRISPRs used in this study. We find a correlation between free energy potential and the capacity of single-stranded oligonucleotides to inhibit specific DNA cleavage activity, thereby indirectly reducing gene editing activity. Our data provide novel information that might be taken into consideration in the design and usage of CRISPR/Cas9 systems with ssODNs for gene editing.
Genetic spell-checking: gene editing using single-stranded DNA oligonucleotides.

PubMed

Rivera-Torres, Natalia; Kmiec, Eric B

2016-02-01

Single-stranded oligonucleotides (ssODNs) can be used to direct the exchange of a single nucleotide or the repair of a single base within the coding region of a gene in a process that is known, generically, as gene editing. These molecules are composed of either all DNA residues or a mixture of RNA and DNA bases and utilize inherent metabolic functions to execute the genetic alteration within the context of a chromosome. The mechanism of action of gene editing is now being elucidated as well as an understanding of its regulatory circuitry, work that has been particularly important in establishing a foundation for designing effective gene editing strategies in plants. Double-strand DNA breakage and the activation of the DNA damage response pathway play key roles in determining the frequency with which gene editing activity takes place. Cellular regulators respond to such damage and their action impacts the success or failure of a particular nucleotide exchange reaction. A consequence of such activation is the natural slowing of replication fork progression, which naturally creates a more open chromatin configuration, thereby increasing access of the oligonucleotide to the DNA template. Herein, how critical reaction parameters influence the effectiveness of gene editing is discussed. Functional interrelationships between DNA damage, the activation of DNA response pathways and the stalling of replication forks are presented in detail as potential targets for increasing the frequency of gene editing by ssODNs in plants and plant cells. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
A Novel Computational Strategy to Identify A-to-I RNA Editing Sites by RNA-Seq Data: De Novo Detection in Human Spinal Cord Tissue

PubMed Central

Picardi, Ernesto; Gallo, Angela; Galeano, Federica; Tomaselli, Sara; Pesole, Graziano

2012-01-01

RNA editing is a post-transcriptional process occurring in a wide range of organisms. In human brain, the A-to-I RNA editing, in which individual adenosine (A) bases in pre-mRNA are modified to yield inosine (I), is the most frequent event. Modulating gene expression, RNA editing is essential for cellular homeostasis. Indeed, its deregulation has been linked to several neurological and neurodegenerative diseases. To date, many RNA editing sites have been identified by next generation sequencing technologies employing massive transcriptome sequencing together with whole genome or exome sequencing. While genome and transcriptome reads are not always available for single individuals, RNA-Seq data are widespread through public databases and represent a relevant source of yet unexplored RNA editing sites. In this context, we propose a simple computational strategy to identify genomic positions enriched in novel hypothetical RNA editing events by means of a new two-steps mapping procedure requiring only RNA-Seq data and no a priori knowledge of RNA editing characteristics and genomic reads. We assessed the suitability of our procedure by confirming A-to-I candidates using conventional Sanger sequencing and performing RNA-Seq as well as whole exome sequencing of human spinal cord tissue from a single individual. PMID:22957051
Genome editing in pluripotent stem cells: research and therapeutic applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deleidi, Michela, E-mail: michela.deleidi@dzne.de; Hertie Institute for Clinical Brain Research, University of Tübingen; Yu, Cong

Recent progress in human pluripotent stem cell (hPSC) and genome editing technologies has opened up new avenues for the investigation of human biology in health and disease as well as the development of therapeutic applications. Gene editing approaches with programmable nucleases have been successfully established in hPSCs and applied to study gene function, develop novel animal models and perform genetic and chemical screens. Several studies now show the successful editing of disease-linked alleles in somatic and patient-derived induced pluripotent stem cells (iPSCs) as well as in animal models. Importantly, initial clinical trials have shown the safety of programmable nucleases formore » ex vivo somatic gene therapy. In this context, the unlimited proliferation potential and the pluripotent properties of iPSCs may offer advantages for gene targeting approaches. However, many technical and safety issues still need to be addressed before genome-edited iPSCs are translated into the clinical setting. Here, we provide an overview of the available genome editing systems and discuss opportunities and perspectives for their application in basic research and clinical practice, with a particular focus on hPSC based research and gene therapy approaches. Finally, we discuss recent research on human germline genome editing and its social and ethical implications. - Highlights: • Programmable nucleases have proven efficient and specific for genome editing in human pluripotent stem cells (hPSCs). • Genome edited hPSCs can be employed to study gene function in health and disease as well as drug and chemical screens. • Genome edited hPSCs hold great promise for ex vivo gene therapy approaches. • Technical and safety issues should be first addressed to advance the clinical use of gene-edited hPSCs.« less
Cell-type-specific genome editing with a microRNA-responsive CRISPR–Cas9 switch

PubMed Central

Hirosawa, Moe; Fujita, Yoshihiko; Parr, Callum J. C.; Hayashi, Karin; Kashida, Shunnichi; Hotta, Akitsu; Woltjen, Knut

2017-01-01

Abstract The CRISPR–Cas9 system is a powerful genome-editing tool useful in a variety of biotechnology and biomedical applications. Here we developed a synthetic RNA-based, microRNA (miRNA)-responsive CRISPR–Cas9 system (miR-Cas9 switch) in which the genome editing activity of Cas9 can be modulated through endogenous miRNA signatures in mammalian cells. We created miR-Cas9 switches by using a miRNA-complementary sequence in the 5΄-UTR of mRNA encoding Streptococcus pyogenes Cas9. The miR-21-Cas9 or miR-302-Cas9 switches selectively and efficiently responded to miR-21-5p in HeLa cells or miR-302a-5p in human induced pluripotent stem cells, and post-transcriptionally attenuated the Cas9 activity only in the target cells. Moreover, the miR-Cas9 switches could differentially control the genome editing by sensing endogenous miRNA activities within a heterogeneous cell population. Our miR-Cas9 switch system provides a promising framework for cell-type selective genome editing and cell engineering based on intracellular miRNA information. PMID:28525578
In vivo genome editing in animals using AAV-CRISPR system: applications to translational research of human disease

PubMed Central

Lau, Cia-Hin; Suh, Yousin

2017-01-01

Adeno-associated virus (AAV) has shown promising therapeutic efficacy with a good safety profile in a wide range of animal models and human clinical trials. With the advent of clustered regulatory interspaced short palindromic repeat (CRISPR)-based genome-editing technologies, AAV provides one of the most suitable viral vectors to package, deliver, and express CRISPR components for targeted gene editing. Recent discoveries of smaller Cas9 orthologues have enabled the packaging of Cas9 nuclease and its chimeric guide RNA into a single AAV delivery vehicle for robust in vivo genome editing. Here, we discuss how the combined use of small Cas9 orthologues, tissue-specific minimal promoters, AAV serotypes, and different routes of administration has advanced the development of efficient and precise in vivo genome editing and comprehensively review the various AAV-CRISPR systems that have been effectively used in animals. We then discuss the clinical implications and potential strategies to overcome off-target effects, immunogenicity, and toxicity associated with CRISPR components and AAV delivery vehicles. Finally, we discuss ongoing non-viral-based ex vivo gene therapy clinical trials to underscore the current challenges and future prospects of CRISPR/Cas9 delivery for human therapeutics. PMID:29333255
A-to-I RNA editing promotes developmental stage–specific gene and lncRNA expression

PubMed Central

Goldstein, Boaz; Agranat-Tamir, Lily; Light, Dean; Ben-Naim Zgayer, Orna; Fishman, Alla; Lamm, Ayelet T.

2017-01-01

A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions, mainly noncoding. Mutations in ADAR enzymes in Caenorhabditis elegans cause defects in normal development but are not lethal as in human and mouse. Previous studies in C. elegans indicated competition between RNA interference (RNAi) and RNA editing mechanisms, based on the observation that worms that lack both mechanisms do not exhibit defects, in contrast to the developmental defects observed when only RNA editing is absent. To study the effects of RNA editing on gene expression and function, we established a novel screen that enabled us to identify thousands of RNA editing sites in nonrepetitive regions in the genome. These include dozens of genes that are edited at their 3′ UTR region. We found that these genes are mainly germline and neuronal genes, and that they are down-regulated in the absence of ADAR enzymes. Moreover, we discovered that almost half of these genes are edited in a developmental-specific manner, indicating that RNA editing is a highly regulated process. We found that many pseudogenes and other lncRNAs are also extensively down-regulated in the absence of ADARs in the embryo but not in the fourth larval (L4) stage. This down-regulation is not observed upon additional knockout of RNAi. Furthermore, levels of siRNAs aligned to pseudogenes in ADAR mutants are enhanced. Taken together, our results suggest a role for RNA editing in normal growth and development by regulating silencing via RNAi. PMID:28031250
Producing an Online Undergraduate Literary Magazine: A Guide to Using Problem-Based Learning in the Writing and Publishing Classroom

ERIC Educational Resources Information Center

Persichetti, Amy L.

2016-01-01

This article will illustrate how a problem-based learning (PBL) course (Savery, 2006) can be used in a writing program as a vehicle for both creative and preprofessional learning. English 420: Writing, Publishing, and Editing is offered every fall, and its counterpart, English 423: Writing, Publishing, and Editing is offered each spring. The…
Expanding the Interaction Lexicon for 3D Graphics

DTIC Science & Technology

2001-11-01

believe that extending it to work with image-based rendering engines is straightforward. I could modify plenoptic image editing [Seitz] to allow...M. Seitz and Kiriakos N. Kutulakos. Plenoptic Image Editing. International Conference on Computer Vision ‘98, pages 17-24. [ShapeCapture
Harnessing the native type I-B CRISPR-Cas for genome editing in a polyploid archaeon.

PubMed

Cheng, Feiyue; Gong, Luyao; Zhao, Dahe; Yang, Haibo; Zhou, Jian; Li, Ming; Xiang, Hua

2017-11-20

Research on CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated protein) systems has led to the revolutionary CRISPR/Cas9 genome editing technique. However, for most archaea and half of bacteria, exploitation of their native CRISPR-Cas machineries may be more straightforward and convenient. In this study, we harnessed the native type I-B CRISPR-Cas system for precise genome editing in the polyploid haloarchaeon Haloarcula hispanica. After testing different designs, the editing tool was optimized to be a single plasmid that carries both the self-targeting mini-CRISPR and a 600-800 bp donor. Significantly, chromosomal modifications, such as gene deletion, gene tagging or single nucleotide substitution, were precisely introduced into the vast majority of the transformants. Moreover, we showed that simultaneous editing of two genomic loci could also be readily achieved by one step. In summary, our data demonstrate that the haloarchaeal CRISPR-Cas system can be harnessed for genome editing in this polyploid archaeon, and highlight the convenience and efficiency of the native CRISPR-based genome editing strategy. Copyright © 2017 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Reproductive medicine involving genome editing: clinical uncertainties and embryological needs.

PubMed

Ishii, Tetsuya

2017-01-01

Genome editing based on site-directed nucleases facilitated efficient and versatile genetic modifications in human cells. However, recent reports, demonstrating CRISPR/Cas9-mediated genome editing in human embryos have raised profound concerns worldwide. This commentary explores the clinical justification and feasibility of reproductive medicine using germline genome editing. Despite the perceived utility of reproductive medicine for treating intractable infertility, it is difficult to justify germline genome editing from the perspective of the prospective child. As suggested by the UK legalization regarding mitochondrial donation, the prevention of genetic disease in offspring by genome editing might be acceptable in limited cases of serious or life-threatening conditions, where no alternative medicine is available. Nonetheless, the mosaicism underlying human embryos as well as the off-target effect by artificial nucleases will likely hamper preimplantation genetic diagnosis prior to embryo transfer. Such considerations suggest that this type of reproductive medicine should not be developed toward a clinical application. However, the clinical uncertainties underscore the need for embryology that can address fundamental questions regarding germline aneuploidy and mosaicism using genome editing. Copyright © 2016 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.
Protein synthesis editing by a DNA aptamer.

PubMed Central

Hale, S P; Schimmel, P

1996-01-01

Potential errors in decoding genetic information are corrected by tRNA-dependent amino acid recognition processes manifested through editing reactions. One example is the rejection of difficult-to-discriminate misactivated amino acids by tRNA synthetases through hydrolytic reactions. Although several crystal structures of tRNA synthetases and synthetase-tRNA complexes exist, none of them have provided insight into the editing reactions. Other work suggested that editing required active amino acid acceptor hydroxyl groups at the 3' end of a tRNA effector. We describe here the isolation of a DNA aptamer that specifically induced hydrolysis of a misactivated amino acid bound to a tRNA synthetase. The aptamer had no effect on the stability of the correctly activated amino acid and was almost as efficient as the tRNA for inducing editing activity. The aptamer has no sequence similarity to that of the tRNA effector and cannot be folded into a tRNA-like structure. These and additional data show that active acceptor hydroxyl groups in a tRNA effector and a tRNA-like structure are not essential for editing. Thus, specific bases in a nucleic acid effector trigger the editing response. Images Fig. 3 Fig. 4 PMID:8610114
Temperature-Dependence of Air-Broadened Line Widths and Shifts in the nu3 Band of Ozone

NASA Technical Reports Server (NTRS)

Smith, Mary A. H.; Rinsland, Curtis P.; Devi, V. Malathy; Benner, D. Chris; Cox, A. M.

2006-01-01

The 9.6-micron bands of O3 are used by many remote-sensing experiments for retrievals of terrestrial atmospheric ozone concentration profiles. Line parameter errors can contribute significantly to the total errors in these retrievals, particularly for nadir-viewing. The McMath-Pierce Fourier transform spectrometer at the National Solar Observatory on Kitt Peak was used to record numerous high-resolution infrared absorption spectra of O3 broadened by various gases at temperatures between 160 and 300 K. Over 30 spectra were analyzed simultaneously using a multispectrum nonlinear least squares fitting technique to determine Lorentz air-broadening and pressure-induced shift coefficients along with their temperature dependences for selected transitions in the 3 fundamental band of (16)O3. We compare the present results with other measurements reported in the literature and with the ozone parameters on the 2000 and 2004 editions of the HITRAN database.
Postnatal Cardiac Gene Editing Using CRISPR/Cas9 With AAV9-Mediated Delivery of Short Guide RNAs Results in Mosaic Gene Disruption.

PubMed

Johansen, Anne Katrine; Molenaar, Bas; Versteeg, Danielle; Leitoguinho, Ana Rita; Demkes, Charlotte; Spanjaard, Bastiaan; de Ruiter, Hesther; Akbari Moqadam, Farhad; Kooijman, Lieneke; Zentilin, Lorena; Giacca, Mauro; van Rooij, Eva

2017-10-27

CRISPR/Cas9 (clustered regularly interspaced palindromic repeats/CRISPR-associated protein 9)-based DNA editing has rapidly evolved as an attractive tool to modify the genome. Although CRISPR/Cas9 has been extensively used to manipulate the germline in zygotes, its application in postnatal gene editing remains incompletely characterized. To evaluate the feasibility of CRISPR/Cas9-based cardiac genome editing in vivo in postnatal mice. We generated cardiomyocyte-specific Cas9 mice and demonstrated that Cas9 expression does not affect cardiac function or gene expression. As a proof-of-concept, we delivered short guide RNAs targeting 3 genes critical for cardiac physiology, Myh6 , Sav1 , and Tbx20 , using a cardiotropic adeno-associated viral vector 9. Despite a similar degree of DNA disruption and subsequent mRNA downregulation, only disruption of Myh6 was sufficient to induce a cardiac phenotype, irrespective of short guide RNA exposure or the level of Cas9 expression. DNA sequencing analysis revealed target-dependent mutations that were highly reproducible across mice resulting in differential rates of in- and out-of-frame mutations. Finally, we applied a dual short guide RNA approach to effectively delete an important coding region of Sav1 , which increased the editing efficiency. Our results indicate that the effect of postnatal CRISPR/Cas9-based cardiac gene editing using adeno-associated virus serotype 9 to deliver a single short guide RNA is target dependent. We demonstrate a mosaic pattern of gene disruption, which hinders the application of the technology to study gene function. Further studies are required to expand the versatility of CRISPR/Cas9 as a robust tool to study novel cardiac gene functions in vivo. © 2017 American Heart Association, Inc.
Salient Features of Endonuclease Platforms for Therapeutic Genome Editing.

PubMed

Certo, Michael T; Morgan, Richard A

2016-03-01

Emerging gene-editing technologies are nearing a revolutionary phase in genetic medicine: precisely modifying or repairing causal genetic defects. This may include any number of DNA sequence manipulations, such as knocking out a deleterious gene, introducing a particular mutation, or directly repairing a defective sequence by site-specific recombination. All of these edits can currently be achieved via programmable rare-cutting endonucleases to create targeted DNA breaks that can engage and exploit endogenous DNA repair pathways to impart site-specific genetic changes. Over the past decade, several distinct technologies for introducing site-specific DNA breaks have been developed, yet the different biological origins of these gene-editing technologies bring along inherent differences in parameters that impact clinical implementation. This review aims to provide an accessible overview of the various endonuclease-based gene-editing platforms, highlighting the strengths and weakness of each with respect to therapeutic applications.
Salient Features of Endonuclease Platforms for Therapeutic Genome Editing

PubMed Central

Certo, Michael T; Morgan, Richard A

2016-01-01

Emerging gene-editing technologies are nearing a revolutionary phase in genetic medicine: precisely modifying or repairing causal genetic defects. This may include any number of DNA sequence manipulations, such as knocking out a deleterious gene, introducing a particular mutation, or directly repairing a defective sequence by site-specific recombination. All of these edits can currently be achieved via programmable rare-cutting endonucleases to create targeted DNA breaks that can engage and exploit endogenous DNA repair pathways to impart site-specific genetic changes. Over the past decade, several distinct technologies for introducing site-specific DNA breaks have been developed, yet the different biological origins of these gene-editing technologies bring along inherent differences in parameters that impact clinical implementation. This review aims to provide an accessible overview of the various endonuclease-based gene-editing platforms, highlighting the strengths and weakness of each with respect to therapeutic applications. PMID:26796671
A future scenario of the global regulatory landscape regarding genome-edited crops

PubMed Central

Araki, Motoko

2017-01-01

ABSTRACT The global agricultural landscape regarding the commercial cultivation of genetically modified (GM) crops is mosaic. Meanwhile, a new plant breeding technique, genome editing is expected to make genetic engineering-mediated crop breeding more socially acceptable because it can be used to develop crop varieties without introducing transgenes, which have hampered the regulatory review and public acceptance of GM crops. The present study revealed that product- and process-based concepts have been implemented to regulate GM crops in 30 countries. Moreover, this study analyzed the regulatory responses to genome-edited crops in the USA, Argentina, Sweden and New Zealand. The findings suggested that countries will likely be divided in their policies on genome-edited crops: Some will deregulate transgene-free crops, while others will regulate all types of crops that have been modified by genome editing. These implications are discussed from the viewpoint of public acceptance. PMID:27960622
International Community Development Statistical Bulletin. Spring 1968 General Edition.

ERIC Educational Resources Information Center

Community Development Foundation, New York, NY.

The Spring 1968 general edition of the International Community Development Statistical Bulletin describes its reporting system based on the International Standard Classification of Community Development Activities and a special project registration and progress form; briefly summarizes overall international data; and presents statistics on…
Software Assists in Extensive Environmental Auditing

NASA Technical Reports Server (NTRS)

Callac, Christopher; Matherne, Charlie

2002-01-01

The Base Enivronmental Management System (BEMS) is a Web-based application program for managing and tracking audits by the Environmental Office of Stennis Space Center in conformity with standard 14001 of the International Organization for Standardization (ISO 14001). (This standard specifies requirements for an environmental-management system.) BEMS saves time by partly automating what were previously manual processes for creating audit checklists; recording and tracking audit results; issuing, tracking, and implementing corrective-action requests (CARs); tracking continuous improvements (CIs); and tracking audit results and statistics. BEMS consists on an administration module and an auditor module. As its name suggests, the administration module is used to administer the audit. It helps administrators to edit the list of audit questions; edit the list of audit locations; assign manditory questions to locations; track, approve, and edit CARs; and edit completed audits. The auditor module is used by auditors to perform audits and record audit results: It helps the auditors to create audit checklists, complete audits, view completed audits, create CARs, record and acknowledge CIs, and generate reports from audit results.
Software Assists in Extensive Environmental Auditing

NASA Technical Reports Server (NTRS)

Callac, Christopher; Matherne, Charlie

2003-01-01

The Base Environmental Management System (BEMS) is a Web-based application program for managing and tracking audits by the Environmental Office of Stennis Space Center in conformity with standard 14001 of the International Organization for Standardization (ISO 14001). (This standard specifies requirements for an environmental-management system.) BEMS saves time by partly automating what were previously manual processes for creating audit checklists; recording and tracking audit results; issuing, tracking, and implementing corrective-action requests (CARs); tracking continuous improvements (CIs); and tracking audit results and statistics. BEMS consists of an administration module and an auditor module. As its name suggests, the administration module is used to administer the audit. It helps administrators to edit the list of audit questions; edit the list of audit locations; assign mandatory questions to locations; track, approve, and edit CARs; and edit completed audits. The auditor module is used by auditors to perform audits and record audit results: it helps the auditors to create audit checklists, complete audits, view completed audits, create CARs, record and acknowledge CIs, and generate reports from audit results.
Software Assists in Extensive Environmental Auditing

NASA Technical Reports Server (NTRS)

Callac, Christopher; Matherne, Charlie; Selinsky, T.

2002-01-01

The Base Environmental Management System (BEMS) is a Web-based application program for managing and tracking audits by the Environmental Office of Stennis Space Center in conformity with standard 14001 of the International Organization for Standardization (ISO 14001). (This standard specifies requirements for an environmental-management system.) BEMS saves time by partly automating what were previously manual processes for creating audit checklists; recording and tracking audit results; issuing, tracking, and implementing corrective-action requests (CARs); tracking continuous improvements (CIs); and tracking audit results and statistics. BEMS consists of an administration module and an auditor module. As its name suggests, the administration module is used to administer the audit. It helps administrators to edit the list of audit questions; edit the list of audit locations; assign mandatory questions to locations; track, approve, and edit CARs; and edit completed audits. The auditor module is used by auditors to perform audits and record audit results: it helps the auditors to create audit checklists, complete audits, view completed audits, create CARs, record and acknowledge CIs, and generate reports from audit results.
Content-based Music Search and Recommendation System

NASA Astrophysics Data System (ADS)

Takegawa, Kazuki; Hijikata, Yoshinori; Nishida, Shogo

Recently, the turn volume of music data on the Internet has increased rapidly. This has increased the user's cost to find music data suiting their preference from such a large data set. We propose a content-based music search and recommendation system. This system has an interface for searching and finding music data and an interface for editing a user profile which is necessary for music recommendation. By exploiting the visualization of the feature space of music and the visualization of the user profile, the user can search music data and edit the user profile. Furthermore, by exploiting the infomation which can be acquired from each visualized object in a mutually complementary manner, we make it easier for the user to search music data and edit the user profile. Concretely, the system gives to the user an information obtained from the user profile when searching music data and an information obtained from the feature space of music when editing the user profile.
Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles.

PubMed

Wang, Ming; Zuris, John A; Meng, Fantao; Rees, Holly; Sun, Shuo; Deng, Pu; Han, Yong; Gao, Xue; Pouli, Dimitra; Wu, Qi; Georgakoudi, Irene; Liu, David R; Xu, Qiaobing

2016-03-15

A central challenge to the development of protein-based therapeutics is the inefficiency of delivery of protein cargo across the mammalian cell membrane, including escape from endosomes. Here we report that combining bioreducible lipid nanoparticles with negatively supercharged Cre recombinase or anionic Cas9:single-guide (sg)RNA complexes drives the electrostatic assembly of nanoparticles that mediate potent protein delivery and genome editing. These bioreducible lipids efficiently deliver protein cargo into cells, facilitate the escape of protein from endosomes in response to the reductive intracellular environment, and direct protein to its intracellular target sites. The delivery of supercharged Cre protein and Cas9:sgRNA complexed with bioreducible lipids into cultured human cells enables gene recombination and genome editing with efficiencies greater than 70%. In addition, we demonstrate that these lipids are effective for functional protein delivery into mouse brain for gene recombination in vivo. Therefore, the integration of this bioreducible lipid platform with protein engineering has the potential to advance the therapeutic relevance of protein-based genome editing.
PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination

PubMed Central

Lee, Woonghee; Kim, Jin Hae; Westler, William M.; Markley, John L.

2011-01-01

Summary: PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY (13C-edited and/or 15N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. Availability: The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/. Contact: whlee@nmrfam.wisc.edu; markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21511715
Naval Observatory Vector Astrometry Software (NOVAS) Version 3.1:Fortran, C, and Python Editions

NASA Astrophysics Data System (ADS)

Kaplan, G. H.; Bangert, J. A.; Barron, E. G.; Bartlett, J. L.; Puatua, W.; Harris, W.; Barrett, P.

2012-08-01

The Naval Observatory Vector Astrometry Software (NOVAS) is a source - code library that provides common astrometric quantities and transformations to high precision. The library can supply, in one or two subroutine or function calls, the instantaneous celestial position of any star or planet in a variety of coordinate systems. NOVAS also provides access to all of the building blocks that go into such computations. NOVAS is used for a wide variety of applications, including the U.S. portions of The Astronomical Almanac and a number of telescope control systems. NOVAS uses IAU recommended models for Earth orientation, including the IAU 2006 precession theory, the IAU 2000A and 2000B nutation series, and diurnal rotation based on the celestial and terrestrial intermediate origins. Equinox - based quantities, such as sidereal time, are also supported. NOVAS Earth orientation calculations match those from SOFA at the sub - microarcsecond level for comparable transformations. NOVAS algorithms for aberration an d gravitational light deflection are equivalent, at the microarcsecond level, to those inherent in the current consensus VLBI delay algorithm. NOVAS can be easily connected to the JPL planetary/lunar ephemerides (e.g., DE405), and connections to IMCCE and IAA planetary ephemerides are planned. NOVAS Version 3.1 introduces a Python edition alongside the Fortran and C editions. The Python edition uses the computational code from the C edition and currently mimics the function calls of the C edition. Future versions will expand the functionality of the Python edition to exploit the object - oriented features of Python. In the Version 3.1 C edition, the ephemeris - access functions have been revised for use on 64 - bit systems and for improved performance in general. NOVAS source code, auxiliary files, and documentation are available from the USNO website (http://aa.usno.navy.mil/software/novas/novas_info.php).
The changing landscape of gene editing in hematopoietic stem cells: a step towards Cas9 clinical translation.

PubMed

Dever, Daniel P; Porteus, Matthew H

2017-11-01

Since the discovery two decades ago that programmable endonucleases can be engineered to modify human cells at single nucleotide resolution, the concept of genome editing was born. Now these technologies are being applied to therapeutically relevant cell types, including hematopoietic stem cells (HSC), which possess the power to repopulate an entire blood and immune system. The purpose of this review is to discuss the changing landscape of genome editing in hematopoietic stem cells (GE-HSC) from the discovery stage to the preclinical stage, with the imminent goal of clinical translation for the treatment of serious genetic diseases of the blood and immune system. With the discovery that the RNA-programmable (sgRNA) clustered regularly interspace short palindromic repeats (CRISPR)-Cas9 nuclease (Cas9/sgRNA) systems can be easily used to precisely modify the human genome in 2012, a genome-editing revolution of hematopoietic stem cells (HSC) has bloomed. We have observed that over the last 2 years, academic institutions and small biotech companies are developing HSC-based Cas9/sgRNA genome-editing curative strategies to treat monogenic disorders, including β-hemoglobinopathies and primary immunodeficiencies. We will focus on recent publications (within the past 2 years) that employ different genome-editing strategies to 'hijack' the cell's endogenous double-strand repair pathways to confer a disease-specific therapeutic advantage. The number of genome-editing strategies in HSCs that could offer therapeutic potential for diseases of the blood and immune system have dramatically risen over the past 2 years. The HSC-based genome-editing field is primed to enter clinical trials in the subsequent years. We will summarize the major advancements for the development of novel autologous GE-HSC cell and gene therapy strategies for hematopoietic diseases that are candidates for curative allogeneic bone marrow transplantation.
An Efficient, Rapid, and Recyclable System for CRISPR-Mediated Genome Editing in Candida albicans.

PubMed

Nguyen, Namkha; Quail, Morgan M F; Hernday, Aaron D

2017-01-01

Candida albicans is the most common fungal pathogen of humans. Historically, molecular genetic analysis of this important pathogen has been hampered by the lack of stable plasmids or meiotic cell division, limited selectable markers, and inefficient methods for generating gene knockouts. The recent development of clustered regularly interspaced short palindromic repeat(s) (CRISPR)-based tools for use with C. albicans has opened the door to more efficient genome editing; however, previously reported systems have specific limitations. We report the development of an optimized CRISPR-based genome editing system for use with C. albicans . Our system is highly efficient, does not require molecular cloning, does not leave permanent markers in the genome, and supports rapid, precise genome editing in C. albicans . We also demonstrate the utility of our system for generating two independent homozygous gene knockouts in a single transformation and present a method for generating homozygous wild-type gene addbacks at the native locus. Furthermore, each step of our protocol is compatible with high-throughput strain engineering approaches, thus opening the door to the generation of a complete C. albicans gene knockout library. IMPORTANCE Candida albicans is the major fungal pathogen of humans and is the subject of intense biomedical and discovery research. Until recently, the pace of research in this field has been hampered by the lack of efficient methods for genome editing. We report the development of a highly efficient and flexible genome editing system for use with C. albicans . This system improves upon previously published C. albicans CRISPR systems and enables rapid, precise genome editing without the use of permanent markers. This new tool kit promises to expedite the pace of research on this important fungal pathogen.
Empowering file-based radio production through media asset management systems

NASA Astrophysics Data System (ADS)

Muylaert, Bjorn; Beckers, Tom

2006-10-01

In recent years, IT-based production and archiving of media has matured to a level which enables broadcasters to switch over from tape- or CD-based to file-based workflows for the production of their radio and television programs. This technology is essential for the future of broadcasters as it provides the flexibility and speed of execution the customer demands by enabling, among others, concurrent access and production, faster than real-time ingest, edit during ingest, centrally managed annotation and quality preservation of media. In terms of automation of program production, the radio department is the most advanced within the VRT, the Flemish broadcaster. Since a couple of years ago, the radio department has been working with digital equipment and producing its programs mainly on standard IT equipment. Historically, the shift from analogue to digital based production has been a step by step process initiated and coordinated by each radio station separately, resulting in a multitude of tools and metadata collections, some of them developed in-house, lacking integration. To make matters worse, each of those stations adopted a slightly different production methodology. The planned introduction of a company-wide Media Asset Management System allows a coordinated overhaul to a unified production architecture. Benefits include the centralized ingest and annotation of audio material and the uniform, integrated (in terms of IT infrastructure) workflow model. Needless to say, the ingest strategy, metadata management and integration with radio production systems play a major role in the level of success of any improvement effort. This paper presents a data model for audio-specific concepts relevant to radio production. It includes an investigation of ingest techniques and strategies. Cooperation with external, professional production tools is demonstrated through a use-case scenario: the integration of an existing, multi-track editing tool with a commercially available Media Asset Management System. This will enable an uncomplicated production chain, with a recognizable look and feel for all system users, regardless of their affiliated radio station, as well as central retrieval and storage of information and metadata.
Genome editing using CRISPR/Cas9-based knock-in approaches in zebrafish.

PubMed

Albadri, Shahad; Del Bene, Filippo; Revenu, Céline

2017-05-15

With its variety of applications, the CRISPR/Cas9 genome editing technology has been rapidly evolving in the last few years. In the zebrafish community, knock-out reports are constantly increasing but insertion studies have been so far more challenging. With this review, we aim at giving an overview of the homologous directed repair (HDR)-based knock-in generation in zebrafish. We address the critical points and limitations of the procedure such as cutting efficiency of the chosen single guide RNA, use of cas9 mRNA or Cas9 protein, homology arm size etc. but also ways to circumvent encountered issues with HDR insertions by the development of non-homologous dependent strategies. While imprecise, these homology-independent mechanisms based on non-homologous-end-joining (NHEJ) repair have been employed in zebrafish to generate reporter lines or to accurately edit an open reading frame by the use of intron-targeting modifications. Therefore, with higher efficiency and insertion rate, NHEJ-based knock-in seems to be a promising approach to target endogenous loci and to circumvent the limitations of HDR whenever it is possible and appropriate. In this perspective, we propose new strategies to generate cDNA edited or tagged insertions, which once established will constitute a new and versatile toolbox for CRISPR/Cas9-based knock-ins in zebrafish. Copyright © 2017 Elsevier Inc. All rights reserved.
High content analysis platform for optimization of lipid mediated CRISPR-Cas9 delivery strategies in human cells.

PubMed

Steyer, Benjamin; Carlson-Stevermer, Jared; Angenent-Mari, Nicolas; Khalil, Andrew; Harkness, Ty; Saha, Krishanu

2016-04-01

Non-viral gene-editing of human cells using the CRISPR-Cas9 system requires optimized delivery of multiple components. Both the Cas9 endonuclease and a single guide RNA, that defines the genomic target, need to be present and co-localized within the nucleus for efficient gene-editing to occur. This work describes a new high-throughput screening platform for the optimization of CRISPR-Cas9 delivery strategies. By exploiting high content image analysis and microcontact printed plates, multi-parametric gene-editing outcome data from hundreds to thousands of isolated cell populations can be screened simultaneously. Employing this platform, we systematically screened four commercially available cationic lipid transfection materials with a range of RNAs encoding the CRISPR-Cas9 system. Analysis of Cas9 expression and editing of a fluorescent mCherry reporter transgene within human embryonic kidney cells was monitored over several days after transfection. Design of experiments analysis enabled rigorous evaluation of delivery materials and RNA concentration conditions. The results of this analysis indicated that the concentration and identity of transfection material have significantly greater effect on gene-editing than ratio or total amount of RNA. Cell subpopulation analysis on microcontact printed plates, further revealed that low cell number and high Cas9 expression, 24h after CRISPR-Cas9 delivery, were strong predictors of gene-editing outcomes. These results suggest design principles for the development of materials and transfection strategies with lipid-based materials. This platform could be applied to rapidly optimize materials for gene-editing in a variety of cell/tissue types in order to advance genomic medicine, regenerative biology and drug discovery. CRISPR-Cas9 is a new gene-editing technology for "genome surgery" that is anticipated to treat genetic diseases. This technology uses multiple components of the Cas9 system to cut out disease-causing mutations in the human genome and precisely suture in therapeutic sequences. Biomaterials based delivery strategies could help transition these technologies to the clinic. The design space for materials based delivery strategies is vast and optimization is essential to ensuring the safety and efficacy of these treatments. Therefore, new methods are required to rapidly and systematically screen gene-editing efficacy in human cells. This work utilizes an innovative platform to generate and screen many formulations of synthetic biomaterials and components of the CRISPR-Cas9 system in parallel. On this platform, we watch genome surgery in action using high content image analysis. These capabilities enabled us to identify formulation parameters for Cas9-material complexes that can optimize gene-editing in a specific human cell type. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A-to-I RNA editing promotes developmental stage-specific gene and lncRNA expression.

PubMed

Goldstein, Boaz; Agranat-Tamir, Lily; Light, Dean; Ben-Naim Zgayer, Orna; Fishman, Alla; Lamm, Ayelet T

2017-03-01

A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions, mainly noncoding. Mutations in ADAR enzymes in Caenorhabditis elegans cause defects in normal development but are not lethal as in human and mouse. Previous studies in C. elegans indicated competition between RNA interference (RNAi) and RNA editing mechanisms, based on the observation that worms that lack both mechanisms do not exhibit defects, in contrast to the developmental defects observed when only RNA editing is absent. To study the effects of RNA editing on gene expression and function, we established a novel screen that enabled us to identify thousands of RNA editing sites in nonrepetitive regions in the genome. These include dozens of genes that are edited at their 3' UTR region. We found that these genes are mainly germline and neuronal genes, and that they are down-regulated in the absence of ADAR enzymes. Moreover, we discovered that almost half of these genes are edited in a developmental-specific manner, indicating that RNA editing is a highly regulated process. We found that many pseudogenes and other lncRNAs are also extensively down-regulated in the absence of ADARs in the embryo but not in the fourth larval (L4) stage. This down-regulation is not observed upon additional knockout of RNAi. Furthermore, levels of siRNAs aligned to pseudogenes in ADAR mutants are enhanced. Taken together, our results suggest a role for RNA editing in normal growth and development by regulating silencing via RNAi. © 2017 Goldstein et al.; Published by Cold Spring Harbor Laboratory Press.
Intellectual interchanges in the history of the massive online open-editing encyclopedia, Wikipedia

NASA Astrophysics Data System (ADS)

Yun, Jinhyuk; Lee, Sang Hoon; Jeong, Hawoong

2016-01-01

Wikipedia is a free Internet encyclopedia with an enormous amount of content. This encyclopedia is written by volunteers with various backgrounds in a collective fashion; anyone can access and edit most of the articles. This open-editing nature may give us prejudice that Wikipedia is an unstable and unreliable source; yet many studies suggest that Wikipedia is even more accurate and self-consistent than traditional encyclopedias. Scholars have attempted to understand such extraordinary credibility, but usually used the number of edits as the unit of time, without consideration of real time. In this work, we probe the formation of such collective intelligence through a systematic analysis using the entire history of 34 534 110 English Wikipedia articles, between 2001 and 2014. From this massive data set, we observe the universality of both timewise and lengthwise editing scales, which suggests that it is essential to consider the real-time dynamics. By considering real time, we find the existence of distinct growth patterns that are unobserved by utilizing the number of edits as the unit of time. To account for these results, we present a mechanistic model that adopts the article editing dynamics based on both editor-editor and editor-article interactions. The model successfully generates the key properties of real Wikipedia articles such as distinct types of articles for the editing patterns characterized by the interrelationship between the numbers of edits and editors, and the article size. In addition, the model indicates that infrequently referred articles tend to grow faster than frequently referred ones, and articles attracting a high motivation to edit counterintuitively reduce the number of participants. We suggest that this decay of participants eventually brings inequality among the editors, which will become more severe with time.
Intellectual interchanges in the history of the massive online open-editing encyclopedia, Wikipedia.

PubMed

Yun, Jinhyuk; Lee, Sang Hoon; Jeong, Hawoong

2016-01-01

Wikipedia is a free Internet encyclopedia with an enormous amount of content. This encyclopedia is written by volunteers with various backgrounds in a collective fashion; anyone can access and edit most of the articles. This open-editing nature may give us prejudice that Wikipedia is an unstable and unreliable source; yet many studies suggest that Wikipedia is even more accurate and self-consistent than traditional encyclopedias. Scholars have attempted to understand such extraordinary credibility, but usually used the number of edits as the unit of time, without consideration of real time. In this work, we probe the formation of such collective intelligence through a systematic analysis using the entire history of 34534110 English Wikipedia articles, between 2001 and 2014. From this massive data set, we observe the universality of both timewise and lengthwise editing scales, which suggests that it is essential to consider the real-time dynamics. By considering real time, we find the existence of distinct growth patterns that are unobserved by utilizing the number of edits as the unit of time. To account for these results, we present a mechanistic model that adopts the article editing dynamics based on both editor-editor and editor-article interactions. The model successfully generates the key properties of real Wikipedia articles such as distinct types of articles for the editing patterns characterized by the interrelationship between the numbers of edits and editors, and the article size. In addition, the model indicates that infrequently referred articles tend to grow faster than frequently referred ones, and articles attracting a high motivation to edit counterintuitively reduce the number of participants. We suggest that this decay of participants eventually brings inequality among the editors, which will become more severe with time.
Teaching Reading Sourcebook, Second Edition

ERIC Educational Resources Information Center

Honig, Bill; Diamond, Linda; Gutlohn, Linda

2008-01-01

The "Teaching Reading Sourcebook, Second Edition" is a comprehensive reference about reading instruction. Organized according to the elements of explicit instruction (what? why? when? and how?), the "Sourcebook" includes both a research-informed knowledge base and practical sample lesson models. It teaches the key elements of an effective reading…
The Community College Story. Third Edition

ERIC Educational Resources Information Center

Vaughan, George B.

2006-01-01

This concise history of community colleges touches on major themes, including open access and equity, comprehensiveness, community-based philosophy, commitment to teaching, and lifelong learning. The third edition includes revised text as well as updated statistical information, time line, reading list, and Internet resources. In the more than a…
CRISPR-Cas9-Based Genome Editing of Human Induced Pluripotent Stem Cells.

PubMed

Giacalone, Joseph C; Sharma, Tasneem P; Burnight, Erin R; Fingert, John F; Mullins, Robert F; Stone, Edwin M; Tucker, Budd A

2018-02-28

Human induced pluripotent stem cells (hiPSCs) are the ideal cell source for autologous cell replacement. However, for patients with Mendelian diseases, genetic correction of the original disease-causing mutation is likely required prior to cellular differentiation and transplantation. The emergence of the CRISPR-Cas9 system has revolutionized the field of genome editing. By introducing inexpensive reagents that are relatively straightforward to design and validate, it is now possible to correct genetic variants or insert desired sequences at any location within the genome. CRISPR-based genome editing of patient-specific iPSCs shows great promise for future autologous cell replacement therapies. One caveat, however, is that hiPSCs are notoriously difficult to transfect, and optimized experimental design considerations are often necessary. This unit describes design strategies and methods for efficient CRISPR-based genome editing of patient- specific iPSCs. Additionally, it details a flexible approach that utilizes positive selection to generate clones with a desired genomic modification, Cre-lox recombination to remove the integrated selection cassette, and negative selection to eliminate residual hiPSCs with intact selection cassettes. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.
Neurodevelopmental Outcome of Young Children with Biliary Atresia and Native Liver: Results from the ChiLDReN Study.

PubMed

Ng, Vicky L; Sorensen, Lisa G; Alonso, Estella M; Fredericks, Emily M; Ye, Wen; Moore, Jeff; Karpen, Saul J; Shneider, Benjamin L; Molleston, Jean P; Bezerra, Jorge A; Murray, Karen F; Loomes, Kathleen M; Rosenthal, Philip; Squires, Robert H; Wang, Kasper; Arnon, Ronen; Schwarz, Kathleen B; Turmelle, Yumirle P; Haber, Barbara H; Sherker, Averell H; Magee, John C; Sokol, Ronald J

2018-05-01

To assess neurodevelopmental outcomes among participants with biliary atresia with their native liver at ages 12 months (group 1) and 24 months (group 2), and to evaluate variables predictive of neurodevelopmental impairment. Participants enrolled in a prospective, longitudinal, multicenter study underwent neurodevelopmental testing with either the Bayley Scales of Infant Development, 2nd edition, or Bayley Scales of Infant and Toddler Development, 3rd edition. Scores (normative mean = 100 ± 15) were categorized as ≥100, 85-99, and <85 for χ 2 analysis. Risk for neurodevelopmental impairment (defined as ≥1 score of <85 on the Bayley Scales of Infant Development, 2nd edition, or Bayley Scales of Infant and Toddler Development, 3rd edition, scales) was analyzed using logistic regression. There were 148 children who completed 217 Bayley Scales of Infant and Toddler Development, 3rd edition, examinations (group 1, n = 132; group 2, n = 85). Neurodevelopmental score distributions significantly shifted downward compared with test norms at 1 and 2 years of age. Multivariate analysis identified ascites (OR, 3.17; P = .01) and low length z-scores at time of testing (OR, 0.70; P < .04) as risk factors for physical/motor impairment; low weight z-score (OR, 0.57; P = .001) and ascites (OR, 2.89; P = .01) for mental/cognitive/language impairment at 1 year of age. An unsuccessful hepatoportoenterostomy was predictive of both physical/motor (OR, 4.88; P < .02) and mental/cognitive/language impairment (OR, 4.76; P = .02) at 2 years of age. Participants with biliary atresia surviving with native livers after hepatoportoenterostomy are at increased risk for neurodevelopmental delays at 12 and 24 months of age. Those with unsuccessful hepatoportoenterostomy are >4 times more likely to have neurodevelopmental impairment compared with those with successful hepatoportoenterostomy. Growth delays and/or complications indicating advanced liver disease should alert clinicians to the risk for neurodevelopmental delays, and expedite appropriate interventions. Clinicaltrials.gov: NCT00061828 and NCT00294684. Copyright © 2018 Elsevier Inc. All rights reserved.
Effects of Changes in BI-RADS Density Assessment Guidelines (Fourth Versus Fifth Edition) on Breast Density Assessment: Intra- and Interreader Agreements and Density Distribution.

PubMed

Irshad, Abid; Leddy, Rebecca; Ackerman, Susan; Cluver, Abbie; Pavic, Dag; Abid, Ahad; Lewis, Madelene C

2016-12-01

The objective of our study was to determine intra- and interreader agreements for density assessment using the fifth edition of the BI-RADS guidelines and to compare with those for density assessment using the fourth edition of the BI-RADS guidelines. Five radiologists assessed breast density four times in 104 mammographic examinations: twice using the fourth edition of the BI-RADS guidelines and twice using the fifth edition. The intra- and interreader agreements for density assessment based on each guideline were determined and compared. The density distribution pattern under each of the four BI-RADS density categories using each guideline was also noted and compared. The intrareader agreement for density assessment using the fifth-edition criteria was lower than that using the fourth-edition criteria (p = 0.0179). The overall intrareader agreement (weighted kappa) using the old criteria was 0.84 (95% CI, 0.80-0.87), and the individual intrareader agreement values in five readers ranged from 0.78 (95% CI, 0.69-0.88) to 0.92 (95% CI, 0.87-0.97). The overall intrareader agreement using the new BI-RADS criteria was 0.77 (95% CI, 0.73-0.81), and the individual intrareader agreement values in five readers ranged from 0.74 (95% CI, 0.64-0.84) to 0.99 (95% CI, 0.98-1.00). The interreader agreement values obtained using the fifth-edition criteria were also lower than those obtained using the fourth-edition criteria (p = 0.006). The overall interreader agreement using the old BI-RADS criteria was 0.65 (95% CI, 0.61-0.69), whereas the overall interreader agreement using the new BI-RADS criteria was 0.57 (95% CI, 0.53-0.61). Overall a higher number of dense assessments were given when the fifth-edition guidelines were used (p < 0.0001). Compared with the intra- and interreader agreements obtained using the fourth edition of the BI-RADS guidelines, the intra- and interreader agreements were lower using the fifth-edition guidelines. An increased number of dense assessments were given when the fifth-edition guidelines were used.
Cell-type-specific genome editing with a microRNA-responsive CRISPR-Cas9 switch.

PubMed

Hirosawa, Moe; Fujita, Yoshihiko; Parr, Callum J C; Hayashi, Karin; Kashida, Shunnichi; Hotta, Akitsu; Woltjen, Knut; Saito, Hirohide

2017-07-27

The CRISPR-Cas9 system is a powerful genome-editing tool useful in a variety of biotechnology and biomedical applications. Here we developed a synthetic RNA-based, microRNA (miRNA)-responsive CRISPR-Cas9 system (miR-Cas9 switch) in which the genome editing activity of Cas9 can be modulated through endogenous miRNA signatures in mammalian cells. We created miR-Cas9 switches by using a miRNA-complementary sequence in the 5΄-UTR of mRNA encoding Streptococcus pyogenes Cas9. The miR-21-Cas9 or miR-302-Cas9 switches selectively and efficiently responded to miR-21-5p in HeLa cells or miR-302a-5p in human induced pluripotent stem cells, and post-transcriptionally attenuated the Cas9 activity only in the target cells. Moreover, the miR-Cas9 switches could differentially control the genome editing by sensing endogenous miRNA activities within a heterogeneous cell population. Our miR-Cas9 switch system provides a promising framework for cell-type selective genome editing and cell engineering based on intracellular miRNA information. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.

PubMed

Canver, Matthew C; Haeussler, Maximilian; Bauer, Daniel E; Orkin, Stuart H; Sanjana, Neville E; Shalem, Ophir; Yuan, Guo-Cheng; Zhang, Feng; Concordet, Jean-Paul; Pinello, Luca

2018-05-01

CRISPR (clustered regularly interspaced short palindromic repeats) genome-editing experiments offer enormous potential for the evaluation of genomic loci using arrayed single guide RNAs (sgRNAs) or pooled sgRNA libraries. Numerous computational tools are available to help design sgRNAs with optimal on-target efficiency and minimal off-target potential. In addition, computational tools have been developed to analyze deep-sequencing data resulting from genome-editing experiments. However, these tools are typically developed in isolation and oftentimes are not readily translatable into laboratory-based experiments. Here, we present a protocol that describes in detail both the computational and benchtop implementation of an arrayed and/or pooled CRISPR genome-editing experiment. This protocol provides instructions for sgRNA design with CRISPOR (computational tool for the design, evaluation, and cloning of sgRNA sequences), experimental implementation, and analysis of the resulting high-throughput sequencing data with CRISPResso (computational tool for analysis of genome-editing outcomes from deep-sequencing data). This protocol allows for design and execution of arrayed and pooled CRISPR experiments in 4-5 weeks by non-experts, as well as computational data analysis that can be performed in 1-2 d by both computational and noncomputational biologists alike using web-based and/or command-line versions.
Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage

PubMed Central

Cattenoz, Pierre B.; Taft, Ryan J.; Westhof, Eric; Mattick, John S.

2013-01-01

Adenosine to inosine (A > I) RNA editing, which is catalyzed by the ADAR family of proteins, is one of the fundamental mechanisms by which transcriptomic diversity is generated. Indeed, a number of genome-wide analyses have shown that A > I editing is not limited to a few mRNAs, as originally thought, but occurs widely across the transcriptome, especially in the brain. Importantly, there is increasing evidence that A > I editing is essential for animal development and nervous system function. To more efficiently characterize the complete catalog of ADAR events in the mammalian transcriptome we developed a high-throughput protocol to identify A > I editing sites, which exploits the capacity of glyoxal to protect guanosine, but not inosine, from RNAse T1 treatment, thus facilitating extraction of RNA fragments with inosine bases at their termini for high-throughput sequencing. Using this method we identified 665 editing sites in mouse brain RNA, including most known sites and suite of novel sites that include nonsynonymous changes to protein-coding genes, hyperediting of genes known to regulate p53, and alterations to non-protein-coding RNAs. This method is applicable to any biological system for the de novo discovery of A > I editing sites, and avoids the complicated informatic and practical issues associated with editing site identification using traditional RNA sequencing data. This approach has the potential to substantially increase our understanding of the extent and function of RNA editing, and thereby to shed light on the role of transcriptional plasticity in evolution, development, and cognition. PMID:23264566
Key Data on Education in Europe 2009

ERIC Educational Resources Information Center

Ranguelov, Stanislav; de Coster, Isabelle; Forsthuber, Bernadette; Noorani, Sogol; Ruffio, Philippe

2009-01-01

This seventh edition of "Key Data on Education in Europe" retains its main special feature which is the combination of statistical data and qualitative information to describe the organisation and functioning of education systems in Europe. The present 2009 edition maintains the subject-based structure defined by the previous one but…
Multisensory Teaching of Basic Language Skills. Third Edition

ERIC Educational Resources Information Center

Birsh, Judith R., Ed.

2011-01-01

As new research shows how effective systematic and explicit teaching of language-based skills is for students with learning disabilities--along with the added benefits of multisensory techniques--discover the latest on this popular teaching approach with the third edition of this bestselling textbook. Adopted by colleges and universities across…
77 FR 37617 - Updating OSHA Standards Based on National Consensus Standards; Head Protection

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-22

... provisions in the 2009 edition permitting optional testing for helmets worn in the backwards position (``reverse wearing''), optional testing for helmets at colder temperatures than provided in previous editions, and optional testing for the high- visibility coloring of helmets. If manufacturers choose to evaluate...
Power Product Equipment Technician: Construction Equipment. Teacher Edition. Student Edition.

ERIC Educational Resources Information Center

Hilley, Robert

The instructor's guide in this package, which is one in a series of new publications developed to replace the Multistate Academic and Vocational Curriculum Consortium's previous small-engine curricula, contains the materials required to teach a competency-based course in repairing construction equipment. The guide begins with an introduction…
Children in Family Contexts. Second Edition. Perspectives on Treatment

ERIC Educational Resources Information Center

Graham, Lee Combrick, Ed.

2006-01-01

Now in a fully revised and updated second edition, this widely used text and professional resource provides a practical guide to family-based therapy for childhood emotional and behavioral problems. Presented are innovative assessment and treatment strategies that take into account children's developmental needs, different family forms, health and…
ACR Electrical Systems. Teacher Edition [and] Student Edition.

ERIC Educational Resources Information Center

Clemons, Mark

This document contains a teacher's guide and student guide for a high school-level competency-based course in air conditioning and refrigeration (ACR) equipment electrical systems. Presented in the teacher's guide are the following: explanation of the instructional units' use; competency profile for recording students' performance of the tasks in…
Action Research: Improving Schools and Empowering Educators. Third Edition

ERIC Educational Resources Information Center

Mertler, Craig A.

2011-01-01

Written for pre- and in-service educators, this "Third Edition" of Craig A. Mertler's "Action Research: Improving Schools and Empowering Educators" introduces the process of conducting one's own classroom- or school-based action research in conjunction with everyday instructional practices and activities. The text provides educators with the…
Genome editing in pluripotent stem cells: research and therapeutic applications.

PubMed

Deleidi, Michela; Yu, Cong

2016-05-06

Recent progress in human pluripotent stem cell (hPSC) and genome editing technologies has opened up new avenues for the investigation of human biology in health and disease as well as the development of therapeutic applications. Gene editing approaches with programmable nucleases have been successfully established in hPSCs and applied to study gene function, develop novel animal models and perform genetic and chemical screens. Several studies now show the successful editing of disease-linked alleles in somatic and patient-derived induced pluripotent stem cells (iPSCs) as well as in animal models. Importantly, initial clinical trials have shown the safety of programmable nucleases for ex vivo somatic gene therapy. In this context, the unlimited proliferation potential and the pluripotent properties of iPSCs may offer advantages for gene targeting approaches. However, many technical and safety issues still need to be addressed before genome-edited iPSCs are translated into the clinical setting. Here, we provide an overview of the available genome editing systems and discuss opportunities and perspectives for their application in basic research and clinical practice, with a particular focus on hPSC based research and gene therapy approaches. Finally, we discuss recent research on human germline genome editing and its social and ethical implications. Copyright © 2016 Elsevier Inc. All rights reserved.
The Impact of CRISPR/Cas9 Technology on Cardiac Research: From Disease Modelling to Therapeutic Approaches

PubMed Central

Pramstaller, Peter P.; Hicks, Andrew A.; Rossini, Alessandra

2017-01-01

Genome-editing technology has emerged as a powerful method that enables the generation of genetically modified cells and organisms necessary to elucidate gene function and mechanisms of human diseases. The clustered regularly interspaced short palindromic repeats- (CRISPR-) associated 9 (Cas9) system has rapidly become one of the most popular approaches for genome editing in basic biomedical research over recent years because of its simplicity and adaptability. CRISPR/Cas9 genome editing has been used to correct DNA mutations ranging from a single base pair to large deletions in both in vitro and in vivo model systems. CRISPR/Cas9 has been used to increase the understanding of many aspects of cardiovascular disorders, including lipid metabolism, electrophysiology and genetic inheritance. The CRISPR/Cas9 technology has been proven to be effective in creating gene knockout (KO) or knockin in human cells and is particularly useful for editing induced pluripotent stem cells (iPSCs). Despite these progresses, some biological, technical, and ethical issues are limiting the therapeutic potential of genome editing in cardiovascular diseases. This review will focus on various applications of CRISPR/Cas9 genome editing in the cardiovascular field, for both disease research and the prospect of in vivo genome-editing therapies in the future. PMID:29434642

Efficient genome engineering of a virulent Klebsiella bacteriophage using CRISPR-Cas9.

PubMed

Shen, Juntao; Zhou, Jinjie; Chen, Guo-Qiang; Xiu, Zhi-Long

2018-06-13

Klebsiella pneumoniae is one of the most common nosocomial opportunistic pathogens usually with multiple drug-resistance. Phage therapy, a potential new therapeutics to replace or supplement antibiotics, has attracted much attention. However, very few Klebsiella phages have been well-characterized as the lack of efficient genome editing tools. Here, Cas9 from Streptococcus pyogenes and a single guide RNA (sgRNA) were used to modify a virulent Klebsiella bacteriophage phiKpS2. We firstly evaluated the distribution of sgRNA activity in phages and proved that it's largely inconsistent with the predicted activity from current models trained on eukaryotic cell datasets. A simple CRISPR-based phage genome editing procedure was developed based on the discovery that homologous arms as short as 30-60 bp was sufficient to introduce point mutation, gene deletion and swap. We also demonstrated that weak sgRNAs could be used for precise phage genome editing but failed to select random recombinants, possibly because inefficient cleavage can be tolerated through continuous repair by homologous recombination with the uncut genomes. Small frameshift deletion was proved to be an efficient way to evaluate the essentiality of phage genes. By using the above strategies, a putative promoter and nine genes of phiKpS2 were successfully deleted. Interestingly, the holin gene can be deleted with little effect on phiKpS2 infection, but the reason is not yet clear. This study established an efficient, time-saving, and cost-effective procedure for phage genome editing, which is expected to significantly promote the development of bacteriophage therapy. IMPORTANCE In the present study, we have addressed an efficient, time-saving and cost-effective CRISPR-based phage genome editing of Klebsiella phage, which has the potential to significantly expand our knowledge of phage-host interactions and to promote the applications of phage therapy. The distribution of sgRNA activity was first evaluated in phages. Short homologous arms were proved enough to introduce point mutation, small frameshift deletion, gene deletion and swap into phages, and weak sgRNAs were proved useful for precise phage genome editing but failed to select random recombinants, which all make the CRISPR-based phage genome editing easier to use. Copyright © 2018 American Society for Microbiology.
Molecular structure input on the web.

PubMed

Ertl, Peter

2010-02-02

A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential.The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.
Comparison of the 7(th) and proposed 8(th) editions of the AJCC/UICC TNM staging system for non-small cell lung cancer undergoing radical surgery.

PubMed

Jin, Ying; Chen, Ming; Yu, Xinmin

2016-09-19

The present study aims to compare the 7(th) and the proposed 8(th) edition of the AJCC/UICC TNM staging system for NSCLC in a cohort of patients from a single institution. A total of 408 patients with NSCLC who underwent radical surgery were analyzed retrospectively. Survivals were analyzed using the Kaplan -Meier method and were compared using the log-rank test. Multivariate analysis was performed by the Cox proportional hazard model. The Akaike information criterion (AIC) and C-index were applied to compare the two prognostic systems with different numbers of stages. The 7(th) AJCC T categories, the proposed 8(th) AJCC T categories, N categories, visceral pleural invasion, and vessel invasion were found to have statistically significant associations with disease-free survival (DFS) on univariate analysis. In the 7(th) edition staging system as well as in the proposed 8(th) edition, T categories, N categories, and pleural invasion were independent factors for DFS on multivariate analysis. The AIC value was smaller for the 8(th) edition compared to the 7(th) edition staging system. The C-index value was larger for the 8(th) edition compared to the 7(th) edition staging system. Based on the data from our single center, the proposed 8(th) AJCC T classification seems to be superior to the 7(th) AJCC T classification in terms of DFS for patients with NSCLC underwent radical surgery.
Polyglutamine Disease Modeling: Epitope Based Screen for Homologous Recombination using CRISPR/Cas9 System.

PubMed

An, Mahru C; O'Brien, Robert N; Zhang, Ningzhe; Patra, Biranchi N; De La Cruz, Michael; Ray, Animesh; Ellerby, Lisa M

2014-04-15

We have previously reported the genetic correction of Huntington's disease (HD) patient-derived induced pluripotent stem cells using traditional homologous recombination (HR) approaches. To extend this work, we have adopted a CRISPR-based genome editing approach to improve the efficiency of recombination in order to generate allelic isogenic HD models in human cells. Incorporation of a rapid antibody-based screening approach to measure recombination provides a powerful method to determine relative efficiency of genome editing for modeling polyglutamine diseases or understanding factors that modulate CRISPR/Cas9 HR.
Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets.

PubMed

Picardi, Ernesto; Quagliariello, Carla

2008-03-26

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. 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. 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 presented here encourage, thus, the use of genomic mitochondrial rather than cDNA sequences for reconstructing phylogenetic events in land plants.
Genome and Epigenome Editing in Mechanistic Studies of Human Aging and Aging-Related Disease

PubMed Central

Lau, Cia-Hin; Suh, Yousin

2016-01-01

The recent advent of genome and epigenome editing technologies has provided a new paradigm in which the landscape of the human genome and epigenome can be precisely manipulated in their native context. Genome and epigenome editing technologies can be applied to many aspects of aging research and offer the potential to development novel therapeutics against age-related diseases. Here, we discuss the latest technological advances in the CRISPR-based genome and epigenome editing toolbox, and provide an insight into how these synthetic biology tools could facilitate aging research by establishing in vitro cell- and in vivo animal-models to dissect genetic and epigenetic mechanisms underlying aging and age-related diseases. We discuss recent developments in the field with the aims to precisely modulate gene expression and dynamic epigenetic landscapes in a spatial- and temporal- manner in cellular and animal models, by complementing the CRISPR-based editing capability with conditional genetic manipulation tools, including chemically inducible expression system, optogenetics, logic gate genetic circuits, tissue-specific promoters, and serotype-specific adeno-associated virus. We also discuss how the combined use of genome and epigenome editing tools permits investigators to uncover novel molecular pathways involved in pathophysiology and etiology conferred by risk variants associated with aging and aging-related disease. A better understanding of the genetic and epigenetic regulatory mechanisms underlying human aging and age-related disease will significantly contribute to the developments of new therapeutic interventions for extending healthspan and lifespan, ultimately improving the quality of life in the elderly populations. PMID:27974723
Detailed analysis of targeted gene mutations caused by the Platinum-Fungal TALENs in Aspergillus oryzae RIB40 strain and a ligD disruptant.

PubMed

Mizutani, Osamu; Arazoe, Takayuki; Toshida, Kenji; Hayashi, Risa; Ohsato, Shuichi; Sakuma, Tetsushi; Yamamoto, Takashi; Kuwata, Shigeru; Yamada, Osamu

2017-03-01

Transcription activator-like effector nucleases (TALENs), which can generate DNA double-strand breaks at specific sites in the desired genome locus, have been used in many organisms as a tool for genome editing. In Aspergilli, including Aspergillus oryzae, however, the use of TALENs has not been validated. In this study, we performed genome editing of A. oryzae wild-type strain via error of nonhomologous end-joining (NHEJ) repair by transient expression of high-efficiency Platinum-Fungal TALENs (PtFg TALENs). Targeted mutations were observed as various mutation patterns. In particular, approximately half of the PtFg TALEN-mediated deletion mutants had deletions larger than 1 kb in the TALEN-targeting region. We also conducted PtFg TALEN-based genome editing in A. oryzae ligD disruptant (ΔligD) lacking the ligD gene involved in the final step of the NHEJ repair and found that mutations were still obtained as well as wild-type. In this case, the ratio of the large deletions reduced compared to PtFg TALEN-based genome editing in the wild-type. In conclusion, we demonstrate that PtFg TALENs are sufficiently functional to cause genome editing via error of NHEJ in A. oryzae. In addition, we reveal that genome editing using TALENs in A. oryzae tends to cause large deletions at the target region, which were partly suppressed by deletion of ligD. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.
Genome and Epigenome Editing in Mechanistic Studies of Human Aging and Aging-Related Disease.

PubMed

Lau, Cia-Hin; Suh, Yousin

2017-01-01

The recent advent of genome and epigenome editing technologies has provided a new paradigm in which the landscape of the human genome and epigenome can be precisely manipulated in their native context. Genome and epigenome editing technologies can be applied to many aspects of aging research and offer the potential to develop novel therapeutics against age-related diseases. Here, we discuss the latest technological advances in the CRISPR-based genome and epigenome editing toolbox, and provide insight into how these synthetic biology tools could facilitate aging research by establishing in vitro cell and in vivo animal models to dissect genetic and epigenetic mechanisms underlying aging and age-related diseases. We discuss recent developments in the field with the aims to precisely modulate gene expression and dynamic epigenetic landscapes in a spatial and temporal manner in cellular and animal models, by complementing the CRISPR-based editing capability with conditional genetic manipulation tools including chemically inducible expression systems, optogenetics, logic gate genetic circuits, tissue-specific promoters, and the serotype-specific adeno-associated virus. We also discuss how the combined use of genome and epigenome editing tools permits investigators to uncover novel molecular pathways involved in the pathophysiology and etiology conferred by risk variants associated with aging and aging-related disease. A better understanding of the genetic and epigenetic regulatory mechanisms underlying human aging and age-related disease will significantly contribute to the developments of new therapeutic interventions for extending health span and life span, ultimately improving the quality of life in the elderly populations. © 2016 S. Karger AG, Basel.
CERES Single Scanner Satellite Footprint, TOA, Surface Fluxes and Clouds (SSF) data in HDF (CER_SSF_Terra-FM2-MODIS_Edition2A)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The Single Scanner Footprint TOA/Surface Fluxes and Clouds (SSF) product contains one hour of instantaneous Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The SSF combines instantaneous CERES data with scene information from a higher-resolution imager such as Visible/Infrared Scanner (VIRS) on TRMM or Moderate-Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua. Scene identification and cloud properties are defined at the higher imager resolution and these data are averaged over the larger CERES footprint. For each CERES footprint, the SSF contains the number of cloud layers and for each layer the cloud amount, height, temperature, pressure, optical depth, emissivity, ice and liquid water path, and water particle size. The SSF also contains the CERES filtered radiances for the total, shortwave (SW), and window (WN) channels and the unfiltered SW, longwave (LW), and WN radiances. The SW, LW, and WN radiances at spacecraft altitude are converted to Top-of-the-Atmosphere (TOA) fluxes based on the imager defined scene. These TOA fluxes are used to estimate surface fluxes. Only footprints with adequate imager coverage are included on CER_SSF_TRMM-PFM-VIRS_Subset_Edition1the SSF which is much less than the full set of footprints on the CERES ES-8 product. The following CERES SSF data sets are currently available: CER_SSF_TRMM-PFM-VIRS_Edition1 CER_SSF_TRMM-PFM-VIRS_Subset_Edition1 CER_SSF_TRMM-PFM-VIRS_Edition2A CER_SSF_TRMM-SIM-VIRS_Edition2_VIRSonly CER_SSF_TRMM-PFM-VIRS_Edition2A-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition2A CER_SSF_Terra-FM2-MODIS_Edition2A CER_SSF_Terra-FM1-MODIS_Edition2B CER_SSF_Terra-FM2-MODIS_Edition2B CER_SSF_Aqua-FM4-MODIS_Beta1 CER_SSF_Aqua-FM3-MODIS_Beta2 CER_SSF_Aqua-FM4-MODIS_Beta2. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2003-12-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Temporal_Resolution=1 hour; Temporal_Resolution_Range=Hourly - < Daily].
CERES Single Satellite Footprint, TOA and Surface Fluxes, Clouds (SSF) data in HDF (CER_SSF_Aqua-FM4-MODIS_Edition2A)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The Single Scanner Footprint TOA/Surface Fluxes and Clouds (SSF) product contains one hour of instantaneous Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The SSF combines instantaneous CERES data with scene information from a higher-resolution imager such as Visible/Infrared Scanner (VIRS) on TRMM or Moderate-Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua. Scene identification and cloud properties are defined at the higher imager resolution and these data are averaged over the larger CERES footprint. For each CERES footprint, the SSF contains the number of cloud layers and for each layer the cloud amount, height, temperature, pressure, optical depth, emissivity, ice and liquid water path, and water particle size. The SSF also contains the CERES filtered radiances for the total, shortwave (SW), and window (WN) channels and the unfiltered SW, longwave (LW), and WN radiances. The SW, LW, and WN radiances at spacecraft altitude are converted to Top-of-the-Atmosphere (TOA) fluxes based on the imager defined scene. These TOA fluxes are used to estimate surface fluxes. Only footprints with adequate imager coverage are included on CER_SSF_TRMM-PFM-VIRS_Subset_Edition1the SSF which is much less than the full set of footprints on the CERES ES-8 product. The following CERES SSF data sets are currently available: CER_SSF_TRMM-PFM-VIRS_Edition1 CER_SSF_TRMM-PFM-VIRS_Subset_Edition1 CER_SSF_TRMM-PFM-VIRS_Edition2A CER_SSF_TRMM-SIM-VIRS_Edition2_VIRSonly CER_SSF_TRMM-PFM-VIRS_Edition2A-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition2A CER_SSF_Terra-FM2-MODIS_Edition2A CER_SSF_Terra-FM1-MODIS_Edition2B CER_SSF_Terra-FM2-MODIS_Edition2B CER_SSF_Aqua-FM4-MODIS_Beta1 CER_SSF_Aqua-FM3-MODIS_Beta2 CER_SSF_Aqua-FM4-MODIS_Beta2. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-09-16] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Temporal_Resolution=1 hour; Temporal_Resolution_Range=Hourly - < Daily].
CERES Single Scanner Satellite Footprint, TOA, Surface Fluxes and Clouds (SSF) data in HDF (CER_SSF_Aqua-FM4-MODIS_Edition1B)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The Single Scanner Footprint TOA/Surface Fluxes and Clouds (SSF) product contains one hour of instantaneous Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The SSF combines instantaneous CERES data with scene information from a higher-resolution imager such as Visible/Infrared Scanner (VIRS) on TRMM or Moderate-Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua. Scene identification and cloud properties are defined at the higher imager resolution and these data are averaged over the larger CERES footprint. For each CERES footprint, the SSF contains the number of cloud layers and for each layer the cloud amount, height, temperature, pressure, optical depth, emissivity, ice and liquid water path, and water particle size. The SSF also contains the CERES filtered radiances for the total, shortwave (SW), and window (WN) channels and the unfiltered SW, longwave (LW), and WN radiances. The SW, LW, and WN radiances at spacecraft altitude are converted to Top-of-the-Atmosphere (TOA) fluxes based on the imager defined scene. These TOA fluxes are used to estimate surface fluxes. Only footprints with adequate imager coverage are included on CER_SSF_TRMM-PFM-VIRS_Subset_Edition1the SSF which is much less than the full set of footprints on the CERES ES-8 product. The following CERES SSF data sets are currently available: CER_SSF_TRMM-PFM-VIRS_Edition1 CER_SSF_TRMM-PFM-VIRS_Subset_Edition1 CER_SSF_TRMM-PFM-VIRS_Edition2A CER_SSF_TRMM-SIM-VIRS_Edition2_VIRSonly CER_SSF_TRMM-PFM-VIRS_Edition2A-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition2A CER_SSF_Terra-FM2-MODIS_Edition2A CER_SSF_Terra-FM1-MODIS_Edition2B CER_SSF_Terra-FM2-MODIS_Edition2B CER_SSF_Aqua-FM4-MODIS_Beta1 CER_SSF_Aqua-FM3-MODIS_Beta2 CER_SSF_Aqua-FM4-MODIS_Beta2. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-03-29] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Temporal_Resolution=1 hour; Temporal_Resolution_Range=Hourly - < Daily].
CERES Single Scanner Satellite Footprint, TOA, Surface Fluxes and Clouds (SSF)- Test data in HDF (CER_SSF_TRMM-PFM-VIRS_Subset-Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The Single Scanner Footprint TOA/Surface Fluxes and Clouds (SSF) product contains one hour of instantaneous Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The SSF combines instantaneous CERES data with scene information from a higher-resolution imager such as Visible/Infrared Scanner (VIRS) on TRMM or Moderate-Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua. Scene identification and cloud properties are defined at the higher imager resolution and these data are averaged over the larger CERES footprint. For each CERES footprint, the SSF contains the number of cloud layers and for each layer the cloud amount, height, temperature, pressure, optical depth, emissivity, ice and liquid water path, and water particle size. The SSF also contains the CERES filtered radiances for the total, shortwave (SW), and window (WN) channels and the unfiltered SW, longwave (LW), and WN radiances. The SW, LW, and WN radiances at spacecraft altitude are converted to Top-of-the-Atmosphere (TOA) fluxes based on the imager defined scene. These TOA fluxes are used to estimate surface fluxes. Only footprints with adequate imager coverage are included on CER_SSF_TRMM-PFM-VIRS_Subset_Edition1the SSF which is much less than the full set of footprints on the CERES ES-8 product. The following CERES SSF data sets are currently available: CER_SSF_TRMM-PFM-VIRS_Edition1 CER_SSF_TRMM-PFM-VIRS_Subset_Edition1 CER_SSF_TRMM-PFM-VIRS_Edition2A CER_SSF_TRMM-SIM-VIRS_Edition2_VIRSonly CER_SSF_TRMM-PFM-VIRS_Edition2A-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition2A CER_SSF_Terra-FM2-MODIS_Edition2A CER_SSF_Terra-FM1-MODIS_Edition2B CER_SSF_Terra-FM2-MODIS_Edition2B CER_SSF_Aqua-FM4-MODIS_Beta1 CER_SSF_Aqua-FM3-MODIS_Beta2 CER_SSF_Aqua-FM4-MODIS_Beta2. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=1998-08-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Temporal_Resolution=1 hour; Temporal_Resolution_Range=Hourly - < Daily].
CERES Single Scanner Satellite Footprint, TOA, Surface Fluxes and Clouds (SSF) data in HDF (CER_SSF_Terra-FM2-MODIS_Edition2B)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The Single Scanner Footprint TOA/Surface Fluxes and Clouds (SSF) product contains one hour of instantaneous Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The SSF combines instantaneous CERES data with scene information from a higher-resolution imager such as Visible/Infrared Scanner (VIRS) on TRMM or Moderate-Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua. Scene identification and cloud properties are defined at the higher imager resolution and these data are averaged over the larger CERES footprint. For each CERES footprint, the SSF contains the number of cloud layers and for each layer the cloud amount, height, temperature, pressure, optical depth, emissivity, ice and liquid water path, and water particle size. The SSF also contains the CERES filtered radiances for the total, shortwave (SW), and window (WN) channels and the unfiltered SW, longwave (LW), and WN radiances. The SW, LW, and WN radiances at spacecraft altitude are converted to Top-of-the-Atmosphere (TOA) fluxes based on the imager defined scene. These TOA fluxes are used to estimate surface fluxes. Only footprints with adequate imager coverage are included on CER_SSF_TRMM-PFM-VIRS_Subset_Edition1the SSF which is much less than the full set of footprints on the CERES ES-8 product. The following CERES SSF data sets are currently available: CER_SSF_TRMM-PFM-VIRS_Edition1 CER_SSF_TRMM-PFM-VIRS_Subset_Edition1 CER_SSF_TRMM-PFM-VIRS_Edition2A CER_SSF_TRMM-SIM-VIRS_Edition2_VIRSonly CER_SSF_TRMM-PFM-VIRS_Edition2A-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition2A CER_SSF_Terra-FM2-MODIS_Edition2A CER_SSF_Terra-FM1-MODIS_Edition2B CER_SSF_Terra-FM2-MODIS_Edition2B CER_SSF_Aqua-FM4-MODIS_Beta1 CER_SSF_Aqua-FM3-MODIS_Beta2 CER_SSF_Aqua-FM4-MODIS_Beta2. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2006-01-01] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Temporal_Resolution=1 hour; Temporal_Resolution_Range=Hourly - < Daily].
CERES Single Scanner Satellite Footprint, TOA, Surface Fluxes and Clouds (SSF) data in HDF (CER_SSF_TRMM-PFM-VIRS_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The Single Scanner Footprint TOA/Surface Fluxes and Clouds (SSF) product contains one hour of instantaneous Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The SSF combines instantaneous CERES data with scene information from a higher-resolution imager such as Visible/Infrared Scanner (VIRS) on TRMM or Moderate-Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua. Scene identification and cloud properties are defined at the higher imager resolution and these data are averaged over the larger CERES footprint. For each CERES footprint, the SSF contains the number of cloud layers and for each layer the cloud amount, height, temperature, pressure, optical depth, emissivity, ice and liquid water path, and water particle size. The SSF also contains the CERES filtered radiances for the total, shortwave (SW), and window (WN) channels and the unfiltered SW, longwave (LW), and WN radiances. The SW, LW, and WN radiances at spacecraft altitude are converted to Top-of-the-Atmosphere (TOA) fluxes based on the imager defined scene. These TOA fluxes are used to estimate surface fluxes. Only footprints with adequate imager coverage are included on CER_SSF_TRMM-PFM-VIRS_Subset_Edition1the SSF which is much less than the full set of footprints on the CERES ES-8 product. The following CERES SSF data sets are currently available: CER_SSF_TRMM-PFM-VIRS_Edition1 CER_SSF_TRMM-PFM-VIRS_Subset_Edition1 CER_SSF_TRMM-PFM-VIRS_Edition2A CER_SSF_TRMM-SIM-VIRS_Edition2_VIRSonly CER_SSF_TRMM-PFM-VIRS_Edition2A-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition2A CER_SSF_Terra-FM2-MODIS_Edition2A CER_SSF_Terra-FM1-MODIS_Edition2B CER_SSF_Terra-FM2-MODIS_Edition2B CER_SSF_Aqua-FM4-MODIS_Beta1 CER_SSF_Aqua-FM3-MODIS_Beta2 CER_SSF_Aqua-FM4-MODIS_Beta2. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2000-03-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Temporal_Resolution=1 hour; Temporal_Resolution_Range=Hourly - < Daily].
CERES Single Scanner Satellite Footprint, TOA, Surface Fluxes and Clouds (SSF) data in HDF (CER_SSF_Terra-FM1-MODIS_Edition2A)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The Single Scanner Footprint TOA/Surface Fluxes and Clouds (SSF) product contains one hour of instantaneous Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The SSF combines instantaneous CERES data with scene information from a higher-resolution imager such as Visible/Infrared Scanner (VIRS) on TRMM or Moderate-Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua. Scene identification and cloud properties are defined at the higher imager resolution and these data are averaged over the larger CERES footprint. For each CERES footprint, the SSF contains the number of cloud layers and for each layer the cloud amount, height, temperature, pressure, optical depth, emissivity, ice and liquid water path, and water particle size. The SSF also contains the CERES filtered radiances for the total, shortwave (SW), and window (WN) channels and the unfiltered SW, longwave (LW), and WN radiances. The SW, LW, and WN radiances at spacecraft altitude are converted to Top-of-the-Atmosphere (TOA) fluxes based on the imager defined scene. These TOA fluxes are used to estimate surface fluxes. Only footprints with adequate imager coverage are included on CER_SSF_TRMM-PFM-VIRS_Subset_Edition1the SSF which is much less than the full set of footprints on the CERES ES-8 product. The following CERES SSF data sets are currently available: CER_SSF_TRMM-PFM-VIRS_Edition1 CER_SSF_TRMM-PFM-VIRS_Subset_Edition1 CER_SSF_TRMM-PFM-VIRS_Edition2A CER_SSF_TRMM-SIM-VIRS_Edition2_VIRSonly CER_SSF_TRMM-PFM-VIRS_Edition2A-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition2A CER_SSF_Terra-FM2-MODIS_Edition2A CER_SSF_Terra-FM1-MODIS_Edition2B CER_SSF_Terra-FM2-MODIS_Edition2B CER_SSF_Aqua-FM4-MODIS_Beta1 CER_SSF_Aqua-FM3-MODIS_Beta2 CER_SSF_Aqua-FM4-MODIS_Beta2. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2003-12-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Temporal_Resolution=1 hour; Temporal_Resolution_Range=Hourly - < Daily].
Single-Stranded γPNAs for In Vivo Site-Specific Genome Editing via Watson-Crick Recognition

PubMed Central

Bahal, Raman; Quijano, Elias; McNeer, Nicole Ali; Liu, Yanfeng; Bhunia, Dinesh C.; López-Giráldez, Francesco; Fields, Rachel J.; Saltzman, W. Mark; Ly, Danith H.; Glazer, Peter M.

2014-01-01

Triplex-forming peptide nucleic acids (PNAs) facilitate gene editing by stimulating recombination of donor DNAs within genomic DNA via site-specific formation of altered helical structures that further stimulate DNA repair. However, PNAs designed for triplex formation are sequence restricted to homopurine sites. Herein we describe a novel strategy where next generation single-stranded gamma PNAs (γPNAs) containing miniPEG substitutions at the gamma position can target genomic DNA in mouse bone marrow at mixed-sequence sites to induce targeted gene editing. In addition to enhanced binding, γPNAs confer increased solubility and improved formulation into poly(lactic-co-glycolic acid) (PLGA) nanoparticles for efficient intracellular delivery. Single-stranded γPNAs induce targeted gene editing at frequencies of 0.8% in mouse bone marrow cells treated ex vivo and 0.1% in vivo via IV injection, without detectable toxicity. These results suggest that γPNAs may provide a new tool for induced gene editing based on Watson-Crick recognition without sequence restriction. PMID:25174576
Single-stranded γPNAs for in vivo site-specific genome editing via Watson-Crick recognition.

PubMed

Bahal, Raman; Quijano, Elias; McNeer, Nicole A; Liu, Yanfeng; Bhunia, Dinesh C; Lopez-Giraldez, Francesco; Fields, Rachel J; Saltzman, William M; Ly, Danith H; Glazer, Peter M

2014-01-01

Triplex-forming peptide nucleic acids (PNAs) facilitate gene editing by stimulating recombination of donor DNAs within genomic DNA via site-specific formation of altered helical structures that further stimulate DNA repair. However, PNAs designed for triplex formation are sequence restricted to homopurine sites. Herein we describe a novel strategy where next generation single-stranded gamma PNAs (γPNAs) containing miniPEG substitutions at the gamma position can target genomic DNA in mouse bone marrow at mixed-sequence sites to induce targeted gene editing. In addition to enhanced binding, γPNAs confer increased solubility and improved formulation into poly(lactic-co-glycolic acid) (PLGA) nanoparticles for efficient intracellular delivery. Single-stranded γPNAs induce targeted gene editing at frequencies of 0.8% in mouse bone marrow cells treated ex vivo and 0.1% in vivo via IV injection, without detectable toxicity. These results suggest that γPNAs may provide a new tool for induced gene editing based on Watson-Crick recognition without sequence restriction.
Genome-editing Technologies for Gene and Cell Therapy.

PubMed

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.
Genome-editing Technologies for Gene and Cell Therapy

PubMed Central

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
May I Cut in? Gene Editing Approaches in Human Induced Pluripotent Stem Cells.

PubMed

Brookhouser, Nicholas; Raman, Sreedevi; Potts, Christopher; Brafman, David A

2017-02-06

In the decade since Yamanaka and colleagues described methods to reprogram somatic cells into a pluripotent state, human induced pluripotent stem cells (hiPSCs) have demonstrated tremendous promise in numerous disease modeling, drug discovery, and regenerative medicine applications. More recently, the development and refinement of advanced gene transduction and editing technologies have further accelerated the potential of hiPSCs. In this review, we discuss the various gene editing technologies that are being implemented with hiPSCs. Specifically, we describe the emergence of technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 that can be used to edit the genome at precise locations, and discuss the strengths and weaknesses of each of these technologies. In addition, we present the current applications of these technologies in elucidating the mechanisms of human development and disease, developing novel and effective therapeutic molecules, and engineering cell-based therapies. Finally, we discuss the emerging technological advances in targeted gene editing methods.

Use of genome editing tools in human stem cell-based disease modeling and precision medicine.

PubMed

Wei, Yu-da; Li, Shuang; Liu, Gai-gai; Zhang, Yong-xian; Ding, Qiu-rong

2015-10-01

Precision medicine emerges as a new approach that takes into account individual variability. The successful conduct of precision medicine requires the use of precise disease models. Human pluripotent stem cells (hPSCs), as well as adult stem cells, can be differentiated into a variety of human somatic cell types that can be used for research and drug screening. The development of genome editing technology over the past few years, especially the CRISPR/Cas system, has made it feasible to precisely and efficiently edit the genetic background. Therefore, disease modeling by using a combination of human stem cells and genome editing technology has offered a new platform to generate " personalized " disease models, which allow the study of the contribution of individual genetic variabilities to disease progression and the development of precise treatments. In this review, recent advances in the use of genome editing in human stem cells and the generation of stem cell models for rare diseases and cancers are discussed.
Design and assessment of engineered CRISPR-Cpf1 and its use for genome editing.

PubMed

Li, Bin; Zeng, Chunxi; Dong, Yizhou

2018-05-01

Cpf1, a CRISPR endonuclease discovered in Prevotella and Francisella 1 bacteria, offers an alternative platform for CRISPR-based genome editing beyond the commonly used CRISPR-Cas9 system originally discovered in Streptococcus pyogenes. This protocol enables the design of engineered CRISPR-Cpf1 components, both CRISPR RNAs (crRNAs) to guide the endonuclease and Cpf1 mRNAs to express the endonuclease protein, and provides experimental procedures for effective genome editing using this system. We also describe quantification of genome-editing activity and off-target effects of the engineered CRISPR-Cpf1 in human cell lines using both T7 endonuclease I (T7E1) assay and targeted deep sequencing. This protocol enables rapid construction and identification of engineered crRNAs and Cpf1 mRNAs to enhance genome-editing efficiency using the CRISPR-Cpf1 system, as well as assessment of target specificity within 2 months. This protocol may also be appropriate for fine-tuning other types of CRISPR systems.
CRISPR-enabled tools for engineering microbial genomes and phenotypes.

PubMed

Tarasava, Katia; Oh, Eun Joong; Eckert, Carrie A; Gill, Ryan T

2018-06-19

In recent years CRISPR-Cas technologies have revolutionized microbial engineering approaches. Genome editing and non-editing applications of various CRISPR-Cas systems have expanded the throughput and scale of engineering efforts, as well as opened up new avenues for manipulating genomes of non-model organisms. As we expand the range of organisms used for biotechnological applications, we need to develop better, more versatile tools for manipulation of these systems. Here we summarize the current advances in microbial gene editing using CRISPR-Cas based tools, and highlight state-of-the-art methods for high-throughput, efficient genome-scale engineering in model organisms Escherichia coli and Saccharomyces cerevisiae. We also review non-editing CRISPR-Cas applications available for gene expression manipulation, epigenetic remodeling, RNA editing, labeling and synthetic gene circuit design. Finally, we point out the areas of research that need further development in order to expand the range of applications and increase the utility of these new methods. This article is protected by copyright. All rights reserved.
May I Cut in? Gene Editing Approaches in Human Induced Pluripotent Stem Cells

PubMed Central

Brookhouser, Nicholas; Raman, Sreedevi; Potts, Christopher; Brafman, David. A.

2017-01-01

In the decade since Yamanaka and colleagues described methods to reprogram somatic cells into a pluripotent state, human induced pluripotent stem cells (hiPSCs) have demonstrated tremendous promise in numerous disease modeling, drug discovery, and regenerative medicine applications. More recently, the development and refinement of advanced gene transduction and editing technologies have further accelerated the potential of hiPSCs. In this review, we discuss the various gene editing technologies that are being implemented with hiPSCs. Specifically, we describe the emergence of technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 that can be used to edit the genome at precise locations, and discuss the strengths and weaknesses of each of these technologies. In addition, we present the current applications of these technologies in elucidating the mechanisms of human development and disease, developing novel and effective therapeutic molecules, and engineering cell-based therapies. Finally, we discuss the emerging technological advances in targeted gene editing methods. PMID:28178187
Application of CRISPR/Cas9 Gene Editing System on MDV-1 Genome for the Study of Gene Function.

PubMed

Zhang, Yaoyao; Tang, Na; Sadigh, Yashar; Baigent, Susan; Shen, Zhiqiang; Nair, Venugopal; Yao, Yongxiu

2018-05-24

Marek's disease virus (MDV) is a member of alphaherpesviruses associated with Marek's disease, a highly contagious neoplastic disease in chickens. Complete sequencing of the viral genome and recombineering techniques using infectious bacterial artificial chromosome (BAC) clones of Marek's disease virus genome have identified major genes that are associated with pathogenicity. Recent advances in CRISPR/Cas9-based gene editing have given opportunities for precise editing of the viral genome for identifying pathogenic determinants. Here we describe the application of CRISPR/Cas9 gene editing approaches to delete the Meq and pp38 genes from the CVI988 vaccine strain of MDV. This powerful technology will speed up the MDV gene function studies significantly, leading to a better understanding of the molecular mechanisms of MDV pathogenesis.
Soils: An Introduction, Fifth Edition

NASA Astrophysics Data System (ADS)

Baisden, W. Troy

Understanding the links among global biogeochemical cycles, ecology, hydrology and climate demands a knowledge base that has traditionally been considered soil science. However, for soil science to play a role in this understanding, geologists, hydrologists, ecologists, climatologists, and many others must have a fundamental understanding of soil science. Do introductory soil science texts speak to this audience?To address this question, I reviewed the fifth edition of a textbook that set out in its original edition to accomplish just this goal—to be the introductory soil science text for students outside the discipline of soil science. As such, Singer and Munns' Soils:An Introduction must be compared to The Nature and Properties of Soils by N.C. Brady and R.R. Weil, a standard text directly descended from a first edition published in 1922.
Assistive Potencies: Reconfiguring the Scholarly Edition in an Electronic Setting

ERIC Educational Resources Information Center

Lyman, Eugene William

2009-01-01

This dissertation makes the claim that electronic scholarly editions have the potential to produce more reliable scholarly texts than their print-based antecedents. It consists of an introduction, four chapters, and a brief conclusion. It originated in my work creating the Elwood Viewer, a sophisticated software browser written to display TEI…
Safety in Science for Primary Schools. 1st Edition.

ERIC Educational Resources Information Center

Association for Science Education, Cambridge (England).

This packet of teacher education materials is based on the publication "Be Safe!" and is intended for those teaching science to children ages 4 to 12. The pack contains INSET materials that supplement a safety exhibition contained in the second edition of "Be Safe!." Five basic activities include instructions for training…
Linguistic Variability and Intellectual Development. Miami Linguistics Series No. 9.

ERIC Educational Resources Information Center

von Humboldt, Wilhelm

Although this edition of Wilhelm von Humboldt's "Linguistic Variability and Intellectual Development" is based entirely on the original German edition, the translators (George C. Buck and Frithjof A. Raven) and the publisher have attempted to clarify certain aspects of this work for the modern-day reader. These features include the addition of…
Mental Retardation: Definition, Classification, and Systems of Supports. 10th Edition.

ERIC Educational Resources Information Center

Luckasson, Ruth; Borthwick-Duffy, Sharon; Buntinx, Wil H. E.; Coulter, David L.; Craig, Ellis M.; Reeve, Alya; Schalock, Robert L.; Snell, Martha E.; Spitalnik, Deborah M.; Spreat, Scott; Tasse, Marc J.

This manual, the 10th edition of a regularly published definition and classification work on mental retardation, presents five key assumptions upon which the definition of mental retardation is based and a theoretical model of five essential dimensions that explain mental retardation and how to use the companion system. These dimensions include…
Diesel Technology: Electrical and Electronic Systems. Teacher Edition [and] Student Edition.

ERIC Educational Resources Information Center

Ready, Allan; Kauffman, Ricky; Bogle, Jerry

This document contains the materials for a competency-based course in diesel technology and electrical and electronic systems that is tied to measurable and observable learning outcomes identified and validated by an advisory committee of business and industry representatives and teachers. The competencies addressed align with the medium/heavy…
Textbook of Child and Adolescent Psychiatry. 3rd Edition.

ERIC Educational Resources Information Center

Wiener, Jerry M.; Dulcan, Mina K.

The third edition of this textbook continues its tradition of integrating clinical wisdom and scientific research to improve patient care and advocacy for children and families. Each of the 56 chapters presents a summary of a core topic, blending clinical experience with evidence-based practices in assessment and treatment. Divided into 10 parts,…
Improvements in Anatomy Knowledge When Utilizing a Novel Cyclical "Observe-Reflect-Draw-Edit-Repeat" Learning Process

ERIC Educational Resources Information Center

Backhouse, Mark; Fitzpatrick, Michael; Hutchinson, Joseph; Thandi, Charankumal S.; Keenan, Iain D.

2017-01-01

Innovative educational strategies can provide variety and enhance student learning while addressing complex logistical and financial issues facing modern anatomy education. "Observe-Reflect-Draw-Edit-Repeat" (ORDER), a novel cyclical artistic process, has been designed based on cognitivist and constructivist learning theories, and on…
Konkordanz zu Schillers aesthetischen und philosophischen Schriften (Concordance of Schiller's Aesthetic and Philosophical Writings).

ERIC Educational Resources Information Center

Sanford, Gerlinde Ulm

This document provides a computer-based concordance of the vocabulary used in Friedrich von Schiller's "Aesthetic and Philosophical Writings" as they appear in Volumes 20 and 21 of Schiller's "Werke," 1967 edition, edited by Benno von Wiese. The first section includes the entire text, each sentence numbered for research…
Trying to Contain Ourselves: A Dialogic Review of the "MLA Handbook, Eighth Edition"

ERIC Educational Resources Information Center

Walker, Janice R.; Kelly, Erin E.

2017-01-01

Since the 2016 release of the Modern Language Association's new style guidelines, scholars and teachers--along with writing centers, libraries, and editorial staffs--have been familiarizing themselves with the changes. Based on a standardized approach to citation, the eighth edition of the "MLA Handbook" asks us to adjust some…
Answer Markup Algorithms for Southeast Asian Languages.

ERIC Educational Resources Information Center

Henry, George M.

1991-01-01

Typical markup methods for providing feedback to foreign language learners are not applicable to languages not written in a strictly linear fashion. A modification of Hart's edit markup software is described, along with a second variation based on a simple edit distance algorithm adapted to a general Southeast Asian font system. (10 references)…
CRISPR/Cas9-mediated noncoding RNA editing in human cancers.

PubMed

Yang, Jie; Meng, Xiaodan; Pan, Jinchang; Jiang, Nan; Zhou, Chengwei; Wu, Zhenhua; Gong, Zhaohui

2018-01-02

Cancer is characterized by multiple genetic and epigenetic alterations, including a higher prevalence of mutations of oncogenes and/or tumor suppressors. Mounting evidences have shown that noncoding RNAs (ncRNAs) are involved in the epigenetic regulation of cancer genes and their associated pathways. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (CRISPR/Cas9) system, a revolutionary genome-editing technology, has shed light on ncRNA-based cancer therapy. Here, we briefly introduce the classifications and mechanisms of CRISPR/Cas9 system. Importantly, we mainly focused on the applications of CRISPR/Cas9 system as a molecular tool for ncRNA (microRNA, long noncoding RNA and circular RNA, etc.) editing in human cancers, and the novel techniques that are based on CRISPR/Cas9 system. Additionally, the off-target effects and the corresponding solutions as well as the challenges toward CRISPR/Cas9 were also evaluated and discussed. Long- and short-ncRNAs have been employed as targets in precision oncology, and CRISPR/Cas9-mediated ncRNA editing may provide an excellent way to cure cancer.
CRISPR-Cas9 technology: applications and human disease modelling.

PubMed

Torres-Ruiz, Raul; Rodriguez-Perales, Sandra

2017-01-01

Genome engineering is a powerful tool for a wide range of applications in biomedical research and medicine. The development of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has revolutionized the field of gene editing, thus facilitating efficient genome editing through the creation of targeted double-strand breaks of almost any organism and cell type. In addition, CRISPR-Cas9 technology has been used successfully for many other purposes, including regulation of endogenous gene expression, epigenome editing, live-cell labelling of chromosomal loci, edition of single-stranded RNA and high-throughput gene screening. The implementation of the CRISPR-Cas9 system has increased the number of available technological alternatives for studying gene function, thus enabling generation of CRISPR-based disease models. Although many mechanistic questions remain to be answered and several challenges have yet to be addressed, the use of CRISPR-Cas9-based genome engineering technologies will increase our knowledge of disease processes and their treatment in the near future. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.
Enhancing Targeted Genomic DNA Editing in Chicken Cells Using the CRISPR/Cas9 System

PubMed Central

Wang, Ling; Yang, Likai; Guo, Yijie; Du, Weili; Yin, Yajun; Zhang, Tao; Lu, Hongzhao

2017-01-01

The CRISPR/Cas9 system has enabled highly efficient genome targeted editing for various organisms. However, few studies have focused on CRISPR/Cas9 nuclease-mediated chicken genome editing compared with mammalian genomes. The current study combined CRISPR with yeast Rad52 (yRad52) to enhance targeted genomic DNA editing in chicken DF-1 cells. The efficiency of CRISPR/Cas9 nuclease-induced targeted mutations in the chicken genome was increased to 41.9% via the enrichment of the dual-reporter surrogate system. In addition, the combined effect of CRISPR nuclease and yRad52 dramatically increased the efficiency of the targeted substitution in the myostatin gene using 50-mer oligodeoxynucleotides (ssODN) as the donor DNA, resulting in a 36.7% editing efficiency after puromycin selection. Furthermore, based on the effect of yRad52, the frequency of exogenous gene integration in the chicken genome was more than 3-fold higher than that without yRad52. Collectively, these results suggest that ssODN is an ideal donor DNA for targeted substitution and that CRISPR/Cas9 combined with yRad52 significantly enhances chicken genome editing. These findings could be extensively applied in other organisms. PMID:28068387
Efficient CRISPR/Cas9-based gene knockout in watermelon.

PubMed

Tian, Shouwei; Jiang, Linjian; Gao, Qiang; Zhang, Jie; Zong, Mei; Zhang, Haiying; Ren, Yi; Guo, Shaogui; Gong, Guoyi; Liu, Fan; Xu, Yong

2017-03-01

CRISPR/Cas9 system can precisely edit genomic sequence and effectively create knockout mutations in T0 generation watermelon plants. Genome editing offers great advantage to reveal gene function and generate agronomically important mutations to crops. Recently, RNA-guided genome editing system using the type II clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) has been applied to several plant species, achieving successful targeted mutagenesis. Here, we report the genome of watermelon, an important fruit crop, can also be precisely edited by CRISPR/Cas9 system. ClPDS, phytoene desaturase in watermelon, was selected as the target gene because its mutant bears evident albino phenotype. CRISPR/Cas9 system performed genome editing, such as insertions or deletions at the expected position, in transfected watermelon protoplast cells. More importantly, all transgenic watermelon plants harbored ClPDS mutations and showed clear or mosaic albino phenotype, indicating that CRISPR/Cas9 system has technically 100% of genome editing efficiency in transgenic watermelon lines. Furthermore, there were very likely no off-target mutations, indicated by examining regions that were highly homologous to sgRNA sequences. Our results show that CRISPR/Cas9 system is a powerful tool to effectively create knockout mutations in watermelon.

Low incidence of SNVs and indels in trio genomes of Cas9-mediated multiplex edited sheep.

PubMed

Wang, Xiaolong; Liu, Jing; Niu, Yiyuan; Li, Yan; Zhou, Shiwei; Li, Chao; Ma, Baohua; Kou, Qifang; Petersen, Bjoern; Sonstegard, Tad; Huang, Xingxu; Jiang, Yu; Chen, Yulin

2018-05-25

The simplicity of the CRISPR/Cas9 system has enabled its widespread applications in generating animal models, functional genomic screening and in treating genetic and infectious diseases. However, unintended mutations produced by off-target CRISPR/Cas9 nuclease activity may lead to negative consequences. Especially, a very recent study found that gene editing can introduce hundreds of unintended mutations into the genome, and have attracted wide attention. To address the off-target concerns, urgent characterization of the CRISPR/Cas9-mediated off-target mutagenesis is highly anticipated. Here we took advantage of our previously generated gene-edited sheep and performed family trio-based whole genome sequencing which is capable of discriminating variants in the edited progenies that are inherited, naturally generated, or induced by genetic modification. Three family trios were re-sequenced at a high average depth of genomic coverage (~ 25.8×). After developing a pipeline to comprehensively analyze the sequence data for de novo single nucleotide variants, indels and structural variations from the genome; we only found a single unintended event in the form of a 2.4 kb inversion induced by site-specific double-strand breaks between two sgRNA targeting sites at the MSTN locus with a low incidence. We provide the first report on the fidelity of CRISPR-based modification for sheep genomes targeted simultaneously for gene breaks at three coding sequence locations. The trio-based sequencing approach revealed almost negligible off-target modifications, providing timely evidences of the safe application of genome editing in vivo with CRISPR/Cas9.
Mojo Hand, a TALEN design tool for genome editing applications.

PubMed

Neff, Kevin L; Argue, David P; Ma, Alvin C; Lee, Han B; Clark, Karl J; Ekker, Stephen C

2013-01-16

Recent studies of transcription activator-like (TAL) effector domains fused to nucleases (TALENs) demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecting appropriate genetic features, finding pairs of binding sites based on a consensus sequence, and, in some cases, identifying endogenous restriction sites for downstream molecular genetic applications. We present the web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (http://www.talendesign.org). We describe the algorithm and its implementation. The features of Mojo Hand include (1) automatic download of genomic data from the National Center for Biotechnology Information, (2) analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3) selection of restriction-enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4) output files designed for subsequent TALEN construction using the Golden Gate assembly method. Mojo Hand enables the rapid identification of TAL binding sites for use in TALEN design. The assembly of TALEN constructs, is also simplified by using the TAL-site prediction program in conjunction with a spreadsheet management aid of reagent concentrations and TALEN formulation. Mojo Hand enables scientists to more rapidly deploy TALENs for genome editing applications.
BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment

PubMed Central

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

2016-01-01

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. PMID:27461955
Quantification of GABA, glutamate and glutamine in a single measurement at 3 T using GABA‐edited MEGA‐PRESS

PubMed Central

Sanaei Nezhad, Faezeh; Anton, Adriana; Michou, Emilia; Jung, JeYoung; Parkes, Laura M.

2017-01-01

γ‐Aminobutyric acid (GABA) and glutamate (Glu), major neurotransmitters in the brain, are recycled through glutamine (Gln). All three metabolites can be measured by magnetic resonance spectroscopy in vivo, although GABA measurement at 3 T requires an extra editing acquisition, such as Mescher–Garwood point‐resolved spectroscopy (MEGA‐PRESS). In a GABA‐edited MEGA‐PRESS spectrum, Glu and Gln co‐edit with GABA, providing the possibility to measure all three in one acquisition. In this study, we investigated the reliability of the composite Glu + Gln (Glx) peak estimation and the possibility of Glu and Gln separation in GABA‐edited MEGA‐PRESS spectra. The data acquired in vivo were used to develop a quality assessment framework which identified MEGA‐PRESS spectra in which Glu and Gln could be estimated reliably. Phantoms containing Glu, Gln, GABA and N‐acetylaspartate (NAA) at different concentrations were scanned using GABA‐edited MEGA‐PRESS at 3 T. Fifty‐six sets of spectra in five brain regions were acquired from 36 healthy volunteers. Based on the Glu/Gln ratio, data were classified as either within or outside the physiological range. A peak‐by‐peak quality assessment was performed on all data to investigate whether quality metrics can discriminate between these two classes of spectra. The quality metrics were as follows: the GABA signal‐to‐noise ratio, the NAA linewidth and the Glx Cramer–Rao lower bound (CRLB). The Glu and Gln concentrations were estimated with precision across all phantoms with a linear relationship between the measured and true concentrations: R 1 = 0.95 for Glu and R 1 = 0.91 for Gln. A quality assessment framework was set based on the criteria necessary for a good GABA‐edited MEGA‐PRESS spectrum. Simultaneous criteria of NAA linewidth <8 Hz and Glx CRLB <16% were defined as optimum features for reliable Glu and Gln quantification. Glu and Gln can be reliably quantified from GABA‐edited MEGA‐PRESS acquisitions. However, this reliability should be controlled using the quality assessment methods suggested in this work. PMID:29130590
A segmentation editing framework based on shape change statistics

NASA Astrophysics Data System (ADS)

Mostapha, Mahmoud; Vicory, Jared; Styner, Martin; Pizer, Stephen

2017-02-01

Segmentation is a key task in medical image analysis because its accuracy significantly affects successive steps. Automatic segmentation methods often produce inadequate segmentations, which require the user to manually edit the produced segmentation slice by slice. Because editing is time-consuming, an editing tool that enables the user to produce accurate segmentations by only drawing a sparse set of contours would be needed. This paper describes such a framework as applied to a single object. Constrained by the additional information enabled by the manually segmented contours, the proposed framework utilizes object shape statistics to transform the failed automatic segmentation to a more accurate version. Instead of modeling the object shape, the proposed framework utilizes shape change statistics that were generated to capture the object deformation from the failed automatic segmentation to its corresponding correct segmentation. An optimization procedure was used to minimize an energy function that consists of two terms, an external contour match term and an internal shape change regularity term. The high accuracy of the proposed segmentation editing approach was confirmed by testing it on a simulated data set based on 10 in-vivo infant magnetic resonance brain data sets using four similarity metrics. Segmentation results indicated that our method can provide efficient and adequately accurate segmentations (Dice segmentation accuracy increase of 10%), with very sparse contours (only 10%), which is promising in greatly decreasing the work expected from the user.
[Historical changes in the list of plasma fractionation products placed on the WHO Model List of Essential Medicines].

PubMed

Sakagami, Yuichiro; Tsutani, Kiichiro

2014-01-01

The purpose of this study was to summarize the historical changes in the list of plasma fractionation products (PFP) placed on the Model List of Essential Medicines (EML) issued by the World Health Organization (WHO). PFP such as albumin, blood coagulation factors, and immunoglobulins are derived from blood collected from thousands of people. PFP have been listed since the first edition of the EML (1977). However, the PFP listed on the EML have changed dramatically because EML's selection process has changed from experience-based to evidence-based. For example, albumin, which had been listed since the 2nd edition (1979), was deleted in the 11th edition (2000) because of the uncertainty of its efficacy. Human immunoglobulin normal, which had been deleted from the 13th edition (2003), was relisted in the 15th edition (2007). Moreover, the WHO has issued several resolutions and guidelines regarding PFP production, quality, and safety in order to promote the establishment of blood programmes in every nation. The focus of WHO's EML selection process has changed over 30 years. In the 20th century, WHO mainly focused on PFP efficacy, quality, and safety problems. However, currently the focus is on the problem of PFP accessibility, especially in developing countries. Therefore, it would be important to know how to capitalize on established knowledge and production technology to increase the accessibility of PFP worldwide.
Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery.

PubMed

Gaj, Thomas; Staahl, Brett T; Rodrigues, Gonçalo M C; Limsirichai, Prajit; Ekman, Freja K; Doudna, Jennifer A; Schaffer, David V

2017-06-20

Realizing the full potential of genome editing requires the development of efficient and broadly applicable methods for delivering programmable nucleases and donor templates for homology-directed repair (HDR). The RNA-guided Cas9 endonuclease can be introduced into cells as a purified protein in complex with a single guide RNA (sgRNA). Such ribonucleoproteins (RNPs) can facilitate the high-fidelity introduction of single-base substitutions via HDR following co-delivery with a single-stranded DNA oligonucleotide. However, combining RNPs with transgene-containing donor templates for targeted gene addition has proven challenging, which in turn has limited the capabilities of the RNP-mediated genome editing toolbox. Here, we demonstrate that combining RNP delivery with naturally recombinogenic adeno-associated virus (AAV) donor vectors enables site-specific gene insertion by homology-directed genome editing. Compared to conventional plasmid-based expression vectors and donor templates, we show that combining RNP and AAV donor delivery increases the efficiency of gene addition by up to 12-fold, enabling the creation of lineage reporters that can be used to track the conversion of striatal neurons from human fibroblasts in real time. These results thus illustrate the potential for unifying nuclease protein delivery with AAV donor vectors for homology-directed genome editing. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Standards for the Analysis and Processing of Surface-Water Data and Information Using Electronic Methods

USGS Publications Warehouse

Sauer, Vernon B.

2002-01-01

Surface-water computation methods and procedures are described in this report to provide standards from which a completely automated electronic processing system can be developed. To the greatest extent possible, the traditional U. S. Geological Survey (USGS) methodology and standards for streamflow data collection and analysis have been incorporated into these standards. Although USGS methodology and standards are the basis for this report, the report is applicable to other organizations doing similar work. The proposed electronic processing system allows field measurement data, including data stored on automatic field recording devices and data recorded by the field hydrographer (a person who collects streamflow and other surface-water data) in electronic field notebooks, to be input easily and automatically. A user of the electronic processing system easily can monitor the incoming data and verify and edit the data, if necessary. Input of the computational procedures, rating curves, shift requirements, and other special methods are interactive processes between the user and the electronic processing system, with much of this processing being automatic. Special computation procedures are provided for complex stations such as velocity-index, slope, control structures, and unsteady-flow models, such as the Branch-Network Dynamic Flow Model (BRANCH). Navigation paths are designed to lead the user through the computational steps for each type of gaging station (stage-only, stagedischarge, velocity-index, slope, rate-of-change in stage, reservoir, tide, structure, and hydraulic model stations). The proposed electronic processing system emphasizes the use of interactive graphics to provide good visual tools for unit values editing, rating curve and shift analysis, hydrograph comparisons, data-estimation procedures, data review, and other needs. Documentation, review, finalization, and publication of records are provided for with the electronic processing system, as well as archiving, quality assurance, and quality control.
A RecET-assisted CRISPR-Cas9 genome editing in Corynebacterium glutamicum.

PubMed

Wang, Bo; Hu, Qitiao; Zhang, Yu; Shi, Ruilin; Chai, Xin; Liu, Zhe; Shang, Xiuling; Zhang, Yun; Wen, Tingyi

2018-04-23

Extensive modification of genome is an efficient manner to regulate the metabolic network for producing target metabolites or non-native products using Corynebacterium glutamicum as a cell factory. Genome editing approaches by means of homologous recombination and counter-selection markers are laborious and time consuming due to multiple round manipulations and low editing efficiencies. The current two-plasmid-based CRISPR-Cas9 editing methods generate false positives due to the potential instability of Cas9 on the plasmid, and require a high transformation efficiency for co-occurrence of two plasmids transformation. Here, we developed a RecET-assisted CRISPR-Cas9 genome editing method using a chromosome-borne Cas9-RecET and a single plasmid harboring sgRNA and repair templates. The inducible expression of chromosomal RecET promoted the frequencies of homologous recombination, and increased the efficiency for gene deletion. Due to the high transformation efficiency of a single plasmid, this method enabled 10- and 20-kb region deletion, 2.5-, 5.7- and 7.5-kb expression cassette insertion and precise site-specific mutation, suggesting a versatility of this method. Deletion of argR and farR regulators as well as site-directed mutation of argB and pgi genes generated the mutant capable of accumulating L-arginine, indicating the stability of chromosome-borne Cas9 for iterative genome editing. Using this method, the model-predicted target genes were modified to redirect metabolic flux towards 1,2-propanediol biosynthetic pathway. The final engineered strain produced 6.75 ± 0.46 g/L of 1,2-propanediol that is the highest titer reported in C. glutamicum. Furthermore, this method is available for Corynebacterium pekinense 1.563, suggesting its universal applicability in other Corynebacterium species. The RecET-assisted CRISPR-Cas9 genome editing method will facilitate engineering of metabolic networks for the synthesis of interested bio-based products from renewable biomass using Corynebacterium species as cell factories.
CERES Single Satellite Footprint, TOA and Surface Fluxes, Clouds (SSF) data in HDF (CER_SSF_Aqua-FM4-MODIS_Ed2A-NoSW)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The Single Scanner Footprint TOA/Surface Fluxes and Clouds (SSF) product contains one hour of instantaneous Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The SSF combines instantaneous CERES data with scene information from a higher-resolution imager such as Visible/Infrared Scanner (VIRS) on TRMM or Moderate-Resolution Imaging Spectroradiometer (MODIS) on Terra and Aqua. Scene identification and cloud properties are defined at the higher imager resolution and these data are averaged over the larger CERES footprint. For each CERES footprint, the SSF contains the number of cloud layers and for each layer the cloud amount, height, temperature, pressure, optical depth, emissivity, ice and liquid water path, and water particle size. The SSF also contains the CERES filtered radiances for the total, shortwave (SW), and window (WN) channels and the unfiltered SW, longwave (LW), and WN radiances. The SW, LW, and WN radiances at spacecraft altitude are converted to Top-of-the-Atmosphere (TOA) fluxes based on the imager defined scene. These TOA fluxes are used to estimate surface fluxes. Only footprints with adequate imager coverage are included on CER_SSF_TRMM-PFM-VIRS_Subset_Edition1the SSF which is much less than the full set of footprints on the CERES ES-8 product. The following CERES SSF data sets are currently available: CER_SSF_TRMM-PFM-VIRS_Edition1 CER_SSF_TRMM-PFM-VIRS_Subset_Edition1 CER_SSF_TRMM-PFM-VIRS_Edition2A CER_SSF_TRMM-SIM-VIRS_Edition2_VIRSonly CER_SSF_TRMM-PFM-VIRS_Edition2A-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B-TransOps CER_SSF_TRMM-PFM-VIRS_Edition2B CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition1A CER_SSF_Terra-FM1-MODIS_Edition2A CER_SSF_Terra-FM2-MODIS_Edition2A CER_SSF_Terra-FM1-MODIS_Edition2B CER_SSF_Terra-FM2-MODIS_Edition2B CER_SSF_Aqua-FM4-MODIS_Beta1 CER_SSF_Aqua-FM3-MODIS_Beta2 CER_SSF_Aqua-FM4-MODIS_Beta2. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2006-01-01] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Temporal_Resolution=1 hour; Temporal_Resolution_Range=Hourly - < Daily].
Good Questions: Great Ways to Differentiate Mathematics Instruction in the Standards-Based Classroom. Third Edition

ERIC Educational Resources Information Center

Small, Marian

2017-01-01

Now in its Third Edition--expanded with over 100 new tasks and questions--this bestselling resource helps experienced and novice teachers to effectively and efficiently differentiate mathematics instruction in grades K-8. Math education expert Marian Small shows teachers how to get started and become expert at using two powerful and universal…
Education Canada? Higher Education on the Brink. Second Edition = Education Canada? Le Postsecondaire en cirse. Deuxieme edition.

ERIC Educational Resources Information Center

Paquet, Gilles, Ed.; von Zur-Muehlen, Max, Ed.

Crises and opportunities in Canadian higher education and challenges for management are addressed in papers and reactions to the papers, based on two symposia. The following English language papers and authors are presented: "Post-Secondary Education--An Enterprise Less Than Optimally Managed?" (Gilles Paquet); "The Crisis Will Get…
78 FR 56715 - Agency Information Collection Activities; Submission for Office of Management and Budget Review...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-13

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A Model for Flexibly Editing CSCL Scripts

ERIC Educational Resources Information Center

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…
Reading for Understanding: How Reading Apprenticeship Improves Disciplinary Learning in Secondary and College Classrooms. Second Edition

ERIC Educational Resources Information Center

Schoenbach, Ruth; Greenleaf, Cynthia; Murphy, Lynn

2012-01-01

Published in partnership with WestEd, this significantly updated second edition of the bestselling book contains strategies for helping students in middle school through community college gain the reading independence to master subject area textbooks and other material. Features of this book include: (1) Based on the Reading Apprenticeship…
Teaching at Its Best: A Research-Based Resource for College Instructors. Second Edition.

ERIC Educational Resources Information Center

Nilson, Linda B.

This handbook is meant to be a toolbox, a compilation of hundreds of practical teaching techniques, formats, classroom activities, and exercises. This edition is revised and expanded to cover more about topics relevant to today's classroom, such as technology and the Internet. The 31 chapters are grouped into these sections: (1) "Sound…
Using Technology with Classroom Instruction that Works. Second Edition

ERIC Educational Resources Information Center

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,…
Education and Identity. Second Edition. The Jossey-Bass Higher and Adult Education Series.

ERIC Educational Resources Information Center

Chickering, Arthur W.; Reisser, Linda

Developing policies and practices to create higher education environments that will foster broad-based development of human talent and potentials is the focus of this fully revised and updated edition, which adds findings from the last 25 years to a classic work. The volume begins with "A Current Theoretical Context for Student Development," which…
Peak with Books: An Early Childhood Resource for Balanced Literacy. Third Edition.

ERIC Educational Resources Information Center

Nelsen, Marjorie R.; Nelsen-Parish, Jan

This book shows how to use popular children's literature to build reading, writing, and cognitive skills in an inquiry-based environment. This third edition has been expanded to include first and second grades. New features include: (1) new emphasis on culturally diverse storybooks; (2) a description of the experiential learning inquiry process;…
The Ecology and Silviculture of Oaks, Second Edition: A new book

Treesearch

Paul S. Johnson; Stephen R. Shifley; Robert Rogers

2011-01-01

The second edition of The Ecology and Silviculture of Oaks was recently published (Johnson and others 2009). The approach of the book is fundamentally silvicultural, but the content is based on the premise that eff ective and environmentally sound management and protection of oak forests and associated landscapes must be grounded in ecological...

Study Guide--What Great Principals Do Differently: Eighteen Things That Matter Most. Second Edition

ERIC Educational Resources Information Center

Whitaker, Beth; Whitaker, Todd; Zoul, Jeffrey

2012-01-01

Designed to be used by facilitators and participants in seminars, book study groups, or other professional development events, this book guides critical thinking, collaboration, and professional growth based on the concepts in Todd Whitaker's best-selling title, "What Great Principals Do Differently" (2nd edition). Each chapter includes: (1) Key…
Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

PubMed

Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

2002-01-01

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.
[The chapter De Puero virgine (or de homine) of Liber medicinae ex animalibus by Sextus Placidus. Historical study, new critical edition and translation].

PubMed

Ferraces Rodríguez, Arsenio

2012-01-01

The article offers an historical study, a new critical edition and the translation of the chapter De Puero virgine of Liber medicinae ex animalibus by Sextus Placitus, firstly edited by Sigerist and Howald in 1927. The book, dating to Late Antiquity, is part of a phyto -zootherapeutical corpus, trasmitted by the manuscript tradition in a single block of text whose central axis is represented by the Herbarium by Pseudo-Apuleius, the tractatus De herba vettonica attributed to Antonius Musa and the De taxone. Chapter 17 is devoted to pharmacological recipes whose ingredients are organic or human body parts; here is provided a critical edition based on the collation of three texts in the manuscript tradition, well testifying the particular vitality of medical prescription texts in Late Antiquity.
A new user-assisted segmentation and tracking technique for an object-based video editing system

NASA Astrophysics Data System (ADS)

Yu, Hong Y.; Hong, Sung-Hoon; Lee, Mike M.; Choi, Jae-Gark

2004-03-01

This paper presents a semi-automatic segmentation method which can be used to generate video object plane (VOP) for object based coding scheme and multimedia authoring environment. Semi-automatic segmentation can be considered as a user-assisted segmentation technique. A user can initially mark objects of interest around the object boundaries and then the user-guided and selected objects are continuously separated from the unselected areas through time evolution in the image sequences. The proposed segmentation method consists of two processing steps: partially manual intra-frame segmentation and fully automatic inter-frame segmentation. The intra-frame segmentation incorporates user-assistance to define the meaningful complete visual object of interest to be segmentation and decides precise object boundary. The inter-frame segmentation involves boundary and region tracking to obtain temporal coherence of moving object based on the object boundary information of previous frame. The proposed method shows stable efficient results that could be suitable for many digital video applications such as multimedia contents authoring, content based coding and indexing. Based on these results, we have developed objects based video editing system with several convenient editing functions.
A Novel RNA Editing Sensor Tool and a Specific Agonist Determine Neuronal Protein Expression of RNA-Edited Glycine Receptors and Identify a Genomic APOBEC1 Dimorphism as a New Genetic Risk Factor of Epilepsy

PubMed Central

Kankowski, Svenja; Förstera, Benjamin; Winkelmann, Aline; Knauff, Pina; Wanker, Erich E.; You, Xintian A.; Semtner, Marcus; Hetsch, Florian; Meier, Jochen C.

2018-01-01

C-to-U RNA editing of glycine receptors (GlyR) can play an important role in disease progression of temporal lobe epilepsy (TLE) as it may contribute in a neuron type-specific way to neuropsychiatric symptoms of the disease. It is therefore necessary to develop tools that allow identification of neuron types that express RNA-edited GlyR protein. In this study, we identify NH4 as agonist of C-to-U RNA edited GlyRs. Furthermore, we generated a new molecular C-to-U RNA editing sensor tool that detects Apobec-1- dependent RNA editing in HEPG2 cells and rat primary hippocampal neurons. Using this sensor combined with NH4 application, we were able to identify C-to-U RNA editing-competent neurons and expression of C-to-U RNA-edited GlyR protein in neurons. Bioinformatic analysis of 1,000 Genome Project Phase 3 allele frequencies coding for human Apobec-1 80M and 80I variants showed differences between populations, and the results revealed a preference of the 80I variant to generate RNA-edited GlyR protein. Finally, we established a new PCR-based restriction fragment length polymorphism (RFLP) approach to profile mRNA expression with regard to the genetic APOBEC1 dimorphism of patients with intractable temporal lobe epilepsy (iTLE) and found that the patients fall into two groups. Patients with expression of the Apobec-1 80I variant mostly suffered from simple or complex partial seizures, whereas patients with 80M expression exhibited secondarily generalized seizure activity. Thus, our method allows the characterization of Apobec-1 80M and 80l variants in the brain and provides a new way to epidemiologically and semiologically classify iTLE according to the two different APOBEC1 alleles. Together, these results demonstrate Apobec-1-dependent expression of RNA-edited GlyR protein in neurons and identify the APOBEC1 80I/M-coding alleles as new genetic risk factors for iTLE patients. PMID:29375302
Book Review: New Perspectives on Technical Editing

NASA Astrophysics Data System (ADS)

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 skills, or do not have a very broad knowledge base. The language fluency of every contributor makes this book a pleasure to read, and this particular volume of Baywood's Technical Communications Series is very well edited. The subject index covers almost 8 two-column pages.
Genome Editing of Monogenic Neuromuscular Diseases: A Systematic Review.

PubMed

Long, Chengzu; Amoasii, Leonela; Bassel-Duby, Rhonda; Olson, Eric N

2016-11-01

Muscle weakness, the most common symptom of neuromuscular disease, may result from muscle dysfunction or may be caused indirectly by neuronal and neuromuscular junction abnormalities. To date, more than 780 monogenic neuromuscular diseases, linked to 417 different genes, have been identified in humans. Genome-editing methods, especially the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) system, hold clinical potential for curing many monogenic disorders, including neuromuscular diseases such as Duchenne muscular dystrophy, spinal muscular atrophy, amyotrophic lateral sclerosis, and myotonic dystrophy type 1. To provide an overview of genome-editing approaches; to summarize published reports on the feasibility, efficacy, and safety of current genome-editing methods as they relate to the potential correction of monogenic neuromuscular diseases; and to highlight scientific and clinical opportunities and obstacles toward permanent correction of disease-causing mutations responsible for monogenic neuromuscular diseases by genome editing. PubMed and Google Scholar were searched for articles published from June 30, 1989, through June 9, 2016, using the following keywords: genome editing, CRISPR-Cas9, neuromuscular disease, Duchenne muscular dystrophy, spinal muscular atrophy, amyotrophic lateral sclerosis, and myotonic dystrophy type 1. The following sources were reviewed: 341 articles describing different approaches to edit mammalian genomes; 330 articles describing CRISPR-Cas9-mediated genome editing in cell culture lines (in vitro) and animal models (in vivo); 16 websites used to generate single-guide RNA; 4 websites for off-target effects; and 382 articles describing viral and nonviral delivery systems. Articles describing neuromuscular diseases, including Duchenne muscular dystrophy, spinal muscular atrophy, amyotrophic lateral sclerosis, and myotonic dystrophy type 1, were also reviewed. Multiple proof-of-concept studies reveal the feasibility and efficacy of genome-editing-meditated correction of monogenic neuromuscular diseases in cultured cells and animal models. Genome editing is a rapidly evolving technology with enormous translational potential once efficacy, delivery, and safety issues are addressed. The clinical impact of this technology is that genome editing can permanently correct disease-causing mutations and circumvent the hurdles of traditional gene- and cell-based therapies.
The CRISPR-Cas9 technology: Closer to the ultimate toolkit for targeted genome editing.

PubMed

Quétier, Francis

2016-01-01

The first period of plant genome editing was based on Agrobacterium; chemical mutagenesis by EMS (ethyl methanesulfonate) and ionizing radiations; each of these technologies led to randomly distributed genome modifications. The second period is associated with the discoveries of homing and meganuclease enzymes during the 80s and 90s, which were then engineered to provide efficient tools for targeted editing. From 2006 to 2012, a few crop plants were successfully and precisely modified using zinc-finger nucleases. A third wave of improvement in genome editing, which led to a dramatic decrease in off-target events, was achieved in 2009-2011 with the TALEN technology. The latest revolution surfaced in 2013 with the CRISPR-Cas9 system, whose high efficiency and technical ease of use is really impressive; scientists can use in-house kits or commercially available kits; the only two requirements are to carefully choose the location of the DNA double strand breaks to be induced and then to order an oligonucleotide. While this close-to- ultimate toolkit for targeted editing of genomes represents dramatic scientific progress which allows the development of more complex useful agronomic traits through synthetic biology, the social acceptance of genome editing remains regularly questioned by anti-GMO citizens and organizations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
The ADAR RNA editing enzyme controls neuronal excitability in Drosophila melanogaster

PubMed Central

Li, Xianghua; Overton, Ian M.; Baines, Richard A.; Keegan, Liam P.; O’Connell, Mary A.

2014-01-01

RNA editing by deamination of specific adenosine bases to inosines during pre-mRNA processing generates edited isoforms of proteins. Recoding RNA editing is more widespread in Drosophila than in vertebrates. Editing levels rise strongly at metamorphosis, and Adar5G1 null mutant flies lack editing events in hundreds of CNS transcripts; mutant flies have reduced viability, severely defective locomotion and age-dependent neurodegeneration. On the other hand, overexpressing an adult dADAR isoform with high enzymatic activity ubiquitously during larval and pupal stages is lethal. Advantage was taken of this to screen for genetic modifiers; Adar overexpression lethality is rescued by reduced dosage of the Rdl (Resistant to dieldrin), gene encoding a subunit of inhibitory GABA receptors. Reduced dosage of the Gad1 gene encoding the GABA synthetase also rescues Adar overexpression lethality. Drosophila Adar5G1 mutant phenotypes are ameliorated by feeding GABA modulators. We demonstrate that neuronal excitability is linked to dADAR expression levels in individual neurons; Adar-overexpressing larval motor neurons show reduced excitability whereas Adar5G1 null mutant or targeted Adar knockdown motor neurons exhibit increased excitability. GABA inhibitory signalling is impaired in human epileptic and autistic conditions, and vertebrate ADARs may have a relevant evolutionarily conserved control over neuronal excitability. PMID:24137011
A simple and efficient method to visualize and quantify the efficiency of chromosomal mutations from genome editing

PubMed Central

Fu, Liezhen; Wen, Luan; Luu, Nga; Shi, Yun-Bo

2016-01-01

Genome editing with designer nucleases such as TALEN and CRISPR/Cas enzymes has broad applications. Delivery of these designer nucleases into organisms induces various genetic mutations including deletions, insertions and nucleotide substitutions. Characterizing those mutations is critical for evaluating the efficacy and specificity of targeted genome editing. While a number of methods have been developed to identify the mutations, none other than sequencing allows the identification of the most desired mutations, i.e., out-of-frame insertions/deletions that disrupt genes. Here we report a simple and efficient method to visualize and quantify the efficiency of genomic mutations induced by genome-editing. Our approach is based on the expression of a two-color fusion protein in a vector that allows the insertion of the edited region in the genome in between the two color moieties. We show that our approach not only easily identifies developing animals with desired mutations but also efficiently quantifies the mutation rate in vivo. Furthermore, by using LacZα and GFP as the color moieties, our approach can even eliminate the need for a fluorescent microscope, allowing the analysis with simple bright field visualization. Such an approach will greatly simplify the screen for effective genome-editing enzymes and identify the desired mutant cells/animals. PMID:27748423
Editing Citrus Genome via SaCas9/sgRNA System

PubMed Central

Jia, Hongge; Xu, Jin; Orbović, Vladimir; Zhang, Yunzeng; Wang, Nian

2017-01-01

SaCas9/sgRNA, derived from Staphylococcus aureus, is an alternative system for genome editing to Streptococcus pyogenes SpCas9/sgRNA. The smaller SaCas9 recognizes a different protospacer adjacent motif (PAM) sequence from SpCas9. SaCas9/sgRNA has been employed to edit the genomes of Arabidopsis, tobacco and rice. In this study, we aimed to test its potential in genome editing of citrus. Transient expression of SaCas9/sgRNA in Duncan grapefruit via Xcc-facilitated agroinfiltration showed it can successfully modify CsPDS and Cs2g12470. Subsequently, binary vector GFP-p1380N-SaCas9/35S-sgRNA1:AtU6-sgRNA2 was developed to edit two target sites of Cs7g03360 in transgenic Carrizo citrange. Twelve GFP-positive Carrizo transformants were successfully established, designated as #Cz1 to #Cz12. Based on targeted next generation sequencing results, the mutation rates for the two targets ranged from 15.55 to 39.13% for sgRNA1 and 49.01 to 79.67% for sgRNA2. Therefore, SaCas9/sgRNA can be used as an alternative tool to SpCas9/sgRNA for citrus genome editing. PMID:29312390
Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus.

PubMed

Fujita, Toshitsugu; Yuno, Miyuki; Fujii, Hodaka

2016-07-28

The clustered regularly interspaced short palindromic repeats (CRISPR) system has been adopted for a wide range of biological applications including genome editing. In some cases, dissection of genome functions requires allele-specific genome editing, but the use of CRISPR for this purpose has not been studied in detail. In this study, using the p16INK4a gene in HCT116 as a model locus, we investigated whether chromatin states, such as CpG methylation, or a single-nucleotide gap form in a target site can be exploited for allele-specific locus binding and genome editing by CRISPR in vivo. First, we showed that allele-specific locus binding and genome editing could be achieved by targeting allele-specific CpG-methylated regions, which was successful for one, but not all guide RNAs. In this regard, molecular basis underlying the success remains elusive at this stage. Next, we demonstrated that an allele-specific single-nucleotide gap form could be employed for allele-specific locus binding and genome editing by CRISPR, although it was important to avoid CRISPR tolerance of a single nucleotide mismatch brought about by mismatched base skipping. Our results provide information that might be useful for applications of CRISPR in studies of allele-specific functions in the genomes.
The nucleotides they are a-changin': function of RNA binding proteins in post-transcriptional messenger RNA editing and modification in Arabidopsis.

PubMed

Kramer, Marianne C; Anderson, Stephen J; Gregory, Brian D

2018-06-05

During and after transcription, the fate of an RNA molecule is almost entirely directed by the cohorts of interacting RNA-binding proteins (RBPs). RBPs regulate all stages of the life cycle of a messenger RNA (mRNA) molecule, including splicing, polyadenylation, transport out of the nucleus, RNA stability, and translation. In addition to these functions, RBPs can function to modify or edit the sequences encoded by the RNA. While the sequence for each transcript is determined in the genome, by the time an RNA reaches its final fate, the sequence may have been edited, where one nucleotide is converted to another, or modified, where a chemical group, or sometimes others moieties, are covalently linked to a nucleotide base. These changes to the RNA sequence have major consequences on the function of the RNA. Additionally, variation in the levels of the RBPs that perform the editing or modification can drastically affect the fitness of an organism. Here, we review RBPs that are known to edit or modify RNA ribonucleotides, focusing on the RNA editing ability of the pentatricopeptide repeat (PPR) proteins and the RBPs that modify adenosine to N 6 - methyladenosine. Copyright © 2018 Elsevier Ltd. All rights reserved.
Book Review: Reconstructing Quaternary Environments

NASA Astrophysics Data System (ADS)

Bridgland, David R.; Evans, David J. A.; Roberts, David H.

2016-02-01

A third edition of this, the foremost Quaternary textbook, is most welcome, coming seventeen years after the 1997 second edition (which was 13 years after the first). The general impression is one of advancement, not least because of the extensive updating of literature cited and examples used, with the status maintained of an impressive compendium of a specialism with a very wide subject base. Some changes are cosmetic, with chapter and section headers having a more modern style and a profusion of new colour photographs and diagrams. Some of the latter are redrawn from black and white figures in the previous edition, although not all have been improved, as some are smaller and have been simplified. For example, black and white Fig. 3.10 of the Second Edition compares very favourably with the much smaller colour 3.17 in this latest volume (erratic sources). On the plus side, the number change, for a figure that appears in the same place within the chapter, shows that the latest edition is considerably better illustrated than its predecessor, perhaps accounting for a significant proportion of the increased page total (up from 446 to 538).
The teachers at Sea program of the Committee on Education of EGU

NASA Astrophysics Data System (ADS)

Laj, Carlo; Kissel, Catherine; Leau, Hélène

2015-04-01

"Teachers at sea" is an Educational Program making it possible for high school teachers to participate to oceanographic cruises together with the scientists. With the support of the French Polar Insitute (IPEV) and of EGU, 3 editions of this program have taken place on board the R/V Marion Dufresne during cruises PACHIDERME in 2007 (along the Coast and in the fiords of Southern Chile), AMOCINT in 2008 (in the North Atlantic Ocean), and CIRCEA (in the South China Sea in 2012) Another edition took place in 2014, aboard the oceanographic cruise PREPARED (PREsent and PAst flow REgime on contourite Drifts west of Spitsbergen, onboard the Norwegian Research Vessel G.O Sars from 05 to 15 June 2014. The expedition was part of the EUROFLEETS On board, the teachers participated to all the scientific activities. In order to be fully immersed in the scientific work, the teachers also participated together with the scientists and technicians to two 4-hours shifts per day (8h total per day). During these shifts, they were involved in every step of the process of obtaining the cores, cutting, opening and labelling them, archiving, and measuring some of the physical parameters, and finally sediment description. It was possible to establish almost daily reports of the scientific progress of the cruise and to send regular logs to the participating land-based teachers in different schools mainly in Europe and in the USA, taking advantage of a list of addresses of teachers having participated to the Geosciences Information for teachers (GIFT) workshops of the European Geosciences Union. This should bring authentic science in the classroom, and indeed we received enthusiastic responses from many teachers. Exposure to authentic science, such as that the teachers have experienced during these oceanographic cruises, may be a pivotal experience for them, causing them to change at least in part their teaching methods, possibly creating more future scientists or at least adults with positive attitudes towards science. Both the work done on board and the conferences held during the cruise stressed that there are a lot of questions for the future and there are difficulties in making predictions, a message to be transmitted to the next generation. Teachers as multiplicators in educational sectors and partners for students are the best actors to make students (the next generation) aware about these problems in the school.
Quantitative assessment of timing, efficiency, specificity and genetic mosaicism of CRISPR/Cas9-mediated gene editing of hemoglobin beta gene in rhesus monkey embryos.

PubMed

Midic, Uros; Hung, Pei-Hsuan; Vincent, Kailey A; Goheen, Benjamin; Schupp, Patrick G; Chen, Diane D; Bauer, Daniel E; VandeVoort, Catherine A; Latham, Keith E

2017-07-15

Gene editing technologies offer new options for developing novel biomedical research models and for gene and stem cell based therapies. However, applications in many species demand high efficiencies, specificity, and a thorough understanding of likely editing outcomes. To date, overall efficiencies, rates of off-targeting and degree of genetic mosaicism have not been well-characterized for most species, limiting our ability to optimize methods. As a model gene for measuring these parameters of the CRISPR/Cas9 application in a primate species (rhesus monkey), we selected the β-hemoglobin gene (HBB), which also has high relevance to the potential application of gene editing and stem-cell technologies for treating human disease. Our data demonstrate an ability to achieve a high efficiency of gene editing in rhesus monkey zygotes, with no detected off-target effects at selected off-target loci. Considerable genetic mosaicism and variation in the fraction of embryonic cells bearing targeted alleles are observed, and the timing of editing events is revealed using a new model. The uses of Cas9-WT protein combined with optimized concentrations of sgRNAs are two likely areas for further refinement to enhance efficiency while limiting unfavorable outcomes that can be exceedingly costly for application of gene editing in primate species. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Statistical optimisation techniques in fatigue signal editing problem

NASA Astrophysics Data System (ADS)

Nopiah, Z. M.; Osman, M. H.; Baharin, N.; Abdullah, S.

2015-02-01

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.
Statistical optimisation techniques in fatigue signal editing problem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nopiah, Z. M.; Osman, M. H.; Baharin, N.

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 andmore » 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.« less
Cognitive Development and Down Syndrome: Age-Related Change on the Stanford-Binet Test (Fourth Edition)

ERIC Educational Resources Information Center

Couzens, Donna; Cuskelly, Monica; Haynes, Michele

2011-01-01

Growth models for subtests of the Stanford-Binet Intelligence Scale, 4th edition (R. L. Thorndike, E. P. Hagen, & J. M. Sattler, 1986a, 1986b) were developed for individuals with Down syndrome. Models were based on the assessments of 208 individuals who participated in longitudinal and cross-sectional research between 1987 and 2004. Variation…
Video Editing System

NASA Technical Reports Server (NTRS)

Schlecht, Leslie E.; Kutler, Paul (Technical Monitor)

1998-01-01

This is a proposal for a general use system based, on the SGI IRIS workstation platform, for recording computer animation to videotape. In addition, this system would provide features for simple editing and enhancement. Described here are a list of requirements for the system, and a proposed configuration including the SGI VideoLab Integrator, VideoMedia VLAN animation controller and the Pioneer rewritable laserdisc recorder.

Bully Blocking: Six Secrets to Help Children Deal with Teasing and Bullying. Revised Edition

ERIC Educational Resources Information Center

Field, Evelyn M.

2007-01-01

This confidence-boosting book aims to help children overcome the damaging effects of teasing and bullying, and to develop practical skills and attitudes to improve their self-esteem and quality of life. This revised edition of "Bully Blocking" (originally published under the title "Bully Busting") is based on Evelyn Field's "Secrets of Relating,"…
A Collaborative Approach to Experiential Learning in University Newswriting and Editing Classes: A Case Study

ERIC Educational Resources Information Center

Parks, Perry

2015-01-01

This case study examines a creative approach by two journalism professors to enhance experiential learning in separate skills-based newswriting and editing courses by collaborating to produce a live online news report from campus each week on a four-hour deadline. The study builds on previous research into how innovative classroom structures that…
Broadcasting in America; Second Edition. A Survey of Television and Radio.

ERIC Educational Resources Information Center

Head, Sydney W.

The plan of this volume follows that of the first (1956) edition: a section on physical bases of broadcasting, one on the origin and growth of broadcasting, another on the economics of broadcasting, a fourth on the social control of broadcasting, and a final section for an assessment of the effects and influences of broadcasting. Special attention…
Cognitive Profiles in Youth with Autism Spectrum Disorder: An Investigation of Base Rate Discrepancies Using the Differential Ability Scales-Second Edition

ERIC Educational Resources Information Center

Nowell, Kerri P.; Schanding, G. Thomas, Jr.; Kanne, Stephen M.; Goin-Kochel, Robin P.

2015-01-01

Extant data suggest that the cognitive profiles of individuals with ASD may be characterized by variability, particularly in terms of verbal intellectual functioning (VIQ) and non-verbal intellectual functioning (NVIQ) discrepancies. The "Differential Ability Scales, Second Edition" (DAS-II) has limited data available on its use with…
Genome engineering in ophthalmology: Application of CRISPR/Cas to the treatment of eye disease.

PubMed

Hung, Sandy S C; McCaughey, Tristan; Swann, Olivia; Pébay, Alice; Hewitt, Alex W

2016-07-01

The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and CRISPR-associated protein (Cas) system has enabled an accurate and efficient means to edit the human genome. Rapid advances in this technology could results in imminent clinical application, and with favourable anatomical and immunological profiles, ophthalmic disease will be at the forefront of such work. There have been a number of breakthroughs improving the specificity and efficacy of CRISPR/Cas-mediated genome editing. Similarly, better methods to identify off-target cleavage sites have also been developed. With the impending clinical utility of CRISPR/Cas technology, complex ethical issues related to the regulation and management of the precise applications of human gene editing must be considered. This review discusses the current progress and recent breakthroughs in CRISPR/Cas-based gene engineering, and outlines some of the technical issues that must be addressed before gene correction, be it in vivo or in vitro, is integrated into ophthalmic care. We outline a clinical pipeline for CRISPR-based treatments of inherited eye diseases and provide an overview of the important ethical implications of gene editing and how these may influence the future of this technology. Copyright © 2016 Elsevier Ltd. All rights reserved.
CrisprGE: a central hub of CRISPR/Cas-based genome editing.

PubMed

Kaur, Karambir; Tandon, Himani; Gupta, Amit Kumar; Kumar, Manoj

2015-01-01

CRISPR system is a powerful defense mechanism in bacteria and archaea to provide immunity against viruses. Recently, this process found a new application in intended targeting of the genomes. CRISPR-mediated genome editing is performed by two main components namely single guide RNA and Cas9 protein. Despite the enormous data generated in this area, there is a dearth of high throughput resource. Therefore, we have developed CrisprGE, a central hub of CRISPR/Cas-based genome editing. Presently, this database holds a total of 4680 entries of 223 unique genes from 32 model and other organisms. It encompasses information about the organism, gene, target gene sequences, genetic modification, modifications length, genome editing efficiency, cell line, assay, etc. This depository is developed using the open source LAMP (Linux Apache MYSQL PHP) server. User-friendly browsing, searching facility is integrated for easy data retrieval. It also includes useful tools like BLAST CrisprGE, BLAST NTdb and CRISPR Mapper. Considering potential utilities of CRISPR in the vast area of biology and therapeutics, we foresee this platform as an assistance to accelerate research in the burgeoning field of genome engineering. © The Author(s) 2015. Published by Oxford University Press.
Functional Reconstitution of a Fungal Natural Product Gene Cluster by Advanced Genome Editing.

PubMed

Weber, Jakob; Valiante, Vito; Nødvig, Christina S; Mattern, Derek J; Slotkowski, Rebecca A; Mortensen, Uffe H; Brakhage, Axel A

2017-01-20

Filamentous fungi produce varieties of natural products even in a strain dependent manner. However, the genetic basis of chemical speciation between strains is still widely unknown. One example is trypacidin, a natural product of the opportunistic human pathogen Aspergillus fumigatus, which is not produced among different isolates. Combining computational analysis with targeted gene editing, we could link a single nucleotide insertion in the polyketide synthase of the trypacidin biosynthetic pathway and reconstitute its production in a nonproducing strain. Thus, we present a CRISPR/Cas9-based tool for advanced molecular genetic studies in filamentous fungi, exploiting selectable markers separated from the edited locus.
CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences.

PubMed

Chou, A; Burke, J

1999-05-01

DNA sequence clustering has become a valuable method in support of gene discovery and gene expression analysis. Our interest lies in leveraging the sequence diversity within clusters of expressed sequence tags (ESTs) to model gene structure for the study of gene variants that arise from, among other things, alternative mRNA splicing, polymorphism, and divergence after gene duplication, fusion, and translocation events. In previous work, CRAW was developed to discover gene variants from assembled clusters of ESTs. Most importantly, novel gene features (the differing units between gene variants, for example alternative exons, polymorphisms, transposable elements, etc.) that are specialized to tissue, disease, population, or developmental states can be identified when these tools collate DNA source information with gene variant discrimination. While the goal is complete automation of novel feature and gene variant detection, current methods are far from perfect and hence the development of effective tools for visualization and exploratory data analysis are of paramount importance in the process of sifting through candidate genes and validating targets. We present CRAWview, a Java based visualization extension to CRAW. Features that vary between gene forms are displayed using an automatically generated color coded index. The reporting format of CRAWview gives a brief, high level summary report to display overlap and divergence within clusters of sequences as well as the ability to 'drill down' and see detailed information concerning regions of interest. Additionally, the alignment viewing and editing capabilities of CRAWview make it possible to interactively correct frame-shifts and otherwise edit cluster assemblies. We have implemented CRAWview as a Java application across windows NT/95 and UNIX platforms. A beta version of CRAWview will be freely available to academic users from Pangea Systems (http://www.pangeasystems.com). Contact :
Graduate Education in Coastal Science: Then and Now

NASA Astrophysics Data System (ADS)

Inman, D. L.

2002-12-01

Coastal science began in the early 20th century in geology disciplines with descriptive field studies of ancient shorelines (G. K. Gilbert, 1885) and coastal observations (Douglas Johnson, 1919). World War II placed a strong emphasis on the importance of coastal processes in military operations. The most profound impact was associated with the interdisciplinary approach to coastal science demonstrated by The Oceans (1942). The first organized graduate program in oceanography opened at Scripps Institution of Oceanography in 1946 and offered courses in marine geology as well as physical oceanography, biology at the sea, chemistry of sea water and applied mathematics. Those first classes and the new "Sverdrup" curriculum inspired the rapid growth and transfer of knowledge in the new oceanographic sciences. Graduates of these classes established Sverdrup-type interdisciplinary curricula throughout the world. Research and descriptive understanding of the world's oceans and coasts burgeoned during the 1950s. The aqualung, introduced to Shepard's students in 1948 by Jacques Cousteau, became a new scientific tool for studies in nearshore waters, and instruments were designed for studying waves, currents, and sediment transport. A new quantitative coastal science emerged from the concepts of Bagnold and others. Funding came from the Office of Naval Research, coastal engineering (Beach Erosion Board), and the oil industry. A significant contribution to the literature of classical nearshore processes was the series of Conferences on Coastal Engineering sponsored by the University of California and edited by Joe Johnson. Starting with the first conference held in Long Beach in 1950, the conferences brought together researchers from diverse backgrounds and published their findings expeditiously. This research soon was synthesized into textbooks such as Shepard's Submarine Geology (2nd edition, 1963); Hill's 1963 edited volume The Sea v. 3 The Earth Beneath the Sea, with the first discussion of "Beach and Nearshore Processes"; Wiegel's Oceanographical Engineering in 1964; and Ippen's Estuary and Coastline Hydrodynamics in 1966. An excellent example of the transition from descriptive to quantitative nearshore processes is given by comparison between the first edition in 1948 and the second edition in 1963 of Submarine Geology, with sections added on the mechanics of waves, currents, and sediment transport. In the last two decades, the global scale of environmental research and the power of computers have shifted the focus of coastal research to large scale experiments and process modeling.
The applicability of new TNM classification for humanpapilloma virus-related oropharyngeal cancer in the 8th edition of the AJCC/UICC TNM staging system in Japan: A single-centre study.

PubMed

Sano, Daisuke; Yabuki, Kenichiro; Arai, Yasuhiro; Tanabe, Teruhiko; Chiba, Yoshihiro; Nishimura, Goshi; Takahashi, Hideaki; Yamanaka, Shoji; Oridate, Nobuhiko

2018-06-01

The purpose of this study is to validate the applicability of new TNM classification for human papillomavirus (HPV)-related oropharyngeal cancer (OPC) in the 8th edition of the American Joint Committee on Cancer (AJCC)/Union for International Cancer Control (UICC) TNM staging system in Japan. A total of 91 OPC patients treated with radiation-based therapy between November 2001 and July 2015 were analyzed retrospectively in this study. HPV infection status was evaluated using tumor p16 expression. 40 OPC patients (44.0%) had HPV-positive disease in this study. The distribution of disease stage of HPV-positive OPC patients dramatically changed from the 7th edition to the 8th edition of AJCC/UICC TNM classification. However, neither the 8th edition nor the 7th edition of the AJCC/UICC TNM staging system could adequately predict outcomes of HPV-positive OPC patients in our patient series. On the other hand, our multivariate analysis indicated that matted nodes and age ≥63 were independent prognostic factors for progression-free survival. In addition, HPV-positive OPC patients with stage I without matted nodes showed significantly better overall and progression-free survival compared with those with stage I with matted nodes and stages II and III in the 8th edition of the AJCC/UICC TNM staging system (P=0.008, and P=0.043, respectively). Our results suggested that matted nodes of HPV-positive OPC patients might be additionally examined to apply the 8th edition of AJCC/UICC TNM classification for more adequate predicting outcomes of HPV-positive OPC patients. Copyright © 2017 Elsevier B.V. All rights reserved.
e23D: database and visualization of A-to-I RNA editing sites mapped to 3D protein structures.

PubMed

Solomon, Oz; Eyal, Eran; Amariglio, Ninette; Unger, Ron; Rechavi, Gidi

2016-07-15

e23D, a database of A-to-I RNA editing sites from human, mouse and fly mapped to evolutionary related protein 3D structures, is presented. Genomic coordinates of A-to-I RNA editing sites are converted to protein coordinates and mapped onto 3D structures from PDB or theoretical models from ModBase. e23D allows visualization of the protein structure, modeling of recoding events and orientation of the editing with respect to nearby genomic functional sites from databases of disease causing mutations and genomic polymorphism. http://www.sheba-cancer.org.il/e23D CONTACT: oz.solomon@live.biu.ac.il or Eran.Eyal@sheba.health.gov.il. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
The X-windows interactive navigation data editor

NASA Technical Reports Server (NTRS)

Rinker, G. C.

1992-01-01

A new computer program called the X-Windows Interactive Data Editor (XIDE) was developed and demonstrated as a prototype application for editing radio metric data in the orbit-determination process. The program runs on a variety of workstations and employs pull-down menus and graphical displays, which allow users to easily inspect and edit radio metric data in the orbit data files received from the Deep Space Network (DSN). The XIDE program is based on the Open Software Foundation OSF/Motif Graphical User Interface (GUI) and has proven to be an efficient tool for editing radio metric data in the navigation operations environment. It was adopted by the Magellan Navigation Team as their primary data-editing tool. Because the software was designed from the beginning to be portable, the prototype was successfully moved to new workstation environments. It was also itegrated into the design of the next-generation software tool for DSN multimission navigation interactive launch support.
Computer-based desktop system for surgical videotape editing.

PubMed

Vincent-Hamelin, E; Sarmiento, J M; de la Puente, J M; Vicente, M

1997-05-01

The educational role of surgical video presentations should be optimized by linking surgical images to graphic evaluation of indications, techniques, and results. We describe a PC-based video production system for personal editing of surgical tapes, according to the objectives of each presentation. The hardware requirement is a personal computer (100 MHz processor, 1-Gb hard disk, 16 Mb RAM) with a PC-to-TV/video transfer card plugged into a slot. Computer-generated numerical data, texts, and graphics are transformed into analog signals displayed on TV/video. A Genlock interface (a special interface card) synchronizes digital and analog signals, to overlay surgical images to electronic illustrations. The presentation is stored as digital information or recorded on a tape. The proliferation of multimedia tools is leading us to adapt presentations to the objectives of lectures and to integrate conceptual analyses with dynamic image-based information. We describe a system that handles both digital and analog signals, production being recorded on a tape. Movies may be managed in a digital environment, with either an "on-line" or "off-line" approach. System requirements are high, but handling a single device optimizes editing without incurring such complexity that management becomes impractical to surgeons. Our experience suggests that computerized editing allows linking surgical scientific and didactic messages on a single communication medium, either a videotape or a CD-ROM.
The Eighth Edition AJCC Cancer Staging Manual: Continuing to build a bridge from a population-based to a more "personalized" approach to cancer staging.

PubMed

Amin, Mahul B; Greene, Frederick L; Edge, Stephen B; Compton, Carolyn C; Gershenwald, Jeffrey E; Brookland, Robert K; Meyer, Laura; Gress, Donna M; Byrd, David R; Winchester, David P

2017-03-01

The American Joint Committee on Cancer (AJCC) staging manual has become the benchmark for classifying patients with cancer, defining prognosis, and determining the best treatment approaches. Many view the primary role of the tumor, lymph node, metastasis (TNM) system as that of a standardized classification system for evaluating cancer at a population level in terms of the extent of disease, both at initial presentation and after surgical treatment, and the overall impact of improvements in cancer treatment. The rapid evolution of knowledge in cancer biology and the discovery and validation of biologic factors that predict cancer outcome and response to treatment with better accuracy have led some cancer experts to question the utility of a TNM-based approach in clinical care at an individualized patient level. In the Eighth Edition of the AJCC Cancer Staging Manual, the goal of including relevant, nonanatomic (including molecular) factors has been foremost, although changes are made only when there is strong evidence for inclusion. The editorial board viewed this iteration as a proactive effort to continue to build the important bridge from a "population-based" to a more "personalized" approach to patient classification, one that forms the conceptual framework and foundation of cancer staging in the era of precision molecular oncology. The AJCC promulgates best staging practices through each new edition in an effort to provide cancer care providers with a powerful, knowledge-based resource for the battle against cancer. In this commentary, the authors highlight the overall organizational and structural changes as well as "what's new" in the Eighth Edition. It is hoped that this information will provide the reader with a better understanding of the rationale behind the aggregate proposed changes and the exciting developments in the upcoming edition. CA Cancer J Clin 2017;67:93-99. © 2017 American Cancer Society. © 2017 American Cancer Society.
Mutagenesis and Genome Engineering of Epstein-Barr Virus in Cultured Human Cells by CRISPR/Cas9.

PubMed

Yuen, Kit-San; Chan, Chi-Ping; Kok, Kin-Hang; Jin, Dong-Yan

2017-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 nuclease (Cas9) system is a powerful genome-editing tool for both chromosomal and extrachromosomal DNA. DNA viruses such as Epstein-Barr virus (EBV), which undergoes episomal replication in human cells, can be effectively edited by CRISPR/Cas9. We have demonstrated targeted editing of the EBV genome by CRISPR/Cas9 in several lines of EBV-infected cells. CRISPR/Cas9-based mutagenesis and genome engineering of EBV provides a new method for genetic analysis, which has some advantages over bacterial artificial chromosome-based recombineering. This approach might also prove useful in the cure of EBV infection. In this chapter, we use the knockout of the BART promoter as an example to detail the experimental procedures for construction of recombinant EBV in human cells.
Predicting verbal fluency using Word Reading: Implications for premorbid functioning.

PubMed

Davis, Andrew S; Finch, W Holmes; Drapeau, Christopher; Nogin, Margarita; E Moss, Lauren; Moore, Brittney

2016-01-01

The estimation of premorbid general intellectual functioning using word reading tests has a rich history of validation and is a common assessment practice for neuropsychologists. What is less well-researched is the approach used to estimate premorbid functioning of non-intellectual domains, such as executive functions, including verbal fluency. The current study evaluated this relationship with 41 adult college students who completed the Word Reading subtest of the Wechsler Individual Achievement Test-Second Edition (WIAT-II) and the Verbal Fluency test from the Delis-Kaplan Executive Function System (D-KEFS). Path analysis indicated that only Letter Fluency (a measure of phonemic fluency) was statistically significantly related to Word Reading and the relationship was somewhat weak. The relationship between Category Fluency (a measure of semantic fluency) and Category Switching (a measure of verbal fluency cognitive set-shifting) to Word Reading was nonsignificant. Participants also completed the Wechsler Adult Intelligence Scale-Third Edition (WAIS-III), and as expected a strong relationship was found between Word Reading and the Verbal IQ (VIQ), Performance IQ (PIQ), and Full Scale Intelligence Quotient (FSIQ). Results of this study strongly suggest that caution be exercised when extrapolating an estimate of premorbid verbal fluency abilities from measures of word reading.
CRISPR-based technologies for the manipulation of eukaryotic genomes

PubMed Central

Komor, Alexis C.; Badran, Ahmed H.; Liu, David R.

2016-01-01

The CRISPR-Cas9 RNA-guided DNA endonuclease has contributed to an explosion of advances in the life sciences that have grown from the ability to edit genomes within living cells. In this review we summarize CRISPR-based technologies that enable mammalian genome editing and their various applications. We describe recent developments that extend the generality, DNA specificity, product selectivity, and fundamental capabilities of natural CRISPR systems, and some of the remarkable advancements in basic research, biotechnology, and therapeutics development that these developments have facilitated. PMID:27866654
The European guideline on management of major bleeding and coagulopathy following trauma: fourth edition.

PubMed

Rossaint, Rolf; Bouillon, Bertil; Cerny, Vladimir; Coats, Timothy J; Duranteau, Jacques; Fernández-Mondéjar, Enrique; Filipescu, Daniela; Hunt, Beverley J; Komadina, Radko; Nardi, Giuseppe; Neugebauer, Edmund A M; Ozier, Yves; Riddez, Louis; Schultz, Arthur; Vincent, Jean-Louis; Spahn, Donat R

2016-04-12

Severe trauma continues to represent a global public health issue and mortality and morbidity in trauma patients remains substantial. A number of initiatives have aimed to provide guidance on the management of trauma patients. This document focuses on the management of major bleeding and coagulopathy following trauma and encourages adaptation of the guiding principles to each local situation and implementation within each institution. The pan-European, multidisciplinary Task Force for Advanced Bleeding Care in Trauma was founded in 2004 and included representatives of six relevant European professional societies. The group used a structured, evidence-based consensus approach to address scientific queries that served as the basis for each recommendation and supporting rationale. Expert opinion and current clinical practice were also considered, particularly in areas in which randomised clinical trials have not or cannot be performed. Existing recommendations were reconsidered and revised based on new scientific evidence and observed shifts in clinical practice; new recommendations were formulated to reflect current clinical concerns and areas in which new research data have been generated. This guideline represents the fourth edition of a document first published in 2007 and updated in 2010 and 2013. The guideline now recommends that patients be transferred directly to an appropriate trauma treatment centre and encourages use of a restricted volume replacement strategy during initial resuscitation. Best-practice use of blood products during further resuscitation continues to evolve and should be guided by a goal-directed strategy. The identification and management of patients pre-treated with anticoagulant agents continues to pose a real challenge, despite accumulating experience and awareness. The present guideline should be viewed as an educational aid to improve and standardise the care of the bleeding trauma patients across Europe and beyond. This document may also serve as a basis for local implementation. Furthermore, local quality and safety management systems need to be established to specifically assess key measures of bleeding control and outcome. A multidisciplinary approach and adherence to evidence-based guidance are key to improving patient outcomes. The implementation of locally adapted treatment algorithms should strive to achieve measureable improvements in patient outcome.
Genome Editing of Monogenic Neuromuscular Diseases

PubMed Central

Long, Chengzu; Amoasii, Leonela; Bassel-Duby, Rhonda; Olson, Eric N.

2017-01-01

IMPORTANCE Muscle weakness, the most common symptom of neuromuscular disease, may result from muscle dysfunction or may be caused indirectly by neuronal and neuromuscular junction abnormalities. To date, more than 780 monogenic neuromuscular diseases, linked to 417 different genes, have been identified in humans. Genome-editing methods, especially the CRISPR (clustered regularly interspaced short palindromic repeats)–Cas9 (CRISPR-associated protein 9) system, hold clinical potential for curing many monogenic disorders, including neuromuscular diseases such as Duchenne muscular dystrophy, spinal muscular atrophy, amyotrophic lateral sclerosis, and myotonic dystrophy type 1. OBJECTIVES To provide an overview of genome-editing approaches; to summarize published reports on the feasibility, efficacy, and safety of current genome-editing methods as they relate to the potential correction of monogenic neuromuscular diseases; and to highlight scientific and clinical opportunities and obstacles toward permanent correction of disease-causing mutations responsible for monogenic neuromuscular diseases by genome editing. EVIDENCE REVIEW PubMed and Google Scholar were searched for articles published from June 30, 1989, through June 9, 2016, using the following keywords: genome editing, CRISPR-Cas9, neuromuscular disease, Duchenne muscular dystrophy, spinal muscular atrophy, amyotrophic lateral sclerosis, andmyotonic dystrophy type 1. The following sources were reviewed: 341 articles describing different approaches to edit mammalian genomes; 330 articles describing CRISPR-Cas9–mediated genome editing in cell culture lines (in vitro) and animal models (in vivo); 16 websites used to generate single-guide RNA; 4 websites for off-target effects; and 382 articles describing viral and nonviral delivery systems. Articles describing neuromuscular diseases, including Duchenne muscular dystrophy, spinal muscular atrophy, amyotrophic lateral sclerosis, and myotonic dystrophy type 1, were also reviewed. FINDINGS Multiple proof-of-concept studies reveal the feasibility and efficacy of genome-editing–meditated correction of monogenic neuromuscular diseases in cultured cells and animal models. CONCLUSIONS AND RELEVANCE Genome editing is a rapidly evolving technology with enormous translational potential once efficacy, delivery, and safety issues are addressed. The clinical impact of this technology is that genome editing can permanently correct disease-causing mutations and circumvent the hurdles of traditional gene- and cell-based therapies. PMID:27668807
Challenging a dogma; AJCC 8th staging system is not sufficient to predict outcomes of patients with malignant pleural mesothelioma.

PubMed

Abdel-Rahman, Omar

2017-11-01

The 8th edition of malignant pleural mesothelioma (MPM) American Joint Committee on Cancer (AJCC) staging system has been published. The current analysis aims to evaluate its performance in a population-based setting among patients recorded within the surveillance, epidemiology and end results (SEER) database. SEER database (2004-2013) has been accessed through SEER*Stat program and AJCC 8th edition stage groups were reconstructed. Survival analyses (overall and cancer-specific) were conducted according to 6th and 8th editions through Kaplan-Meier analysis. Cox-regression multivariate model was also utilized for pair wise comparisons between different prognostic groups for overall and cancer-specific survival. A total of 5382 patients with MPM were identified in the period from 2004 to 2013. According to the 6th edition, significant pair wise P values for overall survival included: IA vs. III (P=0.027); IA vs. IV: P<0.0001; IB vs. IV: P<0.0001; II vs. III: P<0.0001; II vs. IV: P<0.0001; III vs. IV: P<0.0001). According to the 8th edition, significant pair wise P values for overall survival included: all stages vs. IV: P<0.0001; IA vs. II: P=0.046; IA vs. IIIA: P=0.022; IA vs. IIIB: P <0.0001; IB vs. II: P<0.0001; IB vs. IIIB: P<0.0001; II vs. IIIA: P<0.0001; IIIA vs. IIIB: P<0.0001). C-index for 6th edition was 0.539 (SE: 0.008; 95% CI: 0.524-0.555); while C-index for 8th edition was 0.540 (SE: 0.008; 95% CI: 0.525-0.556). Based on the above findings, a simplified staging system was proposed and overall and cancer-specific survivals were evaluated according to the simplified system. For overall and cancer-specific survival assessment, P values for all pair wise comparisons among different stages were significant (<0.01). The prognostic performance of both the 6th and 8th AJCC editions is unsatisfactory; there is a need for a more practical and prognostically relevant staging system for MPM. Copyright © 2017 Elsevier B.V. All rights reserved.

Motion Pattern Encapsulation for Data-Driven Constraint-Based Motion Editing

NASA Astrophysics Data System (ADS)

Carvalho, Schubert R.; Boulic, Ronan; Thalmann, Daniel

The growth of motion capture systems have contributed to the proliferation of human motion database, mainly because human motion is important in many applications, ranging from games entertainment and films to sports and medicine. However, the captured motions normally attend specific needs. As an effort for adapting and reusing captured human motions in new tasks and environments and improving the animator's work, we present and discuss a new data-driven constraint-based animation system for interactive human motion editing. This method offers the compelling advantage that it provides faster deformations and more natural-looking motion results compared to goal-directed constraint-based methods found in the literature.
Current Progress in Therapeutic Gene Editing for Monogenic Diseases

PubMed Central

Prakash, Versha; Moore, Marc; Yáñez-Muñoz, Rafael J

2016-01-01

Programmable nucleases allow defined alterations in the genome with ease-of-use, efficiency, and specificity. Their availability has led to accurate and widespread genome engineering, with multiple applications in basic research, biotechnology, and therapy. With regard to human gene therapy, nuclease-based gene editing has facilitated development of a broad range of therapeutic strategies based on both nonhomologous end joining and homology-dependent repair. This review discusses current progress in nuclease-based therapeutic applications for a subset of inherited monogenic diseases including cystic fibrosis, Duchenne muscular dystrophy, diseases of the bone marrow, and hemophilia and highlights associated challenges and future prospects. PMID:26765770
Human Genome Editing in the Clinic: New Challenges in Regulatory Benefit-Risk Assessment.

PubMed

Abou-El-Enein, Mohamed; Cathomen, Toni; Ivics, Zoltán; June, Carl H; Renner, Matthias; Schneider, Christian K; Bauer, Gerhard

2017-10-05

As genome editing rapidly progresses toward the realization of its clinical promise, assessing the suitability of current tools and processes used for its benefit-risk assessment is critical. Although current regulations may initially provide an adequate regulatory framework, improvements are recommended to overcome several existing technology-based safety and efficacy issues. Copyright © 2017 Elsevier Inc. All rights reserved.
>venture>: Support for Early Stage Start-ups and Potential Entrepreneurs.

PubMed

Kauz, Lukas

2014-12-01

>venture>, the leading Swiss-wide business plan competition, is an ideal partner for young start-ups and entrepreneurs. For the upcoming tenth anniversary edition the competition will receive an update. Building upon a successful base of the past nine editions and equipped with contemporary networking events and more know-how transferring seminars, >venture> will fit even better into the Swiss start-up ecosystem.
How to Teach Poetry Writing: Workshops for Ages 8-13. Developing Creative Literacy, 2nd Edition

ERIC Educational Resources Information Center

Morgan, Michaela

2011-01-01

Now in a fully revised and extended second edition, "How to Teach Poetry Writing: Workshops for Ages 8-13" is a practical and activity based resource of writing workshops to help you teach poetry in the primary classroom. Designed to help build writing, speaking and listening skills, this book contains a wide selection of workshops exemplifying a…
Is Everyone Really Equal? An Introduction to Key Concepts in Social Justice Education. Second Edition. Multicultural Education Series

ERIC Educational Resources Information Center

Sensoy, Ozlem; DiAngelo, Robin

2017-01-01

This is the new edition of the award-winning guide to social justice education. Based on the authors' extensive experience in a range of settings in the United States and Canada, the book addresses the most common stumbling blocks to understanding social justice. This comprehensive resource includes new features such as a chapter on…
The Impact of Fast ForWord[R] on Sixth Grade Students' Use of Standard Edited American English

ERIC Educational Resources Information Center

Rogowsky, Beth A.

2010-01-01

This study investigated the impact of Fast ForWord[R] products, specifically Fast ForWord[R] Literacy (FFL) and Fast ForWord[R] Reading Level 2 (FFR2), on sixth grade students' use of Standard Edited American English (SEAE). Fast ForWord[R] is a computer-based program that focuses on phonological awareness and makes use of modeled…
Performance Discrepancies on the California Verbal Learning Test-Second Edition (CVLT-II) in the Standardization Sample

ERIC Educational Resources Information Center

Donders, Jacobus

2006-01-01

The standardization data for the California Verbal Learning Test-Second Edition (CVLT-II; D. C. Delis, J. H. Kramer, E. Kaplan, & B. A. Ober, 2000) were used to evaluate the base rate of 6 specific discrepancies between various key variables. The results indicated that CVLT-II performance discrepancies should equal or exceed 1 or 1.5 z score…
Journal of Special Operations Medicine, Volume 6, Edition 3

DTIC Science & Technology

2006-01-01

between the lower leg muscular planes. These are often times located in multiple places and not radiographically detectable. Volume 6, Edition 3...tinged. Physical examination was remarkable for rales and rhonchi at the left base. There was no jugular venous distension or tracheal deviation... muscular or subcutaneous epinephrine are the first-line treatments for these rare but serious conditions; respi- ratory and intravascular fluid may
Metabolic synthetic lethality in cancer therapy.

PubMed

Zecchini, Vincent; Frezza, Christian

2017-08-01

Our understanding of cancer has recently seen a major paradigm shift resulting in it being viewed as a metabolic disorder, and altered cellular metabolism being recognised as a hallmark of cancer. This concept was spurred by the findings that the oncogenic mutations driving tumorigenesis induce a reprogramming of cancer cell metabolism that is required for unrestrained growth and proliferation. The recent discovery that mutations in key mitochondrial enzymes play a causal role in tumorigenesis suggested that dysregulation of metabolism could also be a driver of tumorigenesis. These mutations induce profound adaptive metabolic alterations that are a prerequisite for the survival of the mutated cells. Because these metabolic events are specific to cancer cells, they offer an opportunity to develop new therapies that specifically target tumour cells without affecting healthy tissue. Here, we will describe recent developments in metabolism-based cancer therapy, in particular focusing on the concept of metabolic synthetic lethality. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux. Copyright © 2016 Elsevier B.V. All rights reserved.
Sophisticated Cloning, Fermentation, and Purification Technologies for an Enhanced Therapeutic Protein Production: A Review

PubMed Central

Gupta, Sanjeev K.; Shukla, Pratyoosh

2017-01-01

The protein productions strategies are crucial towards the development of application based research and elucidating the novel purification strategies for industrial production. Currently, there are few innovative avenues are studies for cloning, upstream, and purification through efficient bioprocess development. Such strategies are beneficial for industries as well as proven to be vital for effectual therapeutic protein development. Though, these techniques are well documented, but, there is scope of addition to current knowledge with novel and new approaches and it will pave new avenues in production of recombinant microbial and non-microbial proteins including secondary metabolites. In this review, we have focussed on the recent development in clone selection, various modern fermentation and purification technologies and future directions in these emerging areas. Moreover, we have also highlighted notable perspectives and challenges involved in the bioengineering of such proteins, including quality by design, gene editing and pioneering ideas. The biopharmaceutical industries continue to shift towards more flexible, automated platforms and economical product development, which in turn can help in developing the cost effective processes and affordable drug development for a large community. PMID:28725194
Atmospheric pressure plasma deposition of antimicrobial coatings on non-woven textiles

NASA Astrophysics Data System (ADS)

Nikiforov, Anton Yu.; Deng, Xiaolong; Onyshchenko, Iuliia; Vujosevic, Danijela; Vuksanovic, Vineta; Cvelbar, Uros; De Geyter, Nathalie; Morent, Rino; Leys, Christophe

2016-08-01

A simple method for preparation of nanoparticle incorporated non-woven fabric with high antibacterial efficiency has been proposed based on atmospheric pressure plasma process. In this work direct current plasma jet stabilized by fast nitrogen flow was used as a plasma deposition source. Three different types of the nanoparticles (silver, copper and zinc oxide nanoparticles) were employed as antimicrobial agents. X-ray photoelectron spectroscopy (XPS) measurements have shown a positive chemical shift observed for Ag 3d 5/2 (at 368.1 eV) suggests that silver nanoparticles (AgNPs) are partly oxidized during the deposition. The surface chemistry and the antibacterial activity of the samples against Staphylococcus aureus and Escherichia coli were investigated and analyzed. It is shown that the samples loaded with nanoparticles of Ag and Cu and having the barrier layer of 10 nm characterized by almost 97% of bacterial reduction whereas the samples with ZnO nanoparticles provide 86% reduction of Staphylococcus aureus. Contribution to the topical issue "6th Central European Symposium on Plasma Chemistry (CESPC-6)", edited by Nicolas Gherardi, Ester Marotta and Cristina Paradisi
Estimation and detection information trade-off for x-ray system optimization

NASA Astrophysics Data System (ADS)

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.
Human Germline Genome Editing.

PubMed

Ormond, Kelly E; Mortlock, Douglas P; Scholes, Derek T; Bombard, Yvonne; Brody, Lawrence C; Faucett, W Andrew; Garrison, Nanibaa' A; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E

2017-08-03

With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Genetic Counselors. These groups, as well as the American Society for Reproductive Medicine, Asia Pacific Society of Human Genetics, British Society for Genetic Medicine, Human Genetics Society of Australasia, Professional Society of Genetic Counselors in Asia, and Southern African Society for Human Genetics, endorsed the final statement. The statement includes the following positions. (1) At this time, given the nature and number of unanswered scientific, ethical, and policy questions, it is inappropriate to perform germline gene editing that culminates in human pregnancy. (2) Currently, there is no reason to prohibit in vitro germline genome editing on human embryos and gametes, with appropriate oversight and consent from donors, to facilitate research on the possible future clinical applications of gene editing. There should be no prohibition on making public funds available to support this research. (3) Future clinical application of human germline genome editing should not proceed unless, at a minimum, there is (a) a compelling medical rationale, (b) an evidence base that supports its clinical use, (c) an ethical justification, and (d) a transparent public process to solicit and incorporate stakeholder input. Copyright © 2017 American Society of Human Genetics. All rights reserved.
Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization

PubMed Central

Roberts, Brock; Haupt, Amanda; Tucker, Andrew; Grancharova, Tanya; Arakaki, Joy; Fuqua, Margaret A.; Nelson, Angelique; Hookway, Caroline; Ludmann, Susan A.; Mueller, Irina A.; Yang, Ruian; Horwitz, Rick; Rafelski, Susanne M.; Gunawardane, Ruwanthi N.

2017-01-01

We present a CRISPR/Cas9 genome-editing strategy to systematically tag endogenous proteins with fluorescent tags in human induced pluripotent stem cells (hiPSC). To date, we have generated multiple hiPSC lines with monoallelic green fluorescent protein tags labeling 10 proteins representing major cellular structures. The tagged proteins include alpha tubulin, beta actin, desmoplakin, fibrillarin, nuclear lamin B1, nonmuscle myosin heavy chain IIB, paxillin, Sec61 beta, tight junction protein ZO1, and Tom20. Our genome-editing methodology using Cas9/crRNA ribonuclear protein and donor plasmid coelectroporation, followed by fluorescence-based enrichment of edited cells, typically resulted in <0.1–4% homology-directed repair (HDR). Twenty-five percent of clones generated from each edited population were precisely edited. Furthermore, 92% (36/39) of expanded clonal lines displayed robust morphology, genomic stability, expression and localization of the tagged protein to the appropriate subcellular structure, pluripotency-marker expression, and multilineage differentiation. It is our conclusion that, if cell lines are confirmed to harbor an appropriate gene edit, pluripotency, differentiation potential, and genomic stability are typically maintained during the clonal line–generation process. The data described here reveal general trends that emerged from this systematic gene-tagging approach. Final clonal lines corresponding to each of the 10 cellular structures are now available to the research community. PMID:28814507
Efficient Delivery and Nuclear Uptake Is Not Sufficient to Detect Gene Editing in CD34+ Cells Directed by a Ribonucleoprotein Complex.

PubMed

Modarai, Shirin R; Man, Dula; Bialk, Pawel; Rivera-Torres, Natalia; Bloh, Kevin; Kmiec, Eric B

2018-06-01

CD34+ cells are prime targets for therapeutic strategies for gene editing, because modified progenitor cells have the capacity to differentiate through an erythropoietic lineage. Although experimental advances have been reported, the associated experimental protocols have largely been less than clear or robust. As such, we evaluated the relationships among cellular delivery; nuclear uptake, often viewed as the benchmark metric of successful gene editing; and single base repair. We took a combinatorial approach using single-stranded oligonucleotide and a CRISPR/Cas9 ribonucleoprotein to convert wild-type HBB into the sickle cell genotype by evaluating conditions for two common delivery strategies of gene editing tools into CD34+ cells. Confocal microscopy data show that the CRISPR/Cas9 ribonucleoprotein tends to accumulate at the outer membrane of the CD34+ cell nucleus when the Neon Transfection System is employed, while the ribonucleoproteins do pass into the cell nucleus when nucleofection is used. Despite the high efficiency of cellular transformation, and the traditional view of success in efficient nuclear uptake, neither delivery methodology enabled gene editing activity. Our results indicate that more stringent criteria must be established to facilitate the clinical translation and scientific robustness of gene editing for sickle cell disease. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.
CRISPR/Cas9-mediated 2-sgRNA cleavage facilitates pseudorabies virus editing.

PubMed

Tang, Yan-Dong; Guo, Jin-Chao; Wang, Tong-Yun; Zhao, Kuan; Liu, Ji-Ting; Gao, Jia-Cong; Tian, Zhi-Jun; An, Tong-Qing; Cai, Xue-Hui

2018-03-06

Several groups have used CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) for DNA virus editing. In most cases, one single-guide RNA (sgRNA) is used, which produces inconsistencies in gene editing. In this study, we used a swine herpesvirus, pseudorabies virus, as a model to systematically explore the application of CRISPR/Cas9 in DNA virus editing. In our current report, we demonstrated that cotransfection of 2 sgRNAs and a viral genome resulted in significantly better knockout efficiency than the transfection-infection-based approach. This method could result in 100% knockout of ≤3500 bp of viral nonessential large fragments. Furthermore, knockin efficiency was significantly improved by using 2 sgRNAs and was also correlated with the number of background viruses. We also demonstrated that the background viruses were all 2-sgRNA-mediated knockout mutants. Finally, this study demonstrated that the efficacy of gene knockin is determined by the replicative kinetics of background viruses. We propose that CRISPR/Cas9 coupled with 2 sgRNAs creates a powerful tool for DNA virus editing and offers great potential for future applications.-Tang, Y.-D., Guo, J.-C., Wang, T.-Y., Zhao, K., Liu, J.-T., Gao, J.-C., Tian, Z.-J., An, T.-Q., Cai, X.-H. CRISPR/Cas9-mediated 2-sgRNA cleavage facilitates pseudorabies virus editing.
Genome Editing of Erythroid Cell Culture Model Systems.

PubMed

Yik, Jinfen J; Crossley, Merlin; Quinlan, Kate G R

2018-01-01

Genome editing to introduce specific mutations or to knock out genes in model cell systems has become an efficient platform for research in the fields of molecular biology, genetics, and cell biology. With recent rapid improvements in genome editing techniques, bench-top manipulation of the genome in cell culture has become progressively easier. The application of this knowledge to erythroid cell culture systems now allows the rapid analysis of the downstream effects of virtually any engineered gene disruption or modification in cell systems. Here, we describe a CRISPR/Cas9-based approach to making genomic modifications in erythroid lineage cells which we have successfully used in both murine (MEL) and human (K562) erythroleukaemia immortalized cell lines.
Controlled flexibility in technical editing - The levels-of-edit concept at JPL

NASA Technical Reports Server (NTRS)

Buehler, M. F.

1977-01-01

The levels-of-edit concept, which can be used to specify the amount of editorial effort involved in the preparation of a manuscript for publication, is discussed. Nine types of editing are identified and described. These include coordination edit (preparing estimates, gathering cost data, monitoring production processes), policy edit, integrity edit (making sure that parts of a publication match in a physical or numerical sense), screening edit (ensuring that the quality of camera-ready copy is sufficient for external publication), copy clarification edit, format edit, mechanical style edit, language edit, and substantive edit (reviewing the manuscript for content coherence, emphasis, subordination and parallelism). These functions are grouped into five levels of edit. An edit-level number is assigned to each manuscript, providing a quantitative and qualitative indicator of the editing to be done which is clearly understood by authors, managers, and editors alike. In addition, clear boundaries are drawn between normal and extraordinary editing tasks. Individual organizations will group various edits in different ways to reflect their needs and priorities; the essential element of the system is unambiguous definition and coding of the types and amount of work to be done.
Engineered Viruses as Genome Editing Devices.

PubMed

Chen, Xiaoyu; Gonçalves, Manuel A F V

2016-03-01

Genome editing based on sequence-specific designer nucleases, also known as programmable nucleases, seeks to modify in a targeted and precise manner the genetic information content of living cells. Delivering into cells designer nucleases alone or together with donor DNA templates, which serve as surrogate homologous recombination (HR) substrates, can result in gene knockouts or gene knock-ins, respectively. As engineered replication-defective viruses, viral vectors are having an increasingly important role as delivery vehicles for donor DNA templates and designer nucleases, namely, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated Cas9 (CRISPR-Cas9) nucleases, also known as RNA-guided nucleases (RGNs). We review this dual role played by engineered viral particles on genome editing while focusing on their main scaffolds, consisting of lentiviruses, adeno-associated viruses, and adenoviruses. In addition, the coverage of the growing body of research on the repurposing of viral vectors as delivery systems for genome editing tools is complemented with information regarding their main characteristics, pros, and cons. Finally, this information is framed by a concise description of the chief principles, tools, and applications of the genome editing field as a whole.

Engineered Viruses as Genome Editing Devices

PubMed Central

Chen, Xiaoyu; Gonçalves, Manuel A F V

2016-01-01

Genome editing based on sequence-specific designer nucleases, also known as programmable nucleases, seeks to modify in a targeted and precise manner the genetic information content of living cells. Delivering into cells designer nucleases alone or together with donor DNA templates, which serve as surrogate homologous recombination (HR) substrates, can result in gene knockouts or gene knock-ins, respectively. As engineered replication-defective viruses, viral vectors are having an increasingly important role as delivery vehicles for donor DNA templates and designer nucleases, namely, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated Cas9 (CRISPR−Cas9) nucleases, also known as RNA-guided nucleases (RGNs). We review this dual role played by engineered viral particles on genome editing while focusing on their main scaffolds, consisting of lentiviruses, adeno-associated viruses, and adenoviruses. In addition, the coverage of the growing body of research on the repurposing of viral vectors as delivery systems for genome editing tools is complemented with information regarding their main characteristics, pros, and cons. Finally, this information is framed by a concise description of the chief principles, tools, and applications of the genome editing field as a whole. PMID:26336974
Pre-evaluation and interactive editing of B-spline and GERBS curves and surfaces

NASA Astrophysics Data System (ADS)

Laksâ, Arne

2017-12-01

Interactive computer based geometry editing is very useful for designers and artists. Our goal has been to develop useful tools for geometry editing in a way that increases the ability for creative design. When we interactively editing geometry, we want to see the change happening gradually and smoothly on the screen. Pre-evaluation is a tool for increasing the speed of the graphics when doing interactive affine operation on control points and control surfaces. It is then possible to add details on surfaces, and change shape in a smooth and continuous way. We use pre-evaluation on basis functions, on blending functions and on local surfaces. Pre-evaluation can be made hierarchi-cally and is thus useful for local refinements. Sampling and plotting of curves, surfaces and volumes can today be handled by the GPU and it is therefore important to have a structured organization and updating system to be able to make interactive editing as smooth and user friendly as possible. In the following, we will show a structure for pre-evaluation and an optimal organisation of the computation and we will show the effect of implementing both of these techniques.
Computer-aided field editing in DHS: the Turkey experiment.

PubMed

1995-01-01

A study comparing field editing using a Notebook computer, computer-aided field editing (CAFE), with that done manually in the standard manner, during the 1993 Demographic and Health Survey (DHS) in Turkey, demonstrated that there was less missing data and a lower mean number of errors for teams using CAFE. 6 of 13 teams used CAFE in the Turkey experiment; the computers were equipped with Integrated System for Survey Analysis (ISSA) software for editing the DHS questionnaires. The CAFE teams completed 2466 out of 8619 household questionnaires and 1886 out of 6649 individual questionnaires. The CAFE team editor entered data into the computer and marked any detected errors on the questionnaire; the errors were then corrected by the editor, in the field, based on other responses in the questionnaire, or on corrections made by the interviewer to which the questionnaire was returned. Errors in questionnaires edited manually are not identified until they are sent to the survey office for data processing, when it is too late to ask for clarification from respondents. There was one area where the error rate was higher for CAFE teams; the CAFE editors paid less attention to errors presented as warnings only.
Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria.

PubMed

Edera, Alejandro A; Gandini, Carolina L; Sanchez-Puerta, M Virginia

2018-05-14

Our understanding of the dynamic and evolution of RNA editing in angiosperms is in part limited by the few editing sites identified to date. This study identified 10,217 editing sites from 17 diverse angiosperms. Our analyses confirmed the universality of certain features of RNA editing, and offer new evidence behind the loss of editing sites in angiosperms. RNA editing is a post-transcriptional process that substitutes cytidines (C) for uridines (U) in organellar transcripts of angiosperms. These substitutions mostly take place in mitochondrial messenger RNAs at specific positions called editing sites. By means of publicly available RNA-seq data, this study identified 10,217 editing sites in mitochondrial protein-coding genes of 17 diverse angiosperms. Even though other types of mismatches were also identified, we did not find evidence of non-canonical editing processes. The results showed an uneven distribution of editing sites among species, genes, and codon positions. The analyses revealed that editing sites were conserved across angiosperms but there were some species-specific sites. Non-synonymous editing sites were particularly highly conserved (~ 80%) across the plant species and were efficiently edited (80% editing extent). In contrast, editing sites at third codon positions were poorly conserved (~ 30%) and only partially edited (~ 40% editing extent). We found that the loss of editing sites along angiosperm evolution is mainly occurring by replacing editing sites with thymidines, instead of a degradation of the editing recognition motif around editing sites. Consecutive and highly conserved editing sites had been replaced by thymidines as result of retroprocessing, by which edited transcripts are reverse transcribed to cDNA and then integrated into the genome by homologous recombination. This phenomenon was more pronounced in eudicots, and in the gene cox1. These results suggest that retroprocessing is a widespread driving force underlying the loss of editing sites in angiosperm mitochondria.
Nonviral gene editing via CRISPR/Cas9 delivery by membrane-disruptive and endosomolytic helical polypeptide.

PubMed

Wang, Hong-Xia; Song, Ziyuan; Lao, Yeh-Hsing; Xu, Xin; Gong, Jing; Cheng, Du; Chakraborty, Syandan; Park, Ji Sun; Li, Mingqiang; Huang, Dantong; Yin, Lichen; Cheng, Jianjun; Leong, Kam W

2018-05-08

Effective and safe delivery of the CRISPR/Cas9 gene-editing elements remains a challenge. Here we report the development of PEGylated nanoparticles (named P-HNPs) based on the cationic α-helical polypeptide poly(γ-4-((2-(piperidin-1-yl)ethyl)aminomethyl)benzyl-l-glutamate) for the delivery of Cas9 expression plasmid and sgRNA to various cell types and gene-editing scenarios. The cell-penetrating α-helical polypeptide enhanced cellular uptake and promoted escape of pCas9 and/or sgRNA from the endosome and transport into the nucleus. The colloidally stable P-HNPs achieved a Cas9 transfection efficiency up to 60% and sgRNA uptake efficiency of 67.4%, representing an improvement over existing polycation-based gene delivery systems. After performing single or multiplex gene editing with an efficiency up to 47.3% in vitro, we demonstrated that P-HNPs delivering Cas9 plasmid/sgRNA targeting the polo-like kinase 1 (Plk1) gene achieved 35% gene deletion in HeLa tumor tissue to reduce the Plk1 protein level by 66.7%, thereby suppressing the tumor growth by >71% and prolonging the animal survival rate to 60% within 60 days. Capable of delivering Cas9 plasmids to various cell types to achieve multiplex gene knock-out, gene knock-in, and gene activation in vitro and in vivo, the P-HNP system offers a versatile gene-editing platform for biological research and therapeutic applications. Copyright © 2018 the Author(s). Published by PNAS.
Test Review: D. D. Hammill & S. C. Larsen "Test of Written Language-Fourth Edition." (TOWL-4). Austin, TX--PRO-ED, 2009

ERIC Educational Resources Information Center

McCrimmon, Adam W.; Climie, Emma A.

2011-01-01

This article presents a review of the "Test of Written Language-Fourth Edition" (TOWL-4), a newly updated individual or group-based measure of written language for students aged 9 years, 0 months through 17 years, 11 months. The stated purposes of the measure are to identify students in need of support or intervention in the area of…
A Vector Approach to Euclidean Geometry: Inner Product Spaces, Euclidean Geometry and Trigonometry, Volume 2. Teacher's Edition.

ERIC Educational Resources Information Center

Vaughan, Herbert E.; Szabo, Steven

This is the teacher's edition of a text for the second year of a two-year high school geometry course. The course bases plane and solid geometry and trigonometry on the fact that the translations of a Euclidean space constitute a vector space which has an inner product. Congruence is a geometric topic reserved for Volume 2. Volume 2 opens with an…
Multidimensional Aptitude Battery-Second Edition Intelligence Testing of Remotely Piloted Aircraft Training Candidates Compared with Manned Airframe Training Candidates

DTIC Science & Technology

2015-03-01

assessing the general intelligence and neuropsychological aptitudes of USAF RPA pilot training candidates. Chappelle et al. obtained comprehensive...computer-based intelligence testing (Multidimensional Aptitude Battery-Second Edition [MAB-II]) and neuropsychological screening (MicroCog) on USAF MQ-1... schizophrenia , attention deficit hyperactivity disorder, and autism spectrum disorders) and not on very high functioning populations such as aviators
Seeing the Forest for the Trees: Prevalence of Low Scores on the Wechsler Intelligence Scale for Children, Fourth Edition (WISC-IV)

ERIC Educational Resources Information Center

Brooks, Brian L.

2010-01-01

Low scores across a battery of tests are common in healthy people and vary by demographic characteristics. The purpose of the present article was to present the base rates of low scores for the Wechsler Intelligence Scale for Children, fourth edition (WISC-IV; D. Wechsler, 2003). Participants included 2,200 children and adolescents between 6 and…
The Math We Need to Know and Do in Grades 6-9: Concepts, Skills, Standards, and Assessments. Second Edition

ERIC Educational Resources Information Center

Solomon, Pearl Gold

2007-01-01

In a new edition of her standards-based math workbook, author Pearl Gold Solomon covers essential concepts and skills as defined by the National Council of Teachers of Mathematics for learners in middle schools. Designed as a comprehensive resource for planning curriculum, instruction, and assessment, The Math We Need to Know and Do in Grades 6-9,…
DOE Office of Scientific and Technical Information (OSTI.GOV)

Nadel, S.; Elliott, R.N.; Shepard, M.

This updated and revised book, based on the best-selling first edition, will address how motors and motor systems can achieve greater efficiency through efficient motors, motor management, optimized controls, improved component sizing and repair, better transmission hardware, and comprehensive monitoring and maintenance. In language understandable to non-engineers, this second edition will provide an overview of existing motor stock, chronicle experience with drive power programs and policies, and offer recommendations for future efforts to increase motor system efficiency.
Fluctuations in Wikipedia access-rate and edit-event data

NASA Astrophysics Data System (ADS)

Kämpf, Mirko; Tismer, Sebastian; Kantelhardt, Jan W.; Muchnik, Lev

2012-12-01

Internet-based social networks often reflect extreme events in nature and society by drastic increases in user activity. We study and compare the dynamics of the two major complex processes necessary for information spread via the online encyclopedia ‘Wikipedia’, i.e., article editing (information upload) and article access (information viewing) based on article edit-event time series and (hourly) user access-rate time series for all articles. Daily and weekly activity patterns occur in addition to fluctuations and bursting activity. The bursts (i.e., significant increases in activity for an extended period of time) are characterized by a power-law distribution of durations of increases and decreases. For describing the recurrence and clustering of bursts we investigate the statistics of the return intervals between them. We find stretched exponential distributions of return intervals in access-rate time series, while edit-event time series yield simple exponential distributions. To characterize the fluctuation behavior we apply detrended fluctuation analysis (DFA), finding that most article access-rate time series are characterized by strong long-term correlations with fluctuation exponents α≈0.9. The results indicate significant differences in the dynamics of information upload and access and help in understanding the complex process of collecting, processing, validating, and distributing information in self-organized social networks.
BiCluE - Exact and heuristic algorithms for weighted bi-cluster editing of biomedical data

PubMed Central

2013-01-01

Background The explosion of biological data has dramatically reformed today's biology research. The biggest challenge to biologists and bioinformaticians is the integration and analysis of large quantity of data to provide meaningful insights. One major problem is the combined analysis of data from different types. Bi-cluster editing, as a special case of clustering, which partitions two different types of data simultaneously, might be used for several biomedical scenarios. However, the underlying algorithmic problem is NP-hard. Results Here we contribute with BiCluE, a software package designed to solve the weighted bi-cluster editing problem. It implements (1) an exact algorithm based on fixed-parameter tractability and (2) a polynomial-time greedy heuristics based on solving the hardest part, edge deletions, first. We evaluated its performance on artificial graphs. Afterwards we exemplarily applied our implementation on real world biomedical data, GWAS data in this case. BiCluE generally works on any kind of data types that can be modeled as (weighted or unweighted) bipartite graphs. Conclusions To our knowledge, this is the first software package solving the weighted bi-cluster editing problem. BiCluE as well as the supplementary results are available online at http://biclue.mpi-inf.mpg.de. PMID:24565035
Accelerating glioblastoma drug discovery: Convergence of patient-derived models, genome editing and phenotypic screening.

PubMed

O'Duibhir, Eoghan; Carragher, Neil O; Pollard, Steven M

2017-04-01

Patients diagnosed with glioblastoma (GBM) continue to face a bleak prognosis. It is critical that new effective therapeutic strategies are developed. GBM stem cells have molecular hallmarks of neural stem and progenitor cells and it is possible to propagate both non-transformed normal neural stem cells and GBM stem cells, in defined, feeder-free, adherent culture. These primary stem cell lines provide an experimental model that is ideally suited to cell-based drug discovery or genetic screens in order to identify tumour-specific vulnerabilities. For many solid tumours, including GBM, the genetic disruptions that drive tumour initiation and growth have now been catalogued. CRISPR/Cas-based genome editing technologies have recently emerged, transforming our ability to functionally annotate the human genome. Genome editing opens prospects for engineering precise genetic changes in normal and GBM-derived neural stem cells, which will provide more defined and reliable genetic models, with critical matched pairs of isogenic cell lines. Generation of more complex alleles such as knock in tags or fluorescent reporters is also now possible. These new cellular models can be deployed in cell-based phenotypic drug discovery (PDD). Here we discuss the convergence of these advanced technologies (iPS cells, neural stem cell culture, genome editing and high content phenotypic screening) and how they herald a new era in human cellular genetics that should have a major impact in accelerating glioblastoma drug discovery. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
Drilling deeper into the core: an analysis of journal evaluation methodologies used to create the "Basic List of Veterinary Medical Serials," third edition.

PubMed

Ugaz, Ana G

2011-04-01

The paper analyzes the journal evaluation criteria used to create the third edition of a core list of veterinary serials to determine the impact of each criterion on the final composition of the list in order to assess the value of using multiple criteria in creating a core list. Three additional lists were generated from criteria that were previously combined to prepare the third edition of the "Basic List of Veterinary Medical Serials": a list based on journal recommendations from veterinary specialty organizations, another list based on journals selected by veterinary librarians, and a list based on both indexing coverage and scholarly rank. The top fifteen journals in each of the three lists were then compared to reveal potential biases. Subject representation on the full lists generated by each of these methods was also compared. The list based on journal recommendations from veterinary specialty organizations exhibited a focus on clinically relevant titles. The list based on veterinary librarian recommendations resulted in the broadest subject coverage. The list based on indexing and scholarly rank, while emphasizing research titles, produced the largest number of unique titles. A combination approach that includes objective evaluation measures and practical input, whether from librarians or discipline experts, can improve coverage and can result in a list that balances research-based with clinical practice journals.
CRISPR-Cas9D10A Nickase-Assisted Genome Editing in Lactobacillus casei

PubMed Central

Song, Xin; Huang, He; Xiong, Zhiqiang

2017-01-01

ABSTRACT Lactobacillus casei has drawn increasing attention as a health-promoting probiotic, while effective genetic manipulation tools are often not available, e.g., the single-gene knockout in L. casei still depends on the classic homologous recombination-dependent double-crossover strategy, which is quite labor-intensive and time-consuming. In the present study, a rapid and precise genome editing plasmid, pLCNICK, was established for L. casei genome engineering based on CRISPR-Cas9D10A. In addition to the P23-Cas9D10A and Pldh-sgRNA (single guide RNA) expression cassettes, pLCNICK includes the homologous arms of the target gene as repair templates. The ability and efficiency of chromosomal engineering using pLCNICK were evaluated by in-frame deletions of four independent genes and chromosomal insertion of an enhanced green fluorescent protein (eGFP) expression cassette at the LC2W_1628 locus. The efficiencies associated with in-frame deletions and chromosomal insertion is 25 to 62%. pLCNICK has been proved to be an effective, rapid, and precise tool for genome editing in L. casei, and its potential application in other lactic acid bacteria (LAB) is also discussed in this study. IMPORTANCE The lack of efficient genetic tools has limited the investigation and biotechnological application of many LAB. The CRISPR-Cas9D10A nickase-based genome editing in Lactobacillus casei, an important food industrial microorganism, was demonstrated in this study. This genetic tool allows efficient single-gene deletion and insertion to be accomplished by one-step transformation, and the cycle time is reduced to 9 days. It facilitates a rapid and precise chromosomal manipulation in L. casei and overcomes some limitations of previous methods. This editing system can serve as a basic technological platform and offers the possibility to start a comprehensive investigation on L. casei. As a broad-host-range plasmid, pLCNICK has the potential to be adapted to other Lactobacillus species for genome editing. PMID:28864652
CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes.

PubMed

Komor, Alexis C; Badran, Ahmed H; Liu, David R

2017-01-12

The CRISPR-Cas9 RNA-guided DNA endonuclease has contributed to an explosion of advances in the life sciences that have grown from the ability to edit genomes within living cells. In this Review, we summarize CRISPR-based technologies that enable mammalian genome editing and their various applications. We describe recent developments that extend the generality, DNA specificity, product selectivity, and fundamental capabilities of natural CRISPR systems, and we highlight some of the remarkable advancements in basic research, biotechnology, and therapeutics science that these developments have facilitated. Copyright © 2017 Elsevier Inc. All rights reserved.
The effects of armodafinil on objective sleepiness and performance in a shift work disorder sample unselected for objective sleepiness.

PubMed

Howard, Ryan; Roth, Thomas; Drake, Christopher L

2014-06-01

Armodafinil is a medication used to treat excessive sleepiness in individuals with shift work disorder (SWD). In the present study, we investigate whether armodafinil can normalize nocturnal sleepiness in a group of typical SWD patients. Participants were 12 night workers (aged 33.8 ± 8.57 years, 7 female subjects) with excessive sleepiness (≥10 on the Epworth Sleepiness Scale; mean, 14.8 ± 3.16), meeting the International Classification of Sleep Disorders, Second Edition criteria for SWD, with no other sleep or medical disorders verified by polysomnogram. The multiple sleep latency test (MSLT) was not used as an entry criteria. Armodafinil was administered at 10:30 pm in a randomized, double-blind, placebo-controlled, crossover design with experimental nights separated by 1 week. Primary end point was the MSLT, with naps at 1:30, 3:30, 5:30, and 7:30 am. Other study measures included a sleepiness-alertness visual analog scale administered before each nap, and 2 computer-based performance tests evaluating attention and memory. Subjects with SWD had a mean MSLT of 5.3 ± 3.25 minutes, indicating a mean level of pathological sleepiness. Armodafinil significantly improved MSLT score to 11.1 ± 4.79 minutes (P = 0.006). Subjective levels of alertness on the visual analog scale also improved (P = 0.008). For performance, reaction time to central (P = 0.006) and peripheral (P = 0.003) stimuli and free recall memory (P = 0.05) were also improved. Armodafinil 150 mg administered at the beginning of a night shift normalizes nocturnal sleepiness in individuals with SWD unselected for objective sleepiness. Subjective measures of sleepiness and cognitive performance are also improved. This suggests that armodafinil can improve levels of nocturnal alertness to within normal daytime levels in the majority of patients with SWD.
3D Double-Quantum/Double-Quantum Exchange Spectroscopy of Protons under 100 kHz Magic Angle Spinning.

PubMed

Zhang, Rongchun; Duong, Nghia Tuan; Nishiyama, Yusuke; Ramamoorthy, Ayyalusamy

2017-06-22

Solid-state 1 H NMR spectroscopy has attracted much attention in the recent years due to the remarkable spectral resolution improvement by ultrafast magic-angle-spinning (MAS) as well as due to the sensitivity enhancement rendered by proton detection. Although these developments have enabled the investigation of a variety of challenging chemical and biological solids, the proton spectral resolution is still poor for many rigid solid systems owing to the presence of conformational heterogeneity and the unsuppressed residual proton-proton dipolar couplings even with the use of the highest currently feasible sample spinning speed of ∼130 kHz. Although a further increase in the spinning speed of the sample could be beneficial to some extent, there is a need for alternate approaches to enhance the spectral resolution. Herein, by fully utilizing the benefits of double-quantum (DQ) coherences, we propose a single radio frequency channel proton-based 3D pulse sequence that correlates double-quantum (DQ), DQ, and single-quantum (SQ) chemical shifts of protons. In addition to the two-spin homonuclear proximity information, the proposed 3D DQ/DQ/SQ experiment also enables the extraction of three-spin and four-spin proximities, which could be beneficial for revealing the dipolar coupled proton network in the solid state. Besides, the 2D DQ/DQ spectrum sliced at different isotropic SQ chemical shift values of the 3D DQ/DQ/SQ spectrum will also facilitate the identification of DQ correlation peaks and improve the spectral resolution, as it only provides the local homonuclear correlation information associated with the specific protons selected by the SQ chemical shift frequency. The 3D pulse sequence and its efficiency are demonstrated experimentally on small molecular compounds in the solid state. We expect that this approach would create avenues for further developments by suitably combining the benefits of partial deuteration of samples, selective excitation/decoupling pulses, heteronuclear spins for spectral editing, and nonuniform sampling.
IT disaster recovery: are you prepared?

PubMed

Donley, Elizabeth

2007-10-01

New Web technologies provide new opportunities but also include new risks. In an article in the May 2003 edition of Harvard Business Review, Editor Nicolas G. Carr said, "executives need to shift their attention from IT opportunities to IT risks-from offense to defense." That's probably a bit extreme. A better approach is to look at IT the same way you look at any business proposition. Every decision should be an informed decision. You should weigh the opportunities against the risks in order to select the best option. Then, once you have made your decision, take the necessary steps to minimize and prepare for the risks. This includes preparing for whatever disaster may come your way.

Therapeutic applications of CRISPR RNA-guided genome editing.

PubMed

Koo, Taeyoung; Kim, Jin-Soo

2017-01-01

The rapid development of programmable nuclease-based genome editing technologies has enabled targeted gene disruption and correction both in vitro and in vivo This revolution opens up the possibility of precise genome editing at target genomic sites to modulate gene function in animals and plants. Among several programmable nucleases, the type II clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated nuclease 9 (Cas9) system has progressed remarkably in recent years, leading to its widespread use in research, medicine and biotechnology. In particular, CRISPR-Cas9 shows highly efficient gene editing activity for therapeutic purposes in systems ranging from patient stem cells to animal models. However, the development of therapeutic approaches and delivery methods remains a great challenge for biomedical applications. Herein, we review therapeutic applications that use the CRISPR-Cas9 system and discuss the possibilities and challenges ahead. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.
Application of the CRISPR/Cas9 gene editing technique to research on functional genomes of parasites.

PubMed

Cui, Yubao; Yu, Lili

2016-12-01

The clustered regularly-interspaced short palindromic repeats (CRISPR) structural family functions as an acquired immune system in prokaryotes. Gene editing techniques have co-opted CRISPR and the associated Cas nucleases to allow for the precise genetic modification of human cells, zebrafish, mice, and other eukaryotes. Indeed, this approach has been used to induce a variety of modifications including directed insertion/deletion (InDel) of bases, gene knock-in, introduction of mutations in both alleles of a target gene, and deletion of small DNA fragments. Thus, CRISPR technology offers a precise molecular tool for directed genome modification with a range of potential applications; further, its high mutation efficiency, simple process, and low cost provide additional advantages over prior editing techniques. This paper will provide an overview of the basic structure and function of the CRISPR gene editing system as well as current and potential applications to research on parasites. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
Diving into marine genomics with CRISPR/Cas9 systems.

PubMed

Momose, Tsuyoshi; Concordet, Jean-Paul

2016-12-01

More and more genomes are sequenced and a great range of biological questions can be examined at the genomic level in a growing number of organisms. Testing the function of genome features, from gene networks, genome organization, conserved non-coding sequences to microRNAs, and, more generally, experimentally addressing the genotype-phenotype relationship is now possible owing to the clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 revolution of genome editing. In the present review, we give a brief overview of the CRISPR/Cas9 toolbox and different strategies for genome editing currently available. We list the first examples of applications to marine organisms and also draw from studies in more common laboratory models to suggest both guidelines for design of genome editing experiments as well as discuss challenges specific to marine organisms. In addition, we discuss future perspectives, including applications of CRISPR/Cas9 to base editing and targeted reprogramming of gene transcription. Copyright © 2016 Elsevier B.V. All rights reserved.
Illuminant and observer metamerism and the Hardy-Rand-Rittler color vision test editions.

PubMed

Dain, Stephen J

2006-01-01

A previous study identified a significant metamerism in the several editions of the Hardy-Rand-Rittller pseudoisochromatic plates (HRR) but did not proceed to quantify the consequences of that metamerism (Dain, 2004). Metamerism arises from two sources and is almost inevitable when a printed color vision test is reproduced in several editions. Metamerism has two consequences; these are illuminant/source-based changes in performance and changes in performance with observer (less well known) when assessing anomalous trichromats. This study addresses the effects of illuminant/source and observer metamerism on the fourth editions of HRR. Groups of colors intended to lie on a dichromat confusion line generally remain on a confusion line when the source id changed. The plates appear to be resistant to each form of metamerism, perhaps because the features of the spectral reflectance are similar for figure color and background gray. As a consequence, the clinician needs to be less concerned about using a non-recommended source than was previously believed.
Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing.

PubMed

Zhang, Rui; Deng, Patricia; Jacobson, Dionna; Li, Jin Billy

2017-02-01

Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Here we show the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoint a large number of functional editing sites. We found that the establishment of editing and variation in editing levels across Drosophila species are largely explained and predicted by cis-regulatory elements. Furthermore, editing events that arose early in the species tree tend to be more highly edited in clusters and enriched in slowly-evolved neuronal genes, thus suggesting that the main role of RNA editing is for fine-tuning neurological functions. While nonsynonymous editing events have been long recognized as playing a functional role, in addition to nonsynonymous editing sites, a large fraction of 3'UTR editing sites is evolutionarily constrained, highly edited, and thus likely functional. We find that these 3'UTR editing events can alter mRNA stability and affect miRNA binding and thus highlight the functional roles of noncoding RNA editing. Our work, through evolutionary analyses of RNA editing in Drosophila, uncovers novel insights of RNA editing regulation as well as its functions in both coding and non-coding regions.
Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing

PubMed Central

Jacobson, Dionna

2017-01-01

Adenosine-to-inosine RNA editing diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. Here we show the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoint a large number of functional editing sites. We found that the establishment of editing and variation in editing levels across Drosophila species are largely explained and predicted by cis-regulatory elements. Furthermore, editing events that arose early in the species tree tend to be more highly edited in clusters and enriched in slowly-evolved neuronal genes, thus suggesting that the main role of RNA editing is for fine-tuning neurological functions. While nonsynonymous editing events have been long recognized as playing a functional role, in addition to nonsynonymous editing sites, a large fraction of 3’UTR editing sites is evolutionarily constrained, highly edited, and thus likely functional. We find that these 3’UTR editing events can alter mRNA stability and affect miRNA binding and thus highlight the functional roles of noncoding RNA editing. Our work, through evolutionary analyses of RNA editing in Drosophila, uncovers novel insights of RNA editing regulation as well as its functions in both coding and non-coding regions. PMID:28166241
Occurrence of plastid RNA editing in all major lineages of land plants

PubMed Central

Freyer, Regina; Kiefer-Meyer, Marie-Christine; Kössel, Hans

1997-01-01

RNA editing changes posttranscriptionally single nucleotides in chloroplast-encoded transcripts. Although much work has been done on mechanistic and functional aspects of plastid editing, little is known about evolutionary aspects of this RNA processing step. To gain a better understanding of the evolution of RNA editing in plastids, we have investigated the editing patterns in ndhB and rbcL transcripts from various species comprising all major groups of land plants. Our results indicate that RNA editing occurs in plastids of bryophytes, fern allies, true ferns, gymnosperms, and angiosperms. Both editing frequencies and editing patterns show a remarkable degree of interspecies variation. Furthermore, we have found that neither plastid editing frequencies nor the editing pattern of a specific transcript correlate with the phylogenetic tree of the plant kingdom. The poor evolutionary conservation of editing sites among closely related species as well as the occurrence of single species-specific editing sites suggest that the differences in the editing patterns and editing frequencies are probably due both to independent loss and to gain of editing sites. In addition, our results indicate that RNA editing is a relatively ancient process that probably predates the evolution of land plants. This supposition is in good agreement with the phylogenetic data obtained for plant mitochondrial RNA editing, thus providing additional evidence for common evolutionary roots of the two plant organellar editing systems. PMID:9177209
Global and continental changes of arid areas using the FAO Aridity Index over the periods 1951-1980 and 1981-2010

NASA Astrophysics Data System (ADS)

Spinoni, Jonathan; Micale, Fabio; Carrao, Hugo; Naumann, Gustavo; Barbosa, Paulo; Vogt, Jürgen

2013-04-01

An increase in arid areas and progressing land degradation are two of the main consequences of global climate change. In the 2nd edition of the World Atlas of Desertification (WAD), published by the United Nation Environment Program (UNEP) in 1997, a global aridity map was presented. This map was based on the Food and Agriculture Organization (FAO) Aridity Index (AI) that takes into account the annual ratio between precipitation (RR) and Potential Evapo-Transpiration (PET). According to the long-term mean value of this ratio, climate is therefore classified in hyper-arid (<0.05), arid (0.05-0.2), semi-arid (0.2-0.5), dry sub-humid (0.5-0.65), and humid (>0.65); a special case are cold climates, which occur if the mean annual PET is below 400 mm. In the framework of the 3rd edition of the WAD, we computed new global aridity maps to improve and update the old version that was based on a single dataset (CRU dataset, Climate Research Unit of University of East Anglia) related to the 1951-80 period only. We computed the AI on two different time intervals (1951-80 and 1981-2010) in order to account for shifts in classes between the two periods and we used two different datasets: PET from CRU (version 3.2), and precipitation from the global 0.5˚x0.5˚ gridded monthly precipitation of the Global Precipitation Climatology Center (GPCC) of the Deutscher Wetterdienst (DWD). We used the GPCC Full Data Reanalysis Version 6.0, which showed a high reliability during many quality checks and is based on more stations than the CRU's precipitation counterpart. The results show that the "arid areas" (i.e. AI <0.5) globally increased from 28.4% to 29.6% and in Northern Hemisphere the cold climate areas decreased from 26.6% to 25.4%. Comparing the aridity maps of the two periods, the areas which most remarkably moved to lower AI values ("more arid" conditions) are: Canada, Brazil, the Mediterranean Region, Eastern Europe, almost all of Africa, the Middle East, Eastern China, Borneo, and Australia. At regional or country level, a shift of one class towards a "more arid" class can be found in Alaska (U.S.), Alberta (Canada), Patagonia (Argentina), Pernambuco (Brazil), Western Peru, Spain, the Southern Sahara and North-Eastern Kalahari deserts, Rajasthan and Madhya Pradesh (India), Mongolia, the Yang-Tze Basin (China), and the North-Eastern and South-Western Australian coasts. On the other hand, Central U.S., Paraguay and Northern Argentina, Scandinavia, Northern Australia, and Western China moved to a wetter climate in the last period. Due to the low data availability, we assumed that no changes took place in Antarctica, which is meant to be under a permanent ice cap, excluding the northernmost Graham Land.
[The research on the edition of Daquanbencao (Complete Collection of Materia Medica)].

PubMed

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).
Human coding RNA editing is generally nonadaptive

PubMed Central

Xu, Guixia; Zhang, Jianzhi

2014-01-01

Impairment of RNA editing at a handful of coding sites causes severe disorders, prompting the view that coding RNA editing is highly advantageous. Recent genomic studies have expanded the list of human coding RNA editing sites by more than 100 times, raising the question of how common advantageous RNA editing is. Analyzing 1,783 human coding A-to-G editing sites, we show that both the frequency and level of RNA editing decrease as the importance of a site or gene increases; that during evolution, edited As are more likely than unedited As to be replaced with Gs but not with Ts or Cs; and that among nonsynonymously edited As, those that are evolutionarily least conserved exhibit the highest editing levels. These and other observations reveal the overall nonadaptive nature of coding RNA editing, despite the presence of a few sites in which editing is clearly beneficial. We propose that most observed coding RNA editing results from tolerable promiscuous targeting by RNA editing enzymes, the original physiological functions of which remain elusive. PMID:24567376
HITRAN2016 Database Part II: Overview of the Spectroscopic Parameters of the Trace Gases

NASA Astrophysics Data System (ADS)

Tan, Yan; Gordon, Iouli E.; Rothman, Laurence S.; Kochanov, Roman V.; Hill, Christian

2017-06-01

The 2016 edition of HITRAN database is available now. This new edition of the database takes advantage of the new structure and can be accessed through HITRANonline (www.hitran.org). The line-by-line lists for almost all of the trace atmospheric species were updated in comparison with the previous edition HITRAN2012. These extended update covers not only updating few transitions of the certain molecules, but also complete replacements of the whole line lists, and as well as introduction of new spectroscopic parameters for non-Voigt line shape. The new line lists for NH_3, HNO_3, OCS, HCN, CH_3Cl, C_2H_2, C_2H_6, PH_3, C_2H_4, CH_3CN, CF_4, C_4H_2, and SO_3 feature substantial expansion of the spectral and dynamic ranges in addition of the improved accuracy of the parameters for already existing lines. A semi-empirical procedure was developed to update the air-broadening and self-broadening coefficients of N_2O, SO_2, NH_3, CH_3Cl, H_2S, and HO_2. We draw particular attention to flaws in the commonly used expression n_{air}=0.79n_{N_2}+0.21n_{O_2} to determine the air-broadening temperature dependence exponent in the power law from those for nitrogen and oxygen broadening. A more meaningful approach will be presented. The semi-empirical line width, pressure shifts and temperature-dependence exponents of CO, NH_3, HF, HCl, OCS, C_2H_2, SO_2 perturbed by H_2, He, and CO_2 have been added to the database based on the algorithm described in Wilzewski et al.. The new spectroscopic parameters for HT profile were implemented into the database for hydrogen molecule. The HITRAN database is supported by the NASA AURA program grant NNX14AI55G and NASA PDART grant NNX16AG51G. I. E. Gordon, L. S. Rothman, et al., J Quant Spectrosc Radiat Transf 2017; submitted. Hill C, et al., J Quant Spectrosc Radiat Transf 2013;130:51-61. Wilzewski JS,et al., J Quant Spectrosc Radiat Transf 2016;168:193-206. Wcislo P, et al., J Quant Spectrosc Radiat Transf 2016;177:75-91.
Targeted Gene Editing of Glia Maturation Factor in Microglia: a Novel Alzheimer's Disease Therapeutic Target.

PubMed

Raikwar, Sudhanshu P; Thangavel, Ramasamy; Dubova, Iuliia; Selvakumar, Govindhasamy Pushpavathi; Ahmed, Mohammad Ejaz; Kempuraj, Duraisamy; Zaheer, Smita A; Iyer, Shankar S; Zaheer, Asgar

2018-04-27

Alzheimer's disease (AD) is a devastating, progressive neurodegenerative disorder that leads to severe cognitive impairment in elderly patients. Chronic neuroinflammation plays an important role in the AD pathogenesis. Glia maturation factor (GMF), a proinflammatory molecule discovered in our laboratory, is significantly upregulated in various regions of AD brains. We have previously reported that GMF is predominantly expressed in the reactive glial cells surrounding the amyloid plaques (APs) in the mouse and human AD brain. Microglia are the major source of proinflammatory cytokines and chemokines including GMF. Recently clustered regularly interspaced short palindromic repeats (CRISPR) based genome editing has been recognized to study the functions of genes that are implicated in various diseases. Here, we investigated if CRISPR-Cas9-mediated GMF gene editing leads to inhibition of GMF expression and suppression of microglial activation. Confocal microscopy of murine BV2 microglial cell line transduced with an adeno-associated virus (AAV) coexpressing Staphylococcus aureus (Sa) Cas9 and a GMF-specific guide RNA (GMF-sgRNA) revealed few cells expressing SaCas9 while lacking GMF expression, thereby confirming successful GMF gene editing. To further improve GMF gene editing efficiency, we developed lentiviral vectors (LVs) expressing either Streptococcus pyogenes (Sp) Cas9 or GMF-sgRNAs. BV2 cells cotransduced with LVs expressing SpCas9 and GMF-sgRNAs revealed reduced GMF expression and the presence of indels in the exons 2 and 3 of the GMF coding sequence. Lipopolysaccharide (LPS) treatment of GMF-edited cells led to reduced microglial activation as shown by reduced p38 MAPK phosphorylation. We believe that targeted in vivo GMF gene editing has a significant potential for developing a unique and novel AD therapy.
Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium glutamicum.

PubMed

Liu, Jiao; Wang, Yu; Lu, Yujiao; Zheng, Ping; Sun, Jibin; Ma, Yanhe

2017-11-16

Corynebacterium glutamicum is an important industrial workhorse and advanced genetic engineering tools are urgently demanded. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) have revolutionized the field of genome engineering. The CRISPR/Cas9 system that utilizes NGG as protospacer adjacent motif (PAM) and has good targeting specificity can be developed into a powerful tool for efficient and precise genome editing of C. glutamicum. Herein, we developed a versatile CRISPR/Cas9 genome editing toolbox for C. glutamicum. Cas9 and gRNA expression cassettes were reconstituted to combat Cas9 toxicity and facilitate effective termination of gRNA transcription. Co-transformation of Cas9 and gRNA expression plasmids was exploited to overcome high-frequency mutation of cas9, allowing not only highly efficient gene deletion and insertion with plasmid-borne editing templates (efficiencies up to 60.0 and 62.5%, respectively) but also simple and time-saving operation. Furthermore, CRISPR/Cas9-mediated ssDNA recombineering was developed to precisely introduce small modifications and single-nucleotide changes into the genome of C. glutamicum with efficiencies over 80.0%. Notably, double-locus editing was also achieved in C. glutamicum. This toolbox works well in several C. glutamicum strains including the widely-used strains ATCC 13032 and ATCC 13869. In this study, we developed a CRISPR/Cas9 toolbox that could facilitate markerless gene deletion, gene insertion, precise base editing, and double-locus editing in C. glutamicum. The CRISPR/Cas9 toolbox holds promise for accelerating the engineering of C. glutamicum and advancing its application in the production of biochemicals and biofuels.
Revision concepts and distinctive points of the new Japanese classification for biliary tract cancers in comparison with the 7(th) edition of the Union for International Cancer Control and the American Joint Committee on Cancer staging system.

PubMed

Ohtsuka, Masayuki; Miyakawa, Shuichi; Nagino, Masato; Takada, Tadahiro; Miyazaki, Masaru

2015-03-01

The 3(rd) English edition of the Japanese classification of the biliary tract cancers (JC) is now available in this journal. The primary aim of this revision is to provide all clinicians and researchers with a common language of cancer staging at an international level. On the other hand, there are several important issues that should be solved for the optimization of the staging system. Revision concepts and major revision points of the 3(rd) English edition of the JC were reviewed. Furthermore, comparing with the 7(th) edition of staging system developed by the Union for International Cancer Control (UICC) and the American Joint Committee on Cancer (AJCC), distinctive points in the JC was discussed. In this edition of the JC, the same stage groupings as those in the UICC/AJCC staging system were basically adopted. T, N, and M categories were also identical in principle with those in the UICC/AJCC staging system, although slight modifications were proposed as the "Japanese rules". As distinctive points, perihilar cholangiocarcinomas and ampullary region carcinomas were clearly defined. Intraepithelial tumor was discriminated from invasive carcinoma at ductal resection margins. Classifications of site-specific surgical margin status remained in this edition. Histological classification was based on that in the former editions of the JC, but adopted some parts of the World Health Organization classification. The JC now share its staging system of the biliary tact carcinomas with the UICC/AJCC staging system. Future validation of the "Japanese rules" could provide important evidence to make globally standardized staging system. © 2015 Japanese Society of Hepato-Biliary-Pancreatic Surgery.
Screening accuracy of the parent-completed Ages and Stages Questionnaires - second edition as a broadband screener for motor problems in preschoolers with autism spectrum disorders.

PubMed

Vanvuchelen, Marleen; Van Schuerbeeck, Lise; Braeken, Marijke Aka

2017-01-01

Children with autism spectrum disorders are at risk for motor problems. However, this area is often overlooked in the developmental evaluation in autism diagnostic clinics. An alternative can be to identify children who should receive intensive motor assessment by using a parent-based screener. The aim of this study was to examine whether the Ages and Stages Questionnaires - second edition may be used to identify gross and fine motor problems in children. High-functioning children with autism spectrum disorder (n = 43, 22-54 m) participated in this study. Sensitivity, specificity, predictive values and areas under the receiver operating characteristic curve were calculated by comparing the Ages and Stages Questionnaires - second edition scores to the developmental evaluation of the Peabody Developmental Motor Scale - second edition. The results revealed that both the Ages and Stages Questionnaires - second edition gross and fine motor domain may be used to identify children without motor problems. In contrast, sensitivity analyses revealed the likelihood of under screening motor problems in this population. The Ages and Stages Questionnaires - second edition met only the criteria of a fair to good accuracy to identify poor gross motor (sensitivity = 100%) and below-average fine motor development (sensitivity = 71%) in this sample. Hence, the capacity of the Ages and Stages Questionnaires - second edition to identify motor problems in preschoolers with autism spectrum disorder appears to be limited. It is recommended to include a formal standardized motor test in the diagnostic procedure for all children with autism spectrum disorder. © The Author(s) 2016.
Cas9-based tools for targeted genome editing and transcriptional control.

PubMed

Xu, Tao; Li, Yongchao; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong

2014-03-01

Development of tools for targeted genome editing and regulation of gene expression has significantly expanded our ability to elucidate the mechanisms of interesting biological phenomena and to engineer desirable biological systems. Recent rapid progress in the study of a clustered, regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) protein system in bacteria has facilitated the development of newly facile and programmable platforms for genome editing and transcriptional control in a sequence-specific manner. The core RNA-guided Cas9 endonuclease in the type II CRISPR system has been harnessed to realize gene mutation and DNA deletion and insertion, as well as transcriptional activation and repression, with multiplex targeting ability, just by customizing 20-nucleotide RNA components. Here we describe the molecular basis of the type II CRISPR/Cas system and summarize applications and factors affecting its utilization in model organisms. We also discuss the advantages and disadvantages of Cas9-based tools in comparison with widely used customizable tools, such as Zinc finger nucleases and transcription activator-like effector nucleases.
Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing

PubMed Central

Lee, Ciaran M; Cradick, Thomas J; Fine, Eli J; Bao, Gang

2016-01-01

The rapid advancement in targeted genome editing using engineered nucleases such as ZFNs, TALENs, and CRISPR/Cas9 systems has resulted in a suite of powerful methods that allows researchers to target any genomic locus of interest. A complementary set of design tools has been developed to aid researchers with nuclease design, target site selection, and experimental validation. Here, we review the various tools available for target selection in designing engineered nucleases, and for quantifying nuclease activity and specificity, including web-based search tools and experimental methods. We also elucidate challenges in target selection, especially in predicting off-target effects, and discuss future directions in precision genome editing and its applications. PMID:26750397
PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

PubMed

Lee, Jonas; Kim, Sung Hou

2009-04-01

The Protein Data Bank file format is the format most widely used by protein crystallographers and biologists to disseminate and manipulate protein structures. Despite this, there are few user-friendly software packages available to efficiently edit and extract raw information from PDB files. This limitation often leads to many protein crystallographers wasting significant time manually editing PDB files. PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is a stand-alone application written in Java which frees users from the hassles associated with platform/operating system-dependent installation and usage. PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/.
Genome Editing in Escherichia coli with Cas9 and synthetic CRISPRs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Ze; Richardson, Sarah; Robinson, David

Recently, the Cas9-CRISPR system has proven to be a useful tool for genome editing in eukaryotes, which repair the double stranded breaks made by Cas9 with non-homologous end joining or homologous recombination. Escherichia coli lacks non-homologous end joining and has a very low homologous recombination rate, effectively rendering targeted Cas9 activity lethal. We have developed a heat curable, serializable, plasmid based system for selectionless Cas9 editing in arbitrary E. coli strains that uses synthetic CRISPRs for targeting and -red to effect repairs of double stranded breaks. We have demonstrated insertions, substitutions, and multi-target deletions with our system, which we havemore » tested in several strains.« less
Efficient engineering of a bacteriophage genome using the type I-E CRISPR-Cas system.

PubMed

Kiro, Ruth; Shitrit, Dror; Qimron, Udi

2014-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) system has recently been used to engineer genomes of various organisms, but surprisingly, not those of bacteriophages (phages). Here we present a method to genetically engineer the Escherichia coli phage T7 using the type I-E CRISPR-Cas system. T7 phage genome is edited by homologous recombination with a DNA sequence flanked by sequences homologous to the desired location. Non-edited genomes are targeted by the CRISPR-Cas system, thus enabling isolation of the desired recombinant phages. This method broadens CRISPR Cas-based editing to phages and uses a CRISPR-Cas type other than type II. The method may be adjusted to genetically engineer any bacteriophage genome.

Narrowing the Gender Gap:Empowering Women through Literacy Programmes: Case Studies from the UNESCO Effective Literacy and Numeracy Practices Database (LitBase) http://www.unesco.org/uil/litbase/. 2nd Edition

ERIC Educational Resources Information Center

Hanemann, Ulrike, Ed.

2015-01-01

UIL has published a second edition of a collection of case studies of promising literacy programmes that seek to empower women. "Narrowing the Gender Gap: Empowering Women through Literacy Programmes" (originally published in 2013 as "Literacy Programmes with a Focus on Women to Reduce Gender Disparities") responds to the…
A Translational Pathway Toward a Clinical Trial Using the Second-Generation AAV Micro Dystrophin Vector

DTIC Science & Technology

2017-09-01

future experimental therapeutic studies in the canine model such as CRISPR -mediated gene editing, stem cell therapy, dystrophin-independent disease...There is no scientific/budget overlap with the current proposal.) CRISPR /Cas9-based gene editing for the correction of Duchenne muscular dystrophy...lab will perform in vivo gene delivery and functional outcome measurements in mice treated by AAV- CRISPR gene repair vectors and if needed will also
Environmental Assessment: San Antonio Creek Restoration at Vandenberg Air Force Base, California

DTIC Science & Technology

2008-09-08

than larger populations because their low abundance renders them susceptible to inbreeding, loss of genetic variation, high variability in age and...master’s thesis, University of California, Santa Barbara. Grant, C. 1978a. Chumash: Introduction. In California, edited by Robert F. Heizer , pp. 505...Eastern Coastal Chumash. In California, edited by Robert F. Heizer , pp. 509–519. Handbook of North American Indians, vol. 8, William C. Sturtevant
Shift work, night work and sleep disorders among pastry cookers and shopkeepers in France: a cross-sectional survey

PubMed Central

Pepin, Emilie; Gillet, Pascal; Sauvet, Fabien; Gomez-Merino, Danielle; Thaon, Isabelle; Chennaoui, Mounir; Leger, Damien

2018-01-01

Objective Most research on night and shift work focuses on employee health in large companies, primarily in the healthcare and transportation sectors. However, many night workers work on their own or in small businesses related to services or food. This survey focuses on sleep habits and disorders concerning night work in pastry production and sales. Methods An epidemiological telephone cross-sectional survey of night shift workers and their sleep habits was proposed to all employers and employees in the French pastry industry via their insurance health prevention company. Sleep logs allow us to estimate the total sleep time (TST) on workdays and enquire on napping episodes and length. In order to estimate the ideal TST, we added a question on the ideal amount of sleep the subjects need to be in good shape in the morning. We also define sleep debt as the difference between the ideal TST and TST on workdays, and considered a sleep debt when the difference was above 60 min and severe sleep debt above 90 min. Finally we retained subjects as long sleepers for those with a TSTof more than 7 hours and short sleepers when TST was under 5 hours. Insomnia, sleepiness and sleep apnoea have been defined based on the International Classification of Sleep Disorders-Third Edition and the classification of mental disorders (Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition). Bivariate and multivariate logistic regression models were applied to investigate the association with short TST, long TST, sleep debt and napping. Results We analysed 2622 complete questionnaires from 1313 men and 1309 women aged 22–50 years old. 1397 workers began work before 07:00, whereas 1225 began later. The 24-hour TST was 6.7±1.4 hours, whereas the ideal TST was 7.0±1.2 hours. Severe sleep debt (>90 min) was reported by 6% women versus 5% men, whereas moderate sleep debt (>60 min) was reported by 11.5% women versus 9.3% men. Napping is one way to improve 24-hour TST for 58% of pastry producers (75±13 min) and 23% of shopkeepers (45±8 min). Nevertheless, 26.2% of the respondents complained of chronic insomnia, especially women aged 45–54 years old (31%). Finally, 29.6% had evocative criteria for obstructive sleep apnoea, although only 9.1% had a high score on the Berlin Questionnaire. Conclusion Our study demonstrates that both pastry producers and shopkeepers can have disturbed sleep schedules and a high prevalence of sleep disorders, although many have used napping as a behavioural countermeasure to fight sleep debt. The results of our survey lead us to conclude that, besides the need to take care of night workers in big industries, more information and occupational prevention must be focused on night workers in individual and small businesses. PMID:29743318
High GC Content Cas9-Mediated Genome-Editing and Biosynthetic Gene Cluster Activation in Saccharopolyspora erythraea.

PubMed

Liu, Yong; Wei, Wen-Ping; Ye, Bang-Ce

2018-05-18

The overexpression of bacterial secondary metabolite biosynthetic enzymes is the basis for industrial overproducing strains. Genome editing tools can be used to further improve gene expression and yield. Saccharopolyspora erythraea produces erythromycin, which has extensive clinical applications. In this study, the CRISPR-Cas9 system was used to edit genes in the S. erythraea genome. A temperature-sensitive plasmid containing the PermE promoter, to drive Cas9 expression, and the Pj23119 and PkasO promoters, to drive sgRNAs, was designed. Erythromycin esterase, encoded by S. erythraea SACE_1765, inactivates erythromycin by hydrolyzing the macrolactone ring. Sequencing and qRT-PCR confirmed that reporter genes were successfully inserted into the SACE_1765 gene. Deletion of SACE_1765 in a high-producing strain resulted in a 12.7% increase in erythromycin levels. Subsequent PermE- egfp knock-in at the SACE_0712 locus resulted in an 80.3% increase in erythromycin production compared with that of wild type. Further investigation showed that PermE promoter knock-in activated the erythromycin biosynthetic gene clusters at the SACE_0712 locus. Additionally, deletion of indA (SACE_1229) using dual sgRNA targeting without markers increased the editing efficiency to 65%. In summary, we have successfully applied Cas9-based genome editing to a bacterial strain, S. erythraea, with a high GC content. This system has potential application for both genome-editing and biosynthetic gene cluster activation in Actinobacteria.
Gene editing by CRISPR/Cas9 in the obligatory outcrossing Medicago sativa.

PubMed

Gao, Ruimin; Feyissa, Biruk A; Croft, Mana; Hannoufa, Abdelali

2018-04-01

The CRISPR/Cas9 technique was successfully used to edit the genome of the obligatory outcrossing plant species Medicago sativa L. (alfalfa). RNA-guided genome engineering using Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)/Cas9 technology enables a variety of applications in plants. Successful application and validation of the CRISPR technique in a multiplex genome, such as that of M. sativa (alfalfa) will ultimately lead to major advances in the improvement of this crop. We used CRISPR/Cas9 technique to mutate squamosa promoter binding protein like 9 (SPL9) gene in alfalfa. Because of the complex features of the alfalfa genome, we first used droplet digital PCR (ddPCR) for high-throughput screening of large populations of CRISPR-modified plants. Based on the results of genome editing rates obtained from the ddPCR screening, plants with relatively high rates were subjected to further analysis by restriction enzyme digestion/PCR amplification analyses. PCR products encompassing the respective small guided RNA target locus were then sub-cloned and sequenced to verify genome editing. In summary, we successfully applied the CRISPR/Cas9 technique to edit the SPL9 gene in a multiplex genome, providing some insights into opportunities to apply this technology in future alfalfa breeding. The overall efficiency in the polyploid alfalfa genome was lower compared to other less-complex plant genomes. Further refinement of the CRISPR technology system will thus be required for more efficient genome editing in this plant.
MindEdit: A P300-based text editor for mobile devices.

PubMed

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. Copyright © 2016 Elsevier Ltd. All rights reserved.
Using Appendicitis to Improve Estimates of Childhood Medicaid Participation Rates.

PubMed

Silber, Jeffrey H; Zeigler, Ashley E; Reiter, Joseph G; Hochman, Lauren L; Ludwig, Justin M; Wang, Wei; Calhoun, Shawna R; Pati, Susmita

2018-03-23

Administrative data are often used to estimate state Medicaid/Children's Health Insurance Program duration of enrollment and insurance continuity, but they are generally not used to estimate participation (the fraction of eligible children enrolled) because administrative data do not include reasons for disenrollment and cannot observe eligible never-enrolled children, causing estimates of eligible unenrolled to be inaccurate. Analysts are therefore forced to either utilize survey information that is not generally linkable to administrative claims or rely on duration and continuity measures derived from administrative data and forgo estimating claims-based participation. We introduce appendectomy-based participation (ABP) to estimate statewide participation rates using claims by taking advantage of a natural experiment around statewide appendicitis admissions to improve the accuracy of participation rate estimates. We used Medicaid Analytic eXtract (MAX) for 2008-2010; and the American Community Survey for 2008-2010 from 43 states to calculate ABP, continuity ratio, duration, and participation based on the American Community Survey (ACS). In the validation study, median participation rate using ABP was 86% versus 87% for ACS-based participation estimates using logical edits and 84% without logical edits. Correlations between ABP and ACS with or without logical edits was 0.86 (P < .0001). Using regression analysis, ABP alone was a significant predictor of ACS (P < .0001) with or without logical edits, and adding duration and/or the continuity ratio did not significantly improve the model. Using the ABP rate derived from administrative claims (MAX) is a valid method to estimate statewide public insurance participation rates in children. Copyright © 2018 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.
Genome-wide identification of RNA editing in hepatocellular carcinoma.

PubMed

Kang, Lin; Liu, Xiaoqiao; Gong, Zhoulin; Zheng, Hancheng; Wang, Jun; Li, Yingrui; Yang, Huanming; Hardwick, James; Dai, Hongyue; Poon, Ronnie T P; Lee, Nikki P; Mao, Mao; Peng, Zhiyu; Chen, Ronghua

2015-02-01

We did whole-transcriptome sequencing and whole-genome sequencing on nine pairs of Hepatocellular carcinoma (HCC) tumors and matched adjacent tissues to identify RNA editing events. We identified mean 26,982 editing sites with mean 89.5% canonical A→G edits in each sample using an improved bioinformatics pipeline. The editing rate was significantly higher in tumors than adjacent normal tissues. Comparing the difference between tumor and normal tissues of each patient, we found 7 non-synonymous tissue specific editing events including 4 tumor-specific edits and 3 normal-specific edits in the coding region, as well as 292 edits varying in editing degree. The significant expression changes of 150 genes associated with RNA editing were found in tumors, with 3 of the 4 most significant genes being cancer related. Our results show that editing might be related to higher gene expression. These findings indicate that RNA editing modification may play an important role in the development of HCC. Copyright © 2014 Elsevier Inc. All rights reserved.
In VivoLactate Editing with Simultaneous Detection of Choline, Creatine, NAA, and Lipid Singlets at 1.5 T Using PRESS Excitation with Applications to the Study of Brain and Head and Neck Tumors

NASA Astrophysics Data System (ADS)

Star-Lack, Josh; Spielman, Daniel; Adalsteinsson, Elfar; Kurhanewicz, John; Terris, David J.; Vigneron, Daniel B.

1998-08-01

Two T2-independentJ-difference lactate editing schemes for the PRESS magnetic resonance spectroscopy localization sequence are introduced. The techniques, which allow for simultaneous acquisition of the lactate doublet (1.3 ppm) and edited singlets upfield of and including choline (3.2 ppm), exploit the dependence of the in-phase intensity of the methyl doublet upon the time interval separating two inversion (BASING) pulses applied to its coupling partner after initial excitation. Editing method 1, which allows for echo times TE =n/J(n= 1, 2, 3, …), alters the BASING carrier frequency for each of two cycles so that, for one cycle, the quartet is inverted, whereas, for the other cycle, the quartet is unaffected. Method 2, which also provides water suppression, allows for editing for TE > 1/Jby alternating, between cycles, the time interval separating the inversion pulses. Experimental results were obtained at 1.5 T using a Shinnar Le-Roux-designed maximum phase inversion pulse with a filter transition bandwidth of 55 Hz. Spectra were acquired from phantoms andin vivofrom the human brain and neck. In a neck muscle study, the lipid suppression factor, achieved partly through the use of a novel phase regularization algorithm, was measured to be over 103. Spectra acquired from a primary brain and a metastatic neck tumor demonstrated the presence of lactate and choline signals consistent with abnormal spectral patterns. The advantages and limitations of the methods are analyzed theoretically and experimentally, and significance of the results is discussed.
The gene-editing of super-ego.

PubMed

Hofmann, Bjørn

2018-04-17

New emerging biotechnologies, such as gene editing, vastly extend our ability to alter the human being. This comes together with strong aspirations to improve humans not only physically, but also mentally, morally, and socially. These conjoined ambitions aggregate to what can be labelled "the gene editing of super-ego." This article investigates a general way used to argue for new biotechnologies, such as gene-editing: if it is safe and efficacious to implement technology X for the purpose of a common good Y, why should we not do so? This is a rhetorical question with a conditional, and may be dismissed as such. Moreover, investigating the question transformed into a formal argument reveals that the argument does not hold either. Nonetheless, the compelling force of the question calls for closer scrutiny, revealing that this way of arguing for biotechnology is based on five assumptions. Analysis of these assumptions shows their significant axiological, empirical, and philosophical challenges. This makes it reasonable to claim that these kinds of question based promotions of specific biotechnologies fail. Hence, the aspirations to make a super-man with a super-ego appear fundamentally flawed. As these types of moral bioenhancement arguments become more prevalent, a revealing hype test is suggested: What is special with this technology (e.g., gene editing), compared to existing methods, that makes it successful in improving human social characteristics in order to make the world a better place for all? Valid answers to this question will provide good reasons to pursue such technologies. Hence, the aim is not to bar the development of modern biotechnology, but rather to ensure good developments and applications of highly potent technologies. So far, we still have a long way to go to make persons with goodness gene(s).
Optimization of genome editing through CRISPR-Cas9 engineering.

PubMed

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

PubMed Central

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
Why is the Diagnostic and Statistical Manual of Mental Disorders so hard to revise? Path-dependence and "lock-in" in classification.

PubMed

Cooper, Rachel

2015-06-01

The latest edition of the Diagnostic and Statistical Manual of Mental Disorders, the D.S.M.-5, was published in May 2013. In the lead up to publication, radical changes to the classification were anticipated; there was widespread dissatisfaction with the previous edition and it was accepted that a "paradigm shift" might be required. In the end, however, and despite huge efforts at revision, the published D.S.M.-5 differs far less than originally envisaged from its predecessor. This paper considers why it is that revising the D.S.M. has become so difficult. The D.S.M. is such an important classification that this question is worth asking in its own right. The case of the D.S.M. can also serve as a study for considering stasis in classification more broadly; why and how can classifications become resistant to change? I suggest that classifications like the D.S.M. can be thought of as forming part of the infrastructure of science, and have much in common with material infrastructure. In particular, as with material technologies, it is possible for "path dependent" development to cause a sub-optimal classification to become "locked in" and hard to replace. Copyright © 2015 Elsevier Ltd. All rights reserved.
Memory-guided attention during active viewing of edited dynamic scenes.

PubMed

Valuch, Christian; König, Peter; Ansorge, Ulrich

2017-01-01

Films, TV shows, and other edited dynamic scenes contain many cuts, which are abrupt transitions from one video shot to the next. Cuts occur within or between scenes, and often join together visually and semantically related shots. Here, we tested to which degree memory for the visual features of the precut shot facilitates shifting attention to the postcut shot. We manipulated visual similarity across cuts, and measured how this affected covert attention (Experiment 1) and overt attention (Experiments 2 and 3). In Experiments 1 and 2, participants actively viewed a target movie that randomly switched locations with a second, distractor movie at the time of the cuts. In Experiments 1 and 2, participants were able to deploy attention more rapidly and accurately to the target movie's continuation when visual similarity was high than when it was low. Experiment 3 tested whether this could be explained by stimulus-driven (bottom-up) priming by feature similarity, using one clip at screen center that was followed by two alternative continuations to the left and right. Here, even the highest similarity across cuts did not capture attention. We conclude that following cuts of high visual similarity, memory-guided attention facilitates the deployment of attention, but this effect is (top-down) dependent on the viewer's active matching of scene content across cuts.
RNA Editing and Its Molecular Mechanism in Plant Organelles

PubMed Central

Ichinose, Mizuho; Sugita, Mamoru

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 editing events can restore the evolutionarily conserved amino acid residues in mRNAs or create translation start and stop codons. Therefore, RNA editing is an essential process to maintain genetic information at the RNA level. Individual RNA editing sites are recognized by plant-specific pentatricopeptide repeat (PPR) proteins that are encoded in the nuclear genome. These PPR proteins are characterized by repeat elements that bind specifically to RNA sequences upstream of target editing sites. In flowering plants, non-PPR proteins also participate in multiple RNA editing events as auxiliary factors. C-to-U editing can be explained by cytidine deamination. The proteins discovered to date are important factors for RNA editing but a bona fide RNA editing enzyme has yet to be identified. PMID:28025543
Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization. | Office of Cancer Genomics

Cancer.gov

The CRISPR/Cas9 system is a powerful tool for studying gene function. Here, we describe a method that allows temporal control of CRISPR/Cas9 activity based on conditional Cas9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 (DD-Cas9) enables conditional Cas9 expression and temporal control of gene editing in the presence of an FKBP12 synthetic ligand. This system can be easily adapted to co-express, from the same promoter, DD-Cas9 with any other gene of interest without co-modulation of the latter.
Photovoltaic System Pricing Trends: Historical, Recent, and Near-Term Projections. 2014 Edition (Presentation)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feldman, D.; Barbose, G.; Margolis, R.

2014-09-01

This presentation, based on research at Lawrence Berkeley National Laboratory and the National Renewable Energy Laboratory, provides a high-level overview of historical, recent, and projected near-term PV pricing trends in the United States focusing on the installed price of PV systems. It also attempts to provide clarity surrounding the wide variety of potentially conflicting data available about PV system prices. This PowerPoint is the third edition from this series.
Photovoltaic System Pricing Trends. Historical, Recent, and Near-Term Projections, 2015 Edition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feldman, David; Barbose, Galen; Margolis, Robert

2015-08-25

This presentation, based on research at Lawrence Berkeley National Laboratory and the National Renewable Energy Laboratory, provides a high-level overview of historical, recent, and projected near-term PV pricing trends in the United States focusing on the installed price of PV systems. It also attempts to provide clarity surrounding the wide variety of potentially conflicting data available about PV system prices. This PowerPoint is the fourth edition from this series.
Real-Time Modeling of Cross-Body Flow for Torpedo Tube Recovery of the Phoenix Autonomous Underwater Vehicle (AUV)

DTIC Science & Technology

1998-03-01

34Numerical Recipes in C," second edition, Cambridge University Press, Cambridge England, 1992. Marco, David , "Autonomous Control of Underwater...in the viewer. -202- LIST OF REFERENCES Ames, Andrea L., Nadeau, David R., Moreland, John L., VRML 2.0 Sourcebook, Second edition, John Wiley...McGhee, Bob, "The Phoenix Autonomous Underwater Vehicle," AI-Based Mobile Robots, editors David Kortenkamp, Pete Bonasso and Robin Murphy, MJT/AAAI

Proposed Closure of Los Angeles Air Force Base, California and Relocation of Space Systems Division

DTIC Science & Technology

1990-07-01

rendered temporarily out of service in accordance with state and federal regulations. Aboveground ground tanks associated with Building 130 would...Lowell, and Charles R. Smith 1978 Gabrielino. In Handbook of North American Indians-California, edited by Robert F.3 Heizer . Smithsonian Institution...8, California, edited3 by R.F. Heizer , p. 575-587. Smithsonian Institution, Washington DC. Bean, L.J. and F. Shipek 1978 Luiseno. In The Handbook of
The ethics of genome editing in the clinic: A dose of realism for healthcare leaders.

PubMed

Bubela, Tania; Mansour, Yael; Nicol, Dianne

2017-05-01

Genome editing technologies promise therapeutic advances for genetic diseases. We discuss the ethical and societal issues raised by these technologies, including their use in preclinical research, their potential to address mutations in somatic cells, and their potential to make germ line alterations that may be passed to subsequent generations. We call for a proportionate response from health leaders based on a realistic assessment of benefits, risks, and timelines for clinical translation.
Nonviral Genome Editing Based on a Polymer-Derivatized CRISPR Nanocomplex for Targeting Bacterial Pathogens and Antibiotic Resistance.

PubMed

Kang, Yoo Kyung; Kwon, Kyu; Ryu, Jea Sung; Lee, Ha Neul; Park, Chankyu; Chung, Hyun Jung

2017-04-19

The overuse of antibiotics plays a major role in the emergence and spread of multidrug-resistant bacteria. A molecularly targeted, specific treatment method for bacterial pathogens can prevent this problem by reducing the selective pressure during microbial growth. Herein, we introduce a nonviral treatment strategy delivering genome editing material for targeting antibacterial resistance. We apply the CRISPR-Cas9 system, which has been recognized as an innovative tool for highly specific and efficient genome engineering in different organisms, as the delivery cargo. We utilize polymer-derivatized Cas9, by direct covalent modification of the protein with cationic polymer, for subsequent complexation with single-guide RNA targeting antibiotic resistance. We show that nanosized CRISPR complexes (= Cr-Nanocomplex) were successfully formed, while maintaining the functional activity of Cas9 endonuclease to induce double-strand DNA cleavage. We also demonstrate that the Cr-Nanocomplex designed to target mecA-the major gene involved in methicillin resistance-can be efficiently delivered into Methicillin-resistant Staphylococcus aureus (MRSA), and allow the editing of the bacterial genome with much higher efficiency compared to using native Cas9 complexes or conventional lipid-based formulations. The present study shows for the first time that a covalently modified CRISPR system allows nonviral, therapeutic genome editing, and can be potentially applied as a target specific antimicrobial.
Understanding Editing Behaviors in Multilingual Wikipedia.

PubMed

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.
Understanding Editing Behaviors in Multilingual Wikipedia

PubMed Central

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. PMID:27171158
Presenting the 3rd edition of WRB

NASA Astrophysics Data System (ADS)

Schad, Peter

2014-05-01

The third edition of the international soil classification system "World Reference Base for Soil Resources" (WRB) will be presented during der 20th World Congress of Soil Science, Jeju, Korea, June 9-12. The second edition was published in 2006 and the first in 1998, which, in turn, was based on the Legends of the FAO Soil Map of the World. Now, after eight years of experience with the second edition, time was due for a revision. The major changes are: 1. The second edition had two different qualifier sequences for naming soils (IUSS Working Group WRB, 2006, update 2007) and for creating map legends (Guidelines for creating small-scale map legends using the WRB; IUSS Working Group WRB, 2010). The third edition has one sequence for both. The qualifiers for every Reference Soil Group are subdivided into a small number of main qualifiers that are ranked and a larger number of additional qualifiers that are not ranked and given in an alphabetical order. The name of a pedon must comprise all applying qualifiers. The name of a map unit comprises a specified small number of main qualifiers, depending on scale, whereas all other qualifiers are optional. 2. For some soils, problems have been reported. Albeluvisols are difficult to detect in the field and cover only small surfaces. They have been replaced by Retisols, which have a broader definition that is easier to identify in the field. 3. The use of some diagnostics was difficult. Examples are: The argic horizon had too low limit values, so we had much more soils with argic horizons than justified. The definitions of the cambic horizon and the gleyic and stagnic properties were not precise enough. Organic material, mollic and umbric horizons had an unnecessary complicated definition. 4. Some changes in the key to the Reference Soil Groups seemed to be justified. Fluvisols were moved further down, Durisols and Gypsisols switched their position, also Arenosols and Cambisols. The soils with an argic horizon were brought into a new sequence. 5. The umbrella function of WRB aims to allow the allocation of soil classes existing in a national classification system within the WRB. Characteristics that in a national system are regarded to be important must be considered in WRB - not necessarily at the highest level, but at least somewhere. The third edition of WRB allows a better accommodation of soil types, e.g., of the Australian and the Brazilian system. 6. Some environments or even ecoregions had not been well represented in WRB. The third edition allows a better accommodation of soils of ultra-continental permafrost regions, acid-sulphate soils and Technosols. 7. How to explain complicated sets of characteristics? For the third edition, efforts were made to give better structured definitions that can be more easily grasped. The editors of the third edition are convinced that the new WRB allows a more precise classification of soils including both, a better naming of pedons and a better elaboration of soil map legends.
Genetic mapping uncovers cis-regulatory landscape of RNA editing.

PubMed

Ramaswami, Gokul; Deng, Patricia; Zhang, Rui; Anna Carbone, Mary; Mackay, Trudy F C; Li, Jin Billy

2015-09-16

Adenosine-to-inosine (A-to-I) RNA editing, catalysed by ADAR enzymes conserved in metazoans, plays an important role in neurological functions. Although the fine-tuning mechanism provided by A-to-I RNA editing is important, the underlying rules governing ADAR substrate recognition are not well understood. We apply a quantitative trait loci (QTL) mapping approach to identify genetic variants associated with variability in RNA editing. With very accurate measurement of RNA editing levels at 789 sites in 131 Drosophila melanogaster strains, here we identify 545 editing QTLs (edQTLs) associated with differences in RNA editing. We demonstrate that many edQTLs can act through changes in the local secondary structure for edited dsRNAs. Furthermore, we find that edQTLs located outside of the edited dsRNA duplex are enriched in secondary structure, suggesting that distal dsRNA structure beyond the editing site duplex affects RNA editing efficiency. Our work will facilitate the understanding of the cis-regulatory code of RNA editing.
High-Content Analysis of CRISPR-Cas9 Gene-Edited Human Embryonic Stem Cells.

PubMed

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. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
CERES ERBE-like Instantaneous TOA Estimates (ES-8) in HDF (CER_ES4_TRMM-PFM_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=1998-08-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_PFM+FM1_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2000-03-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_FM1+FM4_Edition2)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-03-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_Terra-FM2_Edition1-CV)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2006-10-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_Aqua-FM3_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-10-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_Aqua-FM3_Edition2)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-12-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_Aqua-FM4_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-03-29] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_FM1+FM2_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2003-12-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_Terra-FM1_Edition2)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-12-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_Aqua-FM4_Edition2)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-03-29] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_Aqua-FM4_Edition1-CV)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-03-29] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_Terra-FM2_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-10-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].

CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_Terra-FM1_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-10-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_PFM+FM2_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2000-03-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_FM1+FM2_Edition2)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2002-12-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
CERES ERBE-like Monthly Geographical Averages (ES-4) in HDF (CER_ES4_FM1+FM3_Edition2)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Geographical Averages (ES-4) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-4 is also produced for combinations of scanner instruments. For each observed 2.5-degree spatial region, the daily average, the hourly average over the month, and the overall monthly average of shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-9 product are spatially nested up from 2.5-degree regions to 5- and 10-degree regions, to 2.5-, 5-, and 10-degree zonal averages, and to global monthly averages. For each nested area, the albedo and net flux are given. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The following CERES ES4 data sets are currently available: CER_ES4_FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition1 CER_ES4_PFM+FM1+FM2_Edition2 CER_ES4_PFM+FM1_Edition1 CER_ES4_PFM+FM2_Edition1 CER_ES4_TRMM-PFM_Edition1 CER_ES4_TRMM-PFM_Edition2 CER_ES4_Terra-FM1_Edition1 CER_ES4_Terra-FM2_Edition1 CER_ES4_FM1+FM2_Edition2 CER_ES4_Terra-FM1_Edition2 CER_ES4_Terra-FM2_Edition2 CER_ES4_Aqua-FM3_Edition1 CER_ES4_Aqua-FM4_Edition1 CER_ES4_FM1+FM2+FM3+FM4_Edition1 CER_ES4_Aqua-FM3_Edition2 CER_ES4_Aqua-FM4_Edition2 CER_ES4_FM1+FM3_Edition2 CER_ES4_FM1+FM4_Edition2 CER_ES4_PFM+FM1_Edition2 CER_ES4_PFM+FM2_Edition2 CER_ES4_Aqua-FM3_Edition1-CV CER_ES4_Aqua-FM4_Edition1-CV CER_ES4_Terra-FM1_Edition1-CV CER_ES4_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-12-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=1 month; Temporal_Resolution_Range=Monthly - < Annual].
Water quality management library. 2. edition

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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 formore » 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.« less
Genome engineering in human cells.

PubMed

Song, Minjung; Kim, Young-Hoon; Kim, Jin-Soo; Kim, Hyongbum

2014-01-01

Genome editing in human cells is of great value in research, medicine, and biotechnology. Programmable nucleases including zinc-finger nucleases, transcription activator-like effector nucleases, and RNA-guided engineered nucleases recognize a specific target sequence and make a double-strand break at that site, which can result in gene disruption, gene insertion, gene correction, or chromosomal rearrangements. The target sequence complexities of these programmable nucleases are higher than 3.2 mega base pairs, the size of the haploid human genome. Here, we briefly introduce the structure of the human genome and the characteristics of each programmable nuclease, and review their applications in human cells including pluripotent stem cells. In addition, we discuss various delivery methods for nucleases, programmable nickases, and enrichment of gene-edited human cells, all of which facilitate efficient and precise genome editing in human cells.
Dynamic landscape and regulation of RNA editing in mammals

PubMed Central

Tan, Meng How; Li, Qin; Shanmugam, Raghuvaran; Piskol, Robert; Kohler, Jennefer; Young, Amy N.; Liu, Kaiwen Ivy; Zhang, Rui; Ramaswami, Gokul; Ariyoshi, Kentaro; Gupte, Ankita; Keegan, Liam P.; George, Cyril X.; Ramu, Avinash; Huang, Ni; Pollina, Elizabeth A.; Leeman, Dena S.; Rustighi, Alessandra; Sharon Goh, Y. P.; Chawla, Ajay; Del Sal, Giannino; Peltz, Gary; Brunet, Anne; Conrad, Donald F.; Samuel, Charles E.; O’Connell, Mary A.; Walkley, Carl R.; Nishikura, Kazuko; Li, Jin Billy

2017-01-01

Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules1. Although many editing sites have recently been discovered2–7, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood8–10. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. We show that editing levels in non-repetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 is the primary editor of repetitive sites and ADAR2 is the primary editor of non-repetitive coding sites, whereas the catalytically inactive ADAR3 predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. In addition, we curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. Further analysis of the GTEx data revealed several potential regulators of editing, such as AIMP2, which reduces editing in muscles by enhancing the degradation of the ADAR proteins. Collectively, our work provides insights into the complex cis- and trans-regulation of A-to-I editing. PMID:29022589
Dynamic landscape and regulation of RNA editing in mammals.

PubMed

Tan, Meng How; Li, Qin; Shanmugam, Raghuvaran; Piskol, Robert; Kohler, Jennefer; Young, Amy N; Liu, Kaiwen Ivy; Zhang, Rui; Ramaswami, Gokul; Ariyoshi, Kentaro; Gupte, Ankita; Keegan, Liam P; George, Cyril X; Ramu, Avinash; Huang, Ni; Pollina, Elizabeth A; Leeman, Dena S; Rustighi, Alessandra; Goh, Y P Sharon; Chawla, Ajay; Del Sal, Giannino; Peltz, Gary; Brunet, Anne; Conrad, Donald F; Samuel, Charles E; O'Connell, Mary A; Walkley, Carl R; Nishikura, Kazuko; Li, Jin Billy

2017-10-11

Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules. Although many editing sites have recently been discovered, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. We show that editing levels in non-repetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 is the primary editor of repetitive sites and ADAR2 is the primary editor of non-repetitive coding sites, whereas the catalytically inactive ADAR3 predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. In addition, we curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. Further analysis of the GTEx data revealed several potential regulators of editing, such as AIMP2, which reduces editing in muscles by enhancing the degradation of the ADAR proteins. Collectively, our work provides insights into the complex cis- and trans-regulation of A-to-I editing.
Assessment of the American Joint Commission on Cancer 8th Edition Staging System for Patients with Pancreatic Neuroendocrine Tumors: A Surveillance, Epidemiology, and End Results analysis.

PubMed

Li, Xiaogang; Gou, Shanmiao; Liu, Zhiqiang; Ye, Zeng; Wang, Chunyou

2018-03-01

Although several staging systems have been proposed for pancreatic neuroendocrine tumors (pNETs), the optimal staging system remains unclear. Here, we aimed to assess the application of the newly revised 8th edition American Joint Committee on Cancer (AJCC) staging system for exocrine pancreatic carcinoma (EPC) to pNETs, in comparison with that of other staging systems. We identified pNETs patients from the Surveillance, Epidemiology, and End Results (SEER) database (2004-2014). Overall survival was analyzed using Kaplan-Meier curves with the log-rank test. The predictive accuracy of each staging system was assessed by the concordance index (c-index). Cox proportional hazards regression was conducted to calculate the impact of different stages. In total, 2424 patients with pNETs, including 2350 who underwent resection, were identified using SEER data. Patients with different stages were evenly stratified based on the 8th edition AJCC staging system for EPC. Kaplan-Meier curves were well separated in all patients and patients with resection using the 8th edition AJCC staging system for EPC. Moreover, the hazard ratio increased with worsening disease stage. The c-index of the 8th edition AJCC staging system for EPC was similar to that of the other systems. For pNETs patients, the 8th edition AJCC staging system for EPC exhibits good prognostic discrimination among different stages in both all patients and those with resection. © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.
An analysis of teacher’s preparation in implementing 2013 revision edition curriculum on mathematics specialization learning

NASA Astrophysics Data System (ADS)

Susilo, T.; Suryawan, A.

2018-05-01

This study aimed to determine the pedagogical competence of teachers, the readiness of planning and implementation of learning related to the implementation 2013 revised edition curriculum on mathematics specialization learning for senior high schools Wonogiri. Informants in this study there are 6 high school mathematics teachers X and XI class who teach in the school district Wonogiri. Data were collected using questionnaire method, interview, observation and documentation. Qualitative data analysis is done interactively through 4 paths: data collection, data reduction, data display, drawing conclusion. The results showed that high school mathematics teacher class X and XI in school district of Wonogiri City. The results show that most high school mathematics teachers in grade X and XI are ready to implement the 2013 revised edition curriculum and a few have not been able to implement due to internal or external factors. High school math teachers at Wonogiri district who are ready to face the 2013 revised edition curriculum have applied 10 teacher pedagogic competency indicators according to Regulation of the national education ministry Number 16 Year 2007 in learning. The readiness and implementation of mathematics learning is in line with the demands of the 2013 revised edition curriculum. Based on the teachers who are not ready, data on issues that arise in the implementation of the 2013 revised edition curriculum. Especially the problems in learning, namely mismatch of Core Competence (KI) and Basic Competence (KD) in teacher manual, material disregard in student handbook and lack of examples of problems that exist in teacher manual.
The Thomas A. Edison Papers at Rutgers University

Science.gov Websites

Contact Us Research Digital Edition Microfilm Edition Book Edition Motion Picture Catalogs Document Microfilm Edition Book Edition Motion Picture Catalogs Document Sampler Thomas Edison's Life Biography
Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

PubMed

Mehedi, Masfique; Hoenen, Thomas; Robertson, Shelly; Ricklefs, Stacy; Dolan, Michael A; Taylor, Travis; Falzarano, Darryl; Ebihara, Hideki; Porcella, Stephen F; Feldmann, Heinz

2013-01-01

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.
Baculoviral delivery of CRISPR/Cas9 facilitates efficient genome editing in human cells

PubMed Central

Hindriksen, Sanne; Bramer, Arne J.; Truong, My Anh; Vromans, Martijn J. M.; Post, Jasmin B.; Verlaan-Klink, Ingrid; Snippert, Hugo J.; Lens, Susanne M. A.

2017-01-01

The CRISPR/Cas9 system is a highly effective tool for genome editing. Key to robust genome editing is the efficient delivery of the CRISPR/Cas9 machinery. Viral delivery systems are efficient vehicles for the transduction of foreign genes but commonly used viral vectors suffer from a limited capacity in the genetic information they can carry. Baculovirus however is capable of carrying large exogenous DNA fragments. Here we investigate the use of baculoviral vectors as a delivery vehicle for CRISPR/Cas9 based genome-editing tools. We demonstrate transduction of a panel of cell lines with Cas9 and an sgRNA sequence, which results in efficient knockout of all four targeted subunits of the chromosomal passenger complex (CPC). We further show that introduction of a homology directed repair template into the same CRISPR/Cas9 baculovirus facilitates introduction of specific point mutations and endogenous gene tags. Tagging of the CPC recruitment factor Haspin with the fluorescent reporter YFP allowed us to study its native localization as well as recruitment to the cohesin subunit Pds5B. PMID:28640891
Efficient genomic correction methods in human iPS cells using CRISPR-Cas9 system.

PubMed

Li, Hongmei Lisa; Gee, Peter; Ishida, Kentaro; Hotta, Akitsu

2016-05-15

Precise gene correction using the CRISPR-Cas9 system in human iPS cells holds great promise for various applications, such as the study of gene functions, disease modeling, and gene therapy. In this review article, we summarize methods for effective editing of genomic sequences of iPS cells based on our experiences correcting dystrophin gene mutations with the CRISPR-Cas9 system. Designing specific sgRNAs as well as having efficient transfection methods and proper detection assays to assess genomic cleavage activities are critical for successful genome editing in iPS cells. In addition, because iPS cells are fragile by nature when dissociated into single cells, a step-by-step confirmation during the cell recovery process is recommended to obtain an adequate number of genome-edited iPS cell clones. We hope that the techniques described here will be useful for researchers from diverse backgrounds who would like to perform genome editing in iPS cells. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
CERES ERBE-like Monthly Regional Averages (ES-9) in HDF (CER_ES9_Aqua-FM3_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Regional Averages (ES-9) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-9 is also produced for combinations of scanner instruments. All instantaneous shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-8 product for a month are sorted by 2.5-degree spatial regions, by day number, and by the local hour of observation. The mean of the instantaneous fluxes for a given region-day-hour bin is determined and recorded on the ES-9 along with other flux statistics and scene information. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The ES-9 also contains hourly average fluxes for the month and an overall monthly average for each region. These average fluxes are given for both clear-sky and total-sky scenes. The following CERES ES9 data sets are currently available: CER_ES9_FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition2 CER_ES9_PFM+FM1_Edition1 CER_ES9_PFM+FM2_Edition1 CER_ES9_PFM+FM1_Edition2 CER_ES9_PFM+FM2_Edition2 CER_ES9_TRMM-PFM_Edition1 CER_ES9_TRMM-PFM_Edition2 CER_ES9_Terra-FM1_Edition1 CER_ES9_Terra-FM2_Edition1 CER_ES9_FM1+FM2_Edition2 CER_ES9_Terra-FM1_Edition2 CER_ES9_Terra-FM2_Edition2 CER_ES9_Aqua-FM3_Edition1 CER_ES9_Aqua-FM4_Edition1 CER_ES9_FM1+FM2+FM3+FM4_Edition1 CER_ES9_Aqua-FM3_Edition2 CER_ES9_Aqua-FM4_Edition2 CER_ES9_FM1+FM3_Edition2 CER_ES9_FM1+FM4_Edition2 CER_ES9_Aqua-FM3_Edition1-CV CER_ES9_Aqua-FM4_Edition1-CV CER_ES9_Terra-FM1_Edition1-CV CER_ES9_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-10-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=hourly, daily, monthly; Temporal_Resolution_Range=Hourly - < Daily, Daily - < Weekly, Monthly - < Annual].
CERES ERBE-like Monthly Regional Averages (ES-9) in HDF (CER_ES9_FM1+FM4_Edition2)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Regional Averages (ES-9) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-9 is also produced for combinations of scanner instruments. All instantaneous shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-8 product for a month are sorted by 2.5-degree spatial regions, by day number, and by the local hour of observation. The mean of the instantaneous fluxes for a given region-day-hour bin is determined and recorded on the ES-9 along with other flux statistics and scene information. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The ES-9 also contains hourly average fluxes for the month and an overall monthly average for each region. These average fluxes are given for both clear-sky and total-sky scenes. The following CERES ES9 data sets are currently available: CER_ES9_FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition2 CER_ES9_PFM+FM1_Edition1 CER_ES9_PFM+FM2_Edition1 CER_ES9_PFM+FM1_Edition2 CER_ES9_PFM+FM2_Edition2 CER_ES9_TRMM-PFM_Edition1 CER_ES9_TRMM-PFM_Edition2 CER_ES9_Terra-FM1_Edition1 CER_ES9_Terra-FM2_Edition1 CER_ES9_FM1+FM2_Edition2 CER_ES9_Terra-FM1_Edition2 CER_ES9_Terra-FM2_Edition2 CER_ES9_Aqua-FM3_Edition1 CER_ES9_Aqua-FM4_Edition1 CER_ES9_FM1+FM2+FM3+FM4_Edition1 CER_ES9_Aqua-FM3_Edition2 CER_ES9_Aqua-FM4_Edition2 CER_ES9_FM1+FM3_Edition2 CER_ES9_FM1+FM4_Edition2 CER_ES9_Aqua-FM3_Edition1-CV CER_ES9_Aqua-FM4_Edition1-CV CER_ES9_Terra-FM1_Edition1-CV CER_ES9_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-03-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=hourly, daily, monthly; Temporal_Resolution_Range=Hourly - < Daily, Daily - < Weekly, Monthly - < Annual].
CERES ERBE-like Monthly Regional Averages (ES-9) in HDF ( CER_ES9_Aqua-FM4_Edition1-CV)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Regional Averages (ES-9) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-9 is also produced for combinations of scanner instruments. All instantaneous shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-8 product for a month are sorted by 2.5-degree spatial regions, by day number, and by the local hour of observation. The mean of the instantaneous fluxes for a given region-day-hour bin is determined and recorded on the ES-9 along with other flux statistics and scene information. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The ES-9 also contains hourly average fluxes for the month and an overall monthly average for each region. These average fluxes are given for both clear-sky and total-sky scenes. The following CERES ES9 data sets are currently available: CER_ES9_FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition2 CER_ES9_PFM+FM1_Edition1 CER_ES9_PFM+FM2_Edition1 CER_ES9_PFM+FM1_Edition2 CER_ES9_PFM+FM2_Edition2 CER_ES9_TRMM-PFM_Edition1 CER_ES9_TRMM-PFM_Edition2 CER_ES9_Terra-FM1_Edition1 CER_ES9_Terra-FM2_Edition1 CER_ES9_FM1+FM2_Edition2 CER_ES9_Terra-FM1_Edition2 CER_ES9_Terra-FM2_Edition2 CER_ES9_Aqua-FM3_Edition1 CER_ES9_Aqua-FM4_Edition1 CER_ES9_FM1+FM2+FM3+FM4_Edition1 CER_ES9_Aqua-FM3_Edition2 CER_ES9_Aqua-FM4_Edition2 CER_ES9_FM1+FM3_Edition2 CER_ES9_FM1+FM4_Edition2 CER_ES9_Aqua-FM3_Edition1-CV CER_ES9_Aqua-FM4_Edition1-CV CER_ES9_Terra-FM1_Edition1-CV CER_ES9_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-03-29] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=hourly, daily, monthly; Temporal_Resolution_Range=Hourly - < Daily, Daily - < Weekly, Monthly - < Annual].
CERES ERBE-like Monthly Regional Averages (ES-9) in HDF ( CER_ES9_Terra-FM1_Edition1-CV)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Regional Averages (ES-9) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-9 is also produced for combinations of scanner instruments. All instantaneous shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-8 product for a month are sorted by 2.5-degree spatial regions, by day number, and by the local hour of observation. The mean of the instantaneous fluxes for a given region-day-hour bin is determined and recorded on the ES-9 along with other flux statistics and scene information. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The ES-9 also contains hourly average fluxes for the month and an overall monthly average for each region. These average fluxes are given for both clear-sky and total-sky scenes. The following CERES ES9 data sets are currently available: CER_ES9_FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition2 CER_ES9_PFM+FM1_Edition1 CER_ES9_PFM+FM2_Edition1 CER_ES9_PFM+FM1_Edition2 CER_ES9_PFM+FM2_Edition2 CER_ES9_TRMM-PFM_Edition1 CER_ES9_TRMM-PFM_Edition2 CER_ES9_Terra-FM1_Edition1 CER_ES9_Terra-FM2_Edition1 CER_ES9_FM1+FM2_Edition2 CER_ES9_Terra-FM1_Edition2 CER_ES9_Terra-FM2_Edition2 CER_ES9_Aqua-FM3_Edition1 CER_ES9_Aqua-FM4_Edition1 CER_ES9_FM1+FM2+FM3+FM4_Edition1 CER_ES9_Aqua-FM3_Edition2 CER_ES9_Aqua-FM4_Edition2 CER_ES9_FM1+FM3_Edition2 CER_ES9_FM1+FM4_Edition2 CER_ES9_Aqua-FM3_Edition1-CV CER_ES9_Aqua-FM4_Edition1-CV CER_ES9_Terra-FM1_Edition1-CV CER_ES9_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2006-09-30] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=hourly, daily, monthly; Temporal_Resolution_Range=Hourly - < Daily, Daily - < Weekly, Monthly - < Annual].
CERES ERBE-like Monthly Regional Averages (ES-9) in HDF (CER_ES9_TRMM-PFM_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Regional Averages (ES-9) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-9 is also produced for combinations of scanner instruments. All instantaneous shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-8 product for a month are sorted by 2.5-degree spatial regions, by day number, and by the local hour of observation. The mean of the instantaneous fluxes for a given region-day-hour bin is determined and recorded on the ES-9 along with other flux statistics and scene information. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The ES-9 also contains hourly average fluxes for the month and an overall monthly average for each region. These average fluxes are given for both clear-sky and total-sky scenes. The following CERES ES9 data sets are currently available: CER_ES9_FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition2 CER_ES9_PFM+FM1_Edition1 CER_ES9_PFM+FM2_Edition1 CER_ES9_PFM+FM1_Edition2 CER_ES9_PFM+FM2_Edition2 CER_ES9_TRMM-PFM_Edition1 CER_ES9_TRMM-PFM_Edition2 CER_ES9_Terra-FM1_Edition1 CER_ES9_Terra-FM2_Edition1 CER_ES9_FM1+FM2_Edition2 CER_ES9_Terra-FM1_Edition2 CER_ES9_Terra-FM2_Edition2 CER_ES9_Aqua-FM3_Edition1 CER_ES9_Aqua-FM4_Edition1 CER_ES9_FM1+FM2+FM3+FM4_Edition1 CER_ES9_Aqua-FM3_Edition2 CER_ES9_Aqua-FM4_Edition2 CER_ES9_FM1+FM3_Edition2 CER_ES9_FM1+FM4_Edition2 CER_ES9_Aqua-FM3_Edition1-CV CER_ES9_Aqua-FM4_Edition1-CV CER_ES9_Terra-FM1_Edition1-CV CER_ES9_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=1998-08-31] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=hourly, daily, monthly; Temporal_Resolution_Range=Hourly - < Daily, Daily - < Weekly, Monthly - < Annual].
CERES ERBE-like Monthly Regional Averages (ES-9) in HDF (CER_ES9_Aqua-FM4_Edition1)

NASA Technical Reports Server (NTRS)

Wielicki, Bruce A. (Principal Investigator)

The ERBE-like Monthly Regional Averages (ES-9) product contains a month of space and time averaged Clouds and the Earth's Radiant Energy System (CERES) data for a single scanner instrument. The ES-9 is also produced for combinations of scanner instruments. All instantaneous shortwave and longwave fluxes at the Top-of-the-Atmosphere (TOA) from the CERES ES-8 product for a month are sorted by 2.5-degree spatial regions, by day number, and by the local hour of observation. The mean of the instantaneous fluxes for a given region-day-hour bin is determined and recorded on the ES-9 along with other flux statistics and scene information. For each region, the daily average flux is estimated from an algorithm that uses the available hourly data, scene identification data, and diurnal models. This algorithm is 'like' the algorithm used for the Earth Radiation Budget Experiment (ERBE). The ES-9 also contains hourly average fluxes for the month and an overall monthly average for each region. These average fluxes are given for both clear-sky and total-sky scenes. The following CERES ES9 data sets are currently available: CER_ES9_FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition1 CER_ES9_PFM+FM1+FM2_Edition2 CER_ES9_PFM+FM1_Edition1 CER_ES9_PFM+FM2_Edition1 CER_ES9_PFM+FM1_Edition2 CER_ES9_PFM+FM2_Edition2 CER_ES9_TRMM-PFM_Edition1 CER_ES9_TRMM-PFM_Edition2 CER_ES9_Terra-FM1_Edition1 CER_ES9_Terra-FM2_Edition1 CER_ES9_FM1+FM2_Edition2 CER_ES9_Terra-FM1_Edition2 CER_ES9_Terra-FM2_Edition2 CER_ES9_Aqua-FM3_Edition1 CER_ES9_Aqua-FM4_Edition1 CER_ES9_FM1+FM2+FM3+FM4_Edition1 CER_ES9_Aqua-FM3_Edition2 CER_ES9_Aqua-FM4_Edition2 CER_ES9_FM1+FM3_Edition2 CER_ES9_FM1+FM4_Edition2 CER_ES9_Aqua-FM3_Edition1-CV CER_ES9_Aqua-FM4_Edition1-CV CER_ES9_Terra-FM1_Edition1-CV CER_ES9_Terra-FM2_Edition1-CV. [Location=GLOBAL] [Temporal_Coverage: Start_Date=1998-01-01; Stop_Date=2005-03-29] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=2.5 degree; Longitude_Resolution=2.5 degree; Horizontal_Resolution_Range=250 km - < 500 km or approximately 2.5 degrees - < 5.0 degrees; Temporal_Resolution=hourly, daily, monthly; Temporal_Resolution_Range=Hourly - < Daily, Daily - < Weekly, Monthly - < Annual].

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