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Sample records for additional open reading

  1. Results with Open Court Reading.

    ERIC Educational Resources Information Center

    McGraw-Hill Companies, New York, NY. Educational and Professional Publishing Group.

    This publication tells the stories of eight schools from around the nation that have used the Open Court Reading program, describing the history of the schools, the challenges they faced, and their attempts to meet those challenges. The schools are located in California, Florida, Texas, and New York. Each of the school stories includes a focus on…

  2. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 19 Customs Duties 2 2011-04-01 2011-04-01 false Opening of letter class mail; reading of... Opening of letter class mail; reading of correspondence prohibited. (a) Matter in addition to... addressee has given written authorization for the opening. (c) Reading of correspondence. No Customs...

  3. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Opening of letter class mail; reading of... Opening of letter class mail; reading of correspondence prohibited. (a) Matter in addition to... addressee has given written authorization for the opening. (c) Reading of correspondence. No Customs...

  4. Children's Patterns of Reasoning about Reading and Addition Concepts

    ERIC Educational Resources Information Center

    Farrington-Flint, Lee; Canobi, Katherine H.; Wood, Clare; Faulkner, Dorothy

    2010-01-01

    Children's reasoning was examined within two educational contexts (word reading and addition) so as to understand the factors that contribute to relational reasoning in the two domains. Sixty-seven 5- to 7-year-olds were given a series of related words to read or single-digit addition items to solve (interspersed with unrelated items). The…

  5. Children's patterns of reasoning about reading and addition concepts.

    PubMed

    Farrington-Flint, Lee; Canobi, Katherine H; Wood, Clare; Faulkner, Dorothy

    2010-06-01

    Children's reasoning was examined within two educational contexts (word reading and addition) so as to understand the factors that contribute to relational reasoning in the two domains. Sixty-seven 5- to 7-year-olds were given a series of related words to read or single-digit addition items to solve (interspersed with unrelated items). The frequency, accuracy, and response times of children's self-reports on the conceptually related items provided a measure of relational reasoning, while performance on the unrelated addition and reading items provided a measure of procedural skill. The results indicated that the children's ability to use conceptual relations to solve both reading and addition problems enhanced speed and accuracy levels, increased with age, and was related to procedural skill. However, regression analyses revealed that domain-specific competencies can best explain the use of conceptual relations in both reading and addition. Moreover, a cluster analysis revealed that children differ according to the academic domain in which they first apply conceptual relations and these differences are related to individual variation in their procedural skills within these particular domains. These results highlight the developmental significance of relational reasoning in the context of reading and addition and underscore the importance of concept-procedure links in explaining children's literacy and arithmetical development. PMID:20481396

  6. Open Court Reading[c]. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2012

    2012-01-01

    "Open Court Reading"[c] is a core reading program for grades K-6 developed by SRA/McGraw-Hill that is designed to teach decoding, comprehension, inquiry, and writing in a logical progression. Part 1 of each unit, Preparing to Read, focuses on phonemic awareness, sounds and letters, phonics, fluency, and word knowledge. Part 2, Reading and…

  7. Reading Skills and Reading Habits: A Study of New Open University Undergraduate Reservees.

    ERIC Educational Resources Information Center

    Datta, Saroj; Macdonald-Ross, Michael

    2002-01-01

    Describes the use of cloze procedures to investigate the reading skills and reading habits of Open University (United Kingdom) reservees (potential undergraduate students). Discusses correlations between reading habits and other student characteristics and identifying reservees at risk based on the results of cloze tests. (Author/LRW)

  8. Open the Door for Reading (Motivational Activities).

    ERIC Educational Resources Information Center

    Voorhees, Roxy

    Designed to help elementary teachers motivate students to read, this illustrated booklet presents a store of classroom ideas that promote and enrich reading. Materials presented include (1) instructions for making a "bookworm" bookmark for each student; (2) various animated bulletin board games intended to accompany the reading process and to help…

  9. Translational control of Nrf2 within the open reading frame

    PubMed Central

    Perez-Leal, Oscar; Barrero, Carlos A.; Merali, Salim

    2013-01-01

    Nuclear Factor Erythroid 2-Related Factor 2 (Nrf2) is a transcription factor that is essential for the regulation of an effective antioxidant and detoxifying response. The regulation of its activity can occur at transcription, translation and post-translational levels. Evidence suggests that under environmental stress conditions, new synthesis of Nrf2 is required - a process that is regulated by translational control and is not fully understood. Here we described the identification of a novel molecular process that under basal conditions strongly represses the translation of Nrf2 within the open reading frame (ORF). This mechanism is dependent on the mRNA sequence within the 3’ portion of the ORF of Nrf2 but not in the encoded amino acid sequence. The Nrf2 translational repression can be reversed with the use of synonymous codon substitutions. This discovery suggests an additional layer of control to explain the reason for the low Nrf2 concentration under quiescent state. PMID:23806685

  10. Open Reading Frame Phylogenetic Analysis on the Cloud

    PubMed Central

    2013-01-01

    Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

  11. Open reading frame phylogenetic analysis on the cloud.

    PubMed

    Hung, Che-Lun; Lin, Chun-Yuan

    2013-01-01

    Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

  12. A Multisite Cluster Randomized Field Trial of Open Court Reading

    ERIC Educational Resources Information Center

    Borman, Geoffrey D.; Dowling, N. Maritza; Schneck, Carrie

    2008-01-01

    In this article, the authors report achievement outcomes of a multisite cluster randomized field trial of Open Court Reading 2005 (OCR), a K-6 literacy curriculum published by SRA/McGraw-Hill. The participants are 49 first-grade through fifth-grade classrooms from predominantly minority and poor contexts across the nation. Blocking by grade level…

  13. Translational control of Nrf2 within the open reading frame

    SciTech Connect

    Perez-Leal, Oscar Barrero, Carlos A.; Merali, Salim

    2013-07-19

    Highlights: •Identification of a novel Nrf2 translational repression mechanism. •The repressor is within the 3′ portion of the Nrf2 ORF. •The translation of Nrf2 or eGFP is reduced by the regulatory element. •The translational repression can be reversed with synonymous codon substitutions. •The molecular mechanism requires the mRNA sequence, but not the encoded amino acids. -- Abstract: Nuclear Factor Erythroid 2-Related Factor 2 (Nrf2) is a transcription factor that is essential for the regulation of an effective antioxidant and detoxifying response. The regulation of its activity can occur at transcription, translation and post-translational levels. Evidence suggests that under environmental stress conditions, new synthesis of Nrf2 is required – a process that is regulated by translational control and is not fully understood. Here we described the identification of a novel molecular process that under basal conditions strongly represses the translation of Nrf2 within the open reading frame (ORF). This mechanism is dependent on the mRNA sequence within the 3′ portion of the ORF of Nrf2 but not in the encoded amino acid sequence. The Nrf2 translational repression can be reversed with the use of synonymous codon substitutions. This discovery suggests an additional layer of control to explain the reason for the low Nrf2 concentration under quiescent state.

  14. Hundreds of putatively functional small open reading frames in Drosophila

    PubMed Central

    2011-01-01

    Background The relationship between DNA sequence and encoded information is still an unsolved puzzle. The number of protein-coding genes in higher eukaryotes identified by genome projects is lower than was expected, while a considerable amount of putatively non-coding transcription has been detected. Functional small open reading frames (smORFs) are known to exist in several organisms. However, coding sequence detection methods are biased against detecting such very short open reading frames. Thus, a substantial number of non-canonical coding regions encoding short peptides might await characterization. Results Using bio-informatics methods, we have searched for smORFs of less than 100 amino acids in the putatively non-coding euchromatic DNA of Drosophila melanogaster, and initially identified nearly 600,000 of them. We have studied the pattern of conservation of these smORFs as coding entities between D. melanogaster and Drosophila pseudoobscura, their presence in syntenic and in transcribed regions of the genome, and their ratio of conservative versus non-conservative nucleotide changes. For negative controls, we compared the results with those obtained using random short sequences, while a positive control was provided by smORFs validated by proteomics data. Conclusions The combination of these analyses led us to postulate the existence of at least 401 functional smORFs in Drosophila, with the possibility that as many as 4,561 such functional smORFs may exist. PMID:22118156

  15. Upstream open reading frames: Molecular switches in (patho)physiology

    PubMed Central

    Wethmar, Klaus; Smink, Jeske J; Leutz, Achim

    2010-01-01

    Conserved upstream open reading frames (uORFs) are found within many eukaryotic transcripts and are known to regulate protein translation. Evidence from genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of human diseases. A genetic mouse model has recently provided proof-of-principle support for the physiological relevance of uORF-mediated translational control in mammals. The targeted disruption of the uORF initiation codon within the transcription factor CCAAT/enhancer binding protein β (C/EBPβ) gene resulted in deregulated C/EBPβ protein isoform expression, associated with defective liver regeneration and impaired osteoclast differentiation. The high prevalence of uORFs in the human transcriptome suggests that intensified search for mutations within 5′ RNA leader regions may reveal a multitude of alterations affecting uORFs, causing pathogenic deregulation of protein expression. PMID:20726009

  16. Open Court Reading©. What Works Clearinghouse Intervention Report. Updated October 2014

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2014

    2014-01-01

    "Open Court Reading©" is a reading program for grades K-6 published by McGraw-Hill Education that is designed to teach decoding, comprehension, inquiry, and writing in a three-part logical progression. Part One of each unit, Preparing to Read, focuses on phonemic awareness, sounds and letters, phonics, fluency, and word knowledge. Part…

  17. The Effect of Noise in an Open Space School on Reading Comprehension.

    ERIC Educational Resources Information Center

    Weinstein, Carol S.; Weinstein, Neil D.

    Parents and educators have expressed fears that high noise levels in open space schools may interfere with academic achievement. This investigation compared the reading comprehension of 60 fourth grade students in an open space school during periods both of quiet and of naturally occurring background noise. The reading tasks resembled normal…

  18. 16. INTERIOR OF BEDROOM NO. 3 (1965 ADDITION). OPEN DOOR ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    16. INTERIOR OF BEDROOM NO. 3 (1965 ADDITION). OPEN DOOR LEADS TO BEDROOM NO. 2. WALLS AND CEILING IN THIS ROOM DO NOT HAVE THE DECORATIVE WOOD STRIPPING FOUND IN THE ORIGINAL PORTIONS OF THE HOUSE. VIEW TO NORTHEAST. - Bishop Creek Hydroelectric System, Plant 4, Worker Cottage, Bishop Creek, Bishop, Inyo County, CA

  19. An Investigation of the Additive Benefits of Parent Dialogic Reading Techniques in Older Preschool Children

    ERIC Educational Resources Information Center

    Switalski, Sarah O'Neill

    2012-01-01

    This study examined the additive benefit of parent dialogic reading techniques in older, high-risk preschool children using multiple baseline design across participants, a single subject research design, as was as well as pre-test and post-test measures. Five preschoolers age-eligible to begin kindergarten the following school year participated.…

  20. Computational discovery of small open reading frames in Bacillus lehensis

    NASA Astrophysics Data System (ADS)

    Zainuddin, Nurhafizhoh; Illias, Rosli Md.; Mahadi, Nor Muhammad; Firdaus-Raih, Mohd

    2015-09-01

    Bacillus lehensis is a Gram-positive and endospore-forming alkalitolerant bacterial strain. In recent years there has been increasing interest in alkaliphilic bacteria and their ability to grow under extreme conditions as well as their ability to serve various important functions in industrial biology especially enzyme production. Small open reading frames (sORFs) have emerged as important regulators in various biological roles such as tumor progression, hormone signalling and stress response. Over the past decade, many biocomputational tools have been developed to predict genes in bacterial genomes. In this study, three softwares were used to predict sORF (≤ 80 aa) in B. lehensis by using whole genome sequence. We used comparative analysis to identify the sORFs in B. lehensis that conserved across all other bacterial genomes. We extended the analysis by doing the homology analysis against protein database. This study established the sORFs in B. lehensis that are conserved across bacteria which might has important biological function which still remain elusive in biological field.

  1. Detecting actively translated open reading frames in ribosome profiling data.

    PubMed

    Calviello, Lorenzo; Mukherjee, Neelanjan; Wyler, Emanuel; Zauber, Henrik; Hirsekorn, Antje; Selbach, Matthias; Landthaler, Markus; Obermayer, Benedikt; Ohler, Uwe

    2016-02-01

    RNA-sequencing protocols can quantify gene expression regulation from transcription to protein synthesis. Ribosome profiling (Ribo-seq) maps the positions of translating ribosomes over the entire transcriptome. We have developed RiboTaper (available at https://ohlerlab.mdc-berlin.de/software/), a rigorous statistical approach that identifies translated regions on the basis of the characteristic three-nucleotide periodicity of Ribo-seq data. We used RiboTaper with deep Ribo-seq data from HEK293 cells to derive an extensive map of translation that covered open reading frame (ORF) annotations for more than 11,000 protein-coding genes. We also found distinct ribosomal signatures for several hundred upstream ORFs and ORFs in annotated noncoding genes (ncORFs). Mass spectrometry data confirmed that RiboTaper achieved excellent coverage of the cellular proteome. Although dozens of novel peptide products were validated in this manner, few of the currently annotated long noncoding RNAs appeared to encode stable polypeptides. RiboTaper is a powerful method for comprehensive de novo identification of actively used ORFs from Ribo-seq data. PMID:26657557

  2. The Effects of Providing Additional Reading Opportunities for Struggling Readers at Their Independent Reading Levels within Content Areas

    ERIC Educational Resources Information Center

    Vasinko, Teresa

    2013-01-01

    A mixed-methods study was conducted to determine if extra reading practice incorporated into fifth-and sixth-grade social studies and science content classes would have a positive impact on reading assessments for readers at risk. At-risk readers' independent reading levels were assessed using Dynamic Indicator of Basic Early Literacy Skills or…

  3. Influence of progressive addition lenses on reading posture in myopic children

    PubMed Central

    Bao, Jinhua; Wang, Yuwen; Zhuo, Zuopao; Yang, Xianling; Tan, Renjing; Drobe, Björn; Chen, Hao

    2016-01-01

    Aims To determine the influence of single-vision lenses (SVLs) and progressive addition lenses (PALs) on the near vision posture of myopic children based on their near phoria. Methods Sixty-two myopic children were assigned to wear SVLs followed by PALs. Eighteen children were esophoric (greater than +1), 18 were orthophoric (−1 to 1) and 26 were exophoric (less than −1) at near. Reading distance, head tilt and ocular gaze angles were measured using an electromagnetic system after adaptation to each lens type. Results The lens type did not influence reading distance or head tilt angle (p>0.05 for both), but ocular gaze angle decreased significantly with the PALs (F=9.25, p=0.004). With the PALs, exophoric children exhibited significantly increased head tilt angle (p=0.003) and reduced ocular gaze angle (p=0.004) compared with esophoric children. Near non-exophoric children exhibited similar eye and head postures when wearing SVLs and PALs, whereas exophoric children exhibited reduced ocular gaze angle (t=−3.18, p=0.04) with PALs compared with SVLs. Using PALs for reading, the mean addition power employed by esophoric children was significantly greater than exophoric children (p=0.04). Conclusions The lens type and the near phoria state affected near vision posture. During reading, myopic esophoric children used a lower portion of their PALs compared with exophoric children, resulting in greater addition power. These results may partially explain why myopic children with near esophoria exhibited superior treatment effects in myopia control trials using PALs. PMID:26608026

  4. Reading-Related Behavior in an Open Classroom: Effects of Novelty and Modeling on Preschoolers

    ERIC Educational Resources Information Center

    Haskett, G. J.; Lenfestey, W.

    1975-01-01

    Preschool reading behavior did not arise necessarily or spontaneously in an open classroom where a set of books was continually available. Because the open classroom acquires new properties and meanings when contrasted with the traditional school, complex factors influencing behavior, such as novelty and modeling, must be examined. (BJG)

  5. Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides.

    PubMed

    Ma, Jiao; Diedrich, Jolene K; Jungreis, Irwin; Donaldson, Cynthia; Vaughan, Joan; Kellis, Manolis; Yates, John R; Saghatelian, Alan

    2016-04-01

    Computational, genomic, and proteomic approaches have been used to discover nonannotated protein-coding small open reading frames (smORFs). Some novel smORFs have crucial biological roles in cells and organisms, which motivates the search for additional smORFs. Proteomic smORF discovery methods are advantageous because they detect smORF-encoded polypeptides (SEPs) to validate smORF translation and SEP stability. Because SEPs are shorter and less abundant than average proteins, SEP detection using proteomics faces unique challenges. Here, we optimize several steps in the SEP discovery workflow to improve SEP isolation and identification. These changes have led to the detection of several new human SEPs (novel human genes), improved confidence in the SEP assignments, and enabled quantification of SEPs under different cellular conditions. These improvements will allow faster detection and characterization of new SEPs and smORFs. PMID:27010111

  6. Reading.

    ERIC Educational Resources Information Center

    Mulford, Jeremy, Ed.

    1971-01-01

    A collection of articles reflecting the underlying concern of British contributors with continuity--conceiving reading and learning as a whole throughout the school years--comprises this special issue of "English in Education." Specific topics treated are: "What Children Learn in Learning to Read" by R. Morris; "Reading without Primers" by W.…

  7. Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes.

    PubMed

    Steigele, Stephan; Nieselt, Kay

    2005-01-01

    Natural antisense transcripts are reported from all kingdoms of life and several recent reports of genomewide screens indicate that they are widely distributed. These transcripts seem to be involved in various biological functions and may govern the expression of their respective sense partner. Very little, however, is known about the degree of evolutionary conservation of antisense transcripts. Furthermore, none of the earlier analyses has studied whether antisense relationships are solely dual or involved in more complex relationships. Here we present a systematic screen for cis- and trans-located antisense transcripts based on open reading frames (ORFs) from five fungal species. The relative number of ORFs involved in antisense relationships varies greatly between the five species. In addition, other significant differences are found between the species, such as the mean length of the antisense region. The majority of trans-located antisense transcripts is found to be involved in complex relationships, resulting in highly connected networks. The analysis of the degree of evolutionary conservation of antisense transcripts shows that most antisense transcripts have no ortholog in any other species. An annotation of antisense transcripts based on Gene Ontology directs to common terms and shows that proteins of genes involved in antisense relationships preferentially localize to the nucleus with common functions in the regulation or maintenance of nucleic acids. PMID:16147987

  8. Translational control of protein kinase Ceta by two upstream open reading frames.

    PubMed

    Raveh-Amit, Hadas; Maissel, Adva; Poller, Jonathan; Marom, Liraz; Elroy-Stein, Orna; Shapira, Michal; Livneh, Etta

    2009-11-01

    Protein kinase C (PKC) represents a family of serine/threonine kinases that play a central role in the regulation of cell growth, differentiation, and transformation. Posttranslational control of the PKC isoforms and their activation have been extensively studied; however, not much is known about their translational regulation. Here we report that the expression of one of the PKC isoforms, PKCeta, is regulated at the translational level both under normal growth conditions and during stress imposed by amino acid starvation, the latter causing a marked increase in its protein levels. The 5' untranslated region (5' UTR) of PKCeta is unusually long and GC rich, characteristic of many oncogenes and growth regulatory genes. We have identified two conserved upstream open reading frames (uORFs) in its 5' UTR and show their effect in suppressing the expression of PKCeta in MCF-7 growing cells. While the two uORFs function as repressive elements that maintain low basal levels of PKCeta in growing cells, they are required for its enhanced expression upon amino acid starvation. We show that the translational regulation during stress involves leaky scanning and is dependent on eIF-2alpha phosphorylation by GCN2. Our work further suggests that translational regulation could provide an additional level for controlling the expression of PKC family members, being more common than currently recognized. PMID:19797084

  9. A Study of the Effect of Additional Reading Assistance on Student Achievement

    ERIC Educational Resources Information Center

    Gillan-Sanderson, Nicole A.

    2012-01-01

    This study describes a procedure one school district used to increase students' reading abilities through reviewing data and adjusting the instruction to give students intensive services, as needed. This school worked in a problem-solving team approach to develop a comprehensive team that followed the progression of student achievement.…

  10. Comprehensive translational control of tyrosine kinase expression by upstream open reading frames

    PubMed Central

    Wethmar, K; Schulz, J; Muro, E M; Talyan, S; Andrade-Navarro, M A; Leutz, A

    2016-01-01

    Post-transcriptional control has emerged as a major regulatory event in gene expression and often occurs at the level of translation initiation. Although overexpression or constitutive activation of tyrosine kinases (TKs) through gene amplification, translocation or mutation are well-characterized oncogenic events, current knowledge about translational mechanisms of TK activation is scarce. Here, we report the presence of translational cis-regulatory upstream open reading frames (uORFs) in the majority of transcript leader sequences of human TK mRNAs. Genetic ablation of uORF initiation codons in TK transcripts resulted in enhanced translation of the associated downstream main protein-coding sequences (CDSs) in all cases studied. Similarly, experimental removal of uORF start codons in additional non-TK proto-oncogenes, and naturally occurring loss-of-uORF alleles of the c-met proto-oncogene (MET) and the kinase insert domain receptor (KDR), was associated with increased CDS translation. Based on genome-wide sequence analyses we identified polymorphisms in 15.9% of all human genes affecting uORF initiation codons, associated Kozak consensus sequences or uORF-related termination codons. Together, these data suggest a comprehensive role of uORF-mediated translational control and delineate how aberrant induction of proto-oncogenes through loss-of-function mutations at uORF initiation codons may be involved in the etiology of cancer. We provide a detailed map of uORFs across the human genome to stimulate future research on the pathogenic role of uORFs. PMID:26096937

  11. Comprehensive translational control of tyrosine kinase expression by upstream open reading frames.

    PubMed

    Wethmar, K; Schulz, J; Muro, E M; Talyan, S; Andrade-Navarro, M A; Leutz, A

    2016-03-31

    Post-transcriptional control has emerged as a major regulatory event in gene expression and often occurs at the level of translation initiation. Although overexpression or constitutive activation of tyrosine kinases (TKs) through gene amplification, translocation or mutation are well-characterized oncogenic events, current knowledge about translational mechanisms of TK activation is scarce. Here, we report the presence of translational cis-regulatory upstream open reading frames (uORFs) in the majority of transcript leader sequences of human TK mRNAs. Genetic ablation of uORF initiation codons in TK transcripts resulted in enhanced translation of the associated downstream main protein-coding sequences (CDSs) in all cases studied. Similarly, experimental removal of uORF start codons in additional non-TK proto-oncogenes, and naturally occurring loss-of-uORF alleles of the c-met proto-oncogene (MET) and the kinase insert domain receptor (KDR), was associated with increased CDS translation. Based on genome-wide sequence analyses we identified polymorphisms in 15.9% of all human genes affecting uORF initiation codons, associated Kozak consensus sequences or uORF-related termination codons. Together, these data suggest a comprehensive role of uORF-mediated translational control and delineate how aberrant induction of proto-oncogenes through loss-of-function mutations at uORF initiation codons may be involved in the etiology of cancer. We provide a detailed map of uORFs across the human genome to stimulate future research on the pathogenic role of uORFs. PMID:26096937

  12. Deletion mutants of herpesvirus saimiri define an open reading frame necessary for transformation.

    PubMed Central

    Murthy, S C; Trimble, J J; Desrosiers, R C

    1989-01-01

    Analysis of a 5,549-base-pair sequence at the left end of herpesvirus saimiri unique (L-) DNA revealed two open reading frames and genes for five small nuclear U RNAs (herpesvirus saimiri U RNAs). Replication-competent deletion mutants were constructed in order to assess the importance of these genetic features for transformation by this oncogenic herpesvirus. Although not required for replication, one of the open reading frames was found to be required for immortalization of marmoset T lymphocytes into continuously growing cell lines. The protein predicted by this reading frame (STP; saimiri transformation-associated protein) has a highly hydrophobic stretch of 26 amino acids sufficient for a membrane-spanning domain near its carboxy terminus; this domain is immediately preceded by a sequence appropriate for formation of a metal-binding domain (His X2 His X6 Cys X2 Cys, where Xs are other amino acids). One of two poly(A)+ RNAs that could encode STP is bicistronic, while the other has a long 5' untranslated region (approximately 1.5 kilobases). Although some analogies can be drawn between STP and LMP (lymphocyte membrane protein) of Epstein-Barr virus, STP is not related in sequence to LMP. Images PMID:2545905

  13. OrfM: a fast open reading frame predictor for metagenomic data

    PubMed Central

    Woodcroft, Ben J.; Boyd, Joel A.

    2016-01-01

    Summary: Finding and translating stretches of DNA lacking stop codons is a task common in the analysis of sequence data. However, the computational tools for finding open reading frames are sufficiently slow that they are becoming a bottleneck as the volume of sequence data grows. This computational bottleneck is especially problematic in metagenomics when searching unassembled reads, or screening assembled contigs for genes of interest. Here, we present OrfM, a tool to rapidly identify open reading frames (ORFs) in sequence data by applying the Aho–Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical ORFs to similar tools (‘GetOrf’ and ‘Translate’) but is four-five times faster. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers. Availability and Implementation: Source code and binaries are freely available for download at http://github.com/wwood/OrfM or through GNU Guix under the LGPL 3+ license. OrfM is implemented in C and supported on GNU/Linux and OSX. Contacts: b.woodcroft@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153669

  14. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.

    PubMed

    Raj, Anil; Wang, Sidney H; Shim, Heejung; Harpak, Arbel; Li, Yang I; Engelmann, Brett; Stephens, Matthew; Gilad, Yoav; Pritchard, Jonathan K

    2016-01-01

    Accurate annotation of protein coding regions is essential for understanding how genetic information is translated into function. We describe riboHMM, a new method that uses ribosome footprint data to accurately infer translated sequences. Applying riboHMM to human lymphoblastoid cell lines, we identified 7273 novel coding sequences, including 2442 translated upstream open reading frames. We observed an enrichment of footprints at inferred initiation sites after drug-induced arrest of translation initiation, validating many of the novel coding sequences. The novel proteins exhibit significant selective constraint in the inferred reading frames, suggesting that many are functional. Moreover, ~40% of bicistronic transcripts showed negative correlation in the translation levels of their two coding sequences, suggesting a potential regulatory role for these novel regions. Despite known limitations of mass spectrometry to detect protein expressed at low level, we estimated a 14% validation rate. Our work significantly expands the set of known coding regions in humans. PMID:27232982

  15. Identification of small open reading frames in the Glaciozyma antarctica genome

    NASA Astrophysics Data System (ADS)

    Mat-Sharani, Shuhaila; Bharudin, Izwan; Zainuddin, Nursyafiqi; Abdul-Murad, Abdul-Munir; Abu-Bakar, Farah-Diba; Najimuddin, Nazalan; Mahadi, Nor-Muhammad; Firdaus-Raih, Mohd

    2015-09-01

    Glaciozyma antarctica is an obligate psychrophilic yeast that was isolated from Casey Research Station, Antarctica. The objective of this study was to identify small Open Reading Frames (sORFs) in the G. antarctica genome. Small ORFs have been found in other organisms including Saccharomyces cerevisiae and human and they have been known to partake in a diverse variety of functions. In this study, ORFs were searched from the existing G. antarctica genome annotations and this resulted 294 sORFs (of at most 100 amino acids) which represented 4% of the 7857 annotated ORFs. Several of these sORFs were validated by mapping to EST and transcriptome of G. antarctica.

  16. Varicella-Zoster Virus Open Reading Frame 48 Encodes an Active Nuclease

    PubMed Central

    Mueller, Niklaus H.; Gilden, Don

    2013-01-01

    Based on a DNA sequence and relative genomic position similar to those other herpesviruses, varicella-zoster virus (VZV) open reading frame 48 (ORF48) is predicted to encode an alkaline nuclease. Here we report the cloning, expression, purification, and characterization of recombinant VZV ORF48 protein and a VZV ORF48 point mutation (T172P). Protein encoded by wild-type ORF48, but not mutant protein, displayed both endo- and exonuclease activity, identifying ORF48 as a potential therapeutic target in VZV disease since efficient viral replication requires viral nuclease activity. PMID:23966396

  17. A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation.

    PubMed

    Ivanov, Ivaylo P; Atkins, John F; Michael, Antony J

    2010-01-01

    In many eukaryotic mRNAs one or more short 'upstream' open reading frames, uORFs, precede the initiator of the main coding sequence. Upstream ORFs are functionally diverse as illustrated by their variety of features in polyamine pathway biosynthetic mRNAs. Their propensity to act as sensors for regulatory circuits and to amplify the signals likely explains their occurrence in most polyamine pathway mRNAs. The uORF-mediated polyamine responsive autoregulatory circuits found in polyamine pathway mRNAs exemplify the translationally regulated dynamic interface between components of the proteome and metabolism. PMID:19920120

  18. An Upstream Open Reading Frame Is Essential for Feedback Regulation of Ascorbate Biosynthesis in Arabidopsis

    PubMed Central

    Laing, William A.; Martínez-Sánchez, Marcela; Wright, Michele A.; Bulley, Sean M.; Brewster, Di; Dare, Andrew P.; Rassam, Maysoon; Wang, Daisy; Storey, Roy; Macknight, Richard C.; Hellens, Roger P.

    2015-01-01

    Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. PMID:25724639

  19. Identification and characterization of Kaposi's sarcoma-associated herpesvirus open reading frame 11 promotor activation

    SciTech Connect

    Chen, Lei

    2008-01-01

    Open reading frame 11 (ORF11) of Kaposi's sarcoma-associated herpesvirus belongs to a herpesviral homologous protein family shared by some members of the gamma- herpesvirus subfamily. Little is known about this ORF11 homologous protein family. We have characterized an unknown open reading frame, ORF11, located adjacent and in the opposite orientation to a well-characterized viral IL-6 gene. Northern blot analysis reveals that ORF11 is expressed during the KSHV lytic cycle with delayed-early transcription kinetics. We have determined the 5{prime} and 3{prime} untranslated region of the unspliced ORF11 transcript and identified both the transcription start site and the transcription termination site. Core promoter region, representing ORF11 promoter activity, was mapped to a 159nt fragment 5{prime} most proximal to the transcription start site. A functional TATA box was identified in the core promoter region. Interestingly, we found that ORF11 transcriptional activation is not responsive to Rta, the KSHV lytic switch protein. We also discovered that part of the ORF11 promoter region, the 209nt fragment upstream of the transcription start site, was repressed by phorbol esters. Our data help to understand transcription regulation of ORF11 and to elucidate roles of ORF11 in KSHV pathogenesis and life cycle.

  20. Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana.

    PubMed

    Hu, Qiwen; Merchante, Catharina; Stepanova, Anna N; Alonso, Jose M; Heber, Steffen

    2016-03-01

    Upstream open reading frames (uORFs) are open reading frames that occur within the 5' UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes. It is believed that translated uORFs reduce the translational efficiency of the main coding region. However, only few uORFs are experimentally characterized. In this paper, we use ribosome footprinting together with a semi-supervised approach based on stacking classification models to identify translated uORFs in Arabidopsis thaliana. Our approach identified 5360 potentially translated uORFs in 2051 genes. GO terms enriched in genes with translated uORFs include catalytic activity, binding, transferase activity, phosphotransferase activity, kinase activity, and transcription regulator activity. The reported uORFs occur with a higher frequency in multi-isoform genes, and some uORFs are affected by alternative transcript start sites or alternative splicing events. Association rule mining revealed sequence features associated with the translation status of the uORFs. We hypothesize that uORF translation is a complex process that might be regulated by multiple factors. The identified uORFs are available online at:https://www.dropbox.com/sh/zdutupedxafhly8/AABFsdNR5zDfiozB7B4igFcja?dl=0. This paper is the extended version of our research presented at ISBRA 2015. PMID:26886998

  1. The Random Nature of Genome Architecture: Predicting Open Reading Frame Distributions

    PubMed Central

    McCoy, Michael W.; Allen, Andrew P.; Gillooly, James F.

    2009-01-01

    Background A better understanding of the size and abundance of open reading frames (ORFS) in whole genomes may shed light on the factors that control genome complexity. Here we examine the statistical distributions of open reading frames (i.e. distribution of start and stop codons) in the fully sequenced genomes of 297 prokaryotes, and 14 eukaryotes. Methodology/Principal Findings By fitting mixture models to data from whole genome sequences we show that the size-frequency distributions for ORFS are strikingly similar across prokaryotic and eukaryotic genomes. Moreover, we show that i) a large fraction (60–80%) of ORF size-frequency distributions can be predicted a priori with a stochastic assembly model based on GC content, and that (ii) size-frequency distributions of the remaining “non-random” ORFs are well-fitted by log-normal or gamma distributions, and similar to the size distributions of annotated proteins. Conclusions/Significance Our findings suggest stochastic processes have played a primary role in the evolution of genome complexity, and that common processes govern the conservation and loss of functional genomics units in both prokaryotes and eukaryotes. PMID:19649247

  2. An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis.

    PubMed

    Laing, William A; Martínez-Sánchez, Marcela; Wright, Michele A; Bulley, Sean M; Brewster, Di; Dare, Andrew P; Rassam, Maysoon; Wang, Daisy; Storey, Roy; Macknight, Richard C; Hellens, Roger P

    2015-03-01

    Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. PMID:25724639

  3. The upstream open reading frame of cyclin-dependent kinase inhibitor 1A mRNA negatively regulates translation of the downstream main open reading frame

    SciTech Connect

    Kim, Kyoung Mi; Cho, Hana; Kim, Yoon Ki

    2012-08-03

    Highlights: Black-Right-Pointing-Pointer CDKN1A mRNA is a bona fide NMD substrate. Black-Right-Pointing-Pointer The uORF of CDKN1A mRNA is efficiently translated. Black-Right-Pointing-Pointer Translation of downstream main ORF is negatively regulated by translation of uORF in CDKN1A mRNA. -- Abstract: The first round of translation occurs on mRNAs bound by nuclear cap-binding complex (CBC), which is composed of nuclear cap-binding protein 80 and 20 (CBP80/20). During this round of translation, aberrant mRNAs are recognized and downregulated in abundance by nonsense-mediated mRNA decay (NMD), which is one of the mRNA quality control mechanisms. Here, our microarray analysis reveals that the level of cyclin-dependent kinase inhibitor 1A (CDKN1A; also known as Waf1/p21) mRNAs increases in cells depleted of cellular NMD factors. Intriguingly, CDKN1A mRNA contains an upstream open reading frame (uORF), which is a NMD-inducing feature. Using chimeric reporter constructs, we find that the uORF of CDKN1A mRNA negatively modulates translation of the main downstream ORF. These findings provide biological insights into the possible role of NMD in diverse biological pathways mediated by CDKN1A.

  4. The TGA codons are present in the open reading frame of selenoprotein P cDNA

    SciTech Connect

    Hill, K.E.; Lloyd, R.S.; Read, R.; Burk, R.F. )

    1991-03-11

    The TGA codon in DNA has been shown to direct incorporation of selenocysteine into protein. Several proteins from bacteria and animals contain selenocysteine in their primary structures. Each of the cDNA clones of these selenoproteins contains one TGA codon in the open reading frame which corresponds to the selenocysteine in the protein. A cDNA clone for selenoprotein P (SeP), obtained from a {gamma}ZAP rat liver library, was sequenced by the dideoxy termination method. The correct reading frame was determined by comparison of the deduced amino acid sequence with the amino acid sequence of several peptides from SeP. Using SeP labelled with {sup 75}Se in vivo, the selenocysteine content of the peptides was verified by the collection of carboxymethylated {sup 77}Se-selenocysteine as it eluted from the amino acid analyzer and determination of the radioactivity contained in the collected samples. Ten TGA codons are present in the open reading frame of the cDNA. Peptide fragmentation studies and the deduced sequence indicate that selenium-rich regions are located close to the carboxy terminus. Nine of the 10 selenocysteines are located in the terminal 26% of the sequence with four in the terminal 15 amino acids. The deduced sequence codes for a protein of 385 amino acids. Cleavage of the signal peptide gives the mature protein with 366 amino acids and a calculated mol wt of 41,052 Da. Searches of PIR and SWISSPROT protein databases revealed no similarity with glutathione peroxidase or other selenoproteins.

  5. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  6. Identification and characterization of the herpes simplex virus type 1 protein encoded by the UL37 open reading frame.

    PubMed Central

    Shelton, L S; Pensiero, M N; Jenkins, F J

    1990-01-01

    The UL37 open reading frame of the herpes simplex virus type 1 (HSV-1) DNA genome is located between map units 0.527 and 0.552. We have identified and characterized the UL37 protein product in HSV-1-infected cells. The presence of the UL37 protein was detected by using a polyclonal rabbit antiserum directed against an in vitro-translated product derived from an in vitro-transcribed UL37 mRNA. The UL37 open reading frame encodes for a protein with an apparent molecular mass of 120 kDa in HSV-1-infected cells; the protein's mass was assigned on the basis of its migration in sodium dodecyl sulfate-polyacrylamide gels. The UL37 protein is not present at detectable levels in purified HSV-1 virions, suggesting that it is not a structural protein. Analysis of time course experiments and experiments using DNA synthesis inhibitors demonstrated that the UL37 protein is expressed prior to the onset of viral DNA synthesis, reaching maximum levels late in infection, classifying it as a gamma 1 gene. Elution of HSV-1-infected cell proteins from single-stranded DNA agarose columns by using a linear KCl gradient demonstrated that the UL37 protein elutes from this matrix at a salt concentration similar to that observed for ICP8, the major HSV-1 DNA-binding protein. In addition, computer-assisted analysis revealed a potential ATP-binding domain in the predicted UL37 amino acid sequence. On the basis of the kinetics of appearance and DNA-binding properties, we hypothesize that UL37 represents a newly recognized HSV-1 DNA-binding protein that may be involved in late events in viral replication. Images PMID:2173782

  7. Re(de)fining the orthographic neighborhood: the role of addition and deletion neighbors in lexical decision and reading.

    PubMed

    Davis, Colin J; Perea, Manuel; Acha, Joana

    2009-10-01

    The influence of addition and deletion neighbors on visual word identification was investigated in four experiments. Experiments 1 and 2 used Spanish stimuli. In Experiment 1, lexical decision latencies were slower and less accurate for words and nonwords with higher-frequency deletion neighbors (e.g., jugar in juzgar), relative to control stimuli. Experiment 2 showed a similar interference effect for words and nonwords with higher-frequency addition neighbors (e.g., conejo, which has the addition neighbor consejo), relative to control stimuli. Experiment 3 replicated this addition neighbor interference effect in a lexical decision experiment with English stimuli. Across all three experiments, interference effects were always evident for addition/deletion neighbors with word-outer overlap, usually present for those with word-initial overlap, but never present for those with word-final overlap. Experiment 4 replicated the addition/deletion neighbor inhibitory effects in a Spanish sentence reading task in which the participants' eye movements were monitored. These findings suggest that conventional orthographic neighborhood metrics should be redefined. In addition to its methodological implications, this conclusion has significant theoretical implications for input coding schemes and the mechanisms underlying word recognition. PMID:19803656

  8. Additive Effects of Stimulus Quality and Word Frequency on Eye Movements during Chinese Reading

    ERIC Educational Resources Information Center

    Liu, Pingping; Li, Xingshan; Han, Buxin

    2015-01-01

    Eye movements of Chinese readers were recorded for sentences in which high- and low-frequency target words were presented normally or with reduced stimulus quality in two experiments. We found stimulus quality and word frequency produced strong additive effects on fixation durations for target words. The results demonstrate that stimulus quality…

  9. [Identification of the open reading frame coding transposase of Bordetella pertussis RS-element].

    PubMed

    Vorontsov, V V; Sivov, I G; Umiarov, A M; Siniashina, L N; Bol'shakova, T N; Dobrynina, O Iu; Molchanova, M L; Amelina, I P; Rudnev, I A; Karataev, G I

    2004-01-01

    A computer-aided analysis of the repeating sequence of Bordetella pertussis chromosome (RSBP3) revealed 3 open reading frames, one of whose (ORF1) can code a protein whose structure and properties are similar to those of transposasas, i.e. enzymes in charges for the traveling of migrating genetic elements of pro- and eukaryote. Mutants of the RSBP3 insertion sequence with the affected and unaffected ORF1 sequence were constructed in order to substantiate the above assumption. Two independent experimental models (formation of inter-plasmid co-integrates and of co-integrates between plasmid and E. coli chromosome) were used to show that the RSBP3-stimulated formation of co-integrates is only true for plasmids containing RSBP3 with the unaffected ORF1 sequence. An activity of the Hpr protein (a component of the phosphoenolpyruvate-dependent phosphotransferase) was proven to influence the formation process of inter-plasmid co-integrates. PMID:15164716

  10. Antisense overlapping open reading frames in genes from bacteria to humans.

    PubMed Central

    Merino, E; Balbás, P; Puente, J L; Bolívar, F

    1994-01-01

    Long Open Reading Frames (ORFs) in antisense DNA strands have been reported in the literature as being rare events. However, an extensive analysis of the GenBank database revealed that a substantial number of genes from several species contain an in-phase ORF in the antisense strand, that overlaps entirely the coding sequence of the sense strand, or even extends beyond. The findings described in this paper show that this is a frequent, non-random phenomenon, which is primarily dependent on codon usage, and to a lesser extent on gene size and GC content. Examination of the sequence database for several prokaryotic and eukaryotic organisms, demonstrates that coding sequences with in-phase, 100% overlapping antisense ORFs are present in every genome studied so far. PMID:8208617

  11. Minimum probe length for unique identification of all open reading frames in a microbial genome

    SciTech Connect

    Sokhansanj, B A; Ng, J; Fitch, J P

    2000-03-05

    In this paper, we determine the minimum hybridization probe length to uniquely identify at least 95% of the open reading frame (ORF) in an organism. We analyze the whole genome sequences of 17 species, 11 bacteria, 4 archaea, and 2 eukaryotes. We also present a mathematical model for minimum probe length based on assuming that all ORFs are random, of constant length, and contain an equal distribution of bases. The model accurately predicts the minimum probe length for all species, but it incorrectly predicts that all ORFs may be uniquely identified. However, a probe length of just 9 bases is adequate to identify over 95% of the ORFs for all 15 prokaryotic species we studied. Using a minimum probe length, while accepting that some ORFs may not be identified and that data will be lost due to hybridization error, may result in significant savings in microarray and oligonucleotide probe design.

  12. The Equine Herpesvirus 2 E1 Open Reading Frame Encodes a Functional Chemokine Receptor

    PubMed Central

    Camarda, Grazia; Spinetti, Gaia; Bernardini, Giovanni; Mair, Catherine; Davis-Poynter, Nick; Capogrossi, Maurizio C.; Napolitano, Monica

    1999-01-01

    Several herpesviruses contain open reading frames (ORFs) that encode potential homologs of eucaryotic genes. Equine herpesvirus 2 (EHV-2) is a gammaherpesvirus related to other lymphotropic herpesviruses such as herpesvirus saimiri and Epstein-Barr virus. The E1 ORF of EHV-2, a G protein-coupled receptor homolog, shows 31 to 47% amino acid identity with known CC chemokine receptors. To investigate whether E1 may encode a functional receptor, we cloned the E1 ORF and expressed it in stably transfected cell lines. We report here the identification of the CC chemokine eotaxin as a functional ligand for the EHV-2 E1 receptor. Chemokines are likely to play a role in the regulation of immune functions in equine hosts during EHV-2 infection and, via interaction with E1, may affect viral replication and/or escape from immune responses. PMID:10559296

  13. Fission yeast retrotransposon Tf1 integration is targeted to 5′ ends of open reading frames

    PubMed Central

    Behrens, Ralf; Hayles, Jacky; Nurse, Paul

    2000-01-01

    Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100–420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed. PMID:11095681

  14. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

    PubMed Central

    Raj, Anil; Wang, Sidney H; Shim, Heejung; Harpak, Arbel; Li, Yang I; Engelmann, Brett; Stephens, Matthew; Gilad, Yoav; Pritchard, Jonathan K

    2016-01-01

    Accurate annotation of protein coding regions is essential for understanding how genetic information is translated into function. We describe riboHMM, a new method that uses ribosome footprint data to accurately infer translated sequences. Applying riboHMM to human lymphoblastoid cell lines, we identified 7273 novel coding sequences, including 2442 translated upstream open reading frames. We observed an enrichment of footprints at inferred initiation sites after drug-induced arrest of translation initiation, validating many of the novel coding sequences. The novel proteins exhibit significant selective constraint in the inferred reading frames, suggesting that many are functional. Moreover, ~40% of bicistronic transcripts showed negative correlation in the translation levels of their two coding sequences, suggesting a potential regulatory role for these novel regions. Despite known limitations of mass spectrometry to detect protein expressed at low level, we estimated a 14% validation rate. Our work significantly expands the set of known coding regions in humans. DOI: http://dx.doi.org/10.7554/eLife.13328.001 PMID:27232982

  15. Mitochondrial intronic open reading frames in Podospora: Mobility and consecutive exonic sequence variations

    SciTech Connect

    Sellem, C.H.; Rossignol, M.; Belcour, L.

    1996-06-01

    The mitochondrial genome of 23 wild-type strains belonging to three different species of the filamentous fungus Podospora was examined. Among the 15 optical sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes. 46 refs., 5 figs., 2 tabs.

  16. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics

    PubMed Central

    Fermin, Damian; Allen, Baxter B; Blackwell, Thomas W; Menon, Rajasree; Adamski, Marcin; Xu, Yin; Ulintz, Peter; Omenn, Gilbert S; States, David J

    2006-01-01

    Background Defining the location of genes and the precise nature of gene products remains a fundamental challenge in genome annotation. Interrogating tandem mass spectrometry data using genomic sequence provides an unbiased method to identify novel translation products. A six-frame translation of the entire human genome was used as the query database to search for novel blood proteins in the data from the Human Proteome Organization Plasma Proteome Project. Because this target database is orders of magnitude larger than the databases traditionally employed in tandem mass spectra analysis, careful attention to significance testing is required. Confidence of identification is assessed using our previously described Poisson statistic, which estimates the significance of multi-peptide identifications incorporating the length of the matching sequence, number of spectra searched and size of the target sequence database. Results Applying a false discovery rate threshold of 0.05, we identified 282 significant open reading frames, each containing two or more peptide matches. There were 627 novel peptides associated with these open reading frames that mapped to a unique genomic coordinate placed within the start/stop points of previously annotated genes. These peptides matched 1,110 distinct tandem MS spectra. Peptides fell into four categories based upon where their genomic coordinates placed them relative to annotated exons within the parent gene. Conclusion This work provides evidence for novel alternative splice variants in many previously annotated genes. These findings suggest that annotation of the genome is not yet complete and that proteomics has the potential to further add to our understanding of gene structures. PMID:16646984

  17. Expression and strain variation of the novel “Small Open Reading Frame” 3 (smorf) multigene family in Babesia bovis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Small open reading frame (smorf) genes comprise the second largest Babesia bovis multigene family. All known 44 variant smorf genes are located in close chromosomal proximity to ves1 genes, which encode proteins that mediate cytoadhesion and contribute to immune evasion. In this study, we characte...

  18. Openness to Experience and Night-Sky Watching Interest as Predictors of Reading for Pleasure: Path Analysis of a Mediation Model

    ERIC Educational Resources Information Center

    Kelly, William E.

    2010-01-01

    The relation between reading for pleasure, night-sky watching interest, and openness to experience were examined in a sample of 129 college students. Results of a path analysis examining a mediation model indicated that the influence of night-sky interest on reading for pleasure was not mediated by the broad personality domain openness to…

  19. Implementation Work at Scale: An Examination of the Fidelity of Implementation Study of the Scale-Up Effectiveness Trial of Open Court Reading

    ERIC Educational Resources Information Center

    Sullivan, Kate; Bell, Nance; Jones, Debra Hughes; Caverly, Sarah; Vaden-Kiernan, Michael

    2016-01-01

    The Fidelity of Implementation (FOI) study that is the focus of this report was conducted as a component of a scale-up effectiveness trial of the SRA/McGraw-Hill Open Court Reading program. The overall purpose of the FOI study was to support and provide context for findings from the larger experimental impact study of Open Court Reading (OCR). To…

  20. Expression and strain variation of the novel “small open reading frame” (smorf) multigene family in Babesia bovis

    PubMed Central

    Ferreri, Lucas M.; Brayton, Kelly A.; Sondgeroth, Kerry S.; Lau, Audrey O.T.; Suarez, Carlos E.; McElwain, Terry F.

    2012-01-01

    Small open reading frame (smorf) genes comprise the second largest Babesia bovis multigene family. All known 44 variant smorf genes are located in close chromosomal proximity to ves1 genes, which encode proteins that mediate cytoadhesion and contribute to immune evasion. In this study, we characterised the general topology of smorf genes and investigated the gene repertoire, transcriptional profile and SMORF expression in two distinct strains, T2Bo and Mo7. Sequence analysis using degenerate primers identified additional smorf genes in each strain and demonstrated that the smorf gene repertoire varies between strains, with conserved and unique genes in both. Smorf genes have multiple semi-conserved and variable blocks, and a large hypervariable insertion in 20 of the 44 genes defines two major branches of the family, termed smorf A and smorf B. A total of 32 smorf genes are simultaneously transcribed in T2Bo strain B. bovis merozoites obtained from deep brain tissue of an acutely infected animal. SMORF peptide-specific antiserum bound in immunoblots to multiple proteins with a range of sizes predicted by smorf genes, confirming translation of smorf gene products from these transcripts. These results indicate that the smorf multigene family is larger than previously described and demonstrate that smorf genes are expressed and are undergoing variation, both within strains and in a lineage-specific pattern independent of strain specificity. The function of these novel proteins is unknown. PMID:22138017

  1. Translation of the human erythropoietin transcript is regulated by an upstream open reading frame in response to hypoxia.

    PubMed

    Barbosa, Cristina; Romão, Luísa

    2014-05-01

    Erythropoietin (EPO) is a key mediator hormone for hypoxic induction of erythropoiesis that also plays important nonhematopoietic functions. It has been shown that EPO gene expression regulation occurs at different levels, including transcription and mRNA stabilization. In this report, we show that expression of EPO is also regulated at the translational level by an upstream open reading frame (uORF) of 14 codons. As judged by comparisons of protein and mRNA levels, the uORF acts as a cis-acting element that represses translation of the main EPO ORF in unstressed HEK293, HepG2, and HeLa cells. However, in response to hypoxia, this repression is significantly released, specifically in HeLa cells, through a mechanism that involves processive scanning of ribosomes from the 5' end of the EPO transcript and enhanced ribosome bypass of the uORF. In addition, we demonstrate that in HeLa cells, hypoxia induces the phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) concomitantly with a significant increase of EPO protein synthesis. These findings provide a framework for understanding that production of high levels of EPO induced by hypoxia also involves regulation at the translational level. PMID:24647661

  2. A novel sweet potato potyvirus open reading frame (ORF) is expressed via polymerase slippage and suppresses RNA silencing

    PubMed Central

    Untiveros, Milton; Olspert, Allan; Artola, Katrin

    2016-01-01

    Summary The single‐stranded, positive‐sense RNA genome of viruses in the genus Potyvirus encodes a large polyprotein that is cleaved to yield 10 mature proteins. The first three cleavage products are P1, HCpro and P3. An additional short open reading frame (ORF), called pipo, overlaps the P3 region of the polyprotein ORF. Four related potyviruses infecting sweet potato (Ipomoea batatas) are predicted to contain a third ORF, called pispo, which overlaps the 3′ third of the P1 region. Recently, pipo has been shown to be expressed via polymerase slippage at a conserved GA6 sequence. Here, we show that pispo is also expressed via polymerase slippage at a GA6 sequence, with higher slippage efficiency (∼5%) than at the pipo site (∼1%). Transient expression of recombinant P1 or the ‘transframe’ product, P1N‐PISPO, in Nicotiana benthamiana suppressed local RNA silencing (RNAi), but only P1N‐PISPO inhibited short‐distance movement of the silencing signal. These results reveal that polymerase slippage in potyviruses is not limited to pipo expression, but can be co‐opted for the evolution and expression of further novel gene products. PMID:26757490

  3. A novel sweet potato potyvirus open reading frame (ORF) is expressed via polymerase slippage and suppresses RNA silencing.

    PubMed

    Untiveros, Milton; Olspert, Allan; Artola, Katrin; Firth, Andrew E; Kreuze, Jan F; Valkonen, Jari P T

    2016-09-01

    The single-stranded, positive-sense RNA genome of viruses in the genus Potyvirus encodes a large polyprotein that is cleaved to yield 10 mature proteins. The first three cleavage products are P1, HCpro and P3. An additional short open reading frame (ORF), called pipo, overlaps the P3 region of the polyprotein ORF. Four related potyviruses infecting sweet potato (Ipomoea batatas) are predicted to contain a third ORF, called pispo, which overlaps the 3' third of the P1 region. Recently, pipo has been shown to be expressed via polymerase slippage at a conserved GA6 sequence. Here, we show that pispo is also expressed via polymerase slippage at a GA6 sequence, with higher slippage efficiency (∼5%) than at the pipo site (∼1%). Transient expression of recombinant P1 or the 'transframe' product, P1N-PISPO, in Nicotiana benthamiana suppressed local RNA silencing (RNAi), but only P1N-PISPO inhibited short-distance movement of the silencing signal. These results reveal that polymerase slippage in potyviruses is not limited to pipo expression, but can be co-opted for the evolution and expression of further novel gene products. PMID:26757490

  4. Flatworms have lost the right open reading frame kinase 3 gene during evolution

    PubMed Central

    Breugelmans, Bert; Ansell, Brendan R. E.; Young, Neil D.; Amani, Parisa; Stroehlein, Andreas J.; Sternberg, Paul W.; Jex, Aaron R.; Boag, Peter R.; Hofmann, Andreas; Gasser, Robin B.

    2015-01-01

    All multicellular organisms studied to date have three right open reading frame kinase genes (designated riok-1, riok-2 and riok-3). Current evidence indicates that riok-1 and riok-2 have essential roles in ribosome biosynthesis, and that the riok-3 gene assists this process. In the present study, we conducted a detailed bioinformatic analysis of the riok gene family in 25 parasitic flatworms (platyhelminths) for which extensive genomic and transcriptomic data sets are available. We found that none of the flatworms studied have a riok-3 gene, which is unprecedented for multicellular organisms. We propose that, unlike in other eukaryotes, the loss of RIOK-3 from flatworms does not result in an evolutionary disadvantage due to the unique biology and physiology of this phylum. We show that the loss of RIOK-3 coincides with a loss of particular proteins associated with essential cellular pathways linked to cell growth and apoptosis. These findings indicate multiple, key regulatory functions of RIOK-3 in other metazoan species. Taking advantage of a known partial crystal structure of human RIOK-1, molecular modelling revealed variability in nucleotide binding sites between flatworm and human RIOK proteins. PMID:25976756

  5. Overlapping open reading frames revealed by complete nucleotide sequencing of turnip yellow mosaic virus genomic RNA.

    PubMed Central

    Morch, M D; Boyer, J C; Haenni, A L

    1988-01-01

    The complete nucleotide sequence of turnip yellow mosaic virus (TYMV) genomic RNA has been determined on a set of overlapping cDNA clones using a sequential sequencing strategy. The RNA is 6318 nucleotides long, excluding the cap structure. The genome organization deduced from the sequence confirms previous results of in vitro translation. A novel open reading frame (ORF) putatively encoding a Pro-rich and very basic 69K (K = kilodalton) protein is detected at the 5' end of the genome. It is initiated at the first AUG codon on the RNA and overlaps the major ORF that encodes the non structural 206K (previously referred to as 195K) protein of TYMV; its function is unknown. Several amino acid consensus sequences already described among plant and animal viruses are also found in the TYMV-encoded polypeptides. A comparison with other viruses whose RNA sequence is known leads to the conclusion that TYMV belongs to the "Sindbis-like" supergroup of viruses and could be related to Semliki forest virus. PMID:3399388

  6. Open reading frame 2 of porcine circovirus type 2 encodes a major capsid protein.

    PubMed

    Nawagitgul, P; Morozov, I; Bolin, S R; Harms, P A; Sorden, S D; Paul, P S

    2000-09-01

    Porcine circovirus 2 (PCV2), a single-stranded DNA virus associated with post-weaning multisystemic wasting syndrome of swine, has two potential open reading frames, ORF1 and ORF2, greater than 600 nucleotides in length. ORF1 is predicted to encode a replication-associated protein (Rep) essential for replication of viral DNA, while ORF2 contains a conserved basic amino acid sequence at the N terminus resembling that of the major structural protein of chicken anaemia virus. Thus far, the structural protein(s) of PCV2 have not been identified. In this study, a viral structural protein of 30 kDa was identified in purified PCV2 particles. ORF2 of PCV2 was cloned into a baculovirus expression vector and the gene product was expressed in insect cells. The expressed ORF2 gene product had a molecular mass of 30 kDa, similar to that detected in purified virus particles. The recombinant ORF2 protein self-assembled to form capsid-like particles when viewed by electron microscopy. Antibodies against the ORF2 protein were detected in samples of sera obtained from pigs as early as 3 weeks after experimental infection with PCV2. These results show that the major structural protein of PCV2 is encoded by ORF2 and has a molecular mass of 30 kDa. PMID:10950986

  7. Translation efficiency of mRNAs is increased by antisense oligonucleotides targeting upstream open reading frames.

    PubMed

    Liang, Xue-Hai; Shen, Wen; Sun, Hong; Migawa, Michael T; Vickers, Timothy A; Crooke, Stanley T

    2016-08-01

    Increasing the levels of therapeutic proteins in vivo remains challenging. Antisense oligonucleotides (ASOs) are often used to downregulate gene expression or to modify RNA splicing, but antisense technology has not previously been used to directly increase the production of selected proteins. Here we used a class of modified ASOs that bind to mRNA sequences in upstream open reading frames (uORFs) to specifically increase the amounts of protein translated from a downstream primary ORF (pORF). Using ASO treatment, we increased the amount of proteins expressed from four genes by 30-150% in a dose-dependent manner in both human and mouse cells. Notably, systemic treatment of mice with ASO resulted in an ∼80% protein increase of LRPPRC. The ASO-mediated increase in protein expression was sequence-specific, occurred at the level of translation and was dependent on helicase activity. We also found that the type of RNA modification and the position of modified nucleotides in ASOs affected translation of a pORF. ASOs are a useful class of therapeutic agents with broad utility. PMID:27398791

  8. A Conserved Upstream Open Reading Frame Mediates Sucrose-Induced Repression of TranslationW⃞

    PubMed Central

    Wiese, Anika; Elzinga, Nico; Wobbes, Barry; Smeekens, Sjef

    2004-01-01

    Sugars have been shown to regulate transcription of numerous genes in plants. Sucrose controls translation of the group S basic region leucine zipper (bZIP)-type transcription factor ATB2/AtbZIP11 (Rook et al., 1998a). This control requires the unusually long 5′ untranslated region (UTR) of the gene. Point mutations and deletions of the 5′UTR have uncovered the sequences involved. A highly conserved upstream open reading frame (uORF) coding for 42 amino acids is essential for the repression mechanism. It is conserved in 5′UTRs of bZIP transcription factors from other Arabidopsis thaliana genes and many other plants. ATB2/AtbZIP11 is normally expressed in association with vascular tissues. Ectopic expression of a 5′UTR construct shows that the sucrose repression system is functional in all tissues. AtbZIP2 is another Arabidopsis bZIP transcription factor gene harboring the conserved uORF, which is regulated similarly via sucrose-induced repression of translation. This suggests a general function of the conserved uORF in sucrose-controlled regulation of expression. Our findings imply the operation of a sucrose-sensing pathway that controls translation of several plant bZIP transcription factor genes harboring the conserved uORF in their 5′UTRs. Target genes of such transcription factors will then be regulated in sucrose-dependent way. PMID:15208401

  9. Accumulation of RNA homologous to human papillomavirus type 16 open reading frames in genital precancers

    SciTech Connect

    Crum, C.P.; Nuovo, G.; Friedman, D.; Silverstein, S.J.

    1988-01-01

    The accumulation of human papillomavirus type 16 (HPV-16)-specific RNAs in tissue sections from biopsies of patients with genital precancers was studied by in situ hybridization with single-stranded /sup 35/S-labeled RNA. These analyses revealed that the most abundant early-region RNAs were derived from the E4 and E5 open reading frames (ORFs). RNAs homologous to the E6/E7 ORFs were also detected, whereas RNAs homologous to the intervening E1 ORF were not. This suggest that the E4 and E5 mRNAs are derived by splicing to the upstream E6/E7 ORFs, consistent with studies of HPV-11 in condylomata. Abundant RNAs homologous to the 5' portion of L1 were also detected. These RNAs were localized to the apical strata of the epithelium. HPV-16 RNAs accumulated in discrete regions of these lesions, and when present were most abundant in the upper cell layers of the precancerous epithelium. RNAs homologous to early ORFs were also detected in some germinal cells within the basal layer of the epithelium.

  10. Increasing Word-Reading Speed in Poor Readers: No Additional Benefits of Explicit Letter-Cluster Training

    ERIC Educational Resources Information Center

    Marinus, Eva; de Jong, Peter; van der Leij, Aryan

    2012-01-01

    The present study examined whether explicit training of letter-clusters leads to more gains in word-reading speed than training of the separate letters of the same clusters. Ninety-nine poor reading second-grade children were randomly assigned to a cluster-training, a parallel letter-training, or a no-training condition. The cluster-training…

  11. The Maize TFome – development of a transcription factor open reading frame collection for functional genomics

    PubMed Central

    Burdo, Brett; Gray, John; Goetting-Minesky, Mary P; Wittler, Bettina; Hunt, Matthew; Li, Tai; Velliquette, David; Thomas, Julie; Gentzel, Irene; Brito, Michael dos Santos; Mejía-Guerra, Maria Katherine; Connolly, Layne N; Qaisi, Dalya; Li, Wei; Casas, Maria I; Doseff, Andrea I; Grotewold, Erich

    2014-01-01

    Establishing the architecture of the gene regulatory networks (GRNs) responsible for controlling the transcription of all genes in an organism is a natural development that follows elucidation of the genome sequence. Reconstruction of the GRN requires the availability of a series of molecular tools and resources that so far have been limited to a few model organisms. One such resource consists of collections of transcription factor (TF) open reading frames (ORFs) cloned into vectors that facilitate easy expression in plants or microorganisms. In this study, we describe the development of a publicly available maize TF ORF collection (TFome) of 2034 clones corresponding to 2017 unique gene models in recombination-ready vectors that make possible the facile mobilization of the TF sequences into a number of different expression vectors. The collection also includes several hundred co-regulators (CoREGs), which we classified into well-defined families, and for which we propose here a standard nomenclature, as we have previously done for TFs. We describe the strategies employed to overcome the limitations associated with cloning ORFs from a genome that remains incompletely annotated, with a partial full-length cDNA set available, and with many TF/CoREG genes lacking experimental support. In many instances this required the combination of genome-wide expression data with gene synthesis approaches. The strategies developed will be valuable for developing similar resources for other agriculturally important plants. Information on all the clones generated is available through the GRASSIUS knowledgebase (http://grassius.org/). PMID:25053252

  12. Borrelia burgdorferi supercoiled plasmids encode multicopy tandem open reading frames and a lipoprotein gene family.

    PubMed Central

    Porcella, S F; Popova, T G; Akins, D R; Li, M; Radolf, J D; Norgard, M V

    1996-01-01

    DNA sequencing and Southern blot analyses of a Borrelia burgdorferi DNA fragment encoding a signal sequence led to the discovery of a genetic locus, designated 2.9, which appears to be present in at least seven copies in virulent B. burgdorferi 297. DNA sequence analysis of these regions revealed that each 2.9 locus contained an operon of four genes (ABCD) and open reading frames designated rep+ (positive strand) and rep- (negative strand) which encoded multiple repeat motifs. Downstream of the rep+ gene(s) in six of the completely cloned and sequenced 2.9 loci also were lipoprotein (LP) genes possessing highly similar signal sequences but encoding variable mature polypeptides. The lipoproteins could he separated into two classes on the basis of hydrophilicity profiles, sequence similarities, and reactivity with specific antibodies. The 2.9 loci were localized to two (20- and 30-kb) supercoiled plasmids in B. burgdorferi 297. Northern (RNA) blot analysis established that the 2.9 ABCD operon was only minimally expressed, whereas the rep- gene(s) and at least three of the seven LP genes were expressed by B. burgdorferi in vitro. A single putative promoter element was identified by RNA primer extension analysis upstream of the ABCD operon, whereas a number of potential promoter regions existed upstream of the LP genes. The combined data indicate that the ABCD operon, rep+ and rep- genes, and LP genes are separately transcribed during in vitro growth. The 2.9 loci possess a repetitiveness, diversity, and complexity not previously described for B. burgdorferi; differential expression of these genes may facilitate the spirochete's ability to survive in diverse host environments. PMID:8655511

  13. Phenotypic properties of herpes simplex virus 1 containing a derepressed open reading frame P gene.

    PubMed Central

    Lagunoff, M; Randall, G; Roizman, B

    1996-01-01

    Open reading frame P (ORF P) maps in the viral DNA sequences transcribed during latency and is located antisense to the gamma 1 34.5 gene. Earlier studies have shown that the expression of ORF P is repressed by an infected cell protein no. 4 binding site straddling the transcription initiation site. We have made monospecific polyclonal antibodies to the protein and constructed a virus, designated ORF P++, in which the infected cell protein no. 4 binding site has been mutagenized, thereby allowing full expression of an unmodified ORF P gene from its natural promoter. We report the following findings. (i) The native protein forms multiple bands on denaturing polyacrylamide gels suggestive of extensive processing and aggregation of the protein; (ii) the protein accumulates in the nucleus in rod-shaped structures perpendicular to the axis of attachment of the infected cell to the solid matrix; (iii) the virus was highly attenuated on inoculation into mice by the intracerebral or ocular route, and virus was not recovered upon explantation of trigeminal ganglia; (iv) although protein synthesis was not prematurely shut off in the human neuroblastoma cell line SK-N-SH, gamma 1 34.5 protein was not detected in immunoblasts. Analyses of electrophoretically separated denatured RNAs indicated that in cells infected with the ORF P++ virus, there was a large increase in the amount of ORF P RNA and a corresponding decrease in the amount of gamma 1 34.5 RNA. We conclude that either the overproduction of ORF P protein blocks the expression of some herpes simplex virus 1 genes or derepression of the transcription of ORF P has a negative effect on the transcription of the antisense gamma 1 34.5 RNA. PMID:8627705

  14. Tying Down Loose Ends in the Chlamydomonas Genome: Functional Significance of Abundant Upstream Open Reading Frames

    PubMed Central

    Cross, Frederick R.

    2015-01-01

    The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. The annotated genome is very rich in open reading frames upstream of the annotated coding sequence (‘uORFs’): almost three quarters of the assigned transcripts have at least one uORF, and frequently more than one. This is problematic with respect to the standard ‘scanning’ model for eukaryotic translation initiation. These uORFs can be grouped into three classes: class 1, initiating in-frame with the coding sequence (CDS) (thus providing a potential in-frame N-terminal extension); class 2, initiating in the 5′ untranslated sequences (5UT) and terminating out-of-frame in the CDS; and class 3, initiating and terminating within the 5UT. Multiple bioinformatics criteria (including analysis of Kozak consensus sequence agreement and BLASTP comparisons to the closely related Volvox genome, and statistical comparison to cds and to random sequence controls) indicate that of ∼4000 class 1 uORFs, approximately half are likely in vivo translation initiation sites. The proposed resulting N-terminal extensions in many cases will sharply alter the predicted biochemical properties of the encoded proteins. These results suggest significant modifications in ∼2000 of the ∼20,000 transcript models with respect to translation initiation and encoded peptides. In contrast, class 2 uORFs may be subject to purifying selection, and the existent ones (surviving selection) are likely inefficiently translated. Class 3 uORFs are found in more than half of transcripts, frequently multiple times per transcript; however, they are remarkably similar to random sequence expectations with respect to size, number, and composition, and therefore may in most cases be selectively neutral. PMID:26701783

  15. Tying Down Loose Ends in the Chlamydomonas Genome: Functional Significance of Abundant Upstream Open Reading Frames.

    PubMed

    Cross, Frederick R

    2016-02-01

    The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. The annotated genome is very rich in open reading frames upstream of the annotated coding sequence ('uORFs'): almost three quarters of the assigned transcripts have at least one uORF, and frequently more than one. This is problematic with respect to the standard 'scanning' model for eukaryotic translation initiation. These uORFs can be grouped into three classes: class 1, initiating in-frame with the coding sequence (CDS) (thus providing a potential in-frame N-terminal extension); class 2, initiating in the 5' untranslated sequences (5UT) and terminating out-of-frame in the CDS; and class 3, initiating and terminating within the 5UT. Multiple bioinformatics criteria (including analysis of Kozak consensus sequence agreement and BLASTP comparisons to the closely related Volvox genome, and statistical comparison to cds and to random sequence controls) indicate that of ∼4000 class 1 uORFs, approximately half are likely in vivo translation initiation sites. The proposed resulting N-terminal extensions in many cases will sharply alter the predicted biochemical properties of the encoded proteins. These results suggest significant modifications in ∼2000 of the ∼20,000 transcript models with respect to translation initiation and encoded peptides. In contrast, class 2 uORFs may be subject to purifying selection, and the existent ones (surviving selection) are likely inefficiently translated. Class 3 uORFs are found in more than half of transcripts, frequently multiple times per transcript; however, they are remarkably similar to random sequence expectations with respect to size, number, and composition, and therefore may in most cases be selectively neutral. PMID:26701783

  16. A large interspersed repeat found in mouse DNA contains a long open reading frame that evolves as if it encodes a protein.

    PubMed Central

    Martin, S L; Voliva, C F; Burton, F H; Edgell, M H; Hutchison, C A

    1984-01-01

    DNA sequence analysis of a region contained within a large, interspersed repetitive family of mice reveals a long open reading frame. This sequence extends 978 base pairs between two stop codons, creating a reading frame that is open for 326 amino acids. The DNA sequence in this region is conserved between three distantly related Mus species, as well as between mouse and monkey, in a manner that is characteristic of regions undergoing selection for protein function. PMID:6326120

  17. Sequence variability of Borna disease virus open reading frame II found in human peripheral blood mononuclear cells.

    PubMed Central

    Kishi, M; Arimura, Y; Ikuta, K; Shoya, Y; Lai, P K; Kakinuma, M

    1996-01-01

    A cDNA fragment of the Borna disease virus (BDV) open reading frame II (ORF-II), which encodes a 24-kDa phosphoprotein (p24 [P protein]), was amplified from total RNA of peripheral blood mononuclear cells (PBMC) from three psychiatric inpatients. The amplified cDNA fragments were cloned, sequenced, and analyzed. A total of 15 clones, 5 from each patient, were studied. Intrapatient divergencies of the BDV ORF-II nucleotide sequence were 4.2 to 7.3%, 4.8 to 7.3%, and 2.8 to 7.1% for the three patients, leading to differences of 7.7 to 14.5%, 10.3 to 17.1%, and 6.0 to 16.2%, respectively, in the deduced amino acid sequence for BDV p24. Interpatient divergencies among the 15 clones were 5.9 to 12.7% at the nucleotide level and 12.8 to 28.2% at the amino acid level. Thus, in p24, BDV in human PBMC of the patients undergoes mutation at high rates in vivo. Additionally, we found that the nucleotide sequence of the 15 human BDV ORF-II cDNA clones differed from those of the horse strains V and He/80-1 by 4.2 to 9.3%. However, comparison of the consensus amino acid sequence deduced from the 15 human clones with those of the horse strains revealed no human-specific amino acid residue, suggesting that the BDV infecting humans may be related to that infecting horses. PMID:8523585

  18. Nucleotide sequence of the rpoN gene and characterization of two downstream open reading frames in Pseudomonas aeruginosa.

    PubMed Central

    Jin, S; Ishimoto, K; Lory, S

    1994-01-01

    The rpoN gene of Pseudomonas aeruginosa is required for the expression of a number of diverse genes, ranging from several classes of bacterial adhesins to enzymes for amino acid biosynthesis. The nucleotide sequence of the rpoN gene and its flanking region has been determined. The deduced amino acid sequence of the rpoN product is highly homologous to sequences of RpoN proteins of other microorganisms. Moreover, two open reading frames (ORF1 and ORF2) encoding peptides of 103 and 154 amino acids long, respectively, were found downstream of the rpoN gene. These two ORF products have a high degree of amino acid sequence homology with products of similar ORFs located adjacent to the rpoN genes in other microorganisms. Mutations in either ORF lead to a significant increase in P. aeruginosa generation time when propagated on minimal medium. These mutations had no effect on the expression of pilin or flagellin genes, whose expression depends on RpoN. Complementation analysis showed that the two ORFs are in the same transcriptional unit and the growth defects of the two ORF mutants on minimal medium are due to mutational effects on ORF2. The adverse effect of the ORF mutations on the growth of P. aeruginosa in minimal media can be suppressed by the addition of glutamine but not arginine, glutamate, histidine, or proline. Since rpoN mutants of P. aeruginosa display this same amino acid requirement for growth, the ORF2 product very likely functions as a coinducer of some but not all of the RpoN-controlled genes. Images PMID:8113171

  19. Additivity of Factor Effects in Reading Tasks Is Still a Challenge for Computational Models: Reply to Ziegler, Perry, and Zorzi (2009)

    ERIC Educational Resources Information Center

    Besner, Derek; O'Malley, Shannon

    2009-01-01

    J. C. Ziegler, C. Perry, and M. Zorzi (2009) have claimed that their connectionist dual process model (CDP+) can simulate the data reported by S. O'Malley and D. Besner. Most centrally, they have claimed that the model simulates additive effects of stimulus quality and word frequency on the time to read aloud when words and nonwords are randomly…

  20. Bovine herpesvirus 1 U(s) open reading frame 4 encodes a glycoproteoglycan.

    PubMed Central

    Keil, G M; Engelhardt, T; Karger, A; Enz, M

    1996-01-01

    Sequence analysis of the short unique (Us) segment of the bovine herpesvirus 1 (BHV-1) genome predicted that the Us open reading frame (ORF) 4 encodes a protein with homology to glycoprotein G (gG) of other alpha-herpesviruses (P. Leung-Tack, J.-C. Audonnet, and M. Riviere, Virology 199:409-421, 1994). RNA analysis showed that the Us ORF4 is contained within two transcripts of 3.5 and 1.8 kb. The 3.5 kb RNA represents a structurally bicistronic RNA which encompasses the Us ORF3 and Us ORF4, whereas the 1.8-kb RNA constitutes the monocistronic Us ORF4 mRNA. To identify the predicted BHV-I gG, recombinant vaccinia virus expressing the Us ORF4 was used to raise specific antibodies in rabbits. The antiserum recognized a 65-kDa polypeptide and a very diffusely migrating species of proteins with an apparent molecular mass of between 90 and greater than 240 kDa in supernatants of BHV-1-infected cells which was also precipitated together with 61- and 70-kDa polypeptides from cell-associated proteins. The specificity of the reaction was demonstrated by the absence of these proteins from the supernatant of cells infected with the Us ORF4 deletion mutant BHV-l/gp1-8. Treatment of the immunoprecipitated proteins with glycosidases and chondroitinase AC showed that the 65-kDa protein constitutes gG, which contains both N- and O-linked carbohydrates, and that the high-molecular-mass proteins contain glycosaminoglycans linked to a 65-kDa glycoprotein that is antigenically related to gG. These molecules were therefore named glycoproteoglycan C (gpgG). Pulse chase experiments indicated that gG and gpgG were processed from a common precursor molecule with an apparent molecular mass of 61 kDa via a 70-kDa intermediate. Both gG and gpgG could not be found associated with purified virions. In summary, our results identify the BHV-I gG protein and demonstrate the presence of a form of posttranslational modification, glycosamino-glycosylation, that has not yet been described for a

  1. Opening a Window into Reading Development: Eye Movements' Role Within a Broader Literacy Research Framework.

    PubMed

    Miller, Brett; O'Donnell, Carol

    2013-01-01

    The cumulative body of eye movement research provides significant insight into how readers process text. The heart of this work spans roughly 40 years reflecting the maturity of both the topics under study and experimental approaches used to investigate reading. Recent technological advancements offer increased flexibility to the field providing the potential to more concertedly study reading and literacy from an individual differences perspective. Historically, eye movement research focused far less on developmental issues related to individual differences in reading; however, this issue and the broader change it represents signal a meaningful transition inclusive of individual differences. The six papers in this special issue signify the recent, increased attention to and recognition of eye movement research's transition to emphasize individual differences in reading while appreciating early contributions (e.g., Rayner, 1986) in this direction. We introduce these six papers and provide some historical context for the use of eye movement methodology to examine reading and context for the eye movement field's early transition to examining individual differences, culminating in future research recommendations. PMID:24391304

  2. Prazosin addition to fluvoxamine: A preclinical study and open clinical trial in OCD.

    PubMed

    Feenstra, Matthijs G P; Klompmakers, André; Figee, Martijn; Fluitman, Sjoerd; Vulink, Nienke; Westenberg, Herman G M; Denys, Damiaan

    2016-02-01

    The efficacy of selective serotonin reuptake inhibitors (SRIs) in psychiatric disorders may be "augmented" through the addition of atypical antipsychotic drugs. A synergistic increase in dopamine (DA) release in the prefrontal cortex has been suggested to underlie this augmentation effect, though the mechanism of action is not clear yet. We used in vivo microdialysis in rats to study DA release following the administration of combinations of fluvoxamine (10 mg/kg) and quetiapine (10 mg/kg) with various monoamine-related drugs. The results confirmed that the selective 5-HT1A antagonist WAY-100635 (0.05 mg/kg) partially blocked the fluvoxamine-quetiapine synergistic effect (maximum DA increase dropped from 325% to 214%). A novel finding is that the α1-adrenergic blocker prazosin (1 mg/kg), combined with fluvoxamine, partially mimicked the effect of augmentation (maximum DA increase 205%; area-under-the-curve 163%). As this suggested that prazosin augmentation might be tested in a clinical study, we performed an open clinical trial of prazosin 20 mg addition to SRI in therapy-resistant patients with obsessive-compulsive disorder applying for neurosurgery. A small, non-significant reduction in Yale Brown Obsessive Compulsive Scale (Y-BOCS) scores was observed in 10 patients and one patient was classified as a responder with a reduction in Y-BOCS scores of more than 25%. We suggest that future clinical studies augmenting SRIs with an α1-adrenergic blocker in less treatment resistant cases should be considered. The clinical trial "Prazosin in combination with a serotonin reuptake inhibitor for patients with Obsessive Compulsive disorder: an open label study" was registered at 24/05/2011 under trial number ISRCTN61562706: http://www.controlled-trials.com/ISRCTN61562706. PMID:26712326

  3. Sustaining Composition: Studying Content-Based, Ecological, and Economical Sustainability of Open-Source Textbooks through "Writing Spaces: Readings on Writing"

    ERIC Educational Resources Information Center

    Munson, Margaret

    2013-01-01

    Writing programs in institutions of higher education work to prepare students for real-world writing within any field of study. The composition of "Writing Spaces: Readings on Writing" offers an open-source text for students, teachers, and policy-makers at all levels. Exposure to an open space for learning encourages access to information,…

  4. A cis-Acting Element Present within the gag Open Reading Frame Negatively Impacts on the Activity of the HIV-1 IRES

    PubMed Central

    Valiente-Echeverría, Fernando; Vallejos, Maricarmen; Monette, Anne; Pino, Karla; Letelier, Alejandro; Huidobro-Toro, J. Pablo; Mouland, Andrew J.; López-Lastra, Marcelo

    2013-01-01

    Translation initiation from the human immunodeficiency virus type-1 (HIV-1) mRNA can occur through a cap or an IRES dependent mechanism. Cap-dependent translation initiation of the HIV-1 mRNA can be inhibited by the instability element (INS)-1, a cis-acting regulatory element present within the gag open reading frame (ORF). In this study we evaluated the impact of the INS-1 on HIV-1 IRES-mediated translation initiation. Using heterologous bicistronic mRNAs, we show that the INS-1 negatively impact on HIV-1 IRES-driven translation in in vitro and in cell-based experiments. Additionally, our results show that the inhibitory effect of the INS-1 is not general to all IRESes since it does not hinder translation driven by the HCV IRES. The inhibition by the INS-1 was partially rescued in cells by the overexpression of the viral Rev protein or hnRNPA1. PMID:23451120

  5. Awareness of Inner Dialogues Can Alter Reading Behaviors (Open to Suggestion).

    ERIC Educational Resources Information Center

    Ortiz, Rose Katz

    1996-01-01

    Describes an activity in which students generate questions they ask themselves with regard to reading, becoming aware of their own inner dialog and thus of what they can do to be successful and what they unwittingly do to inhibit their own success. (SR)

  6. Tutoring Opened My Eyes: Tutor Experiences in the America Reads Challenge

    ERIC Educational Resources Information Center

    Lane, Holly B.; Hudson, Roxanne F.; McCray, Erica D.; Tragash, Jennifer R.; Zeig, Jacqueline L.

    2011-01-01

    The America Reads Challenge offers colleges and universities an opportunity to make a contribution to the community while enhancing the education of their students, employing tutoring as a service learning experience. At the same time, their efforts will help the institution develop and sustain community partnerships. This paper reports an…

  7. Open-Trial Pilot of "Mind Reading" and in Vivo Rehearsal for Children with HFASD

    ERIC Educational Resources Information Center

    Thomeer, Marcus L.; Rodgers, Jonathan D.; Lopata, Christopher; McDonald, Christin A.; Volker, Martin A.; Toomey, Jennifer A.; Smith, Rachael A.; Gullo, Gaetano

    2011-01-01

    In this pilot study, the authors evaluated a manualized administration of the "Mind Reading" (MR) program with in vivo rehearsal to determine the effects on emotion recognition and autism features of eleven 7- to 12-year-old children with High-Functioning Autism Spectrum Disorders (HFASD), and to determine the overall feasibility of the…

  8. Quantity, Quality, and Variety of Pupil Responses during an Open-Communication Structured Group Directed Reading-Thinking Activity and a Closed Communication Structured Group Directed Reading Activity.

    ERIC Educational Resources Information Center

    Petre, Richard M.

    The quality, quantity, and variety of pupil responses while using two different group directed reading activities, the Directed Reading Activity (DRA), and the Directed Reading-Thinking Activity (DRTA) were investigated in this study. The subjects, all fourth graders in two nearby communities, were grouped into above-grade-level, at-grade-level,…

  9. Conserved nucleotide sequences in the open reading frame and 3' untranslated region of selenoprotein P mRNA.

    PubMed Central

    Hill, K E; Lloyd, R S; Burk, R F

    1993-01-01

    Rat liver selenoprotein P contains 10 selenocysteine residues in its primary structure (deduced). It is the only selenoprotein characterized to date that has more than one selenocysteine residue. Selenoprotein P cDNA has been cloned from human liver and heart cDNA libraries and sequenced. The open reading frames are identical and contain a signal peptide, indicating that the protein is secreted by both organs and is therefore not exclusively produced in the liver. Ten selenocysteine residues (deduced) are present. Comparison of the open reading frame of the human cDNA with the rat cDNA reveals a 69% identity of the nucleotide sequence and 72% identity of the deduced amino acid sequence. Two regions in the 3' untranslated portion have high conservation between human and rat. Each of these regions contains a predicted stable stem-loop structure similar to the single stem-loop structures reported in 3' untranslated regions of type I iodothyronine 5'-deiodinase and glutathione peroxidase. The stem-loop structure of type I iodothyronine 5'-deiodinase has been shown to be necessary for incorporation of the selenocysteine residue at the UGA codon. Because only two stem-loop structures are present in the 3' untranslated region of selenoprotein P mRNA, it can be concluded that a separate stem-loop structure is not required for each selenocysteine residue. Images PMID:8421687

  10. Additivity of factor effects in reading tasks is still a challenge for computational models: Reply to Ziegler, Perry, and Zorzi (2009).

    PubMed

    Besner, Derek; O'Malley, Shannon

    2009-01-01

    J. C. Ziegler, C. Perry, and M. Zorzi (2009) have claimed that their connectionist dual process model (CDP+) can simulate the data reported by S. O'Malley and D. Besner. Most centrally, they have claimed that the model simulates additive effects of stimulus quality and word frequency on the time to read aloud when words and nonwords are randomly intermixed. This work represents an important attempt given that computational models of reading processes have to date largely ignored the issue of whether it is possible to simulate additive effects. Despite CDP+'s success at capturing many other phenomena, it is clear that CDP+ fails to capture the full pattern seen with skilled readers in these experiments. PMID:19210105

  11. Evolution of rbcL group IA introns and intron open reading frames within the colonial Volvocales (Chlorophyceae).

    PubMed

    Nozaki, Hisayoshi; Takahara, Manabu; Nakazawa, Atsushi; Kita, Yoko; Yamada, Takashi; Takano, Hiroyoshi; Kawano, Shigeyuki; Kato, Masahiro

    2002-06-01

    Mobile group I introns sometimes contain an open reading frame (ORF) possibly encoding a site-specific DNA endonuclease. However, previous phylogenetic studies have not clearly deduced the evolutionary roles of the group I intron ORFs. In this paper, we examined the phylogeny of group IA2 introns inserted in the position identical to that of the chloroplast-encoded rbcL coding region (rbcL-462 introns) and their ORFs from 13 strains of five genera (Volvox, Pleodorina, Volvulina, Astrephomene, and Gonium) of the colonial Volvocales (Chlorophyceae) and a related unicellular green alga, Vitreochlamys. The rbcL-462 introns contained an intact or degenerate ORF of various sizes except for the Gonium multicoccum rbcL-462 intron. Partial amino acid sequences of some rbcL-462 intron ORFs exhibited possible homology to the endo/excinuclease amino acid terminal domain. The distribution of the rbcL-462 introns is sporadic in the phylogenetic trees of the colonial Volvocales based on the five chloroplast exon sequences (6021 bp). Phylogenetic analyses of the conserved intron sequences resolved that the G. multicoccum rbcL-462 intron had a phylogenetic position separate from those of other colonial volvocalean rbcL-462 introns, indicating the recent horizontal transmission of the intron in the G. multicoccum lineage. However, the combined data set from conserved intron sequences and ORFs from most of the rbcL-462 introns resolved robust phylogenetic relationships of the introns that were consistent with those of the host organisms. Therefore, most of the extant rbcL-462 introns may have been vertically inherited from the common ancestor of their host organisms, whereas such introns may have been lost in other lineages during evolution of the colonial Volvocales. In addition, apparently higher synonymous substitutions than nonsynonymous substitutions in the rbcL-462 intron ORFs indicated that the ORFs might evolve under functional constraint, which could result in homing of the

  12. Identification and characterization of the herpes simplex virus type 1 virion protein encoded by the UL35 open reading frame.

    PubMed

    McNabb, D S; Courtney, R J

    1992-05-01

    The UL35 open reading frame (ORF) of herpes simplex virus type 1 (HSV-1) has been predicted from DNA sequence analysis to encode a small polypeptide with a molecular weight of 12,095. We have investigated the protein product of the UL35 ORF by using a trpE-UL35 gene fusion to produce a corresponding fusion protein in Escherichia coli. The TrpE-UL35 chimeric protein was subsequently isolated and used as a source of immunogen for the production of rabbit polyclonal antiserum directed against the UL35 gene product. The TrpE-UL35 antiserum was found to recognize a 12-kDa protein which was specifically present in HSV-1-infected cells. By utilizing the TrpE-UL35 antiserum, the kinetics of synthesis of the UL35 gene product was examined, and these studies indicate that UL35 is expressed as a gamma 2 (true late) gene. The 12-kDa protein recognized by the TrpE-UL35 antiserum was associated with purified HSV-1 virions and type A and B capsids, suggesting that the UL35 ORF may encode the 12-kDa capsid protein variably designated p12, NC7, or VP26. To confirm this assignment, immunoprecipitation and immunoblotting studies were performed to demonstrate that the TrpE-UL35 antiserum reacts with the same polypeptide as an antiserum directed against the purified p12 capsid protein (anti-NC7) (G.H. Cohen, M. Ponce de Leon, H. Diggelmann, W.C. Lawrence, S.K. Vernon, and R.J. Eisenberg, J. Virol. 34:521-531, 1980). Furthermore, the anti-NC7 serum was also found to react with the TrpE-UL35 chimeric protein isolated from E. coli, providing additional evidence that the UL35 gene encodes p12. On the basis of these studies, we conclude that UL35 represents a true late gene which encodes the 12-kDa capsid protein of HSV-1. PMID:1313892

  13. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map.

    PubMed

    Reymond, A; Friedli, M; Henrichsen, C N; Chapot, F; Deutsch, S; Ucla, C; Rossier, C; Lyle, R; Guipponi, M; Antonarakis, S E

    2001-11-01

    A supernumerary copy of human chromosome 21 (HC21) causes Down syndrome. To understand the molecular pathogenesis of Down syndrome, it is necessary to identify all HC21 genes. The first annotation of the sequence of 21q confirmed 127 genes, and predicted an additional 98 previously unknown "anonymous" genes (predictions (PREDs) and open reading frames (C21orfs)), which were foreseen by exon prediction programs and/or spliced expressed sequence tags. These putative gene models still need to be confirmed as bona fide transcripts. Here we report the characterization and expression pattern of the putative transcripts C21orf7, C21orf11, C21orf15, C21orf18, C21orf19, C21orf22, C21orf42, C21orf50, C21orf51, C21orf57, and C21orf58, the GC-rich sequence DNA-binding factor candidate GCFC (also known as C21orf66), PRED12, PRED31, PRED34, PRED44, PRED54, and PRED56. Our analysis showed that most of the C21orfs originally defined by matching spliced expressed sequence tags were correctly predicted, whereas many of the PREDs, defined solely by computer prediction, do not correspond to genuine genes. Four of the six PREDs were incorrectly predicted: PRED44 and C21orf11 are portions of the same transcript, PRED31 is a pseudogene, and PRED54 and PRED56 were wrongly predicted. In contrast, PRED12 (now called C21orf68) and PRED34 (C21orf63) are now confirmed transcripts. We identified three new genes, C21orf67, C21orf69, and C21orf70, not previously predicted by any programs. This revision of the HC21 transcriptome has consequences for the entire genome regarding the quality of previous annotations and the total number of transcripts. It also provides new candidates for genes involved in Down syndrome and other genetic disorders that map to HC21. PMID:11707072

  14. Chicken repeat 1 elements contain a pol-like open reading frame and belong to the non-long terminal repeat class of retrotransposons.

    PubMed Central

    Burch, J B; Davis, D L; Haas, N B

    1993-01-01

    Chicken genomes contain approximately 30,000 chicken repeat 1 (CR1) elements scattered among single-copy sequences, but no information has yet been presented to account for how these elements could have dispersed. The fact that CR1 elements have common (although atypical) 3' ends and variable 5' truncations suggested to us that they might belong to the class of non-long terminal repeat retrotransposons that encode reverse transcriptases. From an analysis of unusually large CR1 elements, we now provide evidence for the presence of such a reverse transcriptase open reading frame. CR1 elements are distantly related to previously described non-long terminal repeat retrotransposons; however, we find that frog and torpedo ray genomes contain dispersed open reading frame segments that have > 50% identity to the CR1 open reading frame. This result suggests that CR1-like elements exist in several vertebrate classes that have evolved independently for approximately 400 million years. PMID:8396264

  15. Varicella-Zoster Virus Open Reading Frame 66 Protein Kinase and Its Relationship to Alphaherpesvirus US3 Kinases

    PubMed Central

    Erazo, Angela

    2014-01-01

    The varicella-zoster virus (VZV) open reading frame (ORF) 66 encodes a basophilic kinase orthologous to the US3 protein kinases found in all alphaherpesviruses. This review summarizes current information on the ORF66 kinase, and outlines apparent differences from other US3 kinases, as well as some of the conserved functions. One critical difference is the VZV ORF66 kinase targeting of the major regulatory VZV IE62 protein to control its nuclear import and assembly into the VZV virion, which is so far unprecedented in the alphaherpesviruses. However, ORF66 targets some cellular targets which are also targeted by US3 kinases of other herpesviruses, including the histone deacetylase-1 and 2 proteins, pathways that lead to changes in actin dynamics, and the targeting of substrates of protein kinase A, including the nuclear matrix protein matrin 3. PMID:20186610

  16. General Open Systems Theory and the Substrata-Factor Theory of Reading.

    ERIC Educational Resources Information Center

    Kling, Martin

    This study was designed to extend the generality of the Substrata-Factor Theory by two methods of investigation: (1) theoretically, to est"blish the validity of the hypothesis that an isomorphic relationship exists between the Substrata-Factor Theory and the General Open Systems Theory, and (2) experimentally, to disc"ver through a series of…

  17. What Oral Text Reading Fluency Can Reveal about Reading Comprehension

    ERIC Educational Resources Information Center

    Veenendaal, Nathalie J.; Groen, Margriet A.; Verhoeven, Ludo

    2015-01-01

    Text reading fluency--the ability to read quickly, accurately and with a natural intonation--has been proposed as a predictor of reading comprehension. In the current study, we examined the role of oral text reading fluency, defined as text reading rate and text reading prosody, as a contributor to reading comprehension outcomes in addition to…

  18. Stimulus modality and working memory performance in Greek children with reading disabilities: additional evidence for the pictorial superiority hypothesis.

    PubMed

    Constantinidou, Fofi; Evripidou, Christiana

    2012-01-01

    This study investigated the effects of stimulus presentation modality on working memory performance in children with reading disabilities (RD) and in typically developing children (TDC), all native speakers of Greek. It was hypothesized that the visual presentation of common objects would result in improved learning and recall performance as compared to the auditory presentation of stimuli. Twenty children, ages 10-12, diagnosed with RD were matched to 20 TDC age peers. The experimental tasks implemented a multitrial verbal learning paradigm incorporating three modalities: auditory, visual, and auditory plus visual. Significant group differences were noted on language, verbal and nonverbal memory, and measures of executive abilities. A mixed-model MANOVA indicated that children with RD had a slower learning curve and recalled fewer words than TDC across experimental modalities. Both groups of participants benefited from the visual presentation of objects; however, children with RD showed the greatest gains during this condition. In conclusion, working memory for common verbal items is impaired in children with RD; however, performance can be facilitated, and learning efficiency maximized, when information is presented visually. The results provide further evidence for the pictorial superiority hypothesis and the theory that pictorial presentation of verbal stimuli is adequate for dual coding. PMID:21942734

  19. Preliminary Findings from a Multi-Year Scale-Up Effectiveness Trial of Open-Court Reading (Imagine It!)

    ERIC Educational Resources Information Center

    Borman, Geoffrey; Vaden-Kiernan, Michael; Caverly, Sarah; Bell, Nance; de Castilla, Veronica Ruiz; Sullivan, Kate

    2015-01-01

    This study addresses the effectiveness of a nationally used core reading program that reflects the research-based practices recommended by the National Reading Panel. This and other similar programs are increasingly used to prevent reading difficulties and ensure that all children are reading at or above grade level by the end of third grade. The…

  20. The Development and Implementation of an Applied Psychology Course Utilizing Behavior Modification Procedures to Supplement a Community College Reading Program for Open Enrollment Students.

    ERIC Educational Resources Information Center

    Kahn, Gloria Batkin

    This study attempted to assess the effect of behavior modification techniques on community college open enrollment students with severe educational deficits. Of 30 suburban New York members of a reading class, half were exposed to direct teaching, instructor praise, peer partners, self and peer ratings, role playing, Premack contracts,…

  1. The expression of the open reading frame of "Arabidopsis" CAX1, but not its cDNA, confers metal tolerance in yeast

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The biochemical properties and regulation of several plant CAX (CAtion eXchanger)-type vacuolar Ca (2+)/H (+) exchangers have been extensively analyzed in yeast expression assays. In the present study, we compare and contrast the phenotypes of yeast cells expressing the CAX1 cDNA and open reading fr...

  2. From Pan-Reactive KV7 Channel Opener to Subtype Selective Opener/Inhibitor by Addition of a Methyl Group

    PubMed Central

    Blom, Sigrid Marie; Rottländer, Mario; Kehler, Jan; Bundgaard, Christoffer; Schmitt, Nicole; Jensen, Henrik Sindal

    2014-01-01

    The voltage-gated potassium channels of the KV7 family (KV7.1–5) play important roles in controlling neuronal excitability and are therefore attractive targets for treatment of CNS disorders linked to hyperexcitability. One of the main challenges in developing KV7 channel active drugs has been to identify compounds capable of discriminating between the neuronally expressed subtypes (KV7.2–5), aiding the identification of the subunit composition of KV7 currents in various tissues, and possessing better therapeutic potential for particular indications. By taking advantage of the structure-activity relationship of acrylamide KV7 channel openers and the effects of these compounds on mutant KV7 channels, we have designed and synthesized a novel KV7 channel modulator with a unique profile. The compound, named SMB-1, is an inhibitor of KV7.2 and an activator of KV7.4. SMB-1 inhibits KV7.2 by reducing the current amplitude and increasing the time constant for the slow component of the activation kinetics. The activation of KV7.4 is seen as an increase in the current amplitude and a slowing of the deactivation kinetics. Experiments studying mutant channels with a compromised binding site for the KV7.2–5 opener retigabine indicate that SMB-1 binds within the same pocket as retigabine for both inhibition of KV7.2 and activation of KV7.4. SMB-1 may serve as a valuable tool for KV7 channel research and may be used as a template for further design of better subtype selective KV7 channel modulators. A compound with this profile could hold novel therapeutic potential such as the treatment of both positive and cognitive symptoms in schizophrenia. PMID:24956197

  3. Characterization of a second open reading frame in genome segment 10 of bluetongue virus

    PubMed Central

    Stewart, Meredith; Hardy, Alexandra; Barry, Gerald; Pinto, Rute Maria; Caporale, Marco; Melzi, Eleonora; Hughes, Joseph; Taggart, Aislynn; Janowicz, Anna; Varela, Mariana

    2015-01-01

    Viruses have often evolved overlapping reading frames in order to maximize their coding capacity. Until recently, the segmented dsRNA genome of viruses of the Orbivirus genus was thought to be monocistronic, but the identification of the bluetongue virus (BTV) NS4 protein changed this assumption. A small ORF in segment 10, overlapping the NS3 ORF in the +1 position, is maintained in more than 300 strains of the 27 different BTV serotypes and in more than 200 strains of the phylogenetically related African horse sickness virus (AHSV). In BTV, this ORF (named S10-ORF2 in this study) encodes a putative protein 50–59 residues in length and appears to be under strong positive selection. HA- or GFP-tagged versions of S10-ORF2 expressed from transfected plasmids localized within the nucleoli of transfected cells, unless a putative nucleolar localization signal was mutated. S10-ORF2 inhibited gene expression, but not RNA translation, in transient transfection reporter assays. In both mammalian and insect cells, BTV S10-ORF2 deletion mutants (BTV8ΔS10-ORF2) displayed similar replication kinetics to wt virus. In vivo, S10-ORF2 deletion mutants were pathogenic in mouse models of disease. Although further evidence is required for S10-ORF2 expression during infection, the data presented provide an initial characterization of this ORF. PMID:26290332

  4. Characterization of a second open reading frame in genome segment 10 of bluetongue virus.

    PubMed

    Stewart, Meredith; Hardy, Alexandra; Barry, Gerald; Pinto, Rute Maria; Caporale, Marco; Melzi, Eleonora; Hughes, Joseph; Taggart, Aislynn; Janowicz, Anna; Varela, Mariana; Ratinier, Maxime; Palmarini, Massimo

    2015-11-01

    Viruses have often evolved overlapping reading frames in order to maximize their coding capacity. Until recently, the segmented dsRNA genome of viruses of the Orbivirus genus was thought to be monocistronic, but the identification of the bluetongue virus (BTV) NS4 protein changed this assumption. A small ORF in segment 10, overlapping the NS3 ORF in the +1 position, is maintained in more than 300 strains of the 27 different BTV serotypes and in more than 200 strains of the phylogenetically related African horse sickness virus (AHSV). In BTV, this ORF (named S10-ORF2 in this study) encodes a putative protein 50-59 residues in length and appears to be under strong positive selection. HA- or GFP-tagged versions of S10-ORF2 expressed from transfected plasmids localized within the nucleoli of transfected cells, unless a putative nucleolar localization signal was mutated. S10-ORF2 inhibited gene expression, but not RNA translation, in transient transfection reporter assays. In both mammalian and insect cells, BTV S10-ORF2 deletion mutants (BTV8ΔS10-ORF2) displayed similar replication kinetics to wt virus. In vivo, S10-ORF2 deletion mutants were pathogenic in mouse models of disease. Although further evidence is required for S10-ORF2 expression during infection, the data presented provide an initial characterization of this ORF. PMID:26290332

  5. Re(de)fining the Orthographic Neighborhood: The Role of Addition and Deletion Neighbors in Lexical Decision and Reading

    ERIC Educational Resources Information Center

    Davis, Colin J.; Perea, Manuel; Acha, Joana

    2009-01-01

    The influence of addition and deletion neighbors on visual word identification was investigated in four experiments. Experiments 1 and 2 used Spanish stimuli. In Experiment 1, lexical decision latencies were slower and less accurate for words and nonwords with higher-frequency deletion neighbors (e.g., "jugar" in "juzgar"), relative to control…

  6. Genomic interspecies microarray hybridization: rapid discovery of three thousand genes in the maize endophyte, Klebsiella pneumoniae 342, by microarray hybridization with Escherichia coli K-12 open reading frames.

    PubMed

    Dong, Y; Glasner, J D; Blattner, F R; Triplett, E W

    2001-04-01

    In an effort to efficiently discover genes in the diazotrophic endophyte of maize, Klebsiella pneumoniae 342, DNA from strain 342 was hybridized to a microarray containing 96% (n = 4,098) of the annotated open reading frames from Escherichia coli K-12. Using a criterion of 55% identity or greater, 3,000 (70%) of the E. coli K-12 open reading frames were also found to be present in strain 342. Approximately 24% (n = 1,030) of the E. coli K-12 open reading frames are absent in strain 342. For 1.6% (n = 68) of the open reading frames, the signal was too low to make a determination regarding the presence or absence of the gene. Genes with high identity between the two organisms are those involved in energy metabolism, amino acid metabolism, fatty acid metabolism, cofactor synthesis, cell division, DNA replication, transcription, translation, transport, and regulatory proteins. Functions that were less highly conserved included carbon compound metabolism, membrane proteins, structural proteins, putative transport proteins, cell processes such as adaptation and protection, and central intermediary metabolism. Open reading frames of E. coli K-12 with little or no identity in strain 342 included putative regulatory proteins, putative chaperones, surface structure proteins, mobility proteins, putative enzymes, hypothetical proteins, and proteins of unknown function, as well as genes presumed to have been acquired by lateral transfer from sources such as phage, plasmids, or transposons. The results were in agreement with the physiological properties of the two strains. Whole genome comparisons by genomic interspecies microarray hybridization are shown to rapidly identify thousands of genes in a previously uncharacterized bacterial genome provided that the genome of a close relative has been fully sequenced. This approach will become increasingly more useful as more full genome sequences become available. PMID:11282649

  7. The Trypanosoma brucei DNA polymerase alpha core subunit gene is developmentally regulated and linked to a constitutively expressed open reading frame.

    PubMed Central

    Leegwater, P A; Strating, M; Murphy, N B; Kooy, R F; van der Vliet, P C; Overdulve, J P

    1991-01-01

    As an initial step towards the characterization of replicative DNA polymerases of trypanosomes, we have cloned, sequenced and examined the expression of the Trypanosoma (Trypanozoon) brucei brucei gene that encodes the DNA polymerase alpha catalytic core (pol alpha). The protein sequence contains the six conserved regions that have been recognized previously in eukaryotic and viral replicative DNA polymerases. In addition, we have identified a seventh region which appears to be conserved primarily in alpha-type DNA polymerases. The T.brucei DNA pol alpha core N-terminus is 123 and 129 amino acids smaller than that of the human and yeast homologue, respectively. The gene is separated by 386 bp from an upstream open reading frame (ORF) of 442 codons. Stable transcripts of the upstream sequence are detected in both dividing and non-dividing forms, while pol alpha transcripts are detected principally in dividing forms. Allelic copies of the T.brucei pol alpha region exhibit restriction site polymorphisms; one such sequence polymorphism affects the amino acid sequence of the T.brucei DNA pol alpha core. The T.brucei pol alpha region cross-hybridizes weakly with that of T.(Nannomonas) congolense and T.(Duttonella) vivax. Images PMID:1754381

  8. A symptom variant of beet curly top geminivirus produced by mutation of open reading frame C4.

    PubMed

    Stanley, J; Latham, J R

    1992-09-01

    Two beet curly top virus (BCTV) mutants have been constructed in vitro that contain G-to-T transversions either at nucleotide 2682 or at nucleotide 2802 within the overlapping open reading frames (ORFs) C1 and C4. The mutations introduce termination codons in ORF C4 without affecting the amino acids encoded by ORF C1. When agroinoculated into Nicotiana benthamiana the mutants caused stunting and yellowing of the plant and downward leaf curl but not the vein swelling and upward leaf curl symptoms that are characteristic of wild-type BCTV infection in this host. Levels of viral single- and double-stranded DNA forms were similar in mutant and wild-type infections. Symptoms induced by one such mutant in Nicotiana clevelandii and Datura stramonium were less severe than those in wild-type infections and were again qualitatively distinct. The mutants caused symptomless infections in Beta vulgaris, contrasting with stunting, severe leaf curl, and vein swelling symptoms associated with wild-type infection of this host. The levels of mutant DNA in newly expanding asymptomatic leaves frequently reached those of wild-type virus in leaves showing severe symptoms. The results suggest that ORF C4 encodes a protein that is a major determinant of pathogenesis that might affect the hyperplastic response of the host to BCTV infection. PMID:1529551

  9. Responses of Nontransformed Human Hepatocytes to Conditional Expression of Full-Length Hepatitis C Virus Open Reading Frame

    PubMed Central

    Tang, Weiliang; Lázaro, Catherine A.; Campbell, Jean S.; Parks, W. Tony; Katze, Michael G.; Fausto, Nelson

    2007-01-01

    Hepatitis C virus (HCV) is a major cause of chronic hepatitis that can lead to cirrhosis and hepatocellular carcinoma. To study the effects of HCV protein expression on host cells, we established conditional expression of the full-length open reading frame (ORF) of an infectious cDNA clone of HCV (genotype 1a, H77 strain) in the nontransformed human hepatocyte line cell HH4 using the ecdysone receptor regulatory system. Treatment with the ecdysone analog ponasterone-A induced tightly regulated and dose-dependent full-length HCV ORF expression and properly processed HCV proteins. HCV Core, NS3, and NS5A colocalized in perinuclear regions and associated with the early endosomal protein EEA1. HCV ORF expression caused marked growth inhibition, increased intracellular reactive oxygen species, up-regulation of glutamate-l-cysteine ligase activity, increased glutathione level, and activation of nuclear factor κB. Although it was not directly cytotoxic, HCV ORF expression sensitized HH4 cells to Fas at certain concentrations but not to tumor necrosis factor-related apoptosis-inducing ligand. HCV ORF expression in HH4 cells up-regulated genes involved in innate immune response/inflammation and oxidative stress responses and down-regulated cell growth-related genes. Expression of HCV ORF in host cells may contribute to HCV pathogenesis by producing oxidative stress and increasing the expression of genes related to the innate immune response and inflammation. PMID:17991716

  10. Functional Analysis of the env Open Reading Frame in Human Endogenous Retrovirus IDDMK1,222 Encoding Superantigen Activity

    PubMed Central

    Lapatschek, Matthias; Dürr, Susanne; Löwer, Roswitha; Magin, Christine; Wagner, Hermann; Miethke, Thomas

    2000-01-01

    Mice harbor a family of endogenous retroviruses, the mouse mammary tumor viruses (MMTV), which encode superantigens. These superantigens are responsible for the deletion of T cells expressing certain Vβ chains of the T-cell receptor in the thymus. Human T cells are able to recognize MMTV-encoded superantigens presented by human major histocompatibility complex class II-positive cells. Owing to this and to the similarity of the human and murine immune systems, it was speculated that human endogenous retroviruses might also code for superantigens. Recently, it was reported that a proviral clone (IDDMK1,222) of the human endogenous retrovirus family HTDV/HERV-K encodes a superantigen. The putative superantigen gene was located within the env region of the virus. Stimulated by these findings, we amplified by PCR and cloned into eucaryotic expression vectors open reading frames (ORFs) which were identical or very similar to IDDMK1,222. When we transfected these vectors into A20 cells, a murine B-cell lymphoma, we were able to demonstrate mRNA expression and protein production. However, we did not find any evidence that the ORF stimulated human or murine T cells in a Vβ-specific fashion, the most prominent feature of superantigens. PMID:10864649

  11. A 5'-upstream short open reading frame encoded peptide regulates angiotensin type 1a receptor production and signalling via the β-arrestin pathway.

    PubMed

    Yosten, Gina L C; Liu, Jun; Ji, Hong; Sandberg, Kathryn; Speth, Robert; Samson, Willis K

    2016-03-15

    AUG sequences and short open reading frames are commonly present in the 5'-leader sequence of G protein-coupled receptor mRNAs. The presence of these upstream AUG sequences has been demonstrated to inhibit downstream receptor translation efficiency and, most recently, receptor signal transduction. A seven amino acid peptide encoded by a short open reading frame in exon 2 of the angiotensin type 1a receptor has been shown to inhibit non-G protein-coupled signalling of angiotensin II, without altering the classical G protein-coupled pathway activated by the ligand. This finding may lead to the development of a new class of angiotensin receptor antagonists with activities biased for one, but not all, of the signalling cascades activated by angiotensin II, which could have therapeutic implications for the myriad hormones and neurotransmitters that signal through G protein-coupled receptors. PMID:26333095

  12. Subunits I and II of Dictyostelium cytochrome c oxidase are specified by a single open reading frame transcribed into a large polycistronic RNA.

    PubMed

    Pellizzari, R; Anjard, C; Bisson, R

    1997-05-16

    A single open reading frame (ORF) encoding cytochrome c oxidase subunit I and II (cox1/2) was identified in the mitochondrial genome of the slime mold Dictyostelium discoideum. The cox1 coding region shares intron positions with its counterparts in fungi and algae. Northern blot analysis, using exon and intron-specific probes, suggests that the cox1/2 gene is transcribed as part of a large, efficiently processed, polycistronic RNA. PMID:9186775

  13. The urease structural gene ureA in Rhizobium meliloti is preceded by an open reading frame necessary for urease activity.

    PubMed

    Miksch, G

    1994-12-01

    An open reading frame (ORF1) located upstream of the urease structural gene ureA in Rhizobium meliloti strain AK631 was cloned and characterized by DNA sequencing. Comparison of the amino acid sequence revealed partial homology with the urease accessory gene ureD of Klebsiella aerogenes and Proteus mirabilis. Mutational analysis of ORF1 showed that the gene is necessary for urease activity. Its function is still unknown. PMID:7813887

  14. Open Reading Frame S/L of Varicella-Zoster Virus Encodes a Cytoplasmic Protein Expressed in Infected Cells

    PubMed Central

    Kemble, George W.; Annunziato, Paula; Lungu, Octavian; Winter, Ruth E.; Cha, Tai-An; Silverstein, Saul J.; Spaete, Richard R.

    2000-01-01

    We report the discovery of a novel gene in the varicella-zoster virus (VZV) genome, designated open reading frame (ORF) S/L. This gene, located at the left end of the prototype VZV genome isomer, expresses a polyadenylated mRNA containing a splice within the 3′ untranslated region in virus-infected cells. Sequence analysis reveals significant differences between the ORF S/Ls of wild-type and attenuated strains of VZV. Antisera raised to a bacterially expressed portion of ORF S/L reacted specifically with a 21-kDa protein synthesized in cells infected with a VZV clinical isolate and with the original vaccine strain of VZV (Oka-ATCC). Cells infected with other VZV strains, including a wild-type strain that has been extensively passaged in tissue culture and commercially produced vaccine strains of Oka, synthesize a family of proteins ranging in size from 21 to 30 kDa that react with the anti-ORF S/L antiserum. MeWO cells infected with recombinant VZV harboring mutations in the C-terminal region of the ORF S/L gene lost adherence to the stratum and adjacent cells, resulting in an altered plaque morphology. Immunohistochemical analysis of VZV-infected cells demonstrated that ORF S/L protein localizes to the cytoplasm. ORF S/L protein was present in skin lesions of individuals with primary or reactivated infection and in the neurons of a dorsal root ganglion during virus reactivation. PMID:11070031

  15. Adenovirus E4 Open Reading Frame 4–Induced Apoptosis Involves Dysregulation of Src Family Kinases

    PubMed Central

    Lavoie, Josée N.; Champagne, Claudia; Gingras, Marie-Claude; Robert, Amélie

    2000-01-01

    The adenoviral early region 4 open reading frame 4 (E4orf4) death factor induces p53-independent apoptosis in many cell types and appears to kill selectively transformed cells. Here we show that expression of E4orf4 in transformed epithelial cells results in early caspase-independent membrane blebbing, associated with changes in the organization of focal adhesions and actin cytoskeleton. Evidence that E4orf4 can associate with and modulate Src family kinase activity, inhibiting Src-dependent phosphorylation of focal adhesion kinase (FAK) and paxillin while increasing phosphorylation of cortactin and some other cellular proteins, is presented. Furthermore, E4orf4 dramatically inhibited the ability of FAK and c-src to cooperate in induction of tyrosine phosphorylation of cellular substrates, suggesting that E4orf4 can interfere with the formation of a signaling complex at focal adhesion sites. Consistent with a functional role for E4orf4–Src interaction, overexpression of activated c-src dramatically potentiated E4orf4-induced membrane blebbing and apoptosis, whereas kinase dead c-src constructs inhibited E4orf4 effects on cell morphology and death. Moreover treatment of E4orf4-expressing cells with PP2, a selective Src kinase inhibitor, led to inhibition of E4orf4-dependent membrane blebbing and later to a marked decrease in E4orf4-induced nuclear condensation. Taken together, these observations indicate that expression of adenovirus 2 E4orf4 can initiate caspase-independent extranuclear manifestations of apoptosis through a modulation of Src family kinases and that these are involved in signaling E4orf4-dependent apoptosis. This study also suggests that Src family kinases are likely to play a role in the cytoplasmic execution of apoptotic programs. PMID:10973994

  16. Functional characterization of Kaposi's sarcoma-associated herpesvirus open reading frame K8 by bacterial artificial chromosome-based mutagenesis.

    PubMed

    Wang, Yan; Sathish, Narayanan; Hollow, Charles; Yuan, Yan

    2011-03-01

    The open reading frame K8 of Kaposi's sarcoma-associated herpesvirus (KSHV) encodes a basic leucine zipper (bZip) protein that binds to the origin of viral DNA replication and is an integral component of viral lytic DNA replication complex. Moreover, K8 physically interacts with replication and transcription activator (RTA) and represses its transactivation activity on several viral promoters. To investigate the role of this protein in viral life cycle, we constructed two K8-null recombinant mutant viruses (BAC-ΔK8 and BAC-stopK8) by using a bacterial artificial chromosome (BAC) system. Latent viral infection can be reconstituted in 293T and BJAB cells with wild-type and the K8-null recombinant viruses by introducing the cloned viral genomes into the cells. When the cells carrying these viruses were induced with 12-O-tetradecanoylphorbol-13-acetate (TPA) and sodium butyrate, no significant difference was seen in overall viral gene expression between wild-type and K8-null viruses, with lytic DNA replication still active in the latter. However, 293T cells harboring K8-null mutant viruses, either BAC-ΔK8 or BAC-stopK8, displayed lower copy numbers of latent KSHV genome in comparison with wild-type viruses. Furthermore, although K8 deficiency appeared to not affect infectivity when K8-null viruses were used to infect 293T, primary human microvascular dermal endothelial and human foreskin fibroblast cells, they exhibited much lower viral genome copy numbers in all types of cell compared to wild-type viruses. Taken together, these data suggest a possible role of K8 in abortive lytic DNA replication occurring in early stages of de novo infection or in the maintenance of latent viral genomes. PMID:21159864

  17. Individualization of Instruction in a Reading and Study Skills Center with Junior College and/or Open Door Policy Students.

    ERIC Educational Resources Information Center

    Cartwright, Hyla D.

    The analysis of individual learning styles and the application of the results of the analyses to realistic learning situations are the basic goals of a Wisconsin college reading and study skills program. In the 1-year required program, beginning college students deficient in reading hear a series of lectures on effective study habits, reading…

  18. Preparing Teachers of Reading and Reading Specialists.

    ERIC Educational Resources Information Center

    Austin, Mary C.

    There is an immediate need for improving the training of reading teachers and specialists. A new program should provide additional instruction at the undergraduate and graduate levels. Preservice teachers whether elementary or secondary, need some formal education in the teaching of reading. Graduate reading specialists should have (1) a minimum…

  19. A Rapid Phenotypic Assay for Detection of Acyclovir-Resistant Varicella-Zoster Virus with Mutations in the Thymidine Kinase Open Reading Frame

    PubMed Central

    Sahli, Roland; Andrei, Graciela; Estrade, Christine; Snoeck, Robert; Meylan, Pascal R. A.

    2000-01-01

    Susceptibility assays by cell culture methods are time-consuming and are particularly difficult to perform with varicella-zoster virus (VZV). To overcome this limitation, we have adapted a functional test of the viral thymidine kinase (TK) in TK-deficient (tdk mutant) bacteria to detect ACV-resistant VZV in clinical samples. After PCR amplification, the complete viral TK open reading frame (ORF) is purified from PCR primers, digested with two restriction enzymes, and ligated in an oriented fashion into a bacterial expression vector. The ligation products are then used to transform tdk mutant bacteria. After transformation, an aliquot of the bacteria is plated onto a plate with minimal medium containing (i) ampicillin to select for plasmids carrying the viral TK ORF and (ii) isopropyl β-d-thiogalactopyranoside (IPTG) to induce its expression. An identical aliquot of bacteria is also plated onto a medium containing, in addition to the components described above, 5-fluorodeoxyuridine (FUdR). Compared to the number of transformants on FUdR-free medium, the number of colonies carrying TK derived from susceptible strains was reduced by 86%, on average, in the presence of FUdR. In contrast, the number of transformants carrying TK from resistant strains with a mutant TK were reduced by only 4%, on average, on FUdR-containing plates. We have assessed the validity of this assay with cell culture isolates and several clinical samples including two cerebrospinal fluid samples from which no virus could be isolated. This colony reduction assay allowed the correct identification of the TK phenotype of each VZV isolate tested and can be completed within 3 days of receipt of the sample. PMID:10722484

  20. Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice.

    PubMed

    Yount, Boyd; Roberts, Rhonda S; Sims, Amy C; Deming, Damon; Frieman, Matthew B; Sparks, Jennifer; Denison, Mark R; Davis, Nancy; Baric, Ralph S

    2005-12-01

    SARS coronavirus (SARS-CoV) encodes several unique group-specific open reading frames (ORFs) relative to other known coronaviruses. To determine the significance of the SARS-CoV group-specific ORFs in virus replication in vitro and in mice, we systematically deleted five of the eight group-specific ORFs, ORF3a, OF3b, ORF6, ORF7a, and ORF7b, and characterized recombinant virus replication and gene expression in vitro. Deletion of the group-specific ORFs of SARS-CoV, either alone or in various combinations, did not dramatically influence replication efficiency in cell culture or in the levels of viral RNA synthesis. The greatest reduction in virus growth was noted following ORF3a deletion. SARS-CoV spike (S) glycoprotein does not encode a rough endoplasmic reticulum (rER)/Golgi retention signal, and it has been suggested that ORF3a interacts with and targets S glycoprotein retention in the rER/Golgi apparatus. Deletion of ORF3a did not alter subcellular localization of the S glycoprotein from distinct punctuate localization in the rER/Golgi apparatus. These data suggest that ORF3a plays little role in the targeting of S localization in the rER/Golgi apparatus. In addition, insertion of the 29-bp deletion fusing ORF8a/b into the single ORF8, noted in early-stage SARS-CoV human and civet cat isolates, had little if any impact on in vitro growth or RNA synthesis. All recombinant viruses replicated to wild-type levels in the murine model, suggesting that either the group-specific ORFs play little role in in vivo replication efficiency or that the mouse model is not of sufficient quality for discerning the role of the group-specific ORFs in disease origin and development. PMID:16282490

  1. Teaching Reading

    ERIC Educational Resources Information Center

    Day, Richard R.

    2013-01-01

    "Teaching Reading" uncovers the interactive processes that happen when people learn to read and translates them into a comprehensive easy-to-follow guide on how to teach reading. Richard Day's revelations on the nature of reading, reading strategies, reading fluency, reading comprehension, and reading objectives make fascinating…

  2. The Effects of Extensive Reading and Reading Strategies on Reading Self-Efficacy

    ERIC Educational Resources Information Center

    Burrows, Lance

    2012-01-01

    This study is a quasi-experimental, longitudinal investigation into the role that extensive reading and reading strategies play in the cultivation of reading self-efficacy. Conducted over the course of one academic year, how changes in reading self-efficacy translate into changes in reading comprehension was examined. In addition, the…

  3. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    SciTech Connect

    Lee, Jumin; Cheng, Xi; Swails, Jason M.; Yeom, Min Sun; Eastman, Peter K.; Lemkul, Justin A.; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; Jo, Sunhwan; Pande, Vijay S.; Case, David A.; Brooks, Charles L.; MacKerell, Alexander D.; Klauda, Jeffery B.; Im, Wonpil

    2015-11-12

    Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

  4. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    PubMed Central

    2015-01-01

    Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules. PMID:26631602

  5. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    DOE PAGESBeta

    Lee, Jumin; Cheng, Xi; Swails, Jason M.; Yeom, Min Sun; Eastman, Peter K.; Lemkul, Justin A.; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; et al

    2015-11-12

    Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find themore » optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.« less

  6. Activation of RNA polymerase III transcription of human Alu repetitive elements by adenovirus type 5: Requirement for the E1b 58-Kilodalton protein and the products of E4 open reading frames 3 and 6

    SciTech Connect

    Panning, B.; Smiley, J.R. )

    1993-06-01

    Alu elements are the single most abundant class of dispersed repeated sequences in the human genome, comprising 5-10% of the mass of human DNA. This report demonstrates that Ad5 infection strongly stimulates Pol III transcription of human Alu elements in HeLa and 293 cells. In contrast to the cases of Ad5-induced Pol III transcriptional activation, this process requires the E1b 58-kDa protein and the products of E4 open reading frames (ORFs) 3 and 6 in addition to the E1a 289-residue product. These findings suggest novel regulatory properties of the Ad5 E1b and E4 proteins and raise the possibility that analogous cellular trans-acting factors serve to modulate Alu expression in vivo.

  7. Physiological Expression and Accumulation of the Products of Two Upstream Open Reading Frames mrtl and MycHex1 Along With p64 and p67 Myc From the Human c-myc Locus.

    PubMed

    Ji, Mi Hong; Kim, Seung-Ki; Kim, Chae-Yong; Phi, Ji Hoon; Jun, Hyun Jin; Blume, Scott W; Choi, Hyoung Soo

    2016-06-01

    In addition to the canonical c-Myc p64 and p67 proteins, the human c-myc locus encodes two distinct proteins, mrtl (myc-related translation/localization regulatory factor) and MycHex1 (Myc Human Exon 1), from the upstream open reading frames within the 5'-untranslated region of the c-myc P0 mRNA. The aim of this study is to examine simultaneously, for the first time, mrtl, MycHex1, c-Myc p64, and p67 in human tumor cell lines and pediatric brain tumor tissues. Western blot analysis demonstrated endogenous mrtl, MycHex1, c-Myc p64, and p67 simultaneously. The relative abundance of mrtl and MycHex1 were consistent among a variety of human tumor cell lines, and the relative intensities of mrtl and MycHex1 correlated positively. Confocal imaging revealed mrtl predominantly localized to the nuclear envelope, along with prominent reticular pattern in the cytoplasm. MycHex1 was observed as a series of bright foci located within the nucleus, a subset of which colocalized with fibrillarin. mrtl and MycHex1 co-immunoprecipitated with RACK1, c-Myc, fibrillarin, coilin, and with each other. These findings suggest that mrtl and MycHex1 have multiple interaction partners in both the nucleus and cytoplasm. Sequence analyses confirmed a known polymorphism of mrtl at base 1965 (G>T) and new mutations at bases 1900 (C>G) and 1798 (C>G). Evidence is presented for expression and stable accumulation of all four proteins encoded by three distinct non-overlapping open reading frames within the human c-myc locus. Additional work is warranted to further elucidate the functional or regulatory roles of these molecules in regulation of c-Myc and in oncogenesis. J. Cell. Biochem. 117: 1407-1418, 2016. © 2015 Wiley Periodicals, Inc. PMID:26552949

  8. Open Your Cupboards to Learning Center Games: Activities for Reinforcing Math and Reading Skills for Teacher and Parent Involvement.

    ERIC Educational Resources Information Center

    Langham, Martha A.; Peterson, Nancy M.

    This book has been developed to furnish teachers and parents with ideas for activities and games which aid children in the transition from oral language to printed language for reading and math. These games are designed to provide children with activities and experiences that increase vocabularies and make them useful in communication, language…

  9. Opening a Window into Reading Development: Eye Movements' Role within a Broader Literacy Research Framework

    ERIC Educational Resources Information Center

    Miller, Brett; O'Donnell, Carol

    2013-01-01

    insight into how readers process text. The heart of this work spans roughly 40 years reflecting the maturity of both the topics under study and experimental approaches used to investigate reading. Recent technological advancements offer increased flexibility to the field, providing…

  10. Supervising the Reading Clinician.

    ERIC Educational Resources Information Center

    Ridout, Susan Ramp; Bailey, Kevin Sue

    Designed for graduate students supervising undergraduate work in a reading clinic, this practicum manual provides guidelines and materials needed for the graduate section of the Reading Practicum (Methods of Teaching Reading II) at Indiana University Southeast. In addition to the syllabus, which includes course description and objectives, course…

  11. The Reading Clinic.

    ERIC Educational Resources Information Center

    Ridout, Susan Ramp; Bailey, Kevin Sue

    Organized to allow undergraduate and graduate students to work together in helping children learn to read, this practicum manual provides guidelines and materials needed for the undergraduate section of the Methods of Teaching Reading II Reading Practicum at Indiana University Southeast. In addition to the syllabus, which includes a course…

  12. An antisense promoter in mouse L1 retrotransposon open reading frame-1 initiates expression of diverse fusion transcripts and limits retrotransposition

    PubMed Central

    Li, Jingfeng; Kannan, Manoj; Trivett, Anna L.; Liao, Hongling; Wu, Xiaolin; Akagi, Keiko; Symer, David E.

    2014-01-01

    Between 6 and 30% of human and mouse transcripts are initiated from transposable elements. However, the promoters driving such transcriptional activity are mostly unknown. We experimentally characterized an antisense (AS) promoter in mouse L1 retrotransposons for the first time, oriented antiparallel to the coding strand of L1 open reading frame-1. We found that AS transcription is mediated by RNA polymerase II. Rapid amplification of cDNA ends cloning mapped transcription start sites adjacent to the AS promoter. We identified >100 novel fusion transcripts, of which many were conserved across divergent mouse lineages, suggesting conservation of potential functions. To evaluate whether AS L1 transcription could regulate L1 retrotransposition, we replaced portions of native open reading frame-1 in donor elements by synonymously recoded sequences. The resulting L1 elements lacked AS promoter activity and retrotransposed more frequently than endogenous L1s. Overexpression of AS L1 transcripts also reduced L1 retrotransposition. This suppression of retrotransposition was largely independent of Dicer. Our experiments shed new light on how AS fusion transcripts are initiated from endogenous L1 elements across the mouse genome. Such AS transcription can contribute substantially both to natural transcriptional variation and to endogenous regulation of L1 retrotransposition. PMID:24493738

  13. An upstream open reading frame represses expression of Lc, a member of the R/B family of maize transcriptional activators

    SciTech Connect

    Damiani, R.D. Jr.; Wessler, S.R. )

    1993-09-01

    The R/B genes of maize encode a family of basic helix-loop-helix proteins that determine where and when the anthocyanin-pigment pathway will be expressed in the plant. Previous studies showed that allelic diversity among family members reflects differences in gene expression, specifically in transcription initiation. The authors present evidence that the R gene Lc is under translational control. They demonstrate that the 235-nt transcript leader of Lc represses expression 25- to 30-fold in an in vivo assay. Repression is mediated by the presence in cis of a 38-codon upstream open reading frame. Furthermore, the coding capacity of the upstream open reading frame influences the magnitude of repression. It is proposed that translational control does not contribute to tissue specificity but prevents overexpression of the Lc protein. The diversity of promoter and 5' untranslated leader sequences among the R/B genes provides an opportunity to study the coevolution of transcriptional and translational mechanisms of gene regulation. 36 refs., 5 figs.

  14. Effective Beginning Reading Programs. [Educator's Summary

    ERIC Educational Resources Information Center

    Center for Data-Driven Reform in Education (NJ3), 2009

    2009-01-01

    What beginning reading programs have been proven to help students in grades K-1 to succeed? To find out, this review summarizes evidence on four types of programs designed to improve beginning reading achievement: (1) Reading Curricula (Curr), such as "Open Court Reading," "Reading Street," and other standard and alternative textbooks; (2)…

  15. [Reading Teacher Education.

    ERIC Educational Resources Information Center

    Palmatier, Robert A., Ed.

    1976-01-01

    This issue of "Epistle," the publication forum of Professors of Reading Teacher Educators, contains three papers as well as the regular features on job openings and on miscellaneous facts. Titles and authors of the articles are: "Doctoral Education in Reading: The State of the Art," by Richard Allington; "The Virtues of Being a Toad and What That…

  16. Human adenovirus early region 4 open reading frame 1 genes encode growth-transforming proteins that may be distantly related to dUTP pyrophosphatase enzymes.

    PubMed Central

    Weiss, R S; Lee, S S; Prasad, B V; Javier, R T

    1997-01-01

    An essential oncogenic determinant of subgroup D human adenovirus type 9 (Ad9), which uniquely elicits estrogen-dependent mammary tumors in rats, is encoded by early region 4 open reading frame 1 (E4 ORF1). Whereas Ad9 E4 ORF1 efficiently induces transformed foci on the established rat embryo fibroblast cell line CREF, the related subgroup A Ad12 and subgroup C Ad5 E4 ORF1s do not (R. T. Javier, J. Virol. 68:3917-3924, 1994). In this study, we found that the lack of transforming activity associated with non-subgroup D adenovirus E4 ORF1s in CREF cells correlated with significantly reduced protein levels compared to Ad9 E4 ORF1 in these cells. In the human cell line TE85, however, the non-subgroup D adenovirus E4 ORF1s produced protein levels higher than those seen in CREF cells as well as transforming activities similar to that of Ad9 E4 ORF1, suggesting that all adenovirus E4 ORF1 polypeptides possess comparable cellular growth-transforming activities. In addition, searches for known proteins related to these novel viral transforming proteins revealed that the E4 ORF1 proteins had weak sequence similarity, over the entire length of the E4 ORF1 polypeptides, with a variety of organismal and viral dUTP pyrophosphatase (dUTPase) enzymes. Even though adenovirus E4 ORF1 proteins lacked conserved protein motifs of dUTPase enzymes or detectable enzymatic activity, E4 ORF1 and dUTPase proteins were predicted to possess strikingly similar secondary structure arrangements. It was also established that an avian adenovirus protein, encoded within a genomic location analogous to that of the human adenovirus E4 ORF1s, was a genuine dUTPase enzyme. Although no functional similarity was found for the E4 ORF1 and dUTPase proteins, we propose that human adenovirus E4 ORF1 genes have evolved from an ancestral adenovirus dUTPase and, from this structural framework, developed novel transforming properties. PMID:9032316

  17. The Role of Speech Prosody and Text Reading Prosody in Children's Reading Comprehension

    ERIC Educational Resources Information Center

    Veenendaal, Nathalie J.; Groen, Margriet A.; Verhoeven, Ludo

    2014-01-01

    Background: Text reading prosody has been associated with reading comprehension. However, text reading prosody is a reading-dependent measure that relies heavily on decoding skills. Investigation of the contribution of speech prosody--which is independent from reading skills--in addition to text reading prosody, to reading comprehension could…

  18. Reading(s).

    ERIC Educational Resources Information Center

    Summerfield, Geoffrey; Summerfield, Judith

    Developed for college English courses, this book presents selections of poetry, short stories, and commentary intended to invite different ways of reading and interpreting literature. An introduction provides an overview of the book's content, as well as a discussion of how to read. The first section, "Entering a Language," considers the…

  19. Pulsed-addition ring-opening metathesis polymerization: catalyst-economical syntheses of homopolymers and block copolymers.

    PubMed

    Matson, John B; Virgil, Scott C; Grubbs, Robert H

    2009-03-11

    Poly(tert-butyl ester norbornene imide) homopolymers and poly(tert-butyl ester norbornene imide-b-N-methyloxanorbornene imide) copolymers were prepared by pulsed-addition ring-opening metathesis polymerization (PA-ROMP). PA-ROMP is a unique polymerization method that employs a symmetrical cis-olefin chain transfer agent (CTA) to simultaneously cap a living polymer chain and regenerate the ROMP initiator with high fidelity. Unlike traditional ROMP with chain transfer, the CTA reacts only with the living chain end, resulting in narrowly dispersed products. The regenerated initiator can then initiate polymerization of a subsequent batch of monomer, allowing for multiple polymer chains with controlled molecular weight and low polydispersity to be generated from one metal initiator. Using the fast-initiating ruthenium metathesis catalyst (H(2)IMes)(Cl)(2)(pyr)(2)RuCHPh and cis-4-octene as a CTA, the capabilities of PA-ROMP were investigated with a Symyx robotic system, which allowed for increased control and precision of injection volumes. The results from a detailed study of the time required to carry out the end-capping/initiator-regeneration step were used to design several experiments in which PA-ROMP was performed from one to ten cycles. After determination of the rate of catalyst death, a single, low polydispersity polymer was prepared by adjusting the amount of monomer injected in each cycle, maintaining a constant monomer/catalyst ratio. Additionally, PA-ROMP was used to prepare nearly perfect block copolymers by quickly injecting a second monomer at a specific time interval after the first monomer injection, such that chain transfer had not yet occurred. Polymers were characterized by gel permeation chromatography with multiangle laser light scattering. PMID:19215131

  20. Up to Four Distinct Polypeptides Are Produced from the γ34.5 Open Reading Frame of Herpes Simplex Virus 2

    PubMed Central

    Korom, Maria; Davis, Katie L.

    2014-01-01

    ABSTRACT The herpes simplex virus 1 (HSV-1) ICP34.5 protein strongly influences neurovirulence and regulates several cellular antiviral responses. Despite the clinical importance of HSV-2, relatively little is known about its ICP34.5 ortholog. We found that HSV-2 produces up to four distinct forms of ICP34.5 in infected cells: a full-length protein, one shorter form sharing the N terminus, and two shorter forms sharing the C terminus. These forms appeared with similar kinetics and accumulated in cells over much of the replication cycle. We confirmed that the N-terminal form is translated from the primary unspliced transcript to a stop codon within the intron unique to HSV-2 γ34.5. We found that the N-terminal form was produced in a variety of cell types and by 9 of 10 clinical isolates. ICP27 influenced but was not required for expression of the N-terminal form. Western blotting and reverse transcription-PCR indicated the C-terminal forms did not contain the N terminus and were not products of alternative splicing or internal transcript initiation. Expression plasmids encoding methionine at amino acids 56 and 70 generated products that comigrated in SDS-PAGE with the C1 and C2 forms, respectively, and mutation of these sites abolished C1 and C2. Using a recombinant HSV-2 encoding hemagglutinin (HA)-tagged ICP34.5, we demonstrated that the C-terminal forms were also produced during infection of many human and mouse cell types but were not detectable in mouse primary neurons. The protein diversity generated from the HSV-2 γ34.5 open reading frame implies additional layers of cellular regulation through potential independent activities associated with the various forms of ICP34.5. IMPORTANCE The herpes simplex virus 1 (HSV-1) protein ICP34.5, encoded by the γ34.5 gene, interferes with several host defense mechanisms by binding cellular proteins that would otherwise stimulate the cell's autophagic, translational-arrest, and type I interferon responses to virus

  1. Translation of the mRNA of the maize transcriptional activator Opaque-2 is inhibited by upstream open reading frames present in the leader sequence.

    PubMed Central

    Lohmer, S; Maddaloni, M; Motto, M; Salamini, F; Thompson, R D

    1993-01-01

    The protein encoded by the Opaque-2 (O2) gene is a transcription factor, translated from an mRNA that possesses an unusually long 5' leader sequence containing three upstream open reading frames (uORFs). The efficiency of translation of O2 mRNA has been tested in vivo by a transient assay in which the level of activation of the b32 promoter, a natural target of O2 protein, is measured. We show that uORF-less O2 alleles possess a higher transactivation value than the wild-type allele and that the reduction in transactivation due to the uORFs is a cis-dominant effect. The data presented indicate that both uORF1 and uORF2 are involved in the reducing effect and suggest that both are likely to be translated. PMID:8439744

  2. The positive regulatory function of the 5'-proximal open reading frames in GCN4 mRNA can be mimicked by heterologous, short coding sequences.

    PubMed Central

    Williams, N P; Mueller, P P; Hinnebusch, A G

    1988-01-01

    Translational control of GCN4 expression in the yeast Saccharomyces cerevisiae is mediated by multiple AUG codons present in the leader of GCN4 mRNA, each of which initiates a short open reading frame of only two or three codons. Upstream AUG codons 3 and 4 are required to repress GCN4 expression in normal growth conditions; AUG codons 1 and 2 are needed to overcome this repression in amino acid starvation conditions. We show that the regulatory function of AUG codons 1 and 2 can be qualitatively mimicked by the AUG codons of two heterologous upstream open reading frames (URFs) containing the initiation regions of the yeast genes PGK and TRP1. These AUG codons inhibit GCN4 expression when present singly in the mRNA leader; however, they stimulate GCN4 expression in derepressing conditions when inserted upstream from AUG codons 3 and 4. This finding supports the idea that AUG codons 1 and 2 function in the control mechanism as translation initiation sites and further suggests that suppression of the inhibitory effects of AUG codons 3 and 4 is a general consequence of the translation of URF 1 and 2 sequences upstream. Several observations suggest that AUG codons 3 and 4 are efficient initiation sites; however, these sequences do not act as positive regulatory elements when placed upstream from URF 1. This result suggests that efficient translation is only one of the important properties of the 5' proximal URFs in GCN4 mRNA. We propose that a second property is the ability to permit reinitiation following termination of translation and that URF 1 is optimized for this regulatory function. Images PMID:3065626

  3. Reading Faster

    ERIC Educational Resources Information Center

    Nation, Paul

    2009-01-01

    This article describes the visual nature of the reading process as it relates to reading speed. It points out that there is a physical limit on normal reading speed and beyond this limit the reading process will be different from normal reading where almost every word is attended to. The article describes a range of activities for developing…

  4. Reading Recovery.

    ERIC Educational Resources Information Center

    Jones, Joanna R., Ed.

    1992-01-01

    This issue of the Arizona Reading Journal focuses on the theme "reading recovery" and includes the following articles: "Why Is an Inservice Programme for Reading Recovery Teachers Necessary?" (Marie M. Clay); "What Is Reading Recovery?" (Gay Su Pinnell); "Teaching a Hard To Teach Child" (Constance A. Compton); "Reading Recovery in Arizona--A…

  5. Production of Candida antaractica Lipase B Gene Open Reading Frame using Automated PCR Gene Assembly Protocol on Robotic Workcell & Expression in Ethanologenic Yeast for use as Resin-Bound Biocatalyst in Biodiesel Production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A synthetic Candida antarctica lipase B (CALB) gene open reading frame (ORF) for expression in yeast was produced using an automated PCR assembly and DNA purification protocol on an integrated robotic workcell. The lycotoxin-1 (Lyt-1) C3 variant gene ORF was added in-frame with the CALB ORF to pote...

  6. Combination Antisense Treatment for Destructive Exon Skipping of Myostatin and Open Reading Frame Rescue of Dystrophin in Neonatal mdx Mice.

    PubMed

    Lu-Nguyen, Ngoc B; Jarmin, Susan A; Saleh, Amer F; Popplewell, Linda; Gait, Michael J; Dickson, George

    2015-08-01

    The fatal X-linked Duchenne muscular dystrophy (DMD), characterized by progressive muscle wasting and muscle weakness, is caused by mutations within the DMD gene. The use of antisense oligonucleotides (AOs) modulating pre-mRNA splicing to restore the disrupted dystrophin reading frame, subsequently generating a shortened but functional protein has emerged as a potential strategy in DMD treatment. AO therapy has recently been applied to induce out-of-frame exon skipping of myostatin pre-mRNA, knocking-down expression of myostatin protein, and such an approach is suggested to enhance muscle hypertrophy/hyperplasia and to reduce muscle necrosis. Within this study, we investigated dual exon skipping of dystrophin and myostatin pre-mRNAs using phosphorodiamidate morpholino oligomers conjugated with an arginine-rich peptide (B-PMOs). Intraperitoneal administration of B-PMOs was performed in neonatal mdx males on the day of birth, and at weeks 3 and 6. At week 9, we observed in treated mice (as compared to age-matched, saline-injected controls) normalization of muscle mass, a recovery in dystrophin expression, and a decrease in muscle necrosis, particularly in the diaphragm. Our data provide a proof of concept for antisense therapy combining dystrophin restoration and myostatin inhibition for the treatment of DMD. PMID:25959011

  7. Combination antisense treatment for destructive exon skipping of myostatin and open reading frame rescue of dystrophin in neonatal mdx mice

    PubMed Central

    Lu-Nguyen, Ngoc B.; Jarmin, Susan A.; Saleh, Amer F.; Popplewell, Linda; Gait, Michael J.; Dickson, George

    2015-01-01

    The fatal X-linked Duchenne muscular dystrophy (DMD), characterized by progressive muscle wasting and muscle weakness, is caused by mutations within the DMD gene. The use of antisense oligonucleotides (AOs) modulating pre-mRNA splicing to restore the disrupted dystrophin reading frame, subsequently generating a shortened but functional protein has emerged as a potential strategy in DMD treatment. AO therapy has recently been applied to induce out-of-frame exon skipping of myostatin pre-mRNA, knocking-down expression of myostatin protein, and such an approach is suggested to enhance muscle hypertrophy/hyperplasia and to reduce muscle necrosis. Within this study, we investigated dual exon skipping of dystrophin and myostatin pre-mRNAs using phosphorodiamidate morpholino oligomers conjugated with an arginine-rich peptide (B-PMOs). Intraperitoneal administration of B-PMOs was performed in neonatal mdx males on the day of birth, and at weeks 3 and 6. At week 9, we observed in treated mice (as compared to age-matched, saline-injected controls) normalization of muscle mass, a recovery in dystrophin expression, and a decrease in muscle necrosis, particularly in the diaphragm. Our data provide a proof of concept for antisense therapy combining dystrophin restoration and myostatin inhibition for the treatment of DMD. PMID:25959011

  8. Automated Yeast Mating Protocol Using Open Reading Frames from Saccharomyces cerevisiae Genome to Improve Yeast Strains for Cellulosic Ethanol Production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Engineering the industrial ethanologen Saccharomyces cerevisiae to utilize pentose sugars from lignocellulosic biomass is critical for commercializing cellulosic fuel ethanol production. Approaches to engineer pentose-fermenting yeasts have required expression of additional genes. We implemented a...

  9. A unique open reading frame within the comX gene of Streptococcus mutans regulates genetic competence and oxidative stress tolerance

    PubMed Central

    Kaspar, Justin; Ahn, Sang-Joon; Palmer, Sara R.; Choi, Sang Chul; Stanhope, Michael J.; Burne, Robert A.

    2015-01-01

    Streptococcus mutans displays complex regulation of genetic competence, with ComX controlling late competence gene transcription. The rcrRPQ operon has been shown to link oxidative stress tolerance, (p)ppGpp metabolism and competence in S. mutans. Importantly, an rcrR polar (ΔrcrR-P) mutant is hyper-transformable, but an rcrR non-polar (ΔrcrR-NP) mutant cannot be transformed. Transcriptome comparisons of the rcrR mutants using RNA-Seq and quantitative real-time polymerase chain reaction revealed little expression in the 5′ region of comX in ΔrcrR-NP, but high level expression in the 3′ region. Northern blotting with comX probes revealed two distinct transcripts in the ΔrcrR-P and ΔrcrR-NP strains, and 5′ Rapid Amplification of cDNA Ends mapped the 5′ terminus of the shorter transcript to nt +140 of the comX structural gene, where a unique 69-aa open reading frame, termed XrpA, was encoded in a different reading frame than ComX. Two single-nucleotide substitution mutants (comX::T162C; comX::T210A) were introduced to disrupt XrpA without affecting the sequence of ComX. When the mutations were in the ΔrcrR-NP genetic background, ComX production and transformation were restored. Overexpression of xrpA led to impaired growth in aerobic conditions and decreased transformability. These results reveal an unprecedented mechanism for competence regulation and stress tolerance by a gene product encoded within the comX gene that appears unique to S. mutans. PMID:25620525

  10. Reading Comics

    ERIC Educational Resources Information Center

    Tilley, Carol L.

    2008-01-01

    Many adults, even librarians who willingly add comics to their collections, often dismiss the importance of comics. Compared to reading "real" books, reading comics appears to be a simple task and compared to reading no books, reading comics might be preferable. After all, comics do have words, but the plentiful pictures seem to carry most of the…

  11. Reading Rituals

    ERIC Educational Resources Information Center

    Manzo, Kathleen Kennedy

    2007-01-01

    The Ogden, Utah schools have used the mandates of the federal Reading First grant program to transform reading instruction and student achievement in low-performing schools. Reading First was approved by Congress in 2001 under the No Child Left Behind Act to bring scientifically based reading methods and materials to struggling schools. The $1…

  12. Comparative Complete Genome Analysis of Chicken and Turkey Megriviruses (Family Picornaviridae): Long 3′ Untranslated Regions with a Potential Second Open Reading Frame and Evidence for Possible Recombination

    PubMed Central

    Boros, Ákos; Pankovics, Péter; Knowles, Nick J.; Nemes, Csaba; Delwart, Eric

    2014-01-01

    ABSTRACT Members of the family Picornaviridae consist of small positive-sense single-stranded RNA (+ssRNA) viruses capable of infecting various vertebrate species, including birds. One of the recently identified avian picornaviruses, with a remarkably long (>9,040-nucleotide) but still incompletely sequenced genome, is turkey hepatitis virus 1 (THV-1; species Melegrivirus A, genus Megrivirus), a virus associated with liver necrosis and enteritis in commercial turkeys (Meleagris gallopavo). This report presents the results of the genetic analysis of three complete genomes of megriviruses from fecal samples of chickens (chicken/B21-CHV/2012/HUN, GenBank accession no. KF961186, and chicken/CHK-IV-CHV/2013/HUN, GenBank accession no. KF961187) (Gallus gallus domesticus) and turkey (turkey/B407-THV/2011/HUN, GenBank accession no. KF961188) (Meleagris gallopavo) with the largest picornavirus genome (up to 9,739 nucleotides) so far described. The close phylogenetic relationship to THV-1 in the nonstructural protein-coding genome region and possession of the same internal ribosomal entry site type (IVB-like) suggest that the study strains belong to the genus Megrivirus. However, the genome comparisons revealed numerous unique variations (e.g., different numbers of potential 2A peptides, unusually long 3′ genome parts with various lengths of a potential second open reading frame, and multiple repeating sequence motifs in the 3′ untranslated region) and heterogeneous sequence relationships between the structural and nonstructural genome regions. These differences suggest the classification of chicken megrivirus-like viruses into a candidate novel species in the genus Megrivirus. Based on the different phylogenetic positions of chicken megrivirus-like viruses at the structural and nonstructural genome regions, the recombinant nature of these viruses is plausible. IMPORTANCE The comparative genome analysis of turkey and novel chicken megriviruses revealed numerous unique

  13. Entrepreneurship Education: Supplementary Readings.

    ERIC Educational Resources Information Center

    Scanlan, Thomas J.; And Others

    This third volume in the Entrepreneurship Education curriculum materials includes readings and suggested additional resources which complement the instructional strategies contained in the first two volumes. Three sections are included in the guide: critical incidents, readings in entrepreneurial skills, and management skill area resources.…

  14. American Reading Instruction.

    ERIC Educational Resources Information Center

    Smith, Nila Banton

    A presentation of the history of reading instruction in the United States, this book is a special edition of Nila Banton Smith's original 1965 volume with the addition of a prologue on her life, and an epilogue which updates the history of reading instruction from 1965 to 1985. Chapter headings consist of: (1) The Beginnings of Reading…

  15. Sensitization to Food Additives in Patients with Allergy: A Study Based on Skin Test and Open Oral Challenge.

    PubMed

    Moghtaderi, Mozhgan; Hejrati, Zinatosadat; Dehghani, Zahra; Dehghani, Faranak; Kolahi, Niloofar

    2016-06-01

    There has been a great increase in the consumption of various food additives in recent years. The purpose of this study was to identify the incidence of sensitization to food additives by using skin prick test in patients with allergy and to determine the concordance rate between positive skin tests and oral challenge in hypersensitivity to additives. This cross-sectional study included 125 (female 71, male 54) patients aged 2-76 years with allergy and 100 healthy individuals. Skin tests were performed in both patient and control groups with 25 fresh food additives. Among patients with allergy, 22.4% showed positive skin test at least to one of the applied materials. Skin test was negative to all tested food additives in control group. Oral food challenge was done in 28 patients with positive skin test, in whom 9 patients showed reaction to culprit (Concordance rate=32.1%). The present study suggested that about one-third of allergic patients with positive reaction to food additives showed positive oral challenge; it may be considered the potential utility of skin test to identify the role of food additives in patients with allergy. PMID:27424134

  16. Open reading frame 5 (ORF5), encoding a ferredoxinlike protein, and nifQ are cotranscribed with nifE, nifN, nifX, and ORF4 in Rhodobacter capsulatus.

    PubMed

    Moreno-Vivian, C; Hennecke, S; Pühler, A; Klipp, W

    1989-05-01

    DNA sequence analysis of a 1,600-base-pair fragment located downstream of nifENX in nif region A of Rhodobacter capsulatus revealed two additional open reading frames (ORFs): ORF5, encoding a ferredoxinlike protein, and nifQ. The ferredoxinlike gene product contained two cysteine motifs, typical of ferredoxins coordinating two 4Fe-4S clusters, but the distance between these two motifs was unusual for low-molecular-weight ferredoxins. The R. capsulatus nifQ gene product shared a high degree of homology with Klebsiella pneumoniae and Azotobacter vinelandii NifQ, including a typical cysteine motif located in the C-terminal part. nifQ insertion mutants and also an ORF5-nifQ double deletion mutant showed normal diazotrophic growth only in the presence of high concentrations of molybdate. This demonstrated that the gene encoding the ferredoxinlike protein is not essential for nitrogen fixation. No NifA-activated consensus promoter could be found in the intergenic region between nifENX-ORF4 and ORF5-nifQ. Analyses of a nifQ-lacZYA fusion revealed that transcription of nifQ was initiated at a promoter in front of nifE. In contrast to other nitrogen-fixing organisms, R. capsulatus nifE, nifN, nifX, ORF4, ORF5, and nifQ were organized in one transcriptional unit. PMID:2708314

  17. Open reading frame 5 (ORF5), encoding a ferredoxinlike protein, and nifQ are cotranscribed with nifE, nifN, nifX, and ORF4 in Rhodobacter capsulatus.

    PubMed Central

    Moreno-Vivian, C; Hennecke, S; Pühler, A; Klipp, W

    1989-01-01

    DNA sequence analysis of a 1,600-base-pair fragment located downstream of nifENX in nif region A of Rhodobacter capsulatus revealed two additional open reading frames (ORFs): ORF5, encoding a ferredoxinlike protein, and nifQ. The ferredoxinlike gene product contained two cysteine motifs, typical of ferredoxins coordinating two 4Fe-4S clusters, but the distance between these two motifs was unusual for low-molecular-weight ferredoxins. The R. capsulatus nifQ gene product shared a high degree of homology with Klebsiella pneumoniae and Azotobacter vinelandii NifQ, including a typical cysteine motif located in the C-terminal part. nifQ insertion mutants and also an ORF5-nifQ double deletion mutant showed normal diazotrophic growth only in the presence of high concentrations of molybdate. This demonstrated that the gene encoding the ferredoxinlike protein is not essential for nitrogen fixation. No NifA-activated consensus promoter could be found in the intergenic region between nifENX-ORF4 and ORF5-nifQ. Analyses of a nifQ-lacZYA fusion revealed that transcription of nifQ was initiated at a promoter in front of nifE. In contrast to other nitrogen-fixing organisms, R. capsulatus nifE, nifN, nifX, ORF4, ORF5, and nifQ were organized in one transcriptional unit. PMID:2708314

  18. Complete Nucleotide Sequence and Genome Organization of Hibiscus Chlorotic Ringspot Virus, a New Member of the Genus Carmovirus: Evidence for the Presence and Expression of Two Novel Open Reading Frames

    PubMed Central

    Huang, Mei; Koh, Dora Chin-Yen; Weng, Li-Juan; Chang, Min-Li; Yap, Yun-Kiam; Zhang, Lee; Wong, Sek-Man

    2000-01-01

    The complete nucleotide sequence of hibiscus chlorotic ringspot virus (HCRSV) was determined. The genomic RNA (gRNA) is 3,911 nucleotides long and has the potential to encode seven viral proteins in the order of 28 (p28), 23 (p23), 81 (p81), 8 (p8), 9 (p9), 38 (p38), and 25 (p25) kDa. Excluding two unique open reading frames (ORFs) encoding p23 and p25, the ORFs encode proteins with high amino acid similarity to those of carmoviruses. In addition to gRNA, two 3′-coterminated subgenomic RNA (sgRNA) species were identified. Full-length cDNA clones derived from gRNA and sgRNA were constructed under the control of a T7 promoter. Both capped and uncapped transcripts derived from the full-length genomic cDNA clone were infectious. In vitro translation and mutagenesis assays confirmed that all the predicted ORFs except the ORF encoding p8 are translatable, and the two novel ORFs (those encoding p23 and p25) may be functionally indispensable for the viral infection cycle. Based on virion morphology and genome organization, we propose that HCRSV be classified as a new member of the genus Carmovirus in family Tombusviridae. PMID:10708431

  19. A single inhibitory upstream open reading frame (uORF) is sufficient to regulate Candida albicans GCN4 translation in response to amino acid starvation conditions.

    PubMed

    Sundaram, Arunkumar; Grant, Chris M

    2014-04-01

    Candida albicans is a major fungal pathogen that responds to various environmental cues as part of its infection mechanism. We show here that the expression of C. albicans GCN4, which encodes a transcription factor that regulates morphogenetic and metabolic responses, is translationally regulated in response to amino acid starvation induced by exposure to the histidine analog 3-aminotriazole (3AT). However, in contrast to the well-known translational control mechanisms that regulate yeast GCN4 and mammalian ATF4 expression via multiple upstream open reading frames (uORFs) in their 5'-leader sequences, a single inhibitory uORF is necessary and sufficient for C. albicans GCN4 translational control. The 5'-leader sequence of GCN4 contains three uORFs, but uORF3 alone is sufficient for translational regulation. Under nonstress conditions, uORF3 inhibits GCN4 translation. Amino acid starvation conditions promote Gcn2-mediated phosphorylation of eIF2α and leaky ribosomal scanning to bypass uORF3, inducing GCN4 translation. GCN4 expression is also transcriptionally regulated, although maximal induction is observed at higher concentrations of 3AT compared with translational regulation. C. albicans GCN4 expression is therefore highly regulated by both transcriptional and translational control mechanisms. We suggest that it is particularly important that Gcn4 levels are tightly controlled since Gcn4 regulates morphogenetic changes during amino acid starvation conditions, which are important determinants of virulence in this fungus. PMID:24570481

  20. Open reading frames 1a and 1b of the porcine reproductive and respiratory syndrome virus (PRRSV) collaboratively initiate viral minus-strand RNA synthesis.

    PubMed

    Tang, Yan-Dong; Fang, Qiong-Qiong; Liu, Ji-Ting; Wang, Tong-Yun; Wang, Yu; Tao, Ye; Liu, Yong-Gang; Cai, Xue-Hui

    2016-09-01

    The porcine reproductive and respiratory syndrome virus (PRRSV) causes a persistent threat to the swine industry, especially when highly pathogenic PRRSV (HP-PRRSV) emerges. Previous studies have indicated that PRRSV RNA synthesis was correlated with HP-PRRSV virulence. PRRSV RNA synthesis includes genomic RNA and sub-genomic mRNA, and these processes require minus-strand RNA as a template. However, the mechanisms involved in PRRSV minus-strand RNA synthesis are not fully understood. A mini-genome system can be used to assess viral replication mechanisms and to evaluate the effects of potential antiviral drugs on viral replicase activities. In this study, we developed a mini-genome system that uses firefly luciferase as a reporter. Based on this system, we found that PRRSV RNA-dependent RNA polymerase nsp9 alone failed to activate virus minus-strand RNA synthesis. We also demonstrated that combinations of open reading frames 1a (ORF1a) and ORF1b are necessary for viral minus-strand RNA synthesis. PMID:27378424

  1. Expression of a second open reading frame present in the genome of tick-borne encephalitis virus strain Neudoerfl is not detectable in infected cells.

    PubMed

    Černý, Jiří; Selinger, Martin; Palus, Martin; Vavrušková, Zuzana; Tykalová, Hana; Bell-Sakyi, Lesley; Štěrba, Ján; Grubhoffer, Libor; Růžek, Daniel

    2016-06-01

    A short upstream open reading frame (uORF) was recently identified in the 5' untranslated region of some tick-borne encephalitis virus (TBEV) strains. However, it is not known if the peptide encoded by TBEV uORF (TuORF) is expressed in infected cells. Here we show that TuORF forms three phylogenetically separated clades which are typical of European, Siberian, and Far-Eastern TBEV subtypes. Analysis of selection pressure acting on the TuORF area showed that it is under positive selection pressure. Theoretically, TuORF may code for a short hydrophobic peptide embedded in a biological membrane. However, expression of TuORF was detectable neither by immunoblotting in tick and mammalian cell lines infected with TBEV nor by immunofluorescence in TBEV-infected mammalian cell lines. These results support the idea that TuORF is not expressed in TBEV-infected cell or expressed in undetectably low concentrations. Therefore we can assume that TuORF has either minor or no biological role in the TBEV life cycle. PMID:26924586

  2. Immortalization and altered differentiation of human keratinocytes in vitro by the E6 and E7 open reading frames of human papillomavirus type 18.

    PubMed Central

    Hudson, J B; Bedell, M A; McCance, D J; Laiminis, L A

    1990-01-01

    The E6-E7 region of human papillomavirus types 16 and 18 is selectively retained and expressed in cervical carcinoma cells. In cultured human keratinocytes, expression of the E6 and E7 open reading frames of human papillomavirus type 18, under the control of its homologous promoter, resulted in high-frequency immortalization. Furthermore, by using a system that allows for stratification of keratinocytes in vitro (raft system), we observed that the morphological differentiation of these E6-E7 immortalized cells was altered such that parabasal cells extended throughout most of the epithelium, with abnormal nuclei present in the upper regions. Examination of E6-E7-expressing cell lines in the raft system at a later passage revealed that complete loss of morphological differentiation had occurred. E7 alone was a much less effective immortalizing agent than E6 and E7 together and acted only minimally to alter morphological differentiation in vitro. No such activities were found for E6 alone. High-frequency transformation of human epithelial cells thus appears to require expression of both E6 and E7 gene products. Images PMID:2153221

  3. Expression, nucleotide sequence and mutational analysis of two open reading frames in the nif gene region of Anabaena sp. strain PCC7120.

    PubMed

    Borthakur, D; Basche, M; Buikema, W J; Borthakur, P B; Haselkorn, R

    1990-04-01

    A 1.8 kb transcript corresponding to a region of the Anabaena 7120 chromosome 4 kb downstream of the nifHDK operon appears 12-18 h after heterocyst induction. The DNA corresponding to this transcript was sequenced and found to contain two open reading frames, designated ORF 1 and ORF 2. Two polypeptides, of 30 kDa and 13 kDa, encoded by these ORFs were expressed in Escherichia coli. An apparent start site for the transcript, detected by S1 nuclease protection, was located 42 bp upstream of the ATG start codon of ORF 1. ORF 2 shows strong sequence similarity to ORF 6 in the nif gene region of Azotobacter vinelandii. ORF 1 was interrupted using a 1.4 kb neomycin resistance cassette and the resulting mutant grew very slowly on medium lacking combined nitrogen. The mutant had 45% of wild-type acetylene reduction activity, which could be complemented by a 2.8 kb EcoRI fragment of wild-type Anabaena DNA containing only ORF 1 and ORF 2. Thus, one or both of these ORFs is required for efficient nitrogen fixation in Anabaena. PMID:2115111

  4. CFTR mRNA expression is regulated by an upstream open reading frame and RNA secondary structure in its 5' untranslated region.

    PubMed

    Lukowski, Samuel W; Rothnagel, Joseph A; Trezise, Ann E O

    2015-02-15

    Post-transcriptional regulation of gene expression through 5' untranslated region (5'UTR)-encoded cis-acting elements is an important mechanism for the control of protein expression levels. Through controlling specific aspects of translation initiation, expression can be tightly regulated while remaining responsive to cellular requirements. With respect to cystic fibrosis (CF), the overexpression of cystic fibrosis transmembrane conductance regulator (CFTR) protein trafficking mutants, such as delta-F508, is of great biological and clinical interest. By understanding the post-transcriptional mechanisms that regulate CFTR expression, new procedures can be developed to enhance CFTR expression in homozygous delta-F508 CF patients. We have identified the key elements of a complex negative regulatory mechanism that is encoded within the human CFTR 5'UTR and show how these elements act in combination to restrict CFTR gene expression to a consistently low level in a transcript-specific manner. This study shows, for the first time, that endogenous human CFTR expression is post-transcriptionally regulated through a 5'UTR-mediated mechanism. We show that the very low levels of endogenous CFTR expression, compared with other low expression genes, are maintained through the co-operative inhibitory effects of an upstream open reading frame and a thermodynamically stable RNA secondary structure. PMID:25274779

  5. A 9359 bp fragment from the right arm of Saccharomyces cerevisiae chromosome VII includes the FOL2 and YTA7 genes and three unknown open reading frames.

    PubMed

    Agostoni Carbone, M L; Lucchini, G; Melchioretto, P; Nardese, V; Vanoni, M; Panzeri, L

    1998-04-30

    In the framework of the EU programme for systematic sequencing of the Saccharomyces cervisiae genome we determined the sequence of a 9359 bp fragment of the right arm of chromosome VII. Five open reading frames (ORFs) of at least 300 nucleotides were found in this region. YGR267c encodes a protein with significant similarity to the enzyme GTP-cyclohydrolase I, that controls the first step in the biosynthetic pathway leading to various pterins and shows a high degree of sequence conservation from bacteria to mammals. We have recently demonstrated (Nardese et al., 1996) that YGR267c corresponds to the FOL2 gene, previously localized in the same chromosomal region by genetic mapping. The protein deduced from YGR270w belongs to the superfamily of putative ATPases associated with diverse cellular activities. It corresponds to the YTA7 gene, a member of a set of yeast genes coding for putative ATPases with high similarity to constituents of the 26S protease. The three ORFs YGR266w, YGR268c and YGR269w encode putative products of unknown function, with neither significant similarity to proteins in databases nor recognizable domains. YGR268c and YGR269w are partially overlapping ORFs: YGR268c seems to correspond to a real gene. whereas YGR269w is probably a fortuitous ORF. PMID:9605509

  6. Fine mapping of the latency-related gene of herpes simplex virus type 1: alternative splicing produces distinct latency-related RNAs containing open reading frames

    SciTech Connect

    Wechsler, S.L.; Nesburn, A.B.; Watson, R.; Slanina, S.M.; Ghiasi, H.

    1988-11-01

    The latency-related (LR) gene of herpes simplex virus type 1 (HSV-1) is transcriptionally active during HSV-1 latency, producing at least two LR-RNAs. The LR gene partially overlaps the immediate-early gene ICP0 and is transcribed in the opposite direction from ICP0, producing LR-RNAs that are complementary (antisense) to ICP0 mRNA. The LR gene is thought to be involved in HSV-1 latency. The authors report here the time mapping and partial sequence analysis of this HSV-1 LR gene. /sup 32/P-labeled genomic DNA restriction fragments and synthetic oligonucleotides were used as probes for in situ hybridizations and Northern (RNA) blot hybridizations of RNA from trigeminal ganglia of rabbits latently infected with HSV-1. The two most abundant LR-RNAs appeared to share their 5' and 3' ends and to be produced by alternative splicing. These LR-RNAs were approximately 2 and 1.3 to 1.5 kilobases in length and were designated LR-RNA 1 and LF-RNA 2, respectively. LR-RNA 1 appeared to have at least one intron removed, while LR-RNA 2 appeared to have at least two introns removed. The LR-RNAs contained two potential long open reading frames, suggesting the possibility that one or more of the LR-RNAs may be a functional mRNA.

  7. A stable hairpin preceded by a short open reading frame promotes nonlinear ribosome migration on a synthetic mRNA leader.

    PubMed Central

    Hemmings-Mieszczak, M; Hohn, T

    1999-01-01

    The regulation of cauliflower mosaic virus (CaMV) pregenomic 35S RNA translation occurs via nonlinear ribosome migration (ribosome shunt) and is mediated by an elongated hairpin structure in the leader. The replacement of the viral leader by a series of short, low-energy stems in either orientation supports efficient ribosomal shunting, showing that the stem per se, and not its sequence, is recognized by the translation machinery. The requirement for cis-acting sequences from the unstructured terminal regions of the viral leader was analyzed: the 5'-terminal polypyrimidine stretch and the short upstream open reading frame (uORF) A stimulate translation, whereas the 3'-flanking region seems not to be essential. Based on these results, an artificial leader was designed with a stable stem flanked by unstructured sequences derived from parts of the 5'- and 3'-proximal regions of the CaMV 35S RNA leader. This artificial leader is shunt-competent in translation assays in vivo and in vitro, indicating that a low-energy stem, broadly used as a device to successfully interfere with ribosome scanning, can efficiently support translation, if preceded by a short uORF. The synthetic 140-nt leader can functionally replace the CaMV 35S RNA 600-nt leader, thus implicating the universal role that nonlinear ribosome scanning could play in translation initiation in eukaryotes. PMID:10496216

  8. Forced Evolution Reveals the Importance of Short Open Reading Frame A and Secondary Structure in the Cauliflower Mosaic Virus 35S RNA Leader

    PubMed Central

    Pooggin, Mikhail M.; Hohn, Thomas; Fütterer, Johannes

    1998-01-01

    Cauliflower mosaic virus pregenomic 35S RNA begins with a long leader sequence containing an extensive secondary structure and up to nine short open reading frames (sORFs), 2 to 35 codons in length. To test whether any of these sORFs are required for virus viability, their start codons were mutated either individually or in various combinations. The resulting viral mutants were tested for infectivity on mechanically inoculated turnip plants. Viable mutants were passaged several times, and the stability of the introduced mutations was analyzed by PCR amplification and sequencing. Mutations at the 5′-proximal sORF A and in the center of the leader resulted in delayed symptom development and in the appearance of revertants. In the central leader region, the predicted secondary structure, rather than the sORF organization, was restored, while true reversions or second-site substitutions in response to mutations of sORF A restored this sORF. Involvement of sORF A and secondary structure of the leader in the virus replication cycle, and especially in translation of the 35S RNA via ribosome shunting, is discussed. PMID:9557705

  9. Expression of Human Hemojuvelin (HJV) Is Tightly Regulated by Two Upstream Open Reading Frames in HJV mRNA That Respond to Iron Overload in Hepatic Cells

    PubMed Central

    Onofre, Cláudia; Tomé, Filipa; Barbosa, Cristina; Silva, Ana Luísa

    2015-01-01

    The gene encoding human hemojuvelin (HJV) is one of the genes that, when mutated, can cause juvenile hemochromatosis, an early-onset inherited disorder associated with iron overload. The 5′ untranslated region of the human HJV mRNA has two upstream open reading frames (uORFs), with 28 and 19 codons formed by two upstream AUGs (uAUGs) sharing the same in-frame stop codon. Here we show that these uORFs decrease the translational efficiency of the downstream main ORF in HeLa and HepG2 cells. Indeed, ribosomal access to the main AUG is conditioned by the strong uAUG context, which results in the first uORF being translated most frequently. The reach of the main ORF is then achieved by ribosomes that resume scanning after uORF translation. Furthermore, the amino acid sequences of the uORF-encoded peptides also reinforce the translational repression of the main ORF. Interestingly, when iron levels increase, translational repression is relieved specifically in hepatic cells. The upregulation of protein levels occurs along with phosphorylation of the eukaryotic initiation factor 2α. Nevertheless, our results support a model in which the increasing recognition of the main AUG is mediated by a tissue-specific factor that promotes uORF bypass. These results support a tight HJV translational regulation involved in iron homeostasis. PMID:25666510

  10. Cis-Acting Sequence Elements and Upstream Open Reading Frame in Mouse Utrophin-A 5'-UTR Repress Cap-Dependent Translation

    PubMed Central

    Ghosh, Trinath; Basu, Utpal

    2015-01-01

    Utrophin, the autosomal homologue of dystrophin can functionally compensate for dystrophin deficiency. Utrophin upregulation could therefore be a therapeutic strategy in Duchenne Muscular Dystrophy (DMD) that arises from mutation in dystrophin gene. In contrast to its transcriptional regulation, mechanisms operating at post-transcriptional level of utrophin expression have not been well documented. Although utrophin-A 5'-UTR has been reported with internal ribosome entry site (IRES), its inhibitory effect on translation is also evident. In the present study we therefore aimed to compare relative contribution of cap-independent and cap-dependent translation with mouse utrophin-A 5'-UTR through m7G-capped and A-capped mRNA transfection based reporter assay. Our results demonstrate that cap-independent translation with utrophin-A 5'-UTR is not as strong as viral IRES. However, cap-independent mode has significant contribution as cap-dependent translation is severely repressed with utrophin-A 5'-UTR. We further identified two sequence elements and one upstream open reading frame in utrophin-A 5'-UTR responsible for repression. The repressor elements in utrophin-A 5'-UTR may be targeted for utrophin upregulation. PMID:26230628

  11. Fluency Interventions for Developmental Readers: Repeated Readings and Wide Reading

    ERIC Educational Resources Information Center

    Ari, Omer

    2011-01-01

    Despite recent findings that show fluency deficits in developmental readers, the field of developmental reading remains remiss in fluency instruction. This article provides a summary intended to increase college reading teachers' understanding of reading fluency and fluency instruction. In addition, included are the step-by-step procedures of…

  12. Additivity of detector responses of a portable direct-reading 10. 2 eV photoionization detector and a flame ionization gas chromatograph for atmospheres of multicomponent organics: use of PID/FID ratios

    SciTech Connect

    Lee, I.N.; Hee, S.S.Q.; Clark, C.S.

    1987-05-01

    The H-Nu PI-101 with a photoionization detector (PID) of 10.2 eV and Century OVA-128 equipped with a flame ionization detector (FID) were evaluated for the additivity of their responses to a defined mixtures of dissimilar organic vapors at a 0 and 90% relative humidity (RH). The responses of both instruments were additive as long as the effect of RH was accounted for the PID. The PI-101 was not as precise as the Century OVA-128 for 90% RH atmospheres. PID/FID ratios did not change in the presence of 90% RH as long as the effect of RH also was accounted for in the PID reading. The compounds investigated included: toluene, benzaldehyde; 1,2,4-trichlorobenzene, methyl chloroform, methylene dichloride, methyl ethyl ketone, ethanol and acetonitrile.

  13. Who's Reading and Why: Reading Habits of 1st Grade through Graduate Students

    ERIC Educational Resources Information Center

    Camp, Deanne

    2007-01-01

    The habit of reading develops over a period of time. This study explored reading habits across a wide range of students. An open-ended survey of reading habits involved 242 participants from grades 1, 4, 6, 8, 11, undergraduate non-education majors, undergraduate elementary majors, and graduate reading majors. As data were analyzed, themes emerged…

  14. Openings

    PubMed Central

    Selwyn, Peter A.

    2015-01-01

    Reviewing his clinic patient schedule for the day, a physician reflects on the history of a young woman he has been caring for over the past 9 years. What starts out as a routine visit then turns into a unique opening for communication and connection. A chance glimpse out the window of the exam room leads to a deeper meditation on parenthood, survival, and healing, not only for the patient but also for the physician. How many missed opportunities have we all had, without even realizing it, to allow this kind of fleeting but profound opening? PMID:26195687

  15. Openings.

    PubMed

    Selwyn, Peter A

    2015-01-01

    Reviewing his clinic patient schedule for the day, a physician reflects on the history of a young woman he has been caring for over the past 9 years. What starts out as a routine visit then turns into a unique opening for communication and connection. A chance glimpse out the window of the exam room leads to a deeper meditation on parenthood, survival, and healing, not only for the patient but also for the physician. How many missed opportunities have we all had, without even realizing it, to allow this kind of fleeting but profound opening? PMID:26195687

  16. Short-term effects of acupuncture on open-angle glaucoma in retrobulbar circulation: additional therapy to standard medication.

    PubMed

    Takayama, Shin; Seki, Takashi; Nakazawa, Toru; Aizawa, Naoko; Takahashi, Seri; Watanabe, Masashi; Izumi, Masayuki; Kaneko, Soichiro; Kamiya, Tetsuharu; Matsuda, Ayane; Kikuchi, Akiko; Yambe, Tomoyuki; Yoshizawa, Makoto; Nitta, Shin-Ichi; Yaegashi, Nobuo

    2011-01-01

    Background. The relation between glaucoma and retrobulbar circulation in the prognosis has been indicated. Purpose. To investigate the effects of acupuncture on retrobulbar circulation in open-angle glaucoma (OAG) patients. Methods. Eleven OAG patients (20 eyes with OAG) who were treated by topical antiglaucoma medications for at least 3 months were enrolled. Acupuncture was performed once at acupoints BL2, M-HN9, ST2, ST36, SP6, KI3, LR3, GB20, BL18, and BL23 bilaterally. Retrobulbar circulation was measured with color Doppler imaging, and intraocular pressure (IOP) was also measured at rest and one hour after rest or before and after acupuncture. Results. The Δ value of the resistive index in the short posterior ciliary artery (P < .01) and the Δ value of IOP (P < .01) were decreased significantly by acupuncture compared with no acupuncture treatment. Conclusions. Acupuncture can improve the retrobulbar circulation and IOP, which may indicate the efficacy of acupuncture for OAG. PMID:21437193

  17. Rekindle the Love of Reading

    ERIC Educational Resources Information Center

    Isero, Mark

    2014-01-01

    This author describes a reading project using Kindles that was designed to increase the reading habits of 9th graders. With a selection of 500 titles for classroom usage, students were encouraged to read any book they chose--in addition to those required for their school term. Isero states that, in the past, many of his students would not risk…

  18. Recent Additions in the Modeling Capabilities of an Open-Source Wave Energy Converter Design Tool: Preprint

    SciTech Connect

    Tom, N.; Lawson, M.; Yu, Y. H.

    2015-04-20

    WEC-Sim is a midfidelity numerical tool for modeling wave energy conversion devices. The code uses the MATLAB SimMechanics package to solve multibody dynamics and models wave interactions using hydrodynamic coefficients derived from frequency-domain boundary-element methods. This paper presents the new modeling features introduced in the latest release of WEC-Sim. The first feature discussed conversion of the fluid memory kernel to a state-space form. This enhancement offers a substantial computational benefit after the hydrodynamic body-to-body coefficients are introduced and the number of interactions increases exponentially with each additional body. Additional features include the ability to calculate the wave-excitation forces based on the instantaneous incident wave angle, allowing the device to weathervane, as well as import a user-defined wave elevation time series. A review of the hydrodynamic theory for each feature is provided and the successful implementation is verified using test cases.

  19. A Novel Mutation in the Upstream Open Reading Frame of the CDKN1B Gene Causes a MEN4 Phenotype

    PubMed Central

    Occhi, Gianluca; Regazzo, Daniela; Trivellin, Giampaolo; Boaretto, Francesca; Ciato, Denis; Bobisse, Sara; Ferasin, Sergio; Cetani, Filomena; Pardi, Elena; Korbonits, Márta; Pellegata, Natalia S.; Sidarovich, Viktoryia; Quattrone, Alessandro; Opocher, Giuseppe; Mantero, Franco; Scaroni, Carla

    2013-01-01

    The CDKN1B gene encodes the cyclin-dependent kinase inhibitor p27KIP1, an atypical tumor suppressor playing a key role in cell cycle regulation, cell proliferation, and differentiation. Impaired p27KIP1 expression and/or localization are often observed in tumor cells, further confirming its central role in regulating the cell cycle. Recently, germline mutations in CDKN1B have been associated with the inherited multiple endocrine neoplasia syndrome type 4, an autosomal dominant syndrome characterized by varying combinations of tumors affecting at least two endocrine organs. In this study we identified a 4-bp deletion in a highly conserved regulatory upstream ORF (uORF) in the 5′UTR of the CDKN1B gene in a patient with a pituitary adenoma and a well-differentiated pancreatic neoplasm. This deletion causes the shift of the uORF termination codon with the consequent lengthening of the uORF–encoded peptide and the drastic shortening of the intercistronic space. Our data on the immunohistochemical analysis of the patient's pancreatic lesion, functional studies based on dual-luciferase assays, site-directed mutagenesis, and on polysome profiling show a negative influence of this deletion on the translation reinitiation at the CDKN1B starting site, with a consequent reduction in p27KIP1 expression. Our findings demonstrate that, in addition to the previously described mechanisms leading to reduced p27KIP1 activity, such as degradation via the ubiquitin/proteasome pathway or non-covalent sequestration, p27KIP1 activity can also be modulated by an uORF and mutations affecting uORF could change p27KIP1 expression. This study adds the CDKN1B gene to the short list of genes for which mutations that either create, delete, or severely modify their regulatory uORFs have been associated with human diseases. PMID:23555276

  20. Multicultural Reading

    ERIC Educational Resources Information Center

    Veltze, Linda

    2004-01-01

    Multicultural reading advocates believe in the power of literature to transform and to change people's lives. They take seriously the arguments that racism and prejudice can be lessened through multicultural reading, and also that children from undervalued societal groups who read books that depict people like themselves in a positive light will…

  1. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 19 Customs Duties 1 2011-04-01 2011-04-01 false Public reading rooms. 103.1 Section 103.1 Customs... reading rooms. Each office listed below will maintain a public reading room or public reading area where... Angeles Street, Los Angeles, California 90012. The reading rooms are open to the public during...

  2. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Public reading rooms. 103.1 Section 103.1 Customs... reading rooms. Each office listed below will maintain a public reading room or public reading area where... Angeles Street, Los Angeles, California 90012. The reading rooms are open to the public during...

  3. The anticentre old open clusters Berkeley 27, Berkeley 34 and Berkeley 36: new additions to the BOCCE project

    NASA Astrophysics Data System (ADS)

    Donati, P.; Bragaglia, A.; Cignoni, M.; Cocozza, G.; Tosi, M.

    2012-08-01

    In this paper, we present the investigation of the evolutionary status of three open clusters: Berkeley 27, Berkeley 34 and Berkeley 36, all located in the Galactic anticentre direction. All of them were observed with SUperb Seeing Imager 2 at the New Technology Telescope using the Bessel B, V and I filters. The cluster parameters have been obtained using the synthetic colour-magnitude diagram (CMD) method, i.e. the direct comparison of the observational CMDs with a library of synthetic CMDs generated with different evolutionary sets (Padova, FRANEC and FST). This analysis shows that Berkeley 27 has an age between 1.5 and 1.7 Gyr, a reddening E(B-V) in the range 0.40-0.50 and a distance modulus (m-M)0 between 13.1 and 13.3; Berkeley 34 is older with an age in the range 2.1-2.5 Gyr, E(B-V) between 0.57 and 0.64 and (m-M)0 between 14.1 and 14.3; Berkeley 36, with an age between 7.0 and 7.5 Gyr, has a reddening of E(B-V) ˜ 0.50 and a distance modulus (m-M)0 between 13.1 and 13.2. For all the clusters, our analysis suggests a subsolar metallicity in accord with their position in the outer Galactic disc. This work is based on data collected at the European Southern Observatory (ESO) telescopes under programme 076.D-0119.

  4. Book Clubs in Developmental Reading: Building Reading Comprehension, Fostering Reading Enjoyment, and Engaging Students

    ERIC Educational Resources Information Center

    Maldonado, Michele

    2012-01-01

    The use of book clubs in college developmental reading classes is an effective way to encourage reluctant readers to build and strengthen reading skills, foster reading enjoyment, and engage students. In addition, book clubs build a sense of community within the classroom as the students converse and share their interpretations of the reading…

  5. Identification of the human papillomavirus type 6b L1 open reading frame protein in condylomas and corresponding antibodies in human sera.

    PubMed

    Li, C C; Shah, K V; Seth, A; Gilden, R V

    1987-09-01

    Genital warts (condylomata acuminata) are among the most frequent sexually transmitted infections. Human papillomavirus type 6 (HPV-6), which is etiologically related to a majority of these lesions, has not been propagated in tissue culture. We generated two forms of HPV-6 viral antigens: a chemically synthesized oligopeptide (referred to as the C-terminal synthetic peptide) corresponding to residues 482 to 495 of the 500-amino-acid-long L1 open reading frame (ORF), and a bacterially expressed 54-kilodalton (kDa) fusion protein containing the N-terminal 13 amino acids encoded by the lambda bacteriophage cII gene followed by one vector-insert junctional residue and 462 amino acids of the L1 ORF sequence (residues 39 to 500). The cII-L1 fusion protein was specifically recognized by an antipeptide serum directed against the N-terminal 13 amino acids derived from the cII gene, an antiserum raised against the C-terminal synthetic peptide, and a genus-specific serum prepared by immunization with disrupted viral capsids. The 54-kDa fusion protein was purified, and the sequence of its first 36 amino acids was determined and found to be as predicted by the DNA sequence. Both the genus-specific anticapsid serum and the antiserum raised against the fusion protein identified authentic L1 ORF proteins in HPV-1-induced (58 kDa) and HPV-6/11-induced (56 kDa) papillomas. The synthetic peptide antiserum recognized the 56- to 58-kDa protein in HPV-6-induced warts, but not in HPV-1- or HPV-11-infected specimens. Using the fusion protein as antigen in immunoassays, we were able to detect the corresponding antibodies in human sera. PMID:3039162

  6. Pretreatment sequence diversity differences in the full-length hepatitis C virus open reading frame correlate with early response to therapy.

    PubMed

    Donlin, Maureen J; Cannon, Nathan A; Yao, Ermei; Li, Jia; Wahed, Abdus; Taylor, Milton W; Belle, Steven H; Di Bisceglie, Adrian M; Aurora, Rajeev; Tavis, John E

    2007-08-01

    Pegylated alpha interferon and ribavirin therapy for hepatitis C virus (HCV) genotype 1 infection fails for half of Caucasian American patients (CA) and more often for African Americans (AA). The reasons for these low response rates are unknown. HCV is highly genetically variable, but it is unknown how this variability affects response to therapy. To assess effects of viral diversity on response to therapy, the complete pretreatment genotype 1 HCV open reading frame was sequenced using samples from 94 participants in the Virahep-C study. Sequences from patients with >3.5 log declines in viral RNA levels by day 28 (marked responders) were more variable than those from patients with declines of <1.4 log (poor responders) in NS3 and NS5A for genotype 1a and in core and NS3 for genotype 1b. These correlations remained when all T-cell epitopes were excluded, indicating that these differences were not due to differential immune selection. When the sequences were compared by race of the patients, higher diversity in CA patients was found in E2 and NS2 but only for genotype 1b. Core, NS3, and NS5A can block the action of alpha interferon in vitro; hence, these genetic patterns are consistent with multiple amino acid variations independently impairing the function of HCV proteins that counteract interferon responses in humans, resulting in HCV strains with variable sensitivity to therapy. No evidence was found for novel HCV strains in the AA population, implying that AA patients may be infected with a higher proportion of the same resistant strains that are found in CA patients. PMID:17522222

  7. Analysis and mapping of a family of 3'-coterminal transcripts containing coding sequences for human cytomegalovirus open reading frames UL93 through UL99.

    PubMed Central

    Wing, B A; Huang, E S

    1995-01-01

    Human cytomegalovirus (HCMV) open reading frames (ORFs) UL93 through UL99 are contained within a region of viral genome that is well conserved in all herpesviruses. Previous reports detailing the expression of ORF UL99 (also referred to as the 28-kDa virion phosphoprotein or pp28) indicated that the pattern of transcription proximal to pp28 is extremely complex and involves a number of large overlapping transcripts, none of which have been characterized. We have used an RNA-mapping approach consisting of Northern (RNA) hybridization, RNase protection, and primer extensions to determine the coding capacity of several large-molecular-weight transcripts which overlap the 1.3- and 1.6-kb UL99-specific transcripts. Our results suggest that six differentially regulated transcripts with sizes of 2.6, 4.7, 5.6, 7.3, 9.1, and 10.5 kb, and derived from the same strand of the viral genome overlap, are 3'-coterminal with the smaller UL99-specific transcripts. On the basis of 5'-end mapping via primer extension and RNase protection, we have determined that the 2.6- to 10.5-kb messages initiate upstream of each of the potential ORFs in this region, UL98, UL97, UL96, UL95, UL94, and UL93. By using cycloheximide and ganciclovir [9-(1,3-dihydroxy-2-propoxymethyl)guanine] to block de novo viral protein synthesis and viral DNA replication, respectively, we have determined that the 2.6-, 4.7-, 5.6-, and 7.3-kb messages have characteristics of early or early-late transcripts, whereas the 9.1- and 10.5-kb messages appear to be true late transcripts. The evolutionary conservation of ORFs UL93 through UL99 and their transcriptional regulation in other herpesviruses are discussed. PMID:7853485

  8. A Short Open Reading Frame Encompassing the MicroRNA173 Target Site Plays a Role in trans-Acting Small Interfering RNA Biogenesis.

    PubMed

    Yoshikawa, Manabu; Iki, Taichiro; Numa, Hisataka; Miyashita, Kyoko; Meshi, Tetsuo; Ishikawa, Masayuki

    2016-05-01

    trans-Acting small interfering RNAs (tasiRNAs) participate in the regulation of organ morphogenesis and determination of developmental timing in plants by down-regulating target genes through mRNA cleavage. The production of tasiRNAs is triggered by microRNA173 (miR173) and other specific microRNA-mediated cleavage of 5'-capped and 3'-polyadenylated primary TAS transcripts (pri-TASs). Although pri-TASs are not thought to encode functional proteins, they contain multiple short open reading frames (ORFs). For example, the primary TAS2 transcript (pri-TAS2) contains 11 short ORFs, and the third ORF from the 5' terminus (ORF3) encompasses the miR173 target site. Here, we show that nonsense mutations in ORF3 of pri-TAS2 upstream of the miR173 recognition site suppress tasiRNA accumulation and that ORF3 is translated in vitro. Glycerol gradient centrifugation analysis of Arabidopsis (Arabidopsis thaliana) plant extracts revealed that pri-TAS2 and its miR173-cleaved 5' and 3' fragments are fractionated together in the polysome fractions. These and previous results suggest that the 3' fragment of pri-TAS2, which is a source of tasiRNAs, forms a huge complex containing SGS3, miR173-programmed AGO1 RNA-induced silencing complex, the 5' fragment, and ribosomes. This complex overaccumulated, moderately accumulated, and did not accumulate in rdr6, sde5, and sgs3 mutants, respectively. The sgs3 sde5 and rdr6 sde5 double mutants showed phenotypes similar to those of sgs3 and sde5 single mutants, respectively, with regard to the TAS2-related RNA accumulation, suggesting that the complex is formed in an SGS3-dependent manner, somehow modified and stabilized by SDE5, and becomes competent for RDR6 action. Ribosomes in this complex likely play an important role in this process. PMID:26966170

  9. Open reading frame 3, which is adjacent to the mycocerosic acid synthase gene, is expressed as an acyl coenzyme A synthase in Mycobacterium bovis BCG.

    PubMed Central

    Fitzmaurice, A M; Kolattukudy, P E

    1997-01-01

    The aim of this study was to test for expression of a 900-bp open reading frame (ORF), ORF3, located at the 5' end of the mycocerosic acid synthase gene in Mycobacterium bovis BCG and to determine the nature of the ORF3 protein. ORF3 was expressed as a 61-kDa C-terminal fusion protein with glutathione S-transferase in Escherichia coli. Polyclonal rabbit antiserum, prepared against this fusion protein, cross-reacted with a 65-kDa protein in M. bovis BCG crude extracts. Since this protein was larger than that predicted from the nucleotide sequence (32 kDa), ORF3 was resequenced, revealing an ORF of 1,749 bp that encodes a 64.8-kDa protein containing 583 amino acids. Reverse transcription-PCR revealed that ORF3 is expressed in M. bovis BCG. The ORF3 product has a high degree of similarity to the acyladenylate family of enzymes. Immunoaffinity absorption chromatography was used to isolate the 65-kDa cross-reacting protein from M. bovis BCG. This purified protein catalyzed coenzyme A (CoA) ester synthesis of n-C10 to n-C18 fatty acids but not mycocerosic acids. ORF3 antibodies severely inhibited acyl-CoA synthase activities of the purified protein and extracts of M. bovis BCG, Mycobacterium smegmatis, and E. coli. They also showed immunological cross-reactivity with proteins in these extracts. Both the ORF3 protein and the acyl-CoA synthase activity were located in the cell cytosol or were loosely associated with the cell membrane. These results indicate that ORF3 encodes an acyl-CoA synthase-like protein. PMID:9098059

  10. Zm908p11, encoded by a short open reading frame (sORF) gene, functions in pollen tube growth as a profilin ligand in maize

    PubMed Central

    Dong, Xue; Wang, Dongxue; Liu, Peng; Li, Chengxia; Zhao, Qian; Zhu, Dengyun; Yu, Jingjuan

    2013-01-01

    Double fertilization of flowering plants depends on the targeted transportation of sperm to the embryo sac by the pollen tube. Currently, little is known about the underlying molecular mechanisms that regulate pollen germination and pollen tube growth in maize (Zea mays). Here, a maize pollen-predominant gene Zm908, with several putative short open reading frames (sORFs), was isolated and characterized. The longest ORF of Zm908 encodes a small protein of 97 amino acids. This was designated as Zm908p11 and is distributed throughout the maize pollen tube. Western blot detected the small peptide in mature pollen. Quantitative reverse transcription–PCR and northern blot analysis revealed that Zm908p11 was expressed predominantly in mature pollen grains. Ectopic overexpression of full-length Zm908 and Zm908p11 in tobacco resulted in defective pollen, while transgenic tobacco plants with a site-specific mutation or a frameshift mutation of Zm908p11 showed normal pollen development. Overexpression of Zm908p11 in maize decreased pollen germination efficiency. Maize pollen cDNA library screening and protein–protein interaction assays demonstrated that Zm908p11 interacts with maize profilin 1 (ZmPRO1). A microarray analysis identified 273 up-regulated and 203 down-regulated genes in the overexpressing transgenic Zm908p11 pollen. Taken together, these results indicate that Zm908 functions as Zm908p11, and binds to profilins as a novel ligand, with a required role during pollen tube growth in maize. Accordingly, a model is proposed for the role of Zm908p11 during pollen tube growth in maize. PMID:23676884

  11. The Herpes Simplex Virus Type 1 UL3 Transcript Starts within the UL3 Open Reading Frame and Encodes a 224-Amino-Acid Protein▿

    PubMed Central

    Markovitz, Nancy S.

    2007-01-01

    Several different herpes simplex viruses (HSVs) and vectors are being explored as therapeutic products for use in the treatment of cancer and neurological disorders. The viral strain and the combination of mutant viral genes that ultimately may serve as a safe and optimal backbone for such products are still being explored. The large genome size and complexity of the viral life cycle make such determinations difficult, because the significance of differences between proposed products is difficult to evaluate. For example, we previously reported that two lineages of γ34.5-deleted HSVs used in clinical studies differ from each other in the size of the UL3 protein expressed (M. J. Dambach et al., Mol. Ther. 13:891-898, 2006). Because the function of UL3 is not known and UL3 gene expression is poorly understood, the significance of such a difference cannot be predicted. Here, I begin to address the function of UL3 by investigating UL3 gene expression. I report that the transcript start site of UL3 mRNA isolated from HSV type 1 (HSV-1)-infected cells maps to a position downstream of the predicted translation start site. By constructing and characterizing the recombinant virus CB8116, which has a mutation in the first in-frame start codon of this UL3 transcript, I demonstrated that UL3 protein translation initiates at the second in-frame start codon of the UL3 open reading frame. This information adds to the body of basic knowledge of HSV-1 biology that forms the foundation for our current understanding of HSV-based products. Future research on HSV-1 biology will facilitate the rational design and evaluation of future generations of therapeutic viruses. PMID:17626086

  12. New PCR-Based Open Reading Frame Typing Method for Easy, Rapid, and Reliable Identification of Acinetobacter baumannii International Epidemic Clones without Performing Multilocus Sequence Typing

    PubMed Central

    Suzuki, Masahiro; Hosoba, Eriko; Matsui, Mari

    2014-01-01

    Antimicrobial resistance issues have become a global health concern. The rapid identification of multidrug-resistant microbes, which depends on microbial genomic information, is essential for overcoming growing antimicrobial resistance challenges. However, genotyping methods, such as multilocus sequence typing (MLST), for identifying international epidemic clones of Acinetobacter baumannii are not easily performed as routine tests in ordinary clinical laboratories. In this study, we aimed to develop a novel genotyping method that can be performed in ordinary microbiology laboratories. Several open reading frames (ORFs) specific to certain bacterial genetic lineages or species, together with their unique distribution patterns on the chromosomes showing a good correlation with the results of MLST, were selected in A. baumannii and other Acinetobacter spp. by comparing their genomic data. The distribution patterns of the ORFs were visualized by agarose gel electrophoresis after multiplex PCR amplification and digitized. A. baumannii sequence types (STs) corresponding to international clones I and II were successfully discriminated from other STs and Acinetobacter species by detecting the distribution patterns of their ORFs using the multiplex PCR developed here. Since bacterial STs can be easily expressed as digitized numeric data with plus (+) expressed as 1 and minus (−) expressed as 0, the results of the method can be easily compared with those obtained by different tests or laboratories. This PCR-based ORF typing (POT) method can easily and rapidly identify international epidemic clones of A. baumannii and differentiate this microbe from other Acinetobacter spp. Since this POT method is easy enough to be performed even in ordinary clinical laboratories, it would also contribute to daily infection control measures and surveillance. PMID:24899031

  13. Positive expression of protein chromosome 9 open reading frame 86 (C9orf86) correlated with poor prognosis in non-small cell lung cancer patients

    PubMed Central

    Peng, Gui-Lin; Tao, Ya-Lan; Wu, Qi-Nian; Zhang, Yu

    2016-01-01

    Background Chromosome 9 open reading frame 86 (C9orf86) is a novel subfamily of GTPases. Previous studies have implicated C9orf86 as a potential oncogene. Methods C9orf86 expression was detected in non-small cell lung cancer (NSCLC) cell lines and human bronchial epithelial (16HBE) cell lines by RT-PCR and western blotting. Immunohistochemistry (IHC) was used to detect 180 consecutive NSCLC specimens and 16 normal lung tissues. The correlation between C9orf86 expression and clinicopathological parameters was evaluated. Kaplan-Meier survival analysis and Cox hazards ratio models were used to estimate the effect of C9orf86 expression on survival. Results C9orf86 was expressed in the cytoplasm in 74 of 180 (41.11%) NSCLC specimens. In clinical pathology analysis, C9orf86 expression significantly correlated with lymph node metastasis and clinical stage significantly (P<0.05). Multivariable analysis confirmed that C9orf86 expression increased the risk of death after adjusting for other clinicopathological factors (P<0.01). Overall survival (OS) and disease-free survival (DFS) were significantly prolonged in the C9orf86 negative group compared to the C9orf86 positive group (P<0.001). Adjuvant chemotherapy prolonged OS and DFS in resected NSCLC patients with C9orf86 negative expression (P<0.001) but not C9orf86 positive. Conclusions Positive expression of C9orf86 is an independent prognostic factor for NSCLC patients, and C9orf86 may serve as a prognostic biomarker for patients with NSCLC. PMID:27499931

  14. Functional Characterization of Kaposi's Sarcoma-Associated Herpesvirus Open Reading Frame K8 by Bacterial Artificial Chromosome-Based Mutagenesis▿ †

    PubMed Central

    Wang, Yan; Sathish, Narayanan; Hollow, Charles; Yuan, Yan

    2011-01-01

    The open reading frame K8 of Kaposi's sarcoma-associated herpesvirus (KSHV) encodes a basic leucine zipper (bZip) protein that binds to the origin of viral DNA replication and is an integral component of viral lytic DNA replication complex. Moreover, K8 physically interacts with replication and transcription activator (RTA) and represses its transactivation activity on several viral promoters. To investigate the role of this protein in viral life cycle, we constructed two K8-null recombinant mutant viruses (BAC-ΔK8 and BAC-stopK8) by using a bacterial artificial chromosome (BAC) system. Latent viral infection can be reconstituted in 293T and BJAB cells with wild-type and the K8-null recombinant viruses by introducing the cloned viral genomes into the cells. When the cells carrying these viruses were induced with 12-O-tetradecanoylphorbol-13-acetate (TPA) and sodium butyrate, no significant difference was seen in overall viral gene expression between wild-type and K8-null viruses, with lytic DNA replication still active in the latter. However, 293T cells harboring K8-null mutant viruses, either BAC-ΔK8 or BAC-stopK8, displayed lower copy numbers of latent KSHV genome in comparison with wild-type viruses. Furthermore, although K8 deficiency appeared to not affect infectivity when K8-null viruses were used to infect 293T, primary human microvascular dermal endothelial and human foreskin fibroblast cells, they exhibited much lower viral genome copy numbers in all types of cell compared to wild-type viruses. Taken together, these data suggest a possible role of K8 in abortive lytic DNA replication occurring in early stages of de novo infection or in the maintenance of latent viral genomes. PMID:21159864

  15. Characterization of the Tupaia Rhabdovirus Genome Reveals a Long Open Reading Frame Overlapping with P and a Novel Gene Encoding a Small Hydrophobic Protein

    PubMed Central

    Springfeld, Christoph; Darai, Gholamreza; Cattaneo, Roberto

    2005-01-01

    Rhabdoviruses are negative-stranded RNA viruses of the order Mononegavirales and have been isolated from vertebrates, insects, and plants. Members of the genus Lyssavirus cause the invariably fatal disease rabies, and a member of the genus Vesiculovirus, Chandipura virus, has recently been associated with acute encephalitis in children. We present here the complete genome sequence and transcription map of a rhabdovirus isolated from cultivated cells of hepatocellular carcinoma tissue from a moribund tree shrew. The negative-strand genome of tupaia rhabdovirus is composed of 11,440 nucleotides and encodes six genes that are separated by one or two intergenic nucleotides. In addition to the typical rhabdovirus genes in the order N-P-M-G-L, a gene encoding a small hydrophobic putative type I transmembrane protein of approximately 11 kDa was identified between the M and G genes, and the corresponding transcript was detected in infected cells. Similar to some Vesiculoviruses and many Paramyxovirinae, the P gene has a second overlapping reading frame that can be accessed by ribosomal choice and encodes a protein of 26 kDa, predicted to be the largest C protein of these virus families. Phylogenetic analyses of the tupaia rhabdovirus N and L genes show that the virus is distantly related to the Vesiculoviruses, Ephemeroviruses, and the recently characterized Flanders virus and Oita virus and further extends the sequence territory occupied by animal rhabdoviruses. PMID:15890917

  16. West Nile alternative open reading frame (N-NS4B/WARF4) is produced in infected West Nile Virus (WNV) cells and induces humoral response in WNV infected individuals

    PubMed Central

    2012-01-01

    Background West Nile Virus (WNV) is a flavivirus that requires an efficient humoral and cellular host response for the control of neuroinvasive infection. We previously reported the existence of six alternative open reading frame proteins in WNV genome, one of which entitled WARF4 is exclusively restricted to the lineage I of the virus. WARF4 is able to elicit antibodies in WNV infected horses; however, there was no direct experimental proof of the existence of this novel protein. The purpose of this study was to demonstrate the in vitro production of WARF4 protein following WNV infection of cultured VERO cells and its immunity in WNV infected individuals. Results We produced a monoclonal antibody against WARF4 protein (MAb 3A12) which detected the novel protein in WNV lineage I-infected, cultured VERO cells while it did not react with WNV lineage II infected cells. MAb 3A12 specificity to WARF4 protein was confirmed by its reactivity to only one peptide among four analyzed that cover the full WARF4 amino acids sequence. In addition, WARF4 protein was expressed in the late phase of WNV lineage I infection. Western blotting and bioinformatics analyses strongly suggest that the protein could be translated by programmed −1 ribosomal frameshifting process. Since WARF4 is embedded in the NS4B gene, we rename this novel protein N-NS4B/WARF4. Furthermore, serological analysis shows that N-NS4B/WARF4 is able to elicit antibodies in WNV infected individuals. Conclusions N-NS4B/WARF4 is the second Alternative Reading Frame (ARF) protein that has been demonstrated to be produced following WNV infection and might represent a novel tool for a better characterization of immune response in WNV infected individuals. Further serological as well as functional studies are required to characterize the function of the N-NS4B/WARF4 protein. Since the virus might actually make an extensive use of ARFs, it appears important to investigate the novel six ARF putative proteins of WNV. PMID

  17. Genetic change in the open reading frame of bovine viral diarrhea virus is introduced more rapidly during the establishment of a single persistent infection than from multiple acute infections.

    PubMed

    Neill, John D; Newcomer, Benjamin W; Marley, Shonda D; Ridpath, Julia F; Givens, M Daniel

    2011-06-01

    Bovine viral diarrhea viruses (BVDV) are ubiquitous viral pathogens of cattle with a high degree of sequence diversity amongst strains circulating in livestock herds. The driving force behind change in sequence is not well established but the inaccurate replication of the genomic RNA by a viral RNA polymerase without proof-reading capabilities as well as immune pressure on immunodominant proteins are thought to play major roles. Additionally, it is not clear when the majority of changes are introduced, whether during acute infections with exposure to innate and adaptive immune responses or in establishment of persistent infections (PI) in utero. To examine which generates greater sequence diversity, two groups of viruses were compared. The first was six isolates of a single strain of BVDV-2 that were isolated over greater than a year's time. These viruses caused a series of severe acute (SA) BVD outbreaks over a large geographic area. Changes in nucleotide sequence were determined by comparison of the sequence of each strain to the six virus consensus sequence. The second group was composed of six BVDV strains isolated from PI calves whose dams were exposed to PI cattle. Changes were identified by comparison of the sequence of the progenitor PI virus to that of the progeny viruses from the single in vivo 'passage'. The open reading frames (ORF) of the six SA isolates were >99% identical at the nucleotide level with 30% of the changes being nonsynonymous changes. The amount of genetic change increased with time and distance from the original outbreak. Similarly, the PI viruses isolated from single passage PI calves had >99% identity with the progenitor virus. The number of nucleotide changes in these viruses was equal to or greater than that observed in the SA viruses. The majority of the nonsynonymous changes were found in the structural proteins, with 65% of these occurring in the immunodominant E2 protein. Antigenic mapping studies using a monoclonal antibody

  18. Implementation of the Realized Genomic Relationship Matrix to Open-Pollinated White Spruce Family Testing for Disentangling Additive from Nonadditive Genetic Effects

    PubMed Central

    Gamal El-Dien, Omnia; Ratcliffe, Blaise; Klápště, Jaroslav; Porth, Ilga; Chen, Charles; El-Kassaby, Yousry A.

    2016-01-01

    The open-pollinated (OP) family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates’ offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of “half-sibling” in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench) Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure. PMID:26801647

  19. Additional Therapy with a Mistletoe Product during Adjuvant Chemotherapy of Breast Cancer Patients Improves Quality of Life: An Open Randomized Clinical Pilot Trial.

    PubMed

    Tröger, Wilfried; Zdrale, Zdravko; Tišma, Nevena; Matijašević, Miodrag

    2014-01-01

    Background. Breast cancer patients receiving adjuvant chemotherapy often experience a loss of quality of life. Moreover chemotherapy may induce neutropenia. Patients report a better quality of life when additionally treated with mistletoe products during chemotherapy. Methods. In this prospective randomized open-label pilot study 95 patients were randomized into three groups. All patients were treated with an adjuvant chemotherapy. The primary objective of the study was quality of life, the secondary objective was neutropenia. Here we report the comparison of HxA (n = 34) versus untreated control (n = 31). Results. In the explorative analysis ten of 15 scores of the EORTC QLQ-C30 showed a better quality of life in the HxA group compared to the control group (P < 0.001 to P = 0.038 in Dunnett-T3 test). The difference was clinically relevant (difference of at least 5 points, range 5.4-12.2) in eight of the ten scores. Neutropenia occurred in 7/34 HxA patients and in 8/31 control patients (P = 0.628). Conclusions. This pilot study showed an improvement of quality of life by treating breast cancer patients with HxA additionally to CAF. Although the open design may be a limitation, the findings show the feasibility of a confirmatory study using the methods described here. PMID:24701238

  20. Additional Therapy with a Mistletoe Product during Adjuvant Chemotherapy of Breast Cancer Patients Improves Quality of Life: An Open Randomized Clinical Pilot Trial

    PubMed Central

    Tröger, Wilfried; Ždrale, Zdravko; Tišma, Nevena; Matijašević, Miodrag

    2014-01-01

    Background. Breast cancer patients receiving adjuvant chemotherapy often experience a loss of quality of life. Moreover chemotherapy may induce neutropenia. Patients report a better quality of life when additionally treated with mistletoe products during chemotherapy. Methods. In this prospective randomized open-label pilot study 95 patients were randomized into three groups. All patients were treated with an adjuvant chemotherapy. The primary objective of the study was quality of life, the secondary objective was neutropenia. Here we report the comparison of HxA (n = 34) versus untreated control (n = 31). Results. In the explorative analysis ten of 15 scores of the EORTC QLQ-C30 showed a better quality of life in the HxA group compared to the control group (P < 0.001 to P = 0.038 in Dunnett-T3 test). The difference was clinically relevant (difference of at least 5 points, range 5.4–12.2) in eight of the ten scores. Neutropenia occurred in 7/34 HxA patients and in 8/31 control patients (P = 0.628). Conclusions. This pilot study showed an improvement of quality of life by treating breast cancer patients with HxA additionally to CAF. Although the open design may be a limitation, the findings show the feasibility of a confirmatory study using the methods described here. PMID:24701238

  1. The Protein Phosphatases of Synechocystis sp. Strain PCC 6803: Open Reading Frames sll1033 and sll1387 Encode Enzymes That Exhibit both Protein-Serine and Protein-Tyrosine Phosphatase Activity In Vitro.

    SciTech Connect

    Li, Ruiliang; Potters, M B.; Shi, Liang; Kennelly, Peter J.

    2005-09-01

    The open reading frames (ORFs) encoding two potential protein-serine/threonine phosphatases from the cyanobacterium Synechocystis sp. strain PCC 6803 were cloned and their protein products expressed in Escherichia coli cells. The product of ORF sll1033, SynPPM3, is a homologue of the PPM family of protein-serine/threonine phosphatases found in all eukaryotes as well as many members of the Bacteria. Surprisingly, the recombinant protein phosphatase dephosphorylated phosphotyrosine- as well as phosphoserine-containing proteins in vitro. While kinetic analyses indicate that the enzyme was more efficient at dephosphorylating the latter, replacement of Asp(608) by asparagine enhanced activity toward a phosphotyrosine-containing protein fourfold. The product of ORF sll1387, SynPPP1, is the sole homolog of the PPP family of protein phosphatases encoded by the genome of Synechocystis sp. strain PCC 6803. Like many other bacterial PPPs, the enzyme dephosphorylated phosphoserine- and phosphotyrosine-containing proteins with comparable efficiencies. However, while previously described PPPs from prokaryotic organisms required the addition of exogenous metal ion cofactors, such as Mg(2+) or Mn(2+), for activity, recombinantly produced SynPPP1 displayed near-maximal activity in the absence of added metals. Inductively coupled plasma mass spectrometry indicated that recombinant SynPPP1 contained significant quantities, 0.32 to 0.44 mol/mole total, of Mg and Mn. In this respect, the cyanobacterial enzyme resembled eukaryotic members of the PPP family, which are metalloproteins. mRNA encoding SynPPP1 or SynPPM3 could be detected in cells grown under many, but not all, environmental conditions.

  2. Molecular identification and genetic diversity of open reading frame 7 field isolated porcine reproductive and respiratory syndrome in North Sumatera, Indonesia, in the period of 2008-2014

    PubMed Central

    Faisal, Faisal; Widayanti, Rini; Haryanto, Aris; Tabu, Charles Rangga

    2015-01-01

    Aim: Molecular identification and genetic diversity of open reading frame 7 (ORF7) of field isolated porcine reproductive and respiratory syndrome virus (PRRSV) in North Sumatera, Indonesia, in the period of 2008-2014. Materials and Methods: A total of 47 PRRSV samples were collected from the death case of pigs. The samples were collected from different districts in the period of 2008-2014 from North Sumatera province. Two pairs of primer were designed to amplify ORF7 of Type 1 and 2 PRRSV based on the sequence of reference viruses VR2332 and Lelystad. Viral RNAs were extracted from samples using PureLink™ micro-to-Midi total RNA purification system (Invitrogen). To amplify the ORF7 of PRRSV, the synthesis cDNA and DNA amplification were performed by reverse transcription polymerase chain reaction (RT-PCR) and nested PCR method. Then the DNA sequencing of PCR products and phylogenetic analysis were accomplished by molecular evolutionary genetics analysis version 6.0 software program. Results: RT-: PCR and nested PCR used in this study had successfully detected of 18 samples positive PRRS virus with the amplification products at 703bp and 508bp, respectively. Sequencing of the ORF7 shows that 18 PRRS viruses isolated from North Sumatera belonged to North American (NA). JXA1 Like and classic NA type viruses. Several mutations were detected, particularly in the area of nuclear localization signal (NLS1) and in NLS2. In the local viruses, which were related closed to JXA1 virus; there are two differences in amino acids in position 12 and 43 of ORF7. Our tested viruses showed that the amino acid positions 12 and 43 are Asparagine and Arginine, while the reference virus (VR2332, Lelystad, and JXA1) occupied both by Lysine. Based on differences in two amino acids at position 12 and 43 showed that viruses from North Sumatera has its own uniqueness and related closed to highly pathogenic PRRS (HP-PRRS) virus (JXA1). Conclusion: The results demonstrated that North Sumatera

  3. Murine Gammaherpesvirus 68 Encoding Open Reading Frame 11 Targets TANK Binding Kinase 1 To Negatively Regulate the Host Type I Interferon Response

    PubMed Central

    Kang, Hye-Ri; Cheong, Woo-Chang; Park, Ji-Eun; Ryu, Seungbo; Cho, Hye-Jeong; Youn, Hyunyee; Ahn, Jin-Hyun

    2014-01-01

    ABSTRACT Upon viral infection, type I interferons, such as alpha and beta interferon (IFN-α and IFN-β, respectively), are rapidly induced and activate multiple antiviral genes, thereby serving as the first line of host defense. Many DNA and RNA viruses counteract the host interferon system by modulating the production of IFNs. In this study, we report that murine gammaherpesvirus 68 (MHV-68), a double-stranded DNA virus, encodes open reading frame 11 (ORF11), a novel immune modulator, to block IFN-β production. ORF11-deficient recombinant viruses induced more IFN-β production in fibroblast and macrophage cells than the MHV-68 wild type or a marker rescue virus. MHV-68 ORF11 decreased IFN-β promoter activation by various factors, the signaling of which converges on TBK1-IRF3 activation. MHV-68 ORF11 directly interacted with both overexpressed and endogenous TBK1 but not with IRF3. Physical interactions between ORF11 and endogenous TBK1 were further confirmed during virus replication in fibroblasts using a recombinant virus expressing FLAG-ORF11. ORF11 efficiently reduced interaction between TBK1 and IRF3 and subsequently inhibited activation of IRF3, thereby negatively regulating IFN-β production. Our domain-mapping study showed that the central domain of ORF11 was responsible for both TBK1 binding and inhibition of IFN-β induction, while the kinase domain of TBK1 was sufficient for ORF11 binding. Taken together, these results suggest a mechanism underlying inhibition of IFN-β production by a gammaherpesvirus and highlight the importance of TBK1 in DNA virus replication. IMPORTANCE Gammaherpesviruses are important human pathogens, as they are associated with various kinds of tumors. Upon virus infection, the type I interferon pathway is activated by a series of signaling molecules and stimulates antiviral gene expression. To subvert such interferon antiviral responses, viruses are equipped with multiple factors that can inhibit its critical steps. In this

  4. Microstructural architecture developed in the fabrication of solid and open-cellular copper components by additive manufacturing using electron beam melting

    NASA Astrophysics Data System (ADS)

    Ramirez, Diana Alejandra

    The fabrication of Cu components were first built by additive manufacturing using electron beam melting (EBM) from low-purity, atomized Cu powder containing a high density of Cu2O precipitates leading to a novel example of precipitate-dislocation architecture. These microstructures exhibit cell-like arrays (1-3microm) in the horizontal reference plane perpendicular to the build direction with columnar-like arrays extending from ~12 to >60 microm in length and corresponding spatial dimensions of 1-3 microm. These observations were observed by the use of optical metallography, and scanning and transmission electron microscopy. The hardness measurements were taken both on the atomized powder and the Cu components. The hardness for these architectures ranged from ~HV 83 to 88, in contrast to the original Cu powder microindentation hardness of HV 72 and the commercial Cu base plate hardness of HV 57. These observations were utilized for the fabrication of open-cellular copper structures by additive manufacturing using EBM and illustrated the ability to fabricate some form of controlled microstructural architecture by EBM parameter alteration or optimizing. The fabrication of these structures ranged in densities from 0.73g/cm3 to 6.67g/cm3. These structures correspond to four different articulated mesh arrays. While these components contained some porosity as a consequence of some unmelted regions, the Cu2O precipitates also contributed to a reduced density. Using X-ray Diffraction showed the approximate volume fraction estimated to be ~2%. The addition of precipitates created in the EBM melt scan formed microstructural arrays which contributed to hardening contributing to the strength of mesh struts and foam ligaments. The measurements of relative stiffness versus relative density plots for Cu compared very closely with Ti-6Al-4V open cellular structures - both mesh and foams. The Cu reticulated mesh structures exhibit a slope of n = 2 in contrast to a slope of n = 2

  5. Read Arizona.

    ERIC Educational Resources Information Center

    Arizona State Dept. of Library, Archives and Public Records, Phoenix.

    This manual, designed to help public libraries in Arizona to plan their summer reading programs for children, celebrates the 25th anniversary of the Arizona Reading Program. The material in the manual is prepared for libraries to adapt for their own uses. Chapters of the manual include: (1) Introductory Materials; (2) Goals, Objectives and…

  6. Required Reading

    ERIC Educational Resources Information Center

    Janko, Edmund

    2002-01-01

    In this article, the author insists that those seeking public office prove their literary mettle. As an English teacher, he does have a litmus test for all public officials, judges and senators included--a reading litmus test. He would require that all candidates and nominees have read and reflected on a nucleus of works whose ideas and insights…

  7. Reading Lab.

    ERIC Educational Resources Information Center

    Burt, Lorna

    This guide is intended for use in conducting a reading lab for a broad group of workers ranging from nonreaders to persons reading at a fifth-grade level. Presented first is a course overview that includes the following: information on the course's targeted population, student selection process, and demographics; strategies for adult remediation;…

  8. Repeated Reading.

    ERIC Educational Resources Information Center

    Moyer, Sandra B.

    1982-01-01

    The article reviews research on the use of multiple oral rereading (MOR) with reading disabled students. MOR uses daily practice on a selection of little difficulty. Its effectiveness in increasing fluency (accuracy and speed) is examined, and the role of redundancy in three types of reading models is analyzed. (CL)

  9. Against Readings

    ERIC Educational Resources Information Center

    Edmundson, Mark

    2009-01-01

    Edmundson states that if he could make one wish for the members of his profession, college and university professors of literature, he would wish that for one year, two, three, or five, they would give up readings. By "a reading," he means the application of an analytical vocabulary to describe and (usually) to judge a work of literary art.…

  10. Reading Aloud

    ERIC Educational Resources Information Center

    Delo, Lynda

    2008-01-01

    Many resources are available to elementary teachers who wish to support science learning with literature. Unfortunately, somewhere between middle school and high school, the emphasis on using literature to teach science content--particularly the exercise of reading aloud--has all but disappeared. However, the practice of reading aloud is helpful…

  11. Reading Programs.

    ERIC Educational Resources Information Center

    Au, Kathryn

    2001-01-01

    Notes that a major issue in literacy instruction today is whether commercial reading programs emphasizing phonemic awareness and phonics are more effective than teacher-designed programs that focus on literature-based reading and process writing with integrated skill instruction. Reviews two books that address this controversy. Presents seven…

  12. Reading Remixed

    ERIC Educational Resources Information Center

    Valenza, Joyce Kasman; Stephens, Wendy

    2012-01-01

    Critics claim that digital technologies are killing reading, but these teacher-librarians have observed that teens are as excited about reading as they ever were. Online communities give these readers opportunities to get to know authors, communicate with other fans, and learn more about books of interest. Publishers and authors are responding to…

  13. Teaching Reading.

    ERIC Educational Resources Information Center

    Ricketts, Mary

    1980-01-01

    Described are five approaches to teaching reading: Language Experience, Modified Alphabet, Linguistic, Programmed, and Basal. It is suggested that a good teacher, well trained, certified in his or her profession, an active participant in professional organizations, can teach reading successfully using almost any approach. (KC)

  14. Training of component reading skills.

    PubMed

    Fiedorowicz, C A

    1986-01-01

    Fifteen reading-disabled boys, classified according to reading subskill deficits, formed three subgroups: Oral Reading, Associative, and Sequential. On the rationale that training procedures emphasizing accuracy and speed of response to letters, syllables, and words would improve reading skills, the children were trained daily for two and one-half months. Two schedules of testing and training allowed for an untrained control group and a follow-up group. The results indicated that the computer-assisted training procedures were not only effective in improving component reading skills, but in addition there was a transfer of training to achievement measures of reading word recognition. This study lends support to the hypothesis that training according to subgroup classification, using training procedures which incorporate an application of the automaticity theory and a combination of task-analytic and process-oriented models, is an effective training approach for reading-disabled children. PMID:24243467

  15. Interruptions disrupt reading comprehension.

    PubMed

    Foroughi, Cyrus K; Werner, Nicole E; Barragán, Daniela; Boehm-Davis, Deborah A

    2015-06-01

    Previous research suggests that being interrupted while reading a text does not disrupt the later recognition or recall of information from that text. This research is used as support for Ericsson and Kintsch's (1995) long-term working memory (LT-WM) theory, which posits that disruptions while reading (e.g., interruptions) do not impair subsequent text comprehension. However, to fully comprehend a text, individuals may need to do more than recognize or recall information that has been presented in the text at a later time. Reading comprehension often requires individuals to connect and synthesize information across a text (e.g., successfully identifying complex topics such as themes and tones) and not just make a familiarity-based decision (i.e., recognition). The goal for this study was to determine whether interruptions while reading disrupt reading comprehension when the questions assessing comprehension require participants to connect and synthesize information across the passage. In Experiment 1, interruptions disrupted reading comprehension. In Experiment 2, interruptions disrupted reading comprehension but not recognition of information from the text. In Experiment 3, the addition of a 15-s time-out prior to the interruption successfully removed these negative effects. These data suggest that the time it takes to process the information needed to successfully comprehend text when reading is greater than that required for recognition. Any interference (e.g., an interruption) that occurs during the comprehension process may disrupt reading comprehension. This evidence supports the need for transient activation of information in working memory for successful text comprehension and does not support LT-WM theory. PMID:25867225

  16. Emerging Concerns in Reading; Highlights of the 21st Annual Reading Conference of Lehigh University.

    ERIC Educational Resources Information Center

    Kender, Joseph P., Ed.

    Addressing the question, "How can we teach all educable children to read effectively?" the papers in the first part of this volume look at several topical concerns in reading: "On Relocating the Reading Program: Finding a Better Barn for Our Sacred Cow,""The Transitional Open Classroom,""A Computer Program for Initial Screening of Problem…

  17. Reading with New Tools: An Evaluation of Personal Digital Assistants as Tools for Reading Course Materials.

    ERIC Educational Resources Information Center

    Waycott, Jenny

    2002-01-01

    Discussion of using Personal Digital Assistants (PDAs) to read electronic text focuses on a study that evaluated the use of PDAs for reading course materials in an Open University (United Kingdom) master's course. Considers activity theory and how the PDA changed reading, including portability, screen display, navigation difficulties, and…

  18. Does E-Reading Enhance Reading Fluency?

    ERIC Educational Resources Information Center

    Akbar, Rahima S.; Taqi, Hanan A.; Dashti, Abdulmohsin A.; Sadeq, Taiba M.

    2015-01-01

    Extensive reading is reading as much as possible, for one's own pleasure, at a difficulty level at which one can read smoothly and quickly. In the domain of reading, this paper investigates the effect of extensive reading from e-books, through utilizing a number of downloadable reading application programs on the students' e-devices, as opposed to…

  19. How Does Speed and Accuracy in Reading Relate to Reading Comprehension in Arabic?

    ERIC Educational Resources Information Center

    Abu-Leil, Aula Khateeb; Share, David L.; Ibrahim, Raphiq

    2014-01-01

    The purpose of this study was to investigate the potential contribution of decoding efficiency to the development of reading comprehension among skilled adult native Arabic speakers. In addition, we tried to investigate the influence of Arabic vowels on reading accuracy, reading speed, and therefore to reading comprehension. Seventy-five Arabic…

  20. Oral Reading Fluency and Comprehension in Kenya: Reading Acquisition in a Multilingual Environment

    ERIC Educational Resources Information Center

    Piper, Benjamin; Schroeder, Leila; Trudell, Barbara

    2016-01-01

    Reading research has shown that variable relationships exist between measures of oral reading fluency and reading comprehension, depending on whether the language of the text is the reader's first language or an additional language. This paper explores this phenomenon, using reading assessment data for 2,000 Kenyan children in two or three…

  1. Reading Research in Hungary.

    ERIC Educational Resources Information Center

    Kamaras, Istvan; Nagy, Attila

    1981-01-01

    Notes that most recent reading research conducted in Hungary has focused on the formation of readers' attitudes and value judgments. Discusses studies conducted in the areas of reading psychology, children's reading, reading habits, reading motivation, and readers' responses. (FL)

  2. Network-based reading system for lung cancer screening CT

    NASA Astrophysics Data System (ADS)

    Fujino, Yuichi; Fujimura, Kaori; Nomura, Shin-ichiro; Kawashima, Harumi; Tsuchikawa, Megumu; Matsumoto, Toru; Nagao, Kei-ichi; Uruma, Takahiro; Yamamoto, Shinji; Takizawa, Hotaka; Kuroda, Chikazumi; Nakayama, Tomio

    2006-03-01

    This research aims to support chest computed tomography (CT) medical checkups to decrease the death rate by lung cancer. We have developed a remote cooperative reading system for lung cancer screening over the Internet, a secure transmission function, and a cooperative reading environment. It is called the Network-based Reading System. A telemedicine system involves many issues, such as network costs and data security if we use it over the Internet, which is an open network. In Japan, broadband access is widespread and its cost is the lowest in the world. We developed our system considering human machine interface and security. It consists of data entry terminals, a database server, a computer aided diagnosis (CAD) system, and some reading terminals. It uses a secure Digital Imaging and Communication in Medicine (DICOM) encrypting method and Public Key Infrastructure (PKI) based secure DICOM image data distribution. We carried out an experimental trial over the Japan Gigabit Network (JGN), which is the testbed for the Japanese next-generation network, and conducted verification experiments of secure screening image distribution, some kinds of data addition, and remote cooperative reading. We found that network bandwidth of about 1.5 Mbps enabled distribution of screening images and cooperative reading and that the encryption and image distribution methods we proposed were applicable to the encryption and distribution of general DICOM images via the Internet.

  3. Making Higher Education More Affordable, One Course Reading at a Time: Academic Libraries as Key Advocates for Open Access Textbooks and Educational Resources

    ERIC Educational Resources Information Center

    Okamoto, Karen

    2013-01-01

    Open access textbooks (OATs) and educational resources (OERs) are being lauded as a viable alternative to costly print textbooks. Some academic libraries are joining the OER movement by creating guides to open repositories. Others are promoting OATs and OERs, reviewing them, and even helping to create them. This article analyzes how academic…

  4. How Reading Volume Affects Both Reading Fluency and Reading Achievement

    ERIC Educational Resources Information Center

    Allington, Richard L.

    2014-01-01

    Long overlooked, reading volume is actually central to the development of reading proficiencies, especially in the development of fluent reading proficiency. Generally no one in schools monitors the actual volume of reading that children engage in. We know that the commonly used commercial core reading programs provide only material that requires…

  5. Iconic Prosody in Story Reading

    ERIC Educational Resources Information Center

    Perlman, Marcus; Clark, Nathaniel; Falck, Marlene Johansson

    2015-01-01

    Recent experiments have shown that people iconically modulate their prosody corresponding with the meaning of their utterance (e.g., Shintel et al., 2006). This article reports findings from a story reading task that expands the investigation of iconic prosody to abstract meanings in addition to concrete ones. Participants read stories that…

  6. Accurate reading comprehension rate as an indicator of broad reading in students in first, second, and third grades.

    PubMed

    Ciancio, Dennis; Thompson, Kelly; Schall, Megan; Skinner, Christopher; Foorman, Barbara

    2015-10-01

    The relationship between reading comprehension rate measures and broad reading skill development was examined using data from approximately 1425 students (grades 1-3). Students read 3 passages, from a pool of 30, and answered open-ended comprehension questions. Accurate reading comprehension rate (ARCR) was calculated by dividing the percentage of questions answered correctly (%QC) by seconds required to read the passage. Across all 30 passages, ARCR and its two components, %QC correct and time spent reading (1/seconds spent reading the passage), were significantly correlated with broad reading scores, with %QC resulting in the lowest correlations. Two sequential regressions supported previous findings which suggest that ARCR measures consistently produced meaningful incremental increases beyond %QC in the amount of variance explained in broad reading skill; however, ARCR produced small or no incremental increases beyond reading time. Discussion focuses on the importance of the measure of reading time embedded in brief accurate reading rate measures and directions for future research. PMID:26407836

  7. The Effects of L2 Reading Skills on L1 Reading Skills through Transfer

    ERIC Educational Resources Information Center

    Altmisdort, Gonca

    2016-01-01

    This study investigated whether transfer from L2 to L1 in reading occurs, and if so, which reading sub-skills are transferred into L1 reading. The aim is to identify the role of second language reading skills in L1 reading skills by means of transfer. In addition, the positive effects of the second language transfer to the first language in the…

  8. Does Extensive Reading Promote Reading Speed?

    ERIC Educational Resources Information Center

    He, Mu

    2014-01-01

    Research has shown a wide range of learning benefits accruing from extensive reading. Not only is there improvement in reading, but also in a wide range of language uses and areas of language knowledge. However, few research studies have examined reading speed. The existing literature on reading speed focused on students' reading speed…

  9. Oral Reading Fluency in Second Language Reading

    ERIC Educational Resources Information Center

    Jeon, Eun Hee

    2012-01-01

    This study investigated the role of oral reading fluency in second language reading. Two hundred and fifty-five high school students in South Korea were assessed on three oral reading fluency (ORF) variables and six other reading predictors. The relationship between ORF and other reading predictors was examined through an exploratory factor…

  10. Reading Transformation

    ERIC Educational Resources Information Center

    Reeves, Melinda

    2006-01-01

    The parents of students who attend Decatur High School thought that there was little hope of their kids going on to college. After a year or so in Decatur's reading program, their sons and daughters were both transformed and college bound. In this article, the author describes how Decatur was able to successfully transform their students. Seven…

  11. Reading Poverty.

    ERIC Educational Resources Information Center

    Shannon, Patrick

    The central purpose of this book is to challenge current social constructions of poverty, reading education, and the putative relationship between the two. It explores how official and popular representations of poverty are bound to specific historical, social, and economic conditions of their own production. The book offers four stances of…

  12. The Right to Read Effort in Ohio.

    ERIC Educational Resources Information Center

    Nemeth, Joseph S., Ed.

    1973-01-01

    The federal Right to Read program is funding five school-based reading programs for the third consecutive year in Ohio. In addition to money, Right to Read provides technical assistance and materials to each site. Ball State University coordinates Ohio's team. Dr. Joseph Nemeth is the federally appointed technical assistant for Ohio's five…

  13. Teaching Reading to the Upward Bound Student.

    ERIC Educational Resources Information Center

    Palmer, Princess A.

    Three steps in teaching reading to Upward Bound students are considered in this paper: individualized needs assessment, determination of students' attitudes toward reading, and the actual instruction. In discussing the diagnosis of students' individual needs, the paper describes the Nelson Reading Test and additional diagnostic tests that may be…

  14. Keys to Reading among Middle School Children

    ERIC Educational Resources Information Center

    Smith, Nichole; Day, Barbara

    2013-01-01

    A recent decline in reading has become a major issue, as Americans are not reading out of necessity or as a leisure activity. In addition, a connection has been found between children's leisure reading habits and their level of academic achievement, causing even more concern. (Contains 1 table.)

  15. Interaction Quality during Partner Reading

    PubMed Central

    Meisinger, Elizabeth B.; Schwanenflugel, Paula J.; Bradley, Barbara A.; Stahl, Steven A.

    2009-01-01

    The influence of social relationships, positive interdependence, and teacher structure on the quality of partner reading interactions was examined. Partner reading, a scripted cooperative learning strategy, is often used in classrooms to promote the development of fluent and automatic reading skills. Forty-three pairs of second grade children were observed during partner reading sessions taking place in 12 classrooms. The degree to which the partners displayed social cooperation (instrumental support, emotional support, and conflict management) and on/off task behavior was evaluated. Children who chose their own partners showed greater social cooperation than those children whose teacher selected their partner. However, when the positive interdependence requirements of the task were not met within the pair (neither child had the skills to provide reading support or no one needed support), lower levels of on-task behavior were observed. Providing basic partner reading script instruction at the beginning of the year was associated with better social cooperation during partner reading, but providing elaborated instruction or no instruction was associated with poorer social cooperation. It is recommended that teachers provide basic script instruction and allow children to choose their own partners. Additionally, pairings of low ability children with other low ability children and high ability children with other high ability children should be avoided. Teachers may want to suggest alternate partners for children who inadvertently choose such pairings or adjust the text difficulty to the pair. Overall, partner reading seems to be an enjoyable pedagogical strategy for teaching reading fluency. PMID:19830259

  16. Viewing Reading Recovery as a Restructuring Phenomenon

    ERIC Educational Resources Information Center

    Rinehart, James S.; Short, Paula Myrick

    2010-01-01

    This study investigated components of Reading Recovery that relate to a restructuring paradigm. Specifically, Reading Recovery was analyzed as a way to redesign teachers' work, empower teachers, and affect the core technology of teaching. Data were collected by a survey that consisted of open-ended questions and of categorical response items.…

  17. DNA sequence analysis of a 10 624 bp fragment of the left arm of chromosome XV from Saccharomyces cerevisiae reveals a RNA binding protein, a mitochondrial protein, two ribosomal proteins and two new open reading frames.

    PubMed

    Lafuente, M J; Gamo, F J; Gancedo, C

    1996-09-01

    We have determined the sequence of a 10624 bp DNA segment located in the left arm of chromosome XV of Saccharomyces cerevisiae. The sequence contains eight open reading frames (ORFs) longer than 100 amino acids. Two of them do not present significant homology with sequences found in the databases. The product of ORF o0553 is identical to the protein encoded by the gene SMF1. Internal to it there is another ORF, o0555 that is apparently expressed. The proteins encoded by ORFs o0559 and o0565 are identical to ribosomal proteins S19.e and L18 respectively. ORF o0550 encodes a protein with an RNA binding signature including RNP motifs and stretches rich in asparagine, glutamine and arginine. PMID:8896268

  18. Analysis of the DNA sequence of a 15,500 bp fragment near the left telomere of chromosome XV from Saccharomyces cerevisiae reveals a putative sugar transporter, a carboxypeptidase homologue and two new open reading frames.

    PubMed

    Gamo, F J; Lafuente, M J; Casamayor, A; Ariño, J; Aldea, M; Casas, C; Herrero, E; Gancedo, C

    1996-06-15

    We report the sequence of a 15.5 kb DNA segment located near the left telomere of chromosome XV of Saccharomyces cerevisiae. The sequence contains nine open reading frames (ORFs) longer than 300 bp. Three of them are internal to other ones. One corresponds to the gene LGT3 that encodes a putative sugar transporter. Three adjacent ORFs were separated by two stop codons in frame. These ORFs presented homology with the gene CPS1 that encodes carboxypeptidase S. The stop codons were not found in the same sequence derived from another yeast strain. Two other ORFs without significant homology in databases were also found. One of them, O0420, is very rich in serine and threonine and presents a series of repeated or similar amino acid stretches along the sequence. PMID:8810044

  19. Reading acceleration training changes brain circuitry in children with reading difficulties

    PubMed Central

    Horowitz-Kraus, Tzipi; Vannest, Jennifer J; Kadis, Darren; Cicchino, Nicole; Wang, Yingying Y; Holland, Scott K

    2014-01-01

    Introduction Dyslexia is characterized by slow, inaccurate reading. Previous studies have shown that the Reading Acceleration Program (RAP) improves reading speed and accuracy in children and adults with dyslexia and in typical readers across different orthographies. However, the effect of the RAP on the neural circuitry of reading has not been established. In the current study, we examined the effect of the RAP training on regions of interest in the neural circuitry for reading using a lexical decision task during fMRI in children with reading difficulties and typical readers. Methods Children (8–12 years old) with reading difficulties and typical readers were studied before and after 4 weeks of training with the RAP in both groups. Results In addition to improvements in oral and silent contextual reading speed, training-related gains were associated with increased activation of the left hemisphere in both children with reading difficulties and typical readers. However, only children with reading difficulties showed improvements in reading comprehension, which were associated with significant increases in right frontal lobe activation. Conclusions Our results demonstrate differential effects of the RAP on neural circuits supporting reading in both children with reading difficulties and typical readers and suggest that the intervention may stimulate use of typical neural circuits for reading and engage compensatory pathways to support reading in the developing brain of children with reading difficulties. PMID:25365797

  20. Slow Reading: Reading along "Lectio" Lines

    ERIC Educational Resources Information Center

    Badley, K. Jo-Ann; Badley, Ken

    2011-01-01

    The medieval monastic movement preserved and developed reading practices--lectio--from ancient Greek pedagogy as a slow, mindful approach to reading for formation. This ancient way of reading, now better known as lectio divina, challenges the fast, pragmatic reading so characteristic of our time. We propose that the present moment may be ripe for…

  1. Reading Together: A Successful Reading Fluency Intervention

    ERIC Educational Resources Information Center

    Young, Chase; Mohr, Kathleen A. J.; Rasinski, Timothy

    2015-01-01

    The article describes a reading fluency intervention called Reading Together that combines the method of repeated readings (Samuels, 1979) and the Neurological Impress Method (Heckelman, 1969). Sixteen volunteers from various backgrounds were recruited and trained to deliver the Reading Together intervention to struggling readers in third through…

  2. Pleasure Reading and Reading Rate Gains

    ERIC Educational Resources Information Center

    Beglar, David; Hunt, Alan

    2014-01-01

    This study investigated the effects of (a) the amount of pleasure reading completed, (b) the type of texts read (i.e., simplified or unsimplified books), and (c) the level of simplified texts read by 14 Japanese university students who made the largest reading rate gains over one academic year. The findings indicated that the participants who made…

  3. Is Oral/Text Reading Fluency a “Bridge” to Reading Comprehension?

    PubMed Central

    Kim, Young-Suk Grace; Park, Chea Hyeong; Wagner, Richard K.

    2015-01-01

    In the present study we investigated developmental relations among word reading fluency, listening comprehension, and text reading fluency to reading comprehension in a relatively transparent language, Korean. A total of 98 kindergartners and 170 first graders in Korea were assessed on a series of tasks involving listening comprehension, word reading fluency, text reading fluency, and reading comprehension. Results from multigroup structural equation models showed that text reading fluency was a dissociable construct for both kindergartners and first graders. In addition, a developmental pattern emerged: listening comprehension was not uniquely related to text reading fluency for first graders, but not for kindergartners, over and above word reading fluency. In addition, text reading fluency was uniquely related to reading comprehension for kindergartners, but not for first graders, after accounting for word reading fluency and listening comprehension. For first graders, listening comprehension dominated the relations. There were no differences in the pattern of relations for skilled and less skilled readers in first grade. Results are discussed from a developmental perspective for reading comprehension component skills including text reading fluency. PMID:25653474

  4. Effects of an Intervention Program on Reading and Math Achievement

    ERIC Educational Resources Information Center

    Johnson, Anthony C.

    2010-01-01

    This action research project examined the effects of an intervention program on student reading and math achievement. TCAP reading and math assessments and ThinkLink Learning reading and math assessments were used for the measures on student achievement. Student perceptions and attitudes were measured with a questionnaire and four open-ended…

  5. Cognitive flexibility predicts early reading skills

    PubMed Central

    Colé, Pascale; Duncan, Lynne G.; Blaye, Agnès

    2014-01-01

    An important aspect of learning to read is efficiency in accessing different kinds of linguistic information (orthographic, phonological, and semantic) about written words. The present study investigates whether, in addition to the integrity of such linguistic skills, early progress in reading may require a degree of cognitive flexibility in order to manage the coordination of this information effectively. Our study will look for evidence of a link between flexibility and both word reading and passage reading comprehension, and examine whether any such link involves domain-general or reading-specific flexibility. As the only previous support for a predictive relationship between flexibility and early reading comes from studies of reading comprehension in the opaque English orthography, another possibility is that this relationship may be largely orthography-dependent, only coming into play when mappings between representations are complex and polyvalent. To investigate these questions, 60 second-graders learning to read the more transparent French orthography were presented with two multiple classification tasks involving reading-specific cognitive flexibility (based on words) and non-specific flexibility (based on pictures). Reading skills were assessed by word reading, pseudo-word decoding, and passage reading comprehension measures. Flexibility was found to contribute significant unique variance to passage reading comprehension even in the less opaque French orthography. More interestingly, the data also show that flexibility is critical in accounting for one of the core components of reading comprehension, namely, the reading of words in isolation. Finally, the results constrain the debate over whether flexibility has to be reading-specific to be critically involved in reading. PMID:24966842

  6. The Impact of Technology-Based Reading Programs on Lower Achievers' State Reading Assessment

    ERIC Educational Resources Information Center

    Jacobs, Rhonda Suzanne

    2012-01-01

    Research concerning technology-based reading intervention is limited and additional studies are needed in this area of study. This study examined the individual intervention programs (Read 180 and Thinking Reader) for diverse 6th, 7th, and 8th graders in order to determine the gains per grade level on state standardized reading tests. This study…

  7. Are Read-Alouds and Free Reading "Natural Partners"?: An Experimental Study

    ERIC Educational Resources Information Center

    Cho, Kyung Sook; Choi, Dong Seop

    2008-01-01

    The positive effects of read-alouds and storytelling on literacy development and second-language acquisition have been confirmed many times in the research literature. In addition, there is consistent evidence that in-school free voluntary reading (sustained silent reading) is effective for both first- and second-language acquisition. Trelease…

  8. Phonological Awareness and Reading Speed Deficits in Reading Disabled Greek-Speaking Children

    ERIC Educational Resources Information Center

    Constantinidou, Maria; Stainthorp, Rhona

    2009-01-01

    There is evidence that phonological awareness skills secure decoding ability and that phonological deficits underlie failure to acquire adequate word recognition. Slow word-reading rate may be an additional defining characteristic of reading disability. The present study aimed to investigate whether: (1) reading disabled (RD) Greek-speaking…

  9. Reading Fluency and Self-Efficacy: A Case Study

    ERIC Educational Resources Information Center

    Ferrara, Sandra L. Nes

    2005-01-01

    In this case study, reading fluency was examined within the context of a paired reading instructional intervention. Additionally, this study explored reader self perceptions and the nature of the lived experience of reading for a less skilled reader. A single subject changing criterion design was employed. Baseline reading fluency data were…

  10. How Brain-Injured Children Learn to Read.

    ERIC Educational Resources Information Center

    Doman, Glenn

    This paper discusses the place of reading instruction in the education of brain-injured children and presents some arguments for early reading instruction for children in general. Reading instruction is especially suitable for brain-injured children because reading presents an additional means of stimulating the brain. Meaning is attached to…

  11. READING IN THE ELEMENTARY SCHOOL--SOME BASIC DIMENSIONS.

    ERIC Educational Resources Information Center

    Denver County Public Schools, CO.

    THE READING INSTRUCTION PROGRAM OF THE DENVER PUBLIC SCHOOLS IS SUMMARIZED. OBJECTIVES INCLUDE TEACHING WORD RECOGNITION SKILLS, DEVELOPING THE HABIT OF READING, AND DEVELOPING READING SPEED AND EFFICIENCY. IN ADDITION TO DEFINING THE OBJECTIVES AND BASIC DIMENSIONS OF THE ELEMENTARY READING PROGRAM, THIS REPORT ALSO DISCUSSES THE FOUR COMPONENT…

  12. Beyond Cognition: Reading Motivation and Reading Comprehension

    PubMed Central

    Wigfield, Allan; Gladstone, Jessica; Turci, Lara

    2016-01-01

    The authors review research on children’s reading motivation and its relation to their reading comprehension. They begin by discussing work on the development of school motivation in general and reading motivation in particular, reviewing work showing that many children’s reading motivation declines over the school years. Girls tend to have more positive motivation for reading than do boys, and there are ethnic differences in children’s reading motivation. Over the last 15 years researchers have identified in both laboratory and classroom-based research instructional practices that positively impact students’ reading motivation and ultimately their reading comprehension. There is a strong need for researchers to build on this work and develop and study in different age groups of children effective classroom-based reading motivation instructional programs for a variety of narrative and informational materials.

  13. Assessment of Reading Comprehension, Panel 5; Conference on Studies in Reading (Washington, D.C., August 1974).

    ERIC Educational Resources Information Center

    Smith, Marshall S., Ed.

    The aim of the panel on reading comprehension, sponsored by the National Institute of Education Conference on Studies in Reading, was to determine the influence of intellectual factors, general experiences with the world, knowledge specific to the particular reading task, and general decoding skills to successful reading performance. In addition,…

  14. From Decoding to Reading Comprehension: An Assessment of the Effectiveness of the Training of Intervention Providers to Teach Reading Comprehension

    ERIC Educational Resources Information Center

    Gold, Carol

    2010-01-01

    Research indicates that the most effective instruction in basic reading skills and reading comprehension should take place in the classroom. For some students, however, additional reading instruction outside of the regular classroom may be needed and should begin early in a student's educational career. Since reading comprehension is the goal of…

  15. Reading with Love: Reading of Life Narrative of a Mother of a Child with Cerebral Palsy

    ERIC Educational Resources Information Center

    Mercieca, Daniela; Mercieca, Duncan P.

    2014-01-01

    This paper draws upon Deleuze and Guattari's ideas to suggest a different kind of reading of a narrative of a mother of a child with severe disability, and thus a different kind of ethical response to them. This reading gives readers the possibility of opening up experiences of parents and children with disability, rather than…

  16. Reading Recovery. [Fact Sheets].

    ERIC Educational Resources Information Center

    Reading Recovery Council of North America, Columbus, OH.

    This set of 10 fact sheets (each 2 to 4 pages long) addresses aspects of Reading Recovery, a program that helps children to be proficient readers and writers by the end of the first grade. It discusses the basic facts of Reading Recovery; Reading Recovery for Spanish literacy; Reading Recovery lessons; Reading Recovery professional development;…

  17. Reading Consultant's Handbook.

    ERIC Educational Resources Information Center

    Bourgeois, Penny, Comp.; And Others

    This handbook contains brief essays concerning aspects of reading and reading skills, activities designed to promote those skills, and biographies of reading specialists. The first section of the handbook discusses reading readiness, word recognition, word analysis, word meaning, comprehension, and content area reading. After discussion of each…

  18. Reading and Reality. Proceedings of the Annual Reading Conference (14th, Terre Haute, Indiana, June 14, 1984).

    ERIC Educational Resources Information Center

    Gibbs, Vanita M., Comp.; Waterman, David C., Comp.

    Intended for reading teachers, this pamphlet contains the presentations of the 14th annual reading conference at Indiana State University, beginning with opening remarks by David C. Waterman and welcoming comments by J. Stephen Hazlett. In the opening address, "What Good is Comprehension without Composition?" by Sharon and David Moore, the role of…

  19. Mapping RNA-seq Reads with STAR.

    PubMed

    Dobin, Alexander; Gingeras, Thomas R

    2015-01-01

    Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems. PMID:26334920

  20. Stimulation of sulfate-reducing bacteria in lake water from a former open-pit mine through addition of organic wastes

    SciTech Connect

    Castro, J.M.; Wielinga, B.W.; Gannon, J.E.; Moore, J.N.

    1999-03-01

    A method to improve water quality in a lake occupying a former open-pit mine was evaluated in a laboratory-scale study. Untreated pit lake water contained high levels of sulfate, iron, and arsenic and was mildly acidic ({approximately} pH 6). Varying amounts of two locally available organic waste products were added to pit water and maintained in microcosms under anoxic conditions. In selected microcosms, populations of sulfate-reducing bacteria increased with time; sulfide was generated by sulfate reduction; sulfate, iron, and arsenic concentrations approached zero; and pH approached neutrality. Best results were obtained with intermediate amounts of waste potato skin.

  1. NGSI student activities in open source information analysis in support of the training program of the U.S. DOE laboratories for the entry into force of the additional protocol

    SciTech Connect

    Sandoval, M Analisa; Uribe, Eva C; Sandoval, Marisa N; Boyer, Brian D; Stevens, Rebecca S

    2009-01-01

    In 2008 a joint team from Los Alamos National Laboratory (LANL) and Brookhaven National Laboratory (BNL) consisting of specialists in training of IAEA inspectors in the use of complementary access activities formulated a training program to prepare the U.S. Doe laboratories for the entry into force of the Additional Protocol. As a major part of the support of the activity, LANL summer interns provided open source information analysis to the LANL-BNL mock inspection team. They were a part of the Next Generation Safeguards Initiative's (NGSI) summer intern program aimed at producing the next generation of safeguards specialists. This paper describes how they used open source information to 'backstop' the LANL-BNL team's effort to construct meaningful Additional Protocol Complementary Access training scenarios for each of the three DOE laboratories, Lawrence Livermore National Laboratory, Idaho National Laboratory, and Oak Ridge National Laboratory.

  2. Children Can Love Reading.

    ERIC Educational Resources Information Center

    Zibart, Rosemary

    1980-01-01

    Describes the Reading Is Fundamental Program (RIF), whose reading motivation concept is simple: young people who get the opportunity to freely choose and to own books may begin to experience reading as a pleasurable activity. (Author/LLS)

  3. Reading: The Human Touch.

    ERIC Educational Resources Information Center

    Roswell, Florence G.

    1978-01-01

    Reading programs must be reassessed, and fragmented, isolated, and repetitive exercises must be eliminated. The goal of any reading program is to get the child to experience the joys of reading and learning. (Author/WI)

  4. Cosmetology Reading Strategies. 1980 Vocational Reading Series.

    ERIC Educational Resources Information Center

    Thornton, L. Jay; And Others

    Cosmetology Reading Strategies is one of five instructional guides in the Reading Strategies in Vocational Education Series. Developed to assist teachers working with students considered disadvantaged because of reading deficiency, the guide contains several strategies, suitable for adaptation, specifically related to cosmetology instruction. Each…

  5. Promoting Reading Motivation by Reading Together

    ERIC Educational Resources Information Center

    Monteiro, Vera

    2013-01-01

    In the present project we tested the hypothesis that tutorial situations with peers would benefit children's reading motivation. Participants were from elementary school--80 fourth-graders and 80 second-graders. We used a questionnaire to assess reading motivation. In the tutorial sessions we developed a Paired Reading Program. The children who…

  6. Teaching Reading Comprehension through Collaborative Strategic Reading.

    ERIC Educational Resources Information Center

    Vaughn, Sharon; Klingner, Janette Kettman

    1999-01-01

    Provides an overview of collaborative strategic reading (CSR) as an approach to enhancing the reading-comprehension skills of students with learning disabilities. Procedures for implementing CSR with collaborative groups and techniques for teaching reading-comprehension skills are provided. The role of the teacher is described and sample teaching…

  7. Extensive Reading Quizzes and Reading Attitudes

    ERIC Educational Resources Information Center

    Stoeckel, Tim; Reagan, Nevitt; Hann, Fergus

    2012-01-01

    Extensive reading (ER) has become a common feature of many English as a second or foreign language (ESL/EFL) programs. There is evidence that reading large amounts of easy, interesting material may improve foreign language skills, most notably in vocabulary, reading rates, and overall proficiency. However, teacher evaluation of extensive reading…

  8. RAPSearch: a fast protein similarity search tool for short reads

    PubMed Central

    2011-01-01

    Background Next Generation Sequencing (NGS) is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets. Results We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. For short reads (translated in 6 frames) we tested, RAPSearch achieved ~20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (~1.3-3.2%) of BLASTX similarity hits, but it also discovered additional homologous proteins (~0.3-2.1%) that BLASTX missed. By contrast, BLAT, a tool that is even slightly faster than RAPSearch, had significant loss of sensitivity as compared to RAPSearch and BLAST. Conclusions RAPSearch is implemented as open-source software and is accessible at http://omics.informatics.indiana.edu/mg/RAPSearch. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated. PMID:21575167

  9. Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.

    PubMed Central

    Ogasawara, N; Moriya, S; Yoshikawa, H

    1985-01-01

    We have determined nucleotide sequence of some 10,000 base pairs (bp) in the oriC region of the Bacillus subtilis chromosome. Initiation sites of transcription from this region were determined in vivo by the S1-mapping method. Five major initiation sites were found in the leader sequences of five open reading frames (ORF) deduced from the nucleotide sequence. The sixth site is located inside the ORF323("recF"). Putative promoters were found for each transcript. Function of these promoters was demonstrated in Escherichia coli by the Maxi-cell method using appropriate fragments cloned in pBR vectors. Based on these results, genes in 10,000 bp oriC region are divided into 4 transcriptional units. GyrB composes one unit with two other ORFs, while gyrA constitutes a single unit by itself. The promoters for ORF446("dnaA") and ORF378("dnaN") are located within the putative signal sequences for oriC. Transcription from these promoters is dependent on a dna-initiation gene, dnaB. Images PMID:2987848

  10. Production of Candida antarctica lipase B gene open reading frame using automated PCR gene assembly protocol on robotic workcell and expression in an ethanologenic yeast for use as resin-bound biocatalyst in biodiesel production.

    PubMed

    Hughes, Stephen R; Moser, Bryan R; Harmsen, Amanda J; Bischoff, Kenneth M; Jones, Marjorie A; Pinkelman, Rebecca; Bang, Sookie S; Tasaki, Ken; Doll, Kenneth M; Qureshi, Nasib; Saha, Badal C; Liu, Siqing; Jackson, John S; Robinson, Samantha; Cotta, Michael C; Rich, Joseph O; Caimi, Paolo

    2011-02-01

    A synthetic Candida antarctica lipase B (CALB) gene open reading frame (ORF) for expression in yeast was constructed, and the lycotoxin-1 (Lyt-1) C3 variant gene ORF, potentially to improve the availability of the active enzyme at the surface of the yeast cell, was added in frame with the CALB ORF using an automated PCR assembly and DNA purification protocol on an integrated robotic workcell. Saccharomyces cerevisiae strains expressing CALB protein or CALB Lyt-1 fusion protein were first grown on 2% (w/v) glucose, producing 9.3 g/L ethanol during fermentation. The carbon source was switched to galactose for GAL1-driven expression, and the CALB and CALB Lyt-1 enzymes expressed were tested for fatty acid ethyl ester (biodiesel) production. The synthetic enzymes catalyzed the formation of fatty acid ethyl esters from ethanol and either corn or soybean oil. It was further demonstrated that a one-step-charging resin, specifically selected for binding to lipase, was capable of covalent attachment of the CALB Lyt-1 enzyme, and that the resin-bound enzyme catalyzed the production of biodiesel. High-level expression of lipase in an ethanologenic yeast strain has the potential to increase the profitability of an integrated biorefinery by combining bioethanol production with coproduction of a low-cost biocatalyst that converts corn oil to biodiesel. PMID:21609683

  11. Immunization with DNA vaccines containing porcine reproductive and respiratory syndrome virus open reading frames 5, 6, and 7 may be related to the exacerbation of clinical disease after an experimental challenge.

    PubMed

    Díaz, Ivan; Ganges, Llilianne; Galindo-Cardiel, Iván; Tarradas, Joan; Alvarez, Belén; Lorca-Oró, Cristina; Pujols, Joan; Gimeno, Mariona; Darwich, Laila; Domingo, Mariano; Domínguez, Javier; Mateu, Enric

    2013-02-01

    Pigs were immunized with DNA plasmids containing different open reading frames (ORFs) of a porcine reproductive and respiratory syndrome virus (PRRSV) genotype I strain. One group was injected with three inoculations of ORF7, a second group was immunized with three inoculations of plasmids containing ORF5 and ORF6, and a third group was kept as controls. Later, +21 days after the last inoculation, animals were challenged with the homologous strain. After the challenge, PRRSV-specific interferon (IFN)-γ-secreting cells and anti-PRRSV IgG antibodies developed faster in DNA vaccinated pigs (p<0.05). However, DNA-immunized pigs showed an exacerbation of the disease compared to the unvaccinated challenged pigs. The data suggest that previous immunization with DNA vaccines against glycoprotein 5 and/or matrix protein of PRRSV, as well as nucleoprotein but to a lesser degree, could result in an exacerbation of the clinical course in terms of fever upon challenge. PMID:23409932

  12. Viral culture and p24 antigenemia of human immunodeficiency virus (HIV)-infected individuals correlated with antibody profiles determined with recombinant polypeptides of all HIV-1 open-reading frames.

    PubMed

    Baur, A; Vornhagen, R; Korn, K; Sonneborn, H H; Eberlein, B; Harrer, T; Brockhaus, W; Jahn, G

    1992-03-01

    The association between viral activity and antibody profiles was investigated in 202 individuals infected by the human immunodeficiency virus (HIV) grouped according to their Walter Reed clinical stage. Each study group was subdivided into subjects positive or negative for markers of active viral replication: presence of serum p24 antigen and viral culture. In Western blots using recombinant antigens, sera of HIV-positive individuals with positive viral markers had a significantly lower antibody reactivity to several viral proteins than did individuals without viral markers. Noticeably, proteins of the gag (p24, p17) and env (gp120, COOH-terminal part of gp41) open-reading frames revealed a decreased reactivity. The antibody response to the regulatory proteins revealed no or poor association with viral activity in the host. The results suggest that seroreactivity is mainly influenced by factors reflecting the viral activity of an HIV-infected individual, while the clinical stage of the patient is less important. Especially, reductions in antibodies against gp120 and p17 were useful markers associated with increased viral activity. PMID:1371534

  13. Beyond the Basics: Effective Reading Programs for the Upper Elementary Grades. [Educator's Summary

    ERIC Educational Resources Information Center

    Center for Data-Driven Reform in Education (NJ3), 2009

    2009-01-01

    What reading programs have been proven to help students in grades 2-5 to succeed? To find out, this review summarizes evidence on three types of programs designed to improve the reading achievement of students in grades 2-5: (1) Reading Curricula (Curr), such as "Open Court," "Harcourt," "Reading Street" and other standard and alternative…

  14. Food additives

    MedlinePlus

    Food additives are substances that become part of a food product when they are added during the processing or making of that food. "Direct" food additives are often added during processing to: Add nutrients ...

  15. Talker-specific auditory imagery during reading

    NASA Astrophysics Data System (ADS)

    Nygaard, Lynne C.; Duke, Jessica; Kawar, Kathleen; Queen, Jennifer S.

    2001-05-01

    The present experiment was designed to determine if auditory imagery during reading includes talker-specific characteristics such as speaking rate. Following Kosslyn and Matt (1977), participants were familiarized with two talkers during a brief prerecorded conversation. One talker spoke at a fast speaking rate and one spoke at a slow speaking rate. During familiarization, participants were taught to identify each talker by name. At test, participants were asked to read two passages and told that either the slow or fast talker wrote each passage. In one condition, participants were asked to read each passage aloud, and in a second condition, they were asked to read each passage silently. Participants pressed a key when they had completed reading the passage, and reading times were collected. Reading times were significantly slower when participants thought they were reading a passage written by the slow talker than when reading a passage written by the fast talker. However, the effects of speaking rate were only present in the reading-aloud condition. Additional experiments were conducted to investigate the role of attention to talker's voice during familiarization. These results suggest that readers may engage in auditory imagery while reading that preserves perceptual details of an author's voice.

  16. The regulatory element READ1 epistatically influences reading and language, with both deleterious and protective alleles

    PubMed Central

    Powers, Natalie R; Eicher, John D; Miller, Laura L; Kong, Yong; Smith, Shelley D; Pennington, Bruce F; Willcutt, Erik G; Olson, Richard K; Ring, Susan M; Gruen, Jeffrey R

    2016-01-01

    Background Reading disability (RD) and language impairment (LI) are heritable learning disabilities that obstruct acquisition and use of written and spoken language, respectively. We previously reported that two risk haplotypes, each in strong linkage disequilibrium (LD) with an allele of READ1, a polymorphic compound short tandem repeat within intron 2 of risk gene DCDC2, are associated with RD and LI. Additionally, we showed a non-additive genetic interaction between READ1 and KIAHap, a previously reported risk haplotype in risk gene KIAA0319, and that READ1 binds the transcriptional regulator ETV6. Objective To examine the hypothesis that READ1 is a transcriptional regulator of KIAA0319. Methods We characterised associations between READ1 alleles and RD and LI in a large European cohort, and also assessed interactions between READ1 and KIAHap and their effect on performance on measures of reading, language and IQ. We also used family-based data to characterise the genetic interaction, and chromatin conformation capture (3C) to investigate the possibility of a physical interaction between READ1 and KIAHap. Results and conclusions READ1 and KIAHap show interdependence—READ1 risk alleles synergise with KIAHap, whereas READ1 protective alleles act epistatically to negate the effects of KIAHap. The family data suggest that these variants interact in trans genetically, while the 3C results show that a region of DCDC2 containing READ1 interacts physically with the region upstream of KIAA0319. These data support a model in which READ1 regulates KIAA0319 expression through KIAHap and in which the additive effects of READ1 and KIAHap alleles are responsible for the trans genetic interaction. PMID:26660103

  17. Food additives

    PubMed Central

    Spencer, Michael

    1974-01-01

    Food additives are discussed from the food technology point of view. The reasons for their use are summarized: (1) to protect food from chemical and microbiological attack; (2) to even out seasonal supplies; (3) to improve their eating quality; (4) to improve their nutritional value. The various types of food additives are considered, e.g. colours, flavours, emulsifiers, bread and flour additives, preservatives, and nutritional additives. The paper concludes with consideration of those circumstances in which the use of additives is (a) justified and (b) unjustified. PMID:4467857

  18. Additional considerations to the model of musical empathic engagement: Empathy facets, preferences, and openness. Comment on "Music, empathy, and cultural understanding" by E. Clarke et al.

    NASA Astrophysics Data System (ADS)

    Greenberg, David M.

    2015-12-01

    Recent research has shown that empathy plays an important role in musical experience including perception, preference, and performance [9,11,13,16,17]. Clarke, DeNora, and Vuoskoski's [4] timely review extends this work by establishing a framework for how "music empathic engagement" can facilitate cultural understanding. In this commentary I raise attention to some additional factors that may be at play in their model.

  19. Focus on Reading.

    ERIC Educational Resources Information Center

    Sheridan, Harriet W., Ed.

    1972-01-01

    The theme of this issue of the "Minnesota English Journal" is reading. The contents include "Preamblings," which discusses some of the current concerns in reading instruction; "The State of Minnesota's Right to Read Program," which looks at the Minnesota plan for building the reading program in conjunction with inservice education, and for…

  20. What Should Students Read?

    ERIC Educational Resources Information Center

    Wolk, Steven

    2010-01-01

    The reading students are required to do for school bears little semblance to the reading they do outside of school. Students today are reading the same texts in school that students read a generation ago, but the varieties of text used outside of school are much different. One result is that many students are unmotivated to become readers.…

  1. Designing the Reading Curriculum.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    The design of the reading curriculum presents a vision of what will be stressed in reading instruction. A first ingredient to discuss in developing the reading curriculum emphasizes the degree to which different curriculum areas should be related in teaching and learning. Reading then could be taught as a separate subject matter area from the…

  2. Failure Free Reading.

    ERIC Educational Resources Information Center

    Education Commission of the States, Denver, CO.

    This paper provides an overview of Failure Free Reading, a program with the primary goal of providing a basic understanding of the reading process to students in grades K-12 with pronounced reading difficulty and move them into traditional reading programs. The program is targeted to and most effective with at-risk and English as a Second Language…

  3. Big Read, Big ROI

    ERIC Educational Resources Information Center

    Dempsey, Beth

    2008-01-01

    In 2004, the National Endowment for the Arts (NEA) released a grim report on the state of literary reading in America. "Reading at Risk" (www.nea.gov/pub/ReadingAtRisk.pdf) detailed a dramatic decline in recreational reading across all segments of the American population--young and old, black, brown, and white. It also included the projected…

  4. Narration in Reading Remediation.

    ERIC Educational Resources Information Center

    Kersting, Frank; Ferguson, Janice

    A case study examined the whole-part application of the language experience approach to reading as used for students whose reading development is severely delayed. The subject, a third-grade female student reading on the first-grade level as determined by the Woodcock Reading Mastery Tests-Revised (Woodcock, 1987), participated in a reading…

  5. Reading Assessment: Looking Ahead

    ERIC Educational Resources Information Center

    Afflerbach, Peter

    2016-01-01

    In this article, I focus on three areas of reading assessment that I believe to be crucial for students' reading development: developing comprehensive formative assessments, assessing the wide array of factors that contribute to students' reading development, and fostering student independence by helping students learn to use reading assessment on…

  6. Reading and Comprehension.

    ERIC Educational Resources Information Center

    Eagan, Ruth L.

    For years, reading teachers in the schools have emphasized word identification skills and believed that reading is comprised of a set of subskills that a child must master before he or she can learn to read. To teach a child to read, however, instruction must focus on comprehension. Therefore, word attack skills should be taught in conjunction…

  7. Reading Therapy Project.

    ERIC Educational Resources Information Center

    McCarty, Roxanne

    2002-01-01

    Examines the results of using the Phono-Graphix reading method, designed for students with reading disabilities, to teach nine prison inmates to read. Reports that inmates' average basic reading skills standard score gains were 17 points (more than one standard deviation) after 33 one-hour sessions, an average gain of 1.9 standard points per…

  8. Translation Regulation of the Glutamyl-prolyl-tRNA Synthetase Gene EPRS through Bypass of Upstream Open Reading Frames with Noncanonical Initiation Codons.

    PubMed

    Young, Sara K; Baird, Thomas D; Wek, Ronald C

    2016-05-13

    In the integrated stress response, phosphorylation of eIF2α (eIF2α-P) reduces protein synthesis while concomitantly promoting preferential translation of specific transcripts associated with stress adaptation. Translation of the glutamyl-prolyl-tRNA synthetase gene EPRS is enhanced in response to eIF2α-P. To identify the underlying mechanism of translation control, we employed biochemical approaches to determine the regulatory features by which upstream ORFs (uORFs) direct downstream translation control and expression of the EPRS coding region. Our findings reveal that translation of two inhibitory uORFs encoded by noncanonical CUG and UUG initiation codons in the EPRS mRNA 5'-leader serve to dampen levels of translation initiation at the EPRS coding region. By a mechanism suggested to involve increased translation initiation stringency during stress-induced eIF2α-P, we observed facilitated ribosome bypass of these uORFs, allowing for increased translation of the EPRS coding region. Importantly, EPRS protein expression is enhanced through this preferential translation mechanism in response to multiple known activators of eIF2α-P and likely serves to facilitate stress adaptation in response to a variety of cellular stresses. The rules presented here for the regulated ribosome bypass of noncanonical initiation codons in the EPRS 5'-leader add complexity into the nature of uORF-mediated translation control mechanisms during eIF2α-P and additionally illustrate the roles that previously unexamined uORFs with noncanonical initiation codons can play in modulating gene expression. PMID:27002157

  9. The Influence of Black English on Diagnosis of Reading in Learning Disabled and Normal Readers.

    ERIC Educational Resources Information Center

    Burke, Suzanne M.; And Others

    A study was undertaken to determine if the removal of black English dialect as oral reading errors would influence the scores obtained on three oral reading diagnostic tests: the Gray Oral Reading Test, the Gilmore Oral Reading Test, and the Spache Diagnostic Reading Scales. In addition, the study investigated whether there were differences in the…

  10. Individual and group sensitivity to remedial reading program design: Examining reading gains across three middle school reading projects

    PubMed Central

    Calhoon, Mary Beth; Petscher, Yaacov

    2015-01-01

    The purpose of this project was to examine group- and individual-level responses by struggling adolescents readers (6th – 8th grades; N = 155) to three different modalities of the same reading program, Reading Achievement Multi-Component Program (RAMP-UP). The three modalities differ in the combination of reading components (phonological decoding, spelling, fluency, comprehension) that are taught and their organization. Latent change scores were used to examine changes in phonological decoding, fluency, and comprehension for each modality at the group level. In addition, individual students were classified as gainers versus non-gainers (a reading level increase of a year or more vs. less than one year) so that characteristics of gainers and differential sensitivity to instructional modality could be investigated. Findings from both group and individual analyses indicated that reading outcomes were related to modalities of reading instruction. Furthermore, differences in reading gains were seen between students who began treatment with higher reading scores than those with lower reading scores; dependent on modality of treatment. Results, examining group and individual analyses similarities and differences, and the effect the different modalities have on reading outcomes for older struggling readers will be discussed. PMID:25657503

  11. Manual for a Summer Reading Program.

    ERIC Educational Resources Information Center

    Medina, Sue O.

    This manual provides suggestions for materials and projects to carry out a summer reading program for children based on a monster theme. The planning process outlined may be used as a "how-to" guide for developing summer reading programs on other themes as well. In addition to general guidelines, the manual provides information on the following…

  12. An additional middle cuneiform?

    PubMed Central

    Brookes-Fazakerley, S.D.; Jackson, G.E.; Platt, S.R.

    2015-01-01

    Additional cuneiform bones of the foot have been described in reference to the medial bipartite cuneiform or as small accessory ossicles. An additional middle cuneiform has not been previously documented. We present the case of a patient with an additional ossicle that has the appearance and location of an additional middle cuneiform. Recognizing such an anatomical anomaly is essential for ruling out second metatarsal base or middle cuneiform fractures and for the preoperative planning of arthrodesis or open reduction and internal fixation procedures in this anatomical location. PMID:26224890

  13. The Effects of Extensive Reading via E-Books on Tertiary Level EFL Students' Reading Attitude, Reading Comprehension, and Vocabulary

    ERIC Educational Resources Information Center

    Chen, Chin-Neng; Chen, Shu-Chu; Chen, Shu-Hui Eileen; Wey, Shyh-Chyi

    2013-01-01

    This study investigates the effects of extensive reading of e-books on tertiary level EFL students' English reading attitude, reading comprehension and vocabulary. Eighty-nine participants were assigned in two groups, with 46 students in the experimental group and the other 43 students in the control group. In addition to a traditional…

  14. A 4.6 kb DNA region of Rhizobium meliloti involved in determining urease and hydrogenase activities carries the structural genes for urease (ureA, ureB, ureC) interrupted by other open reading frames.

    PubMed

    Miksch, G; Arnold, W; Lentzsch, P; Priefer, U B; Pühler, A

    1994-03-01

    A 4.6 kb DNA region of the Rhizobium meliloti strain AK631 was found to contain seven open reading frames (ORFs), all oriented in the same direction. The putative gene products of four of these ORFs were highly homologous to UreA, UreB and UreC of Klebsiella aerogenes, Proteus mirabilis, Proteus vulgaris and Canavalia ensiformis. The overall organisation of the DNA region analysed was ORF1, ureA (ORF2), ORF3, ureB (ORF4), ORF5, ORF6 and ureC (ORF7), indicating that the organisation of the urease structural genes in R. meliloti differs from that of other urease genes so far characterized. ORF1 was incomplete; only the 3' end of the coding region was present. The six complete ORFs coded for polypeptides of 11.1 (UreA), 8.9 (ORF3), 10.8 (UreB), 15.0 (ORF5), 13.8 (ORF6) and 60.7 kDa (UreC). No sequence homology to known polypeptides could be detected for the gene products of ORF1, ORF3, ORF5 and ORF6. Using a lacZ fusion and insertional mutagenesis it was shown that the seven ORFs identified were all located in the same transcription unit. For mutational analysis a resistance gene cassette was introduced into each of the complete ORFs resulting in apolar mutations. Mutations in ureA, ureB and ureC, but not in ORF3, ORF5 and ORF6, abolished urease activity in R. meliloti. The determination of hydrogen uptake in these R. meliloti mutants revealed that only ORF6 and ureB are necessary for hydrogen uptake. PMID:8121412

  15. A Short-Term Longitudinal Study of the Relationship between Motivation to Read and Reading Fluency Skill in Second Grade.

    PubMed

    Quirk, Matthew; Schwanenflugel, Paula J; Webb, Mi-Young

    2009-04-01

    This short-term longitudinal study investigated the relationships between students' reading self-concept, goals for reading, and reading fluency skill over the course of the second grade year. Second grade children (N=185) were administered the Test of Word Reading Efficiency, the second grade Dynamic Indicators of Basic Early Literacy Skills, and an adapted version of Motivation to Read Profile at the beginning, middle, and end of the school year. Results showed that students' goals for reading were related to reading self-concept, but unrelated to reading fluency. In addition, reading self-concept was significantly related to reading fluency at each time point. Latent-variable path analysis was used to test four potential relationships between students' reading self-concept and reading fluency skill: (a) an independence model; (b) a skill development model; (c) a self-enhancement model; and (d) a reciprocal effects model. Support for a reciprocal model was found between students' reading fluency skill and reading self-concept over the second grade year. This finding also indicated that students' reading self-concept begins to influence their reading achievement earlier than previous research had indicated. Implications for educational practice and future research will also be discussed. PMID:20300541

  16. Food additives.

    PubMed

    Berglund, F

    1978-01-01

    The use of additives to food fulfils many purposes, as shown by the index issued by the Codex Committee on Food Additives: Acids, bases and salts; Preservatives, Antioxidants and antioxidant synergists; Anticaking agents; Colours; Emulfifiers; Thickening agents; Flour-treatment agents; Extraction solvents; Carrier solvents; Flavours (synthetic); Flavour enhancers; Non-nutritive sweeteners; Processing aids; Enzyme preparations. Many additives occur naturally in foods, but this does not exclude toxicity at higher levels. Some food additives are nutrients, or even essential nutritents, e.g. NaCl. Examples are known of food additives causing toxicity in man even when used according to regulations, e.g. cobalt in beer. In other instances, poisoning has been due to carry-over, e.g. by nitrate in cheese whey - when used for artificial feed for infants. Poisonings also occur as the result of the permitted substance being added at too high levels, by accident or carelessness, e.g. nitrite in fish. Finally, there are examples of hypersensitivity to food additives, e.g. to tartrazine and other food colours. The toxicological evaluation, based on animal feeding studies, may be complicated by impurities, e.g. orthotoluene-sulfonamide in saccharin; by transformation or disappearance of the additive in food processing in storage, e.g. bisulfite in raisins; by reaction products with food constituents, e.g. formation of ethylurethane from diethyl pyrocarbonate; by metabolic transformation products, e.g. formation in the gut of cyclohexylamine from cyclamate. Metabolic end products may differ in experimental animals and in man: guanylic acid and inosinic acid are metabolized to allantoin in the rat but to uric acid in man. The magnitude of the safety margin in man of the Acceptable Daily Intake (ADI) is not identical to the "safety factor" used when calculating the ADI. The symptoms of Chinese Restaurant Syndrome, although not hazardous, furthermore illustrate that the whole ADI

  17. Opening the Gates: Reading "The Gulag"

    ERIC Educational Resources Information Center

    Iannone, Carol

    2009-01-01

    The year 2008 saw the death of one of the towering figures of the twentieth century, Aleksandr Solzhenitsyn. More than any other single man, Solzhenitsyn helped morally delegitimize what had seemed the unchallengeable monolith that was the Union of Soviet Socialist Republics. His life is a standing example and inspiration to those American…

  18. Reading: Putting the Pieces Together.

    ERIC Educational Resources Information Center

    Hayes, Bernard L., Ed.; Camperell, Kay, Ed.

    1994-01-01

    The papers in this yearbook focus on the strategies, practices, and research related to elementary reading, secondary reading, adult reading, literature, philosophy of reading, psychology of reading, affective issues, administration, supervision, research, teacher training, assessment that affect reading and reading instruction. Papers in the book…

  19. Iconic Prosody in Story Reading.

    PubMed

    Perlman, Marcus; Clark, Nathaniel; Johansson Falck, Marlene

    2015-08-01

    Recent experiments have shown that people iconically modulate their prosody corresponding with the meaning of their utterance (e.g., Shintel et al., 2006). This article reports findings from a story reading task that expands the investigation of iconic prosody to abstract meanings in addition to concrete ones. Participants read stories that contrasted along concrete and abstract semantic dimensions of speed (e.g., a fast drive, slow career progress) and size (e.g., a small grasshopper, an important contract). Participants read fast stories at a faster rate than slow stories, and big stories with a lower pitch than small stories. The effect of speed was distributed across the stories, including portions that were identical across stories, whereas the size effect was localized to size-related words. Overall, these findings enrich the documentation of iconicity in spoken language and bear on our understanding of the relationship between gesture and speech. PMID:25351919

  20. Lights, Camera, Read! Arizona Reading Program Manual.

    ERIC Educational Resources Information Center

    Arizona State Dept. of Library, Archives and Public Records, Phoenix.

    This document is the manual for the Arizona Reading Program (ARP) 2003 entitled "Lights, Camera, Read!" This theme spotlights books that were made into movies, and allows readers to appreciate favorite novels and stories that have progressed to the movie screen. The manual consists of eight sections. The Introduction includes welcome letters from…

  1. Beginning Readers' Reading Performance and Reading Habits

    ERIC Educational Resources Information Center

    Leppanen, Ulla; Aunola, Kaisa; Nurmi, Jari-Erik

    2005-01-01

    This study investigated the prospective relationships between reading performance and reading habits among Finnish children during the first and second grades of primary school. One hundred and ninety-five children were examined twice during their first primary school year and once during the spring term of Grade 2. The results showed, first, that…

  2. Reading Disabilities and PASS Reading Enhancement Programme

    ERIC Educational Resources Information Center

    Mahapatra, Shamita

    2016-01-01

    Children experience difficulties in reading either because they fail to decode the words and thus are unable to comprehend the text or simply fail to comprehend the text even if they are able to decode the words and read them out. Failure in word decoding results from a failure in phonological coding of written information, whereas reading…

  3. Reading Assessment--The Third Dimension.

    ERIC Educational Resources Information Center

    Johns, Jerry L.

    1979-01-01

    Suggests that teacher observations form a valid and integral part of student assessment and that, in addition to standardized tests and informal tests, this "inner-ocular technique" is an important means for assessing the effectiveness of reading instruction. (MKM)

  4. How To...Celebrate Reading--Electronically!

    ERIC Educational Resources Information Center

    Lindroth, Linda

    2005-01-01

    This column describes technology resources that teachers can use to support a celebration of reading throughout the year. In addition to online sites, other tools such as word processors, graphic drawing tools, and photo editors are suggested.

  5. Recreational Reading of International Students in Academic Libraries

    ERIC Educational Resources Information Center

    Bordonaro, Karen

    2011-01-01

    Recreational reading as a method of language learning has been a focus of investigation in second language education. This article considers recreational reading through the additional perspective of academic librarianship. Its purpose is to discover if recreational reading is a topic that lends itself to research through both perspectives. This…

  6. Critical Thinking... and the Art of Close Reading, Part III

    ERIC Educational Resources Information Center

    Paul, Richard; Elder, Linda

    2004-01-01

    The "Critical Thinking and the Art of Close Reading" series (which includes this column and three others) focuses on some of the most basic understandings necessary for close reading (Paul & Elder, 2003). To read well, in addition to having these understandings, students must be able to identify the big picture within a text, to determine the key…

  7. What Are Preschool Teachers Reading in Their Classrooms?

    ERIC Educational Resources Information Center

    Pentimonti, Jill M.; Zucker, Tricia A.; Justice, Laura M.

    2011-01-01

    The present study describes preschool read-alouds in terms of the types of texts to which children are exposed. The methods involved analyzing the genre and instructional foci of 426 titles read by 13 teachers throughout an entire academic year. Additionally, associations between teacher characteristics and texts teachers read in their classrooms…

  8. Is the Simple View of Reading Too Simple?

    ERIC Educational Resources Information Center

    Hoien-Tengesdal, Ingjerd

    2010-01-01

    According to the Simple View of Reading (SVR), reading comprehension is the product of word decoding ability and linguistic comprehension (R = D x C). However, there is also evidence showing that an additive model (R = D + C) explains just as much or even more of the variance in reading comprehension than the product model. To further evaluate…

  9. Close Readings and Children's Literature

    ERIC Educational Resources Information Center

    Serafini, Frank

    2014-01-01

    The concept of close reading is an important consideration when addressing the Common Core State Standards. In addition, "close reading" permeates the CCSS and suggests a particular way of reading and responding to texts. Trying to help students become successful readers in both school based settings and in the world outside of school is…

  10. Toddler Reading Time

    MedlinePlus

    ... Studies show that kids with active exposure to language have social and educational advantages over their peers — ... reading is one of the best exposures to language. Reading to toddlers sets the foundation for later ...

  11. Understanding Blood Pressure Readings

    MedlinePlus

    ... Pressure Tools & Resources Stroke More Understanding Blood Pressure Readings Updated:Aug 17,2016 Blood pressure is typically ... Your doctor should evaluate unusually low blood pressure readings. How is high blood pressure diagnosed? Your healthcare ...

  12. What Are Reading Disorders?

    MedlinePlus

    ... Information Clinical Trials Resources and Publications What are reading disorders? Skip sharing on social media links Share ... for more information about these problems. Types of Reading Disorders Dyslexia is a brain-based type of ...

  13. Assessing Motivation to Read.

    ERIC Educational Resources Information Center

    Gambrell, Linda B.; And Others

    1996-01-01

    Describes the Motivation to Read Profile (MRP), which assesses children's self-concepts as readers and the value they see in reading. Discusses its development and offers suggestions for its use with elementary students. Includes the MRP. (SR)

  14. Colorado longitudinal twin study of reading disability.

    PubMed

    Wadsworth, Sally J; DeFries, John C; Olson, Richard K; Willcutt, Erik G

    2007-12-01

    The primary objectives of the present study are to introduce the Colorado Longitudinal Twin Study of Reading Disability, the first longitudinal twin study in which subjects have been specifically selected for having a history of reading difficulties, and to present some initial assessments of the stability of reading performance and cognitive abilities in this sample. Preliminary examination of the test scores of 124 twins with a history of reading difficulties and 154 twins with no history of reading difficulties indicates that over the 5- to 6-year interval between assessments, cognitive and reading performance are highly stable. As a group, those subjects with a history of reading difficulties had substantial deficits relative to control subjects on all measures at initial assessment, and significant deficits remained at follow-up. The stability noted for all cognitive and achievement measures was highest for a composite measure of reading, whose average stability correlation across groups was 0.80. Results of preliminary behavior genetic analyses for this measure indicated that shared genetic influences accounted for 86% and 49% of the phenotypic correlations between the two assessments for twin pairs with and without reading difficulties, respectively. In addition, genetic correlations reached unity for both groups, suggesting that the same genetic influences are manifested at both time points. PMID:18060583

  15. Potlining Additives

    SciTech Connect

    Rudolf Keller

    2004-08-10

    In this project, a concept to improve the performance of aluminum production cells by introducing potlining additives was examined and tested. Boron oxide was added to cathode blocks, and titanium was dissolved in the metal pool; this resulted in the formation of titanium diboride and caused the molten aluminum to wet the carbonaceous cathode surface. Such wetting reportedly leads to operational improvements and extended cell life. In addition, boron oxide suppresses cyanide formation. This final report presents and discusses the results of this project. Substantial economic benefits for the practical implementation of the technology are projected, especially for modern cells with graphitized blocks. For example, with an energy savings of about 5% and an increase in pot life from 1500 to 2500 days, a cost savings of $ 0.023 per pound of aluminum produced is projected for a 200 kA pot.

  16. Phosphazene additives

    SciTech Connect

    Harrup, Mason K; Rollins, Harry W

    2013-11-26

    An additive comprising a phosphazene compound that has at least two reactive functional groups and at least one capping functional group bonded to phosphorus atoms of the phosphazene compound. One of the at least two reactive functional groups is configured to react with cellulose and the other of the at least two reactive functional groups is configured to react with a resin, such as an amine resin of a polycarboxylic acid resin. The at least one capping functional group is selected from the group consisting of a short chain ether group, an alkoxy group, or an aryloxy group. Also disclosed are an additive-resin admixture, a method of treating a wood product, and a wood product.

  17. Learning to Read Again.

    ERIC Educational Resources Information Center

    Adams, O. F., McCreery, Liz

    1988-01-01

    A project was developed which successfully taught individuals with visual impairments to read commercial large-print books, with either their own reading spectacles or with lower levels of magnification than usually prescribed. Over the course of the project, print sizes were systematically reduced and healthy reading habits were re-taught. (JDD)

  18. Reading/Language Arts.

    ERIC Educational Resources Information Center

    Illinois State Office of Education, Springfield.

    These seven projects comprise the reading and language arts section of a report on Elementary Secondary Education Act Title IV programs for the state of Illinois. Complete descriptions are furnished for the following: a multi-text, individualized reading skills program for grades four through eight; a reading program which stresses phonetic and…

  19. Reading in Mathematics.

    ERIC Educational Resources Information Center

    Taschow, Horst G.

    Difficulties inherent in the reading of mathematics at secondary and college levels are discussed. Special emphasis is placed on the reading of arithmetic numerals, literal numbers, operational symbols, and expressions of relationships, as well as the reading of technical vocabularies and specialized meanings of general words. While each…

  20. Family Reading Night

    ERIC Educational Resources Information Center

    Hutchins, Darcy; Greenfeld, Marsha; Epstein, Joyce

    2007-01-01

    This book offers clear and practical guidelines to help engage families in student success. It shows families how to conduct a successful Family Reading Night at their school. Family Night themes include Scary Stories, Books We Love, Reading Olympics, Dr. Seuss, and other themes. Family reading nights invite parents to come to school with their…

  1. Monster Moose Reading.

    ERIC Educational Resources Information Center

    Finney, Frank

    Monster Moose (MM) Reading is a program specifically aimed at improving children's language, beginning reading, and self-concept development through the creation and utilization of student-authored reading materials which feature a series of wordless picture books about a magical moose. The MM Program is based on the following general principles…

  2. Reading and Writing Connections.

    ERIC Educational Resources Information Center

    Mason, Jana M., Ed.

    This collection of papers, from a conference on reading and writing connections held at the University of Illinois in October 1986, reflects the value of demonstrating connections between reading instruction and writing. The book shows practitioners how writing can be blended with reading instruction and how writing activities can be used not just…

  3. Time for Reading?

    ERIC Educational Resources Information Center

    Fowler, William R.

    1989-01-01

    Reading for pleasure and enlightenment is a critical, and endangered, element in a well-informed citizenry. As a basis for intellectual growth, reading is threatened by media misuse and lack of encouragement of recreational reading. Solutions include emphasis on integrated skills, improved time allocation, and cooperation among parents, teachers,…

  4. Guided Reading and Motivation

    ERIC Educational Resources Information Center

    Hauptman, Allyson L.

    2012-01-01

    The purpose of this study was to determine the relationship between Guided Reading and student motivation to read across fourth, fifth, and sixth grades. The study defined literacy motivation as: (a) task value; (b) self-perceived competence; (c) students' perceptions of the Guided Reading format. Factor analysis and repeated measures ANOVAs were…

  5. ELLs' Perceptions of Reading

    ERIC Educational Resources Information Center

    Howard, Rachael M.

    2012-01-01

    This research investigated reading support and book preferences of fourth grade English language learners (ELLs) who were struggling readers. This qualitative research focused on three case studies. Interviews were conducted to explore ELLs' perceptions on reading motivation, reading programs, and types of support they received. Descriptions of…

  6. Reading, Language Arts & Literacy.

    ERIC Educational Resources Information Center

    Matthew, Kathy, Ed.

    This document contains the following papers on educational technology issues related to reading, language arts, and literacy: (1) "The Infusion of Technology into a Teacher Education Course: Issues and Strategies" (Mary Ann Kolloff); (2) "Project READ: Developing Online Course Materials for a Reading Methods Class" (Judith A. Crowe); (3) "Reading…

  7. Free Reading Is UTOPIA

    ERIC Educational Resources Information Center

    LeCrone, Nancy

    2010-01-01

    In high school students get tied up in extracurricular activities and have little time for pleasure reading. It is true that with rigorous academic schedules they have little time for pleasure reading. Thus began a conversation with a sophomore English teacher at the author's high school. As they were discussing the plight of free reading he was…

  8. The Future of Reading

    ERIC Educational Resources Information Center

    Peters, Tom

    2009-01-01

    The future of reading is very much in doubt. In this century, reading could soar to new heights or crash and burn. Some educators and librarians fear that sustained reading for learning, for work, and for pleasure may be slowly dying out as a widespread social practice. Several social and technological developments of the 20th century, such as…

  9. The Roots of Reading.

    ERIC Educational Resources Information Center

    Segel, Elizabeth

    2000-01-01

    School-community partnership programs can help teachers reach children in the crucial years from birth to 4, thereby preventing reading difficulties and raising future test scores. Many organizations help families in starting their children on the road to lifetime reading by distributing free books and pamphlets on reading aloud to children. (SM)

  10. Content Reading Strategies

    ERIC Educational Resources Information Center

    Belk, Elizabeth Joann; Seed, Allen H.; Abdi, Wali

    2005-01-01

    Reading comprehension skills promote achievement in science, so how can teachers help students to develop these skills? Research indicates that students who read well are more likely to be successful in school and in life (Belk 1999). Furthermore, there is a direct link between science skills and reading skills (Carter and Simpson 1978). There are…

  11. Summer Library Reading Programs

    ERIC Educational Resources Information Center

    Fiore, Carole D.

    2007-01-01

    Virtually all public libraries in the United States provide some type of summer library reading program during the traditional summer vacation period. Summer library reading programs provide opportunities for students of many ages and abilities to practice their reading skills and maintain skills that are developed during the school year. Fiore…

  12. Developing a Reading Course.

    ERIC Educational Resources Information Center

    Creemers, F. H. Th.; And Others

    A course for improving Dutch reading proficiency of entering university students was developed by the Linguistic and Literacy Studies department of the University of Tilburg in the Netherlands. Dutch secondary school students receive instruction in text-specific approaches to reading but no instruction in reading methodology. The course focuses on…

  13. The Reading Book.

    ERIC Educational Resources Information Center

    Barrs, Myra, Ed.; Thomas, Anne, Ed.

    Noting the persistent tendency to polarize questions of reading instruction into diametrically opposed or simplified positions, this book (developed in the United Kingdom) is a teacher's guide to learning to read. The first part of the book surveys what is known about reading, in chapters corresponding to the four major partners in the reading…

  14. Reading difficulties in Albanian.

    PubMed

    Avdyli, Rrezarta; Cuetos, Fernando

    2012-10-01

    Albanian is an Indo-European language with a shallow orthography, in which there is an absolute correspondence between graphemes and phonemes. We aimed to know reading strategies used by Albanian disabled children during word and pseudoword reading. A pool of 114 Kosovar reading disabled children matched with 150 normal readers aged 6 to 11 years old were tested. They had to read 120 stimuli varied in lexicality, frequency, and length. The results in terms of reading accuracy as well as in reading times show that both groups were affected by lexicality and length effects. In both groups, length and lexicality effects were significantly modulated by school year being greater in early grades and later diminish in length and just the opposite in lexicality. However, the reading difficulties group was less accurate and slower than the control group across all school grades. Analyses of the error patterns showed that phonological errors, when the letter replacement leading to new nonwords, are the most common error type in both groups, although as grade rises, visual errors and lexicalizations increased more in the control group than the reading difficulties group. These findings suggest that Albanian normal children use both routes (lexical and sublexical) from the beginning of reading despite of the complete regularity of Albanian, while children with reading difficulties start using sublexical reading and the lexical reading takes more time to acquire, but finally both routes are functional. PMID:22739980

  15. Reading Difficulties in Albanian

    ERIC Educational Resources Information Center

    Avdyli, Rrezarta; Cuetos, Fernando

    2012-01-01

    Albanian is an Indo-European language with a shallow orthography, in which there is an absolute correspondence between graphemes and phonemes. We aimed to know reading strategies used by Albanian disabled children during word and pseudoword reading. A pool of 114 Kosovar reading disabled children matched with 150 normal readers aged 6 to 11 years…

  16. Current Issues in Reading.

    ERIC Educational Resources Information Center

    French, Michael P., Ed.

    1985-01-01

    Articles in this journal issue focus on reading acquisition and instruction. The titles and authors are as follows: (1) "10 Good Ways to Involve Parents in the Reading Program," by Nickolas Criscuolo; (2) "A Parent Guide for Helping the Child with A Reading Disability," by Frederick Duffelmeyer and Dale Baum; (3) "Promoting a Good Attitude toward…

  17. Reading to Learn

    ERIC Educational Resources Information Center

    Herman, Phillip; Wardrip, Peter

    2012-01-01

    Science teachers expect high school students to know how to read, understand, and learn from texts at the core of the curriculum. But though students learn to read in grade school, many do not know how to "read to learn" science. And science teachers are often too busy teaching science to actively help students increase their science reading…

  18. Psycholinguistics and Reading.

    ERIC Educational Resources Information Center

    Smith, Frank, (Ed.)

    Psycholinguistics has offered many new insights into the development of reading, e.g., only a small part of the information necessary for reading comprehension comes from the printed page, comprehension must precede the identification of individual words, and reading is not decoding to spoken language. These views are elaborated in this collection…

  19. Creative Reading: Other Voices.

    ERIC Educational Resources Information Center

    Padgett, Ron

    1990-01-01

    Discusses subvocalization and other ways in which people read silently. Comments on authorial voice and offers ways to experiment with creative reading aloud. Notes how the proliferation of advertising, the media "explosion," and the influence of modernism in literature has changed the fundamental sense of what reading is and how to do it. (MG)

  20. Literature without Reading.

    ERIC Educational Resources Information Center

    Knighten, Katherine W.

    During one term at a laboratory school, reading was systematically deleted from activites in one secondary level class and replaced with film, lecture, oral reading, slides, and other audiovisual aids. The Nelson-Denny Reading Test served as pretest-posttest for the twelve-week experiment, with 19 of 25 students completing both tests. The results…

  1. Issues in Reading Instruction.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    Presently, reading is much discussed by senators, representatives, and state legislatures--the debate is on the following issues in reading instruction: (1) having all students in public school achieve at grade level as a reading minimum; (2) accountability of teachers for student achievement; (3) teachers having high achievement expectations from…

  2. Sequence analysis of a near-subtelomeric 35.4 kb DNA segment on the right arm of chromosome VII from Saccharomyces cerevisiae carrying the MAL1 locus reveals 15 complete open reading frames, including ZUO1, BGL2 and BIO2 genes and an ABC transporter gene.

    PubMed

    Volckaert, G; Voet, M; Robben, J

    1997-03-15

    The nucleotide sequence of 35,400 bp at approximately 10 kb from the right telomere of chromosome VII was determined. The segment contains the MAL1 locus, one of the five unlinked loci sufficient for maltose utilization. Until now, each of these loci was considered to contain three genes (for regulator, permease and alpha-glucosidase), but a fourth gene, presumably an extra alpha-glucosidase gene, was found at MAL1 adjacent to the usual cluster of three genes. The two glucosidase genes are present in opposite orientation, forming an inverted repeat structure. In addition to the four genes at MAL1, there are 11 complete, non-overlapping open reading frames (ORFs) longer than 300 bp in the sequence presented here. A new ABC transporter gene (YGR281w), required for oligomycin resistance was found (YOR1; Katzman et al., 1995), and the previously sequenced BGL2 (YGR282c), ZUO1 (YGR285c) and BIO2 (YGR286c) genes were located. The sequence of BIO2, a biotin synthetase gene, required substantial correction and the size of Bio2p is 375, rather than 356, amino acids. Two ORFs show rather weak similarities to animal genes: YGR278w to an unknown ORF of Caenorhabditis elegans and YGR284c to the murine Surf-4, a member of a cluster of at least four housekeeping genes. The remaining five ORFs do not encode known functions, but three of these show weak to high similarities to other ORFs in the Saccharomyces cerevisiae genome and one (YGR280c) codes for a particularly lysine-rich protein. PMID:9090054

  3. Effects of the deletion of early region 4 (E4) open reading frame 1 (orf1), orf1-2, orf1-3 and orf1-4 on virus-host cell interaction, transgene expression, and immunogenicity of replicating adenovirus HIV vaccine vectors.

    PubMed

    Thomas, Michael A; Song, Rui; Demberg, Thorsten; Vargas-Inchaustegui, Diego A; Venzon, David; Robert-Guroff, Marjorie

    2013-01-01

    The global health burden engendered by human immunodeficiency virus (HIV)-induced acquired immunodeficiency syndrome (AIDS) is a sobering reminder of the pressing need for a preventative vaccine. In non-human primate models replicating adenovirus (Ad)-HIV/SIV recombinant vaccine vectors have been shown to stimulate potent immune responses culminating in protection against challenge exposures. Nonetheless, an increase in the transgene carrying capacity of these Ad vectors, currently limited to approximately 3000 base pairs, would greatly enhance their utility. Using a replicating, E3-deleted Ad type 5 host range mutant (Ad5 hr) encoding full-length single-chain HIVBaLgp120 linked to the D1 and D2 domains of rhesus macaque CD4 (rhFLSC) we systematically deleted the genes encoding early region 4 open reading frame 1 (E4orf1) through E4orf4. All the Ad-rhFLSC vectors produced similar levels of viral progeny. Cell cycle analysis of infected human and monkey cells revealed no differences in virus-host interaction. The parental and E4-deleted viruses expressed comparable levels of the transgene with kinetics similar to Ad late proteins. Similar levels of cellular immune responses and transgene-specific antibodies were elicited in vaccinated mice. However, differences in recognition of Ad proteins and induced antibody subtypes were observed, suggesting that the E4 gene products might modulate antibody responses by as yet unknown mechanisms. In short, we have improved the transgene carrying capacity by one thousand base pairs while preserving the replicability, levels of transgene expression, and immunogenicity critical to these vaccine vectors. This additional space allows for flexibility in vaccine design that could not be obtained with the current vector and as such should facilitate the goal of improving vaccine efficacy. To the best of our knowledge, this is the first report describing the effects of these E4 deletions on transgene expression and immunogenicity in a

  4. Oral Reading Fluency: Accuracy of Assessing Errors and Classification of Readers Using a 1-Min Timed Reading Sample

    ERIC Educational Resources Information Center

    Coulter, Gail; Shavin, Karen; Gichuru, Margaret

    2009-01-01

    Children in general education are classified by measures of oral reading fluency (ORF) to determine the level of support needed for reading. In addition, teachers use ORF measures with children who receive special education services to determine whether they are making progress toward their reading goals. In this descriptive study, the authors…

  5. Relationships Between Selected Oral Reading Errors and Levels of Reading Comprehension for Good, Average, and Poor Readers.

    ERIC Educational Resources Information Center

    Packman, Linda Arlene

    Some oral reading errors were found to be more significant than others in evaluating a pupil's performance in reading at six comprehension levels. The percentage of seven kinds of errors (pronunciation, mispronunciation, omission, substitution, addition, repetition, and punctuation) was computed to the levels of reading comprehension for good,…

  6. Anaphoric inference during reading.

    PubMed

    O'Brien, E J; Duffy, S A; Myers, J L

    1986-07-01

    Three experiments provide evidence that an anaphoric noun phrase reinstates its antecedent in the course of comprehension. Subjects read a series of texts each containing a target item. Immediately after the last line of each text, the item was probed using a recognition task in Experiment 1 and a naming task in Experiment 2. Subjects were faster to respond to the item when the last line contained an anaphoric reference to it than when the last line referred to a different item from the text. Additional control conditions ensured that the effect was not due to semantic priming and that the probed item was not in working memory when the last line was encountered. A third experiment suggested that previous evidence for reinstatement reflected interference from a change of topic in the last line rather than facilitation due to reinstatement of the probed item. PMID:2942624

  7. Investigating the Relationship between Connectives and Readers' Reading Comprehension Level

    ERIC Educational Resources Information Center

    Gençer, Yusuf; ÇetiInkaya, Gökhan

    2015-01-01

    The purpose of this study is to investigate the relationship between connectives in Turkish texts and readers' reading comprehension. Research was conducted with a total of 50 teachers. In the study group, readers' reading comprehension was determined through 10 descriptive texts by using open-ended questions. The results of the analysis revealed…

  8. Standardized Reading Tests and the Postsecondary Reading Curriculum.

    ERIC Educational Resources Information Center

    Wood, Nancy V.

    To help college reading teachers develop an awareness of what standardized reading tests do and do not reveal about students' reading abilities, a study examined the testing of reading and criticized four major standardized tests. Results indicated that reading is tested through (1) reading passages accompanied by multiple choice questions, (2)…

  9. A single 13-kilobase divergent locus in the Kaposi sarcoma-associated herpesvirus (human herpesvirus 8) genome contains nine open reading frames that are homologous to or related to cellular proteins.

    PubMed Central

    Nicholas, J; Ruvolo, V; Zong, J; Ciufo, D; Guo, H G; Reitz, M S; Hayward, G S

    1997-01-01

    Two small fragments of a novel human gammaherpesvirus genome known as Kaposi's sarcoma (KS)-associated herpesvirus or human herpesvirus 8 (HHV-8) have been shown to be present in virtually all AIDS and non-AIDS KS lesions, as well as in body cavity-based lymphomas (BCBL) and in multicentric Castleman's disease. We have extended those studies by identifying and sequencing a third fragment of HHV-8 DNA encoding a viral thymidylate synthetase (TS) gene. Use of this viral TS fragment as a probe led to the identification and mapping of a cluster of overlapping phage lambda clones from a BCBL tumor DNA genomic library that spanned 48 kb on the left-hand side of the HHV-8 genome between the equivalents of open reading frame 6 (ORF6) and ORF31 of herpesvirus saimiri (HVS). DNA sequencing of a 17-kb segment encompassing a gammaherpesvirus divergent locus (DL-B) between ORF11 and ORF17 revealed the presence of nine viral ORFs with predicted gene products related to cellular proteins. These include the complete TS gene and a dihydrofolate reductase (DHFR) gene, four novel cytokine genes (encoding viral interleukin-6, viral MIP-1A, viral MIP-1B, and BCK) that have not previously been found to be encoded by a virus, and a bcl-2 homolog. This region in HHV-8 also contains the T1.1 abundant lytic cycle nuclear RNA gene and encompasses two genes (or exons) encoding proteins with C4HC3 zinc finger domains of the PHD/leukemia-associated protein subtype. The latter are related to the spliced immediate-early IE1 protein of the gamma-2 class herpesvirus bovine herpesvirus type 4 and a similar motif found in HVS ORF12. Although genes for TS and DHFR enzymes are also encoded by HVS (ORF70 and ORF2), both occur at different genomic loci than in HHV-8, and the HHV-8 DHFR protein is much farther diverged from human DHFR than is the HVS version, implying that they were probably acquired as host cell cDNAs by independent evolutionary events. Transcripts from the IE1-A, IE1-B, DHFR, and MIP-1B

  10. How to Read Drug Labels

    MedlinePlus

    ... and alternative medicine Healthy Aging How to read drug labels Printer-friendly version How to Read Drug ... read drug labels How to read a prescription drug label View a text version of this picture. ...

  11. Do reading and spelling share a lexicon?

    PubMed

    Jones, Angela C; Rawson, Katherine A

    2016-05-01

    In the reading and spelling literature, an ongoing debate concerns whether reading and spelling share a single orthographic lexicon or rely upon independent lexica. Available evidence tends to support a single lexicon account over an independent lexica account, but evidence is mixed and open to alternative explanation. In the current work, we propose another, largely ignored account--separate-but-shared lexica--according to which reading and spelling have separate orthographic lexica, but information can be shared between them. We report three experiments designed to competitively evaluate these three theoretical accounts. In each experiment, participants learned new words via reading training and/or spelling training. The key manipulation concerned the amount of reading versus spelling practice a given item received. Following training, we assessed both response time and accuracy on final outcome measures of reading and spelling. According to the independent lexica account, final performance in one modality will not be influenced by the level of practice in the other modality. According to the single lexicon account, final performance will depend on the overall amount of practice regardless of modality. According to the separate-but-shared account, final performance will be influenced by the level of practice in both modalities but will benefit more from same-modality practice. Results support the separate-but-shared account, indicating that reading and spelling rely upon separate lexica, but information can be shared between them. PMID:26999066

  12. Improving Reading Comprehension in Reading and Listening Settings: The Effect of Two Training Programmes Focusing on Metacognition and Working Memory

    ERIC Educational Resources Information Center

    Carretti, Barbara; Caldarola, Nadia; Tencati, Chiara; Cornoldi, Cesare

    2014-01-01

    Background: Metacognition and working memory (WM) have been found associated with success in reading comprehension, but no studies have examined their combined effect on the training of reading comprehension. Another open question concerns the role of listening comprehension: In particular, it is not clear whether training to improve reading…

  13. What, Why, and How They Read: Reading Preferences and Patterns of Rural Young Adults

    ERIC Educational Resources Information Center

    Becnel, Kim; Moeller, Robin A.

    2015-01-01

    The purpose of this study is to better understand the reading patterns and preferences of rural teen readers and the cultures of reading that do or do not exist in the rural communities in which the teens reside. In addition, the researchers sought to discover, by conducting a series of focus groups, whether rural teen readers felt connected to…

  14. The Potential Impact of Structured Read-Aloud on Middle School Reading Achievement

    ERIC Educational Resources Information Center

    Marchessault, Jennifer Kohart; Larwin, Karen H.

    2014-01-01

    Read-aloud is a technique predominantly utilized at the elementary level. This study was designed to research the effectiveness of this technique at the middle school level, specifically, students who were not receiving special education or additional reading intervention services. For the current investigation, students in two middle schools…

  15. Structured Read-Aloud in Middle School: The Potential Impact on Reading Achievement

    ERIC Educational Resources Information Center

    Marchessault, Jennifer Kohart; Larwin, Karen H.

    2013-01-01

    Read-aloud is a technique predominantly utilized at the elementary level. This study was designed to research the effectiveness of this technique at the middle school level, specifically students who were not receiving special education or additional reading intervention services. For the current investigation, students in two middle schools…

  16. Reading Motivation and Reading Comprehension in Chinese and English among Bilingual Students

    ERIC Educational Resources Information Center

    Lin, Dan; Wong, Ka Ki; McBride-Chang, Catherine

    2012-01-01

    One hundred four Hong Kong Chinese fifth graders completed a questionnaire on eight separate motivational subscales related to reading separately for Chinese as a first language (L1) and English as a foreign language (EFL) in addition to measures of both Chinese and English reading comprehension. Motivations related to self-efficacy, curiosity,…

  17. Explicit Reading Comprehension Instruction in Elementary Classrooms: Teacher Use of Reading Comprehension Strategies

    ERIC Educational Resources Information Center

    Ness, Molly

    2011-01-01

    The purpose of this observational study was to identify the frequency of reading comprehension instruction in elementary classrooms. Additional objectives were to determine which reading comprehension instructional strategies were most employed by teachers in elementary classrooms. In 3,000 minutes of direct classroom observation in 20 first-…

  18. Pre-Service Teachers' Use of Reading Strategies in Their Own Readings and Future Classrooms

    ERIC Educational Resources Information Center

    Akyol, Hayati; Ulusoy, Mustafa

    2010-01-01

    The main purpose of this study was to determine pre-service teachers' use of reading strategies in their own readings. In addition, pre-service teachers' use of these strategies in their future teaching practices was also investigated. The subjects for this study were 505 pre-service teachers enrolled in one of the major universities in Ankara.…

  19. High School Science Teachers' Perceptions of Teaching Content-Related Reading Comprehension Instruction

    NASA Astrophysics Data System (ADS)

    Williams, Theresa

    In order to achieve academic success, students must be able to comprehend written material in content-area textbooks. However, a large number of high school students struggle to comprehend science content. Research findings have demonstrated that students make measurable gains in comprehending content-area textbooks when provided quality reading comprehension instruction. The purpose of this study was to gain an understanding of how high school science teachers perceived their responsibility to provide content-related comprehension instruction and 10 high school science teachers were interviewed for this study. Data analysis consisted of open, axial, and selective coding. The findings revealed that 8 out of the 10 participants believed that it is their responsibility to provide reading comprehension. However, the findings also revealed that the participants provided varying levels of reading comprehension instruction as an integral part of their science instruction. The potential for positive social change could be achieved by teachers and administrators. Teachers may use the findings to reflect upon their own personal feelings and beliefs about providing explicit reading comprehension. In addition to teachers' commitment to reading comprehension instruction, administrators could deliberate about professional development opportunities that might improve necessary skills, eventually leading to better comprehension skills for students and success in their education.

  20. Cost-Effectiveness of Double Reading versus Single Reading of Mammograms in a Breast Cancer Screening Programme

    PubMed Central

    Posso, Margarita; Carles, Misericòrdia; Rué, Montserrat; Puig, Teresa; Bonfill, Xavier

    2016-01-01

    Objectives The usual practice in breast cancer screening programmes for mammogram interpretation is to perform double reading. However, little is known about its cost-effectiveness in the context of digital mammography. Our purpose was to evaluate the cost-effectiveness of double reading versus single reading of digital mammograms in a population-based breast cancer screening programme. Methods Data from 28,636 screened women was used to establish a decision-tree model and to compare three strategies: 1) double reading; 2) double reading for women in their first participation and single reading for women in their subsequent participations; and 3) single reading. We calculated the incremental cost-effectiveness ratio (ICER), which was defined as the expected cost per one additionally detected cancer. We performed a deterministic sensitivity analysis to test the robustness of the ICER. Results The detection rate of double reading (5.17‰) was similar to that of single reading (4.78‰; P = .768). The mean cost of each detected cancer was €8,912 for double reading and €8,287 for single reading. The ICER of double reading versus single reading was €16,684. The sensitivity analysis showed variations in the ICER according to the sensitivity of reading strategies. The strategy that combines double reading in first participation with single reading in subsequent participations was ruled out due to extended dominance. Conclusions From our results, double reading appears not to be a cost-effective strategy in the context of digital mammography. Double reading would eventually be challenged in screening programmes, as single reading might entail important net savings without significantly changing the cancer detection rate. These results are not conclusive and should be confirmed in prospective studies that investigate long-term outcomes like quality adjusted life years (QALYs). PMID:27459663

  1. A Machine that Reads (Reading Technology).

    ERIC Educational Resources Information Center

    Rickelman, Robert J.; Henk, William A.

    1990-01-01

    Discusses the Xerox/Kurzweil Personal Reader which is an advanced optical scanner that reads a greater range of typeset or typewritten text than its predecessors, and converts it into highly naturalistic speech. (MG)

  2. Teachers Sourcebook for Extensive Reading

    ERIC Educational Resources Information Center

    Jacobs, George; Farrell, Thomas S. C.

    2012-01-01

    The best way for students to learn to read and to come to love reading is--surprise, surprise--by reading in quantity. Unfortunately, many of today's students read far too little. This lack of time spent reading is particularly unfortunate, as reading constitutes a bedrock skill, essential in all subject areas. Thus, we teachers need to devote…

  3. Exploring the Relationship between Adolescent's Reading Skills, Reading Motivation and Reading Habits

    ERIC Educational Resources Information Center

    McGeown, Sarah P.; Duncan, Lynne G.; Griffiths, Yvonne M.; Stothard, Sue E.

    2015-01-01

    The present study examines the extent to which adolescents' reading affect (reading motivation) and behaviour (reading habits) predict different components of reading (word reading, comprehension, summarisation and text reading speed) and also adds to the limited research examining group differences (gender, age, ability) in adolescents' reading…

  4. The effects of reading comprehension and launch site on frequency-predictability interactions during paragraph reading.

    PubMed

    Whitford, Veronica; Titone, Debra

    2014-01-01

    We used eye movement measures of paragraph reading to examine whether word frequency and predictability interact during the earliest stages of lexical processing, with a specific focus on whether these effects are modulated by individual differences in reading comprehension or launch site (i.e., saccade length between the prior and currently fixated word--a proxy for the amount of parafoveal word processing). The joint impact of frequency and predictability on reading will elucidate whether these variables additively or multiplicatively affect the earliest stages of lexical access, which, in turn, has implications for computational models of eye movements during reading. Linear mixed effects models revealed additive effects during both early- and late-stage reading, where predictability effects were comparable for low- and high-frequency words. Moreover, less cautious readers (e.g., readers who engaged in skimming, scanning, mindless reading) demonstrated smaller frequency effects than more cautious readers. Taken together, our findings suggest that during extended reading, frequency and predictability exert additive influences on lexical and postlexical processing, and that individual differences in reading comprehension modulate sensitivity to the effects of word frequency. PMID:24205888

  5. Interhemispheric communication influences reading behavior.

    PubMed

    Van der Haegen, Lise; Cai, Qing; Stevens, Michaël A; Brysbaert, Marc

    2013-09-01

    We can read words at an amazing speed, with the left hemisphere taking the burden of the processing in most readers (i.e., over 95% of right-handers and about 75% of left-handers). Yet, it is a long-standing question whether word reading in central vision is possible without information transfer between the left and right hemispheres (LH/RH). Here we show that such communication is required by comparing word naming latencies and eye movement data of people with LH language dominance and a unique sample of healthy RH dominant people. The results reveal that individuals with LH speech dominance name words faster when they are allowed to fixate at the word beginning, whereas RH dominants are faster for fixations toward the end. In text reading, the eyes of LH dominants land more to the left than the eyes of RH dominants, making more information directly available to the dominant hemisphere. We conclude that the traditional view of bilateral projections in central vision is incorrect. In contrast, interhemispheric communication is needed in central vision, and eye movements are adjusted to optimize information uptake. Our findings therefore call into question the explanation of macular sparing in hemianopia based on a bilaterally projecting fovea. In addition, these results are in line with the increase of white matter in the splenium of the corpus callosum when people learn to read. PMID:23647517

  6. Additional insights. Commentary on “the musical stroop effect: opening a new avenue to research on automatisms” by l. Grégoire, P. Perruchet, and B. Poulin-Charronnat (Experimental Psychology, 2013, vol. 60, pp. 269–278).

    PubMed

    Akiva-Kabiri, Lilach; Henik, Avishai

    2014-01-01

    In their paper "The Musical Stroop Effect: Opening a New Avenue to Research on Automatisms," Grégoire, Perruchet, and Poulin-Charronnat (2013) use a musical Stroop-like task to demonstrate the automaticity of musical note naming in musicians. In addition, the authors suggest that music training can serve as a tool in order to study the acquisition of automaticity. In the following commentary, we aim to address three main issues concerning the paper by Grégoire et al. (2013). First, we will suggest some additional interpretations of the results; specifically, we will relate to the association between music and space. Second, we will discuss a methodological issue dealing with interference, facilitation, and the role of the neutral condition. We suggest that the study by Grégoire et al. (2013) lacks a proper neutral condition and thus it is impossible to assert that the congruency effect is interference based. Third, we will discuss the authors' suggestion of using the musical Stroop effect as a tool for studying automatism. We consider the practical relevance of music training as a tool for studying the acquisition of automaticity by pointing out that music training is highly heterogeneous. PMID:24449650

  7. Can Read, Can Write

    ERIC Educational Resources Information Center

    Melia, Ed

    2008-01-01

    Linda Worden always loved books. She liked the way they felt in her hands and the way they smelled. The only problem was she could not read them--until she took part in Channel 4's "Can't Read, Can't Write". This article tells the story of Linda Worden and how learning to read changed her life. Her attempts to learn as an adult are a shocking…

  8. Reading and General Cognitive Ability: A Multivariate Analysis of 7-Year-Old Twins

    ERIC Educational Resources Information Center

    Harlaar, Nicole; Hayiou-Thomas, Marianna E.; Plomin, Robert

    2005-01-01

    We examined the association between reading and general cognitive ability (g) in a population-based sample of 6,476 pairs of 7-year-old twins. Additive genetic influences largely accounted for individual differences in reading and the covariation between reading and g. Furthermore, both genetic and shared environmental influences on reading and g…

  9. University Student Reading Preferences in Relation to the Big Five Personality Dimensions

    ERIC Educational Resources Information Center

    Schutte, Nicola S.; Malouff, John M.

    2004-01-01

    In this study 251 Australian university students, with a mean age of 26.46, indicated their preference for different types of reading material. A subset of 136 participants additionally reported how many hours per week they typically engage in recreational reading and non-recreational reading, indicated their motivation for recreational reading,…

  10. What Motivates Reading? How Library Media Specialists Can Contribute to the Development of Good Readers

    ERIC Educational Resources Information Center

    Fitzgibbons, Shirley A

    2004-01-01

    Since the significant report "Becoming a Nation of Readers: The Report of the Commission on Reading" (Anderson, Hiebert, Scott, and Wilkinson 1985), more attention has been given to the need to motivate and encourage reading in addition to teaching reading skills. That report concluded that the best predictor of reading comprehension, vocabulary…

  11. Weaving the Literacy Web: Changes in Reading from Page to Screen.

    ERIC Educational Resources Information Center

    Sutherland-Smith, Wendy

    2002-01-01

    Explores the unique reading strategies needed for the World Wide Web. Considers additions needed in the repertoire of teaching reading strategies when computers are the medium. Argues that Internet technology has had a significant impact upon reading strategies, resulting in a need to reshape thinking about classroom reading practices. (SG)

  12. Read Hard, Play Later: Putting Summer Reading into Action.

    ERIC Educational Resources Information Center

    Wemett, Lisa C.; Bolan, Kimberly

    1998-01-01

    Provides an overview of "Read on the Wild Side," a summer reading program for young adults established by the Webster (New York) Public Library, and "Read Hard, Play Later," a young adult summer reading program of the Pioneer Library System (New York). Highlights include reading logs, T-shirts, publicity, program evaluation, benefits, summer…

  13. Invent the Future--READ! 2000 Texas Reading Club Manual.

    ERIC Educational Resources Information Center

    Bass, Martha; Davis, Robin Works; Harris, Marlive; Marcum, Paul

    The Texas Reading Club is designed to encourage youth to read for pleasure and to promote library usage.A statewide theme is selected each year that emphasizes ways in which reading expands young minds and encourages children to use their imaginations. The year 2000's theme, "Invent the future! READ!," emphasizes ways in which reading expands…

  14. Motivating Reading Comprehension: Concept-Oriented Reading Instruction

    ERIC Educational Resources Information Center

    Guthrie, John T., Ed.; Wigfield, Allan, Ed.; Perencevich, Kathleen C., Ed.

    2004-01-01

    Concept Oriented Reading Instruction (CORI) is a unique, classroom-tested model of reading instruction that breaks new ground by explicitly showing how content knowledge, reading strategies, and motivational support all merge in successful reading instruction. A theoretical perspective (engagement in reading) frames the book and provides a…

  15. The Effect of Guided Reading Instruction on Reading Achievement

    ERIC Educational Resources Information Center

    Underwood, Vanda Lea

    2010-01-01

    Although reading achievement correlates highly with a student's ability to do well in school, not all children achieve in reading. The purpose of this mixed-method study was to investigate whether reading instruction provided in small groups at the child's own reading level, known as "guided reading instruction," would result in significant…

  16. Assisted Reading with Digital Audiobooks for Students with Reading Disabilities

    ERIC Educational Resources Information Center

    Esteves, Kelli J.; Whitten, Elizabeth

    2011-01-01

    The goal of this study was to compare the efficacy of assisted reading with digital audiobooks with the traditional practice of sustained silent reading (SSR) in terms of reading fluency and reading attitude with upper elementary students with reading disabilities. Treatment group participants selected authentic children's literature and engaged…

  17. A Survey of Reading Achievement in a Secondary School Population.

    ERIC Educational Resources Information Center

    Moodie, Allan G.

    Reading achievement of students from open plan and traditional elementary classes were compared in three areas; speed and accuracy, vocabulary, and comprehension. The first evaluation (Grade 7) indicated that the mean score of the speed and accuracy scale was significantly lower for "open-area" students than for traditional pupils. Score…

  18. Open Access and beyond.

    PubMed

    Mathur, Shawn; Schmidt, Christian; Das, Chhaya; Tucker, Philip W

    2006-01-01

    Uncensored exchange of scientific results hastens progress. Open Access does not stop at the removal of price and permission barriers; still, censorship and reading disabilities, to name a few, hamper access to information. Here, we invite the scientific community and the public to discuss new methods to distribute, store and manage literature in order to achieve unfettered access to literature. PMID:16956402

  19. Diver First Class Reading Ability.

    ERIC Educational Resources Information Center

    Bain, E. C., III; Berghage, T. E.

    The Nelson-Denny reading test was administered to thirty Navy first class diver candidates to evaluate the group's vocabulary, reading comprehension, reading rate and over-all reading ability. Reading rate and comprehension were at the twelfth grade level, while vocabulary ability was equal to the college freshman norm. (Author)

  20. SILENT SPEECH DURING SILENT READING.

    ERIC Educational Resources Information Center

    MCGUIGAN, FRANK J.

    EFFORTS WERE MADE IN THIS STUDY TO (1) RELATE THE AMOUNT OF SILENT SPEECH DURING SILENT READING TO LEVEL OF READING PROFICIENCY, INTELLIGENCE, AGE, AND GRADE PLACEMENT OF SUBJECTS, AND (2) DETERMINE WHETHER THE AMOUNT OF SILENT SPEECH DURING SILENT READING IS AFFECTED BY THE LEVEL OF DIFFICULTY OF PROSE READ AND BY THE READING OF A FOREIGN…

  1. The Beginning Stages of Reading.

    ERIC Educational Resources Information Center

    Wilkie, Fiona, Comp.

    Noting that in the beginning stages of reading it is helpful for children to be surrounded by the written word and to be read to by adults, this article offers brief encapsulations of and responses to five articles about beginning reading and reading readiness. The five articles are as follows: (1) "Three-Year-Olds in Their Reading Corner" by…

  2. A School Policy for Reading.

    ERIC Educational Resources Information Center

    Medwell, Jane

    1992-01-01

    Offers a school policy for reading, arrived at as a product of a whole school inservice program. Discusses word recognition, sound-symbol correspondence, prediction, classroom environment, reading with an adult, parents and reading, assessment of reading, and reading material selection. (RS)

  3. Reading with a Special Touch.

    ERIC Educational Resources Information Center

    McCool, Mary

    Disadvantaged secondary school students with special reading needs can be motivated in the reading room. The school year can start with "popcorn" reading involving materials that are funny, interesting, and exciting. The teacher reads to the students or the students read silently, using materials on the students' independent rather than…

  4. Reading Activities of American Adults.

    ERIC Educational Resources Information Center

    Sharon, Amiel T.

    A reading activities survey as part of the Targeted Research and Development Reading Program was done by interviewing 3,504 adults, aged 16 years or older, selected by area probability sampling. Among the preliminary findings was that the most frequent type of reading is newspaper reading. Seven out of 10 people read or look at a newspaper during…

  5. Paraprofessionals and Reading.

    ERIC Educational Resources Information Center

    Vick, Marian L.

    This pamphlet suggests guidelines to follow for the selection, training, and supervision of paraprofessionals and volunteers in teaching reading and reading-related activities. The contents include: criteria by which paraprofessionals should be selected (emotional stability, ability to relate well to people, ethics, and formal and informal…

  6. Television and Reading.

    ERIC Educational Resources Information Center

    Shaughnessy, Michael F.

    While the influence of television on reading has only been minimally researched, it is obvious that the more television watching children do, the less time is spent on reading. Over 10 years, the cumulative effects of television viewing can be devastating. Watching television is a passive, receptive activity. Children also watch MTV, rent movies,…

  7. EXPERIMENTS IN KINDERGARTEN READING.

    ERIC Educational Resources Information Center

    BAKER, EVA L.; AND OTHERS

    FOUR PAPERS GIVEN AT THE READING SYMPOSIUM OF THE 1968 AMERICAN EDUCATIONAL RESEARCH ASSOCIATION PRESENT DISCUSSIONS OF THE SOUTHWEST REGIONAL LABORATORY (SWRL) READING PROGRAM. THE FIRST PAPER DESCRIBES OBJECTIVES, CLASSROOM MATERIALS, AND PROCEDURES. OBJECTIVES FOR SIGHT-RECOGNITION, WORD-ATTACK SKILLS, AND COMPREHENSION SKILLS ARE EXPRESSED IN…

  8. Keep Them Reading

    ERIC Educational Resources Information Center

    Vanneman, Susan

    2010-01-01

    The relentless quest of the school librarian is finding the right book for each student, searching for the home-run book for every child, and keeping students reading book after book after book. A considerable amount of the school librarian's time, effort, and creativity are devoted not only to motivating students to read, but to keeping them…

  9. Books for Summer Reading.

    ERIC Educational Resources Information Center

    Phi Delta Kappan, 1996

    1996-01-01

    Suggests several novels for educators' summer reading enjoyment, including classics by Robert Pirsig, Robertson Davies, John Steinbeck, Albert Camus, and Charles Dickens. Educators might also read Alex Kotlowitz's "There Are No Children Here" (Doubleday, 1991) and Sharon Quint's "Schooling Homeless Children" (Teachers College Press, 1994) to gain…

  10. Philosophy of Reading Instruction.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    Reading teachers need to provide for individual differences so that each pupil might attain optimally. Methods of teaching reading should be varied and thus reflect diverse philosophies of instruction. These philosophies should be analyzed and used to guide optimal pupil achievement. A philosophy of phoneme/grapheme relationships should be…

  11. Reading: Process and Program.

    ERIC Educational Resources Information Center

    Goodman, Kenneth S.; Niles, Olive S.

    Broad and major concerns dealing with reading are set forth in this monograph to provoke discussion and examination by both researchers and practitioners. In Part 1, Kenneth S. Goodman presents a psycholinguistic view of language and reading (within a transformational-generative framework) as essentially a set of processes of recoding, decoding,…

  12. Visual Search and Reading.

    ERIC Educational Resources Information Center

    Calfee, Robert C.; Jameson, Penny

    The effect on reading speed of the number of target items being searched for and the number of target occurrences in the text was examined. The subjects, 24 college undergraduate volunteers, were presented with a list of target words, and then they read a passage for comprehension which contained occurrences of the target words (Experiment1) or…

  13. Maryland Reading First.

    ERIC Educational Resources Information Center

    Maryland State Dept. of Education, Baltimore.

    In years past, Maryland has provided little guidance toward adoption and implementation of Scientifically Based Reading Research (SBRR) programs. Only recently, with the implementation of the Comprehensive School Reform Demonstration program and the Reading Excellence Act (REA) program, have schools or local education agencies been required to…

  14. Savoring Reading Schoolwide

    ERIC Educational Resources Information Center

    Reis, Sally M.; Fogarty, Elizabeth A.

    2006-01-01

    Over the past four years, educators and researchers from the University of Connecticut have worked with urban high-poverty schools to implement an alternative reading instruction program called the Schoolwide Enrichment Model in Reading (SEM-R). Based on Renzulli's Enrichment Triad Model, the SEM-R works through planned enrichment experiences to…

  15. INTERMEDIATE READINGS IN TAGALOG.

    ERIC Educational Resources Information Center

    BOWEN, J. DONALD, ED.

    THE SECOND IN A SERIES OF TEXTS DESIGNED TO HELP THE STUDENT ACHIEVE AN UNDERSTANDING OF FILIPINO CULTURE AND ACQUIRE ENOUGH PROFICIENCY IN TAGALOG TO COMMUNICATE EASILY AND MEANINGFULLY, THESE INTERMEDIATE READINGS ARE COORDINATED WITH THE EDITOR'S "BEGINNING TAGALOG" (ED 014 696). INCLUDED IN PART I ARE READINGS WRITTEN ESPECIALLY FOR THIS TEXT…

  16. Reading Is Fundamental, 1977.

    ERIC Educational Resources Information Center

    Smithsonian Institution, Washington, DC. National Reading is Fun-damental Program.

    Reading Is Fundamental (RIF) is a national, nonprofit organization designed to motivate children to read by making a wide variety of inexpensive books available to them and allowing the children to choose and keep books that interest them. This annual report for 1977 contains the following information on the RIF project: an account of the…

  17. Can India's "Literate" Read?

    ERIC Educational Resources Information Center

    Kothari, Brij; Bandyopadhyay, Tathagata

    2010-01-01

    This paper takes a close look at India's literacy rate by exploring whether the officially "literate" can read and at what level. In a large sample, aged 7+, drawn from four Hindi-speaking states, two methods were used to measure literacy. One was the standard Census Method (CM) which relies on self-reporting and the other was a Reading Method…

  18. Summer Reading Loss

    ERIC Educational Resources Information Center

    Mraz, Maryann; Rasinski, Timothy V.

    2007-01-01

    Summer reading loss is a documented reality for many students. It is often of greatest concern for those who are already at risk, who typically have limited access to reading materials at home and whose parents or caregivers may be reluctant or unsure of how to help. By raising parents' awareness of the importance of supporting their children's…

  19. Reading and Postmodernism.

    ERIC Educational Resources Information Center

    Alexander, James C.

    One of the main differences between the whole language position and the more traditional views lies in the epistemological base upon which whole language is rooted. Although whole language proponents may not have clearly put forth an epistemology upon which their views of reading acquisition and the reading process are based, still a careful…

  20. Reading for Meaning: Questioning

    ERIC Educational Resources Information Center

    Trinkle, Catherine

    2009-01-01

    An essential literacy skill is asking questions. Because reading comprehension strategies should be taught directly and explicitly, students need to be told that they should ask questions throughout their research and that all questions are valid. While library media specialists are not reading teachers, the work they do with students in the…

  1. Using Collaborative Strategic Reading.

    ERIC Educational Resources Information Center

    Klingner, Janette K.; Vaughn, Sharon

    1998-01-01

    Describes collaborative strategic reading (CSR), a technique for teaching students, such as those with learning disabilities, reading comprehension and vocabulary skills in a cooperative setting. Covers teaching the four strategies of CSR (preview, click and clunk, get the gist, and wrap up), as well as teaching students cooperative learning group…

  2. Making Textbook Reading Meaningful

    ERIC Educational Resources Information Center

    Guthrie, John T.; Klauda, Susan Lutz

    2012-01-01

    When students enter middle school, they are confronted with the necessity of learning from complex content-area textbooks. Many students find these texts boring, and they may lack the higher-order reading comprehension skills they need to tackle complex text. Yet the ability to read informational text is essential to success in middle school and…

  3. VISION AND READING ABILITY.

    ERIC Educational Resources Information Center

    MANGRUM, CHARLES T.

    SIGNIFICANT RESEARCH ON THE PHYSIOLOGICAL AND FUNCTIONAL ASPECTS OF VISION AND READING DISABILITY IS SURVEYED. CONCLUSIONS BASED ON THE LITERATURE IN THE FIELD ARE DISCUSSED. A BIBLIOGRAPHY OF 70 REFERENCES AND A GLOSSARY OF TERMS ARE APPENDED. A TABLE SUMMARIZING REFRACTIVE ERRORS AND EYE DEFECTS CONTRIBUTING TO READING DISABILITY IS INCLUDED.…

  4. CRITICAL READING DEVELOPS EARLY.

    ERIC Educational Resources Information Center

    LEE, DORRIS; AND OTHERS

    THIS ISSUE OF THE READING AIDS SERIES PRESENTS A DISCUSSION OF THE POTENTIAL FOR CRITICAL READING AMONG YOUNG CHILDREN AND HOW IT CAN BE DEVELOPED. IT OFFERS SUGGESTIONS FOR THE MAXIMUM DEVELOPMENT OF THINKING SKILLS AND ATTITUDES OF INQUIRY AND EVALUATION. SOME OF THE TOPICS DISCUSSED ARE -- (1) THE DEVELOPMENT OF PERCEPTS, CONCEPTS, AND COMMON…

  5. The Virtues of Reading

    ERIC Educational Resources Information Center

    Kupfer, Joseph

    2002-01-01

    In Danny DeVito's film "Matilda," Harry Wormwood berates his young daughter, the title character, when she insists on reading. He tells her, "There's nothing you can get from a book that you can't get faster from television." Matilda's would-be visionary father, however, is blind to crucial habits of mind fostered by reading books that are not…

  6. An Individualized Reading Program.

    ERIC Educational Resources Information Center

    Davis, Nancy B.

    The operating procedures of a university reading and study skills center for completely individualized reading instruction are described. The program is offered as a student service (no fee) on a voluntary, noncredit basis. A prepared set of instructional tapes is used whereby students can largely serve themselves, proceeding at their own rates,…

  7. Against Reading Lists

    ERIC Educational Resources Information Center

    Davis, Lennard J.

    2012-01-01

    A course's reading list is the skeleton of a semester's body of thought, the inventory that a professor writes up for the departmental Web site and the schedule of courses that lists the goods. Despite the obvious utility of fixed reading lists, one should jettison them when possible. The author has been conducting an informal experiment using a…

  8. Teaching Reading in Homeschool.

    ERIC Educational Resources Information Center

    Yambo, Idalia

    This paper discusses the home-schooling trend and identifies reading instructional methods used by home-schooling parents. Interviews were conducted with 5 home-schooling families of children ranging in age from 1 to 14 years. Parents reported that they began reading instruction with their child at about age 5 and agreed that instruction in…

  9. Reading in Kazakhstan.

    ERIC Educational Resources Information Center

    Beisembaeva, Zhanat Abaevna

    1995-01-01

    Analyzes sociological research conducted by Kazakhstan libraries between 1991 and 1994. Highlights include discussions on the sociology of reading, research results, and library facilities. It was found that reading is characterized by frequent changes in demands of readers caused by dramatic shifts in ideology, politics, and economics in the…

  10. Anything but Reading

    ERIC Educational Resources Information Center

    Krashen, Stephen

    2009-01-01

    Both the popular media and professional literature are filled with suggestions on how to improve reading, but the one approach that always works is rarely mentioned: provide readers with a supply of interesting and comprehensible books. Instead, people are given advice that is dead wrong as a means of improving reading (e.g., roller skating and…

  11. Reading Field Experience Program.

    ERIC Educational Resources Information Center

    Ceaser, Lisbeth

    The lessons included in this collection were written by California Polytechnic State University Reading Specialist Credential candidates in the Salinas Cohort Project of 1992 as partial fulfillment for an education course titled "Bilingual Special Education Reading Problems." Each lesson is research-based. A rationale describes the reading…

  12. The Reading Tutor.

    ERIC Educational Resources Information Center

    Rosberg, Merilee A.

    As a direct result of the passage of the America Reads Challenge Act in 1997, Mt. Mercy College, Cedar Rapids, Iowa, has developed a reading tutor program. The program includes a college credit course and on-site visits by college faculty supervising student tutors. This article includes the rationale for development of a credit course for reading…

  13. Reading with an Infant.

    ERIC Educational Resources Information Center

    Lamme, Linda Leonard

    1980-01-01

    Emphasizes that parents' reading to infants fosters interest in literature and provides foundation for basic reading skills. Titles of musical books, point-and-say books, touch and smell books, cardboard books, cloth books, plastic books, and early stories are provided. (Author/DB)

  14. Connecting Males and Reading

    ERIC Educational Resources Information Center

    Buddy, Juanita Warren

    2011-01-01

    The problems facing males and reading continues to be a topic of concern and discussion in communities across the country. The author has interviewed school librarians and teachers, however, who are coordinating programs that are successfully connecting male students and reading. This article includes summaries of those interviews. The author has…

  15. Little Herder Reading Series.

    ERIC Educational Resources Information Center

    Bureau of Indian Affairs (Dept. of Interior), Washington, DC.

    The Little Herder Reading Series is comprised of 4 volumes based on the life of a Navajo Indian girl. The books are written in English blank verse and describe many facets of Indian life. The volumes contain illustrations by Hoke Denetsosie which give a pictorial representation of the printed verse. The reading level is for the middle and upper…

  16. Teaching Reading and Writing.

    ERIC Educational Resources Information Center

    Manning, Maryann; Manning, Gary

    1996-01-01

    Introduces Earth Day. Encourages the use of reading, writing, and theme immersion to increase student participation in such activities. Provides information on several organizations which students can obtain concerning environmental awareness. Recommends reading materials that can be obtained in hard copy as well as on the Internet. (MOK)

  17. Reading and Math.

    ERIC Educational Resources Information Center

    Baldwin, Anna; And Others

    This publication contains materials used in the three phases of the reading and mathematics components of work-specific classes. Each section begins with an overview of developments in that phase. Section 1 focuses on Phase 1 during which math and reading were taught as separate components. It contains a math placement appraisal, worksheets and…

  18. Education: Is Reading Important?

    ERIC Educational Resources Information Center

    USA Today, 1980

    1980-01-01

    Summarizes arguments in favor of teaching people to read. Arguments include that television and radio cannot help individuals adapt and retrain quickly in their jobs; promotion in the armed services and elsewhere depends upon a certain degree of reading expertise; and people are unable to fill out income tax and other forms if they do not possess…

  19. Motivating Students To Read.

    ERIC Educational Resources Information Center

    Kane, Roberta S.; Warner, Dori

    This action research project implemented a program for motivating students to read so that they would become enthusiastic, lifelong readers. The targeted population consisted of first- and second-grade students in a middle class community located in a western suburb of Chicago, Illinois. The problem of lack of motivation in reading was documented…

  20. Children's Reading Strategies.

    ERIC Educational Resources Information Center

    Brown, Rexel E., Ed.

    1980-01-01

    This issue of the "Journal of Children and Youth" focuses on children's strategies for decoding and comprehending written language and teacher's strategies for facilitating this process. The issue includes eleven papers by members of the Indiana Reading Professors division of the Indiana State Reading Council and several invited guests. Peggy…

  1. Reading and Perestroika.

    ERIC Educational Resources Information Center

    Plotnikov, Sergei N.

    1992-01-01

    Presents a short historical and sociological analysis of reading in the Soviet Union from the beginning of the twentieth century to perestroika. Discusses some sociocultural problems associated with reading, including the prevailing social, economic and political crises in all spheres of life, particularly the cultural. (RS)

  2. Reading Where It Counts

    ERIC Educational Resources Information Center

    Miller, Harry

    2014-01-01

    In this article, teachers are reminded that their content subject areas require acquainting children with special words or symbols related to that subject area (e.g. mathematics or social studies). Because children can read well does not mean they would be understanding of any special reading skill required in a content subject area; that the…

  3. Reading Methods Comparison

    ERIC Educational Resources Information Center

    Montgomery, Joel R.

    2008-01-01

    This working paper explores contemporary research related to methods for teaching reading in Spanish and English in bilingual, foreign language, and English as a second language (ESL) classrooms. Changes stemming from innovations in research and learning are identified and a table is provided to compare methods of teaching reading in Spanish and…

  4. Reading for Life

    ERIC Educational Resources Information Center

    McKearney, Miranda

    2009-01-01

    The Reading Agency has been backing and building a movement in libraries called reader development. The movement is creating a livelier, more interventionist reading service that's both much more attractive and socially relevant. A focus on reader development is changing the way public libraries work, and transforming people's lives in the…

  5. Cerebral Laterality and Reading.

    ERIC Educational Resources Information Center

    Mackworth, Jane F.

    Recent research has confirmed that hemispheric patterns of dominance are related to reading skills. Reading is more complex than speech because it includes a visuo-spatial element. In the great majority of people, the left hemisphere deals with speech and sequencing skills. Visual matching of printed words requires the spatial skills of the right…

  6. Reading Stars. 2013 Report

    ERIC Educational Resources Information Center

    National Literacy Trust, 2013

    2013-01-01

    The National Literacy Trust's Premier League Reading Stars has now been running for 10 years. During this time, hundreds of thousands of children and families have been inspired by the power of football to develop a love of reading. Although the programme has grown and evolved over this period, the premise remains the same: harnessing the…

  7. Extending Extensive Reading

    ERIC Educational Resources Information Center

    Day, Richard R.

    2015-01-01

    The April 2015 issue of "Reading in a Foreign Language" featured a discussion forum on extensive reading (ER). Most of the authors, recognized authorities on ER, discussed their views of the principles of ER, particularly in establishing and conducting ER programs. The purpose of this discussion is to review developments in the practice…

  8. The Roots of Reading.

    ERIC Educational Resources Information Center

    Montoya, Colleen, Ed.

    2002-01-01

    This newsletter covers educational issues affecting schools in the Western Regional Educational Laboratory's 4-state region (Arizona, California, Nevada, and Utah) and nationwide. The following articles appear in the Volume 4, Number 1 issue: (1) "The Roots of Reading"; (2) "Breaking the Code: Reading Literacy in K-3"; (3) "Improving Secondary…

  9. Superheroes and Summer Reading.

    ERIC Educational Resources Information Center

    Meyer, Ron; Buckner, Joyce

    1980-01-01

    To combat summer learning loss among remedial readers, teachers and consultants in the Omaha, Nebraska, Title I program designed a series of comic-book reading units and mailed them to students' homes. Parents were pleased with the project and it appeared that less reading skill had been lost by September. (SJL)

  10. Learn to Read.

    ERIC Educational Resources Information Center

    Appelson, Marilyn; And Others

    The Learn to Read project was designed to provide a supportive setting in which functionally illiterate adult students from suburban Cook County, Illinois, and surrounding areas could develop reading and writing skills. The target population included English-dominant adults with basic oral competency but no literacy skills, as well as…

  11. PASS and Reading Achievement.

    ERIC Educational Resources Information Center

    Kirby, John R.

    Two studies examined the effectiveness of the PASS (Planning, Attention, Simultaneous, and Successive cognitive processes) theory of intelligence in predicting reading achievement scores of normally achieving children and distinguishing children with reading disabilities from normally achieving children. The first study dealt with predicting…

  12. Measuring Reading Performance Informally.

    ERIC Educational Resources Information Center

    Powell, William R.

    To improve the accuracy of the informal reading inventory (IRI), a differential set of criteria is necessary for both word recognition and comprehension scores for different levels and reading conditions. In initial evaluation, word recognition scores should reflect only errors of insertions, omissions, mispronunciations, substitiutions, unkown…

  13. Readings in Reading: Practice, Theory, Research.

    ERIC Educational Resources Information Center

    Schubert, Delwyn G., Ed.; Torgerson, Theodore L., Ed.

    Designed to give teachers, specialists, and students insight into the historical development of trends, theory, research, and current practices in reading instruction, 82 selections written over a period of nearly 150 years have been compiled from books, monographs, pamphlets, yearbooks, conference proceedings, and education periodicals. The…

  14. Nystagmus Does Not Limit Reading Ability in Albinism

    PubMed Central

    Dysli, Muriel; Abegg, Mathias

    2016-01-01

    Purpose Subjects with albinism usually suffer from nystagmus and reduced visual acuity, which may impair reading performance. The contribution of nystagmus to decreased reading ability is not known. Low vision and nystagmus may have an additive effect. We aimed to address this question by motion compensation of the nystagmus in affected subjects and by simulating nystagmus in healthy controls. Methods Reading speed and eye movements were assessed in 9 subjects with nystagmus associated with albinism and in 12 healthy controls. We compared the reading ability with steady word presentation and with words presented on a gaze contingent display where words move in parallel to the nystagmus and thus correct for the nystagmus. As the control, healthy subjects were asked to read words and texts in steady reading conditions as well as text passages that moved in a pattern similar to nystagmus. Results Correcting nystagmus with a gaze contingent display neither improved nor reduced the reading speed for single words. Subjects with nystagmus and healthy participants achieved comparable reading speed when reading steady texts. However, movement of text in healthy controls caused a significantly reduced reading speed and more regressive saccades. Conclusions Our results argue against nystagmus as the rate limiting factor for reading speed when words were presented in high enough magnification and support the notion that other sensory visual impairments associated with albinism (for example reduced visual acuity) might be the primary causes for reading impairment. PMID:27391149

  15. Effects of Differentiated Reading on Elementary Students' Reading Comprehension and Attitudes toward Reading

    ERIC Educational Resources Information Center

    Shaunessy-Dedrick, Elizabeth; Evans, Linda; Ferron, John; Lindo, Myriam

    2015-01-01

    In this investigation, we examined the effects of a differentiated reading approach on fourth grade students' reading comprehension and attitudes toward reading. Eight Title I schools within one urban district were randomly assigned to treatment (Schoolwide Enrichment Model-Reading [SEM-R]) or control (district reading curriculum) conditions.…

  16. The Effects of Sustained Silent Reading on Reading Achievement and Reading Attitudes of Fourth Grade Students

    ERIC Educational Resources Information Center

    Gray, Holly Lynn

    2012-01-01

    This study tested the effects of a Sustained Silent Reading program on reading achievement and reading attitude. The study accessed scores from the DIBELS Oral Reading Fluency (Good, Kaminski, & Dill, 2007) to measure reading achievement. This measure was given before and after a twelve week period, during which the treatment group…

  17. Role of Reading Engagement in Mediating Effects of Reading Comprehension Instruction on Reading Outcomes

    ERIC Educational Resources Information Center

    Wigfield, Allan; Guthrie, John T.; Perencevich, Kathleen C.; Taboada, Ana; Klauda, Susan Lutz; McRae, Angela; Barbosa, Pedro

    2008-01-01

    The engagement model of reading development suggests that instruction improves students' reading comprehension to the extent that it increases students' engagement processes in reading. We compared how Concept-Oriented Reading Instruction (CORI) (support for cognitive and motivational processes in reading), strategy instruction (support for…

  18. Photometry using Kepler ``superstamps'' of open clusters NGC 6791 & NGC 6819

    NASA Astrophysics Data System (ADS)

    Kuehn, Charles A.; Drury, Jason; Stello, Dennis; Bedding, Timothy R.

    2014-02-01

    The Kepler space telescope has proven to be a gold mine for the study of variable stars. Unfortunately, Kepler only returns a handful of pixels surrounding each star on the target list, which omits a large number of stars in the Kepler field. For the open clusters NGC 6791 and NGC 6819, Kepler also reads out larger superstamps which contain complete images of the central region of each cluster. These cluster images can potentially be used to study additional stars in the open clusters. We present preliminary results from using traditional photometric techniques to identify and analyze additional variable stars from these images.

  19. Formulating secondary-level reading interventions.

    PubMed

    Kamps, Debra M; Greenwood, Charles R

    2005-01-01

    Recent advances concerning emerging/beginning reading skills, positive behavioral support (PBS), and three-tiered schoolwide prevention models combined with federal mandates (i.e., IDEA and No Child Left Behind) have stimulated interest in providing early and intensive instructional intervention services to children at risk for reading and behavior problems. New measures for identifying students as early as kindergarten who are not acquiring early basic literacy skills make this possible. However, questions regarding exactly how to formulate, deliver, sustain, and manage secondary-level interventions remain to be addressed. This paper describes first-year, first-grade findings for students participating in secondary-level interventions (i.e., small-group reading instruction) in a randomized trial of the efficacy of secondary and tertiary reading and behavior interventions under way at the Center for Early Intervention in Reading and Behavior, University of Kansas. The formulation of the experimental secondary-level intervention was guided by evidence supporting the efficacy of (a) small groups of 3 to 6 participating students and low student-teacher ratio combined with (b) explicit, phonics-based instruction. Selected curricula were Reading Mastery, Proactive Reading, Programmed Reading, and Read Well, use of which varied by choice across experimental-group schools. PBS was an additional intervention context in experimental schools. Comparison schools and first-grade teachers did not employ the three-tiered model, early screening, or PBS; most students were taught using conventional whole-group instruction, little or no individualization, and curricula with weak scientific evidence. Initial results indicate significantly larger growth for experimental secondary-level at-risk students than for comparisons. Experimental-group first graders not showing growth were those identified with disabilities or behavioral risks and English language learners. Implications are

  20. The additive effect of dorzolamide hydrochloride (Trusopt) and a morning dose of bimatoprost (Lumigan) on intraocular pressure and retrobulbar blood flow in patients with primary open-angle glaucoma

    PubMed Central

    Stankiewicz, Andrzej; Siemiątkowska, Anna; Fuksińska, Beata; Robaszkiewicz, Jacek; Zegadło, Arkadiusz; Ehrlich, Rita; Siesky, Brent; Harris, Alon

    2010-01-01

    Aims To assess the additive effect of dorzolamide hydrochloride 2% on the diurnal intraocular pressure (IOP) curve and retrobulbar haemodynamics in patients with primary open-angle glaucoma (POAG) treated with morning-dosed bimatoprost 0.03%. Methods Twenty-five patients with POAG were evaluated in a prospective, single-masked study. After a 1 week run-in period with bimatoprost all patients were treated with bimatoprost dosed once in the morning for 1 month, after which dorzolamide was added twice daily for 2 months. Goldmann applanation IOP, arterial blood pressure (ABP) and heart rate were measured every 2 h for 24 h and diurnal ocular perfusion pressure (OPP) was calculated. Colour Doppler imaging (CDI) of the ophthalmic artery (OA) and the central retinal artery (CRA) was recorded five times daily. All measurements were taken after the two phases of treatment and were compared. Results The mean baseline IOP was 14.8±3.5 mm Hg. Mean IOP following bimatoprost monotherapy (12.8±2.9 mm Hg) and after 2 months of dorzolamide adjunctive therapy (12.2±2.6 mm Hg) were not statistically significantly different (p=0.544). Only at the 4:00 h time point was IOP significantly reduced using the bimatoprost/dorzolamide combined treatment (p=0.013). The 24 h IOP fluctuations were lower when dorzolamide was added (6.0±2.3 mm Hg vs 4.6±1.5 mm Hg, p=0.0016). Repeated analysis of variance detected a significant decrease of vascular resistance in the OA (p=0.0167) with adjunctive dorzolamide treatment. Conclusions The addition of dorzolamide to morning-dosed bimatoprost had an additive hypotensive effect only on the night-time IOP curve at 4:00 h and resulted in a lower IOP fluctuation. Dorzolamide added to bimatoprost may reduce vascular resistance in the OA. PMID:20558428

  1. Attention and reading skills.

    PubMed

    Commodari, Elena; Guarnera, Maria

    2005-04-01

    Attention plays a critical role in information processing. Its adequate functioning is required for correct development of complex cognitive abilities and regular scholastic progress. Children with attention deficits often have difficulties in reading, writing, and arithmetic. The present study investigated interactions among reading skills, overall scholastic performance as rated by teachers, and components of attention: visual reaction time, simple immediate span of attention, and selectivity. The sample was 98 students in the first and second years of public junior high school (age range 11-14 years, M = 12.6, SD = 1.2), i.e., with expected already well-established reading. Reading was evaluated using Comprehension, Accuracy, and Speed tests. Overall scholastic performance was obtained by means of teachers' ratings. Simple Reaction Time, Digit Span, and Color-Word Interference, included in a multitask computerized test, assessed attention. Analysis confirmed the hypothesis that the reading skills are strongly predictive of the Scholastic Assessment rated by the teachers. High scholastic ratings were correlated with Reading Speed and Accuracy rather than Reading Comprehension. Poor readers showed worse performances on the Digit Span test which measures simple immediate span of attention. Good and poor readers obtained a similar score on the Color-Word Interference task. This observation seems to contrast with the more common interpretation of this effect, suggesting that reading is an automatic process and, therefore, the semantic dimension overcomes the controlled perceptual one. According to other studies, an alternative explanation is suggested. In conclusion, present results confirm the hypothesis of a strong link among reading speed and accuracy, scholastic assessment as rated by teachers, simple immediate span of attention, and visual reaction time. PMID:15974348

  2. The impacts of read length and transcriptome complexity for de novo assembly: a simulation study.

    PubMed

    Chang, Zheng; Wang, Zhenjia; Li, Guojun

    2014-01-01

    Transcriptome assembly using RNA-seq data - particularly in non-model organisms has been dramatically improved, but only recently have the pre-assembly procedures, such as sequencing depth and error correction, been studied. Increasing read length is viewed as a crucial condition to further improve transcriptome assembly, but it is unknown whether the read length really matters. In addition, though many assembly tools are available now, it is unclear whether the existing assemblers perform well enough for all data with different transcriptome complexities. In this paper, we studied these two open problems using two high-performing assemblers, Velvet/Oases and Trinity, on several simulated datasets of human, mouse and S.cerevisiae. The results suggest that (1) the read length of paired reads does not matter once it exceeds a certain threshold, and interestingly, the threshold is distinct in different organisms; (2) the quality of de novo assembly decreases sharply with the increase of transcriptome complexity, all existing de novo assemblers tend to corrupt whenever the genes contain a large number of alternative splicing events. PMID:24736633

  3. Reading, Writing, and Running.

    ERIC Educational Resources Information Center

    Detherage, Jim

    1980-01-01

    Describes an English course that capitalizes on the popularity of running, integrating running with reading and writing activities. Notes the positive results of this interdisciplinary approach. Provides samples of student writings. (RL)

  4. Developmental reading disorder

    MedlinePlus

    ... important. Many students with learning disabilities have poor self-esteem. Psychological counseling may be helpful. ... Problems in school, including behavior problems Loss of self-esteem Reading problems that continue Problems with job performance

  5. Reading the Future

    ERIC Educational Resources Information Center

    Marturano, Arlene

    1976-01-01

    A learning activity is described in which the children become involved in dialogs with the Earth and its resources, and in turn the eye reads the surroundings and becomes more skilled at observation. (EB)

  6. Reading the Body.

    ERIC Educational Resources Information Center

    Dressman, Mark; Abbott, Judy

    2001-01-01

    Presents brief summaries of 26 children's books (published between 1996 and 2001) about physiology, health and sexuality, and sports and recreation. Also presents new books of professional interest that might provoke some visceral reaction from their reading. (SG)

  7. Can India's ``literate'' read?

    NASA Astrophysics Data System (ADS)

    Kothari, Brij; Bandyopadhyay, Tathagata

    2010-12-01

    This paper takes a close look at India's literacy rate by exploring whether the officially "literate" can read and at what level. In a large sample, aged 7+, drawn from four Hindi-speaking states, two methods were used to measure literacy. One was the standard Census Method (CM) which relies on self-reporting and the other was a Reading Method (RM) which required the same individuals to actually read a simple text at grade 2 level. The findings revealed a substantial difference between the reading literacy rates obtained by CM and RM. CM over-reported RM by 16%. The overestimation was higher for males. Decoding skills were found to erode in most cases after completion of primary schooling, assuming no further education. A minimum grade 8-9 education was required for decoding skills to not deteriorate after schooling.

  8. A School Reading Policy.

    ERIC Educational Resources Information Center

    Dawson, Alan

    1978-01-01

    Defines a school-based reading policy and explores the issues involved in setting up a program, including awareness and use of school resources, recording student progress, evaluation, parental involvement, and classroom organization and teaching methods. (FL)

  9. The "Enigma" Reading Program.

    ERIC Educational Resources Information Center

    Sachs, Frances Greenberg; Banas, Norma

    1985-01-01

    Approaches are discussed for constructing and implementing the ENIGMA (Engineering Individual Growth Through Manipulative Associations) reading program, a language-based activity using teacher-made puzzles and stories in a manipulative-associative manner. (CL)

  10. Reading Improvement Through Art

    ERIC Educational Resources Information Center

    Corwin, Sylvia K.

    1977-01-01

    A team of enthusiastic, dedicated teachers proved that for problem readers in today's high schools, in a setting where trained reading teachers collaborated with studio teachers, the visual arts can be an important tool for learning. (Author)

  11. Philosophy of Teaching Reading.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    2003-01-01

    Lists advantages and disadvantages of statewide testing. Presents examples of highly specific objectives, as emphasized by realism as a philosophy of education. Considers the advantages idealism/perennialism, as a philosophy of instruction, has in a quality reading curriculum. (SG)

  12. Reading-Boxing Class

    ERIC Educational Resources Information Center

    Kravitz, Richard; Shapiro, Marvin

    1969-01-01

    The physical education department of the Pennsylvania Advancement School of Philadelphia has established a reading and communication skill project that uses the appeal of sports to help students improve their basic skills. (Author)

  13. Developmental reading disorder

    MedlinePlus

    ... people with DRD have normal or above-average intelligence. DRD may appear with other problems. These can ... causes of learning and reading disabilities, such as: Emotional disorders Intellectual disability Brain diseases Certain cultural and ...

  14. Teachers' Role in Fostering Reading Skill: Effective and Successful Reading

    ERIC Educational Resources Information Center

    Jose, G. Rexlin; Raja, B. William Dharma

    2011-01-01

    Reading bestows enjoyment and enlightenment. It unlocks the unknown. It is a complex cognitive activity that is indispensable for the kind of knowledge society. So the students of today's world must know how to learn from reading and to enter the present literate society. One who reads can lead others to light. People who read can be free because…

  15. Developing New Reading Assessments to Promote Beginning Reading in Singapore

    ERIC Educational Resources Information Center

    Koh, Kim H.; Paris, Scott G.

    2011-01-01

    Effective reading instruction and intervention are rooted in effective assessments of children's developing skills in reading. The article aims to describe the development of new reading assessments to help promote beginning reading in Singapore primary schools. We begin with an introduction to the educational landscape and policies before…

  16. The Potency of "READS" to Inform Students' Reading Ability

    ERIC Educational Resources Information Center

    Mohamed, Abdul Rashid; Eng, Lin Siew; Mohamed Ismail, Shaik Abdul Malik

    2012-01-01

    This paper shares an initiative conducted in Malaysia in terms of knowledge to gauge students' Reading Age and to inform teachers of their students' reading progress and learning. Ensuring teachers understand the needs of students' reading ability and preparing students to read and comprehend texts are the two most fundamental parallel tasks in…

  17. Improving EFL Learners' Reading Levels through Extensive Reading

    ERIC Educational Resources Information Center

    Mermelstein, Aaron David

    2014-01-01

    Today there is an increasing amount of research promoting the effectiveness of extensive reading (ER) towards increasing learners' vocabulary, comprehension, reading speed, and motivation towards reading. However, little has been done to measure the effects of ER on learners' reading levels. This quantitative study examined the effects…

  18. When Reading Gets Ruff: Canine-Assisted Reading Programs

    ERIC Educational Resources Information Center

    Lane, Holly B.; Zavada, Shannon D. W.

    2013-01-01

    Canine-assisted reading programs show promise as an innovative method for engaging reluctant readers and motivating them to practice. In such programs, specially trained dogs visit classrooms and libraries, and children read to them. Children who struggle with reading may be motivated to read more because they find dogs to be calming and…

  19. Parents' Reading-Related Knowledge and Children's Reading Acquisition

    ERIC Educational Resources Information Center

    Ladd, Megan; Martin-Chang, Sandra; Levesque, Kyle

    2011-01-01

    Teacher reading-related knowledge (phonological awareness and phonics knowledge) predicts student reading, however little is known about the reading-related knowledge of parents. Participants comprised 70 dyads (children from kindergarten and grade 1 and their parents). Parents were administered a questionnaire tapping into reading-related…

  20. Summer Reading Summer Not: How Project READS Can Advance Equity

    ERIC Educational Resources Information Center

    Kim, James S.

    2010-01-01

    This paper has three goals. First, it describes the broader research on summer reading loss. Second, it discusses how research and development efforts informed the key components of Project READS (Reading Enhances Achievement During Summer), a scaffolded voluntary summer reading intervention for children in grades 3 to 5. The second part of the…

  1. A Developmental Path to Reading: Reading the Signs.

    ERIC Educational Resources Information Center

    Mitchell, Kevin, Ed.

    2000-01-01

    This issue focuses on the developmental path that children typically take when learning to read. The purpose is to help parents take steps to ensure that their children will make the transition from learning to read to reading to learn by the end of third grade. An introductory section includes two articles: "Parents, Children, and Reading" (Carol…

  2. Reading Motivation and Reading Engagement: Clarifying Commingled Conceptions

    ERIC Educational Resources Information Center

    Unrau, Norman J.; Quirk, Matthew

    2014-01-01

    The constructs of motivation for reading and reading engagement have frequently become blurred and ambiguous in both research and discussions of practice. To address this commingling of constructs, the authors provide a concise review of the literature on motivation for reading and reading engagement and illustrate the blurring of those concepts…

  3. Teen Summer Reading Program, 1999. Read around the World.

    ERIC Educational Resources Information Center

    Virginia State Library, Richmond.

    This guide for the 1999 Virginia teen summer reading program for public libraries, "Read around the World," includes the following chapters: (1) "Reading and Teens," including serving the underserved, tips for teens, and a recipe for choosing a book to read for fun; (2) "Programming and Teens," including "The Why of YA [Youth Adult] Programming"…

  4. Reading Every Single Day: A Journey to Authentic Reading

    ERIC Educational Resources Information Center

    Hudson, Alida K.; Williams, Joan A.

    2015-01-01

    This article details one teacher's implementation of reading workshop in her second grade classroom. She provided a framework for authentic reading using the five components of reading workshop: time, choice, response, community, and structure. She found that reading workshop is a highly effective practice for not only increasing students'…

  5. Family Reading Habits and Children's Progress in Reading.

    ERIC Educational Resources Information Center

    Lamme, Linda; Olmsted, Pat

    This study examined the influences of the home on children's attitudes toward reading, perceptions of reading, reading habits, and reading achievement. Participating in the study were 38 low-income white children (and their parents) from nine first-grade classrooms involved in the Florida Parent Education Follow Through project. Data were obtained…

  6. Reading Acts: An Inquiry into Reading and Teaching

    ERIC Educational Resources Information Center

    Sams, Brandon L.

    2012-01-01

    This text performs reading for teaching in an audit culture. Two teachers, myself and Steven, read the memoir "Hole in My Life" by Jack Gantos and, while reading, recorded our experiences as readers and planned to teach the book to Steven's English class. This study is an inquiry into the phenomenon of "reading to teach,"…

  7. READING MANUAL, A GUIDEBOOK FOR ILLINOIS WORKSHOPS IN READING REMEDIATION.

    ERIC Educational Resources Information Center

    COVEY, CATHERINE

    THE IMPORTANCE OF ADAPTING READING INSTRUCTION TO EACH CHILD'S NEEDS IS STRESSED IN THIS HANDBOOK FOR TEACHERS OF REMEDIAL READING. INFORMATION IS ORGANIZED AROUND SIX TOPICS--(1) THE NATURE OF THE READING PROCESS, (2) CRITERIA FOR A GOOD ELEMENTARY READING PROGRAM, (3) REMEDIAL READERS, THE SYMPTOMS AND CAUSES (PHYSICAL, INTELLECTUAL,…

  8. Reconsidering Children's Readings: Insights into the Reading Process

    ERIC Educational Resources Information Center

    Arya, Poonam; Feathers, Karen M.

    2012-01-01

    This study highlights the complex reading processes of two primary grade struggling readers. It provides a more complete picture of the readers' use of all parts of a text, verbal and visual, to construct meaning during reading. The oral reading data show that students used various linguistic strategies to read words, and the eye-tracking data…

  9. Reading Rates of Young Braille-Reading Children.

    ERIC Educational Resources Information Center

    Wormsley, D. P.

    1996-01-01

    Three tables present data from 22 braille-reading blind children, ages 6 to 12, including demographic data (such as years of braille use, IQ, age, hand movement type, and reading rate); highest and lowest reading rates, by years of braille instruction and IQ scores; and oral reading rates. The methodology used is suggested for teachers doing…

  10. Reading Knee-Deep

    ERIC Educational Resources Information Center

    Jewett, Pamela

    2007-01-01

    Freire told his audience at a seminar at the University of Massachusetts, "You need to read knee-deep in texts, for deeper than surface meanings, and you need to know the words to be able to do it" (quoted in Cleary, 2003). In a children's literature class, fifteen teachers and I traveled along a path that moved us toward reading knee-deep as we…

  11. Reading Networks at Rest

    PubMed Central

    Kelly, Clare; Shehzad, Zarrar; Penesetti, Deepak; Castellanos, F. Xavier; Milham, Michael P.

    2010-01-01

    Resting-state functional connectivity (RSFC) approaches offer a novel tool to delineate distinct functional networks in the brain. In the present functional magnetic resonance imaging (fMRI) study, we elucidated patterns of RSFC associated with 6 regions of interest selected primarily from a meta-analysis on word reading (Bolger DJ, Perfetti CA, Schneider W. 2005. Cross-cultural effect on the brain revisited: universal structures plus writing system variation. Hum Brain Mapp. 25: 92–104). In 25 native adult readers of English, patterns of positive RSFC were consistent with patterns of task-based activity and functional connectivity associated with word reading. Moreover, conjunction analyses highlighted the posterior left inferior frontal gyrus and the posterior left middle temporal gyrus (post-LMTG) as potentially important loci of functional interaction among 5 of the 6 reading networks. The significance of the post-LMTG has typically been unappreciated in task-based studies on unimpaired readers but is frequently reported to be a locus of hypoactivity in dyslexic readers and exhibits intervention-induced changes of activity in dyslexic children. Finally, patterns of negative RSFC included not only regions of the so-called default mode network but also regions involved in effortful controlled processes, which may not be required once reading becomes automatized. In conclusion, the current study supports the utility of resting-state fMRI for investigating reading networks and has direct relevance for the understanding of reading disorders such as dyslexia. PMID:20139150

  12. Binocular advantages in reading.

    PubMed

    Jainta, Stephanie; Blythe, Hazel I; Liversedge, Simon P

    2014-03-01

    Reading, an essential skill for successful function in today's society, is a complex psychological process involving vision, memory, and language comprehension. Variability in fixation durations during reading reflects the ease of text comprehension, and increased word frequency results in reduced fixation times. Critically, readers not only process the fixated foveal word but also preprocess the parafoveal word to its right, thereby facilitating subsequent foveal processing. Typically, text is presented binocularly, and the oculomotor control system precisely coordinates the two frontally positioned eyes online. Binocular, compared to monocular, visual processing typically leads to superior performance, termed the "binocular advantage"; few studies have investigated the binocular advantage in reading. We used saccade-contingent display change methodology to demonstrate the benefit of binocular relative to monocular text presentation for both parafoveal and foveal lexical processing during reading. Our results demonstrate that denial of a unified visual signal derived from binocular inputs provides a cost to the efficiency of reading, particularly in relation to high-frequency words. Our findings fit neatly with current computational models of eye movement control during reading, wherein successful word identification is a primary determinant of saccade initiation. PMID:24530062

  13. ARYANA: Aligning Reads by Yet Another Approach

    PubMed Central

    2014-01-01

    Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

  14. The Many Fibers of Reading

    ERIC Educational Resources Information Center

    Leloup, Dennis

    2009-01-01

    How can library media specialists encourage kids to read outside the curriculum and maintain this reading beyond elementary school? What does it take to get children involved in recreational reading and turn their focus to books? At Sycamore Elementary School in Avon, Indiana, library media specialists have organized reading programs which have…

  15. Woodcock Diagnostic Reading Battery (WDRB).

    ERIC Educational Resources Information Center

    Simon, Janet

    1999-01-01

    This article describes the Woodcock Diagnostic Reading Battery, an instrument designed to assess the abilities and achievements of individuals ages 4 through 90 in the areas of basic reading skills, reading comprehension, phonological awareness, oral language comprehension, and reading aptitude. Its administration, standardization, reliability,…

  16. Focus on Reading. New Edition.

    ERIC Educational Resources Information Center

    Hood, Susan; Solomon, Nicky; Burns, Anne

    The handbook is designed as an introductory text on reading instruction for teachers of English as a Second Language. The first chapter explores the nature of reading through a series of activities that help identify the kind of knowledge one draws on and the strategies one uses in reading. Chapter 2 reviews key theories of reading that have…

  17. Reading and the Slow Learner.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    Advocates of high standards and expectations usually believe that gaps in reading achievement can be eliminated with good teaching, but slow readers need a specially designed reading curriculum. The teacher first needs to use an informal reading inventory to determine the student's reading level. Functioning generally on a higher level than…

  18. DEVELOPING HIGH SCHOOL READING PROGRAMS.

    ERIC Educational Resources Information Center

    DAWSON, MILDRED A.

    FORTY-FOUR REPRINTS CONCERNING HIGH SCHOOL READING PROGRAMS SELECTED FROM "THE READING TEACHER" AND THE "JOURNAL OF READING" AND THE PROCEEDINGS OF THE INTERNATIONAL READING ASSOCIATION ARE PRESENTED. THE CRITERIA FOR SELECTION WERE CONSISTENCY WITH ACCEPTED CURRICULAR AND INSTRUCTIONAL PRINCIPLES, CURRENT APPROPRIATENESS, DUPLICATION, AND…

  19. Reading and the Special Learner.

    ERIC Educational Resources Information Center

    Hedley, Carolyn N., Ed.; Hicks, John S., Ed.

    Compiled from papers presented at the annual Reading/Special Education Institute at Fordham University, this collection of essays addresses reading problems of special education students. The book is divided into three sections. The first section covers reading assessment and reading intervention; section 2 addresses the specific learner and the…

  20. Dyslexia: Problems of Reading Disabilities.

    ERIC Educational Resources Information Center

    Goldberg, Herman K.; Schiffman, Gilbert B.

    The purpose of this book is to provide an understanding of both the educational and medical aspects of reading and to show how they are interrelated in reading disabilities. The various aspects of reading disabilities are presented in the following chapters: Introduction to the Reading Problem; Early Predictive Studies; Psychological Evaluation;…

  1. What Is a Reading Error?

    ERIC Educational Resources Information Center

    Labov, William; Baker, Bettina

    2010-01-01

    Early efforts to apply knowledge of dialect differences to reading stressed the importance of the distinction between differences in pronunciation and mistakes in reading. This study develops a method of estimating the probability that a given oral reading that deviates from the text is a true reading error by observing the semantic impact of the…

  2. Explorations in Second Language Reading

    ERIC Educational Resources Information Center

    Cohen, Roger, Ed.

    2009-01-01

    The chapters in "Explorations in Second Language Reading" reveal the importance of reading in the classroom and how instructors can use reading as a bridge to improve learners' other linguistic and interpersonal skills. Most significantly, each author prompts us to rediscover how enjoyable ESOL reading can be and how it can increase learner…

  3. Paired Reading: Psycholinguistics in Practice.

    ERIC Educational Resources Information Center

    Barrett, James Martin

    1987-01-01

    Contends that children need to learn phonic skills, not necessarily through early direct teaching, but through reading experience. Suggests using Paired Reading, which is validated by psycholinguistic reading theory and provides opportunities to learn to read from context and use innate syntactic and semantic knowledge. (SKC)

  4. Effective interventions for reading disability.

    PubMed

    Williams, M C; Lecluyse, K; Rock-Faucheux, A

    1992-06-01

    A simple, readily accessible, and inexpensive intervention which produces immediate improvements in the reading comprehension abilities of reading-disabled children has been found. The intervention consists of colored overlays, or overlays which reduce the contrast of printed materials. This intervention produces reading comprehension gains in approximately 80 percent of the reading-disabled children tested. PMID:1378860

  5. Improving Reading to Improve Math

    ERIC Educational Resources Information Center

    Glenberg, Arthur; Willford, Jonathan; Gibson, Bryan; Goldberg, Andrew; Zhu, Xiaojin

    2012-01-01

    Reading provides information across the curriculum. Thus, to the extent that fundamental (i.e., generalizable) reading comprehension strategies can be taught, the benefits should be found in multiple domains. To test this claim, children in the third and fourth grades read by simulating text content using the two-part, embodied "Moved by Reading"…

  6. Student Accountability: Guided Reading Kidstations

    ERIC Educational Resources Information Center

    Guastello, E. Francine; Lenz, Claire

    2005-01-01

    Guided reading is a major component of a comprehensive or balanced reading program. Most teachers understand the value of guided reading in the classroom but have difficulty managing effective implementation. They often ask, "What will the other students be doing when I am working with a guided reading group, and how do I manage all the children…

  7. Reading in the Geography Curriculum.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    To become an efficient reader of subject matter in geography, students need to have adequate background information to read the ensuing content. Vocabulary considerations thoroughly enter into the reading act. A major problem for the teacher when students read geographical content is to develop meaning. To assist students in reading and…

  8. Reading in the Secondary School.

    ERIC Educational Resources Information Center

    Teaching English, 1976

    1976-01-01

    The topic of discussion of this issue of the journal "Teaching English" is reading instruction in the secondary school. Articles include "Reading in the Primary School" (Alastair Hendry), "Patterns of Progress" (Fergus McBride), "Teaching Reading--Whose Business?" (James Maxwell), "A Reading Policy for the Secondary School" (Iain McGillivray),…

  9. Early Reading and Concrete Operations.

    ERIC Educational Resources Information Center

    Polk, Cindy L. Howes; Goldstein, David

    1980-01-01

    Indicated that early readers are more likely to be advanced in cognitive development than are nonearly-reading peers. After one year of formal reading instruction, early readers maintained their advantage in reading achievement. Measures of concrete operations were found to predict reading achievement for early and nonearly readers. (Author/DB)

  10. When Do Children Read Books?

    ERIC Educational Resources Information Center

    van Ours, Jan C.

    2008-01-01

    This paper investigates the reading of fiction books by 15 year olds in 18 OECD countries. It appears that girls read fiction books more often than boys, whereas boys read comic books more often than girls. Parental education, family structure, and the number of books and televisions at home influence the intensity with which children read fiction…

  11. Reading Interventions With Behavioral and Social Skill Outcomes: A Synthesis of Research

    PubMed Central

    Roberts, Garrett J.; Solis, Michael; Ciullo, Stephen; McKenna, John W.; Vaughn, Sharon

    2015-01-01

    Research findings have suggested that reading deficits and problem behaviors are positively related. This synthesis investigated how reading interventions impact behavioral/social skill outcomes by reviewing studies that included (a) a reading intervention without behavioral/social skill components, (b) behavioral/social skill dependent variables, and (c) students in Grades K-12. Fifteen articles were evaluated by the type of reading intervention, associations between positive reading effects and behavioral/social skill outcomes, and The What Works Clearinghouse (WWC) determinants of study ratings. Findings suggested that reading interventions tended to have positive reading outcomes, while behavioral/social skill outcomes were small or negative. Research did not suggest an association between improved reading and behavioral performance, regardless of the WWC study determinants rating. Implications include reading instruction may not be sufficient to improve behavioral and social skill outcomes. Additional research is warranted to investigate the long-term impact of reading on behavioral and social skill outcomes. PMID:25548392

  12. Updated Perspectives on Educational Diagnosticians' Understanding of Reading Assessments

    ERIC Educational Resources Information Center

    Rueter, Jessica A.; McWhorter, Rochell R.; Lamb, John H.; Dykes, Frank O.

    2016-01-01

    Chappell, Stephens, Kinnison, and Pettigrew (2009) conducted a study investigating educational diagnosticians knowledge of early reading development. Our study replicated the work of Chappell et al. through a mixed methods design that investigated educational diagnosticians' perceptions and knowledge of early reading development. Additionally, our…

  13. Helping Your Child in Reading in the Social Studies.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    There are numerous ways in which parents can assist students in social studies. Parents can read aloud library books that deal with social studies; older peers can also read aloud, providing practice to the older student as well. Parents can relate current events to a nearby globe, locating places mentioned in newscasts. In addition, parents and…

  14. Readings in Public School Collective Bargaining. Volume 2.

    ERIC Educational Resources Information Center

    Educational Service Bureau, Inc., Washington, DC.

    This report contains a variety of readings related to different aspects of collective negotiations in public education. Subject areas covered include (1) State labor laws, (2) emerging roles of educators, (3) teacher militancy, (4) impasse resolution, and (5) public policy on teacher strikes. For additional readings on collective negotiations see…

  15. The Role of Independent Reading in a "Balanced" Reading Program: Re-Thinking California's Reading Initiative.

    ERIC Educational Resources Information Center

    Jonson, Kathleen F.

    1998-01-01

    Notes that California undertook a new commitment to improve the basic reading skills of its elementary students; lists several components of this commitment, the "California Reading Initiative." Describes the state's definition of a balanced and comprehensive approach to reading. Argues that independent reading is a crucial component and should…

  16. Reading to Learn and Reading to Integrate: New Tasks for Reading Comprehension Tests?

    ERIC Educational Resources Information Center

    Trites, Latricia; McGroarty, Mary

    2005-01-01

    To address the concern that most traditional reading comprehension tests only measure basic comprehension, this study designed measures to assess more complex reading tasks: Reading to Learn and Reading to Integrate. The new measures were taken by 251 participants: 105 undergraduate native speakers of English, 106 undergraduate nonnative speakers,…

  17. Reading Improvement in English- and Hebrew-Speaking Children with Reading Difficulties after Reading Acceleration Training

    ERIC Educational Resources Information Center

    Horowitz-Kraus, Tzipi; Cicchino, Nicole; Amiel, Merav; Holland, Scott K.; Breznitz, Zvia

    2014-01-01

    A reading acceleration program known to improve reading fluency in Hebrew-speaking adults was tested for its effect on children. Eighty-nine Hebrew- and English-speaking children with reading difficulties were divided into a waiting list group and two training groups (Hebrew and English) and underwent 4 weeks of reading acceleration training.…

  18. Improving Reading Rate Activities for EFL Students: Timed Reading and Repeated Oral Reading

    ERIC Educational Resources Information Center

    Chang, Anna C. -S.

    2012-01-01

    This study investigates the effect of timed reading (TR) and repeated oral reading (RR) on 35 adult students of English as a foreign language. Students in the TR (n =18) and RR (n =17) groups read 52 and 26 passages respectively over a 13-week period. Reading rates and comprehension levels were measured at three occasions: pre-intervention,…

  19. Developing Reading Fluency in EFL: How Assisted Repeated Reading and Extensive Reading Affect Fluency Development

    ERIC Educational Resources Information Center

    Taguchi, Etsuo; Takayasu-Maass, Miyoko; Gorsuch, Greta J.

    2004-01-01

    Extensive research on reading in a first language has shown the critical role fluency plays in successful reading. Fluency alone, however, does not guarantee successful reading. Cognitive and metacognitive reading strategies and schemata that readers utilize also play important roles in constructing meaning from text. Most research, however,…

  20. Students' Self-Perception of Reading Ability, Enjoyment of Reading and Reading Achievement

    ERIC Educational Resources Information Center

    Smith, Jeffrey K.; Smith, Lisa F.; Gilmore, Alison; Jameson, Madgerie

    2012-01-01

    Using data from New Zealand's National Education Monitoring Project, a light sampling, low stakes performance based national school assessment program, reading self-efficacy, reading enjoyment, and reading achievement were examined in samples of 8 and 12 year old children. Sample sizes were n = 480 for each group. While reading achievement…