Science.gov

Sample records for additional open reading

  1. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 19 Customs Duties 2 2014-04-01 2014-04-01 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...

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

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... sender or the addressee has given written authorization for the reading. (d) Other types of... 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...

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

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... sender or the addressee has given written authorization for the reading. (d) Other types of... 19 Customs Duties 2 2013-04-01 2013-04-01 false Opening of letter class mail; reading of... Opening of letter class mail; reading of correspondence prohibited. (a) Matter in addition...

  4. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... sender or the addressee has given written authorization for the reading. (d) Other types of... 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...

  5. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... sender or the addressee has given written authorization for the reading. (d) Other types of... 19 Customs Duties 2 2012-04-01 2012-04-01 false Opening of letter class mail; reading of... Opening of letter class mail; reading of correspondence prohibited. (a) Matter in addition...

  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. Addition lens alleviates reading-induced ocular stress.

    PubMed

    Choy, Camus K; Siu, Andrew W; Lam, Frankie Y; Tse, Jesse T; Lau, Sylvania Y

    2000-01-01

    BACKGROUND: Near tasks have been associated with binocular stress to induce myopia. The aim of this study was to investigate the effects of accommodation on reading-induced near heterophoria. METHODS: We measured the near heterophoria of 22 young adults before and after 30 minutes of reading. The reading task comprised a column of local English newsletter studied monocularly at 33 cm. One of three addition lenses (that is, 0.00 D, +1.50 D and +3.00 D) was randomly incorporated into the optical prescription. The difference in near heterophoria between the pre- and post-reading task was recorded. The experiment was completed on separate days for the other lens powers. RESULTS: Reading for 30 minutes with a plano lens addition (control) increased the near heterophoria by 3.81 +/- 0.95 prism dioptres (SEM) toward exo-deviation (p < 0.002). Addition of a +3.00 D lens significantly decreased the reading-induced exophoric shift to 1.36 +/- 0.55 prism dioptres (SEM). Similarly, a +1.50 D lens reduced the exophoric shift to 3.14 +/- 0.85 prism dioptres (SEM) but the difference was not statistically significant when compared with the control. CONCLUSIONS: The results showed that close work might cause eye strain via the extraocular muscles. Incorporation of plus lens into the optical correction caused a power-dependent reduction in the stress, that is, smaller exophoric shift. Whether binocular stress contributes to myopia and its response to addition lens therapy deserve further investigation.

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

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2008

    2008-01-01

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

  9. 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…

  10. What about Reading "Interests" in the Open Classroom?

    ERIC Educational Resources Information Center

    Kirsch, Dorothy Italie

    To determine what happens to a student's reading interests in an open classroom setting, three studies were conducted into the expressed reading interests of 1,078 first and second grade children in twelve public schools located in the urban and suburban areas of New York, Detroit, and Los Angeles. The children were interviewed individually and…

  11. Open-Ended Questions in Reading. ERIC/TM Digest.

    ERIC Educational Resources Information Center

    Badger, Elizabeth; Thomas, Brenda

    In this digest a rationale is given for using open-ended questions in the assessment of student achievement, the use of open-ended questions in reading is discussed, and some implications for the classroom are outlined. Research has helped shift the focus from learning as content knowledge per se to learning as the ability to use and interpret…

  12. 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

  13. 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

  14. 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…

  15. 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.

  16. Using Reading Skills To Open the World of Art.

    ERIC Educational Resources Information Center

    Sacks, Kathleen

    A total reading program must provide for the sequential development of reading skills and the deliberate development of interest in reading. The prime means of accomplishing the goals of skills and interest in reading is use of a basal reading program along with independent reading. The basal reader is designed to provide for the sequential…

  17. 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

  18. 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…

  19. 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

  20. The Effectiveness of "Open Court" on Improving the Reading Achievement of Economically-Disadvantaged Children.

    ERIC Educational Resources Information Center

    Moustafa, Margaret; Land, Robert

    This study compares average SAT 9 reading scores of second through fifth grade English-only children in schools using "Open Court" (a program for teaching young children to read) with the scores of comparable schools using non-scripted programs in one very large urban school district in California. Findings show that schools using "Open Court" are…

  1. 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…

  2. 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.

  3. 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.…

  4. 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

  5. Fluent Reading as the Improvement of Stimulus Control: Additive Effects of Performance-Based Interventions to Repeated Reading on Students' Reading and Error Rates

    ERIC Educational Resources Information Center

    Chafouleas, Sandra M.; Martens, Brian K.; Dobson, Robin L.; Weinstein, Kristen S.; Gardner, Kate B.

    2004-01-01

    The impact of adding performance-based interventions to a skill-based intervention on oral reading fluency was examined with 3 elementary students identified as having difficulty with reading. Two performance-based interventions were combined with the skill-based intervention Repeated Reading (RR) to create the three instructional packages…

  6. Insights into the translational regulation of biologically active open reading frames of Pelargonium line pattern virus.

    PubMed

    Castaño, Aurora; Ruiz, Leticia; Hernández, Carmen

    2009-04-10

    Pelargonium line pattern virus (PLPV), a proposed member of a prospective genus (Pelarspovirus) within family Tombusviridae, has a positive-sense, single-stranded genomic RNA. According to previous predictions, it contains six open reading frames (ORFs) potentially encoding proteins of 27 (p27), 13 (p13), 87 (p87), 7 (p7), 6 (p6), and 37 kDa (p37). Using a variety of techniques we demonstrate that all predicted ORFs are functional, with the exception of (p13) and (p6). We also characterize a previously unidentified ORF which encodes a 9.7 kDa protein (p9.7) that is essential for viral movement. Furthermore, we present evidence that the single subgenomic RNA (sgRNA) produced by the virus directs synthesis of p7, p9.7 and p37. Remarkably, the translation of these totally unrelated proteins is coordinated via leaky-scanning. This mechanism seems to be favoured by the poor translation context of the start codon of ORF(p7), the non-AUG weak initiation codon of ORF(p9.7) and the lack of additional AUG codons in any reading frame preceding ORF(p37). The results also suggest that precise regulation of protein production from the sgRNA is critical for virus viability. Altogether, the data supports the notion that PLPV belongs to a new genus of plant viruses.

  7. 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.…

  8. Reading.

    ERIC Educational Resources Information Center

    Gee, James Paul

    1992-01-01

    Explores what is meant by reading, noting that to read is to respond appropriately to a specific consensus centered on certain values and that the consensus is achieved among persons whose paths through life have come together with members of dominant discourses in society. (SLD)

  9. A translation-attenuating intraleader open reading frame is selected on coronavirus mRNAs during persistent infection.

    PubMed Central

    Hofmann, M A; Senanayake, S D; Brian, D A

    1993-01-01

    Short open reading frames within the 5' leader of some eukaryotic mRNAs are known to regulate the rate of translation initiation on the downstream open reading frame. By employing the polymerase chain reaction, we learned that the 5'-terminal 5 nt on the common leader sequence of bovine coronavirus subgenomic mRNAs were heterogeneous and hypervariable throughout early infection in cell culture and that as a persistent infection became established, termini giving rise to a common 33-nt intraleader open reading frame were selected. Since the common leader is derived from the genomic 5' end during transcription, a common focus of origin for the heterogeneity is expected. The intraleader open reading frame was shown by in vitro translation studies to attenuate translation of downstream open reading frames in a cloned bovine coronavirus mRNA molecule. Selection of an intraleader open reading frame resulting in a general attenuation of mRNA translation and a consequent attenuation of virus replication may, therefore, be a mechanism by which coronaviruses and possibly other RNA viruses with a similar transcriptional strategy maintain a persistent infection. Images Fig. 1 Fig. 3 PMID:8265618

  10. The use of Open Reading frame ESTs (ORESTES) for analysis of the honey bee transcriptome

    PubMed Central

    Nunes, Francis MF; Valente, Valeria; Sousa, Josane F; Cunha, Marco AV; Pinheiro, Daniel G; Maia, Rafaela M; Araujo, Daniela D; Costa, Maria CR; Martins, Waleska K; Carvalho, Alex F; Monesi, Nadia; Nascimento, Adriana M; Peixoto, Pablo MV; Silva, Maria FR; Ramos, Ricardo GP; Reis, Luis FL; Dias-Neto, Emmanuel; Souza, Sandro J; Simpson, Andrew JG; Zago, Marco A; Soares, Ademilson EE; Bitondi, Marcia MG; Espreafico, Enilza M; Espindola, Foued S; Paco-Larson, Maria L; Simoes, Zila LP; Hartfelder, Klaus; Silva, Wilson A

    2004-01-01

    Background The ongoing efforts to sequence the honey bee genome require additional initiatives to define its transcriptome. Towards this end, we employed the Open Reading frame ESTs (ORESTES) strategy to generate profiles for the life cycle of Apis mellifera workers. Results Of the 5,021 ORESTES, 35.2% matched with previously deposited Apis ESTs. The analysis of the remaining sequences defined a set of putative orthologs whose majority had their best-match hits with Anopheles and Drosophila genes. CAP3 assembly of the Apis ORESTES with the already existing 15,500 Apis ESTs generated 3,408 contigs. BLASTX comparison of these contigs with protein sets of organisms representing distinct phylogenetic clades revealed a total of 1,629 contigs that Apis mellifera shares with different taxa. Most (41%) represent genes that are in common to all taxa, another 21% are shared between metazoans (Bilateria), and 16% are shared only within the Insecta clade. A set of 23 putative genes presented a best match with human genes, many of which encode factors related to cell signaling/signal transduction. 1,779 contigs (52%) did not match any known sequence. Applying a correction factor deduced from a parallel analysis performed with Drosophila melanogaster ORESTES, we estimate that approximately half of these no-match ESTs contigs (22%) should represent Apis-specific genes. Conclusions The versatile and cost-efficient ORESTES approach produced minilibraries for honey bee life cycle stages. Such information on central gene regions contributes to genome annotation and also lends itself to cross-transcriptome comparisons to reveal evolutionary trends in insect genomes. PMID:15527499

  11. 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

  12. 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.

  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

    2016-05-27

    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.

  15. 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

  16. Upstream open reading frames regulate the expression of the nuclear Wnt13 isoforms

    SciTech Connect

    Tang Tao; Rector, Kyle; Barnett, Corey D.; Mao, Catherine D.

    2008-02-22

    Wnt proteins control cell survival and cell fate during development. Although Wnt expression is tightly regulated in a spatio-temporal manner, the mechanisms involved both at the transcriptional and translational levels are poorly defined. We have identified a downstream translation initiation codon, AUG(+74), in Wnt13B and Wnt13C mRNAs responsible for the expression of Wnt13 nuclear forms. In this report, we demonstrate that the expression of the nuclear Wnt13C form is translationally regulated in response to stress and apoptosis. Though the 5'-leaders of both Wnt13C and Wnt13B mRNAs have an inhibitory effect on translation, they did not display an internal ribosome entry site activity as demonstrated by dicistronic reporter assays. However, mutations or deletions of the upstream AUG(-99) and AUG(+1) initiation codons abrogate these translation inhibitory effects, demonstrating that Wnt13C expression is controlled by upstream open reading frames. Since long 5'-untranslated region with short upstream open reading frames characterize other Wnt transcripts, our present data on the translational control of Wnt13 expression open the way to further studies on the translation control of Wnt expression as a modulator of their subcellular localization and activity.

  17. 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.

  18. Informal Reading-Thinking Inventory: An Informal Reading Inventory (IRI) with Options for Assessing Additional Elements of Higher-Order Literacy.

    ERIC Educational Resources Information Center

    Manzo, Anthony V.; And Others

    Focusing on better assessing the thinking, or meaning-making, aspects of reading that are emphasized in current views of the reading process, this book presents the Informal Reading-Thinking Inventory (IR-TI) which offers options to enhance assessment beyond assessing students' listening level, oral reading of words, and basic comprehension. The…

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. A human cDNA expression library in yeast enriched for open reading frames.

    PubMed

    Holz, C; Lueking, A; Bovekamp, L; Gutjahr, C; Bolotina, N; Lehrach, H; Cahill, D J

    2001-10-01

    We developed a high-throughput technique for the generation of cDNA libraries in the yeast Saccharomyces cerevisiae which enables the selection of cloned cDNA inserts containing open reading frames (ORFs). For direct screening of random-primed cDNA libraries, we have constructed a yeast shuttle/expression vector, the so-called ORF vector pYEXTSH3, which allows the enriched growth of protein expression clones. The selection system is based on the HIS3 marker gene fused to the C terminus of the cDNA insert. The cDNAs cloned in-frame result in histidine prototrophic yeast cells growing on minimal medium, whereas clones bearing the vector without insert or out-of-frame inserts should not grow on this medium. A randomly primed cDNA library from human fetal brain tissue was cloned in this novel vector, and using robot technology the selected clones were arrayed in microtiter plates and were analyzed by sequencing and for protein expression. In the constructed cDNA expression library, about 60% of clones bear an insert in the correct reading frame. In comparison to unselected libraries it was possible to increase the clones with inserts in the correct reading frame more than fourfold, from 14% to 60%. With the expression system described here, we could avoid time-consuming and costly techniques for identification of clones expressing protein by using antibody screening on high-density filters and subsequently rearraying the selected clones in a new "daughter" library. The advantage of this ORF vector is that, in a one-step screening procedure, it allows the generation of expression libraries enriched for clones with correct reading frames as sources of recombinant proteins.

  4. Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110

    PubMed Central

    Hahn, Julia; Tsoy, Olga V.; Thalmann, Sebastian; Čuklina, Jelena; Gelfand, Mikhail S.

    2016-01-01

    Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. Stabilizing selection was demonstrated for sORFs with proteomic evidence and bll1319_ISGA which is conserved at the nucleotide level in 16 alphaproteobacterial species, 79 species from other taxa and 49 other Proteobacteria. Further we used Northern blot hybridization to validate ten small RNAs (BjsR1 to BjsR10) belonging to new RNA families. We found that BjsR1 and BjsR3 have homologs outside the genus Bradyrhizobium, and BjsR5, BjsR6, BjsR7, and BjsR10 have up to four imperfect copies in Bradyrhizobium genomes. BjsR8, BjsR9, and BjsR10 are present exclusively in nodules, while the other sRNAs are also expressed in liquid cultures. We also found that the level of BjsR4 decreases after exposure to tellurite and iron, and this down-regulation contributes to survival under high iron conditions. Analysis of additional small RNAs overlapping with 3’-UTRs revealed two new repetitive elements named Br-REP1 and Br-REP2. These REP elements may play roles in the genomic plasticity and gene regulation and could be useful for strain identification by PCR-fingerprinting. Furthermore, we studied two potential toxin genes in the symbiotic island and confirmed toxicity of the yhaV homolog bll1687 but not of the newly annotated higB homolog blr0229_ISGA in E. coli. Finally, we revealed transcription interference resulting in an antisense RNA complementary to blr1853, a gene induced in symbiosis. The presented results expand our knowledge on sORFs, non-coding RNAs and repetitive elements in B. japonicum and related bacteria. PMID

  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. 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

  7. 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.

  8. 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

  9. 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…

  10. 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

  11. Escherichia coli gpt gene provides dominant selection for vaccinia virus open reading frame expression vectors.

    PubMed

    Falkner, F G; Moss, B

    1988-06-01

    Mycophenolic acid, an inhibitor of purine metabolism, was shown to block the replication of vaccinia virus in normal cell lines. This observation led to the development of a dominant one-step plaque selection system, based on expression of the Escherichia coli gpt gene, for the isolation of recombinant vaccinia viruses. Synthesis of xanthine-guanine phosphoribosyltransferase enabled only the recombinant viruses to form large plaques in a selective medium containing mycophenolic acid, xanthine, and hypoxanthine. To utilize the selection system efficiently, we constructed a series of plasmids that contain the E. coli gpt gene and allow insertion of foreign genes into multiple unique restriction endonuclease sites in all three reading frames between the translation initiation codon of a strong late promoter and synthetic translation termination sequences. The selection-expression cassette is flanked by vaccinia virus DNA that directs homologous recombination into the virus genome. The new vectors allow high-level expression of complete or partial open reading frames and rapid construction of recombinant viruses by facilitating the cloning steps and by simplifying their isolation. The system was tested by cloning the E. coli beta-galactosidase gene; in 24 h, this enzyme accounted for approximately 3.5% of the total infected-cell protein.

  12. 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...

  13. 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…

  14. 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…

  15. Rereadings and Literacy: How Students' Second Readings Might Open Third Spaces

    ERIC Educational Resources Information Center

    Lynch, Tom Liam

    2008-01-01

    A secondary English teacher tells how he and his students confronted the question, How do we reclaim the joy of reading? After admitting that they didn't read very much for his assignments, the students were invited to help figure out where the joy of reading goes as students grow older. As the teacher and students discussed their experiences as…

  16. 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

  17. The Mycobacterium tuberculosis recA intein can be used in an ORFTRAP to select for open reading frames.

    PubMed Central

    Daugelat, S.; Jacobs, W. R.

    1999-01-01

    The DNA repair protein RecA of Mycobacterium tuberculosis contains an intein, a self-splicing protein element. We have employed this Mtu recA intein to create a selection system for successful intein splicing by inserting it into a kanamycin-resistance gene so that functional antibiotic resistance can only be restored upon protein splicing. We then proceeded to develop an ORFTRAP, i.e., a selection system for the cloning of open reading frames (ORFs). The ORFTRAP exploits the self-splicing properties of inteins (which depend on full-length in-frame translation of a precursor protein) by allowing protein splicing to occur when DNA fragments encoding ORFs are inserted into the Mtu recA intein, whereas DNA fragments containing non-ORFs are selected against. Regions of the Mtu recA intein that tolerate the insertion of additional amino acids were identified by Bgl II linker scanning mutagenesis, and a respective construct was chosen as the ORFTRAP. To test the maximum insert size that could be cloned into ORFTRAP, DNA fragments of increasing length from the Listeria monocytogenes hly gene as well as a genomic library of Haemophilus influenzae were inserted and it was found that the longest permissive inserts were 425 bp and 251 bp, respectively. The H. influenzae ORFTRAP library also demonstrated the strength (strong selection power) and weakness (insertion of very small fragments) of the system. Further modifications should make the ORFTRAP useful for protein expression, epitope mapping, and antigen screening. PMID:10091667

  18. 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

  19. 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

  20. 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

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

    PubMed

    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.

  2. 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

  3. Simultaneous cloning of open reading frames into several different expression vectors.

    PubMed

    Stanyon, Clement A; Limjindaporn, Thawornchai; Finley, Russell L

    2003-09-01

    Genomic sequencing has enabled the prediction of thousands of genes, most of which either cannot be assigned a function or can be only broadly categorized on the basis of sequence alone. High-throughput strategies for elucidating protein function are of high priority, and numerous approaches are being developed. Many of these approaches require the cloning of open reading frames (ORFs) into expression vectors that enable the encoded proteins to be tested for biological and biochemical activities. Typically, more than one type of vector must be employed, as different experiments require different conditions of protein production. Here we show that it is possible to simultaneously transfer a single ORF from a source vector to four target vectors using a commercially available in vitro recombination system. To test the approach, we constructed new vectors for expression of fusion proteins in yeast, including vectors for the LexA two-hybrid system. We show that individual ORFs can be efficiently transferred to four different vectors in a single in vitro reaction. The resulting expression plasmids can be separated using prototrophic markers specific to each vector. Using this system to produce multiple expression constructs simultaneously could greatly facilitate high-throughput subcloning and proteomic studies.

  4. 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.

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

    PubMed

    Cross, Frederick R

    2015-12-23

    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.

  6. 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

  7. 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

  8. 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

  9. Attenuation of the adaptive immune response in rhesus macaques infected with simian varicella virus lacking open reading frame 61.

    PubMed

    Meyer, Christine; Kerns, Amelia; Haberthur, Kristen; Dewane, Jesse; Walker, Joshua; Gray, Wayne; Messaoudi, Ilhem

    2013-02-01

    Varicella zoster virus (VZV) is a neurotropic alphaherpesvirus that causes chickenpox during primary infection and establishes latency in sensory ganglia. Infection of rhesus macaques (RM) with the homologous simian varicella virus (SVV) recapitulates hallmarks of VZV infection. We have shown that an antisense transcript of SVV open reading frame 61 (ORF61), a viral transactivator, was detected most frequently in latently infected RM sensory ganglia. In this study, we compared disease progression, viral replication, immune response, and the establishment of latency following intrabronchial infection with a recombinant SVV lacking ORF61 (SVVΔORF61) to those following infection with wild-type (WT) SVV. Varicella severity and viral latency within sensory ganglia were comparable in RMs infected with SVVΔORF61 and WT SVV. In contrast, viral loads, B and T cell responses, and plasma inflammatory cytokine levels were decreased in RMs infected with SVVΔORF61. To investigate the mechanisms underlying the reduced adaptive immune response, we compared acute SVV gene expression, frequency and proliferation of dendritic cell (DC) subsets, and the expression of innate antiviral genes in bronchoalveolar lavage (BAL) samples. The abundance of SVV transcripts in all kinetic classes was significantly decreased in RMs infected with SVVΔORF61. In addition, we detected a higher frequency and proliferation of plasmacytoid dendritic cells in BAL fluid at 3 days postinfection in RMs infected with SVVΔORF61, which was accompanied by a slight increase in type I interferon gene expression. Taken together, our data suggest that ORF61 plays an important role in orchestrating viral gene expression in vivo and interferes with the host antiviral interferon response.

  10. Role of an upstream open reading frame in mediating arginine-specific translational control in Neurospora crassa.

    PubMed Central

    Luo, Z; Sachs, M S

    1996-01-01

    The Neurospora crassa arg-2 transcript contains an upstream open reading frame (uORF) specifying a 24-residue leader peptide and is subject to a novel form of negative translational regulation in response to arginine. The role of the arg-2 uORF in arginine-specific negative regulation was investigated by using translational fusions of wild-type and mutant arg-2 sequences to the Escherichia coli lacZ reporter gene specifying beta-galactosidase. The wild-type uORF conferred Arg-specific regulation on the reporter gene in N. crassa, but mutated or truncated uORFs did not, as determined by measurements of beta-galactosidase activity produced in N. crassa strains expressing arg-2-lacZ fusion genes. All effects on reporter gene expression were posttranscriptional, as determined by measurement of RNA levels. Both sequence-dependent and sequence-independent effects of uORFs were observed. Genes containing the wild-type uORF or a 21-codon mutated uORF showed reduced translation in comparison with that of a gene lacking a uORF. Both uORF-containing transcripts showed reduced association with polysomes relative to transcripts lacking a uORF, but only the transcript with the wild-type uORF showed a reduced average number of ribosomes associated with it in response to arginine addition. Direct translational fusions between uORF sequences and lacZ sequences indicated that the uORF is translated. Overlapping the uORF with the lacZ initiation codon indicated that ribosome reinitiation at a downstream start codon is not integral to uORF-mediated, Arg-specific translational regulation. These studies provide direct biochemical evidence for arg-2 uORF function in translational control. PMID:8636015

  11. 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

  12. The Development of Comprehension and Reading-Related Skills in Children Learning English as an Additional Language and Their Monolingual, English-Speaking Peers

    ERIC Educational Resources Information Center

    Burgoyne, K.; Whiteley, H. E.; Hutchinson, J. M.

    2011-01-01

    Background: A significant number of pupils in UK schools learn English as an additional language (EAL). Relative differences between the educational attainment of this group and monolingual, English-speaking pupils call for an exploration of the literacy needs of EAL learners. Aims: This study explores the developmental progression of reading and…

  13. 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…

  14. 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

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

    PubMed Central

    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

  16. 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

  17. 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,…

  18. 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…

  19. 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

  20. 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,…

  1. Translation of the mRNA for the sporulation gene spoIIID of Bacillus subtilis is dependent upon translation of a small upstream open reading frame.

    PubMed Central

    Decatur, A; McMurry, M T; Kunkel, B N; Losick, R

    1997-01-01

    We report the existence of a small open reading frame (usd) that is located between the promoter and coding sequence for the sporulation gene spoIIID in Bacillus subtilis. The mRNA from the usd-spoIIID operon contains an inverted repeat sequence that is predicted to form a stem-loop structure that would sequester the ribosome binding site for spoIIID. A mutation eliminating the ribosome binding site for the upstream open reading frame caused an oligosporogenous phenotype and interfered with the translation, but not the transcription, of the downstream gene spoIIID. We propose that efficient synthesis of SpoIIID requires that the putative stem-loop structure be disrupted by translation through the upstream open reading frame. PMID:9023218

  2. 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

  3. 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

  4. In vivo characterisation of a translational enhancer upstream from the coat protein open reading frame of potato virus S.

    PubMed

    Turner, R; Bate, N; Twell, D; Foster, G D

    1994-01-01

    The 101 nucleotide region upstream from the ATG of the potato virus S (PVS) coat protein gene was isolated and the effect of this region on the translation of a downstream open reading frame analysed in vivo. Translation was monitored using the reporter genes B-glucuronidase (GUS) and luciferase (LUC). Translational enhancement was assayed transiently using DNA microprojectile bombardment into both leaf and pollen tissue and also by polyethylene glycol mediated transfection of tobacco protoplasts. In both cases the presence of this region resulted in a 2-3 fold increase in translation when compared to reporter expression with synthetic leader and authentic plant leader constructs. Tobacco plants stability transformed with this PVS 101 nucleotide region and downstream GUS gene gave 4 times the level of translation over synthetic leader GUS control plants. PMID:7979985

  5. Drought stress differentially regulates the expression of small open reading frames (sORFs) in Arabidopsis roots and shoots.

    PubMed

    Rasheed, Sultana; Bashir, Khurram; Nakaminami, Kentaro; Hanada, Kousuke; Matsui, Akihiro; Seki, Motoaki

    2016-08-01

    Characterizing the molecular mechanisms governing the response of plant roots and shoots to drought stress could aid the development of strategies aiming to ameliorate drought stress. Small open reading frames (sORFs), putatively encoding small peptides, may play a significant role in the response to different abiotic stresses. Microarray analyses revealed that after 5, 7 and 9 d of a drought treatment, 2, 77, and 104 sORFs were up-regulated in roots, respectively; while the number of upregulated sORFs in shoots was 12, 45, and 158, respectively. RT-qPCR analysis confirmed the up-regulated expression of ATRIKEN29196 and ATRIKEN32280 specifically in roots. The identified upregulated sORFs, particularly those in roots, may contribute to drought stress tolerance.

  6. 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…

  7. 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…

  8. Reading First: States Report Improvements in Reading Instruction, but Additional Procedures Would Clarify Education's Role in Ensuring Proper Implementation by States. Report to Congressional Requesters. GAO-07-161

    ERIC Educational Resources Information Center

    Ashby, Cornelia M.

    2007-01-01

    The Reading First program was designed to help students in kindergarten through third grade develop stronger reading skills. This report examines the implementation of the Reading First program, including: (1) changes that have occurred to reading instruction; (2) criteria states have used to award sub-grants to districts, and the difficulties, if…

  9. 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,…

  10. 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...

  11. 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

  12. 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

  13. 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.

  14. 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…

  15. Rational genomics I: antisense open reading frames and codon bias in short-chain oxido reductase enzymes and the evolution of the genetic code.

    PubMed

    Duax, William L; Huether, Robert; Pletnev, Vladimir Z; Langs, David; Addlagatta, Anthony; Connare, Sonjay; Habegger, Lukas; Gill, Jay

    2005-12-01

    The short-chain oxidoreductase (SCOR) family of enzymes includes over 6000 members, extending from bacteria and archaea to humans. Nucleic acid sequence analysis reveals that significant numbers of these genes are remarkably free of stopcodons in reading frames other than the coding frame, including those on the antisense strand. The genes from this subset also use almost entirely the GC-rich half of the 64 codons. Analysis of a million hypothetical genes having random nucleotide composition shows that the percentage of SCOR genes having multiple open reading frames exceeds random by a factor of as much as 1 x 10(6). Nevertheless, screening the content of the SWISS-PROT TrEMBL database reveals that 15% of all genes contain multiple open reading frames. The SCOR genes having multiple open reading frames and a GC-rich coding bias exhibit a similar GC bias in the nucleotide triple composition of their DNA. This bias is not correlated with the GC content of the species in which the SCOR genes are found. One possible explanation for the conservation of multiple open reading frames and extreme bias in nucleic acid composition in the family of Rossman folds is that the primordial member of this family was encoded early using only very stable GC-rich DNA and that evolution proceeded with extremely limited introduction of any codons having two or more adenine or thymine nucleotides. These and other data suggest that the SCOR family of enzymes may even have diverged from a common ancestor before most of the AT-rich half of the genetic code was fully defined.

  16. Evolutionary dynamics of introns and their open reading frames in the U7 region of the mitochondrial rnl gene in species of Ceratocystis.

    PubMed

    Sethuraman, Jyothi; Rudski, Shelly M; Wosnitza, Kari; Hafez, Mohamed; Guppy, Brent; Hausner, Georg

    2013-01-01

    The mtDNA rnl-U7 region has been examined for the presence of introns in selected species of the genus Ceratocystis. Comparative sequence analysis identified group I and group II introns encoding single and double motif LAGLIDADG open reading frames (ORFs) at the following positions L1671, L1787, and L1923. In addition downstream of the rnl-U7 region group I introns were detected at positions L1971 and L2231, and a group II intron at L2059. A GIY-YIG type ORF was located within one mL1923 LAGLIDADG type ORF and a degenerated GIY-YIG ORF fused to a nad2 gene fragment was found in association with the mL1971 group I intron. The diversity of composite elements that appear to be sporadically distributed among closely related species of Ceratocystis illustrates the potential for homing endonucleases and their associated introns to invade new sites. Phylogenetic analysis showed that single motif LADGLIDADG ORFs related to the mL1923 ORFs have invaded the L1787 group II intron and the L1671 group I intron. Phylogenetic analysis of intron encoded single and double motif LAGLIDADG ORFs also showed that these ORFs transferred four times from group I into group II B1 type introns.

  17. 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

  18. Inactivation of a Synechocystis sp strain PCC 6803 gene with homology to conserved chloroplast open reading frame 184 increases the photosystem II-to-photosystem I ratio.

    PubMed Central

    Wilde, A; Härtel, H; Hübschmann, T; Hoffmann, P; Shestakov, S V; Börner, T

    1995-01-01

    A gene of the unicellular cyanobacterium Synechocystis sp strain PCC 6803 that is homologous to the conserved chloroplast open reading frame orf184 has been cloned and sequenced. The nucleotide sequence of the gene predicts a protein of 184 amino acids with a calculated molecular mass of 21.5 kD and two membrane-spanning regions. Amino acid sequence analysis showed 46 to 37% homology of the cyanobacterial orf184 with tobacco orf184, rice orf185, liverwort orf184, and Euglena gracilis orf206 sequences. Two orf184-specific mutants of Synechocystis sp PCC 6803 were constructed by insertion mutagenesis. Cells of mutants showed growth characteristics similar to those of the wild type. Their pigment composition was distinctly different from the wild type, as indicated by an increase in the phycocyanin-to-chlorophyll ratio. In addition, mutants also had a two- to threefold increase in photosynthetic electron transfer rates as well as in photosystem II-to-photosystem I ratio-a phenomenon hitherto not reported for mutants with altered photosynthetic characteristics. The observed alterations in the orf184-specific mutants provide strong evidence for a functional role of the orf184 gene product in photosynthetic processes. PMID:7780311

  19. Roles of Epstein-Barr virus BGLF3.5 gene and two upstream open reading frames in lytic viral replication in HEK293 cells.

    PubMed

    Watanabe, Takahiro; Fuse, Kenshiro; Takano, Takahiro; Narita, Yohei; Goshima, Fumi; Kimura, Hiroshi; Murata, Takayuki

    2015-09-01

    The Epstein-Barr virus (EBV) predominantly establishes a latent infection in B lymphocytes, but a small percentage of infected cells switch from the latent state to the lytic cycle, leading to potent viral DNA replication and progeny viruses production. We here focused on a lytic gene BGLF3.5, and first established BGLF3.5 mutants by marker cassette insertion. Unexpectedly, this insertion mutant failed to produce BGLF4 protein and thus progeny production was severely inhibited. Then we carefully made two point mutant viruses (stop codon insertion or frame-shift mutation) and found that BGLF3.5 is not essential for EBV lytic replication processes, such as viral gene expression, DNA replication, or progeny production in the HEK293 cells although its homolog in murine gammaherpesvirus 68 (MHV-68) was reported to be essential. In addition, we examined the roles of two short, upstream open reading frames within the 5'UTR of BGLF3.5 gene in translation of BGLF4.

  20. Varicella-zoster virus (VZV) mediates a delayed host shutoff independent of open reading frame (ORF) 17 expression.

    PubMed

    Waterboer, Tim; Rahaus, Markus; Wolff, Manfred H

    2002-01-01

    Varicella-zoster virus (VZV) open reading frame 17 (ORF 17) is the gene corresponding to Herpes simplex-virus (HSV) UL41. The UL41 gene encodes the virion host shutoff factor (vhs), a RNase that has been the object of detailed studies. In contrast to HSV, knowledge about VZV mediated shutoff effects and the role of ORF 17 is poor. We investigated the ORF 17 expression in infected cells and analyzed shutoff effects. ORF 17 expression could not be proven in infected human fibroblast cell lines and melanoma (MeWo) cells. Only after induction by Phorbol 12-myristate 13-acetate an ORF 17 expression became detectable in MeWo cells. Nevertheless, using stable expressed GAPDH mRNA as a marker for mRNA degradation, a VZV mediated shutoff, independent of ORF 17 expression, became measurable. Transfection experiments demonstrated that transient ORF 17 expression did not decrease the cellular GAPDH mRNA level. We examined whether the VZV shutoff factor is a tegument protein causing an early shutoff or whether it needs to be expressed (delayed shutoff). The GAPDH mRNA level in Actinomycin D pretreated and infected MeWo cells did not decrease even faster than the theoretical decay rate based on a half-life of 24 h. These findings lead to the conclusion that the VZV shutoff factor is not a mature protein localized in the virion and that VZV causes a delayed virion host shutoff effect.

  1. Cytoplasmic male sterility-associated chimeric open reading frames identified by mitochondrial genome sequencing of four Cajanus genotypes.

    PubMed

    Tuteja, Reetu; Saxena, Rachit K; Davila, Jaime; Shah, Trushar; Chen, Wenbin; Xiao, Yong-Li; Fan, Guangyi; Saxena, K B; Alverson, Andrew J; Spillane, Charles; Town, Christopher; Varshney, Rajeev K

    2013-10-01

    The hybrid pigeonpea (Cajanus cajan) breeding technology based on cytoplasmic male sterility (CMS) is currently unique among legumes and displays major potential for yield increase. CMS is defined as a condition in which a plant is unable to produce functional pollen grains. The novel chimeric open reading frames (ORFs) produced as a results of mitochondrial genome rearrangements are considered to be the main cause of CMS. To identify these CMS-related ORFs in pigeonpea, we sequenced the mitochondrial genomes of three C. cajan lines (the male-sterile line ICPA 2039, the maintainer line ICPB 2039, and the hybrid line ICPH 2433) and of the wild relative (Cajanus cajanifolius ICPW 29). A single, circular-mapping molecule of length 545.7 kb was assembled and annotated for the ICPA 2039 line. Sequence annotation predicted 51 genes, including 34 protein-coding and 17 RNA genes. Comparison of the mitochondrial genomes from different Cajanus genotypes identified 31 ORFs, which differ between lines within which CMS is present or absent. Among these chimeric ORFs, 13 were identified by comparison of the related male-sterile and maintainer lines. These ORFs display features that are known to trigger CMS in other plant species and to represent the most promising candidates for CMS-related mitochondrial rearrangements in pigeonpea. PMID:23792890

  2. A novel multicopy suppressor of a groEL mutation includes two nested open reading frames transcribed from different promoters.

    PubMed Central

    Greener, T; Govezensky, D; Zamir, A

    1993-01-01

    When present on a multicopy plasmid, a newly discovered gene (sugE) mapping to 94 min on the Escherichia coli chromosome, suppresses a groEL mutation and mimics the effects of groE overexpression. A groEL mutant of E.coli, transformed with the Klebsiella pneumoniae nif gene cluster, failed to accumulate nitrogenase components [Govezensky et al. (1991) J. Bacteriol., 173, 6339-6346]. Transformation with sugE reversed the mutant phenotype. In wild type K.pneumoniae, transformation with sugE accelerated the rate of nitrogenase biogenesis after nif derepression. In E.coli, transformation with sugE enabled bacteriophage T4 growth in a groEL mutant. A continuous 178 codon open reading frame (ORF) in sugE encloses another, in-frame, 105 codon ORF similar to a predicted ORF in Proteus vulgaris. In vivo products of both sugE ORFs were observed in transformants expressing the gene from a T7 promoter. In non-transformed cells, a typical sigma 70-dependent promoter found upstream of the larger ORF directs sugE transcription during growth at 30 degrees C. At elevated temperatures or in stationary phase cells, another promoter, found within the coding sequence upstream of the smaller ORF, is activated independently of sigma 32. The results suggest that sugE encodes a chaperonin-related system whose composition might vary with temperature and growth phase. Images PMID:8096175

  3. Cytoplasmic male sterility-associated chimeric open reading frames identified by mitochondrial genome sequencing of four Cajanus genotypes.

    PubMed

    Tuteja, Reetu; Saxena, Rachit K; Davila, Jaime; Shah, Trushar; Chen, Wenbin; Xiao, Yong-Li; Fan, Guangyi; Saxena, K B; Alverson, Andrew J; Spillane, Charles; Town, Christopher; Varshney, Rajeev K

    2013-10-01

    The hybrid pigeonpea (Cajanus cajan) breeding technology based on cytoplasmic male sterility (CMS) is currently unique among legumes and displays major potential for yield increase. CMS is defined as a condition in which a plant is unable to produce functional pollen grains. The novel chimeric open reading frames (ORFs) produced as a results of mitochondrial genome rearrangements are considered to be the main cause of CMS. To identify these CMS-related ORFs in pigeonpea, we sequenced the mitochondrial genomes of three C. cajan lines (the male-sterile line ICPA 2039, the maintainer line ICPB 2039, and the hybrid line ICPH 2433) and of the wild relative (Cajanus cajanifolius ICPW 29). A single, circular-mapping molecule of length 545.7 kb was assembled and annotated for the ICPA 2039 line. Sequence annotation predicted 51 genes, including 34 protein-coding and 17 RNA genes. Comparison of the mitochondrial genomes from different Cajanus genotypes identified 31 ORFs, which differ between lines within which CMS is present or absent. Among these chimeric ORFs, 13 were identified by comparison of the related male-sterile and maintainer lines. These ORFs display features that are known to trigger CMS in other plant species and to represent the most promising candidates for CMS-related mitochondrial rearrangements in pigeonpea.

  4. Upstream Open Reading Frames Located in the Leader of Protein Kinase Mζ mRNA Regulate Its Translation

    PubMed Central

    Bal, Natalia V.; Susorov, Denis; Chesnokova, Ekaterina; Kasianov, Artem; Mikhailova, Tatiana; Alkalaeva, Elena; Balaban, Pavel M.; Kolosov, Peter

    2016-01-01

    For protein synthesis that occurs locally in dendrites, the translational control mechanisms are much more important for neuronal functioning than the transcription levels. Here, we show that uORFs (upstream open reading frames) in the 5′ untranslated region (5′UTR) play a critical role in regulation of the translation of protein kinase Mζ (PKMζ). Elimination of these uORFs activates translation of the reporter protein in vitro and in primary cultures of rat hippocampal neurons. Using cell-free translation systems, we demonstrate that translational initiation complexes are formed only on uORFs. Further, we address the mechanism of translational repression of PKMζ translation, by uORFs. We observed an increase in translation of the reporter protein under the control of PKMζ leader in neuronal culture during non-specific activation by picrotoxin. We also show that such a mechanism is similar to the mechanism seen in cell stress, as application of sodium arsenite to neuron cultures induced translation of mRNA carrying PKMζ 5′UTR similarly to picrotoxin activation. Therefore, we suppose that phosphorylation of eIF2a, like in cell stress, is a main regulator of PKMζ translation. Altogether, our findings considerably extend our understanding of the role of uORF in regulation of PKMζ translation in activated neurons, important at early stages of LTP. PMID:27790092

  5. Cytoplasmic Male Sterility-Associated Chimeric Open Reading Frames Identified by Mitochondrial Genome Sequencing of Four Cajanus Genotypes

    PubMed Central

    Tuteja, Reetu; Saxena, Rachit K.; Davila, Jaime; Shah, Trushar; Chen, Wenbin; Xiao, Yong-Li; Fan, Guangyi; Saxena, K. B.; Alverson, Andrew J.; Spillane, Charles; Town, Christopher; Varshney, Rajeev K.

    2013-01-01

    The hybrid pigeonpea (Cajanus cajan) breeding technology based on cytoplasmic male sterility (CMS) is currently unique among legumes and displays major potential for yield increase. CMS is defined as a condition in which a plant is unable to produce functional pollen grains. The novel chimeric open reading frames (ORFs) produced as a results of mitochondrial genome rearrangements are considered to be the main cause of CMS. To identify these CMS-related ORFs in pigeonpea, we sequenced the mitochondrial genomes of three C. cajan lines (the male-sterile line ICPA 2039, the maintainer line ICPB 2039, and the hybrid line ICPH 2433) and of the wild relative (Cajanus cajanifolius ICPW 29). A single, circular-mapping molecule of length 545.7 kb was assembled and annotated for the ICPA 2039 line. Sequence annotation predicted 51 genes, including 34 protein-coding and 17 RNA genes. Comparison of the mitochondrial genomes from different Cajanus genotypes identified 31 ORFs, which differ between lines within which CMS is present or absent. Among these chimeric ORFs, 13 were identified by comparison of the related male-sterile and maintainer lines. These ORFs display features that are known to trigger CMS in other plant species and to represent the most promising candidates for CMS-related mitochondrial rearrangements in pigeonpea. PMID:23792890

  6. 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

  7. The hepatitis E virus open reading frame 3 product interacts with microtubules and interferes with their dynamics.

    PubMed

    Kannan, Harilakshmi; Fan, Sumin; Patel, Deendayal; Bossis, Ioannis; Zhang, Yan-Jin

    2009-07-01

    Hepatitis E virus (HEV) is the causative agent of hepatitis E, a major form of viral hepatitis in developing countries. The open reading frame 3 (ORF3) of HEV encodes a phosphoprotein with a molecular mass of approximately 13 kDa (hereinafter called vp13). vp13 is essential for establishing HEV infections in animals, yet its exact functions are still obscure. Our current study found evidence showing interaction between vp13 and microtubules. Live-cell confocal fluorescence microscopy revealed both filamentous and punctate distribution patterns of vp13 in cells transfected with recombinant ORF3 reporter plasmids. The filamentous pattern of vp13 was altered by a microtubule-destabilizing drug. The vp13 expression led to elevation of acetylated alpha-tubulin, indicating increased microtubule stability. Its association with microtubules was further supported by its presence in microtubule-containing pellets in microtubule isolation assays. Exposure of these pellets to a high-salt buffer caused release of the vp13 to the supernatant, suggesting an electrostatic interaction. Inclusion of ATP and GTP in the lysis buffer during microtubule isolation also disrupted the interaction, indicating its sensitivity to the nucleotides. Further assays showed that motor proteins are needed for the vp13 association with the microtubules because disruption of dynein function abolished the vp13 filamentous pattern. Analysis of ORF3 deletion constructs found that both of the N-terminal hydrophobic domains of vp13 are needed for the interaction. Thus, our findings suggest that the vp13 interaction with microtubules might be needed for establishment of an HEV infection. PMID:19369329

  8. 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

  9. 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

  10. Reselection of a Genomic Upstream Open Reading Frame in Mouse Hepatitis Coronavirus 5′-Untranslated-Region Mutants

    PubMed Central

    Wu, Hung-Yi; Guan, Bo-Jhih; Su, Yu-Pin; Fan, Yi-Hsin

    2014-01-01

    An AUG-initiated upstream open reading frame (uORF) encoding a potential polypeptide of 3 to 13 amino acids (aa) is found within the 5′ untranslated region (UTR) of >75% of coronavirus genomes based on 38 reference strains. Potential CUG-initiated uORFs are also found in many strains. The AUG-initiated uORF is presumably translated following genomic 5′-end cap-dependent ribosomal scanning, but its function is unknown. Here, in a reverse-genetics study with mouse hepatitis coronavirus, the following were observed. (i) When the uORF AUG-initiating codon was replaced with a UAG stop codon along with a U112A mutation to maintain a uORF-harboring stem-loop 4 structure, an unimpaired virus with wild-type (WT) growth kinetics was recovered. However, reversion was found at all mutated sites within five virus passages. (ii) When the uORF was fused with genomic (main) ORF1 by converting three in-frame stop codons to nonstop codons, a uORF-ORF1 fusion protein was made, and virus replicated at WT levels. However, a frameshifting G insertion at virus passage 7 established a slightly 5′-extended original uORF. (iii) When uAUG-eliminating deletions of 20, 30, or 51 nucleotides (nt) were made within stem-loop 4, viable but debilitated virus was recovered. However, a C80U mutation in the first mutant and an A77G mutation in the second appeared by passage 10, which generated alternate uORFs that correlated with restored WT growth kinetics. In vitro, the uORF-disrupting nondeletion mutants showed enhanced translation of the downstream ORF1 compared with the WT. These results together suggest that the uORF represses ORF1 translation yet plays a beneficial but nonessential role in coronavirus replication in cell culture. PMID:24173235

  11. 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…

  12. 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.

    PubMed Central

    Panning, B; Smiley, J R

    1993-01-01

    We found that transcription of endogenous human Alu elements by RNA polymerase III was strongly stimulated following infection of HeLa cells with adenovirus type 5, leading to the accumulation of high levels of Alu transcripts initiated from Alu polymerase III promoters. In contrast to previously reported cases of adenovirus-induced activation of polymerase III transcription, induction required the E1b 58-kDa protein and the products of E4 open reading frames 3 and 6 in addition to the 289-residue E1a protein. In addition, E1a function was not required at high multiplicities of infection, suggesting that E1a plays an indirect role in Alu activation. These results suggest previously unsuspected regulatory properties of the adenovirus E1b and E4 gene products and provide a novel approach to the study of the biology of the most abundant class of dispersed repetitive DNA in the human genome. Images PMID:7684492

  13. 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

  14. Sequence-specific binding of a hormonally regulated mRNA binding protein to cytidine-rich sequences in the lutropin receptor open reading frame.

    PubMed

    Kash, J C; Menon, K M

    1999-12-21

    In previous studies, a lutropin receptor mRNA binding protein implicated in the hormonal regulation of lutropin receptor mRNA stability was identified. This protein, termed LRBP-1, was shown by RNA gel electrophoretic mobility shift assay to specifically interact with lutropin receptor RNA sequences. The present studies have examined the specificity of lutropin receptor mRNA recognition by LRBP-1 and mapped the contact site by RNA footprinting and by site-directed mutagenesis. LRBP-1 was partially purified by cation-exchange chromatography, and the mRNA binding properties of the partially purified LRBP-1 were examined by RNA gel electrophoretic mobility shift assay and hydroxyl-radical RNA footprinting. These data showed that the LRBP-1 binding site is located between nucleotides 203 and 220 of the receptor open reading frame, and consists of the bipartite polypyrimidine sequence 5'-UCUC-X(7)-UCUCCCU-3'. Competition RNA gel electrophoretic mobility shift assays demonstrated that homoribopolymers of poly(rC) were effective RNA binding competitors, while poly(rA), poly(rG), and poly(rU) showed no effect. Mutagenesis of the cytidine residues contained within the LRBP-1 binding site demonstrated that all the cytidines in the bipartite sequence contribute to LRBP-1 binding specificity. Additionally, RNA gel electrophoretic mobility supershift analysis showed that LRBP-1 was not recognized by antibodies against two well-characterized poly(rC) RNA binding proteins, alphaCP-1 and alphaCP-2, implicated in the regulation of RNA stability of alpha-globin and tyrosine hydroxylase mRNAs. In summary, we show that partially purified LRBP-1 binds to a polypyrimidine sequence within nucleotides 203 and 220 of lutropin receptor mRNA with a high degree of specificity which is indicative of its role in posttranscriptional control of lutropin receptor expression.

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

    DOE PAGES

    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

  16. 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.

  17. 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…

  18. 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…

  19. Pulsed-Addition Ring-Opening Metathesis Polymerization: Catalyst-Economical Syntheses of Homopolymers and Block Copolymers

    PubMed Central

    Matson, John B.; Virgil, Scott C.

    2009-01-01

    Poly(tert-butyl ester norbornene imide) homopolymers and poly(tert-butyl ester norbornene imide-b-N-methyl oxanorbornene 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 (H2IMes)(Cl)2(pyr)2RuCHPh 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 determining 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 multi-angle laser light scattering. PMID:19215131

  20. 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.

  1. The complete nucleotide sequence of PEBV RNA2 reveals the presence of a novel open reading frame and provides insights into the structure of tobraviral subgenomic promoters.

    PubMed Central

    Goulden, M G; Lomonossoff, G P; Davies, J W; Wood, K R

    1990-01-01

    The 3374 nucleotide sequence of RNA2 from the British PEBV strain SP5 has been determined. The RNA includes three open reading frames flanked by 5' and 3' noncoding regions of 509 and 480 nucleotides. The open reading frames specify coat protein, a 29.6K product homologous to the 29.1K product of TRV(TCM) RNA2 and a 23K product not homologous to any previously described protein. The homology demonstrated between the coat proteins of PRV, TRV and PEBV indicates a common evolutionary origin for these proteins. Upstream of each ORF are located sequences homologous to those with which subgenomic RNAs of other tobraviruses start. Subgenomic RNAs for the expression of the three ORFs may start at these points. On all five tobraviral RNA2 molecules sequenced to date, these sequences were found upstream of the coat protein ORF in association with a strongly-conserved potential secondary structural element. Similar potential structures were identified upstream of other tobraviral ORFs. These structures may contribute to the activity of the tobraviral subgenomic promoter. Images PMID:2388830

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

    PubMed

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

    2014-04-01

    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.

  3. Comparisons of an open-ended vs. forced-choice 'mind reading' task: implications for measuring perspective-taking and emotion recognition.

    PubMed

    Cassels, Tracy G; Birch, Susan A J

    2014-01-01

    Perspective-taking and emotion recognition are essential for successful social development and have been the focus of developmental research for many years. Although the two abilities often overlap, they are distinct and our understanding of these abilities critically rests upon the efficacy of existing measures. Lessons from the literature differentiating recall versus recognition memory tasks led us to hypothesize that an open-ended emotion recognition measure would be less reliant on compensatory strategies and hence a more specific measure of emotion recognition abilities than a forced-choice task. To this end, we compared an open-ended version of the Reading the Mind in the Eyes Task with the original forced-choice version in two studies: 118 typically-developing 4- to 8-year-olds (Study 1) and 139 5- to 12-year-olds; 85 typically-developing and 54 with learning disorders (Study 2). We found that the open-ended version of the task was a better predictor of empathy and more reliably discriminated typically-developing children from those with learning disorders. As a whole, the results suggest that the open-ended version is a more sensitive measure of emotion recognition specifically.

  4. 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

  5. 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)…

  6. [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…

  7. 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…

  8. 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…

  9. 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

  10. Isolation and expression of human cytokine synthesis inhibitory factor cDNA clones: Homology to Epstein-Barr virus open reading frame BCRFI

    SciTech Connect

    Vieira, P.; De Waal-Malefyt, R.; Dang, M.N.; Johnson, K.E.; Kastelein, R.; Fiorentino, D.F.; DeVries, J.E.; Roncarolo, M.G.; Mosmann, T.R.; Moore, K.W. )

    1991-02-15

    The authors demonstrated the existence of human cytokine synthesis inhibitory factor (DSIF) (interleukin 10 (IL-10)). cDNA clones encoding human IL-10 (hIL-10) were isolated from a tetanus toxin-specific human T-cell clone. Like mouse IL-10, hIL-10 exhibits strong DNA and amino acid sequence homology to an open reading frame in the Epstein-Barr virus, BDRFL. hIL-10 and the BCRFI product inhibit cytokine synthesis by activated human peripheral blood mononuclear cells and by a mouse Th1 clone. Both hIL-10 and mouse IL-10 sustain the viability of a mouse mast cell line in culture, but BCRFI lacks comparable activity in this way, suggesting that BCRFI may have conserved only a subset of hIL-10 activities.

  11. [The influence of mutations at ATG triplets of the open reading frame SUP35 on viability of the yeast Saccharomyces cerevisiae].

    PubMed

    Riabinkova, N A; Borkhsenius, A S; Inge-Vechtomov, S G

    2009-02-01

    The open reading frame SUP35 encoding the translation termination eRF3 factor vital to life contains three ATG codons (ATG1, ATG124, and ATG254). Previously, other authors detected two SUP35 transcripts: a major one that corresponds to the full-length open reading frame and a minor transcript that corresponds to the 3' terminal site of SUP35 starting at the third ATG codon (ATG254). In this work, mutations at triplets ATG1, ATG124, and ATG254 were obtained as well as double mutations, which combine the point mutation in one of three ATG triplets and a deletion at the site for binding with the transcription factor Abf1 within the SUP35 (sup35-deltaAbf1) promoter. The influence of these mutations on the yeast viability was analyzed. Mutations at triplets ATG124 and ATG254 did not affect yeast viability in their own right or in the background of deletion sup35-deltaAbf1. Mutation sup35-AGG1 (ATG1-->AGG) causes the lethal effect in cells grown on media containing glucose as the sole source of carbon. The replacement of glucose by galactose, or histidine starvation, partially restore the viability of sup35-AGG1 mutants, but not that of double mutants sup35-deltaAbf1,AGG1. The restoration of sup35-AGG1 mutant viability under these conditions can be explained by either the appearance (or enhancement) of the production of short peptides synthesized on the mRNA triplets SUP35 AUG124 and AUG254, or by the enhanced production of the full-length SUP35 transcript coupled with translation initiation from the noncanonical AGG1 codon. These data confirm that the expression of gene SUP35 at the transcription and(or) translation level is regulated by environmental conditions.

  12. Transition-metal free reactions of boronic acids: cascade addition - ring-opening of furans towards functionalized γ-ketoaldehydes.

    PubMed

    Roscales, S; Csákÿ, A G

    2016-02-18

    We describe the first ring-opening of furfuryl alcohols with boronic acids to afford functionalized γ-ketoaldehydes. The transformation builds a new C-C bond at the original C-4 of the starting furan, and tolerates ring-substitution at C-3 and C-4 positions. The reaction takes place under metal-free conditions by promotion with tartaric acid.

  13. Reading Laboratories: The Conversion of the Speed Reading Lab into an ESL Reading Lab.

    ERIC Educational Resources Information Center

    Novak, Sigrid Scholtz

    It is proposed that the reading-machine laboratory provides a means for the classroom ESL instructor to continue using his present method in the classroom (intensive, theoretical-grammatical instruction) while providing additional extensive reading and learning practice with the machines in the reading laboratory. Two speed reading systems…

  14. 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…

  15. 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…

  16. The open reading frame VI product of Cauliflower mosaic virus is a nucleocytoplasmic protein: its N terminus mediates its nuclear export and formation of electron-dense viroplasms.

    PubMed

    Haas, Muriel; Geldreich, Angèle; Bureau, Marina; Dupuis, Laurence; Leh, Véronique; Vetter, Guillaume; Kobayashi, Kappei; Hohn, Thomas; Ryabova, Lyubov; Yot, Pierre; Keller, Mario

    2005-03-01

    The Cauliflower mosaic virus (CaMV) open reading frame VI product (P6) is essential for the viral infection cycle. It controls translation reinitiation of the viral polycistronic RNAs and forms cytoplasmic inclusion bodies (viroplasms) where virus replication and assembly occur. In this study, the mechanism involved in viroplasm formation was investigated by in vitro and in vivo experiments. Far protein gel blot assays using a collection of P6 deletion mutants demonstrated that the N-terminal alpha-helix of P6 mediates interaction between P6 molecules. Transient expression in tobacco (Nicotiana tabacum) BY-2 cells of full-length P6 and P6 mutants fused to enhanced green fluorescent protein revealed that viroplasms are formed at the periphery of the nucleus and that the N-terminal domain of P6 is an important determinant in this process. Finally, this study led to the unexpected finding that P6 is a nucleocytoplasmic shuttle protein and that its nuclear export is mediated by a Leu-rich sequence that is part of the alpha-helix domain implicated in viroplasm formation. The discovery that P6 can localize to the nucleus opens new prospects for understanding yet unknown roles of this viral protein in the course of the CaMV infection cycle.

  17. The open reading frame VI product of Cauliflower mosaic virus is a nucleocytoplasmic protein: its N terminus mediates its nuclear export and formation of electron-dense viroplasms.

    PubMed

    Haas, Muriel; Geldreich, Angèle; Bureau, Marina; Dupuis, Laurence; Leh, Véronique; Vetter, Guillaume; Kobayashi, Kappei; Hohn, Thomas; Ryabova, Lyubov; Yot, Pierre; Keller, Mario

    2005-03-01

    The Cauliflower mosaic virus (CaMV) open reading frame VI product (P6) is essential for the viral infection cycle. It controls translation reinitiation of the viral polycistronic RNAs and forms cytoplasmic inclusion bodies (viroplasms) where virus replication and assembly occur. In this study, the mechanism involved in viroplasm formation was investigated by in vitro and in vivo experiments. Far protein gel blot assays using a collection of P6 deletion mutants demonstrated that the N-terminal alpha-helix of P6 mediates interaction between P6 molecules. Transient expression in tobacco (Nicotiana tabacum) BY-2 cells of full-length P6 and P6 mutants fused to enhanced green fluorescent protein revealed that viroplasms are formed at the periphery of the nucleus and that the N-terminal domain of P6 is an important determinant in this process. Finally, this study led to the unexpected finding that P6 is a nucleocytoplasmic shuttle protein and that its nuclear export is mediated by a Leu-rich sequence that is part of the alpha-helix domain implicated in viroplasm formation. The discovery that P6 can localize to the nucleus opens new prospects for understanding yet unknown roles of this viral protein in the course of the CaMV infection cycle. PMID:15746075

  18. 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...

  19. Open complex scrunching before nucleotide addition accounts for the unusual transcription start site of E. coli ribosomal RNA promoters.

    PubMed

    Winkelman, Jared T; Chandrangsu, Pete; Ross, Wilma; Gourse, Richard L

    2016-03-29

    Most Escherichia coli promoters initiate transcription with a purine 7 or 8 nt downstream from the -10 hexamer, but some promoters, including the ribosomal RNA promoter rrnB P1, start 9 nt from the -10 element. We identified promoter and RNA polymerase determinants of this noncanonical rrnB P1 start site using biochemical and genetic approaches including mutational analysis of the promoter, Fe(2+) cleavage assays to monitor template strand positions near the active-site, and Bpa cross-linking to map the path of open complex DNA at amino acid and nucleotide resolution. We find that mutations in several promoter regions affect transcription start site (TSS) selection. In particular, we show that the absence of strong interactions between the discriminator region and σ region 1.2 and between the extended -10 element and σ region 3.0, identified previously as a determinant of proper regulation of rRNA promoters, is also required for the unusual TSS. We find that the DNA in the single-stranded transcription bubble of the rrnB P1 promoter complex expands and is "scrunched" into the active site channel of RNA polymerase, similar to the situation in initial transcribing complexes. However, in the rrnB P1 open complex, scrunching occurs before RNA synthesis begins. We find that the scrunched open complex exhibits reduced abortive product synthesis, suggesting that scrunching and unusual TSS selection contribute to the extraordinary transcriptional activity of rRNA promoters by increasing promoter escape, helping to offset the reduction in promoter activity that would result from the weak interactions with σ.

  20. Open complex scrunching before nucleotide addition accounts for the unusual transcription start site of E. coli ribosomal RNA promoters.

    PubMed

    Winkelman, Jared T; Chandrangsu, Pete; Ross, Wilma; Gourse, Richard L

    2016-03-29

    Most Escherichia coli promoters initiate transcription with a purine 7 or 8 nt downstream from the -10 hexamer, but some promoters, including the ribosomal RNA promoter rrnB P1, start 9 nt from the -10 element. We identified promoter and RNA polymerase determinants of this noncanonical rrnB P1 start site using biochemical and genetic approaches including mutational analysis of the promoter, Fe(2+) cleavage assays to monitor template strand positions near the active-site, and Bpa cross-linking to map the path of open complex DNA at amino acid and nucleotide resolution. We find that mutations in several promoter regions affect transcription start site (TSS) selection. In particular, we show that the absence of strong interactions between the discriminator region and σ region 1.2 and between the extended -10 element and σ region 3.0, identified previously as a determinant of proper regulation of rRNA promoters, is also required for the unusual TSS. We find that the DNA in the single-stranded transcription bubble of the rrnB P1 promoter complex expands and is "scrunched" into the active site channel of RNA polymerase, similar to the situation in initial transcribing complexes. However, in the rrnB P1 open complex, scrunching occurs before RNA synthesis begins. We find that the scrunched open complex exhibits reduced abortive product synthesis, suggesting that scrunching and unusual TSS selection contribute to the extraordinary transcriptional activity of rRNA promoters by increasing promoter escape, helping to offset the reduction in promoter activity that would result from the weak interactions with σ. PMID:26976590

  1. A complex organization of the gene encoding cytochrome oxidase subunit 1 in the mitochondrial genome of the dinoflagellate, Crypthecodinium cohnii: homologous recombination generates two different cox1 open reading frames.

    PubMed

    Norman, J E; Gray, M W

    2001-01-01

    In the course of investigating mitochondrial genome organization in Crypthecodinium cohnii, a non-photosynthetic dinoflagellate, we identified four EcoRI fragments that hybridize to a probe specific for cox1, the gene that encodes subunit 1 of cytochrome oxidase. Cloning and sequence characterization of the four fragments (5.7, 5.1, 4.1, 3.5 kilobase pairs) revealed that cox1 exists in four distinct but related contexts in C. cohnii mtDNA, with a central repeat unit flanked by one of two possible upstream (flanking domain 1 or 2) and downstream (flanking domain 3 or 4) regions. The majority of the cox1 gene is located within the central repeat; however, the C-terminal portion of the open reading frame extends into flanking domains 3 and 4, thereby creating two distinct cox1 coding sequences. The 3'-terminal region of one of the cox1 reading frames can assume an elaborate secondary structure, which potentially could act to stabilize the mature mRNA against nucleolytic degradation. In addition, a high density of small inverted repeats (15-22 base pairs) has been identified at the 5'-end of cox1, further suggesting that hairpin structures could be important for gene regulation. The organization of cox1 in C. cohnii mtDNA appears to reflect homologous recombination events within the central repeat between different cox1 sequence contexts. Such recombining repeats are a characteristic feature of plant (angiosperm) mtDNA, but they have not previously been described in the mitochondrial genomes of protists.

  2. 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.

  3. 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

  4. 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

  5. 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…

  6. 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

  7. Effect of organic matter addition to the pen surface and pen cleaning frequency on nitrogen mass balance in open feedlots.

    PubMed

    Adams, J R; Farran, T B; Erickson, G E; Klopfenstein, T J; Macken, C N; Wilson, C B

    2004-07-01

    Three finishing trials were conducted to determine the effects of dietary manipulation and management on N losses from open feedlots. In each experiment, 96 steers were assigned randomly to 12 nutrient balance pens. In Trial 1, calves were fed for 180 d during the winter/spring months; in Trial 2, yearlings were fed for 132 d in the summer. In Trials 1 and 2, N losses from pens were compared directly by adding OM to the pen surface or indirectly by feeding digestible ingredients designed to increase OM excretion. The dietary treatment (BRAN) included 30% corn bran (DM basis) replacing dry-rolled corn. Pens where OM was directly added received sawdust applications (SAWDUST) at a rate to match OM excretion from the BRAN diet. These two treatments were compared with a conventional, 75% dry-rolled corn diet (CON). Because CON and SAWDUST diets were identical, performance for both treatments was similar during Trials 1 and 2. The BRAN diet decreased (P < 0.10) gain efficiency during Trials 1 and 2 by 9.5% relative to CON. Fecal N excretion was greater (P < 0.01) for calves and yearlings when BRAN was fed compared with CON. Adding OM to the pen surface increased (P < 0.01) the amount of N in manure removed from pens and reduced (P < 0.10) N losses in Trial 1. Nitrogen losses were not significantly different among treatments in Trial 2. In Trial 3, calves were fed for 166 d during the winter/spring months. A 2 x 2 factorial design was used to evaluate pen cleaning frequency and diets similar to CON and BRAN. Pens were either cleaned monthly or once at the end of the feeding period. Daily DMI was greater (P = 0.01) and ADG was lower (P < 0.01) when cattle were fed BRAN compared with CON. Responses from all three trials indicate a negative effect of BRAN on gain efficiency. Dietary treatment and cleaning frequency interacted for N balance in the feedlot. Nitrogen losses decreased and manure N increased (P < 0.10) for cattle fed BRAN compared with CON when pens were cleaned

  8. [Molecular epidemiology of the Methicillin-resistant Staphylococcus aureus(MRSA) by the internal transcribed spacer PCR (ITS-PCR) method and the phage open reading frame typing (POT) method].

    PubMed

    Senda, Yasuko; Takemori, Yukiko; Iwata, Yasunori; Fujita, Shinichi; Sakai, Yoshio; Wada, Takashi

    2014-05-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is the most common causative bacteria of hospital acquired infection, and should be rapidly identified for infection control. For this purpose, in our hospital, the PCR electrophoresis patterns of spacer regions (ITS: internal transcribed spacers) (ITS-PCR) are combined with a toxigenicity assay to establish a strain identification method for outbreak surveillance. In the present study, the usefulness of this method was evaluated in comparison with the POT (phage-open reading frame typing) method. One hundred MRSA strains isolated from inpatients in our hospital between April 2011 and March 2012 were classified into 25 patterns using the ITS-PCR method combined with a toxigenicity assay. The strains could be classified into 46 patterns using the POT method. ITS-PCR type 22 strain producing enterotoxin C and toxic shock syndrome toxin-1 could be further classified into 7 patterns using the POT method. In the outbreak of the type 22 strain, cross-infection could be excluded by additional analysis using the POT method, providing more precise information on strain identification. We identified that some strains of the same POT type consisted of different ITS-PCR types or toxigenicities. Therefore, these results suggest that the combination of ITS-PCR method plus toxigenicity assay with POT method may be a useful technique of MRSA typing.

  9. 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

  10. Covering one eye affects how some children read.

    PubMed

    Cornelissen, P; Bradley, L; Fowler, S; Stein, J

    1992-04-01

    The Dunlop Test was used to identify unstable binocular control in a group of 32 mixed-ability children. They were compared with 32 reading age-matched controls. The children were then asked to read two lists of single real words of equal linguistic difficulty: one with both eyes open and the other with the left eye occluded. Only children who failed the Dunlop Test made fewer non-word errors when they read with one eye. This result provides additional support for the theory that unstable binocular control can directly affect how children read. In addition, these findings suggest that this effect must be due, at least in part, to some interaction between the images from the two eyes.

  11. Co-ordinate expression of glycine betaine synthesis genes linked by the FMDV 2A region in a single open reading frame in Pichia pastoris.

    PubMed

    Wang, Sanhong; Yao, Quanhong; Tao, Jianmin; Qiao, Yushan; Zhang, Zhen

    2007-12-01

    The genes encoding the two enzymes choline monooxygenase (CMO) and betaine aldehyde dehydrogenase (BADH) of glycine betaine synthesis in Suaeda salsa were cloned and fused with the 2A region of foot-and-mouth disease virus in a single open reading frame. The fused genes were placed under the control of the alcohol oxidase (AOX1) promoter in pPIC3B and transformed into P. pastoris GS115. The expression of the fused genes in P. pastoris and the ability of recombinant yeasts to tolerate environmental stresses were studied. The results showed that induced with 0.5% methanol for 96 h, the maximal activities of CMO and BADH in the tested recombinant yeasts were 45- and 44-fold higher than those in the control yeast transformed empty vector only, respectively; the content of glycine betaine in the recombinant yeasts was 28- to 35-fold higher than that in the control. The fused genes linked by 2A region of foot-and-mouth disease virus were expressed in P. pastoris successfully and the polyprotein was 'cleaved' to each functional protein. The yeasts transformed the fused genes, which were more resistant to salt, methanol, and high temperature stresses than the control as result of glycine betaine synthesis genes introduced.

  12. Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner

    PubMed Central

    Ebina, Isao; Takemoto-Tsutsumi, Mariko; Watanabe, Shun; Koyama, Hiroaki; Endo, Yayoi; Kimata, Kaori; Igarashi, Takuya; Murakami, Karin; Kudo, Rin; Ohsumi, Arisa; Noh, Abdul Latif; Takahashi, Hiro; Naito, Satoshi; Onouchi, Hitoshi

    2015-01-01

    Upstream open reading frames (uORFs) are often found in the 5′-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be independent of their encoded peptide sequences, certain uORFs control translation of the main ORF in a peptide sequence-dependent manner. For genome-wide identification of such peptide sequence-dependent regulatory uORFs, exhaustive searches for uORFs with conserved amino acid sequences have been conducted using bioinformatic analyses. However, whether the conserved uORFs identified by these bioinformatic approaches encode regulatory peptides has not been experimentally determined. Here we analyzed 16 recently identified Arabidopsis thaliana conserved uORFs for the effects of their amino acid sequences on the expression of the main ORF using a transient expression assay. We identified five novel uORFs that repress main ORF expression in a peptide sequence-dependent manner. Mutational analysis revealed that, in four of them, the C-terminal region of the uORF-encoded peptide is critical for the repression of main ORF expression. Intriguingly, we also identified one exceptional sequence-dependent regulatory uORF, in which the stop codon position is not conserved and the C-terminal region is not important for the repression of main ORF expression. PMID:25618853

  13. 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

  14. 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

  15. Gramicidin S biosynthesis operon containing the structural genes grsA and grsB has an open reading frame encoding a protein homologous to fatty acid thioesterases.

    PubMed Central

    Krätzschmar, J; Krause, M; Marahiel, M A

    1989-01-01

    The DNA sequence of about 5.9 kilobase pairs (kbp) of the gramicidin S biosynthesis operon (grs) was determined. Three open reading frames were identified; the corresponding genes, called grsT, grsA, and grsB, were found to be organized in one transcriptional unit, not two as previously reported (M. Krause and M. A. Marahiel, J. Bacteriol. 170:4669-4674, 1988). The entire nucleotide sequence of grsA, coding for the 126.663-kilodalton gramicidin S synthetase 1, grsT, encoding a 29.191-kilodalton protein of unknown function, and 732 bp of the 5' end of grsB, encoding the gramicidin S synthetase 2, were determined. A single initiation site of transcription 81 bp upstream of the grsT initiation condon GTG was identified by high-resolution S1 mapping studies. The sequence of the grsA gene product showed a high degree of homology to the tyrocidine synthetase 1 (TycA protein), and that of grsT exhibited a significant degree of homology to vertebrate fatty acid thioesterases. Images PMID:2477357

  16. Single nucleotide polymorphisms in the open reading frame of the stearoyl-CoA desaturase gene and resulting genetic variants in Canadian Holstein and Jersey cows.

    PubMed

    Kgwatalala, Patrick M; Ibeagha-Awemu, Eveline M; Hayes, John F; Zhao, Xin

    2007-10-01

    Stearoyl-CoA desaturase (SCD) catalyzes the synthesis of conjugated linoleic acid (CLA) and mono-unsaturated fatty acids (MUFA) from their saturated counterparts in the mammary gland and adipose tissue of ruminant animals. We hypothesize that single nucleotide polymorphisms (SNPs) in the SCD gene account for some of the differences in SCD activity, and consequently for some of the variations in CLA and MUFA content of milk fat between Holsteins and Jersey cows and within these two breeds. We analyzed the open reading frame of the SCD gene of 44 Holsteins and 48 Jerseys for SNPs by sequencing. Three SNPs: 702A --> G, 762T --> C and 878C --> T were identified in both breeds and a further SNP, 435G --> A, was unique to Holsteins. The SNPs characterized four different genetic variants in Holsteins: A (G(435)A(702)T(762)C(878)), A1 (A(435)A(702)T(762)C(878)), B (G(435)G(702)C(762)T(878)) and B1 (A(435)G(702)C(762)T(878)), with only variants A and B in Jerseys. SNP 878C --> T resulted in a non-synonymous codon change while the rest resulted in synonymous codon changes giving rise to two protein variants, A having alanine and B having valine. Allele A was the most prevalent in the two breeds. These differences may, therefore, contribute to existing variations in CLA and fat content between and within Canadian Holstein and Jersey cows.

  17. Intra- and inter-genotypic size variation in the central variable region of the 9RL open reading frame of diverse African swine fever viruses.

    PubMed

    Phologane, Solomon B; Bastos, Armanda D S; Penrith, Mary-Louise

    2005-12-01

    African swine fever (ASF) viruses are characterised by numerous p72 genotypes, but by low levels of intra-genotypic variation, particularly in domestic pig associated genotypes. As it is precisely these viral lineages that are involved in outbreaks of the disease it is imperative that alternative, more informative gene regions be identified which are suitable for intra-genotypic resolution of relationships. To this end, the central variable region (CVR) of the 9RL open reading frame of diverse ASF viruses was amplified and product sizes scored and compared within and between genotypes. Results indicate that although product sizes are not genotype restricted, there is a high degree of intra-genotypic size variation particularly within the homogeneous p72 genotypes. Within one such genotype, the ESACWA virus genotype, 12 size-discrete CVR products were identified, four corresponding to viruses of west African origin and eight to viruses from countries where the disease is exotic, namely Europe, South America and the Caribbean. The high degree of size heterogeneity in the CVR of this genotype is significant and attests to the usefulness of the CVR gene marker in elucidating the epidemiology of African swine fever.

  18. 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

  19. 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

  20. Abrogation of upstream open reading frame-mediated translational control of a plant S-adenosylmethionine decarboxylase results in polyamine disruption and growth perturbations.

    PubMed

    Hanfrey, Colin; Franceschetti, Marina; Mayer, Melinda J; Illingworth, Crista; Michael, Anthony J

    2002-11-15

    S-Adenosylmethionine decarboxylase (AdoMetDC) is a key enzyme in polyamine biosynthesis. We show that the plant AdoMetDC activity is subject to post-transcriptional control by polyamines. A highly conserved small upstream open reading frame (uORF) in the AdoMetDC mRNA 5' leader is responsible for translational repression of a downstream beta-glucuronidase reporter cistron in transgenic tobacco plants. Elimination of the small uORF from an AdoMetDC cDNA led to increased relative translational efficiency of the AdoMetDC proenzyme in transgenic plants. The resulting increased activity of AdoMetDC caused disruption to polyamine levels with depletion of putrescine, reduction of spermine levels, and a more than 400-fold increase in the level of decarboxylated S-adenosylmethionine. These changes were associated with severe growth and developmental defects. The high level of decarboxylated S-adenosylmethionine was not associated with any change in 5'-methylcytosine content in genomic DNA and S-adenosylmethionine levels were more or less normal, indicating a highly efficient system for maintenance of S-adenosylmethionine levels in plants. This work demonstrates that uORF-mediated translational control of AdoMetDC is essential for polyamine homeostasis and for normal growth and development.

  1. 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.

  2. 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

  3. 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…

  4. 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…

  5. 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…

  6. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 19 Customs Duties 1 2013-04-01 2013-04-01 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...

  7. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 19 Customs Duties 1 2012-04-01 2012-04-01 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...

  8. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 19 Customs Duties 1 2014-04-01 2014-04-01 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...

  9. 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...

  10. The varicella-zoster virus-mediated delayed host shutoff: open reading frame 17 has no major function, whereas immediate-early 63 protein represses heterologous gene expression.

    PubMed

    Desloges, Nathalie; Rahaus, Markus; Wolff, Manfred H

    2005-12-01

    We reported that varicella-zoster virus (VZV) causes a delayed host shutoff during its replicative cycle. VZV open reading frame 17 (ORF17) is the homologue of the herpes simplex virus (HSV) UL41 gene encoding the virion host shutoff (vhs) protein which is responsible for the shutoff effect observed in HSV-infected cells. In the present study, we demonstrated that ORF17 is expressed as a late protein during the VZV replicative cycle in different infected permissive cell lines which showed a delayed shutoff of cellular RNA. A cell line with stable expression of VZV ORF17 was infected with VZV. In these cells, VZV replication and delayed host shutoff remained unchanged when compared to normal infected cells. ORF17 was not capable of repressing the expression of the beta-gal reporter gene under the control of the human cytomegalovirus immediate-early gene promoter or to inhibit the expression of a CAT reporter gene under the control of the human GAPDH promoter, indicating that ORF17 has no major function in the VZV-mediated delayed host shutoff. To determine whether other viral factors are involved in the host shutoff, a series of cotransfection assays was performed. We found that the immediate-early 63 protein (IE63) was able to downregulate the expression of reporter genes under the control of the two heterologous promoters, indicating that this viral factor can be involved in the VZV-mediated delayed host shutoff. Other factors can be also implicated to modulate the repressing action of IE63 to achieve a precise balance between the viral and cellular gene expression.

  11. Deletion of open reading frame UL26 from the human cytomegalovirus genome results in reduced viral growth, which involves impaired stability of viral particles.

    PubMed

    Lorz, Kerstin; Hofmann, Heike; Berndt, Anja; Tavalai, Nina; Mueller, Regina; Schlötzer-Schrehardt, Ursula; Stamminger, Thomas

    2006-06-01

    We previously showed that open reading frame (ORF) UL26 of human cytomegalovirus, a member of the US22 multigene family of betaherpesviruses, encodes a novel tegument protein, which is imported into cells in the course of viral infection. Moreover, we demonstrated that pUL26 contains a strong transcriptional activation domain and is capable of stimulating the major immediate-early (IE) enhancer-promoter. Since this suggested an important function of pUL26 during the initiation of the viral replicative cycle, we sought to ascertain the relevance of pUL26 by construction of a viral deletion mutant lacking the UL26 ORF using the bacterial artificial chromosome mutagenesis procedure. The resulting deletion virus was verified by PCR, enzyme restriction, and Southern blot analyses. After infection of human foreskin fibroblasts, the UL26 deletion mutant showed a small-plaque phenotype and replicated to significantly lower titers than wild-type or revertant virus. In particular, we noticed a striking decrease of infectious titers 7 days postinfection in a multistep growth experiment, whereas the release of viral DNA from infected cells was not impaired. A further investigation of this aspect revealed a significantly diminished stability of viral particles derived from the UL26 deletion mutant. Consistent with this, we observed that the tegument composition of the deletion mutant deviates from that of the wild-type virus. We therefore hypothesize that pUL26 plays a role not only in the onset of IE gene transcription but also in the assembly of the viral tegument layer in a stable and correct manner. PMID:16699023

  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

    Suzuki, Masahiro; Hosoba, Eriko; Matsui, Mari; Arakawa, Yoshichika

    2014-08-01

    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.

  13. Roles of genomic island 3 (GI-3) BAB1_0267 and BAB1_0270 open reading frames (ORFs) in the virulence of Brucella abortus 2308.

    PubMed

    Ortiz-Román, Luisa; Riquelme-Neira, Roberto; RobertoVidal; Oñate, Angel

    2014-08-01

    One of the properties of bacteria is their capacity to acquire large fragments of genomic DNA from other bacteria or to loose important parts of their own genome. Such fragments include genomic islands (GIs); nine GIs are present in Brucella, including genomic island 3 (GI-3), present in B. abortus, B. melitensis and B. ovis. The GI-3 have 29 open reading frames (ORFs) most of them with unknown function. Within the GI-3, the ORFs BAB1_0267 encodes a hypothetical protein sharing a SH3 domain and BAB1_270 a zinc-dependent metallopeptidase. We have obtained deletion mutants for BAB1_0267 and BAB1_0270 ORFs present within GI-3, which have been named the Δ0267 and Δ0270, respectively; in both cases the mutation did not affect the growth of bacteria. Both mutants were evaluated with respect to their growth rates, their ability to invade and replicate in the non-professional and professional phagocytes, HeLa and J774.A1 cells, respectively. Their persistence in the spleens of mice was also evaluated. The mutants efficiently invaded HeLa and J774.A1 cells but both mutants showed a decreased intracellular survival in macrophages and HeLa cells 72 and 96 h post-infection, respectively, and were non-detected in J774.A1 cells 120 h post infection. With respect to in vivo persistence Δ0267 was detected through the fourth week while Δ0270 decreased at 7 days disappearing the second week. Our results indicated that deletion of BAB1_0267 and BAB1_270 are necessary to establish an optimal infectious process in B. abortus 2308, having more effect the deletion of ORF BAB1_0270. Therefore these ORFs, principally BAB1_0270 are important virulent of B. abortus.

  14. 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

  15. Implementation and assessment of a yeast orphan gene research project: involving undergraduates in authentic research experiences and progressing our understanding of uncharacterized open reading frames.

    PubMed

    Bowling, Bethany V; Schultheis, Patrick J; Strome, Erin D

    2016-02-01

    Saccharomyces cerevisiae was the first eukaryotic organism to be sequenced; however, little progress has been made in recent years in furthering our understanding of all open reading frames (ORFs). From October 2012 to May 2015 the number of verified ORFs had only risen from 75.31% to 78%, while the number of uncharacterized ORFs had decreased from 12.8% to 11% (representing > 700 genes still left in this category; http://www.yeastgenome.org/genomesnapshot). Course-based research has been shown to increase student learning while providing experience with real scientific investigation; however, implementation in large, multi-section courses presents many challenges. This study sought to test the feasibility and effectiveness of incorporating authentic research into a core genetics course, with multiple instructors, to increase student learning and progress our understanding of uncharacterized ORFs. We generated a module-based annotation toolkit and utilized easily accessible bioinformatics tools to predict gene function for uncharacterized ORFs within the Saccharomyces Genome Database (SGD). Students were each assigned an uncharacterized ORF, which they annotated using contemporary comparative genomics methodologies, including multiple sequence alignment, conserved domain identification, signal peptide prediction and cellular localization algorithms. Student learning outcomes were measured by quizzes, project reports and presentations, as well as a post-project questionnaire. Our results indicate that the authentic research experience had positive impacts on students' perception of their learning and their confidence to conduct future research. Furthermore, we believe that creation of an online repository and adoption and/or adaptation of this project across multiple researchers and institutions could speed the process of gene function prediction. PMID:26460164

  16. 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

  17. Implementation and assessment of a yeast orphan gene research project: involving undergraduates in authentic research experiences and progressing our understanding of uncharacterized open reading frames.

    PubMed

    Bowling, Bethany V; Schultheis, Patrick J; Strome, Erin D

    2016-02-01

    Saccharomyces cerevisiae was the first eukaryotic organism to be sequenced; however, little progress has been made in recent years in furthering our understanding of all open reading frames (ORFs). From October 2012 to May 2015 the number of verified ORFs had only risen from 75.31% to 78%, while the number of uncharacterized ORFs had decreased from 12.8% to 11% (representing > 700 genes still left in this category; http://www.yeastgenome.org/genomesnapshot). Course-based research has been shown to increase student learning while providing experience with real scientific investigation; however, implementation in large, multi-section courses presents many challenges. This study sought to test the feasibility and effectiveness of incorporating authentic research into a core genetics course, with multiple instructors, to increase student learning and progress our understanding of uncharacterized ORFs. We generated a module-based annotation toolkit and utilized easily accessible bioinformatics tools to predict gene function for uncharacterized ORFs within the Saccharomyces Genome Database (SGD). Students were each assigned an uncharacterized ORF, which they annotated using contemporary comparative genomics methodologies, including multiple sequence alignment, conserved domain identification, signal peptide prediction and cellular localization algorithms. Student learning outcomes were measured by quizzes, project reports and presentations, as well as a post-project questionnaire. Our results indicate that the authentic research experience had positive impacts on students' perception of their learning and their confidence to conduct future research. Furthermore, we believe that creation of an online repository and adoption and/or adaptation of this project across multiple researchers and institutions could speed the process of gene function prediction.

  18. 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

  19. Comparative mitochondrial genomics of freshwater mussels (Bivalvia: Unionoida) with doubly uniparental inheritance of mtDNA: gender-specific open reading frames and putative origins of replication.

    PubMed

    Breton, Sophie; Beaupré, Hélène Doucet; Stewart, Donald T; Piontkivska, Helen; Karmakar, Moumita; Bogan, Arthur E; Blier, Pierre U; Hoeh, Walter R

    2009-12-01

    Doubly uniparental inheritance (DUI) of mitochondrial DNA in marine mussels (Mytiloida), freshwater mussels (Unionoida), and marine clams (Veneroida) is the only known exception to the general rule of strict maternal transmission of mtDNA in animals. DUI is characterized by the presence of gender-associated mitochondrial DNA lineages that are inherited through males (male-transmitted or M types) or females (female-transmitted or F types), respectively. This unusual system constitutes an excellent model for studying basic aspects of mitochondrial DNA inheritance and the evolution of mtDNA genomes in general. Here we compare published mitochondrial genomes of unionoid bivalve species with DUI, with an emphasis on characterizing unassigned regions, to identify regions of the F and M mtDNA genomes that could (i) play a role in replication or transcription of the mtDNA molecule and/or (ii) determine whether a genome will be transmitted via the female or the male gamete. Our results reveal the presence of one F-specific and one M-specific open reading frames (ORFs), and we hypothesize that they play a role in the transmission and/or gender-specific adaptive functions of the M and F mtDNA genomes in unionoid bivalves. Three major unassigned regions shared among all F and M unionoid genomes have also been identified, and our results indicate that (i) two of them are potential heavy-strand control regions (O(H)) for regulating replication and/or transcription and that (ii) multiple and potentially bidirectional light-strand origins of replication (O(L)) are present in unionoid F and M mitochondrial genomes. We propose that unassigned regions are the most promising candidate sequences in which to find regulatory and/or gender-specific sequences that could determine whether a mitochondrial genome will be maternally or paternally transmitted.

  20. Getting Along With Reading Teachers

    ERIC Educational Resources Information Center

    Fenwick, Sara Innis

    1970-01-01

    Some of the stated needs of reading teachers include: more books where students can find them at arm's length, more open Door" hours, more help and time for individual students, more flexibility in borrowing rules, more books and other media relevant to the reading specialists, and more storytelling by librarians. (MF)

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

    PubMed

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

    2016-03-01

    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.

  2. 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

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

    PubMed

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

    2016-03-01

    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

  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. 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

  6. 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

    Springfeld, Christoph; Darai, Gholamreza; Cattaneo, Roberto

    2005-06-01

    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.

  7. 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

  8. 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

  9. 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.

  10. 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…

  11. Bilingual Reading.

    ERIC Educational Resources Information Center

    Garganta, Soledad; Ramirez, Inez

    This report discusses the importance of bilingual reading instruction for limited English speaking ability (LESA) students, and careful testing of their language dominance and reading levels. Bilingual students, and English- and Spanish-dominant students from the Fabens Independent School District, Grades K-13, were tested for the data reported…

  12. Reading Evaluation

    ERIC Educational Resources Information Center

    Fagan, W. T.

    1978-01-01

    The Canadian Institute for Research in Behavioral and Social Sciences of Calgary was awarded a contract by the Provincial Government of Alberta to assess student skills and knowledge in reading and written composition. Here evaluation is defined and the use of standardized and criterion referenced tests for evaluating reading performance are…

  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. 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;…

  15. 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…

  16. Reading Performance.

    ERIC Educational Resources Information Center

    Neuman, Susan B.

    1984-01-01

    Research indicates that factors other than media patterns--including such variables as home environment, role models, and personality characteristics--appear to influence reading behavior. New, sophisticated theoretical models are needed, however, to examine the relationship between television and reading. (Author/GC)

  17. 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.…

  18. 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.

  19. 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…

  20. Effect of solvent and additives on the open-circuit voltage of ZnO-based dye-sensitized solar cells: a combined theoretical and experimental study.

    PubMed

    Le Bahers, Tangui; Labat, Frédéric; Pauporté, Thierry; Ciofini, Ilaria

    2010-11-28

    We have investigated the role of electrolyte composition, in terms of solvent and additive, on the open-circuit voltage (V(oc)) of ZnO-based dye-sensitized solar cells (DSSCs) using a combined experimental and theoretical approach. Calculations based on density functional theory (DFT) have been performed in order to describe the geometries and adsorption energies of various adsorbed solvents (nitromethane, acetonitrile and dimethylformamide) and p-tert-butylpyridine (TBP) (modeled by methylpyridine) on the ZnO (100) surface using a periodic approach. The densities of states (DOS) have been calculated and the energy position of the conduction band edge (CBE) has been evaluated for the different molecules adsorbed. The effect of the electrolyte composition on the standard redox potential of the iodide/triiodide redox couple has been experimentally determined. These two data values (CBE and standard redox potential) allowed us to determine the dependence of V(oc) on the electrolyte composition. The variations determined using this method were in good agreement with the measured V(oc) for cells made of electrodeposited ZnO films sensitized using D149 (indoline) dye. As in the case of TiO(2)-based cells, a correlation of V(oc) with the donor number of the adsorbed species was found. The present study clearly points out that both the CBE energy and the redox potential variation are important for explaining the experimentally observed changes in the V(oc) of DSSCs. PMID:20949189

  1. Organization and partial sequence of a DNA region of the Rhizobium leguminosarum symbiotic plasmid pRL6JI containing the genes fixABC, nifA, nifB and a novel open reading frame.

    PubMed Central

    Grönger, P; Manian, S S; Reiländer, H; O'Connell, M; Priefer, U B; Pühler, A

    1987-01-01

    By hybridization and heteroduplex studies the fixABC and nifA genes of the Rhizobium leguminosarum symbiotic plasmid pRL6JI have been identified. DNA sequencing of the region containing nifA showed an open reading frame of 1557 bp encoding a protein of 56, 178 D. Based on sequence homology, this ORF was confirmed to correspond to the nifA gene. Comparison of three nifA proteins (Klebsiella pneumoniae, Rhizobium meliloti, Rhizobium leguminosarum) revealed only a weak relationship in their N-terminal regions, whereas the C-terminal parts exhibited strong homology. Sequence analysis also showed that the R. leguminosarum nifA gene is followed by nifB and preceded by fixC with an open reading frame inserted in between. This novel ORF of 294 bp was found to be highly conserved also in R. meliloti. No known promoter and termination signals could be defined on the sequenced R. leguminosarum fragment. Images PMID:3029674

  2. Protective effect of a DNA vaccine containing an open reading frame with homology to an ABC-type transporter present in the genomic island 3 of Brucella abortus in BALB/c mice.

    PubMed

    Riquelme-Neira, Roberto; Retamal-Díaz, Angello; Acuña, Francisca; Riquelme, Pablo; Rivera, Alejandra; Sáez, Darwin; Oñate, Angel

    2013-08-12

    The immunogenicity of a DNA vaccine containing an open reading frame (ORF) of genomic island 3 (GI-3), specific for Brucella abortus and Brucella melitensis, has been examined. Intramuscular injection of plasmid DNA carrying the open reading frame with homology to an ABC-type transporter (pV278a) into BALB/c mice elicited both humoral and cellular immune responses. Mice injected with pV278a had a dominant immunoglobulin G2a (IgG2a) response. This DNA vaccine elicited a T-cell-proliferative response and induced significant levels of interferon gamma (INF-γ) upon restimulation with recombinant 278a protein. Upon stimulation with an appropriate recombinant protein or crude Brucella protein, the vaccine did not induce IL-4, suggesting a typical T-helper (TH1) response. Furthermore, the vaccine induced protection in BALB/c mice when challenged with the virulent strain Brucella abortus 2308. Taken together, these data suggest that DNA vaccination offers an improved delivery of the homologous of an ABC-type transporter antigen, and provides the first evidence of a protective effect of this antigen in the construction of vaccines against B. abortus.

  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. 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…

  5. 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…

  6. 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…

  7. Fast and accurate short read alignment with Burrows–Wheeler transform

    PubMed Central

    Li, Heng; Durbin, Richard

    2009-01-01

    Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk PMID:19451168

  8. How to improve reading skills in dyslexics: the effect of high frequency rTMS.

    PubMed

    Costanzo, Floriana; Menghini, Deny; Caltagirone, Carlo; Oliveri, Massimiliano; Vicari, Stefano

    2013-12-01

    The latest progress in understanding remediation of dyslexia underlines how some changes in brain are a necessary mechanism of improvement. We wanted to determine whether high frequency repetitive transcranial magnetic stimulation (hf-rTMS) over areas that are underactive during reading in dyslexics, would improve reading of dyslexic adults. We applied 5Hz-TMS over both left and right inferior parietal lobule (IPL) and superior temporal gyrus (STG) prior to word, non-word and text reading aloud. Results show that hf-rTMS stimulation over the left IPL improves non-word reading accuracy and hf-rTMS stimulation over the left STG increases word reading speed and text reading accuracy. Moreover after right IPL stimulation, non-word reading accuracy also improves. These findings indicate that in dyslexics, L-STG and L-IPL have a differential role in word, non-word and text reading. Even if we would normally expect left-lateralized improvements only, the finding of a right IPL involvement suggests that there is additional compensatory recruitment of this region in dyslexics. In conclusion, we provide the first evidence that distinctive facilitation of neural pathways known to be underactive in dyslexics transitorily improves their reading performance. Such ameliorative effect may open new perspectives for the development of long-term specific treatments for dyslexia.

  9. 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.

  10. Oculomotor and cognitive control of eye movements in reading: evidence from mindless reading.

    PubMed

    Luke, Steven G; Henderson, John M

    2013-08-01

    In the present study, we investigated the influence of cognitive factors on eye-movement behaviors in reading. Participants performed two tasks: a normal-reading task, as well as a mindless-reading task in which letters were replaced with unreadable block shapes. This mindless-reading task served as an oculomotor control condition, simulating the visual aspects of reading but removing higher-level linguistic processing. Fixation durations, word skipping, and some regressions were influenced by cognitive factors, whereas eye movements within words appeared to be less open to cognitive control. Implications for models of eye-movement control in reading are discussed.

  11. 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…

  12. 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…

  13. The Effects of Combining Repeated Reading with "Reading Mastery" on First Graders' Oral Reading Fluency

    ERIC Educational Resources Information Center

    Nanda, Alice O.; Fredrick, Laura D.

    2007-01-01

    The present study replicates and extends the work of Frankhauser, Tso, and Martella (2001) using 6 first-grade students in a multiple baseline design across participants to determine if the addition of three repeated readings following "Reading Mastery I and II" (Engelmann & Bruner, 1995) lessons improves student fluency beyond that expected…

  14. 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.

  15. A theoretical study of cyclohexyne addition to carbonyl-Cα bonds: allowed and forbidden electrocyclic and nonpericyclic ring-openings of strained cyclobutenes.

    PubMed

    Sader, C Avery; Houk, K N

    2012-06-01

    The mechanism of cyclohexyne insertion into a C(O)-C(α) bond of cyclic ketones, explored experimentally by the Carreira group, has been investigated using density functional theory. B3LYP and M06-2X calculations were performed in both gas phase and THF (CPCM, UAKS radii). The reaction proceeds through a stepwise [2 + 2] cycloaddition of cyclohexyne to the enolate, followed by three disparate ring-opening possibilities of the cyclobutene alkoxide to give the product: (1) thermally allowed conrotatory electrocyclic ring-opening, (2) thermally forbidden disrotatory electrocyclic ring-opening, or (3) nonpericyclic C-C bond cleavage. Our computational results for the model alkoxide and potassium alkoxide systems show that the thermally allowed electrocyclic ring-opening pathway is favored by less than 1 kcal/mol. In more complex systems containing a potassium alkoxide (e-f), the barrier of the allowed conrotatory ring-opening is disfavored by 4-8 kcal/mol. This suggests that the thermodynamically more stable disrotatory product can be formed directly through a "forbidden" pathway. Analysis of geometrical parameters and atomic charges throughout the ring-opening pathways provides evidence for a nonpericyclic C-C bond cleavage, rather than a thermally forbidden disrotatory ring-opening. A true forbidden disrotatory ring-opening transition structure was computed for the cyclobutene alcohol; however, it was 19 kcal/mol higher in energy than the allowed conrotatory transition structure. An alternate mechanism in which the disrotatory product forms via isomerization of the conrotatory product was also explored for the alkoxide and potassium alkoxide systems. PMID:22537557

  16. 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…

  17. Assessing Children's Silent Reading

    ERIC Educational Resources Information Center

    Yule, Valerie

    1987-01-01

    Less is known about how children read connected text in silent reading, and the range of reading strategies used in an ordinary primary school classroom, than about the reading of single words, oral reading and reading by skilled adults. This paper describes and evaluates a method of testing children's silent reading in which they are their own…

  18. 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…

  19. 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…

  20. 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…

  1. 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…

  2. Felis domesticus papillomavirus, isolated from a skin lesion, is related to canine oral papillomavirus and contains a 1.3 kb non-coding region between the E2 and L2 open reading frames.

    PubMed

    Terai, Masanori; Burk, Robert D

    2002-09-01

    We have characterized the complete genome (8300 bp) of an isolate of Felis domesticus papillomavirus (FdPV) from a domestic cat with cutaneous papillomatosis. A BLAST homology search using the nucleotide sequence of the L1 open reading frame demonstrated that the FdPV genome was most closely related to canine oral papillomavirus (COPV). A 384 bp non-coding region (NCR) was found between the end of L1 and the beginning of E6, and a 1.3 kbp NCR was located between the end of E2 and the beginning of L2. Phylogenetic analysis placed FdPV in the E3 clade with COPV. Both viruses contain the atypical second NCR, which has no homology with sequences in existing databases. PMID:12185286

  3. 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.

  4. 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.

  5. 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.)

  6. The "Affective Component" of the Reading Program

    ERIC Educational Resources Information Center

    Strickler, Darryl J.

    1977-01-01

    A balanced reading program must--in addition to providing for children's reading skill needs--include a well-planned "affective component" which provides for the development of their interests, attitudes, and personal values in relation to reading for information and enjoyment. (Author)

  7. 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.…

  8. Reading Science

    ERIC Educational Resources Information Center

    Carlson, Kenneth

    2005-01-01

    Reading the average science textbook, one is struck with a question: Why would people devote their lives to the study of a subject as dry as the Sahara Desert? Students in science classes only need to be let in on the great secret of science. It is fun and full of the stuff in page-turner novels--intrigue, mystery, romance, and sometimes just dumb…

  9. Transcription strategy in a Closterovirus: a novel 5'-proximal controller element of Citrus Tristeza Virus produces 5'- and 3'-terminal subgenomic RNAs and differs from 3' open reading frame controller elements.

    PubMed

    Gowda, Siddarame; Ayllón, María A; Satyanarayana, Tatineni; Bar-Joseph, Moshe; Dawson, William O

    2003-01-01

    of both the 3'- and 5'-terminal sgRNAs. These mutations, when introduced in frame in the native 5'TR, similarly abolished the synthesis of the LMT1 RNAs and presumably the large 3'-terminal sgRNA while having no impact on replication, demonstrating that neither 5'- nor 3'-terminal sgRNA is necessary for replication of the replicon or full-length CTV in protoplasts. Differences between the 5'TR, which produced two plus-strand sgRNAs, and the cis-acting elements controlling the 3' open reading frames, which produced additional minus-strand sgRNAs corresponding to the 3'-terminal mRNAs, suggest that the different sgRNA controller elements had different origins in the modular evolution of closteroviruses.

  10. 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…

  11. 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…

  12. Reading To Learn: Study Reading for All?

    ERIC Educational Resources Information Center

    Kelly, Virginia

    This paper discusses the concept of "study reading" as used at a learning disabilities clinic at the University of Southampton, England. Study reading is defined as attentive reading to learn and remember, as different from reading that is performed simply to follow a narrative or browsing for one's own, self-set purposes. Results obtained with…

  13. 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…

  14. Proceedings of the College Reading Association, Volume 2, Summer 1961.

    ERIC Educational Resources Information Center

    Ketcham, Clay A., Ed.

    The proceedings of the fourth annual meeting of the College Reading Association (a fledgling organization in 1961 when this meeting was held) consisted of two symposia, a number of papers, and special reports on research related to reading, as follows: (1) "Opening Remarks" (Albert J. Mazurkiewicz); (2) "Improving Reading in the English Classroom"…

  15. 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…

  16. The Reading First Controversy: Promises and Perils of Federal Leadership

    ERIC Educational Resources Information Center

    Barbash, Shepard

    2008-01-01

    "Reading First is the most effective federal program in history." So reads the opening line of a report that Alabama superintendent of education Joseph Morton sent to his congressional delegation last June, in which he recounts how the program has raised reading achievement for poor students in his charge. Morton's view is shared by leaders in…

  17. 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

  18. 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.

  19. Successful Idiom Solving Strategies While Reading and Reading Time with Trained and Untrained Learners

    ERIC Educational Resources Information Center

    Angel, Rosalina Domínguez

    2014-01-01

    The present article examines the outcomes derived from a task on intensive reading carried out by university students. The main goal is to analyze the frequency of use and the success of idiom solving strategies used by the subjects while reading. Additionally, our interest is to compare the above outcomes and the reading time scores of a group of…

  20. Revisiting the "Simple View of Reading" in a Group of Children with Poor Reading Comprehension

    ERIC Educational Resources Information Center

    Georgiou, George K.; Das, J. P.; Hayward, Denyse

    2009-01-01

    According to Gough and Tunmer's Simple View of Reading, Reading Comprehension = Decoding (D) x Listening Comprehension (C). The purpose of this study was to evaluate the model with a sample of First Nations children, known to have average decoding and listening comprehension but poor reading comprehension. In addition, the authors examined the…

  1. 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…

  2. 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.

  3. Cognitive flexibility predicts early reading skills.

    PubMed

    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.

  4. 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,…

  5. 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…

  6. 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. PMID:27617030

  7. 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.

  8. All About Reading.

    ERIC Educational Resources Information Center

    Insights Into Open Education, 1974

    1974-01-01

    Focusing on reading, this issue of "Insights" contains three sections. The first, by Clara A. Pedersen, lists 20 questions which teachers and administrators should ask themselves before administering reading tests. The second, "What's Wrong with Reading Tests" by Deborah Meier, defines reading, describes learning to read, and analyzes the problems…

  9. 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;…

  10. 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…

  11. Mapping RNA-seq Reads with STAR.

    PubMed

    Dobin, Alexander; Gingeras, Thomas R

    2015-09-03

    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.

  12. Mapping RNA-seq Reads with STAR

    PubMed Central

    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, signal visualization, and so forth. 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

  13. Multisyllabic word reading as a moderator of morphological awareness and reading comprehension.

    PubMed

    Gilbert, Jennifer K; Goodwin, Amanda P; Compton, Donald L; Kearns, Devin M

    2014-01-01

    The purpose of this study was to investigate whether the relation between morphological awareness on reading comprehension is moderated by multisyllabic word reading ability in fifth-grade students (N = 169, 53.7% female, 65.2% minority status, 69.2% free/reduced lunch status), oversampled for poor reading skill, when controlling for general knowledge and vocabulary. Based on the lexical quality hypothesis, it was expected that morphological awareness would have a stronger effect on comprehension for children with poor word reading skills, suggesting possible use of morphological awareness for word identification support. Results indicated that neither morphological awareness nor word reading was uniquely associated with reading comprehension when both were included in the model along with vocabulary and general knowledge. Instead, the interaction between word reading and morphological awareness explained significant additional variance in reading comprehension. By probing this interaction, it was determined that the effect of morphological awareness on reading comprehension was significant for the 39% of the sample that had more difficulty reading multisyllabic words but not for students at the higher end of the multisyllabic word reading continuum. We conclude from these results that the relation between morphological awareness and reading comprehension is moderated by multisyllabic word reading ability, providing support for the lexical quality hypothesis. Although we have only correlational data, we suggest tentative instructional practices for improving the reading skill of upper elementary struggling readers.

  14. Multisyllabic Word Reading as a Moderator of Morphological Awareness and Reading Comprehension

    PubMed Central

    Gilbert, Jennifer K.; Goodwin, Amanda P.; Compton, Donald L.; Kearns, Devin M.

    2013-01-01

    The purpose of this study was to investigate whether the relation between morphological awareness on reading comprehension is moderated by multisyllabic word reading ability in fifth grade students (N = 169, 53.7% female, 65.2% minority status, 69.2% free/reduced lunch status), oversampled for poor reading skill, when controlling for general knowledge and vocabulary. Based on the lexical quality hypothesis (Perfetti, 2007), it was expected that morphological awareness would have a stronger effect on comprehension for children with poor word reading skills, suggesting possible use of morphological awareness for word identification support. Results indicated that neither morphological awareness nor word reading was uniquely associated with reading comprehension when both were included in the model along with vocabulary and general knowledge. Instead, the interaction between word reading and morphological awareness explained significant additional variance in reading comprehension. By probing this interaction, it was determined that the effect of morphological awareness on reading comprehension was significant for the 39% of the sample that had more difficulty reading multisyllabic words), but not for students at the higher end of the multisyllabic word reading continuum. We conclude from these results that the relation between morphological awareness and reading comprehension is moderated by multisyllabic word reading ability, providing support for the lexical quality hypothesis (Perfetti, 2007). Although we have only correlational data, we suggest tentative instructional practices for improving the reading skill of upper elementary struggling readers. PMID:24219914

  15. Sharp microwave frequency dependence in {open_quotes}ionization{close_quotes} of 3d H atoms and the effect of additive noise

    SciTech Connect

    Sirko, L.; Bellermann, M.; Haffmans, A.; Koch, P.M.

    1993-05-01

    For weak broadband (26-40 GHz) added shot noise (rms amplitude F{sub n} {approx_equal} 0.5 V/cm, <5% of the coherent amplitude F), we saw sharp variations around {nu}=30 GHz in e.g., F(10%) for 10%-{open_quotes}ionization{close_quotes} probability (n-cutoff {approx_equal} 89) of n{sub 0}=57 3d H atoms. Sharp means varying {nu} {approx_lt} 1/3 of the Fourier bandwidth 0.35 GHz of the 4.3 ns long half-sinewave pulseshape. Increased noise lowered (raised) F(10%) near sharp maxima (minima). (For some other cases noise did very little.) F{sub n} {approx_equal} 2.2 V/cm. suppressed the sharp {nu}-variation of F(10%). Our bound-basis integration of the 1d Schrodinger equation reproduces the results well, including influence of noise. Leopold, Richards, and Jensen are developing theory for a perturbed pendulum effective Hamiltonian H{sub eff} locally describing the dynamics at the classical nonlinear resonance island centered near n{sub 0}{sup 3}{omega}=1. Our data may be the first spectroscopic glimpse of novel quantal states of H{sub eff}.

  16. Characterization of the tol-pal region of Escherichia coli K-12: translational control of tolR expression by TolQ and identification of a new open reading frame downstream of pal encoding a periplasmic protein.

    PubMed Central

    Vianney, A; Muller, M M; Clavel, T; Lazzaroni, J C; Portalier, R; Webster, R E

    1996-01-01

    The TolQ, TolR, TolA, TolB, and Pal proteins appear to function in maintaining the integrity of the outer membrane, as well as facilitating the uptake of the group A colicins and the DNA of the infecting filamentous bacteriophages. Sequence data showed that these genes are clustered in a 6-kb segment of DNA with the gene order orf1 tolQ tolR tolA tolB pal orf2 (a newly identified open reading frame encoding a 29-kD9 protein). Like those containing orf1, bacteria containing an insertion mutation in this gene showed no obvious phenotype. Analysis of beta-galactosidase activity from fusion constructs in which the lac operon was fused to various genes in the cluster showed that the genes in this region constitute two separate operons: orf1 tolQRA and tolB pal orf2. In the orf1 tolQRA operon, translation of MR was dependent on translation of the upstream tolQ region. Consistent with this result, no functional ribosome-binding site for TolR synthesis was detected. PMID:8763928

  17. Simian Varicella Virus Expresses a Latency-Associated Transcript That Is Antisense to Open Reading Frame 61 (ICP0) mRNA in Neural Ganglia of Latently Infected Monkeys▿

    PubMed Central

    Ou, Yang; Davis, Kara A.; Traina-Dorge, Vicki; Gray, Wayne L.

    2007-01-01

    Simian varicella virus (SVV) and varicella-zoster virus (VZV) are closely related alphaherpesviruses that cause varicella (chickenpox) in nonhuman primates and humans, respectively. After resolution of the primary disease, SVV and VZV establish latent infection of neural ganglia and may later reactivate to cause a secondary disease (herpes zoster). This study investigated SVV gene expression in neural ganglia derived from latently infected vervet monkeys. SVV transcripts were detected in neural ganglia, but not in liver or lung tissues, of latently infected animals. A transcript mapping to open reading frame (ORF) 61 (herpes simplex virus type 1 [HSV-1] ICP0 homolog) was consistently detected in latently infected trigeminal, cervical, and lumbar ganglia by reverse transcriptase PCR. Further analysis confirmed that this SVV latency-associated transcript (LAT) was oriented antisense to the gene 61 mRNA. SVV ORF 21 transcripts were also detected in 42% of neural ganglia during latency. In contrast, SVV ORF 28, 29, 31, 62, and 63 transcripts were not detected in ganglia, liver, or lung tissues of latently infected animals. The results demonstrate that viral gene expression is limited during SVV latency and that a LAT antisense to an ICP0 homolog is expressed. In this regard, SVV gene expression during latency is similar to that of HSV-1 and other neurotropic animal alphaherpesviruses but differs from that reported for VZV. PMID:17507490

  18. Immunogenicity and Protective Response Induced by Recombinant Plasmids Based on the BAB1_0267 and BAB1_0270 Open Reading Frames of Brucella abortus 2308 in BALB/c Mice

    PubMed Central

    Gómez, Leonardo A.; Alvarez, Francisco I.; Fernández, Pablo A.; Flores, Manuel R.; Molina, Raúl E.; Coloma, Roberto F.; Oñate, Angel A.

    2016-01-01

    Immunogenicity induced by recombinant plasmids based on the BAB1_0267 and BAB1_0270 open reading frames (ORFs) of Brucella abortus 2308 was evaluated. Bioinformatics analyses indicate that the BAB1_0267 and BAB1_0270 ORFs encode a protein with a SH3 domain and a Zn-dependent metalloproteinase, respectively. Both ORFs have important effects on intracellular survival and replication of B. abortus 2308, mediated via professional and non-professional phagocytic cells. Our results show that immunization with the recombinant plasmid based on the BAB1_0267 ORF significantly increases the production of IgG1, levels of IFN-γ and the lymphoproliferative response of splenocytes. However, BAB1_0267 did not provide significant levels of protection. The plasmid based on the BAB1_0270 significantly increased IgG2a production, levels of IFN-γ and TNF-α, and the lymphoproliferative response of splenocytes. These results demonstrate that immunization with the BAB1_0270 derived recombinant plasmid induce a Th1-type immune response, correlated with a heightened resistance to B. abortus 2308 infection in mice. It is concluded that the Th1-type immune response against bacterial Zn-dependent metalloproteinase induces a protective response in mice, and that pV270 recombinant plasmid is an effective candidate microbicide against brucellosis. PMID:27747197

  19. The primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus MHV-A59; a highly conserved polymerase is expressed by an efficient ribosomal frameshifting mechanism.

    PubMed Central

    Bredenbeek, P J; Pachuk, C J; Noten, A F; Charité, J; Luytjes, W; Weiss, S R; Spaan, W J

    1990-01-01

    Sequence analysis of a substantial part of the polymerase gene of the murine coronavirus MHV-A59 revealed the 3' end of an open reading frame (ORF1a) overlapping with a large ORF (ORF1b; 2733 amino acids) which covers the 3' half of the polymerase gene. The expression of ORF1b occurs by a ribosomal frameshifting mechanism since the ORF1a/ORF1b overlapping nucleotide sequence is capable of inducing ribosomal frameshifting in vitro as well as in vivo. A stem-loop structure and a pseudoknot are predicted in the nucleotide sequence involved in ribosomal frameshifting. Comparison of the predicted amino acid sequence of MHV ORF1b with the amino acid sequence deduced from the corresponding gene of the avian coronavirus IBV demonstrated that in contrast to the other viral genes this ORF is extremely conserved. Detailed analysis of the predicted amino acid sequence revealed sequence elements which are conserved in many DNA and RNA polymerases. Images PMID:2159623

  20. 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.

  1. 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

  2. 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…

  3. 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…

  4. 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…

  5. 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…

  6. Celebrations in Reading and Writing: Reading Refresher

    ERIC Educational Resources Information Center

    Manning, Maryann

    2005-01-01

    Revising reading program can breathe new life into the classroom and increase students' confidence. This paper describes how one teacher decided to refine her reading curriculum. She had five non-negotiables for the curriculum: the need for self-selection of quality literature; volume of reading; peer interaction; individual conferences; and…

  7. Reading(s) in the Writing Classroom.

    ERIC Educational Resources Information Center

    Foster, David

    1997-01-01

    Interrogates the reading/writing connection by evaluating how three essays by published writers affected the attitude and writing practices of university students in a course on the personal essay. Describes the course. Suggests what findings imply for current rationales about the reading/writing connection and for the use of anthology readings in…

  8. Parents, Reading Partners, Library Advocates

    ERIC Educational Resources Information Center

    Deskins, Liz

    2011-01-01

    According to the author, one of her most important goals as a school librarian is to inspire her students to become lifelong lovers of reading. She recognizes that she cannot do this alone, and one of her most powerful partners is a parent. She can encourage a child to check out a book that may open their eyes to the wonders of literature, but if…

  9. 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…

  10. Braille Reading Rates as a Function of Reading Tasks.

    ERIC Educational Resources Information Center

    Knowlton, M.; Wetzel, R.

    1996-01-01

    This study of the cognitive processes of braille reading compared the reading of 23 adult braille readers in 4 different reading conditions: oral reading, silent reading, studying, and scanning. The findings support the idea that braille reading is process driven and that reading rates vary, depending on the purpose of the reading task. (Author)

  11. 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

  12. Reading with Purpose

    ERIC Educational Resources Information Center

    Linderholm, Tracy

    2006-01-01

    In college-level courses, the vast majority of students read expository textbooks with a primary purpose in mind: to memorize and, hopefully, understand enough information to receive a particular grade on a course exam. Intuitively, this kind of reading is different than the kind of reading that these same students do when reading a novel while…

  13. Measuring Reading Performance.

    ERIC Educational Resources Information Center

    Blanton, William E., Ed.; And Others

    Designed to provide solutions to some of the problems related to measuring reading behavior, this publication explores some of the problems of test selection and usage which confront educators. Contents include "Reading Testing for Reading Evaluation" by Walter R. Hill, "Reading Tests and the Disadvantaged" by Thomas J. Fitzgibbon, "What Is…

  14. 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.…

  15. 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…

  16. Affective Considerations in Reading.

    ERIC Educational Resources Information Center

    Strickler, Darryl J.

    1978-01-01

    Schools can influence beginning readers' concepts, interests, attitudes, and values--these are the raw materials from which reading habits develop. Guidelines for promoting children's interest in reading involve reading/language arts programs, provision of reading materials, classroom climate, and specific teacher behaviors. (CP)

  17. 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…

  18. 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…

  19. 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…

  20. Genotyping of skin and soft tissue infection (SSTI)-associated methicillin-resistant Staphylococcus aureus (MRSA) strains among outpatients in a teaching hospital in Japan: application of a phage-open reading frame typing (POT) kit.

    PubMed

    Maeda, Tadashi; Saga, Tomoo; Miyazaki, Taito; Kouyama, Yuichi; Harada, Sohei; Iwata, Morihiro; Yoshizawa, Sadako; Kimura, Soichiro; Ishii, Yoshikazu; Urita, Yoshihisa; Sugimoto, Motonobu; Yamaguchi, Keizo; Tateda, Kazuhiro

    2012-12-01

    We aimed to elucidate the current epidemiological features of outpatient skin and soft tissue infection (SSTI)-associated methicillin-resistant Staphylococcus aureus (MRSA) in Japan. Altogether, we evaluated the performance of a phage-open reading frame typing (POT) kit for genotyping these MRSA strains. We collected 57 MRSA strains from all outpatients with SSTIs attending a teaching hospital in Japan. Drug susceptibility measurement and genotyping including SCCmec typing, spa typing, multilocus sequence typing, pulsed-field gel electrophoresis, and commercial POT-kit were performed. The majority of strains (39 strains, 68 %) had the SCCmec-II element. Seventeen strains (30 %) with SCCmec-IV accounted for the second largest population. Strains with SCCmec-IV and SCCmec-V appeared multiclonal, and a predominance of Panton-Valentine leukocidin (PVL) gene-negative CC8/spa-CC008 strains, as well as the first isolate of an ST93 strain in Japan, was observed among them. Only one USA300 strain was identified. Strains with SCCmec-IV and SCCmec-V were significantly susceptible to antimicrobials. The PVL gene was found in 5 SCCmec-IV strains and 1 SCCmec-V strain. The POT-kit successfully predicted the SCCmec type in 54 strains (95 %), and typing by POT1 scores was highly concordant with SCCmec typing and spa typing. Moreover, three PVL-positive strains fell into a particular POT type (POT scores, 106-77-113). Simpson's index of the POT-kit was 0.977. In conclusion, the present study clarified the multiclonal nature of outpatient SSTI-associated MRSA in a teaching hospital in Japan. These data also underscore the utility of the POT-kit for non-outbreak surveillance through its simple platform consisting of two multiplex PCRs without sequencing.

  1. Introducing point mutations into the ATGs of the putative open reading frames of the HSV-1 gene encoding the latency associated transcript (LAT) reduces its anti-apoptosis activity.

    PubMed

    Carpenter, Dale; Henderson, Gail; Hsiang, Chinhui; Osorio, Nelson; BenMohamed, Lbachir; Jones, Clinton; Wechsler, Steven L

    2008-02-01

    The herpes simplex virus type 1 (HSV-1) latency associated transcript (LAT) gene has anti-apoptosis activity that directly or indirectly enhances the virus's reactivation phenotype in small animal models. The first 1.5 kb of the primary 8.3 kb LAT is sufficient and some or all of it is necessary for LAT's anti-apoptosis in transient transfection assays and for LAT's ability to enhance the reactivation phenotype. Based on LAT's genomic sequence, the first 1.5 kb contains eight potential open reading frames (ORFs) defined as an ATG followed by an in frame termination codon. In this study, point mutations were introduced into the ATGs of ORFs present in the 1.5 kb fragment of LAT. Mutagenesis of all eight ATGs in LAT ORFs consistently reduced the anti-apoptotic activity of LAT in transiently transfected mouse neuroblastoma cells regardless of whether apoptosis was induced by caspase 8 or caspase 9. Mutation of the six ATGs located in the stable intron sequences within the 1.5 kb LAT had a dramatic effect on caspase 9, but not caspase 8, induced apoptosis. For both caspase 8 and caspase 9 induced apoptosis, mutating the two ATGs in the exon of the LAT 1.5 kb fragment reduced, but did not eliminate the anti-apoptotic activity of LAT. These studies suggest that altering the fine structure of regulatory RNA or expression of a putative LAT ORF regulates the anti-apoptosis activity of LAT. These studies also indicate that more than one function is present in the 1.5 kb LAT fragment.

  2. 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

  3. The Professional Reading Habits of American Librarians.

    ERIC Educational Resources Information Center

    Weaver, Susan M.

    This research project studied the perceived quality of the library and information science literature and asked questions regarding international librarianship. Additionally, it questioned what librarians read, how they choose their reading material, and how they use the literature for their decision making. The sample consisted of librarians from…

  4. Functional Reading Levels: From Graded Word Lists?

    ERIC Educational Resources Information Center

    Froese, Victor

    This study investigated the feasibility of using only the McCracken Word List (MWL), a subtest of the Standard Reading Inventory (SRI), rather than the entire SRI to determine functional grade placement in reading. The MWL is one of the few word lists with well-documented reliability and validity. In addition, the MWL has been shown to be highly…

  5. 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…

  6. 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…

  7. 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…

  8. Phosphazene additives

    DOEpatents

    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.

  9. 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.

  10. Reading without Nonsense. Second Edition.

    ERIC Educational Resources Information Center

    Smith, Frank

    Intended for reading teachers, this book is concerned with the process of reading, with the perceptual and language skills involved in reading, and with the nature of the task confronting children learning to read. It shows that it is only through reading that children learn to read, and that a teacher's role must therefore be to make reading easy…

  11. 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.

  12. 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.

  13. 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…

  14. 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…

  15. 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…

  16. Improving Reading Readiness through Reading and Writing.

    ERIC Educational Resources Information Center

    Dashner, Carol

    A study examined the effectiveness of a project to increase reading readiness skills. The targeted population consisted of kindergarten students in a growing middle class community located in northern Illinois. The problems of lack of reading readiness were documented through teacher observation and district assessment tools. Analysis of probable…

  17. Measuring reading performance.

    PubMed

    Rubin, Gary S

    2013-09-20

    Despite significant changes in the treatment of common eye conditions like cataract and age-related macular degeneration, reading difficulty remains the most common complaint of patients referred for low vision services. Clinical reading tests have been widely used since Jaeger introduced his test types in 1854. A brief review of the major developments in clinical reading tests is provided, followed by a discussion of some of the main controversies in clinical reading assessment. Data for the Salisbury Eye Evaluation (SEE) study demonstrate that standardised clinical reading tests are highly predictive of reading performance under natural, real world conditions, and that discrepancies between self-reported reading ability and measured reading performance may be indicative of people who are at a pre-clinical stage of disability, but are at risk for progression to clinical disability. If measured reading performance is to continue to increase in importance as a clinical outcome measure, there must be agreement on what should be measured (e.g. speed or comprehension) and how it should be measured (e.g. reading silently or aloud). Perhaps most important, the methods for assessing reading performance and the algorithms for scoring reading tests need to be optimised so that the reliability and responsiveness of reading tests can be improved.

  18. 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.

  19. 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…

  20. 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…

  1. 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…

  2. 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…

  3. Cost-Effectiveness Affirmative Reading Skills Program, 1984-85.

    ERIC Educational Resources Information Center

    Gallagher, Michael P.

    The 1984-85 cost-effects study represents the third annual analysis of the components of Cleveland's Affirmative Reading Skills Plan, which offers three instructional strands--developmental (regular reading/language arts), support (additional enrichment, corrective or remedial), and compensatory (instruction for students having reading scores in…

  4. Young Bilinguals Reading Aloud.

    ERIC Educational Resources Information Center

    Parke, Tim

    1991-01-01

    Examines some of the differences between monolingual and bilingual reading. Focuses on some factors that are likely to influence young bilingual readers' capacity to read in their second language. Offers suggestions for pedagogy. (RS)

  5. Can Reading Help?

    ERIC Educational Resources Information Center

    Crowe, Chris

    2003-01-01

    Ponders the effect of September 11th on teenagers. Proposes that reading books can help teenagers sort out complicated issues. Recommends young adult novels that offer hope for overcoming tragedy. Lists 50 short story collections worth reading. (PM)

  6. 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 ...

  7. 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)

  8. 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 ...

  9. 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 ...

  10. 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…

  11. Measuring College Students' Reading Comprehension Ability Using Cloze Tests

    ERIC Educational Resources Information Center

    Williams, Rihana Shiri; Ari, Omer; Santamaria, Carmen Nicole

    2011-01-01

    Recent investigations challenge the construct validity of sustained silent reading tests. Performance of two groups of post-secondary students (e.g. struggling and non-struggling) on a sustained silent reading test and two types of cloze test (i.e. maze and open-ended) was compared in order to identify the test format that contributes greater…

  12. A Comparison of Perceptual Motor Skill with Auditory Comprehension as Correlates of Word Recognition, Oral Reading, and Silent Reading.

    ERIC Educational Resources Information Center

    Tillman, Chester E.

    A study was conducted to examine the relationship of perceptual motor skills as measured by the Bender Visual Motor Gestalt Test to word recognition, oral reading, and silent reading. In addition, perceptual motor skill and auditory comprehension were compared as correlates of the three reading variables. Subjects were 60 primary grade students in…

  13. Read length versus depth of coverage for viral quasispecies reconstruction.

    PubMed

    Zagordi, Osvaldo; Däumer, Martin; Beisel, Christian; Beerenwinkel, Niko

    2012-01-01

    Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus populations. Several sequencing platforms with different underlying technologies and performance characteristics are available for viral diversity studies. Here, we investigate how the differences between two common platforms provided by 454/Roche and Illumina affect viral diversity estimation and the reconstruction of viral haplotypes. Using a mixture of ten HIV clones sequenced with both platforms and additional simulation experiments, we assessed the trade-off between sequencing coverage, read length, and error rate. For fixed costs, short Illumina reads can be generated at higher coverage and allow for detecting variants at lower frequencies. They can also be sufficient to assess the diversity of the sample if sequences are dissimilar enough, but, in general, assembly of full-length haplotypes is feasible only with the longer 454/Roche reads. The quantitative comparison highlights the advantages and disadvantages of both platforms and provides guidance for the design of viral diversity studies.

  14. 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…

  15. Motivating Students To Read.

    ERIC Educational Resources Information Center

    Green, Patricia; Kandyba, Christine; McDonald, Colleen; Stevens, Tricia

    This report describes a research study in which motivational strategies were used to increase student enjoyment of reading and to foster a life-long love of reading. The targeted populations consisted of primary and middle grade students in three different urban midwestern settings. The problem of motivating students to read was documented through…

  16. 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…

  17. 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…

  18. 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…

  19. Reading for Pleasure: Guidelines.

    ERIC Educational Resources Information Center

    Spiegel, Dixie Lee

    Intended for classroom teachers and administrators who want their schools to reflect commitment to the idea that reading for pleasure is an essential part of every successful reading program, this book provides suggestions by which educators can coordinate their efforts with librarians and parents to get children to read voluntarily. The book is…

  20. Evaluation of Reading Progress.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    1999-01-01

    Explores numerous procedures to evaluate a pupil's reading achievement. Discusses different evaluation methods including criterion-referenced tests; contextualism in reading; discussions in the reading curriculum; conferences with pupils; and using portfolios. Concludes that the best objectives, learning opportunities, appraisal procedures, and an…

  1. 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…

  2. 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…

  3. Carbo Reading Styles.

    ERIC Educational Resources Information Center

    Education Commission of the States, Denver, CO.

    This paper provides an overview of the Carbo Reading Styles Program (RSP), a comprehensive reading program that applies learning styles concepts to reading. The program uses themes, activities, and literature to help improve student performance across all subject areas. Main components of RSP include: a variety of instructional strategies to…

  4. Rapid Reading, Yes

    ERIC Educational Resources Information Center

    Frommer, Harvey

    1971-01-01

    Recommends instruction in rapid reading fo high school and college students and asserts that flexibility of speed and reasoning provide the foundation for effective rapid reading. Describes the components of rapid reading as orientation, selection, clarification, arrangement, review, and study. (RW)

  5. 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.

  6. Reading as a Whole.

    ERIC Educational Resources Information Center

    Weaver, Constance

    Underlying virtually all of the basal reading series available in the United States today is the assumption that learning to read is a skill-by-skill and word-by-word process. This part-to-whole approach to teaching reading is based on principles of behavioral psychology and "scientific management" developed a half century ago and treats meaning…

  7. 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…

  8. 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…

  9. 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…

  10. Prose reading in neglect.

    PubMed

    Beschin, Nicoletta; Cisari, Carlo; Cubelli, Roberto; Della Sala, Sergio

    2014-02-01

    Prose reading has been shown to be a very sensitive measure of Unilateral Spatial Neglect. However, little is known about the relationship between prose reading and other measures of neglect and its severity, or between prose reading and single word reading. Thirty participants with a first stroke in the right hemisphere and clear symptoms of spatial neglect in everyday life were assessed with tests of prose reading (text in one column book-like, and in two columns magazine-like), single words reading, and a battery of 13 tests investigating neglect. Seventy percent of these participants omitted words at the beginning of the text (left end), showing Prose Reading Neglect (PRN). The participants showing PRN differed from those not showing PRN only for the overall severity of neglect, and had a lesion centred on the insula, putamen and superior temporal gyrus. Double dissociations emerged between PRN and single word reading neglect, suggesting different cognitive requirements between the two tests: parallel processing in single word reading vs. serial analysis in text reading. Notably, the pattern of neglected text varied dramatically across participants presenting with PRN, including dissociations between reading performance of one and two columns text. Prose reading proved a complex and unique task which should be directly investigated to predict the effects of unilateral neglect. The outcome of this study should also inform clinical assessment and advises given to patients and care-givers.

  11. Reading is Thinking.

    ERIC Educational Resources Information Center

    Winkeljohann, Rosemary

    1979-01-01

    The focus article in this newsletter contains a discussion of the theory of reading as a thinking process and offers practical suggestions for implementing instruction in teaching reading as a thinking process. The section on theory is based on observations of the reading process as perceived by psycholinguists such as Frank Smith and Kenneth…

  12. Philosophies of Reading Instruction

    ERIC Educational Resources Information Center

    Ediger, Marlow

    2013-01-01

    There are selected philosophies of reading instruction which are relevant in providing for individual differences among learners. These need to be studied in-depth by reading teachers in order to best provide for each pupil in the classroom. Pupils differ from each other in reading achievement, interests, and purposes, and it is a challenge to…

  13. 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,…

  14. 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…

  15. Reading: United States.

    ERIC Educational Resources Information Center

    Weber, Rose-Marie

    1983-01-01

    An exploration of the increasingly important role of linguistics in literacy research and instruction reviews literature on reading comprehension, written language, orthography, metalinguistics, classroom language use, reading disabilities, native tongues, nonstandard dialects, bilingual education, adult literacy, and second-language reading. (86…

  16. Reading/Writing Connection.

    ERIC Educational Resources Information Center

    Fernandez, Melanie

    In the past, students and teachers alike viewed reading and writing instruction as two separate entities. Reading and writing instruction was often characterized by linear and behaviorist theories and methods, with students rarely coming away from their schooling experience with confidence in and respect for their own writing. To both read and…

  17. Student Motivation in Reading.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    Motivation is a rather persistent problem in guiding students to read well. If a student lacks motivation, a low energy level will be available for learning to read. Through motivation, a learner is encouraged to achieve definite goals in reading. Attention and retention by the student are important in recognizing new words whether the approach is…

  18. 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…

  19. 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…

  20. Staff Development and Reading.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    Much is being emphasized in staff development in the area of reading instruction. It is important for teachers to study and think reflectively about what can be done to improve the elementary reading curriculum. One procedure that can be used is to hold a quality workshop based on the needs of reading teachers. Teachers might volunteer to serve on…

  1. Writing Workshops and the Teaching of Reading.

    ERIC Educational Resources Information Center

    Shuman, R. Baird

    This paper discusses three types of writing experiences, "Writing Roulette,""The Even-Steven Swap Game," and "The Open-Ended Story with a Slant," that can be used in a writing workshop for disabled readers at the secondary level. Each activity emphasizes writing but provides motivation for students to read each other's work. Students will have…

  2. Formal Specification of the OpenMP Memory Model

    SciTech Connect

    Bronevetsky, G; de Supinski, B R

    2006-05-17

    OpenMP [1] is an important API for shared memory programming, combining shared memory's potential for performance with a simple programming interface. Unfortunately, OpenMP lacks a critical tool for demonstrating whether programs are correct: a formal memory model. Instead, the current official definition of the OpenMP memory model (the OpenMP 2.5 specification [1]) is in terms of informal prose. As a result, it is impossible to verify OpenMP applications formally since the prose does not provide a formal consistency model that precisely describes how reads and writes on different threads interact. This paper focuses on the formal verification of OpenMP programs through a proposed formal memory model that is derived from the existing prose model [1]. Our formalization provides a two-step process to verify whether an observed OpenMP execution is conformant. In addition to this formalization, our contributions include a discussion of ambiguities in the current prose-based memory model description. Although our formal model may not capture the current informal memory model perfectly, in part due to these ambiguities, our model reflects our understanding of the informal model's intent. We conclude with several examples that may indicate areas of the OpenMP memory model that need further refinement however it is specified. Our goal is to motivate the OpenMP community to adopt those refinements eventually, ideally through a formal model, in later OpenMP specifications.

  3. 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…

  4. Factors That Facilitate or Hinder the Use of Computer-Assisted Reading in the L2 Reading Classroom

    ERIC Educational Resources Information Center

    Al-Seghayer, Khalid

    2016-01-01

    This study examined factors associated with whether instructors of English as a second or foreign language (ESL/EFL) incorporate computer-assisted reading (CAR) into their second-language (L2) reading classrooms. To achieve this goal, 70 ESL/EFL instructors completed a survey containing 37 items and 1 open-ended question concerning their…

  5. 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

  6. Speed Reading Scores in Perspective

    ERIC Educational Resources Information Center

    Smith, Brenda Golembesky

    1975-01-01

    Cites the factors that influence reading rates and comprehension scores on timed speed reading tests, concluding that the reading speed achieved for any particular test or timed reading is the speed for that situation only. (RB)

  7. 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. ...

  8. Reading Style: Diagnosis, Evaluation, Prescription.

    ERIC Educational Resources Information Center

    Carbo, Marie L.

    1980-01-01

    Designed for the evaluation of the reading ability of handicapped students, the reading style checklist (RSC) is presented along with lists of abilities a student would need in order to learn to read using different reading methods. (PHR)

  9. Reading Millionaires--It Works!

    ERIC Educational Resources Information Center

    Baumann, Nancy L.

    1995-01-01

    Describes the successful implementation in a Georgia elementary school of the Reading Millionaires Project, a reading incentive program to promote recreational reading and to create student interest in reading. (SR)

  10. 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.

  11. 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…

  12. 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…

  13. 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…

  14. 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,…

  15. 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.…

  16. 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-…

  17. Amblyopic reading is crowded.

    PubMed

    Levi, Dennis M; Song, Shuang; Pelli, Denis G

    2007-10-26

    We measure acuity, crowding, and reading in amblyopic observers to answer four questions. (1) Is reading with the amblyopic eye impaired because of larger required letter size (i.e., worse acuity) or larger required spacing (i.e., worse crowding)? The size or spacing required to read at top speed is called "critical". For each eye of seven amblyopic observers and the preferred eyes of two normal observers, we measure reading rate as a function of the center-to-center spacing of the letters in central and peripheral vision. From these results, we estimate the critical spacing for reading. We also measured traditional acuity for an isolated letter and the critical spacing for identifying a letter among other letters, which is the classic measure of crowding. For both normals and amblyopes, in both central and peripheral vision, we find that the critical spacing for reading equals the critical spacing for crowding. The identical critical spacings, and very different critical sizes, show that crowding, not acuity, limits reading. (2) Does amblyopia affect peripheral reading? No. We find that amblyopes read normally with their amblyopic eye except that abnormal crowding in the fovea prevents them from reading fine print. (3) Is the normal periphery a good model for the amblyopic fovea? No. Reading centrally, the amblyopic eye has an abnormally large critical spacing but reads all larger spacings at normal rates. This is unlike the normal periphery, in which both critical spacing and maximum reading rate are severely impaired relative to the normal fovea. (4) Can the uncrowded-span theory of reading rate explain amblyopic reading? Yes. The case of amblyopia shows that crowding limits reading solely by determining the uncrowded span: the number of characters that are not crowded. Characters are uncrowded if and only if their spacing is more than critical. The text spacing may be uniform, but the observer's critical spacing increases with distance from fixation, so the

  18. 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

  19. 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

  20. 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.

  1. Methodological Variables in Choral Reading

    ERIC Educational Resources Information Center

    Poore, Meredith A.; Ferguson, Sarah Hargus

    2008-01-01

    This preliminary study explored changes in prosodic variability during choral reading and investigated whether these changes are affected by the method of eliciting choral reading. Ten typical adult talkers recorded three reading materials (poetry, fiction and textbook) in three reading conditions: solo (reading aloud alone), track (reading aloud…

  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. Comparison of Genetic Variability at Multiple Loci across the Genomes of the Major Subtypes of Kaposi’s Sarcoma-Associated Herpesvirus Reveals Evidence for Recombination and for Two Distinct Types of Open Reading Frame K15 Alleles at the Right-Hand End

    PubMed Central

    Poole, Lynn J.; Zong, Jian-Chao; Ciufo, Dolores M.; Alcendor, Donald J.; Cannon, Jennifer S.; Ambinder, Richard; Orenstein, Jan M.; Reitz, Marvin S.; Hayward, Gary S.

    1999-01-01

    Kaposi’s sarcoma (KS)-associated herpesvirus or human herpesvirus 8 (HHV8) DNA is found consistently in nearly all classical, endemic, transplant, and AIDS-associated KS lesions, as well as in several AIDS-associated lymphomas. We have previously sequenced the genes for the highly variable open reading frame K1 (ORF-K1) protein from more than 60 different HHV8 samples and demonstrated that they display up to 30% amino acid variability and cluster into four very distinct evolutionary subgroups (the A, B, C, and D subtypes) that correlate with the major migrationary diasporas of modern humans. Here we have extended this type of analysis to six other loci across the HHV8 genome to further evaluate overall genotype patterns and the potential for chimeric genomes. Comparison of the relatively conserved ORF26, T0.7/K12, and ORF75 gene regions at map positions 0.35, 0.85, and 0.96 revealed typical ORF-K1-linked subtype patterns, except that between 20 and 30% of the genomes analyzed proved to be either intertypic or intratypic mosaics. In addition, a 2,500-bp region found at the extreme right-hand side of the unique segment in 45 HHV8 genomes proved to be highly diverged from the 3,500-bp sequence found at this position in the other 18 HHV8 genomes examined. Furthermore, these previously uncharacterized “orphan” region sequences proved to encompass multiexon latent-state mRNAs encoding two highly diverged alleles of the novel ORF-K15 protein. The predominant (P) and minor (M) forms of HHV8 ORF-K15 are structurally related integral membrane proteins that have only 33% overall amino acid identity to one another but retain conserved likely tyrosine kinase signaling motifs and may be distant evolutionary relatives of the LMP2 latency protein of Epstein-Barr virus. The M allele of ORF-K15 is also physically linked to a distinctive M subtype of the adjacent ORF75 gene locus, and in some cases, this linkage extends as far back as the T0.7 locus also. Overall, the results

  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.

  5. 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…

  6. Repeated readings and science: Fluency with expository passages

    NASA Astrophysics Data System (ADS)

    Kostewicz, Douglas E.

    The current study investigated the effects of repeated readings to a fluency criterion (RRFC) for seven students with disabilities using science text. The study employed a single subject design, specifically, two multiple probe multiple baselines across subjects, to evaluate the effects of the RRFC intervention. Results indicated that students met criterion (200 or more correct words per minute with 2 or fewer errors) on four consecutive passages. A majority of students displayed accelerations to correct words per minute and decelerations to incorrect words per minute on successive initial, intervention readings suggesting reading transfer. Students' reading scores during posttest and maintenance out performed pre-test and baseline readings provided additional measures of reading transfer. For a relationship to comprehension, students scored higher on oral retell measures after meeting criterion as compared to initial readings. Overall, the research findings suggested that the RRFC intervention improves science reading fluency for students with disabilities, and may also indirectly benefit comprehension.

  7. 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

  8. 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

  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. 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…

  11. Summer library reading programs.

    PubMed

    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 summarizes some of the research in the field and relates it to library programs and usage by students. Several traditional and innovative programs from U.S. and Canadian libraries are described. She concludes with a call for further research related to summer library reading programs.

  12. Reading Strategy: Tackling Reading through Topic and Main Ideas

    ERIC Educational Resources Information Center

    Naidu, Bharathi; Briewin, Marshal; Embi, Mohamed Amin

    2013-01-01

    Reading comprehension is one of the four skills essential in learning English. In a reading class, students tend to read all the information provided in reading materials, but how much do they actually retain? This study explores whether learners use identification of the topic and main ideas as a reading strategy to assist in reading…

  13. 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…

  14. 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…

  15. 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…

  16. Binocular Coordination during Reading and Non-Reading Tasks

    ERIC Educational Resources Information Center

    Kirkby, Julie A.; Webster, Lisa A. D.; Blythe, Hazel I.; Liversedge, Simon P.

    2008-01-01

    The goal of this review is to evaluate the literature on binocular coordination during reading and non-reading tasks in adult, child, and dyslexic populations. The review begins with a description of the basic characteristics of eye movements during reading. Then, reading and non-reading studies investigating binocular coordination are evaluated.…

  17. 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.

  18. 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

  19. Buffering New Information during Reading.

    ERIC Educational Resources Information Center

    Haberlandt, Karl; Graesser, Arthur C.

    1989-01-01

    Describes two subject-paced reading experiments in which word-reading times were collected using the moving-window method. Finds that reading times of content words increase more steeply than reading times for function words. Discusses results in terms of buffer models of reading, the processing of different lexical classes, and hypotheses which…

  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. 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…

  3. 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…

  4. Improving Science Reading Comprehension

    ERIC Educational Resources Information Center

    Johnson, Jill Caton; Martin-Hansen, Lisa

    2005-01-01

    Students in science classrooms are given numerous opportunities to read expository text in a variety of formats and for a variety of purposes. They read to solve a problem, understand the steps in an experiment, gain base knowledge about a concept, answer their own questions, compare their inquiry results with what others have found, expand their…

  5. Reading Visual Texts

    ERIC Educational Resources Information Center

    Werner, Walter

    2002-01-01

    Visual images within social studies textbooks need to be actively "read" by students. Drawing on literature from cultural studies, this article suggests three instructional conditions for teaching students to read visual texts. Agency implies that readers have the (1) authority, (2) opportunity and capacity, and (3) community for engaging in the…

  6. 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.…

  7. Reading Rate and Comprehension

    ERIC Educational Resources Information Center

    Jodai, Hojat

    2011-01-01

    Reading fluency is one of the most important signs of language proficiency both for native and foreign language speakers (Grabe, 2010; Macalister, 2010; Winston, 2010; Hasbrouck, 2008; Rasinski, 2004; Oakley, 2003; Waldman, 1985; Cited in: Sayenko, 2010, Introduction Para 1). This paper is in the area of reading fluency and tries to investigate…

  8. Supporting Older Students' Reading

    ERIC Educational Resources Information Center

    Gutchewsky, Kim; Curran, Joanne

    2012-01-01

    According to a 2010 report by ACT, "Only 31 percent of students are performing at a college-and-career reading level with respect to successfully understanding complex text" (p. 5). This statistic demonstrates what educators know: Middle and high school students face numerous challenges in reading, understanding, connecting to, and remembering…

  9. 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…

  10. 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…

  11. Mappability and read length

    PubMed Central

    Li, Wentian; Freudenberg, Jan

    2014-01-01

    Power-law distributions are the main functional form for the distribution of repeat size and repeat copy number in the human genome. When the genome is broken into fragments for sequencing, the limited size of fragments and reads may prevent an unique alignment of repeat sequences to the reference sequence. Repeats in the human genome can be as long as 104 bases, or 105 − 106 bases when allowing for mismatches between repeat units. Sequence reads from these regions are therefore unmappable when the read length is in the range of 103 bases. With a read length of 1000 bases, slightly more than 1% of the assembled genome, and slightly less than 1% of the 1 kb reads, are unmappable, excluding the unassembled portion of the human genome (8% in GRCh37/hg19). The slow decay (long tail) of the power-law function implies a diminishing return in converting unmappable regions/reads to become mappable with the increase of the read length, with the understanding that increasing read length will always move toward the direction of 100% mappability. PMID:25426137

  12. 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…

  13. 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…

  14. 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…

  15. 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…

  16. Beginning Reading in Italy.

    ERIC Educational Resources Information Center

    Tutolo, Daniel

    Teaching practices in Italy, where teachers combine three different methods for teaching reading, may provide insight into ways to improve methodologies in the United States. The first method is the natural method, which, unlike American methods, teaches reading and writing simultaneously with the emphasis on writing. The teacher writes as…

  17. Atari: Speed Reading.

    ERIC Educational Resources Information Center

    Oliver, Steve

    1983-01-01

    Reviews "Atari Speed Reading" course materials (which include eight units on four cassettes, 200-page workbook, and cassette with pacer/timer program). Indicates that the course is successful in meeting its goal to help average readers double their reading speed and comprehension. (JN)

  18. Why Should I Read?

    ERIC Educational Resources Information Center

    Cleland, Donald L.

    Reading is defined operationally as the cognitive process of perceiving and ordering our environment. As such it is a psychomotor process involving the reorganization of experiences evoked by some stimulus. Thus defined, reading is equated with perception and has several primary functions, including concept building, which begins with perception…

  19. 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)

  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. 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…

  2. Reading Difficulties in Schools.

    ERIC Educational Resources Information Center

    Clark, Margaret M.

    A longitudinal study of reading difficulties in schools in the county of Dunbarton, Scotland, was conducted in 1966. More than 1,500 children were tested after they had completed two years at school and were just over seven years of age. Important results included: about 15% of the children were without any independent reading skill, boys were…

  3. 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…

  4. 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…

  5. Lippincott Basic Reading Program.

    ERIC Educational Resources Information Center

    Monterey Peninsula Unified School District, Monterey, CA.

    This program, included in "Effective Reading Programs...," serves 459 students in grades 1-3 at 15 elementary schools. The program employs a diagnostic-prescriptive approach to instruction in a nongraded setting through the use of the Lippincott Basic Reading program. When a child enters the program, he is introduced to a decoding process that…

  6. 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…

  7. 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…

  8. 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,…

  9. 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…

  10. Speed Listening and Reading.

    ERIC Educational Resources Information Center

    Bradtmueller, Weldon G.

    Compressed speech (speed listening), in which audiotapes are speeded up, is examined in this paper along with its relationship to the reading process. Among the topics discussed first are the close relationship between reading and listening, the rationale behind compressed speech, and the use of compressed speech in business communication, special…

  11. The Psychology of Reading.

    ERIC Educational Resources Information Center

    Rayner, Keith; Pollatsek, Alexander

    Intended for advanced undergraduates and beginning graduate students, this book summarizes and puts into a coherent framework the research on reading processes conducted by cognitive psychologists since the early 1970s. The book focuses on the process of reading: how information is extracted from the printed page and comprehended. Part 1 provides…

  12. 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)

  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. Uninterrupted Sustained Silent Reading.

    ERIC Educational Resources Information Center

    Meyers, Rick

    A study investigated the effect Sustained Silent Reading (SSR) has had on literacy at Estancia High School in California which recently implemented an SSR program. It also examined the role SSR has on language development, comprehension, vocabulary, student attitudes, and its corollary consequence on the development of reading habits. A survey of…

  15. 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…

  16. A Beginning Reading Strategy.

    ERIC Educational Resources Information Center

    Aldridge, Jerry T.; Rust, Debra

    1987-01-01

    First-graders (identified as high-risk for reading difficulties) were taught to read examples of "environmental print" (words on candy wrappers, grocery bags, newspaper advertisements) and were able to identify and write words when logos and supporting detail were removed, indicating that activities using environmental print can effectively…

  17. Reading, Writing, and Art

    ERIC Educational Resources Information Center

    Reist, Kay M.

    2010-01-01

    With No Child Left Behind, schools are cutting extracurricular activities, doing away with aides, and even getting rid of art and physical education so that reading specialists and writing tutors can be hired. But what can the art teachers do to assist in teaching reading and writing skills? The author believes they need to provide their students…

  18. Reading, Writing, and Understanding.

    ERIC Educational Resources Information Center

    Jacobs, Vicki A.

    2002-01-01

    Describes how secondary-school content-area teachers can improve student comprehension of text material by incorporating reading and writing strategies into their classroom instruction. Illustrates relationships among reading, writing, and understanding. Suggests framework for staff-development program. (Contains 14 references.) (PKP)

  19. 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…

  20. 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,…

  1. 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)

  2. 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…

  3. Get That Brain Reading.

    ERIC Educational Resources Information Center

    Lapin, Gloria

    Noting the National Reading Panel's suggestions on assessing and improving children's phonemic awareness, this paper discusses how reading can be improved through think-alouds and visualizations. Comprehension strategies that teachers can model during think-alouds are: activating prior knowledge; building vocabulary; determining importance;…

  4. Techniques of Efficient Reading.

    ERIC Educational Resources Information Center

    Brown, James I.

    To help students develop techniques which lead to maximum reading efficiency, it is first necessary to help them develop a positive self-image. Growing evidence is focusing attention on self-image as the crucial determiner of progress. Poor progess in reading at the elementary level leads to poor self-image, which in turn hinders the student in…

  5. Reading for Laughs

    ERIC Educational Resources Information Center

    Haigh, Gerald

    1978-01-01

    A successful reading program developed and written by a popular entertainer is improbable. Nevertheless, having observed that the books offered to children were not very interesting, Terry Hall, well known to British television audiences as the man behind Lenny the Lion, invested much creative time and finance to produce a basic reading series…

  6. 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…

  7. 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…

  8. 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…

  9. Effects of Sustained Silent Reading on Attitudes toward Reading.

    ERIC Educational Resources Information Center

    Dwyer, Edward J.; Reed, Valda

    1989-01-01

    Examines the effect of sustained silent reading (SSR) on reading attitudes of boys and girls. Finds that boys have a substantially poorer attitude toward reading than girls and that SSR has no demonstrable effect on either sex. (RS)

  10. 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

  11. Integrating Reading and Writing through Extensive Reading

    ERIC Educational Resources Information Center

    Park, Jeongyeon

    2016-01-01

    This study explores whether an extensive reading (ER) approach can enhance L2 learners' writing performance in an English for Academic Purposes context. Two classes were compared in terms of writing improvement after one semester: a 'traditional' writing class primarily focused on writing practice and grammar instruction, and an ER class in which…

  12. Science Fiction: Serious Reading, Critical Reading

    ERIC Educational Resources Information Center

    Zigo, Diane; Moore, Michael T.

    2004-01-01

    Science fiction deserves a greater respect, serious and critical reading and a better place in high school literature classes. Some of the science fiction books by Isaac Asimov, Alfred Bester, Ray Bradbury and Octavia L. Butler and various activities for incorporating science fiction into the English language arts instruction classroom are…

  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. Forecasting Reading Anxiety for Promoting English-Language Reading Performance Based on Reading Annotation Behavior

    ERIC Educational Resources Information Center

    Chen, Chih-Ming; Wang, Jung-Ying; Chen, Yong-Ting; Wu, Jhih-Hao

    2016-01-01

    To reduce effectively the reading anxiety of learners while reading English articles, a C4.5 decision tree, a widely used data mining technique, was used to develop a personalized reading anxiety prediction model (PRAPM) based on individual learners' reading annotation behavior in a collaborative digital reading annotation system (CDRAS). In…

  15. The Relationships between Korean University Students' Reading Attitude, Reading Strategy Use, and Reading Proficiency

    ERIC Educational Resources Information Center

    Kim, Hyangil

    2016-01-01

    This present study investigated the relationships among L2 readers' reading attitude, reading strategy use, and reading proficiency in order to identify patterns caused by individuals' differences. For this study, 153 Korean university students replied to a reading attitude and reading strategy questionnaire. An ANOVA and frequency analysis were…

  16. Elementary Teachers' Beliefs about Reading and Knowledge of Reading Content: Relationships to Decisions about Reading Outcomes.

    ERIC Educational Resources Information Center

    Rupley, William H.; Logan, John W.

    To explore the relationships between teachers' knowledge of basic reading content, beliefs about reading, and decisions about the importance of specified reading learning outcomes, two existing instruments (Knowledge Test of Reading for Elementary Teachers and Propositions About Reading Instruction Inventory) and one researcher-developed…

  17. 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…

  18. 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…

  19. 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.…

  20. How to Direct Directed Reading.

    ERIC Educational Resources Information Center

    Gerlach, Gail J.

    1981-01-01

    Describes how an elementary teacher can plan and manage directed reading, including selecting appropriate children's books, preparing a reading guidesheet for each, and conducting conferences with each student to reinforce reading comprehension and vocabulary development. (SJL)

  1. 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

  2. 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.

  3. 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

  4. The cold reading technique.

    PubMed

    Dutton, D L

    1988-04-15

    For many people, belief in the paranormal derives from personal experience of face-to-face interviews with astrologers, palm readers, aura and Tarot readers, and spirit mediums. These encounters typically involve cold reading, a process in which a reader makes calculated guesses about a client's background and problems and, depending on the reaction, elaborates a reading which seems to the client so uniquely appropriate that it carries with it the illusion of having been produced by paranormal means. The cold reading process is shown to depend initially on the Barnum effect, the tendency for people to embrace generalized personality descriptions as idiosyncratically their own. Psychological research into the Barnum effect is critically reviewed, and uses of the effect by a professional magician are described. This is followed by detailed analysis of the cold reading performances of a spirit medium. Future research should investigate the degree to which cold readers may have convinced themselves that they actually possess psychic or paranormal abilities.

  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. 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)

  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. 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

  9. Develop Choral Reading Skills.

    ERIC Educational Resources Information Center

    Middleton, James A.

    1984-01-01

    The responsibility for helping students attain competence in music-reading skills must fall on choral directors and choral music teachers from middle schools on up. Teachers must teach rhythmic and tonal vocabularies and pitch accuracies. Methods are described. (RM)

  10. 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)

  11. 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…

  12. 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"…

  13. 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…

  14. Relationships of Three Components of Reading Fluency to Reading Comprehension

    ERIC Educational Resources Information Center

    Klauda, Susan Lutz; Guthrie, John T.

    2008-01-01

    This study examined the relationships of 3 levels of reading fluency--the individual word, the syntactic unit, and the whole passage--to reading comprehension among 278 5th graders heterogeneous in reading ability. Hierarchical regression analyses revealed that reading fluency at each level related uniquely to performance on a standardized reading…

  15. 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…

  16. Improving Reading Rates and Comprehension through Timed Repeated Reading

    ERIC Educational Resources Information Center

    Chang, Anna C-S.; Millett, Sonia

    2013-01-01

    Thirteen English as a foreign language students read 26 passages during a 13-week period. Each passage was read five times, and students answered comprehension questions after the first and the fifth reading. Another 13 students read the same number of passages but without repetition and only answered the comprehension questions once. All students…

  17. 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…

  18. 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'…

  19. Strengthening Reading Services through Increasing Provisions for Elementary Reading Centers.

    ERIC Educational Resources Information Center

    Milwaukee Public Schools, WI. Div. of Curriculum and Instruction.

    The purpose of this project was to strengthen and extend reading services by increasing elementary school reading centers in the culturally disadvantaged areas of Milwaukee. A basic tenet of the program was the belief that continuous growth in reading ability is necessary for good academic progress. Besides furnishing plentiful reading materials,…

  20. 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,"…

  1. 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…

  2. 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…

  3. Georgia Reading Excellence Act Demonstration Sites (GA READS). Executive Summary.

    ERIC Educational Resources Information Center

    Georgia State Dept. of Education, Atlanta.

    This executive summary of Georgia Reading Excellence Act Demonstration Sites (GA READS) includes the Reading Excellence overview; Georgia's plan and goals; state activities; a timeline; local activities; and a budget. The overview states that the Reading Excellence Act was authorized to carry out the following purposes: teach every child to read…

  4. INTERNATIONAL READING ASSOCIATION CONFERENCE PROCEEDINGS REPORTS ON ELEMENTARY READING.

    ERIC Educational Resources Information Center

    HARRIS, LARRY A.

    THE IMPORTANT PAPERS PUBLISHED IN THE YEARLY CONFERENCE PROCEEDINGS OF THE INTERNATIONAL READING ASSOCIATION IN ELEMENTARY READING SINCE 1960 ARE LISTED WITH ANNOTATIONS, AND THE COMPLETE TEXT OF EACH PAPER IS PROVIDED. THE 345 PAPERS ARE PRESENTED WITHIN THE FOLLOWING CATEGORIES--(1) THE OBJECTIVES AND GOALS IN READING, (2) READING PROGRAMS, (3)…

  5. 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…

  6. 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…

  7. 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…

  8. Child-Centered Reading Intervention: See, Talk, Dictate, Read, Write!

    ERIC Educational Resources Information Center

    Bastug, Muhammet; Demirtas, Gonca

    2016-01-01

    Poor reading achievement of children in elementary schools has been one of the major concerns in education. The aim of this study is to examine the effectiveness of a child-centered reading intervention in eliminating the reading problems of a student with poor reading achievement. The research was conducted with a student having difficulty in…

  9. 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…

  10. 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.

  11. 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"…

  12. Peer Tutors Improve Reading Comprehension

    ERIC Educational Resources Information Center

    LaGue, Kristina M.; Wilson, Katrina

    2011-01-01

    The influential report "Teaching Children to Read: An Evidenced-Based Assessment of the Scientific Research Literature on Reading and Its Implications for Reading Instruction," published by the National Reading Panel in 2000, presented recommendations for daily literacy instruction in five key areas: phonemic awareness, phonics, fluency,…

  13. 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…

  14. Secondary School Reading: A Bibliography.

    ERIC Educational Resources Information Center

    Huang, Tsokan, Comp.

    The 55 entries in this bibliography represent books published between 1960 and 1979. The entries deal with a variety of topics, including the following: reading success and personality characteristics; reading instruction; participating in secondary school reading; helping the nonreading student; classroom strategies; remedial reading; developing…

  15. 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…

  16. Reading Practices in Singapore Homes.

    ERIC Educational Resources Information Center

    Mee, Cheah Yin; Gan, Linda

    1998-01-01

    Conducted a pilot questionnaire study on Singaporean family reading practices. Found that in the majority of homes, the mother initiated reading of mostly fictional material borrowed from public libraries. Reading aloud to children occurred in about one-third of homes, with direct reading instruction occurring in over two-thirds of families. Found…

  17. Adding Extras for Reading Achievement.

    ERIC Educational Resources Information Center

    Solo, Len

    1999-01-01

    A Cambridge, Massachusetts, alternative public school's basic reading program is a rich combination of whole language and individualized phonics. Other strategies to hook kids on reading include 20-minute recreational reading periods with parent volunteers, a weekly book-bag program, reading buddies, special projects, and community helpers from…

  18. 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;…

  19. 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…

  20. 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…

  1. 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),…

  2. 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…

  3. 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…

  4. Low vision reading with sequential word presentation.

    PubMed

    Rubin, G S; Turano, K

    1994-07-01

    Individuals with scotomas in the center of their visual fields usually read much more slowly than visually impaired individuals without central scotomas. This study determines the extent to which inefficient eye movements could account for this difference. Using a technique described previously [Rubin and Turano (1992) Vision Research, 32, 895-902] text was presented sequentially, one word at a time at the same location in the visual field. Reading performance for rapid serial visual presentation (RSVP) was compared to conventional text presentation (PAGE) in 14 subjects with dense central scotomas (central field loss, CFL) and 9 without central scotomas (noCFL). Reading rates were faster with RSVP compared to PAGE, but CFL subjects improved less (by a factor of 1.5 +/- 0.41) than noCFL subjects (by a factor of 2.1 +/- 0.38). When reading rate (words/min) was converted to average word duration (msec/word) the reduction in word duration for RSVP compared to PAGE text averaged 150 msec for normal subjects, 171 msec for noCFL subjects, and 250 msec for CFL subjects. We hypothesized that the reduction in word duration was attributable to a reduced number of saccades/word. We confirmed this hypothesis by measuring the number of saccades during RSVP and PAGE reading using a scanning laser ophthalmoscope in four subjects with CFL. All of the subjects made fewer saccades during RSVP than PAGE reading (average reduction = 1.3 +/- 0.5 saccades/word). But even with the reduced number of saccades, CFL subjects required longer word durations than noCFL subjects. These results indicate that inefficient eye movements account for only part of the reduction in reading speed caused by CFL. An additional and potentially more important factor is the limited rate at which peripheral retina can perform the pattern decoding tasks required for reading.

  5. Reading interventions with behavioral and social skill outcomes: a synthesis of research.

    PubMed

    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.

  6. 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

  7. Teacher Prediction of Students' Reading Attitudes: An Examination of Teacher Judgment Compared to Student-Peer Judgment in Assessing Student Reading Attitude and Habit.

    ERIC Educational Resources Information Center

    Mikulecky, Larry J.

    Fifteen high school English teachers and 544 students in their classes participated in a study to determine how well teachers assess student reading habits and attitudes and to compare the accuracy of their judgments with those of student-peers. Each student was administered a measure of reading ability and of reading attitude; additional data…

  8. Characterizing Teacher Feedback to Student Miscues During Oral Reading Instruction.

    ERIC Educational Resources Information Center

    Hoffman, James V.; Baker, Christopher J.

    Noting that the verbal interactions that transpire between teacher and student in the classroom setting are central to the instructional process, this paper offers reading teachers a systematic means of examining their own interactive patterns in the context of oral reading instruction. In addition, it provides teachers with a way of inspecting…

  9. 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…

  10. APPLYING AUDIO-LINGUAL (ORAL) TECHNOLOGY TO BEGINNING READING.

    ERIC Educational Resources Information Center

    KING, EVA; KING, PAUL

    THE ROLE OF EDUCATIONAL TECHNOLOGY IN LANGUAGE COMMUNICATION FOR PRIMARY SCHOOL STUDENTS IS DISCUSSED. IT IS KNOWN THAT COMMUNICATION SKILLS DEVELOP IN SEQUENCE, THAT THERE IS A GAP BETWEEN A 6-YEAR- OLD'S LISTENING AND READING SKILLS, AND THAT READING IS A MULTISENSORY SKILLS. IN ADDITION, THERE ARE STRIKING SIMILARITIES IN MASTERING ORAL…

  11. Physical and Psychological Decrements Affecting Reading in the Aged.

    ERIC Educational Resources Information Center

    Wilson, Molly M.

    While reading has been recognized as a potentially useful and enjoyable pastime for the elderly, physical and psychological decrements affect the ability of the elderly to read. As the eyes age, near-point tasks become more difficult. In addition to reduced sensory intake, perceptual changes occur. The central nervous system slows, and data travel…

  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. THE ROLE OF THE READING COORDINATOR.

    ERIC Educational Resources Information Center

    MCNEIL, SHIRLEY

    AN IMPORTANT PART OF THE READING COORDINATOR'S TASK IS CONCERNED WITH CORRECTIVE WORK IN THE LANGUAGE ARTS. COORDINATORS SERVE AS CONSULTANTS TO TEACHERS. IN ADDITION, THEY MAY BE EXPECTED TO WORK WITH SMALL GROUPS OF UNDER-ACHIEVERS TO MOTIVATE AND STIMULATE THEM TO MEET SCHOOL REQUIREMENTS WITH SOME DEGREE OF SUCCESS. WORK MAY INVOLVE GUIDANCE…

  14. Reading to Speak: Integrating Oral Communication Skills

    ERIC Educational Resources Information Center

    Zhang, Yun

    2009-01-01

    According to Ur (1996, 120), "of all the four skills (listening, speaking, reading and writing), speaking seems intuitively the most important." Indeed, whether for business or pleasure, a primary motivation to learn a second language is to be able to converse with speakers of that language. However, in addition to being an important skill,…

  15. 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…

  16. 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,…

  17. 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,…

  18. Comparing Recreational Reading Levels with Reading Levels from an Informal Reading Inventory.

    ERIC Educational Resources Information Center

    Smith, Lawrence L.; Joyner, C. Rosanne

    1990-01-01

    Compares second grade and fifth grade students' recreational reading levels (when students self-select library books for recreation reading) in relation to independent, instructional, and frustration levels as determined with an informal reading inventory. Concludes that recreational reading levels should not be viewed as synonymous with…

  19. What Are Teenagers Reading? Adolescent Fiction Reading Habits and Reading Choices

    ERIC Educational Resources Information Center

    Hopper, Rosemary

    2005-01-01

    What are adolescents choosing to read? This is an important question because of potential divergence between school students' reading interests and reading expectations in school. This article considers the findings from a study of the reading over one week in May 2002 of 707 school students aged between 11 and 15, undertaken in 30 schools in the…

  20. 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.…