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Sample records for acid open reading

  1. Results with Open Court Reading.

    ERIC Educational Resources Information Center

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

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

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

    PubMed

    Sundaram, Arunkumar; Grant, Chris M

    2014-04-01

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

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

    PubMed Central

    Fitzmaurice, A M; Kolattukudy, P E

    1997-01-01

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

  4. 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…

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

    ERIC Educational Resources Information Center

    Datta, Saroj; Macdonald-Ross, Michael

    2002-01-01

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

  6. 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

  7. 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…

  8. 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

  9. Translational control of Nrf2 within the open reading frame

    PubMed Central

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

    2013-01-01

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

  10. 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.

  11. 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

  12. 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

  13. 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…

  14. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

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

  15. 19 CFR 145.3 - Opening of letter class mail; reading of correspondence prohibited.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

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

  16. 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.

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

    PubMed Central

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

    1989-01-01

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

  18. 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.

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

    PubMed Central

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

    1984-01-01

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

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

    PubMed Central

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

    2010-01-01

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

  1. 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…

  2. 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…

  3. 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.

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

    PubMed

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

    2016-02-01

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

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

    PubMed Central

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

    1999-01-01

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

  6. Acid mine treatment with open limestone channels

    SciTech Connect

    Ziemkiewicz, P.F.; Brant, D.L.; Skousen, J.G.

    1996-12-31

    Acid mine drainage (AMD) is often associated with mining of pyritic coal and metal deposits. Typical AMD associated with coal mines in the eastern US can have acidity and iron concentrations ranging from the teens to the thousands of mg/l. Aluminum and manganese can be present in concentrations ranging from zero to the low hundreds of mg/l. Much attention has been devoted to developing inexpensive, limestone (LS)-based systems for treating AMID with little or no maintenance. However, LS tends to coat with metal hydroxides when exposed to AMID in an oxidized state, a process known as {open_quotes}armoring{close_quotes}. It is generally assumed that once armored, LS ceases to neutralize acid. Another problem is that the hydroxides tend to settle into plug the pore spaces in LS beds forcing water to move around rather than through the LS. While both are caused by the precipitation of metal hydroxides, armoring and plugging are two different problems. Plugging of LS pores can be avoided by maintaining a high flushing rate through the LS bed. Armoring, however, occurs regardless of water velocity. This study investigated the influence of armoring on LS solubility and the implications of armoring and plugging on the construction of open (oxidizing) LS channels for treating AMD. We evaluated the AMID treatment performance of armored and unarmored LS in oxidizing environments both in laboratory and field studies.

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

    ERIC Educational Resources Information Center

    Haskett, G. J.; Lenfestey, W.

    1975-01-01

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

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

    PubMed

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

    2009-11-01

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

  9. 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.…

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

    PubMed

    Steigele, Stephan; Nieselt, Kay

    2005-01-01

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

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

    PubMed Central

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

    1988-01-01

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

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

    PubMed

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

    2000-09-01

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

  13. 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

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

    PubMed

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

    2001-04-01

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

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

    PubMed

    Miksch, G

    1994-12-01

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

  16. 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

  17. A 5-month open study with long-chain polyunsaturated fatty acids in dyslexia.

    PubMed

    Lindmark, Lars; Clough, Peter

    2007-12-01

    This open pilot study investigated effects of a docosahexaenoic acid (DHA)-rich supplement on learning ability in a group of 20 dyslexic children in Sweden. Children formally diagnosed as dyslexic took eight capsules per day of a long-chain polyunsaturated fatty acid (LC-PUFA) supplement containing high-DHA fish oil and evening primrose oil. Subjective assessments by the children and their parents were completed at baseline and 6, 12, and 20 weeks after supplementation. Quantitative evaluation by word-chain test was completed before and after 4 months of supplementation to measure word decoding (speed of reading) and letter decoding (motoric-perceptual speed). Subjective parent and child assessments showed increasing numbers of positive responders over time in reading speed, general schoolwork, and overall perceived benefit. Significant improvements were observed in reading speed and motor-perceptual velocity. Thirteen of 17 children had a significant improvement on the word-chain test (P < .04). Reading speed improved by 60% from 1.76 +/- 0.29 before the study to 2.82 +/- 0.36 after supplementation (P < .01 by Wilcoxon sign test). Motoric-perceptual velocity improved by 23% from a stanine value of 3.76 +/- 0.42 to 4.65 +/- 0.66 after supplementation (P < .05 by Wilcoxon sign test). Thus LC-PUFA supplementation for 5 months provides positive and clear beneficial effect on variables usually impaired by dyslexia. PMID:18158838

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

    PubMed

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

    2016-03-15

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

  19. 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

  20. 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

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

    PubMed Central

    Mueller, Niklaus H.; Gilden, Don

    2013-01-01

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

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

    PubMed

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

    2010-01-01

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

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

    PubMed Central

    Jin, S; Ishimoto, K; Lory, S

    1994-01-01

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

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

    PubMed Central

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

    1990-01-01

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

  5. 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

  6. 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.

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

    PubMed

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

    2016-03-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2015-03-01

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

  10. 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.

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

    PubMed Central

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

    1996-01-01

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

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

    PubMed

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

    2004-01-01

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

  13. 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

  14. 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

  15. 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.

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

    PubMed Central

    Behrens, Ralf; Hayles, Jacky; Nurse, Paul

    2000-01-01

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

  17. 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

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

    SciTech Connect

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

    1996-06-01

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

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

    PubMed Central

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

    2006-01-01

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

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

    PubMed

    Stanley, J; Latham, J R

    1992-09-01

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

  1. 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...

  2. 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…

  3. 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…

  4. Ultrasensitive visual read-out of nucleic acids using electrocatalytic fluid displacement.

    PubMed

    Besant, Justin D; Das, Jagotamoy; Burgess, Ian B; Liu, Wenhan; Sargent, Edward H; Kelley, Shana O

    2015-01-01

    Diagnosis of disease outside of sophisticated laboratories urgently requires low-cost, user-friendly devices. Disposable, instrument-free testing devices are used for home and physician office testing, but are limited in applicability to a small class of highly abundant analytes. Direct, unambiguous visual read-out is an ideal way to deliver a result on a disposable device; however, existing strategies that deliver appropriate sensitivity produce only subtle colour changes. Here we report a new approach, which we term electrocatalytic fluid displacement, where a molecular binding event is transduced into an electrochemical current, which drives the electrodeposition of a metal catalyst. The catalyst promotes bubble formation that displaces a fluid to reveal a high contrast change. We couple the read-out system to a nanostructured microelectrode and demonstrate direct visual detection of 100 fM DNA in 10 min. This represents the lowest limit of detection of nucleic acids reported using high contrast visual read-out. PMID:25901450

  5. Ultrasensitive visual read-out of nucleic acids using electrocatalytic fluid displacement

    PubMed Central

    Besant, Justin D.; Das, Jagotamoy; Burgess, Ian B.; Liu, Wenhan; Sargent, Edward H.; Kelley, Shana O.

    2015-01-01

    Diagnosis of disease outside of sophisticated laboratories urgently requires low-cost, user-friendly devices. Disposable, instrument-free testing devices are used for home and physician office testing, but are limited in applicability to a small class of highly abundant analytes. Direct, unambiguous visual read-out is an ideal way to deliver a result on a disposable device; however, existing strategies that deliver appropriate sensitivity produce only subtle colour changes. Here we report a new approach, which we term electrocatalytic fluid displacement, where a molecular binding event is transduced into an electrochemical current, which drives the electrodeposition of a metal catalyst. The catalyst promotes bubble formation that displaces a fluid to reveal a high contrast change. We couple the read-out system to a nanostructured microelectrode and demonstrate direct visual detection of 100 fM DNA in 10 min. This represents the lowest limit of detection of nucleic acids reported using high contrast visual read-out. PMID:25901450

  6. 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

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

    PubMed

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

    2016-08-01

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

  8. 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.

  9. 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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-03-31

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

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

    PubMed Central

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

    1996-01-01

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

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

    PubMed Central

    Lagunoff, M; Randall, G; Roizman, B

    1996-01-01

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

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

    PubMed Central

    Cross, Frederick R.

    2015-01-01

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

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

    PubMed

    Cross, Frederick R

    2016-02-01

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

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

    PubMed

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

    2002-06-01

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

  17. 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

  18. 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

  19. 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,…

  20. 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

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

    PubMed Central

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

    1988-01-01

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

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

    ERIC Educational Resources Information Center

    Ortiz, Rose Katz

    1996-01-01

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

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  4. 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…

  5. 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,…

  6. 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

  7. 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

  8. 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

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

    ERIC Educational Resources Information Center

    Kling, Martin

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

  10. PREVENTION OF ACID MINE DRAINAGE GENERATION FROM OPEN-PIT MINE HIGHWALLS

    EPA Science Inventory



    Exposed, open pit mine highwalls contribute significantly to the production of acid mine

    drainage (AMD) thus causing environmental concerns upon closure of an operating mine. Available information on the generation of AMD from open-pit mine highwalls is very limit...

  11. 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…

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

    PubMed Central

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

    2015-01-01

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

  13. Catalyzed ring-opening polymerization of epoxidized soybean oil by hydrated and anhydrous fluoroantimonic acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ring-opening polymerization of epoxidized soybean oil (ESO) catalyzed by the super acid, fluroantimonic acid hexahydrate (HSbF6-6H2O), and the anhydrous form (HSbF6) in ethyl acetate was conducted in an effort to develop useful biodegradable polymers. The resulting polymerized ESO (SA-RPESO and SAA-...

  14. 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,…

  15. 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...

  16. 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

  17. 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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    2007-01-01

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

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

    PubMed

    Barbosa, Cristina; Romão, Luísa

    2014-05-01

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

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

    PubMed Central

    Untiveros, Milton; Olspert, Allan; Artola, Katrin

    2016-01-01

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

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

    PubMed

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

    2016-09-01

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

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

    PubMed Central

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

    2000-01-01

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

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

    PubMed

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

    2007-08-01

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

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

    PubMed Central

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

    2013-01-01

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

  7. 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

  8. Graphene oxide as an acid catalyst for the room temperature ring opening of epoxides.

    PubMed

    Dhakshinamoorthy, Amarajothi; Alvaro, Mercedes; Concepción, Patricia; Fornés, Vicente; Garcia, Hermenegildo

    2012-06-01

    The minute amount of hydrogen sulfate groups introduced into the graphene oxide (GO) obtained by Hummers oxidation of graphite renders this material as a highly efficient, recyclable acid catalyst for the ring opening of epoxides with methanol and other primary alcohols as nucleophile and solvent. PMID:22534622

  9. Triarylsulfonium hexafluorophosphate salts as photoactivated acidic catalysts for ring-opening polymerisation.

    PubMed

    Barker, Ian A; Dove, Andrew P

    2013-02-11

    Triarylsulfonium hexafluorophosphate salts were shown to be effective catalysts for the ring-opening polymerisation of various cyclic monomers under UV irradiation. A dual basic/acidic catalytic system demonstrated the potential for UV-triggered formation of poly(δ-valerolactone)-b-poly(L-lactide)-b-poly(δ-valerolactone) in a 'one-pot' reaction. PMID:23283246

  10. MINE WASTE TECHNOLOGY PROGRAM PREVENTION OF ACID MINE DRAINAGE GENERATION FROM OPEN-PIT HIGHWALLS

    EPA Science Inventory

    This document summarizes the results of Mine Waste Technology Program Activity III, Project 26, Prevention of Acid Mine Drainage Generation from Open-Pit Highwalls. The intent of this project was to obtain performance data on the ability of four technologies to prevent the gener...

  11. Sulfuric acid as a catalyst for ring-opening of biobased bis-epoxides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vegetable oils can be relatively and easily transformed into bio-based epoxides. Because of this, the acid-catalyzed epoxide ring-opening has been explored for the preparation of bio-based lubricants and polymers. Detailed model studies are carried out only with mono-epoxide made from methyl oleate,...

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

    PubMed Central

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

    2000-01-01

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

  13. 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

  14. 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

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

    PubMed

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

    1996-09-01

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

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

    PubMed

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

    1996-06-15

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

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

    ERIC Educational Resources Information Center

    Cartwright, Hyla D.

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

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

    PubMed

    McNabb, D S; Courtney, R J

    1992-05-01

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

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

    PubMed

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

    2001-11-01

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

  20. Teaching Reading

    ERIC Educational Resources Information Center

    Day, Richard R.

    2013-01-01

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

  1. Phosphatidic acid inhibits blue light-induced stomatal opening via inhibition of protein phosphatase 1 [corrected].

    PubMed

    Takemiya, Atsushi; Shimazaki, Ken-ichiro

    2010-08-01

    Stomata open in response to blue light under a background of red light. The plant hormone abscisic acid (ABA) inhibits blue light-dependent stomatal opening, an effect essential for promoting stomatal closure in the daytime to prevent water loss. However, the mechanisms and molecular targets of this inhibition in the blue light signaling pathway remain unknown. Here, we report that phosphatidic acid (PA), a phospholipid second messenger produced by ABA in guard cells, inhibits protein phosphatase 1 (PP1), a positive regulator of blue light signaling, and PA plays a role in stimulating stomatal closure in Vicia faba. Biochemical analysis revealed that PA directly inhibited the phosphatase activity of the catalytic subunit of V. faba PP1 (PP1c) in vitro. PA inhibited blue light-dependent stomatal opening but did not affect red light- or fusicoccin-induced stomatal opening. PA also inhibited blue light-dependent H(+) pumping and phosphorylation of the plasma membrane H(+)-ATPase. However, PA did not inhibit the autophosphorylation of phototropins, blue light receptors for stomatal opening. Furthermore, 1-butanol, a selective inhibitor of phospholipase D, which produces PA via hydrolysis of phospholipids, diminished the ABA-induced inhibition of blue light-dependent stomatal opening and H(+) pumping. We also show that hydrogen peroxide and nitric oxide, which are intermediates in ABA signaling, inhibited the blue light responses of stomata and that 1-butanol diminished these inhibitions. From these results, we conclude that PA inhibits blue light signaling in guard cells by PP1c inhibition, accelerating stomatal closure, and that PP1 is a cross talk point between blue light and ABA signaling pathways in guard cells. PMID:20498335

  2. Growth responses of 53 open-pollinated loblolly pine families to ozone and acid rain

    SciTech Connect

    McLaughlin, S.B.; Edwards, N.T.; Hanson, P.J.

    1994-03-01

    Field exposures of 9950 containerized 12-wk-old loblolly pine (Pinustaeda L.) seedlings representing 53 commercially important, open-pollinated families were conducted to evaluate individual and interactive effects of acid rain and O{sub 3} on growth response. A 36-plot field research facility comprised of 33 open-top chambers and three open plots was used to test effects of five O{sub 3} levels that included ambient (A) and seasonally integrated levels that were 0.53, 1.10, 1.58, or 2.15 times ambient. Individual effects of three levels of simulated acid rain (pH 3.3, 4.5, and 5.2) as well as their interaction with O{sub 3} at 0.53A, 1.58A, and 2.15A levels were also included. Exposure to ambient air reduced average growth in height (26%), diameter (5%), and volume (14%) compared with growth of seedlings exposed to a 47% lower dose in charcoal filtered (CF) air. Responses to increasing O{sub 3} above ambient levels varied widely between families, became increasingly inhibitory at the highest O{sub 3} levels, but did not significantly exceed growth reductions found in ambient air. Diameter growth was reduced in most families by all levels of O{sub 3} addition. Acid rain caused a general stimulation of height growth at ambient levels (pH 4.5), while both height and diameter growth were reduced at a mean pH of 3.3. Significant antagonism between rainfall acidity and O{sub 3} effects on height and biomass increment was detected with increasing pollutant concentrations. Ozone reduced root/shoot biomass in most families, while acid rain did not. 51 refs., 6 figs., 6 tabs.

  3. Difference in abscisic acid perception mechanisms between closure induction and opening inhibition of stomata.

    PubMed

    Yin, Ye; Adachi, Yuji; Ye, Wenxiu; Hayashi, Maki; Nakamura, Yoshimasa; Kinoshita, Toshinori; Mori, Izumi C; Murata, Yoshiyuki

    2013-10-01

    Abscisic acid (ABA) induces stomatal closure and inhibits light-induced stomatal opening. The mechanisms in these two processes are not necessarily the same. It has been postulated that the ABA receptors involved in opening inhibition are different from those involved in closure induction. Here, we provide evidence that four recently identified ABA receptors (PYRABACTIN RESISTANCE1 [PYR1], PYRABACTIN RESISTANCE-LIKE1 [PYL1], PYL2, and PYL4) are not sufficient for opening inhibition in Arabidopsis (Arabidopsis thaliana). ABA-induced stomatal closure was impaired in the pyr1/pyl1/pyl2/pyl4 quadruple ABA receptor mutant. ABA inhibition of the opening of the mutant's stomata remained intact. ABA did not induce either the production of reactive oxygen species and nitric oxide or the alkalization of the cytosol in the quadruple mutant, in accordance with the closure phenotype. Whole cell patch-clamp analysis of inward-rectifying K(+) current in guard cells showed a partial inhibition by ABA, indicating that the ABA sensitivity of the mutant was not fully impaired. ABA substantially inhibited blue light-induced phosphorylation of H(+)-ATPase in guard cells in both the mutant and the wild type. On the other hand, in a knockout mutant of the SNF1-related protein kinase, srk2e, stomatal opening and closure, reactive oxygen species and nitric oxide production, cytosolic alkalization, inward-rectifying K(+) current inactivation, and H(+)-ATPase phosphorylation were not sensitive to ABA. PMID:23946352

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

    ERIC Educational Resources Information Center

    Langham, Martha A.; Peterson, Nancy M.

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

  5. 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…

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

    PubMed Central

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

    2014-01-01

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

  7. 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.

  8. 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)…

  9. [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…

  10. Acid digestion of geological and environmental samples using open-vessel focused microwave digestion.

    PubMed

    Taylor, Vivien F; Toms, Andrew; Longerich, Henry P

    2002-01-01

    The application of open vessel focused microwave acid digestion is described for the preparation of geological and environmental samples for analysis using inductively coupled plasma-mass spectrometry (ICP-MS). The method is compared to conventional closed-vessel high pressure methods which are limited in the use of HF to break down silicates. Open-vessel acid digestion more conveniently enables the use of HF to remove Si from geological and plant samples as volatile SiF4, as well as evaporation-to-dryness and sequential acid addition during the procedure. Rock reference materials (G-2 granite, MRG-1 gabbros, SY-2 syenite, JA-1 andesite, and JB-2 and SRM-688 basalts) and plant reference materials (BCR and IAEA lichens, peach leaves, apple leaves, Durham wheat flour, and pine needles) were digested with results comparable to conventional hotplate digestion. The microwave digestion method gave poor results for granitic samples containing refractory minerals, however fusion was the preferred method of preparation for these samples. Sample preparation time was reduced from several days, using conventional hotplate digestion method, to one hour per sample using our microwave method. PMID:11936112

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

    PubMed

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

    2011-02-01

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

  12. 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…

  13. Improvement of Physicochemical Characteristics of Monoepoxide Linoleic Acid Ring Opening for Biolubricant Base Oil

    PubMed Central

    Salimon, Jumat; Salih, Nadia; Abdullah, Bashar Mudhaffar

    2011-01-01

    For environmental reasons, a new class of environmentally acceptable and renewable biolubricant based on vegetable oils is available. In this study, oxirane ring opening reaction of monoepoxide linoleic acid (MEOA) was done by nucleophilic addition of oleic acid (OA) with using p-toluene sulfonic acid (PTSA) as a catalyst for synthesis of 9(12)-hydroxy-10(13)-oleoxy-12(9)-octadecanoic acid (HYOOA) and the physicochemical properties of the resulted HYOOA are reported to be used as biolubricant base oils. Optimum conditions of the experiment using D-optimal design to obtain high yield% of HYOOA and lowest OOC% were predicted at OA/MEOA ratio of 0.30 : 1 (w/w), PTSA/MEOA ratio of 0.50 : 1 (w/w), reaction temperature at 110°C, and reaction time at 4.5 h. The results showed that an increase in the chain length of the midchain ester resulted in the decrease of pour point (PP) −51°C, increase of viscosity index (VI) up to 153, and improvement in oxidative stability (OT) to 180.94°C. PMID:22131799

  14. Insights into the Mechanism of Pore Opening of Acid-sensing Ion Channel 1A*

    PubMed Central

    Tolino, Lindsey A.; Okumura, Sora; Kashlan, Ossama B.; Carattino, Marcelo D.

    2011-01-01

    Acid-sensing ion channels (ASICs) are trimeric cation channels that undergo activation and desensitization in response to extracellular acidification. The underlying mechanism coupling proton binding in the extracellular region to pore gating is unknown. Here we probed the reactivity toward methanethiosulfonate (MTS) reagents of channels with cysteine-substituted residues in the outer vestibule of the pore of ASIC1a. We found that positively-charged MTS reagents trigger pore opening of G428C. Scanning mutagenesis of residues in the region preceding the second transmembrane spanning domain indicated that the MTSET-modified side chain of Cys at position 428 interacts with Tyr-424. This interaction was confirmed by double-mutant cycle analysis. Strikingly, Y424C-G428C monomers were associated by intersubunit disulfide bonds and were insensitive to MTSET. Despite the spatial constraints introduced by these intersubunit disulfide bonds in the outer vestibule of the pore, Y424C-G428C transitions between the resting, open, and desensitized states in response to extracellular acidification. This finding suggests that the opening of the ion conductive pathway involves coordinated rotation of the second transmembrane-spanning domains. PMID:21388961

  15. 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

  16. A Randomised, Open-label, Comparative Study of Tranexamic Acid Microinjections and Tranexamic Acid with Microneedling in Patients with Melasma

    PubMed Central

    Budamakuntla, Leelavathy; Loganathan, Eswari; Suresh, Deepak Hurkudli; Shanmugam, Sharavana; Suryanarayan, Shwetha; Dongare, Aparna; Venkataramiah, Lakshmi Dammaningala; Prabhu, Namitha

    2013-01-01

    Background: Melasma is a common cause of facial hyperpigmentation with significant cosmetic deformity. Although several treatment modalities are available, none is satisfactory. Aim: To compare the therapeutic efficacy and safety of tranexamic acid (TA) microinjections versus tranexamic acid with microneedling in melasma. Materials and Methods: This is a prospective, randomised, open-label study with a sample size of 60; 30 in each treatment arms. Thirty patients were administered with localised microinjections of TA in one arm, and other 30 with TA with microneedling. The procedure was done at monthly intervals (0, 4 and 8 weeks) and followed up for three consecutive months. Clinical images were taken at each visit including modified Melasma Area Severity Index MASI scoring, patient global assessment and physician global assessment to assess the clinical response. Results: In the microinjection group, there was 35.72% improvement in the MASI score compared to 44.41% in the microneedling group, at the end of third follow-up visit. Six patients (26.09%) in the microinjections group, as compared to 12 patients (41.38%) in the microneedling group, showed more than 50% improvement. However, there were no major adverse events observed in both the treatment groups. Conclusions: On the basis of these results, TA can be used as potentially a new, effective, safe and promising therapeutic agent in melasma. The medication is easily available and affordable. Better therapeutic response to treatment in the microneedling group could be attributed to the deeper and uniform delivery of the medication through microchannels created by microneedling. PMID:24163529

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    1993-01-01

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

  19. Docosahexaenoic Acid for Reading, Cognition and Behavior in Children Aged 7–9 Years: A Randomized, Controlled Trial (The DOLAB Study)

    PubMed Central

    Richardson, Alexandra J.; Burton, Jennifer R.; Sewell, Richard P.; Spreckelsen, Thees F.; Montgomery, Paul

    2012-01-01

    Background Omega-3 fatty acids are dietary essentials, and the current low intakes in most modern developed countries are believed to contribute to a wide variety of physical and mental health problems. Evidence from clinical trials indicates that dietary supplementation with long-chain omega-3 may improve child behavior and learning, although most previous trials have involved children with neurodevelopmental disorders such as attention-deficit/hyperactivity disorder (ADHD) or developmental coordination disorder (DCD). Here we investigated whether such benefits might extend to the general child population. Objectives To determine the effects of dietary supplementation with the long-chain omega-3 docosahexaenoic acid (DHA) on the reading, working memory, and behavior of healthy schoolchildren. Design Parallel group, fixed-dose, randomized, double-blind, placebo-controlled trial (RCT). Setting Mainstream primary schools in Oxfordshire, UK (n = 74). Participants Healthy children aged 7–9 years initially underperforming in reading (≤33rd centile). 1376 invited, 362 met study criteria. Intervention 600 mg/day DHA (from algal oil), or taste/color matched corn/soybean oil placebo. Main Outcome Measures Age-standardized measures of reading, working memory, and parent- and teacher-rated behavior. Results ITT analyses showed no effect of DHA on reading in the full sample, but significant effects in the pre-planned subgroup of 224 children whose initial reading performance was ≤20th centile (the target population in our original study design). Parent-rated behavior problems (ADHD-type symptoms) were significantly reduced by active treatment, but little or no effects were seen for either teacher-rated behaviour or working memory. Conclusions DHA supplementation appears to offer a safe and effective way to improve reading and behavior in healthy but underperforming children from mainstream schools. Replication studies are clearly warranted, as such children are known

  20. 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…

  1. 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…

  2. The importance of acid-base management for cardiac and cerebral preservation during open heart operations.

    PubMed

    Swan, H

    1984-04-01

    at that time limit should be used. Probably the best general management of the body for H-CPB is alpha-stat, which preserves biologic neutrality. The uncorrected analyzer reads pH 7.4 and Pco2 at any temperature. However, the need for preservation of the hypoxic heart is overwhelming and, thus, the best acid-base management for cardiac hypothermic operations is significant respiratory alkalosis. The most appropriate sites for the collection of blood samples for gas analysis and measuring temperatures were discussed; "body temperature" is the most unreliable parameter measured. The major characteristics of an "ideal" cardiopreservative solution were described.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:6424251

  3. 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

  4. Efficacy of tranexamic acid as compared to aprotinin in open heart surgery in children

    PubMed Central

    Muthialu, Nagarajan; Balakrishnan, Soundaravalli; Sundar, Rajani; Muralidharan, Srinivasan

    2015-01-01

    Background: Coagulopathy is a major issue in children undergoing high-risk pediatric cardiac surgery. Use of anti-fibrinolytics is well documented in adults, but recently there are questions raised about safety and effectiveness of their use on routine use. Tranexamic acid is a potent anti-fibrinolytic, but its role is not fully understood in children. This study aims to study the benefits tranexamic acid in controlling postoperative bleeding in pediatric cardiac surgical patients. Methods and Results: Fifty consecutive children who underwent cardiac surgery were randomized prospectively to receive either aprotinin (Group A; n = 24) or tranexamic acid (Group B; n = 26) from September 2009 to February 2010 were studied. Primary end points were early mortality, postoperative drainage, reoperation for bleeding and complications. Mean age and body weight was smaller in Group A (Age: 48.55 vs. 64.73 months; weight 10.75 vs. 14.80 kg) respectively. Group A had more cyanotic heart disease than Group B (87.5% vs. 76.92%). Mean cardiopulmonary bypass time (144.33 vs. 84.34 min) and aortic cross-clamp time (78.5 vs. 41.46 min) were significantly higher in group A. While the blood and products usage was significantly higher in Group A, there was no difference in indexed postoperative drainage in first 4, 8 and 12 h and postoperative coagulation parameters. Mean C-reactive protein was less in Group A than B and renal dysfunction was seen more in Group A (25% vs. 7.6%). Mortality in Group A was 16.66% and 7.6% in Group B. Conclusion: Anti-fibrinolytics have a definitive role in high-risk children who undergo open-heart surgery. Tranexamic acid is as equally effective as aprotinin with no additional increase in morbidity or mortality. Ultramini Abstract: Coagulopathy has been a major issue in pediatric cardiac surgery, and anti-fibrinolytics have been used fairly regularly in various settings. This study aims to evaluate the efficacy of tranexamic acid as compared against that

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  6. A Simple and Efficient Synthesis of an Acid-labile Polyphosphoramidate by Organobase-catalyzed Ring-Opening Polymerization and Transformation to Polyphosphoester Ionomers by Acid Treatment

    PubMed Central

    Zhang, Shiyi; Wang, Hai; Shen, Yuefei; Zhang, Fuwu; Seetho, Kellie; Zou, Jiong; Taylor, John-Stephen A.; Dove, Andrew P.; Wooley, Karen L.

    2013-01-01

    The direct synthesis of an acid-labile polyphosphoramidate by organobase-catalyzed ring-opening polymerization and an overall two-step preparation of polyphosphodiester ionomers (PPEI) by acid-assisted cleavage of the phosphoramidate bonds along the backbone of the polyphosphoramidate were developed in this study. The ultrafast organobase-catalyzed ring-opening polymerization of a cyclic phospholane methoxyethyl amidate monomer initiated by benzyl alcohol allowed for the preparation of well-defined polyphosphoramidates (PPA) with predictable molecular weights, narrow molecular weight distributions (PDI<1.10), and well-defined chain ends. Cleavage of the acid-labile phosphoramidate bonds on the polyphosphoramidate repeat units was evaluated under acidic conditions over a pH range of 1–5, and the complete hydrolysis produced polyphosphodiesters. The thermal properties of the resulting polyphosphoester ionomer acid and polyphosphoester ionomer sodium salt exhibited significant thermal stability. The parent PPA and both forms of the PPEIs showed low cytotoxicities toward HeLa cells and RAW 264.7 mouse macrophage cells. The synthetic methodology developed here has enriched the family of water-soluble polymers prepared by rapid and convenient organobase-catalyzed ring-opening polymerizations and straightforward chemical medication reactions, which are designed to be hydrolytically degradable and have promise for numerous biomedical and other applications. PMID:23997276

  7. Open Stomata 1 (OST1) is limiting in abscisic acid responses of Arabidopsis guard cells.

    PubMed

    Acharya, Biswa R; Jeon, Byeong Wook; Zhang, Wei; Assmann, Sarah M

    2013-12-01

    Open Stomata 1 (OST1) (SnRK2.6 or SRK2E), a serine/threonine protein kinase, is a positive regulator in abscisic acid (ABA)-mediated stomatal response, but OST1-regulation of K(+) and Ca(2+) currents has not been studied directly in guard cells and it is unknown whether OST1 activity is limiting in ABA-mediated stomatal responses. We employed loss-of-function and gain-of-function approaches to study native ABA responses of Arabidopsis guard cells. We performed stomatal aperture bioassays, patch clamp analyses and reactive oxygen species (ROS) measurements. ABA inhibition of inward K(+) channels and light-induced stomatal opening are reduced in ost1 mutants while transgenic plants overexpressing OST1 show ABA hypersensitivity in these responses. ost1 mutants are insensitive to ABA-induced stomatal closure, regulation of slow anion currents, Ca(2+) -permeable channel activation and ROS production while OST1 overexpressing lines are hypersensitive for these responses, resulting in accelerated stomatal closure in response to ABA. Overexpression of OST1 in planta in the absence of ABA application does not affect basal apertures or ion currents. Moreover, we demonstrate the physical interaction of OST1 with the inward K(+) channel KAT1, the anion channel SLAC1, and the NADPH oxidases AtrbohD and AtrbohF. Our findings support OST1 as a critical limiting component in ABA regulation of stomatal apertures, ion channels and NADPH oxidases in Arabidopsis guard cells. PMID:24033256

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

    PubMed

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

    2015-08-01

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

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

    PubMed Central

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

    2015-01-01

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

  10. Hepatitis C Virus Frameshift/Alternate Reading Frame Protein Suppresses Interferon Responses Mediated by Pattern Recognition Receptor Retinoic-Acid-Inducible Gene-I

    PubMed Central

    Park, Seung Bum; Seronello, Scott; Mayer, Wasima; Ojcius, David M.

    2016-01-01

    Hepatitis C virus (HCV) actively evades host interferon (IFN) responses but the mechanisms of how it does so are not completely understood. In this study, we present evidence for an HCV factor that contributes to the suppression of retinoic-acid-inducible gene-I (RIG-I)-mediated IFN induction. Expression of frameshift/alternate reading frame protein (F/ARFP) from HCV -2/+1 frame in Huh7 hepatoma cells suppressed type I IFN responses stimulated by HCV RNA pathogen-associated molecular pattern (PAMP) and poly(IC). The suppression occurred independently of other HCV factors; and activation of interferon stimulated genes, TNFα, IFN-λ1, and IFN-λ2/3 was likewise suppressed by HCV F/ARFP. Point mutations in the full-length HCV sequence (JFH1 genotype 2a strain) were made to introduce premature termination codons in the -2/+1 reading frame coding for F/ARFP while preserving the original reading frame, which enhanced IFNα and IFNβ induction by HCV. The potentiation of IFN response by the F/ARFP mutations was diminished in Huh7.5 cells, which already have a defective RIG-I, and by decreasing RIG-I expression in Huh7 cells. Furthermore, adding F/ARFP back via trans-complementation suppressed IFN induction in the F/ARFP mutant. The F/ARFP mutants, on the other hand, were not resistant to exogenous IFNα. Finally, HCV-infected human liver samples showed significant F/ARFP antibody reactivity, compared to HCV-uninfected control livers. Therefore, HCV F/ARFP likely cooperates with other viral factors to suppress type I and III IFN induction occurring through the RIG-I signaling pathway. This study identifies a novel mechanism of pattern recognition receptor modulation by HCV and suggests a biological function of the HCV alternate reading frame in the modulation of host innate immunity. PMID:27404108

  11. 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

  12. 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…

  13. Reading Rituals

    ERIC Educational Resources Information Center

    Manzo, Kathleen Kennedy

    2007-01-01

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

  14. Re-treatment of relapsed Paget's disease of bone with zoledronic acid: results from an open-label study.

    PubMed

    Reid, Ian R; Brown, Jacques P; Levitt, Naomi; Román Ivorra, José A; Bachiller-Corral, Javier; Ross, Ian L; Su, Guoqin; Antunez-Flores, Oscar; Aftring, R Paul

    2013-01-01

    Six patients from the phase 3 trials of zoledronic acid in Paget's disease, who had received zoledronic acid initially and had subsequently relapsed, were entered into an open re-treatment study. Following re-treatment, each patient reached similar absolute nadirs of serum alkaline phosphatase to those recorded after their first dose. No significant adverse events were reported. It is concluded that, while re-treatment of Paget's disease with zoledronic acid is rarely needed, it is safe and effective, with no evidence of treatment resistance based on this small cohort. PMID:24422139

  15. Chiral ligand-exchange separation and determination of malic acid enantiomers in apple juice by open-tubular capillary electrochromatography.

    PubMed

    Aydoğan, Cemil; Karakoç, Veyis; Denizli, Adil

    2015-11-15

    This study describes the application of an open tubular capillary column for chiral ligand-exchange separation and determination of malic acid enantiomers in apple juice by open-tubular capillary electrochromatography (OT-CEC). The open tubular column was prepared by in-situ grafting polymerization of 3-chloro-2-hydroxypropyl methacrylate (HPMA-Cl) and followed by L-Histidine (L-His) modification. L-His was used as a chiral ligand-exchange selector and copper (II) as a central ion. The electrochromatographic characterization of the open tubular column was performed with the use of thiourea as an electroosmotic flow (EOF) marker. Factors affecting electrochromatographic enantioseparation of malic acid were also studied. The running buffer conditions for optimum enantioseparation of malic acid were found to be ACN/5.0mM CuSO4, 20.0mM (NH4)2SO4 (60/40%, v/v) adjusted to pH 3.0. The separation and determination of the enantiomers of malic acid in the apple juice solution diluted 10- to 40-folds were successfully achieved. PMID:25977007

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

    PubMed Central

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

    2014-01-01

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

  17. 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

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

    PubMed

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

    2016-06-01

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

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

    PubMed Central

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

    1990-01-01

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

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

    PubMed

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

    1990-04-01

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

  1. 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

  2. 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

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

    SciTech Connect

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

    1988-11-01

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

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

    PubMed Central

    Hemmings-Mieszczak, M; Hohn, T

    1999-01-01

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

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

    PubMed Central

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

    1998-01-01

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

  6. 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

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

    PubMed

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

    2011-06-01

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

  9. 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…

  10. 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

  11. Openings.

    PubMed

    Selwyn, Peter A

    2015-01-01

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

  12. Multicultural Reading

    ERIC Educational Resources Information Center

    Veltze, Linda

    2004-01-01

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

  13. 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...

  14. 19 CFR 103.1 - Public reading rooms.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

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

  15. Auxin Biosynthesis: Are the Indole-3-Acetic Acid and Phenylacetic Acid Biosynthesis Pathways Mirror Images?1[OPEN

    PubMed Central

    Nichols, David S.; Smith, Jason; Chourey, Prem S.; McAdam, Erin L.; Quittenden, Laura

    2016-01-01

    The biosynthesis of the main auxin in plants (indole-3-acetic acid [IAA]) has been elucidated recently and is thought to involve the sequential conversion of Trp to indole-3-pyruvic acid to IAA. However, the pathway leading to a less well studied auxin, phenylacetic acid (PAA), remains unclear. Here, we present evidence from metabolism experiments that PAA is synthesized from the amino acid Phe, via phenylpyruvate. In pea (Pisum sativum), the reverse reaction, phenylpyruvate to Phe, is also demonstrated. However, despite similarities between the pathways leading to IAA and PAA, evidence from mutants in pea and maize (Zea mays) indicate that IAA biosynthetic enzymes are not the main enzymes for PAA biosynthesis. Instead, we identified a putative aromatic aminotransferase (PsArAT) from pea that may function in the PAA synthesis pathway. PMID:27208245

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

    PubMed Central

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

    2000-01-01

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

  17. 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

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

    PubMed Central

    Wing, B A; Huang, E S

    1995-01-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed Central

    Suzuki, Masahiro; Hosoba, Eriko; Matsui, Mari

    2014-01-01

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

  1. 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

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

    PubMed Central

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

    2011-01-01

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

  3. Efficacy of Folic Acid Supplementation in Autistic Children Participating in Structured Teaching: An Open-Label Trial

    PubMed Central

    Sun, Caihong; Zou, Mingyang; Zhao, Dong; Xia, Wei; Wu, Lijie

    2016-01-01

    Autism spectrum disorders (ASD) are recognized as a major public health issue. Here, we evaluated the effects of folic acid intervention on methylation cycles and oxidative stress in autistic children enrolled in structured teaching. Sixty-six autistic children enrolled in this open-label trial and participated in three months of structured teaching. Forty-four children were treated with 400 μg folic acid (two times/daily) for a period of three months during their structured teaching (intervention group), while the remaining 22 children were not given any supplement for the duration of the study (control group). The Autism Treatment Evaluation Checklist (ATEC) and Psychoeducational Profile-third edition (PEP-3) were measured at the beginning and end of the treatment period. Folic acid, homocysteine, and glutathione metabolism in plasma were measured before and after treatment in 29 autistic children randomly selected from the intervention group and were compared with 29 age-matched unaffected children (typical developmental group). The results illustrated folic acid intervention improved autism symptoms towards sociability, cognitive verbal/preverbal, receptive language, and affective expression and communication. Furthermore, this treatment also improved the concentrations of folic acid, homocysteine, and normalized glutathione redox metabolism. Folic acid supplementation may have a certain role in the treatment of children with autism. PMID:27338456

  4. Nitro-Fatty Acids in Plant Signaling: Nitro-Linolenic Acid Induces the Molecular Chaperone Network in Arabidopsis1[OPEN

    PubMed Central

    Padilla, María N.; Begara-Morales, Juan C.; Luque, Francisco; Melguizo, Manuel; Fierro-Risco, Jesús; Peñas-Sanjuán, Antonio; Valderrama, Raquel

    2016-01-01

    Nitro-fatty acids (NO2-FAs) are the product of the reaction between reactive nitrogen species derived of nitric oxide (NO) and unsaturated fatty acids. In animal systems, NO2-FAs are considered novel signaling mediators of cell function based on a proven antiinflammatory response. Nevertheless, the interaction of NO with fatty acids in plant systems has scarcely been studied. Here, we examine the endogenous occurrence of nitro-linolenic acid (NO2-Ln) in Arabidopsis and the modulation of NO2-Ln levels throughout this plant’s development by mass spectrometry. The observed levels of this NO2-FA at picomolar concentrations suggested its role as a signaling effector of cell function. In fact, a transcriptomic analysis by RNA-seq technology established a clear signaling role for this molecule, demonstrating that NO2-Ln was involved in plant defense response against different abiotic-stress conditions, mainly by inducing heat shock proteins and supporting a conserved mechanism of action in both animal and plant defense processes. Bioinformatics analysis revealed that NO2-Ln was also involved in the response to oxidative stress conditions, mainly depicted by H2O2, reactive oxygen species, and oxygen-containing compound responses, with a high induction of ascorbate peroxidase expression. Closely related to these results, NO2-Ln levels significantly rose under several abiotic-stress conditions such as wounding or exposure to salinity, cadmium, and low temperature, thus validating the outcomes found by RNA-seq technology. Jointly, to our knowledge, these are the first results showing the endogenous presence of NO2-Ln in Arabidopsis (Arabidopsis thaliana) and supporting the strong signaling role of these molecules in the defense mechanism against different abiotic-stress situations. PMID:26628746

  5. Comparative nutrition and metabolism: Explication of open questions with emphasis on protein and amino acids

    PubMed Central

    Baker, David H.

    2005-01-01

    The 20th century saw numerous important discoveries in the nutritional sciences. Nonetheless, many unresolved questions still remain. Fifteen questions dealing with amino acid nutrition and metabolism are posed in this review. The first six deal with the functionality of sulfur amino acids (methionine and cysteine) and related compounds. Other unresolved problems that are discussed include priorities of use for amino acids having multiple functions; interactions among lysine, niacin and tryptophan; amino acid contributions to requirements from gut biosynthesis; the potential for gluconeogenesis to divert amino acids away from protein synthesis; the unique nutritional and metabolic idiosyncrasies of feline species, with emphasis on arginine; controversies surrounding human amino acid requirements; and the potential for maternal diet to influence sex ratio of offspring. PMID:16326801

  6. β-Lactam Ring Opening: A Useful Entry to Amino Acids and Relevant Nitrogen-Containing Compounds

    NASA Astrophysics Data System (ADS)

    Palomo, C.; Oiarbide, M.

    The main strategies for the ring opening of β-lactams by chemical means are described. The discovery of each approach is put into context, sometimes in connection to processes occurring in biological systems, and the synthetic opportunities each approach offers are shown. Thus, this β-lactam route affords a number of synthetically relevant building-blocks, including α-amino acids, β-amino acids, their derived peptides, and other nitrogen containing heterocycles and open chain molecules. The content, which encompases references to initial work, further major development, and the most relevant recent literature contributions, is categorized according to the ring bond cleavaged (N 1-C 2, C 2-C 3, C 3 -C 4 , N 1-C 4), to finish with ring opening strategies leading to large heterocyclic compounds. Within each category, distinction has been made according to the type of nucleophilic agent employed, principally O-, N-, and C-nucleophiles. Also, a variety of applications of the strategy to the synthesis of interesting target compounds are shown.

  7. 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

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

    PubMed Central

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

    2014-01-01

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

  9. Coexpressing Escherichia coli Cyclopropane Synthase with Sterculia foetida Lysophosphatidic Acid Acyltransferase Enhances Cyclopropane Fatty Acid Accumulation1[W][OPEN

    PubMed Central

    Yu, Xiao-Hong; Prakash, Richa Rawat; Sweet, Marie; Shanklin, John

    2014-01-01

    Cyclopropane fatty acids (CPAs) are desirable as renewable chemical feedstocks for the production of paints, plastics, and lubricants. Toward our goal of creating a CPA-accumulating crop, we expressed nine higher plant cyclopropane synthase (CPS) enzymes in the seeds of fad2fae1 Arabidopsis (Arabidopsis thaliana) and observed accumulation of less than 1% CPA. Surprisingly, expression of the Escherichia coli CPS gene resulted in the accumulation of up to 9.1% CPA in the seed. Coexpression of a Sterculia foetida lysophosphatidic acid acyltransferase (SfLPAT) increases CPA accumulation up to 35% in individual T1 seeds. However, seeds with more than 9% CPA exhibit wrinkled seed morphology and reduced size and oil accumulation. Seeds with more than 11% CPA exhibit strongly decreased seed germination and establishment, and no seeds with CPA more than 15% germinated. That previous reports suggest that plant CPS prefers the stereospecific numbering (sn)-1 position whereas E. coli CPS acts on sn-2 of phospholipids prompted us to investigate the preferred positions of CPS on phosphatidylcholine (PC) and triacylglycerol. Unexpectedly, in planta, E. coli CPS acts primarily on the sn-1 position of PC; coexpression of SfLPAT results in the incorporation of CPA at the sn-2 position of lysophosphatidic acid. This enables a cycle that enriches CPA at both sn-1 and sn-2 positions of PC and results in increased accumulation of CPA. These data provide proof of principle that CPA can accumulate to high levels in transgenic seeds and sets the stage for the identification of factors that will facilitate the movement of CPA from PC into triacylglycerol to produce viable seeds with additional CPA accumulation. PMID:24204024

  10. Read Arizona.

    ERIC Educational Resources Information Center

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

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

  11. 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…

  12. 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;…

  13. Repeated Reading.

    ERIC Educational Resources Information Center

    Moyer, Sandra B.

    1982-01-01

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

  14. 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.…

  15. Reading Aloud

    ERIC Educational Resources Information Center

    Delo, Lynda

    2008-01-01

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

  16. Reading Programs.

    ERIC Educational Resources Information Center

    Au, Kathryn

    2001-01-01

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

  17. 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…

  18. 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)

  19. WRINKLED1 Rescues Feedback Inhibition of Fatty Acid Synthesis in Hydroxylase-Expressing Seeds1[OPEN

    PubMed Central

    Browse, John

    2016-01-01

    Previous attempts at engineering Arabidopsis (Arabidopsis thaliana) to produce seed oils containing hydroxy fatty acids (HFA) have resulted in low yields of HFA compared with the native castor (Ricinus communis) plant and caused undesirable effects, including reduced total oil content. Recent studies have led to an understanding of problems involved in the accumulation of HFA in oils of transgenic plants, which include metabolic bottlenecks and a decrease in the rate of fatty acid synthesis. Focusing on engineering the triacylglycerol assembly mechanisms led to modest increases in the HFA content of seed oil, but much room for improvement still remains. We hypothesized that engineering fatty acid synthesis in the plastids to increase flux would facilitate enhanced total incorporation of fatty acids, including HFA, into seed oil. The transcription factor WRINKLED1 (WRI1) positively regulates the expression of genes involved in fatty acid synthesis and controls seed oil levels. We overexpressed Arabidopsis WRI1 in seeds of a transgenic line expressing the castor fatty acid hydroxylase. The proportion of HFA in the oil, the total HFA per seed, and the total oil content of seeds increased to an average of 20.9%, 1.26 µg, and 32.2%, respectively, across five independent lines, compared with 17.6%, 0.83 µg, and 27.9%, respectively, for isogenic segregants. WRI1 and WRI1-regulated genes involved in fatty acid synthesis were up-regulated, providing for a corresponding increase in the rate of fatty acid synthesis. PMID:27208047

  20. Ring-opening polymerization of epoxidized soybean oil catalyzed by the superacid, Fluroantimonic acid hexahydrate (HSbF6-6H2O)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ring-opening polymerization of epoxidized soybean oil (ESO) catalyzed by the super acid, fluroantimonic acid hexahydrate (HSbF6-6H2O), in ethyl acetate was conducted. The resulting polymers, SA-RPESO, were characterized using infrared spectroscopy, differential scanning calorimetry, thermogravimetri...

  1. Effects of pantethine, cysteamine and pantothenic acid on open-field behavior and brain catecholamines in rats.

    PubMed

    Vécsei, L; Widerlöv, E; Alling, C

    1989-01-01

    Cysteamine (1.95 mM/kg) markedly decreased the locomotor, rearing and grooming activities, as well as the number of defecation boluses in an open-field test. An equimolar dose of pantethine reduced the locomotor activity to a lesser extent, but has the same potency in decreasing the number of defecation boluses, whereas pantothenic acid did not affect the behavior of the rats. Cysteamine, and to a lesser extent pantethine, reduced the noradrenaline and increased the dopamine and DOPAC concentrations in the hypothalamus. Pantothenic acid itself did not influence the hypothalamic catecholamine concentrations. These results suggest that the lower efficacy of pantethine compared to cysteamine on both behavioral and neurochemical parameters is probably due to a rate-limiting activity of the enzyme pantetheinase in the conversion of pantetheine to cysteamine. PMID:2619420

  2. Novel human D-amino acid oxidase inhibitors stabilize an active-site lid-open conformation

    PubMed Central

    Terry-Lorenzo, Ryan T.; Chun, Lawrence E.; Brown, Scott P.; Heffernan, Michele L. R.; Fang, Q. Kevin; Orsini, Michael A.; Pollegioni, Loredano; Hardy, Larry W.; Spear, Kerry L.; Large, Thomas H.

    2014-01-01

    The NMDAR (N-methyl-D-aspartate receptor) is a central regulator of synaptic plasticity and learning and memory. hDAAO (human D-amino acid oxidase) indirectly reduces NMDAR activity by degrading the NMDAR co-agonist D-serine. Since NMDAR hypofunction is thought to be a foundational defect in schizophrenia, hDAAO inhibitors have potential as treatments for schizophrenia and other nervous system disorders. Here, we sought to identify novel chemicals that inhibit hDAAO activity. We used computational tools to design a focused, purchasable library of compounds. After screening this library for hDAAO inhibition, we identified the structurally novel compound, ‘compound 2’ [3-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)propanoic acid], which displayed low nM hDAAO inhibitory potency (Ki=7 nM). Although the library was expected to enrich for compounds that were competitive for both D-serine and FAD, compound 2 actually was FAD uncompetitive, much like canonical hDAAO inhibitors such as benzoic acid. Compound 2 and an analog were independently co-crystalized with hDAAO. These compounds stabilized a novel conformation of hDAAO in which the active-site lid was in an open position. These results confirm previous hypotheses regarding active-site lid flexibility of mammalian D-amino acid oxidases and could assist in the design of the next generation of hDAAO inhibitors. PMID:25001371

  3. Lewis Acid Catalyzed Ring-opening Polymerization of Epoxidized Soybean Oil in Liquid Carbon Dioxide

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ring-opening polymerization of epoxidized soybean oil (ESO) catalyzed by boron trifluoride diethyl etherate (BF3•OEt2), in liquid carbon dioxide, was conducted in an effort to develop useful biobased biodegradable polymers. The resulting polymers (RPESO) were characterized by FTIR spectroscopy, diff...

  4. 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…

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

    ERIC Educational Resources Information Center

    Waycott, Jenny

    2002-01-01

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

  6. The restricted DH gene reading frame usage in the expressed human antibody repertoire is selected based upon its amino acid content.

    PubMed

    Benichou, Jennifer; Glanville, Jacob; Prak, Eline T Luning; Azran, Roy; Kuo, Tracy C; Pons, Jaume; Desmarais, Cindy; Tsaban, Lea; Louzoun, Yoram

    2013-06-01

    The Ab repertoire is not uniform. Some variable, diversity, and joining genes are used more frequently than others. Nonuniform usage can result from the rearrangement process, or from selection. To study how the Ab repertoire is selected, we analyzed one part of diversity generation that cannot be driven by the rearrangement mechanism: the reading frame usage of DH genes. We have used two high-throughput sequencing methodologies, multiple subjects and advanced algorithms to measure the DH reading frame usage in the human Ab repertoire. In most DH genes, a single reading frame is used predominantly, and inverted reading frames are practically never observed. The choice of a single DH reading frame is not limited to a single position of the DH gene. Rather, each DH gene participates in rearrangements of differing CDR3 lengths, restricted to multiples of three. In nonproductive rearrangements, there is practically no reading frame bias, but there is still a striking absence of inversions. Biases in DH reading frame usage are more pronounced, but also exhibit greater interindividual variation, in IgG(+) and IgA(+) than in IgM(+) B cells. These results suggest that there are two developmental checkpoints of DH reading frame selection. The first occurs during VDJ recombination, when inverted DH genes are usually avoided. The second checkpoint occurs after rearrangement, once the BCR is expressed. The second checkpoint implies that DH reading frames are subjected to differential selection. Following these checkpoints, clonal selection induces a host-specific DH reading frame usage bias. PMID:23630353

  7. 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…

  8. Acidic calcium stores open for business: expanding the potential for intracellular Ca2+ signaling

    PubMed Central

    Patel, Sandip; Docampo, Roberto

    2010-01-01

    Changes in cytosolic calcium concentration are crucial for a variety of cellular processes in all cells. It has long been appreciated that calcium is stored and released from intracellular calcium stores such as the endoplasmic reticulum. However, emerging evidence indicates that calcium is also dynamically regulated by a seemingly disparate collection of acidic organelles. Here, we review the defining features of these acidic calcium stores and highlight recent progress in understanding the mechanisms of uptake and release of calcium from these stores. We also examine the nature of calcium buffering within the stores and summarize the physiological and patho-physiological significance of these ubiquitous organelles in calcium signaling. PMID:20303271

  9. Scanning electrochemical microscopy: surface interrogation of adsorbed hydrogen and the open circuit catalytic decomposition of formic acid at platinum.

    PubMed

    Rodríguez-López, Joaquín; Bard, Allen J

    2010-04-14

    The surface interrogation mode of scanning electrochemical microscopy (SECM) is extended to the in situ quantification of adsorbed hydrogen, H(ads), at polycrystalline platinum. The methodology consists of the production, at an interrogator electrode, of an oxidized species that is able to react with H(ads) on the Pt surface and report the amounts of this adsorbate through the SECM feedback response. The technique is validated by comparison to the electrochemical underpotential deposition (UPD) of hydrogen on Pt. We include an evaluation of electrochemical mediators for their use as oxidizing reporters for adsorbed species at platinum; a notable finding is the ability of tetramethyl-p-phenylenediamine (TMPD) to oxidize (interrogate) H(ads) on Pt at low pH (0.5 M H(2)SO(4) or 1 M HClO(4)) and with minimal background effects. As a case study, the decomposition of formic acid (HCOOH) in acidic media at open circuit on Pt was investigated. Our results suggest that formic acid decomposes at the surface of unbiased Pt through a dehydrogenation route to yield H(ads) at the Pt surface. The amount of H(ads) depended on the open circuit potential (OCP) of the Pt electrode at the time of interrogation; at a fixed concentration of HCOOH, a more negative OCP yielded larger amounts of H(ads) until reaching a coulomb limiting coverage close to 1 UPD monolayer of H(ads). The introduction of oxygen into the cell shifted the OCP to more positive potentials and reduced the quantified H(ads); furthermore, the system was shown to be chemically reversible, as several interrogations could be run consecutively and reproducibly regardless of the path taken to reach a given OCP. PMID:20225806

  10. On the Opening of Thick Walled Elastic Tubes: A Fluid-Structure Model for Acid Reflux

    NASA Astrophysics Data System (ADS)

    Ghosh, Sudip; Kahrilas, Peter

    2005-11-01

    A coupled fluid-structure mathematical model was developed to quantify rapid opening of thick-walled elastic tubes, a phenomenon underlying biological flows such as gastroesophageal reflux disease (GERD). The wall was modeled using non-linear finite deformation theory to predict space-time radial distention of an axisymmetric tube with luminal fluid flow. Anisotropic azimuthal and longitudinal muscle-induced stresses were incorporated, and interstitial material properties were assumed isotropic and linearly elastic. Fluid flow was modeled using lubrication theory with inertial correction. Opening and flow were driven by a specified inflow pressure and zero pressure gradient was specified at outflow. No-slip and surface force balance were applied at the fluid-wall interface. Viscoelasticity was modeled with ad hoc damping and the evolution of the tube geometry was predicted at mid-layer. A potentially important discovery was made when applied to studies of initiation of opening with GERD: while material stiffness is of minor consequence, small changes in resting lumen distension (˜2 mm diameter) may be a sensitive distinguishing feature of the disease.

  11. Reading Research in Hungary.

    ERIC Educational Resources Information Center

    Kamaras, Istvan; Nagy, Attila

    1981-01-01

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

  12. 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…

  13. 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…

  14. MATE Transporter-Dependent Export of Hydroxycinnamic Acid Amides[OPEN

    PubMed Central

    Eschen-Lippold, Lennart; Gorzolka, Karin; Matern, Andreas; Marillonnet, Sylvestre; Böttcher, Christoph; Rosahl, Sabine

    2016-01-01

    The ability of Arabidopsis thaliana to successfully prevent colonization by Phytophthora infestans, the causal agent of late blight disease of potato (Solanum tuberosum), depends on multilayered defense responses. To address the role of surface-localized secondary metabolites for entry control, droplets of a P. infestans zoospore suspension, incubated on Arabidopsis leaves, were subjected to untargeted metabolite profiling. The hydroxycinnamic acid amide coumaroylagmatine was among the metabolites secreted into the inoculum. In vitro assays revealed an inhibitory activity of coumaroylagmatine on P. infestans spore germination. Mutant analyses suggested a requirement of the p-coumaroyl-CoA:agmatine N4-p-coumaroyl transferase ACT for the biosynthesis and of the MATE transporter DTX18 for the extracellular accumulation of coumaroylagmatine. The host plant potato is not able to efficiently secrete coumaroylagmatine. This inability is overcome in transgenic potato plants expressing the two Arabidopsis genes ACT and DTX18. These plants secrete agmatine and putrescine conjugates to high levels, indicating that DTX18 is a hydroxycinnamic acid amide transporter with a distinct specificity. The export of hydroxycinnamic acid amides correlates with a decreased ability of P. infestans spores to germinate, suggesting a contribution of secreted antimicrobial compounds to pathogen defense at the leaf surface. PMID:26744218

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

    PubMed

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

    2015-10-01

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

  16. Hyperspectral analysis for qualitative and quantitative features related to acid mine drainage at a remediated open-pit mine

    NASA Astrophysics Data System (ADS)

    Davies, G.; Calvin, W. M.

    2015-12-01

    The exposure of pyrite to oxygen and water in mine waste environments is known to generate acidity and the accumulation of secondary iron minerals. Sulfates and secondary iron minerals associated with acid mine drainage (AMD) exhibit diverse spectral properties in the ultraviolet, visible and near-infrared regions of the electromagnetic spectrum. The use of hyperspectral imagery for identification of AMD mineralogy and contamination has been well studied. Fewer studies have examined the impacts of hydrologic variations on mapping AMD or the unique spectral signatures of mine waters. Open-pit mine lakes are an additional environmental hazard which have not been widely studied using imaging spectroscopy. A better understanding of AMD variation related to climate fluctuations and the spectral signatures of contaminated surface waters will aid future assessments of environmental contamination. This study examined the ability of multi-season airborne hyperspectral data to identify the geochemical evolution of substances and contaminant patterns at the Leviathan Mine Superfund site. The mine is located 24 miles southeast of Lake Tahoe and contains remnant tailings piles and several AMD collection ponds. The objectives were to 1) distinguish temporal changes in mineralogy at a the remediated open-pit sulfur mine, 2) identify the absorption features of mine affected waters, and 3) quantitatively link water spectra to known dissolved iron concentrations. Images from NASA's AVIRIS instrument were collected in the spring, summer, and fall seasons for two consecutive years at Leviathan (HyspIRI campaign). Images had a spatial resolution of 15 meters at nadir. Ground-based surveys using the ASD FieldSpecPro spectrometer and laboratory spectral and chemical analysis complemented the remote sensing data. Temporal changes in surface mineralogy were difficult to distinguish. However, seasonal changes in pond water quality were identified. Dissolved ferric iron and chlorophyll

  17. Reducing Isozyme Competition Increases Target Fatty Acid Accumulation in Seed Triacylglycerols of Transgenic Arabidopsis1[OPEN

    PubMed Central

    van Erp, Harrie; Shockey, Jay; Zhang, Meng; Adhikari, Neil D.; Browse, John

    2015-01-01

    One goal of green chemistry is the production of industrially useful fatty acids (FAs) in crop plants. We focus on hydroxy fatty acids (HFAs) and conjugated polyenoic FAs (α-eleostearic acids [ESAs]) using Arabidopsis (Arabidopsis thaliana) as a model. These FAs are found naturally in seed oils of castor (Ricinus communis) and tung tree (Vernicia fordii), respectively, and used for the production of lubricants, nylon, and paints. Transgenic oils typically contain less target FA than that produced in the source species. We hypothesized that competition between endogenous and transgenic isozymes for substrates limits accumulation of unique FAs in Arabidopsis seeds. This hypothesis was tested by introducing a mutation in Arabidopsis diacylglycerol acyltransferase1 (AtDGAT1) in a line expressing castor FA hydroxylase and acyl-Coenzyme A:RcDGAT2 in its seeds. This led to a 17% increase in the proportion of HFA in seed oil. Expression of castor phospholipid:diacylglycerol acyltransferase 1A in this line increased the proportion of HFA by an additional 12%. To determine if our observations are more widely applicable, we investigated if isozyme competition influenced production of ESA. Expression of tung tree FA conjugase/desaturase in Arabidopsis produced approximately 7.5% ESA in seed lipids. Coexpression of VfDGAT2 increased ESA levels to approximately 11%. Overexpression of VfDGAT2 combined with suppression of AtDGAT1 increased ESA accumulation to 14% to 15%. Our results indicate that isozyme competition is a limiting factor in the engineering of unusual FAs in heterologous plant systems and that reduction of competition through mutation and RNA suppression may be a useful component of seed metabolic engineering strategies. PMID:25739701

  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 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…

  1. 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…

  2. Moss Chloroplasts Are Surrounded by a Peptidoglycan Wall Containing D-Amino Acids[OPEN

    PubMed Central

    Hirano, Takayuki; Tanidokoro, Koji; Shimizu, Yasuhiro; Kawarabayasi, Yutaka; Ohshima, Toshihisa; Sato, Momo; Tadano, Shinji; Ishikawa, Hayato; Takio, Susumu; Takechi, Katsuaki; Takano, Hiroyoshi

    2016-01-01

    It is believed that the plastids in green plants lost peptidoglycan (i.e., a bacterial cell wall-containing d-amino acids) during their evolution from an endosymbiotic cyanobacterium. Although wall-like structures could not be detected in the plastids of green plants, the moss Physcomitrella patens has the genes required to generate peptidoglycan (Mur genes), and knocking out these genes causes defects in chloroplast division. Here, we generated P. patens knockout lines (∆Pp-ddl) for a homolog of the bacterial peptidoglycan-synthetic gene encoding d-Ala:d-Ala ligase. ∆Pp-ddl had a macrochloroplast phenotype, similar to other Mur knockout lines. The addition of d-Ala-d-Ala (DA-DA) to the medium suppressed the appearance of giant chloroplasts in ∆Pp-ddl, but the addition of l-Ala-l-Ala (LA-LA), DA-LA, LA-DA, or d-Ala did not. Recently, a metabolic method for labeling bacterial peptidoglycan was established using ethynyl-DA-DA (EDA-DA) and click chemistry to attach an azide-modified fluorophore to the ethynyl group. The ∆Pp-ddl line complemented with EDA-DA showed that moss chloroplasts are completely surrounded by peptidoglycan. Our findings strongly suggest that the moss plastids have a peptidoglycan wall containing d-amino acids. By contrast, no plastid phenotypes were observed in the T-DNA tagged ddl mutant lines of Arabidopsis thaliana. PMID:27325639

  3. Open fermentative production of fuel ethanol from food waste by an acid-tolerant mutant strain of Zymomonas mobilis.

    PubMed

    Ma, Kedong; Ruan, Zhiyong; Shui, Zongxia; Wang, Yanwei; Hu, Guoquan; He, Mingxiong

    2016-03-01

    The aim of present study was to develop a process for open ethanol fermentation from food waste using an acid-tolerant mutant of Zymomonas mobilis (ZMA7-2). The mutant showed strong tolerance to acid condition of food waste hydrolysate and high ethanol production performance. By optimizing fermentation parameters, ethanol fermentation with initial glucose concentration of 200 g/L, pH value around 4.0, inoculum size of 10% and without nutrient addition was considered as best conditions. Moreover, the potential of bench scales fermentation and cell reusability was also examined. The fermentation in bench scales (44 h) was faster than flask scale (48 h), and the maximum ethanol concentration and ethanol yield (99.78 g/L, 0.50 g/g) higher than that of flask scale (98.31 g/L, 0.49 g/g). In addition, the stable cell growth and ethanol production profile in five cycles successive fermentation was observed, indicating the mutant was suitable for industrial ethanol production. PMID:26744803

  4. Open-tubular electrochromatographic chiral separation of amino acids using an organic nanocrystals immobilized capillary.

    PubMed

    Kitagawa, Fumihiko; Sudaki, Hiroshi; Sueyoshi, Kenji; Otsuka, Koji

    2013-01-01

    The preparation of cinchonidine (CCND) nanocrystals and their immobilization onto the inner surface of a fused silica capillary was investigated for use in the enantioseparation by capillary electrochromatography. The CCND nanocrystals were prepared by an emulsion method that utilizes crystal growth in an oil-in-water emulsion without a stabilizer. As a result, white-colored aqueous dispersions of organic nanoparticles were obtained. SEM images showed that the prepared CCND nanocrystals were from 300 to 700 nm in size. When the obtained dispersion was introduced into a poly(diallyldimethylammonium chloride) (PDDAC) coated capillary, the nanocrystals were strongly adsorbed onto the inner surface due to an electrostatic interaction between cationic PDDAC and the negatively charged organic nanocrystals. In CCND nanocrystals coated capillary, CEC enantioseparations of racemic amino acids were successfully achieved. The reproducibilities of the detection times were acceptable with a relative standard deviation of less than 7%, indicating that stable nanocrystal coating could be obtained by our proposed method. PMID:23303094

  5. Abscisic Acid Is a General Negative Regulator of Arabidopsis Axillary Bud Growth1[OPEN

    PubMed Central

    Yao, Chi; Finlayson, Scott A.

    2015-01-01

    Branching is an important process controlled by intrinsic programs and by environmental signals transduced by a variety of plant hormones. Abscisic acid (ABA) was previously shown to mediate Arabidopsis (Arabidopsis thaliana) branching responses to the ratio of red light (R) to far-red light (FR; an indicator of competition) by suppressing bud outgrowth from lower rosette positions under low R:FR. However, the role of ABA in regulating branching more generally was not investigated. This study shows that ABA restricts lower bud outgrowth and promotes correlative inhibition under both high and low R:FR. ABA was elevated in buds exhibiting delayed outgrowth resulting from bud position and low R:FR and decreased in elongating buds. ABA was reduced in lower buds of hyperbranching mutants deficient in auxin signaling (AUXIN RESISTANT1), MORE AXILLARY BRANCHING (MAX) signaling (MAX2), and BRANCHED1 (BRC1) function, and partial suppression of branch elongation in these mutants by exogenous ABA suggested that ABA may act downstream of these components. Bud BRC1 expression was not altered by exogenous ABA, consistent with a downstream function for ABA. However, the expression of genes encoding the indole-3-acetic acid (IAA) biosynthesis enzyme TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1, the auxin transporter PIN-FORMED1, and the cell cycle genes CYCLIN A2;1 and PROLIFERATING CELL NUCLEAR ANTIGEN1 in buds was suppressed by ABA, suggesting that it may inhibit bud growth in part by suppressing elements of the cell cycle machinery and bud-autonomous IAA biosynthesis and transport. ABA was found to suppress bud IAA accumulation, thus confirming this aspect of its action. PMID:26149576

  6. 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.…

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

    SciTech Connect

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

    1993-06-01

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

  8. Reversible Burst of Transcriptional Changes during Induction of Crassulacean Acid Metabolism in Talinum triangulare1[OPEN

    PubMed Central

    Winter, Klaus

    2016-01-01

    Drought tolerance is a key factor for agriculture in the 21st century as it is a major determinant of plant survival in natural ecosystems as well as crop productivity. Plants have evolved a range of mechanisms to cope with drought, including a specialized type of photosynthesis termed Crassulacean acid metabolism (CAM). CAM is associated with stomatal closure during the day as atmospheric CO2 is assimilated primarily during the night, thus reducing transpirational water loss. The tropical herbaceous perennial species Talinum triangulare is capable of transitioning, in a facultative, reversible manner, from C3 photosynthesis to weakly expressed CAM in response to drought stress. The transcriptional regulation of this transition has been studied. Combining mRNA-Seq with targeted metabolite measurements, we found highly elevated levels of CAM-cycle enzyme transcripts and their metabolic products in T. triangulare leaves upon water deprivation. The carbohydrate metabolism is rewired to reduce the use of reserves for growth to support the CAM-cycle and the synthesis of compatible solutes. This large-scale expression dataset of drought-induced CAM demonstrates transcriptional regulation of the C3–CAM transition. We identified candidate transcription factors to mediate this photosynthetic plasticity, which may contribute in the future to the design of more drought-tolerant crops via engineered CAM. PMID:26530316

  9. Rate Motifs Tune Auxin/Indole-3-Acetic Acid Degradation Dynamics1[OPEN

    PubMed Central

    Moss, Britney L.; Mao, Haibin; Guseman, Jessica M.; Hinds, Thomas R.; Hellmuth, Antje; Kovenock, Marlies; Noorassa, Anisa; Lanctot, Amy; Villalobos, Luz Irina A. Calderón; Zheng, Ning; Nemhauser, Jennifer L.

    2015-01-01

    Ubiquitin-mediated protein degradation is a common feature in diverse plant cell signaling pathways; however, the factors that control the dynamics of regulated protein turnover are largely unknown. One of the best-characterized families of E3 ubiquitin ligases facilitates ubiquitination of auxin (aux)/indole-3-acetic acid (IAA) repressor proteins in the presence of auxin. Rates of auxin-induced degradation vary widely within the Aux/IAA family, and sequences outside of the characterized degron (the minimum region required for auxin-induced degradation) can accelerate or decelerate degradation. We have used synthetic auxin degradation assays in yeast (Saccharomyces cerevisiae) and in plants to characterize motifs flanking the degron that contribute to tuning the dynamics of Aux/IAA degradation. The presence of these rate motifs is conserved in phylogenetically distant members of the Arabidopsis (Arabidopsis thaliana) Aux/IAA family, as well as in their putative Brassica rapa orthologs. We found that rate motifs can act by enhancing interaction between repressors and the E3, but that this is not the only mechanism of action. Phenotypes of transgenic plants expressing a deletion in a rate motif in IAA28 resembled plants expressing degron mutations, underscoring the functional relevance of Aux/IAA degradation dynamics in regulating auxin responses. PMID:26149575

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

    PubMed

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

    2016-06-01

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

  11. A Single Amino Acid Substitution in an ORANGE Protein Promotes Carotenoid Overaccumulation in Arabidopsis1[OPEN

    PubMed Central

    Yuan, Hui; Owsiany, Katherine; Sheeja, T.E.; Zhou, Xiangjun; Rodriguez, Caroline; Li, Yongxi; Welsch, Ralf; Chayut, Noam; Yang, Yong; Thannhauser, Theodore W.; Parthasarathy, Mandayam V.; Xu, Qiang; Deng, Xiuxin; Fei, Zhangjun; Schaffer, Ari; Katzir, Nurit; Burger, Joseph; Tadmor, Yaakov; Li, Li

    2015-01-01

    Carotenoids are crucial for plant growth and human health. The finding of ORANGE (OR) protein as a pivotal regulator of carotenogenesis offers a unique opportunity to comprehensively understand the regulatory mechanisms of carotenoid accumulation and develop crops with enhanced nutritional quality. Here, we demonstrated that alteration of a single amino acid in a wild-type OR greatly enhanced its ability to promote carotenoid accumulation. Whereas overexpression of OR from Arabidopsis (Arabidopsis thaliana; AtOR) or from the agronomically important crop sorghum (Sorghum bicolor; SbOR) increased carotenoid levels up to 2-fold, expression of AtORHis (R90H) or SbORHis (R104H) variants dramatically enhanced carotenoid accumulation by up to 7-fold in the Arabidopsis calli. Moreover, we found that AtORAla (R90A) functioned similarly to AtORHis to promote carotenoid overproduction. Neither AtOR nor AtORHis greatly affected carotenogenic gene expression. AtORHis exhibited similar interactions with phytoene synthase (PSY) as AtOR in posttranscriptionally regulating PSY protein abundance. AtORHis triggered biogenesis of membranous chromoplasts in the Arabidopsis calli, which shared structures similar to chromoplasts found in the curd of the orange cauliflower (Brassica oleracea) mutant. By contrast, AtOR did not cause plastid-type changes in comparison with the controls, but produced plastids containing larger and electron-dense plastoglobuli. The unique ability of AtORHis in mediating chromoplast biogenesis is responsible for its induced carotenoid overproduction. Our study demonstrates ORHis/Ala as powerful tools for carotenoid enrichment in plants, and provides insights into the mechanisms underlying ORHis-regulated carotenoid accumulation. PMID:26224804

  12. Ectopic Expression of WRINKLED1 Affects Fatty Acid Homeostasis in Brachypodium distachyon Vegetative Tissues1[OPEN

    PubMed Central

    Yang, Yang; Munz, Jacob; Cass, Cynthia; Zienkiewicz, Agnieszka; Kong, Que; Ma, Wei; Sedbrook, John; Benning, Christoph

    2015-01-01

    Triacylglycerol (TAG) is a storage lipid used for food purposes and as a renewable feedstock for biodiesel production. WRINKLED1 (WRI1) is a transcription factor that governs fatty acid (FA) synthesis and, indirectly, TAG accumulation in oil-storing plant tissues, and its ectopic expression has led to TAG accumulation in vegetative tissues of different dicotyledonous plants. The ectopic expression of BdWRI1 in the grass Brachypodium distachyon induced the transcription of predicted genes involved in glycolysis and FA biosynthesis, and TAG content was increased up to 32.5-fold in 8-week-old leaf blades. However, the ectopic expression of BdWRI1 also caused cell death in leaves, which has not been observed previously in dicotyledonous plants such as Arabidopsis (Arabidopsis thaliana). Lipid analysis indicated that the free FA content was 2-fold elevated in BdWRI1-expressing leaf blades of B. distachyon. The transcription of predicted genes involved in β-oxidation was induced. In addition, linoleic FA treatment caused cell death in B. distachyon leaf blades, an effect that was reversed by the addition of the FA biosynthesis inhibitor cerulenin. Taken together, ectopic expression of BdWRI1 in B. distachyon enhances FA biosynthesis and TAG accumulation in leaves, as expected, but also leads to increased free FA content, which has cytotoxic effects leading to cell death. Thus, while WRI appears to ubiquitously affect FA biosynthesis and TAG accumulation in diverse plants, its ectopic expression can lead to undesired side effects depending on the context of the specific lipid metabolism of the respective plant species. PMID:26419778

  13. Investigation of poly(styrene-divinylbenzene-vinylsulfonic acid) as retentive and electroosmotic flow generating phase in open-tubular electrochromatography.

    PubMed

    De Smet, Seppe; Lynen, Frederic

    2015-07-24

    In this work, a new sulfonated polystyrene based porous layer was synthesized on the wall of a capillary by a single step in situ polymerization process. To obtain a capillary suited for electrochromatography, vinylsulfonic acid (VSA) was, next to divinylbenzene (DVB), copolymerized to induce charges for the electroosmotic flow (EOF) generation. The VSA ratio in the monomer mixture and the polymerization time were optimized while the chromatographic characteristics of the obtained open tubular columns were investigated in electrochromatography. To allow unambiguous study of only chromatographic processes, evaluations were performed with a mixture of sufficiently retained and electrophoretically neutral parabens. Comparison of SEM pictures and chromatograms revealed that the polymerization time had a great influence on the polymer layer morphology and on the chromatographic performance. An increase in the VSA ratio, led to an increase in the mobile phase velocity but simultaneously lowered paraben retention. The novel optimized stationary phase could generate a stable and significant electro-osmotic flow (EOF) of 1.1mm/s over a wide pH range which could be produced in a reproducible manner. Minimal plate heights of 10μm, equivalent to the capillary internal diameter, were obtained. The open-tubular character of this optimized porous layer column allowed successful analyses at elevated temperature, resulting in a maximum efficiency of 85,500 plates for a 75cm capillary and linear velocities up to 1.4mm/s. Finally, a thermal gradient was successfully applied, leading to artificial sharpened peaks with a peak capacity of 55 in a 20min time span. PMID:26065568

  14. Indolyl-3-butyric acid-induced Arabidopsis stomatal opening mediated by 3',5'-cyclic guanosine-monophosphate.

    PubMed

    Cousson, A

    2010-12-01

    It has been pharmacologically suggested that 3',5'-cyclic guanosine-monophosphate (cGMP) mediates indolyl-3-butyric acid (IBA)-induced stomatal opening. In Arabidopsis thaliana (L.) Heynh., such investigations compared the wild type (Columbia and Ws ecotypes) to mutants knockout for either GTP-binding protein (G protein) α subunit 1 (gpa1-4), putative G protein-coupled receptor 1 (gcr1-5), calcineurin B-like isoform 1 (cbl1) or 9 (cbl9), or the NADPH oxidases AtrbohD and AtrbohF (atrbohD/F). Stomatal opening to IBA or the permeant cGMP analogue, 8-bromo-cGMP (8-Br-cGMP) was abolished in the atrbohD/F mutant. The IBA response was fully or partially suppressed, respectively, in the gcr1-5 mutant, or the gpa1-4 and cbl1 mutants. In the cbl9 mutant, the response to IBA or 8-Br-cGMP, respectively, was partially or fully suppressed. Phenylarsine oxide (PAO) affected the IBA response, which the cbl1 mutant overlapped or the gpa1-4 and cbl9 mutants increased up to 100% inhibition. 6-anilino-5,8-quinolinedione, mas17, the (Rp)-diastereomer of 8-bromo-3',5'-cyclic guanosine monophosphorothioate (Rp-8-Br-cGMPS), nicotinamide, ruthenium red (RRed), 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA), cyclosporine A (CsA) and FK506 converged to affect the IBA response, which the gpa1-4 and cbl9 mutants overlapped or the cbl1 mutant and PAO increased up to 100% inhibition. Rp-8-Br-cGMPS, nicotinamide, RRed, BAPTA, CsA or FK506 paralled the cbl9 and atrbohD/F mutants to abolish the 8-Br-cGMP response. Based on so far revealed features of these mutants and pharmacological compounds, these results confirmed cGMP as a Ca(2+)-mobilizing second messenger for apoplastic auxin whose perception and transduction would implicate a seven-transmembrane receptor - G protein - guanylyl cyclase unit at the guard cell plasma membrane. PMID:20951600

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

    PubMed Central

    2011-01-01

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

  16. 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…

  17. 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…

  18. 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…

  19. Regulation of Leaf Starch Degradation by Abscisic Acid Is Important for Osmotic Stress Tolerance in Plants[OPEN

    PubMed Central

    Thalmann, Matthias; Pazmino, Diana; Seung, David; Horrer, Daniel; Nigro, Arianna; Meier, Tiago; Zeeman, Samuel C.; Santelia, Diana

    2016-01-01

    Starch serves functions that range over a timescale of minutes to years, according to the cell type from which it is derived. In guard cells, starch is rapidly mobilized by the synergistic action of β-AMYLASE1 (BAM1) and α-AMYLASE3 (AMY3) to promote stomatal opening. In the leaves, starch typically accumulates gradually during the day and is degraded at night by BAM3 to support heterotrophic metabolism. During osmotic stress, starch is degraded in the light by stress-activated BAM1 to release sugar and sugar-derived osmolytes. Here, we report that AMY3 is also involved in stress-induced starch degradation. Recently isolated Arabidopsis thaliana amy3 bam1 double mutants are hypersensitive to osmotic stress, showing impaired root growth. amy3 bam1 plants close their stomata under osmotic stress at similar rates as the wild type but fail to mobilize starch in the leaves. 14C labeling showed that amy3 bam1 plants have reduced carbon export to the root, affecting osmolyte accumulation and root growth during stress. Using genetic approaches, we further demonstrate that abscisic acid controls the activity of BAM1 and AMY3 in leaves under osmotic stress through the AREB/ABF-SnRK2 kinase-signaling pathway. We propose that differential regulation and isoform subfunctionalization define starch-adaptive plasticity, ensuring an optimal carbon supply for continued growth under an ever-changing environment. PMID:27436713

  20. 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…

  1. 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

  2. High abundances of oxalic, azelaic, and glyoxylic acids and methylglyoxal in the open ocean with high biological activity: Implication for secondary OA formation from isoprene

    NASA Astrophysics Data System (ADS)

    Bikkina, Srinivas; Kawamura, Kimitaka; Miyazaki, Yuzo; Fu, Pingqing

    2014-05-01

    Atmospheric dicarboxylic acids (DCA) are a ubiquitous water-soluble component of secondary organic aerosols (SOA), which can act as cloud condensation nuclei (CCN), affecting the Earth's climate. Despite the high abundances of oxalic acid and related compounds in the marine aerosols, there is no consensus on what controls their distributions over the open ocean. Marine biological productivity could play a role in the production of DCA, but there is no substantial evidence to support this hypothesis. Here we present latitudinal distributions of DCA, oxoacids and α-dicarbonyls in the marine aerosols from the remote Pacific. Their concentrations were found several times higher in more biologically influenced aerosols (MBA) than less biologically influenced aerosols. We propose isoprene and unsaturated fatty acids as sources of DCA as inferred from significantly higher abundances of isoprene-SOA tracers and azelaic acid in MBA. These results have implications toward the reassessment of climate forcing feedbacks of marine-derived SOA.

  3. 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.

  4. Regio- and stereochemically controlled formation of hydroxamic acids from indium triflate-mediated nucleophilic ring-opening reactions with acylnitroso-Diels–Alder adducts

    PubMed Central

    Yang, Baiyuan; Miller, Marvin J.

    2010-01-01

    Treatment of acylnitroso-Diels–Alder [2.2.1] bicyclic adducts 2a–b with indium triflate in an alcohol solvent induces ring opening reactions to afford monocyclic anti-1,2-, anti-1,4- and syn-1,4-hydroxamic acids with good to excellent regio- and stereoselectivity (up to 7:86:7). Treatment of [2.2.2] bicyclic nitroso adducts 2c–d under similar reaction conditions generates only anti-1,2- and anti-1,4-hydroxamic acids with anti-1,4-product predominant (up to 17:83). PMID:20209116

  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. 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;…

  7. 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…

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

    ERIC Educational Resources Information Center

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

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

  9. Omega-3 fatty acids in the management of autism spectrum disorders: findings from an open-label pilot study in Singapore.

    PubMed

    Ooi, Y P; Weng, S-J; Jang, L Y; Low, L; Seah, J; Teo, S; Ang, R P; Lim, C G; Liew, A; Fung, D S; Sung, M

    2015-08-01

    The goal of this open-label trial was to examine the efficacy and safety of a 12-week omega-3 fatty acids supplementation among children suffering with Autism Spectrum Disorders (ASD). A total of 41 children and adolescents aged 7-18 years (36 boys, 5 girls; mean age = 11.66, s.d. = 3.05) diagnosed with ASD participated in the study. At post-treatment, participants showed significant improvements on all subscales of the Social Responsiveness Scale (P < 0.01) and the Social and Attention Problems syndrome scales of the Child Behavior Checklist (P < 0.05). Blood fatty acid levels were significantly correlated with changes in the core symptoms of ASD. Baseline levels of blood fatty acid levels were also predictive of response to the omega-3 treatment. Omega-3 fatty acids supplementation was well-tolerated and did not cause any serious side effects. Our findings lend some preliminary support for the use of omega-3 fatty acids supplementation in addressing ASD. Future randomized controlled trials of omega-3 fatty acids in ASD with blood fatty acid measurements with a larger sample and longer follow-up period is warranted. PMID:25804268

  10. Harnessing Lewis acidic open metal sites of metal-organic frameworks: the foremost route to achieve highly selective benzene sorption over cyclohexane.

    PubMed

    Mukherjee, Soumya; Manna, Biplab; Desai, Aamod V; Yin, Yuefeng; Krishna, Rajamani; Babarao, Ravichandar; Ghosh, Sujit K

    2016-07-01

    π-Complexation triggered Lewis acid-base interactions between open metal sites (OMS) of metal-organic frameworks (MOFs), and π-e(-) rich adsorptive benzene (Bz) is exploited to establish M-MOF-74 as the best Bz-selective MOF sorbent, marking the first report of utilizing OMS behind benzene/cyclohexane separation; a key advance from the energy-economy standpoint of industrial separation. PMID:27188914

  11. Children Can Love Reading.

    ERIC Educational Resources Information Center

    Zibart, Rosemary

    1980-01-01

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

  12. Reading: The Human Touch.

    ERIC Educational Resources Information Center

    Roswell, Florence G.

    1978-01-01

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

  13. 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…

  14. 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…

  15. 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…

  16. Preparing Teachers of Reading and Reading Specialists.

    ERIC Educational Resources Information Center

    Austin, Mary C.

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

  17. 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…

  18. Proteogenomic Discovery of a Small, Novel Protein in Yeast Reveals a Strategy for the Detection of Unannotated Short Open Reading Frames.

    PubMed

    Yagoub, Daniel; Tay, Aidan P; Chen, Zhiliang; Hamey, Joshua J; Cai, Curtis; Chia, Samantha Z; Hart-Smith, Gene; Wilkins, Marc R

    2015-12-01

    In recent years, proteomic data have contributed to genome annotation efforts, most notably in humans and mice, and spawned a field termed "proteogenomics". Yeast, in contrast with higher eukaryotes, has a small genome, which has lent itself to simpler ORF prediction. Despite this, continual advances in mass spectrometry suggest that proteomics should be able to improve genome annotation even in this well-characterized species. Here we applied a proteogenomics workflow to yeast to identify novel protein-coding genes. Specific databases were generated, from intergenic regions of the genome, which were then queried with MS/MS data. This suggested the existence of several putative novel ORFs of <100 codons, one of which we chose to validate. Synthetic peptides, RNA-Seq analysis, and evidence of evolutionary conservation allowed for the unequivocal definition of a new protein of 78 amino acids encoded on chromosome X, which we dub YJR107C-A. It encodes a new type of domain, which ab initio modeling suggests as predominantly α-helical. We show that this gene is nonessential for growth; however, deletion increases sensitivity to osmotic stress. Finally, from the above discovery process, we discuss a generalizable strategy for the identification of short ORFs and small proteins, many of which are likely to be undiscovered. PMID:26554900

  19. Open fermentative production of L-lactic acid by Bacillus sp. strain NL01 using lignocellulosic hydrolyzates as low-cost raw material.

    PubMed

    Ouyang, Jia; Ma, Rui; Zheng, Zhaojuan; Cai, Cong; Zhang, Min; Jiang, Ting

    2013-05-01

    Highly efficient L-lactate production by a thermophilic strain Bacillus sp. NL01 was demonstrated in this study. Lignocellulosic hydrolyzates containing a high content of glucose, which was prepared from corn stover, was used as substrate for L-lactic acid production. The fermentation was carried out under open condition without sterilization and used NaOH as alkaline neutralizing reagent. In batch fermentation, 56.37 g l(-1) L-lactic acid was obtained from lignocellulosic hydrolyzates which contained the solid residues produced in enzymatic saccharification. In fed-batch fermentation, 75.03 g l(-1) L-lactic acid was obtained from lignocellulosic hydrolyzates supernatant. The yield was 74.5% and the average productivity was 1.04 g l(-1) h(-1). PMID:23127843

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

    PubMed Central

    Ogasawara, N; Moriya, S; Yoshikawa, H

    1985-01-01

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

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

    PubMed

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

    1989-05-01

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

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

    PubMed

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

    2013-02-01

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

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

    PubMed Central

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

    1989-01-01

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

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

    PubMed

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

    1992-03-01

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

  5. 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…

  6. Performance of an open limestone channel for treating a stream affected by acid rock drainage (León, Spain).

    PubMed

    Santofimia, Esther; López-Pamo, Enrique

    2016-07-01

    The generation of acid rock drainage (ARD) was observed after the oxidation dissolution of pyrite-rich black shales, which were excavated during the construction of a highway in León (Spain). ARDs are characterized by the presence of high concentrations of sulfate and metals (Al, Fe, Mn, Zn, Cu, Co, Ni, Th, and U) that affect the La Silva stream. Dissolved element concentrations showed values between one and four orders of magnitude higher than those of natural waters of this area. A passive treatment system was constructed; the aim of which was to improve the quality of the water of the stream. This work provides a hydrochemical characterization of the La Silva stream after its transit through the different elements that constitute the passive treatment system (open limestone channel (OLC), small ponds, and a wetland), during its first year of operation. The passive treatment system has two sections separated by a tunnel 230 m long. The first section, which stretches between the highway and the tunnel entrance, is an OLC 350 m long with a slope of 16 %. The second section, which stretches from the tunnel exit to the end wetland, has a length of 700 m and a slope of 6 %; it is in this section where six small ponds are located. In the first section of this passive treatment system, the OLC was effectively increasing the pH from 3 to 4-4.5 and eliminating all of the dissolved Fe and the partially dissolved Al. These elements, after hydrolysis at a pH 3-3.5 and 4-4.5, respectively, had precipitated as schwertmannite and hydrobasaluminite, while other dissolved metals were removed totally or partially for adsorption by the precipitates and/or by coprecipitation. The second section receives different inputs of water such as ARDs and natural waters. After exiting the treatment system, the stream is buffered by Al at a pH of 4-4.3, showing high Al concentrations (19-101 mg/L) but with a complete removal of dissolved Fe. Unfortunately, the outflow shows similar or

  7. 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…

  8. 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.…

  9. Designing the Reading Curriculum.

    ERIC Educational Resources Information Center

    Ediger, Marlow

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

  10. 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…

  11. 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…

  12. Narration in Reading Remediation.

    ERIC Educational Resources Information Center

    Kersting, Frank; Ferguson, Janice

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

  13. 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…

  14. Reading and Comprehension.

    ERIC Educational Resources Information Center

    Eagan, Ruth L.

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

  15. Reading Therapy Project.

    ERIC Educational Resources Information Center

    McCarty, Roxanne

    2002-01-01

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

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

    PubMed

    Volckaert, G; Voet, M; Robben, J

    1997-03-15

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

  17. bZIP67 Regulates the Omega-3 Fatty Acid Content of Arabidopsis Seed Oil by Activating FATTY ACID DESATURASE3[W][OPEN

    PubMed Central

    Mendes, Ana; Kelly, Amélie A.; van Erp, Harrie; Shaw, Eve; Powers, Stephen J.; Kurup, Smita; Eastmond, Peter J.

    2013-01-01

    Arabidopsis thaliana seed maturation is accompanied by the deposition of storage oil, rich in the essential ω-3 polyunsaturated fatty acid α-linolenic acid (ALA). The synthesis of ALA is highly responsive to the level of FATTY ACID DESATURASE3 (FAD3) expression, which is strongly upregulated during embryogenesis. By screening mutants in LEAFY COTYLEDON1 (LEC1)–inducible transcription factors using fatty acid profiling, we identified two mutants (lec1-like and bzip67) with a seed lipid phenotype. Both mutants share a substantial reduction in seed ALA content. Using a combination of in vivo and in vitro assays, we show that bZIP67 binds G-boxes in the FAD3 promoter and enhances FAD3 expression but that activation is conditional on bZIP67 association with LEC1-LIKE (L1L) and NUCLEAR FACTOR-YC2 (NF-YC2). Although FUSCA3 and ABSCISIC ACID INSENSITIVE3 are required for L1L and bZIP67 expression, neither protein is necessary for [bZIP67:L1L:NF-YC2] to activate FAD3. We conclude that a transcriptional complex containing L1L, NF-YC2, and bZIP67 is induced by LEC1 during embryogenesis and specifies high levels of ALA production for storage oil by activating FAD3 expression. PMID:23995083

  18. 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.

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

    PubMed

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

    1994-03-01

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

  20. Deficient glutathione in guard cells facilitates abscisic acid-induced stomatal closure but does not affect light-induced stomatal opening.

    PubMed

    Jahan, Md Sarwar; Ogawa, Ken'ichi; Nakamura, Yoshimasa; Shimoishi, Yasuaki; Mori, Izumi C; Murata, Yoshiyuki

    2008-10-01

    We investigated the role of glutathione (GSH) in stomatal movements using a GSH deficient mutant, chlorinal-1 (ch1-1). Guard cells of ch1-1 mutants accumulated less GSH than wild types did. Light induced stomatal opening in ch1-1 and wild-type plants. Abscisic acid (ABA) induced stomatal closure in ch1-1 mutants more than wild types without enhanced reactive oxygen species (ROS) production. Therefore, GSH functioned downstream of ROS production in the ABA signaling cascade. PMID:18838781

  1. 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…

  2. Synthesis and biological evaluation of ring A and/or C expansion and opening echinocystic acid derivatives for anti-HCV entry inhibitors.

    PubMed

    Wang, Han; Yu, Fei; Peng, Yiyun; Wang, Qi; Han, Xu; Xu, Renyang; Zhou, Xiaoshu; Wan, Chuanxing; Fan, Zibo; Jiao, Pingxuan; Zhang, Yongmin; Zhang, Lihe; Zhou, Demin; Xiao, Sulong

    2015-09-18

    Echinocystic acid (EA), a naturally occurring oleanane-type triterpene isolated from Dipsacus asperoides, was found to have anti-HCV entry activity in our previous study. Expansion of triterpene structural diversity, including the ring A and/or C expansion and opening, was performed. To elucidate the pharmacophore of EA, seven lactones (8, 16, 17, 24, 26, 35 and 41), three 3,28-dioic acids (9, 36 and 42) and two pentols (10 and 27) were synthesized. The anti-HCV entry activities of those derivatives, along with their parental compound EA and analogs α,β-unsaturated ketone (18), were evaluated. All the products showed no improvement but detrimental effect on potency of EA. The results demonstrated that ring A and C of EA are highly conserved, indicating the steric effects of the rigid skeleton have a profound effect on the potency. PMID:26318066

  3. Application of pH-responsive poly(2-dimethyl-aminoethylmethacrylate)-block-poly(acrylic acid) coatings for the open-tubular capillary electrochromatographic analysis of acidic and basic compounds.

    PubMed

    Sepehrifar, Roshanak; Boysen, Reinhard I; Danylec, Basil; Yang, Yuanzhong; Saito, Kei; Hearn, Milton T W

    2016-04-21

    A new type of stimuli-responsive polymeric (SRP) coating has been prepared for use in open tubular capillary electrochromatography (OT-CEC), by grafting poly(2-dimethylaminoethylmethacrylate)-block-poly(acrylic acid) (PDMAEMA-b-PAA) as a Y-shaped block copolymer with two dissimilar chain compositions onto the inner walls of aminopropyl-modified silica capillaries. The grafting process introduced weakly charged functional groups from the PAA and PDMAEMA, enabling the generation of electroendosmotic flow with magnitude and direction adjustable by changing the pH of the running buffer electrolyte. This stimuli-responsive PDMAEMA-b-PAA block copolymer was found to provide excellent resolution of various acidic and basic compounds, leading to efficient analyte separation. When operated in the OT-CEC mode, separation selectivities could be readily manipulated via differential contributions from chromatographic and electrophoretic mechanisms, simply by changing the pH or the ionic strength of the running buffer electrolyte. PMID:27026608

  4. 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…

  5. Reading: Putting the Pieces Together.

    ERIC Educational Resources Information Center

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

    1994-01-01

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

  6. Gibberellic Acid-Stimulated Arabidopsis6 Serves as an Integrator of Gibberellin, Abscisic Acid, and Glucose Signaling during Seed Germination in Arabidopsis1[OPEN

    PubMed Central

    Zhong, Chunmei; Xu, Hao; Ye, Siting; Wang, Shiyi; Li, Lingfei; Zhang, Shengchun; Wang, Xiaojing

    2015-01-01

    The DELLA protein REPRESSOR OF ga1-3-LIKE2 (RGL2) plays an important role in seed germination under different conditions through a number of transcription factors. However, the functions of the structural genes associated with RGL2-regulated germination are less defined. Here, we report the role of an Arabidopsis (Arabidopsis thaliana) cell wall-localized protein, Gibberellic Acid-Stimulated Arabidopsis6 (AtGASA6), in functionally linking RGL2 and a cell wall loosening expansin protein (Arabidopsis expansin A1 [AtEXPA1]), resulting in the control of embryonic axis elongation and seed germination. AtGASA6-overexpressing seeds showed precocious germination, whereas transfer DNA and RNA interference mutant seeds displayed delayed seed germination under abscisic acid, paclobutrazol, and glucose (Glc) stress conditions. The differences in germination rates resulted from corresponding variation in cell elongation in the hypocotyl-radicle transition region of the embryonic axis. AtGASA6 was down-regulated by RGL2, GLUCOSE INSENSITIVE2, and ABSCISIC ACID-INSENSITIVE5 genes, and loss of AtGASA6 expression in the gasa6 mutant reversed the insensitivity shown by the rgl2 mutant to paclobutrazol and the gin2 mutant to Glc-induced stress, suggesting that it is involved in regulating both the gibberellin and Glc signaling pathways. Furthermore, it was found that the promotion of seed germination and length of embryonic axis by AtGASA6 resulted from a promotion of cell elongation at the embryonic axis mediated by AtEXPA1. Taken together, the data indicate that AtGASA6 links RGL2 and AtEXPA1 functions and plays a role as an integrator of gibberellin, abscisic acid, and Glc signaling, resulting in the regulation of seed germination through a promotion of cell elongation. PMID:26400990

  7. 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…

  8. 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…

  9. 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…

  10. Microalgae Synthesize Hydrocarbons from Long-Chain Fatty Acids via a Light-Dependent Pathway1[OPEN

    PubMed Central

    Légeret, Bertrand; Mirabella, Boris; Guédeney, Geneviève; Jetter, Reinhard; Peltier, Gilles

    2016-01-01

    Microalgae are considered a promising platform for the production of lipid-based biofuels. While oil accumulation pathways are intensively researched, the possible existence of a microalgal pathways converting fatty acids into alka(e)nes has received little attention. Here, we provide evidence that such a pathway occurs in several microalgal species from the green and the red lineages. In Chlamydomonas reinhardtii (Chlorophyceae), a C17 alkene, n-heptadecene, was detected in the cell pellet and the headspace of liquid cultures. The Chlamydomonas alkene was identified as 7-heptadecene, an isomer likely formed by decarboxylation of cis-vaccenic acid. Accordingly, incubation of intact Chlamydomonas cells with per-deuterated D31-16:0 (palmitic) acid yielded D31-18:0 (stearic) acid, D29-18:1 (oleic and cis-vaccenic) acids, and D29-heptadecene. These findings showed that loss of the carboxyl group of a C18 monounsaturated fatty acid lead to heptadecene formation. Amount of 7-heptadecene varied with growth phase and temperature and was strictly dependent on light but was not affected by an inhibitor of photosystem II. Cell fractionation showed that approximately 80% of the alkene is localized in the chloroplast. Heptadecane, pentadecane, as well as 7- and 8-heptadecene were detected in Chlorella variabilis NC64A (Trebouxiophyceae) and several Nannochloropsis species (Eustigmatophyceae). In contrast, Ostreococcus tauri (Mamiellophyceae) and the diatom Phaeodactylum tricornutum produced C21 hexaene, without detectable C15-C19 hydrocarbons. Interestingly, no homologs of known hydrocarbon biosynthesis genes were found in the Nannochloropsis, Chlorella, or Chlamydomonas genomes. This work thus demonstrates that microalgae have the ability to convert C16 and C18 fatty acids into alka(e)nes by a new, light-dependent pathway. PMID:27288359

  11. The Impact of the Branched-Chain Ketoacid Dehydrogenase Complex on Amino Acid Homeostasis in Arabidopsis1[OPEN

    PubMed Central

    Peng, Cheng; Uygun, Sahra; Shiu, Shin-Han; Last, Robert L.

    2015-01-01

    The branched-chain amino acids (BCAAs) Leu, Ile, and Val are among nine essential amino acids that must be obtained from the diet of humans and other animals, and can be nutritionally limiting in plant foods. Despite genetic evidence of its importance in regulating seed amino acid levels, the full BCAA catabolic network is not completely understood in plants, and limited information is available regarding its regulation. In this study, transcript coexpression analyses revealed positive correlations among BCAA catabolism genes in stress, development, diurnal/circadian, and light data sets. A core subset of BCAA catabolism genes, including those encoding putative branched-chain ketoacid dehydrogenase subunits, is highly expressed during the night in plants on a diel cycle and in prolonged darkness. Mutants defective in these subunits accumulate higher levels of BCAAs in mature seeds, providing genetic evidence for their function in BCAA catabolism. In addition, prolonged dark treatment caused the mutants to undergo senescence early and overaccumulate leaf BCAAs. These results extend the previous evidence that BCAAs can be catabolized and serve as respiratory substrates at multiple steps. Moreover, comparison of amino acid profiles between mature seeds and dark-treated leaves revealed differences in amino acid accumulation when BCAA catabolism is perturbed. Together, these results demonstrate the consequences of blocking BCAA catabolism during both normal growth conditions and under energy-limited conditions. PMID:25986129

  12. 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 ...

  13. 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 ...

  14. 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 ...

  15. 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)

  16. Jasmonic Acid and Its Precursor 12-Oxophytodienoic Acid Control Different Aspects of Constitutive and Induced Herbivore Defenses in Tomato1[W][OPEN

    PubMed Central

    Bosch, Marko; Wright, Louwrance P.; Gershenzon, Jonathan; Wasternack, Claus; Hause, Bettina; Schaller, Andreas; Stintzi, Annick

    2014-01-01

    The jasmonate family of growth regulators includes the isoleucine (Ile) conjugate of jasmonic acid (JA-Ile) and its biosynthetic precursor 12-oxophytodienoic acid (OPDA) as signaling molecules. To assess the relative contribution of JA/JA-Ile and OPDA to insect resistance in tomato (Solanum lycopersicum), we silenced the expression of OPDA reductase3 (OPR3) by RNA interference (RNAi). Consistent with a block in the biosynthetic pathway downstream of OPDA, OPR3-RNAi plants contained wild-type levels of OPDA but failed to accumulate JA or JA-Ile after wounding. JA/JA-Ile deficiency in OPR3-RNAi plants resulted in reduced trichome formation and impaired monoterpene and sesquiterpene production. The loss of these JA/JA-Ile -dependent defense traits rendered them more attractive to the specialist herbivore Manduca sexta with respect to feeding and oviposition. Oviposition preference resulted from reduced levels of repellant monoterpenes and sesquiterpenes. Feeding preference, on the other hand, was caused by increased production of cis-3-hexenal acting as a feeding stimulant for M. sexta larvae in OPR3-RNAi plants. Despite impaired constitutive defenses and increased palatability of OPR3-RNAi leaves, larval development was indistinguishable on OPR3-RNAi and wild-type plants, and was much delayed compared with development on the jasmonic acid-insensitive1 (jai1) mutant. Apparently, signaling through JAI1, the tomato ortholog of the ubiquitin ligase CORONATINE INSENSITIVE1 in Arabidopsis (Arabidopsis thaliana), is required for defense, whereas the conversion of OPDA to JA/JA-Ile is not. Comparing the signaling activities of OPDA and JA/JA-Ile, we found that OPDA can substitute for JA/JA-Ile in the local induction of defense gene expression, but the production of JA/JA-Ile is required for a systemic response. PMID:25073705

  17. Connecting Source with Sink: The Role of Arabidopsis AAP8 in Phloem Loading of Amino Acids1[OPEN

    PubMed Central

    Santiago, James P.; Tegeder, Mechthild

    2016-01-01

    Allocation of large amounts of nitrogen to developing organs occurs in the phloem and is essential for plant growth and seed development. In Arabidopsis (Arabidopsis thaliana) and many other plant species, amino acids represent the dominant nitrogen transport forms in the phloem, and they are mainly synthesized in photosynthetically active source leaves. Following their synthesis, a broad spectrum of the amino nitrogen is actively loaded into the phloem of leaf minor veins and transported within the phloem sap to sinks such as developing leaves, fruits, or seeds. Controlled regulation of the source-to-sink transport of amino acids has long been postulated; however, the molecular mechanism of amino acid phloem loading was still unknown. In this study, Arabidopsis AMINO ACID PERMEASE8 (AAP8) was shown to be expressed in the source leaf phloem and localized to the plasma membrane, suggesting its function in phloem loading. This was further supported by transport studies with aap8 mutants fed with radiolabeled amino acids and by leaf exudate analyses. In addition, biochemical and molecular analyses revealed alterations in leaf nitrogen pools and metabolism dependent on the developmental stage of the mutants. Decreased amino acid phloem loading and partitioning to sinks led to decreased silique and seed numbers, but seed protein levels were unchanged, demonstrating the importance of AAP8 function for sink development rather than seed quality. Overall, these results show that AAP8 plays an important role in source-to-sink partitioning of nitrogen and that its function affects source leaf physiology and seed yield. PMID:27016446

  18. Folic acid

    MedlinePlus

    ... in the blood vessel to keep it open. Bipolar disorder. Taking folic acid does not appear to improve the antidepressant effects of lithium in people with bipolar disorder. However, taking folate with the medication valproate improves ...

  19. Learning to Read Again.

    ERIC Educational Resources Information Center

    Adams, O. F., McCreery, Liz

    1988-01-01

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

  20. Reading/Language Arts.

    ERIC Educational Resources Information Center

    Illinois State Office of Education, Springfield.

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

  1. Reading in Mathematics.

    ERIC Educational Resources Information Center

    Taschow, Horst G.

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

  2. 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…

  3. 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…

  4. Supervising the Reading Clinician.

    ERIC Educational Resources Information Center

    Ridout, Susan Ramp; Bailey, Kevin Sue

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

  5. The Reading Clinic.

    ERIC Educational Resources Information Center

    Ridout, Susan Ramp; Bailey, Kevin Sue

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

  6. 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…

  7. 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,…

  8. Guided Reading and Motivation

    ERIC Educational Resources Information Center

    Hauptman, Allyson L.

    2012-01-01

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

  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. 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…

  11. 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…

  12. 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…

  13. The Roots of Reading.

    ERIC Educational Resources Information Center

    Segel, Elizabeth

    2000-01-01

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

  14. 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…

  15. 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…

  16. Developing a Reading Course.

    ERIC Educational Resources Information Center

    Creemers, F. H. Th.; And Others

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

  17. 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…

  18. Reading difficulties in Albanian.

    PubMed

    Avdyli, Rrezarta; Cuetos, Fernando

    2012-10-01

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

  19. Reading Difficulties in Albanian

    ERIC Educational Resources Information Center

    Avdyli, Rrezarta; Cuetos, Fernando

    2012-01-01

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

  20. Current Issues in Reading.

    ERIC Educational Resources Information Center

    French, Michael P., Ed.

    1985-01-01

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

  1. 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…

  2. 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…

  3. Creative Reading: Other Voices.

    ERIC Educational Resources Information Center

    Padgett, Ron

    1990-01-01

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

  4. Literature without Reading.

    ERIC Educational Resources Information Center

    Knighten, Katherine W.

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

  5. Issues in Reading Instruction.

    ERIC Educational Resources Information Center

    Ediger, Marlow

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

  6. Arabidopsis MYC Transcription Factors Are the Target of Hormonal Salicylic Acid/Jasmonic Acid Cross Talk in Response to Pieris brassicae Egg Extract1[OPEN

    PubMed Central

    Schmiesing, André; Gouhier-Darimont, Caroline

    2016-01-01

    Arabidopsis (Arabidopsis thaliana) plants recognize insect eggs and activate the salicylic acid (SA) pathway. As a consequence, expression of defense genes regulated by the jasmonic acid (JA) pathway is suppressed and larval performance is enhanced. Cross talk between defense signaling pathways is common in plant-pathogen interactions, but the molecular mechanism mediating this phenomenon is poorly understood. Here, we demonstrate that egg-induced SA/JA antagonism works independently of the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor ORA59, which controls the ERF branch of the JA pathway. In addition, treatment with egg extract did not enhance expression or stability of JASMONATE ZIM-domain transcriptional repressors, and SA/JA cross talk did not involve JASMONATE ASSOCIATED MYC2-LIKEs, which are negative regulators of the JA pathway. Investigating the stability of MYC2, MYC3, and MYC4, three basic helix-loop-helix transcription factors that additively control jasmonate-related defense responses, we found that egg extract treatment strongly diminished MYC protein levels in an SA-dependent manner. Furthermore, we identified WRKY75 as a novel and essential factor controlling SA/JA cross talk. These data indicate that insect eggs target the MYC branch of the JA pathway and uncover an unexpected modulation of SA/JA antagonism depending on the biological context in which the SA pathway is activated. PMID:26884488

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

    ERIC Educational Resources Information Center

    Gençer, Yusuf; ÇetiInkaya, Gökhan

    2015-01-01

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

  8. bHLH transcription factors that facilitate K⁺ uptake during stomatal opening are repressed by abscisic acid through phosphorylation.

    PubMed

    Takahashi, Yohei; Ebisu, Yuta; Kinoshita, Toshinori; Doi, Michio; Okuma, Eiji; Murata, Yoshiyuki; Shimazaki, Ken-Ichiro

    2013-06-18

    Stomata open in response to light and close after exposure to abscisic acid (ABA). They regulate gas exchange between plants and the atmosphere, enabling plants to adapt to changing environmental conditions. ABA binding to receptors initiates a signaling cascade that involves protein phosphorylation. We show that ABA induced the phosphorylation of three basic helix-loop-helix (bHLH) transcription factors, called AKSs (ABA-responsive kinase substrates; AKS1, AKS2, and AKS3), in Arabidopsis guard cells. In their unphosphorylated state, AKSs facilitated stomatal opening through the transcription of genes encoding inwardly rectifying K⁺ channels. aks1aks2-1 double mutant plants showed decreases in light-induced stomatal opening, K⁺ accumulation in response to light, activity of inwardly rectifying K⁺ channels, and transcription of genes encoding major inwardly rectifying K⁺ channels without affecting ABA-mediated stomatal closure. Overexpression of potassium channel in Arabidopsis thaliana 1 (KAT1), which encodes a major inwardly rectifying K⁺ channel in guard cells, rescued the phenotype of aks1aks2-1 plants. AKS1 bound directly to the promoter of KAT1, an interaction that was attenuated after ABA-induced phosphorylation. The ABA agonist pyrabactin induced phosphorylation of AKSs. Our results demonstrate that the AKS family of bHLH transcription factors facilitates stomatal opening through the transcription of genes encoding inwardly rectifying K⁺ channels and that ABA suppresses the activity of these channels by triggering the phosphorylation of AKS family transcription factors. PMID:23779086

  9. Differential expression pattern of an acidic 9/13-lipoxygenase in flower opening and senescence and in leaf response to phloem feeders in the tea plant

    PubMed Central

    2010-01-01

    Background Lipoxygenase (LOXs) is a large family of plant enzymes that catalyse the hydroperoxidation of free polyunsaturated fatty acids into diverse biologically active compounds, collectively named phyto-oxylipins. Although multiple isoforms of LOXs have been identified in a wide range of annual herbaceous plants, the genes encoding these enzymes in perennial woody plants have not received as much attention. In Camellia sinensis (L.) O. Kuntze, no LOX gene of any type has been isolated, and its possible role in tea plant development, senescence, and defence reaction remains unknown. The present study describes the isolation, characterization, and expression of the first tea plant LOX isoform, namely CsLOX1, and seeks to clarify the pattern of its expression in the plant's defence response as well as in flower opening and senescence. Results Based on amino acid sequence similarity to plant LOXs, a LOX was identified in tea plant and named CsLOX1, which encodes a polypeptide comprising 861 amino acids and has a molecular mass of 97.8 kDa. Heterologous expression in yeast analysis showed that CsLOX1 protein conferred a dual positional specificity since it released both C-9 and C-13 oxidized products in equal proportion and hence was named 9/13-CsLOX1. The purified recombinant CsLOX1 protein exhibited optimum catalytic activity at pH 3.6 and 25°C. Real-time quantitative PCR analysis showed that CsLOX1 transcripts were detected predominantly in flowers, up-regulated during petal senescence, and down-regulated during flower bud opening. In leaves, the gene was up-regulated following injury or when treated with methyl jasmonate (MeJA), but salicylic acid (SA) did not induce such response. The gene was also rapidly and highly induced following feeding by the tea green leafhopper Empoasca vitis, whereas feeding by the tea aphid Toxoptera aurantii resulted in a pattern of alternating induction and suppression. Conclusions Analysis of the isolation and expression of the

  10. ECERIFERUM2-LIKE Proteins Have Unique Biochemical and Physiological Functions in Very-Long-Chain Fatty Acid Elongation1[OPEN

    PubMed Central

    Haslam, Tegan M.; Haslam, Richard; Thoraval, Didier; Pascal, Stéphanie; Delude, Camille; Domergue, Frédéric; Fernández, Aurora Mañas; Beaudoin, Frédéric; Napier, Johnathan A.; Kunst, Ljerka; Joubès, Jérôme

    2015-01-01

    The extension of very-long-chain fatty acids (VLCFAs) for the synthesis of specialized apoplastic lipids requires unique biochemical machinery. Condensing enzymes catalyze the first reaction in fatty acid elongation and determine the chain length of fatty acids accepted and produced by the fatty acid elongation complex. Although necessary for the elongation of all VLCFAs, known condensing enzymes cannot efficiently synthesize VLCFAs longer than 28 carbons, despite the prevalence of C28 to C34 acyl lipids in cuticular wax and the pollen coat. The eceriferum2 (cer2) mutant of Arabidopsis (Arabidopsis thaliana) was previously shown to have a specific deficiency in cuticular waxes longer than 28 carbons, and heterologous expression of CER2 in yeast (Saccharomyces cerevisiae) demonstrated that it can modify the acyl chain length produced by a condensing enzyme from 28 to 30 carbon atoms. Here, we report the physiological functions and biochemical specificities of the CER2 homologs CER2-LIKE1 and CER2-LIKE2 by mutant analysis and heterologous expression in yeast. We demonstrate that all three CER2-LIKEs function with the same small subset of condensing enzymes, and that they have different effects on the substrate specificity of the same condensing enzyme. Finally, we show that the changes in acyl chain length caused by each CER2-LIKE protein are of substantial importance for cuticle formation and pollen coat function. PMID:25596184

  11. Lewis acid catalyzed ring-opening polymerization of natural epoxy oil (Euphorbia oil) in carbon dioxide media

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In an attempt to build up useful application of plant oil based polymers, natural epoxy oil (euphorbia oil-EuO) was polymerized in liquid carbon dioxide in the presence of Lewis acid catalyst [Boron trifluoride diethyl etherate (BF3•OEt2)]. The resulting polymers (RPEuO) were characterized by FTIR ...

  12. Effect of zoledronic acid on disseminated tumour cells in women with locally advanced breast cancer: an open label, randomised, phase 2 trial

    PubMed Central

    Aft, Rebecca; Naughton, Michael; Trinkaus, Kathryn; Watson, Mark; Ylagan, Lourdes; Chavez-MacGregor, Mariana; Zhai, Jing; Kuo, Sacha; Shannon, William; Diemer, Kathryn; Herrmann, Virginia; Dietz, Jill; Ali, Amjad; Ellis, Matthew; Weiss, Peter; Eberlein, Timothy; Ma, Cynthia; Fracasso, Paula M; Zoberi, Imran; Taylor, Marie; Gillanders, William; Pluard, Timothy; Mortimer, Joanne; Weilbaecher, Katherine

    2013-01-01

    Summary Background Treatment with bisphosphonates decreases bone loss and can increase disease-free survival in patients with breast cancer. The aim of our study was to assess the effect of zoledronic acid on clearance of disseminated tumour cells (DTCs) from the bone marrow in women undergoing neoadjuvant chemotherapy for breast cancer. Methods Patients were recruited for this open-label, phase 2 randomised trial between March 17, 2003, and May 19, 2006, at a single centre. Eligible patients had clinical stage II–III (≥T2 and/or ≥N1) newly diagnosed breast cancer, Eastern Cooperative Oncology Group performance status of 0 or 1, and normal cardiac, renal, and liver function. 120 women were randomly assigned, using allocation concealment, to receive 4 mg zoledronic acid intravenously every 3 weeks (n=60), or no zoledronic acid (n=60), for 1 year concomitant with four cycles of neoadjuvant epirubicin (75 mg/m²) plus docetaxel (75 mg/m²) and two cycles of adjuvant epirubicin plus docetaxel. The primary endpoint was the number of patients with detectable DTCs at 3 months. Final analysis was done 1 year after the last patient was enrolled. Analyses were done for all patients with available data at 3 months. This study is registered with ClinicalTrials.gov, number NCT00242203. Findings Of the 120 patients initially enrolled, one withdrew after signing consent and one patient’s baseline bone marrow was not available. Both of these patients were in the control group. At 3 months, 109 bone-marrow samples were available for analysis. In the zoledronic acid group, bone marrow was not collected from one patient because of disease progression, one patient was taken off study because of severe diarrhoea, and two patients had not consented at the time of surgery. In the control group, bone marrow was not collected from two patients because of disease progression, one patient withdrew consent, and three patients were not consented at the time of surgery. At baseline

  13. Standardized Reading Tests and the Postsecondary Reading Curriculum.

    ERIC Educational Resources Information Center

    Wood, Nancy V.

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

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

    PubMed Central

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

    1997-01-01

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

  15. 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. ...

  16. 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

  17. 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…

  18. A Machine that Reads (Reading Technology).

    ERIC Educational Resources Information Center

    Rickelman, Robert J.; Henk, William A.

    1990-01-01

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

  19. 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…

  20. Hydrophobic bile acids relax rat detrusor contraction via inhibiting the opening of the Na+/Ca2+ exchanger

    PubMed Central

    Zhu, Jingzhen; Dong, Xingyou; Liu, Qian; Wu, Chao; Wang, Qingqing; Long, Zhou; Li, Longkun

    2016-01-01

    Hydrophobic bile acids (BAs) are thought to inhibit smooth muscle contractility in several organs. The present study was undertaken to investigate the effects of hydrophobic BAs on the detrusor contractility of rat bladder and to explore the possible mechanism. Lithocholic acid (LCA) treatment increased the micturition interval and induced a concentration-dependent relaxation of bladder detrusor strips. In addition, LCA reduced the concentration of intracellular free Ca2+([Ca2+]i) and inhibited both the outward and inward Na+/Ca2+ exchanger (NCX) current (INCX) in primary isolated smooth muscle cells (SMCs). To further investigate the mechanism of action of LCA, several pharmacologic agents were used. We found that the NCX inhibitor 3′,4′-Dichlorobenzamil (DCB) can significantly inhibit the relaxation of detrusor strips and a reduction of the [Ca2+]i induced by LCA, while the antagonist of muscarinic receptor and the agonist of the G protein-coupled bile acid receptor (TGR5) and the farnesoid X receptor (FXR) had no effect. In conclusion, these data suggest that the relaxation of rat detrusor induced by hydrophobic BAs is mediated by NCX. Further research is needed to carry out to demonstrate the possible pathway and provide a potential new strategy to investigation for the treatment of the low urinary tract syndromes. PMID:26892434

  1. Modeling of Open-Circuit Voltage of Phenyl-C61-Butyric Acid Methyl Ester-Like Based Bulk-Heterojunction Solar Cells.

    PubMed

    Ferreira, Rodrigo M; Batagin-Neto, Augusto; Lavarda, Francisco C

    2015-12-01

    New materials are currently being sought for use in active layers of bulk-heterojunction organic solar cells, and computational modeling plays an important role in this search. Although open circuit voltage (V(oc)) is one of the fundamental quantities that determine the efficiency of a solar cell, there is no consensus on the best way to estimate this magnitude for new materials from calculations of the electronic structure. In this paper, we compare ways of predicting V(oc) values employing a diverse group of blends and conclude that it is possible to have a good prediction tool for organic solar cells based on phenyl-C61-butyric acid methyl ester (PCBM) acceptor molecules. PMID:26682440

  2. 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…

  3. Abscisic Acid Flux Alterations Result in Differential Abscisic Acid Signaling Responses and Impact Assimilation Efficiency in Barley under Terminal Drought Stress1[C][W][OPEN

    PubMed Central

    Seiler, Christiane; Harshavardhan, Vokkaliga T.; Reddy, Palakolanu S.; Hensel, Götz; Kumlehn, Jochen; Eschen-Lippold, Lennart; Rajesh, Kalladan; Korzun, Viktor; Wobus, Ulrich; Lee, Justin; Selvaraj, Gopalan; Sreenivasulu, Nese

    2014-01-01

    Abscisic acid (ABA) is a central player in plant responses to drought stress. How variable levels of ABA under short-term versus long-term drought stress impact assimilation and growth in crops is unclear. We addressed this through comparative analysis, using two elite breeding lines of barley (Hordeum vulgare) that show senescence or stay-green phenotype under terminal drought stress and by making use of transgenic barley lines that express Arabidopsis (Arabidopsis thaliana) 9-cis-epoxycarotenoid dioxygenase (AtNCED6) coding sequence or an RNA interference (RNAi) sequence of ABA 8′-hydroxylase under the control of a drought-inducible barley promoter. The high levels of ABA and its catabolites in the senescing breeding line under long-term stress were detrimental for assimilate productivity, whereas these levels were not perturbed in the stay-green type that performed better. In transgenic barley, drought-inducible AtNCED expression afforded temporal control in ABA levels such that the ABA levels rose sooner than in wild-type plants but also subsided, unlike as in the wild type , to near-basal levels upon prolonged stress treatment due to down-regulation of endogenous HvNCED genes. Suppressing of ABA catabolism with the RNA interference approach of ABA 8′-hydroxylase caused ABA flux during the entire period of stress. These transgenic plants performed better than the wild type under stress to maintain a favorable instantaneous water use efficiency and better assimilation. Gene expression analysis, protein structural modeling, and protein-protein interaction analyses of the members of the PYRABACTIN RESISTANCE1/PYRABACTIN RESISTANCE1-LIKE/REGULATORY COMPONENT OF ABA RECEPTORS, TYPE 2C PROTEIN PHOSPHATASE Sucrose non-fermenting1-related protein kinase2, and ABA-INSENSITIVE5/ABA-responsive element binding factor family identified specific members that could potentially impact ABA metabolism and stress adaptation in barley. PMID:24610749

  4. Molecular and Physiological Analysis of Al3+ and H+ Rhizotoxicities at Moderately Acidic Conditions1[W][OPEN

    PubMed Central

    Kobayashi, Yasufumi; Kobayashi, Yuriko; Watanabe, Toshihiro; Shaff, Jon E.; Ohta, Hiroyuki; Kochian, Leon V.; Wagatsuma, Tadao; Kinraide, Thomas B.; Koyama, Hiroyuki

    2013-01-01

    Al3+ and H+ toxicities predicted to occur at moderately acidic conditions (pH [water] = 5–5.5) in low-Ca soils were characterized by the combined approaches of computational modeling of electrostatic interactions of ions at the root plasma membrane (PM) surface and molecular/physiological analyses in Arabidopsis (Arabidopsis thaliana). Root growth inhibition in known hypersensitive mutants was correlated with computed {Al3+} at the PM surface ({Al3+}PM); inhibition was alleviated by increased Ca, which also reduced {Al3+}PM and correlated with cellular Al responses based on expression analysis of genes that are markers for Al stress. The Al-inducible Al tolerance genes ALUMINUM-ACTIVATED MALATE TRANSPORTER1 and ALUMINUM SENSITIVE3 were induced by levels of {Al3+}PM too low to inhibit root growth in tolerant genotypes, indicating that protective responses are triggered when {Al3+}PM was below levels that can initiate injury. Modeling of the H+ sensitivity of the SENSITIVE TO PROTON RHIZOTOXICITY1 knockout mutant identified a Ca alleviation mechanism of H+ rhizotoxicity, possibly involving stabilization of the cell wall. The phosphatidate phosphohydrolase1 (pah1) pah2 double mutant showed enhanced Al susceptibility under low-P conditions, where greater levels of negatively charged phospholipids in the PM occur, which increases {Al3+}PM through increased PM surface negativity compared with wild-type plants. Finally, we found that the nonalkalinizing Ca fertilizer gypsum improved the tolerance of the sensitive genotypes in moderately acidic soils. These findings fit our modeling predictions that root toxicity to Al3+ and H+ in moderately acidic soils involves interactions between both toxic ions in relation to Ca alleviation. PMID:23839867

  5. Mutations in the Prokaryotic Pathway Rescue the fatty acid biosynthesis1 Mutant in the Cold1[OPEN

    PubMed Central

    Gao, Jinpeng; Wallis, James G.; Browse, John

    2015-01-01

    The Arabidopsis (Arabidopsis thaliana) fatty acid biosynthesis1 (fab1) mutant has increased levels of the saturated fatty acid 16:0 due to decreased activity of 3-ketoacyl-acyl carrier protein (ACP) synthase II. In fab1 leaves, phosphatidylglycerol, the major chloroplast phospholipid, contains up to 45% high-melting-point molecular species (molecules that contain only 16:0, 16:1-trans, and 18:0), a trait associated with chilling-sensitive plants, compared with less than 10% in wild-type Arabidopsis. Although they do not exhibit typical chilling sensitivity, when exposed to low temperatures (2°C–6°C) for long periods, fab1 plants do suffer collapse of photosynthesis, degradation of chloroplasts, and eventually death. A screen for suppressors of this low-temperature phenotype has identified 11 lines, some of which contain additional alterations in leaf-lipid composition relative to fab1. Here, we report the identification of two suppressor mutations, one in act1, which encodes the chloroplast acyl-ACP:glycerol-3-phosphate acyltransferase, and one in lpat1, which encodes the chloroplast acyl-ACP:lysophosphatidic acid acyltransferase. These enzymes catalyze the first two steps of the prokaryotic pathway for glycerolipid synthesis, so we investigated whether other mutations in this pathway would rescue the fab1 phenotype. Both the gly1 mutation, which reduces glycerol-3-phosphate supply to the prokaryotic pathway, and fad6, which is deficient in the chloroplast 16:1/18:1 fatty acyl desaturase, were discovered to be suppressors. Analyses of leaf-lipid compositions revealed that mutations at all four of the suppressor loci result in reductions in the proportion of high-melting-point molecular species of phosphatidylglycerol relative to fab1. We conclude that these reductions are likely the basis for the suppressor phenotypes. PMID:26224803

  6. Effect of 2,4-dichlorophenoxyacetic acid (2,4-D) on PCDD/F emissions from open burning of biomass.

    PubMed

    Muñoz, Maria; Gullett, Brian K; Touati, Abderrahmane; Font, Rafael

    2012-09-01

    To understand the effect of leaf-surface pesticides on emissions of PCDD/F during biomass burns, nine combustion experiments simulating the open burning of biomass were conducted. Needles and branches of Pinus taeda (Loblolly pine) were sprayed with the pesticide 2,4-dichlorophenoxyacetic acid (2,4-D) at 1 and 10 times the manufacturer's recommended application concentration. The biomass was then dried overnight, burned in an open burn test facility, and emission samples were collected, analyzed, and compared against emission samples from burning untreated biomass. Blank tests and analysis of PCDD/F in the raw biomass were also performed. Emission results from burning a water-sprayed control show a ~20-fold increase in PCDD/F levels above that of the raw biomass alone, implicating combustive formation versus simple volatilization. Results from burns of pine branches sprayed with pesticide showed a statistically significant increase in the PCDD/F TEQ emissions when burning biomass at ten times the recommended pesticide concentration (from 0.22 to 1.14 ng TEQ/kg carbon burned (C(b)), both ND = 0). Similarly, a 150-fold increase in the total PCDD/F congener mass (tetra- to octa-chlorinated D/F) above that of the control was observed (from 52 to 7800 ng/kg C(b)), confirming combustive formation of PCDD/F from 2,4-D. More replicate testing is needed to evaluate effects at lower pesticide concentrations. PMID:22845342

  7. Structure of a Specialized Acyl Carrier Protein Essential for Lipid A Biosynthesis with Very Long-chain Fatty Acids in Open and Closed Conformations

    SciTech Connect

    Ramelot, Theresa A.; Rossi, Paolo M.; Forouhar, Farhad; Lee, Hsiau-Wei; Yang, Yunhuang; Ni, Shuisong; Unser, Sarah; Lew, Scott; Seetharaman, Jayaraman; Xiao, Rong; Acton, Thomas; Everett, John K.; Prestegard, James H.; Hunt, John F.; Montelione, Gaetano; Kennedy, Michael A.

    2012-09-18

    The solution nuclear magnetic resonance (NMR) structures and backbone (15)N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformation. The structures have an extra α-helix compared to the archetypical ACP from Escherichia coli, which has four helices, resulting in a larger opening to the hydrophobic cavity. Chemical shift differences between apo- and holo-RpAcpXL indicated some differences in the hinge region between α2 and α3 and in the hydrophobic cavity environment, but corresponding changes in nuclear Overhauser effect cross-peak patterns were not detected. In contrast to the NMR structures, apo-RpAcpXL was observed in an open conformation in crystals that diffracted to 2.0 Å resolution, which resulted from movement of α3. On the basis of the crystal structure, the predicted biological assembly is a homodimer. Although the possible biological significance of dimerization is unknown, there is potential that the resulting large shared hydrophobic cavity could accommodate the very long-chain fatty acid (28-30 carbons) that this specialized ACP is known to synthesize and transfer to lipid A. These structures are the first representatives of the AcpXL family and the first to indicate that dimerization may be important for the function of these specialized ACPs.

  8. Application of hyaluronic acid in the healing of non-experimental open wounds: A pilot study on 12 wounds in 10 client-owned dogs

    PubMed Central

    Ferrari, Roberta; Boracchi, Patrizia; Romussi, Stefano; Ravasio, Giuliano; Stefanello, Damiano

    2015-01-01

    Aim: Veterinarians have frequently to deal with wounds to the skin, subcutis, and underlying muscle. The aim was to explore the application of hyaluronic acid (HA)-containing dressing on open skin wounds in dogs. The progress of healing was assessed by wound area reduction and two scoring scales applied in human medicine. Materials and Methods: Ten client-owned dogs with 12 cutaneous open wounds healed by the second intention were included. All wounds were treated using available in commerce HA-containing wound dressing from admission to complete re-epithelialization. At every clinical examination, wound area and scale scoring assessments were performed. Results: After debridement, an increased wound size was obtained while an improvement was determined by both grading systems. The median numbers of return to the clinic for bandage change were 5 times. The median time to complete wound healing was 34.5 days. The mean wound area at day 7, 14, 21, and 28 were, respectively, 90.4%, 47.7%, 22.4%, and 14.8% of the original size (for linear measurement) and 95.5%, 54.4%, 23.10%, and 14.8% of the original size (for software measurement). Regarding wound healing assessment tools, the agreement between two operators was considered high for both scales. Conclusions: HA-containing dressing may be a possible wound treatment for cutaneous open wounds in dogs. The assessment of wound quality using scale scoring system could be useful especially in the 1st week and to direct clinical decision-making process. PMID:27047026

  9. Salicylic acid analogues as chemical exchange saturation transfer MRI contrast agents for the assessment of brain perfusion territory and blood-brain barrier opening after intra-arterial infusion.

    PubMed

    Song, Xiaolei; Walczak, Piotr; He, Xiaowei; Yang, Xing; Pearl, Monica; Bulte, Jeff Wm; Pomper, Martin G; McMahon, Michael T; Janowski, Mirosław

    2016-07-01

    The blood-brain barrier (BBB) is a major obstacle for drug delivery to the brain. Predicted, focal opening of the BBB through intra-arterial infusion of hyperosmolar mannitol is feasible, but there is a need to facilitate imaging techniques (e.g. MRI) to guide interventional procedures and assess the outcomes. Here, we show that salicylic acid analogues (SAA) can depict the brain territory supplied by the catheter and detect the BBB opening, through chemical exchange saturation transfer (CEST) MRI. Hyperosmolar SAA solutions themselves are also capable of opening the BBB, and, when multiple SAA agents were co-injected, their locoregional perfusion could be differentiated. PMID:26980755

  10. Uric acid - urine

    MedlinePlus

    ... to filter fluids and waste normally (chronic glomerulonephritis ) Lead poisoning Long-term (chronic) alcohol use Risks There are ... Elsevier Saunders; 2011:chap 28. Read More Gout Lead poisoning Liver disease Polycythemia vera Uric acid - blood Update ...

  11. Intracellular pH Recovery Rates of Hemocytes from Estuarine and Open Ocean Bivalve Species Following In vitro Acid Challenge

    NASA Astrophysics Data System (ADS)

    Croxton, A.; Wikfors, G.

    2013-12-01

    Decreasing pH in estuarine systems is a growing concern for researchers studying mollusk species. Debates continue on whether estuarine bivalve species are more or less vulnerable to ocean acidification than marine species because estuaries can present multiple environmental stressors. The aim of this study is to understand the homeostatic mechanisms of bivalve hemocytes following exposure to extracellular acid treatment. Previous measurements using fluorescent SNARF probes and flow-cytometry have determined the intracellular pH of hemocytes from several bivalve species (eastern oyster, bay scallop, northern quahog, soft-shell clam, and blue mussel) to range between 7.0-7.4. In the present study of four bivalve species, recovery rate profiles were determined for intracellular hemocyte pH following addition of acid to hemolymph in vitro. These profiles indicate that soft-shell clams and bay scallops maintained homeostasis with very little change in intracellular pH. In contrast, an initial drop in intracellular pH in northern quahogs was followed by a steady recovery of intracellular pH. Contrasting results between species appear to be unrelated to mineral shell composition (aragonite vs. calcite) or habitat location (infaunal vs. epifaunal). The next phase of this study will be to determine if offshore species (surfclams and sea scallops) will have similar responses. Results from these studies will provide a better understanding of the physiological responses of estuarine and marine species exposed to acidified environments.

  12. UDP-Glucosyltransferase71C5, a Major Glucosyltransferase, Mediates Abscisic Acid Homeostasis in Arabidopsis1[OPEN

    PubMed Central

    Liu, Zhen; Yan, Jin-Ping; Li, De-Kuan; Yan, Qiujie; Liu, Zhi-Bin; Ye, Li-Ming; Wang, Jian-Mei; Li, Xu-Feng

    2015-01-01

    Abscisic acid (ABA) plays a key role in plant growth and development. The effect of ABA in plants mainly depends on its concentration, which is determined by a balance between biosynthesis and catabolism of ABA. In this study, we characterize a unique UDP-glucosyltransferase (UGT), UGT71C5, which plays an important role in ABA homeostasis by glucosylating ABA to abscisic acid-glucose ester (GE) in Arabidopsis (Arabidopsis thaliana). Biochemical analyses show that UGT71C5 glucosylates ABA in vitro and in vivo. Mutation of UGT71C5 and down-expression of UGT71C5 in Arabidopsis cause delay in seed germination and enhanced drought tolerance. In contrast, overexpression of UGT71C5 accelerates seed germination and reduces drought tolerance. Determination of the content of ABA and ABA-GE in Arabidopsis revealed that mutation in UGT71C5 and down-expression of UGT71C5 resulted in increased level of ABA and reduced level of ABA-GE, whereas overexpression of UGT71C5 resulted in reduced level of ABA and increased level of ABA-GE. Furthermore, altered levels of ABA in plants lead to changes in transcript abundance of ABA-responsive genes, correlating with the concentration of ABA regulated by UGT71C5 in Arabidopsis. Our work shows that UGT71C5 plays a major role in ABA glucosylation for ABA homeostasis. PMID:25713337

  13. Can Read, Can Write

    ERIC Educational Resources Information Center

    Melia, Ed

    2008-01-01

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

  14. Reduced folate and serum vitamin metabolites in patients with rectal carcinoma: an open-label feasibility study of pemetrexed with folic acid and vitamin B12 supplementation

    PubMed Central

    Odin, Elisabeth A.; Carlsson, Göran U.; Kurlberg, Göran K.; Björkqvist, Hillevi G.; Tångefjord, Maria T.; Gustavsson, Bengt G.

    2016-01-01

    The objectives of this single-center, open-label, phase II study were to evaluate (a) the feasibility and safety of neoadjuvant administration of pemetrexed with oral folic acid and vitamin B12 (FA/B12) in newly diagnosed patients with resectable rectal cancer and (b) intracellular and systemic vitamin metabolism. Patients were treated with three cycles of pemetrexed (500 mg/m2, every 3 weeks) and FA/B12 before surgery. The reduced folates tetrahydrofolate, 5-methyltetrahydrofolate, and 5,10-methylenetetrahydrofolate were evaluated from biopsies in tumor tissue and in adjacent mucosa. Serum levels of homocysteine, cystathionine, and methylmalonic acid were also measured. All 37 patients received three cycles of pemetrexed; 89.2% completed their planned dosage within a 9-week feasibility time frame. Neither dose reductions nor study drug-related serious adverse events were reported. Reduced folate levels were significantly higher in tumor tissue compared with adjacent mucosa at baseline. After FA/B12 administration, tissue levels of reduced folates increased significantly and remained high during treatment in both tumor and mucosa until surgery. Serum levels of cystathionine increased significantly compared with baseline after FA/B12 administration, but then decreased, fluctuating cyclically during pemetrexed therapy. Homocysteine and methylmalonic acid levels decreased significantly after FA/B12 administration, and remained below baseline levels during the study. These results indicate that administration of three neoadjuvant cycles of single-agent pemetrexed, every 3 weeks, with FA/B12 in patients with resectable rectal cancer is feasible and tolerable. Tissue and serum vitamin metabolism results demonstrate the influence of pemetrexed and FA/B12 on vitamin metabolism and warrant further study. PMID:26825869

  15. Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach

    PubMed Central

    Adamala, Katarzyna; Anella, Fabrizio; Wieczorek, Rafal; Stano, Pasquale; Chiarabelli, Cristiano; Luisi, Pier Luigi

    2014-01-01

    In this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From the chemical viewpoint, macromolecules are formed by chemical pathways leading to the condensation of building blocks (amino acids, or nucleotides) in long-chain copolymers (proteins and nucleic acids, respectively). The second difficulty deals with a conceptual problem, namely with the emergence of specific sequences among a vast array of possible ones, the huge “sequence space”, leading to the question “why these macromolecules, and not the others?” We have recently addressed these questions by using a chemical synthetic biology approach. In particular, we have tested the catalytic activity of small peptides, like Ser-His, with respect to peptide- and nucleotides-condensation, as a realistic model of primitive organocatalysis. We have also set up a strategy for exploring the sequence space of random proteins and RNAs (the so-called “never born biopolymer” project) with respect to the production of folded structures. Being still far from solved, the main aspects of these “open questions” are discussed here, by commenting on recent results obtained in our groups and by providing a unifying view on the problem and possible solutions. In particular, we propose a general scenario for macromolecule formation via fragment-condensation, as a scheme for the emergence of specific sequences based on molecular growth and selection. PMID:24757502

  16. Reduced folate and serum vitamin metabolites in patients with rectal carcinoma: an open-label feasibility study of pemetrexed with folic acid and vitamin B12 supplementation.

    PubMed

    Stoffregen, Clemens C; Odin, Elisabeth A; Carlsson, Göran U; Kurlberg, Göran K; Björkqvist, Hillevi G; Tångefjord, Maria T; Gustavsson, Bengt G

    2016-06-01

    The objectives of this single-center, open-label, phase II study were to evaluate (a) the feasibility and safety of neoadjuvant administration of pemetrexed with oral folic acid and vitamin B12 (FA/B12) in newly diagnosed patients with resectable rectal cancer and (b) intracellular and systemic vitamin metabolism. Patients were treated with three cycles of pemetrexed (500 mg/m, every 3 weeks) and FA/B12 before surgery. The reduced folates tetrahydrofolate, 5-methyltetrahydrofolate, and 5,10-methylenetetrahydrofolate were evaluated from biopsies in tumor tissue and in adjacent mucosa. Serum levels of homocysteine, cystathionine, and methylmalonic acid were also measured. All 37 patients received three cycles of pemetrexed; 89.2% completed their planned dosage within a 9-week feasibility time frame. Neither dose reductions nor study drug-related serious adverse events were reported. Reduced folate levels were significantly higher in tumor tissue compared with adjacent mucosa at baseline. After FA/B12 administration, tissue levels of reduced folates increased significantly and remained high during treatment in both tumor and mucosa until surgery. Serum levels of cystathionine increased significantly compared with baseline after FA/B12 administration, but then decreased, fluctuating cyclically during pemetrexed therapy. Homocysteine and methylmalonic acid levels decreased significantly after FA/B12 administration, and remained below baseline levels during the study. These results indicate that administration of three neoadjuvant cycles of single-agent pemetrexed, every 3 weeks, with FA/B12 in patients with resectable rectal cancer is feasible and tolerable. Tissue and serum vitamin metabolism results demonstrate the influence of pemetrexed and FA/B12 on vitamin metabolism and warrant further study. PMID:26825869

  17. Phytochrome A and B Function Antagonistically to Regulate Cold Tolerance via Abscisic Acid-Dependent Jasmonate Signaling1[OPEN

    PubMed Central

    Guo, Zhixin; Li, Huizi; Wang, Mengmeng; Zhou, Jie; Xia, Xiaojian; Shi, Kai; Yu, Jingquan

    2016-01-01

    Light signaling and phytohormones both influence plant growth, development, and stress responses; however, cross talk between these two signaling pathways in response to cold remains underexplored. Here, we report that far-red light (FR) and red light (R) perceived by phytochrome A (phyA) and phyB positively and negatively regulated cold tolerance, respectively, in tomato (Solanum lycopersicum), which were associated with the regulation of levels of phytohormones such as abscisic acid (ABA) and jasmonic acid (JA) and transcript levels of ABA- and JA-related genes and the C-REPEAT BINDING FACTOR (CBF) stress signaling pathway genes. A reduction in the R/FR ratio did not alter cold tolerance, ABA and JA accumulation, and transcript levels of ABA- and JA-related genes and the CBF pathway genes in phyA mutant plants; however, those were significantly increased in wild-type and phyB plants with the reduction in the R/FR ratio. Even though low R/FR treatments did not confer cold tolerance in ABA-deficient (notabilis [not]) and JA-deficient (prosystemin-mediated responses2 [spr2]) mutants, it up-regulated ABA accumulation and signaling in the spr2 mutant, with no effect on JA levels and signaling in the not mutant. Foliar application of ABA and JA further confirmed that JA functioned downstream of ABA to activate the CBF pathway in light quality-mediated cold tolerance. It is concluded that phyA and phyB function antagonistically to regulate cold tolerance that essentially involves FR light-induced activation of phyA to induce ABA signaling and, subsequently, JA signaling, leading to an activation of the CBF pathway and a cold response in tomato plants. PMID:26527654

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

    ERIC Educational Resources Information Center

    Wemett, Lisa C.; Bolan, Kimberly

    1998-01-01

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

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

    ERIC Educational Resources Information Center

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

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

  20. 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…

  1. 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…

  2. 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…

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

    ERIC Educational Resources Information Center

    Moodie, Allan G.

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

  4. 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

  5. Diver First Class Reading Ability.

    ERIC Educational Resources Information Center

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

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

  6. 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…

  7. 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…

  8. A School Policy for Reading.

    ERIC Educational Resources Information Center

    Medwell, Jane

    1992-01-01

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

  9. 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…

  10. Reading Activities of American Adults.

    ERIC Educational Resources Information Center

    Sharon, Amiel T.

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

  11. Temporal-Spatial Interaction between Reactive Oxygen Species and Abscisic Acid Regulates Rapid Systemic Acclimation in Plants[W][OPEN

    PubMed Central

    Suzuki, Nobuhiro; Miller, Gad; Salazar, Carolina; Mondal, Hossain A.; Shulaev, Elena; Cortes, Diego F.; Shuman, Joel L.; Luo, Xiaozhong; Shah, Jyoti; Schlauch, Karen; Shulaev, Vladimir; Mittler, Ron

    2013-01-01

    Being sessile organisms, plants evolved sophisticated acclimation mechanisms to cope with abiotic challenges in their environment. These are activated at the initial site of exposure to stress, as well as in systemic tissues that have not been subjected to stress (termed systemic acquired acclimation [SAA]). Although SAA is thought to play a key role in plant survival during stress, little is known about the signaling mechanisms underlying it. Here, we report that SAA in plants requires at least two different signals: an autopropagating wave of reactive oxygen species (ROS) that rapidly spreads from the initial site of exposure to the entire plant and a stress-specific signal that conveys abiotic stress specificity. We further demonstrate that SAA is stress specific and that a temporal–spatial interaction between ROS and abscisic acid regulates rapid SAA to heat stress in plants. In addition, we demonstrate that the rapid ROS signal is associated with the propagation of electric signals in Arabidopsis thaliana. Our findings unravel some of the basic signaling mechanisms underlying SAA in plants and reveal that signaling events and transcriptome and metabolome reprogramming of systemic tissues in response to abiotic stress occur at a much faster rate than previously envisioned. PMID:24038652

  12. A 7-Deoxyloganetic Acid Glucosyltransferase Contributes a Key Step in Secologanin Biosynthesis in Madagascar Periwinkle[C][W][OPEN

    PubMed Central

    Asada, Keisuke; Salim, Vonny; Masada-Atsumi, Sayaka; Edmunds, Elizabeth; Nagatoshi, Mai; Terasaka, Kazuyoshi; Mizukami, Hajime; De Luca, Vincenzo

    2013-01-01

    Iridoids form a broad and versatile class of biologically active molecules found in thousands of plant species. In addition to the many hundreds of iridoids occurring in plants, some iridoids, such as secologanin, serve as key building blocks in the biosynthesis of thousands of monoterpene indole alkaloids (MIAs) and many quinoline alkaloids. This study describes the molecular cloning and functional characterization of three iridoid glucosyltransfeases (UDP-SUGAR GLYCOSYLTRANSFERASE6 [UGT6], UGT7, and UGT8) from Madagascar periwinkle (Catharanthus roseus) with remarkably different catalytic efficiencies. Biochemical analyses reveal that UGT8 possessed a high catalytic efficiency toward its exclusive iridoid substrate, 7-deoxyloganetic acid, making it better suited for the biosynthesis of iridoids in periwinkle than the other two iridoid glucosyltransfeases. The role of UGT8 in the fourth to last step in secologanin biosynthesis was confirmed by virus-induced gene silencing in periwinkle plants, which reduced expression of this gene and resulted in a large decline in secologanin and MIA accumulation within silenced plants. Localization studies of UGT8 using a carborundum abrasion method for RNA extraction show that its expression occurs preferentially within periwinkle leaves rather than in epidermal cells, and in situ hybridization studies confirm that UGT8 is preferentially expressed in internal phloem associated parenchyma cells of periwinkle species. PMID:24104568

  13. Evaluation of the separation characteristics of application-specific (fatty acid methyl esters) open-tubular columns for gas chromatography.

    PubMed

    Kiridena, Waruna; Qian, Jing; Koziol, Wladyslaw W; Poole, Colin F

    2007-03-01

    The solvation parameter model is used to characterize the separation properties of the polar stationary phases EC-Wax and PAG with a poly(ethylene oxide) backbone (substituted with propylene oxide in the case of PAG) and the cyanopropyl-substituted polysilphenylene-siloxane stationary phase BPX90 at five equally spaced temperatures between 60 and 140 degrees C. The separation characteristics of these stationary phases are compared to four PEG and two poly(cyanopropylsiloxane) stationary phases (HP-20M, HP-Innowax, SolGel-Wax, DB-WAXetr, HP-88, and SP-2340) characterized in the same way. The database of system constants for these polar stationary phases is used to provide insight into the separation mechanism for fatty acid methyl esters and to determine selectivity differences that can be expected for generically similar stationary phase types. The discussion is not structured to indicate which stationary phase should be used for a particular separation but to provide a general framework to demonstrate the relationship between the retention mechanism and stationary phase chemistry. PMID:17461115

  14. Environmental Nitrate Stimulates Abscisic Acid Accumulation in Arabidopsis Root Tips by Releasing It from Inactive Stores[OPEN

    PubMed Central

    2016-01-01

    Abscisic acid (ABA) signaling plays a major role in root system development, regulating growth and root architecture. However, the precise localization of ABA remains undetermined. Here, we present a mechanism in which nitrate signaling stimulates the release of bioactive ABA from the inactive storage form, ABA-glucose ester (ABA-GE). We found that ABA accumulated in the endodermis and quiescent center of Arabidopsis thaliana root tips, mimicking the pattern of SCARECROW expression, and (to lower levels) in the vascular cylinder. Nitrate treatment increased ABA levels in root tips; this stimulation requires the activity of the endoplasmic reticulum-localized, ABA-GE-deconjugating enzyme β-GLUCOSIDASE1, but not de novo ABA biosynthesis. Immunogold labeling demonstrated that ABA is associated with cytoplasmic structures near, but not within, the endoplasmic reticulum. These findings demonstrate a mechanism for nitrate-regulated root growth via regulation of ABA accumulation in the root tip, providing insight into the environmental regulation of root growth. PMID:26887919

  15. Paraprofessionals and Reading.

    ERIC Educational Resources Information Center

    Vick, Marian L.

    This pamphlet suggests guidelines to follow for the selection, training, and supervision of paraprofessionals and volunteers in teaching reading and reading-related activities. The contents include: criteria by which paraprofessionals should be selected (emotional stability, ability to relate well to people, ethics, and formal and informal…

  16. 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,…

  17. EXPERIMENTS IN KINDERGARTEN READING.

    ERIC Educational Resources Information Center

    BAKER, EVA L.; AND OTHERS

    FOUR PAPERS GIVEN AT THE READING SYMPOSIUM OF THE 1968 AMERICAN EDUCATIONAL RESEARCH ASSOCIATION PRESENT DISCUSSIONS OF THE SOUTHWEST REGIONAL LABORATORY (SWRL) READING PROGRAM. THE FIRST PAPER DESCRIBES OBJECTIVES, CLASSROOM MATERIALS, AND PROCEDURES. OBJECTIVES FOR SIGHT-RECOGNITION, WORD-ATTACK SKILLS, AND COMPREHENSION SKILLS ARE EXPRESSED IN…

  18. Keep Them Reading

    ERIC Educational Resources Information Center

    Vanneman, Susan

    2010-01-01

    The relentless quest of the school librarian is finding the right book for each student, searching for the home-run book for every child, and keeping students reading book after book after book. A considerable amount of the school librarian's time, effort, and creativity are devoted not only to motivating students to read, but to keeping them…

  19. 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…

  20. Philosophy of Reading Instruction.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    Reading teachers need to provide for individual differences so that each pupil might attain optimally. Methods of teaching reading should be varied and thus reflect diverse philosophies of instruction. These philosophies should be analyzed and used to guide optimal pupil achievement. A philosophy of phoneme/grapheme relationships should be…

  1. 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,…

  2. Visual Search and Reading.

    ERIC Educational Resources Information Center

    Calfee, Robert C.; Jameson, Penny

    The effect on reading speed of the number of target items being searched for and the number of target occurrences in the text was examined. The subjects, 24 college undergraduate volunteers, were presented with a list of target words, and then they read a passage for comprehension which contained occurrences of the target words (Experiment1) or…

  3. 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…

  4. Savoring Reading Schoolwide

    ERIC Educational Resources Information Center

    Reis, Sally M.; Fogarty, Elizabeth A.

    2006-01-01

    Over the past four years, educators and researchers from the University of Connecticut have worked with urban high-poverty schools to implement an alternative reading instruction program called the Schoolwide Enrichment Model in Reading (SEM-R). Based on Renzulli's Enrichment Triad Model, the SEM-R works through planned enrichment experiences to…

  5. INTERMEDIATE READINGS IN TAGALOG.

    ERIC Educational Resources Information Center

    BOWEN, J. DONALD, ED.

    THE SECOND IN A SERIES OF TEXTS DESIGNED TO HELP THE STUDENT ACHIEVE AN UNDERSTANDING OF FILIPINO CULTURE AND ACQUIRE ENOUGH PROFICIENCY IN TAGALOG TO COMMUNICATE EASILY AND MEANINGFULLY, THESE INTERMEDIATE READINGS ARE COORDINATED WITH THE EDITOR'S "BEGINNING TAGALOG" (ED 014 696). INCLUDED IN PART I ARE READINGS WRITTEN ESPECIALLY FOR THIS TEXT…

  6. 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…

  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. Summer Reading Loss

    ERIC Educational Resources Information Center

    Mraz, Maryann; Rasinski, Timothy V.

    2007-01-01

    Summer reading loss is a documented reality for many students. It is often of greatest concern for those who are already at risk, who typically have limited access to reading materials at home and whose parents or caregivers may be reluctant or unsure of how to help. By raising parents' awareness of the importance of supporting their children's…

  9. Reading and Postmodernism.

    ERIC Educational Resources Information Center

    Alexander, James C.

    One of the main differences between the whole language position and the more traditional views lies in the epistemological base upon which whole language is rooted. Although whole language proponents may not have clearly put forth an epistemology upon which their views of reading acquisition and the reading process are based, still a careful…

  10. 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…

  11. Entrepreneurship Education: Supplementary Readings.

    ERIC Educational Resources Information Center

    Scanlan, Thomas J.; And Others

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

  12. 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…

  13. 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…

  14. 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.…

  15. CRITICAL READING DEVELOPS EARLY.

    ERIC Educational Resources Information Center

    LEE, DORRIS; AND OTHERS

    THIS ISSUE OF THE READING AIDS SERIES PRESENTS A DISCUSSION OF THE POTENTIAL FOR CRITICAL READING AMONG YOUNG CHILDREN AND HOW IT CAN BE DEVELOPED. IT OFFERS SUGGESTIONS FOR THE MAXIMUM DEVELOPMENT OF THINKING SKILLS AND ATTITUDES OF INQUIRY AND EVALUATION. SOME OF THE TOPICS DISCUSSED ARE -- (1) THE DEVELOPMENT OF PERCEPTS, CONCEPTS, AND COMMON…

  16. American Reading Instruction.

    ERIC Educational Resources Information Center

    Smith, Nila Banton

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

  17. 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…

  18. An Individualized Reading Program.

    ERIC Educational Resources Information Center

    Davis, Nancy B.

    The operating procedures of a university reading and study skills center for completely individualized reading instruction are described. The program is offered as a student service (no fee) on a voluntary, noncredit basis. A prepared set of instructional tapes is used whereby students can largely serve themselves, proceeding at their own rates,…

  19. 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…

  20. 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…

  1. Reading in Kazakhstan.

    ERIC Educational Resources Information Center

    Beisembaeva, Zhanat Abaevna

    1995-01-01

    Analyzes sociological research conducted by Kazakhstan libraries between 1991 and 1994. Highlights include discussions on the sociology of reading, research results, and library facilities. It was found that reading is characterized by frequent changes in demands of readers caused by dramatic shifts in ideology, politics, and economics in the…

  2. 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…

  3. Reading Field Experience Program.

    ERIC Educational Resources Information Center

    Ceaser, Lisbeth

    The lessons included in this collection were written by California Polytechnic State University Reading Specialist Credential candidates in the Salinas Cohort Project of 1992 as partial fulfillment for an education course titled "Bilingual Special Education Reading Problems." Each lesson is research-based. A rationale describes the reading…

  4. 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…

  5. 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)

  6. Connecting Males and Reading

    ERIC Educational Resources Information Center

    Buddy, Juanita Warren

    2011-01-01

    The problems facing males and reading continues to be a topic of concern and discussion in communities across the country. The author has interviewed school librarians and teachers, however, who are coordinating programs that are successfully connecting male students and reading. This article includes summaries of those interviews. The author has…

  7. 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…

  8. 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)

  9. 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…

  10. Education: Is Reading Important?

    ERIC Educational Resources Information Center

    USA Today, 1980

    1980-01-01

    Summarizes arguments in favor of teaching people to read. Arguments include that television and radio cannot help individuals adapt and retrain quickly in their jobs; promotion in the armed services and elsewhere depends upon a certain degree of reading expertise; and people are unable to fill out income tax and other forms if they do not possess…

  11. Motivating Students To Read.

    ERIC Educational Resources Information Center

    Kane, Roberta S.; Warner, Dori

    This action research project implemented a program for motivating students to read so that they would become enthusiastic, lifelong readers. The targeted population consisted of first- and second-grade students in a middle class community located in a western suburb of Chicago, Illinois. The problem of lack of motivation in reading was documented…

  12. Children's Reading Strategies.

    ERIC Educational Resources Information Center

    Brown, Rexel E., Ed.

    1980-01-01

    This issue of the "Journal of Children and Youth" focuses on children's strategies for decoding and comprehending written language and teacher's strategies for facilitating this process. The issue includes eleven papers by members of the Indiana Reading Professors division of the Indiana State Reading Council and several invited guests. Peggy…

  13. Reading and Perestroika.

    ERIC Educational Resources Information Center

    Plotnikov, Sergei N.

    1992-01-01

    Presents a short historical and sociological analysis of reading in the Soviet Union from the beginning of the twentieth century to perestroika. Discusses some sociocultural problems associated with reading, including the prevailing social, economic and political crises in all spheres of life, particularly the cultural. (RS)

  14. 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…

  15. 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…

  16. Reading for Life

    ERIC Educational Resources Information Center

    McKearney, Miranda

    2009-01-01

    The Reading Agency has been backing and building a movement in libraries called reader development. The movement is creating a livelier, more interventionist reading service that's both much more attractive and socially relevant. A focus on reader development is changing the way public libraries work, and transforming people's lives in the…

  17. 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…

  18. 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…

  19. Extending Extensive Reading

    ERIC Educational Resources Information Center

    Day, Richard R.

    2015-01-01

    The April 2015 issue of "Reading in a Foreign Language" featured a discussion forum on extensive reading (ER). Most of the authors, recognized authorities on ER, discussed their views of the principles of ER, particularly in establishing and conducting ER programs. The purpose of this discussion is to review developments in the practice…

  20. 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…

  1. 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)

  2. 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…

  3. PASS and Reading Achievement.

    ERIC Educational Resources Information Center

    Kirby, John R.

    Two studies examined the effectiveness of the PASS (Planning, Attention, Simultaneous, and Successive cognitive processes) theory of intelligence in predicting reading achievement scores of normally achieving children and distinguishing children with reading disabilities from normally achieving children. The first study dealt with predicting…

  4. 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…

  5. 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…

  6. Unlocking Short Read Sequencing for Metagenomics

    PubMed Central

    Timberlake, Sonia C.; Blackburn, Matthew C.; Malmstrom, Rex R.; Alm, Eric J.; Chisholm, Sallie W.

    2010-01-01

    Background Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved. Methodology/Principal Findings We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read. Conclusions/Significance This strategy is broadly applicable to sequencing applications that benefit from low-cost high-throughput sequencing, but require longer read lengths. We demonstrate that our approach enables metagenomic analyses using the Illumina Genome Analyzer, with low error rates, and at a fraction of the cost of pyrosequencing. PMID:20676378

  7. An Ancestral Role for CONSTITUTIVE TRIPLE RESPONSE1 Proteins in Both Ethylene and Abscisic Acid Signaling1[OPEN

    PubMed Central

    Yasumura, Yuki; Pierik, Ronald; Kelly, Steven; Sakuta, Masaaki; Voesenek, Laurentius A.C.J.; Harberd, Nicholas P.

    2015-01-01

    Land plants have evolved adaptive regulatory mechanisms enabling the survival of environmental stresses associated with terrestrial life. Here, we focus on the evolution of the regulatory CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) component of the ethylene signaling pathway that modulates stress-related changes in plant growth and development. First, we compare CTR1-like proteins from a bryophyte, Physcomitrella patens (representative of early divergent land plants), with those of more recently diverged lycophyte and angiosperm species (including Arabidopsis [Arabidopsis thaliana]) and identify a monophyletic CTR1 family. The fully sequenced P. patens genome encodes only a single member of this family (PpCTR1L). Next, we compare the functions of PpCTR1L with that of related angiosperm proteins. We show that, like angiosperm CTR1 proteins (e.g. AtCTR1 of Arabidopsis), PpCTR1L modulates downstream ethylene signaling via direct interaction with ethylene receptors. These functions, therefore, likely predate the divergence of the bryophytes from the land-plant lineage. However, we also show that PpCTR1L unexpectedly has dual functions and additionally modulates abscisic acid (ABA) signaling. In contrast, while AtCTR1 lacks detectable ABA signaling functions, Arabidopsis has during evolution acquired another homolog that is functionally distinct from AtCTR1. In conclusion, the roles of CTR1-related proteins appear to have functionally diversified during land-plant evolution, and angiosperm CTR1-related proteins appear to have lost an ancestral ABA signaling function. Our study provides new insights into how molecular events such as gene duplication and functional differentiation may have contributed to the adaptive evolution of regulatory mechanisms in plants. PMID:26243614

  8. Abscisic Acid- and Stress-Induced Highly Proline-Rich Glycoproteins Regulate Root Growth in Rice1[W][OPEN

    PubMed Central

    Tseng, I-Chieh; Hong, Chwan-Yang; Yu, Su-May; Ho, Tuan-Hua David

    2013-01-01

    In the root of rice (Oryza sativa), abscisic acid (ABA) treatment, salinity, or water deficit stress induces the expression of a family of four genes, REPETITIVE PROLINE-RICH PROTEIN (RePRP). These genes encode two subclasses of novel proline-rich glycoproteins with highly repetitive PX1PX2 motifs, RePRP1 and RePRP2. RePRP orthologs exist only in monocotyledonous plants, and their functions are virtually unknown. Rice RePRPs are heavily glycosylated with arabinose and glucose on multiple hydroxyproline residues. They are significantly different from arabinogalactan proteins that have glycan chains composed of arabinose and galactose. Transient and stable expressions of RePRP-green fluorescent protein reveal that a fraction of this protein is localized to the plasma membrane. In rice roots, ABA treatment increases RePRP expression preferentially in the elongation zone. Overexpression of RePRP in transgenic rice reduces root cell elongation in the absence of ABA, similar to the effect of ABA on wild-type roots. Conversely, simultaneous knockdown of the expression of RePRP1 and RePRP2 reduces the root sensitivity to ABA, indicating that RePRP proteins play an essential role in ABA/stress regulation of root growth and development. Moreover, rice RePRPs specifically interact with a polysaccharide, arabinogalactan, in a dosage-dependent manner. It is suggested that RePRP1 and RePRP2 are functionally redundant suppressors of root cell expansion and probably act through interactions with cell wall components near the plasma membrane. PMID:23886623

  9. A Single Amino-Acid Substitution in the Sodium Transporter HKT1 Associated with Plant Salt Tolerance1[OPEN

    PubMed Central

    Ali, Akhtar; Aman, Rashid; Park, Hyeong Cheol; Jan, Masood; Baek, Dongwon; Khan, Irfan Ullah; Oh, Dong-Ha; Lee, Sang Yeol; Bressan, Ray A.; Lee, Keun Woo; Maggio, Albino; Yun, Dae-Jin

    2016-01-01

    A crucial prerequisite for plant growth and survival is the maintenance of potassium uptake, especially when high sodium surrounds the root zone. The Arabidopsis HIGH-AFFINITY K+ TRANSPORTER1 (HKT1), and its homologs in other salt-sensitive dicots, contributes to salinity tolerance by removing Na+ from the transpiration stream. However, TsHKT1;2, one of three HKT1 copies in Thellungiella salsuginea, a halophytic Arabidopsis relative, acts as a K+ transporter in the presence of Na+ in yeast (Saccharomyces cerevisiae). Amino-acid sequence comparisons indicated differences between TsHKT1;2 and most other published HKT1 sequences with respect to an Asp residue (D207) in the second pore-loop domain. Two additional T. salsuginea and most other HKT1 sequences contain Asn (n) in this position. Wild-type TsHKT1;2 and altered AtHKT1 (AtHKT1N-D) complemented K+-uptake deficiency of yeast cells. Mutant hkt1-1 plants complemented with both AtHKT1N-D and TsHKT1;2 showed higher tolerance to salt stress than lines complemented by the wild-type AtHKT1. Electrophysiological analysis in Xenopus laevis oocytes confirmed the functional properties of these transporters and the differential selectivity for Na+ and K+ based on the n/d variance in the pore region. This change also dictated inward-rectification for Na+ transport. Thus, the introduction of Asp, replacing Asn, in HKT1-type transporters established altered cation selectivity and uptake dynamics. We describe one way, based on a single change in a crucial protein that enabled some crucifer species to acquire improved salt tolerance, which over evolutionary time may have resulted in further changes that ultimately facilitated colonization of saline habitats. PMID:27208305

  10. Silicon- and Tin-Containing Open-Chain and Eight-Membered-Ring Compounds as Bicentric Lewis Acids toward Anions.

    PubMed

    Wendji, Anicet Siakam; Dietz, Christina; Kühn, Silke; Lutter, Michael; Schollmeyer, Dieter; Hiller, Wolf; Jurkschat, Klaus

    2016-01-01

    Herein, we report the syntheses of silicon- and tin-containing open-chain and eight-membered-ring compounds Me2 Si(CH2 SnMe2 X)2 (2, X=Me; 3, X=Cl; 4, X=F), CH2 (SnMe2 CH2 I)2 (7), CH2 (SnMe2 CH2 Cl)2 (8), cyclo-Me2 Sn(CH2 SnMe2 CH2 )2 SiMe2 (6), cyclo-(Me2 SnCH2 )4 (9), cyclo-Me(2-n) Xn Sn(CH2 SiMe2 CH2 )2 SnXn Me(2-n) (5, n=0; 10, n=1, X=Cl; 11, n=1, X=F; 12, n=2, X=Cl), and the chloride and fluoride complexes NEt4 [cyclo- Me(Cl)Sn(CH2 SiMe2 CH2 )2 Sn(Cl)Me⋅F] (13), PPh4 [cyclo-Me(Cl)Sn(CH2 SiMe2 CH2 )2 Sn(Cl)Me⋅Cl] (14), NEt4 [cyclo-Me(F)Sn(CH2 SiMe2 CH2 )2 Sn(F)Me⋅F] (15), [NEt4 ]2 [cyclo-Cl2 Sn(CH2 SiMe2 CH2 )2 SnCl2 ⋅2 Cl] (16), M[Me2 Si(CH2 Sn(Cl)Me2 )2 ⋅Cl] (17 a, M=PPh4 ; 17 b, M=NEt4 ), NEt4 [Me2 Si(CH2 Sn(Cl)Me2 )2 ⋅F] (18), NEt4 [Me2 Si(CH2 Sn(F)Me2 )2 ⋅F] (19), and PPh4 [Me2 Si(CH2 Sn(Cl)Me2 )2 ⋅Br] (20). The compounds were characterised by electrospray mass-spectrometric, IR and (1) H, (13) C, (19) F, (29) Si, and (119) Sn NMR spectroscopic analysis, and, except for 15 and 18, single-crystal X-ray diffraction studies. PMID:26616743

  11. 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.…

  12. 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…

  13. 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…

  14. 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…

  15. A genetic scale of reading frame coding.

    PubMed

    Michel, Christian J

    2014-08-21

    The reading frame coding (RFC) of codes (sets) of trinucleotides is a genetic concept which has been largely ignored during the last 50 years. A first objective is the definition of a new and simple statistical parameter PrRFC for analysing the probability (efficiency) of reading frame coding (RFC) of any trinucleotide code. A second objective is to reveal different classes and subclasses of trinucleotide codes involved in reading frame coding: the circular codes of 20 trinucleotides and the bijective genetic codes of 20 trinucleotides coding the 20 amino acids. This approach allows us to propose a genetic scale of reading frame coding which ranges from 1/3 with the random codes (RFC probability identical in the three frames) to 1 with the comma-free circular codes (RFC probability maximal in the reading frame and null in the two shifted frames). This genetic scale shows, in particular, the reading frame coding probabilities of the 12,964,440 circular codes (PrRFC=83.2% in average), the 216 C(3) self-complementary circular codes (PrRFC=84.1% in average) including the code X identified in eukaryotic and prokaryotic genes (PrRFC=81.3%) and the 339,738,624 bijective genetic codes (PrRFC=61.5% in average) including the 52 codes without permuted trinucleotides (PrRFC=66.0% in average). Otherwise, the reading frame coding probabilities of each trinucleotide code coding an amino acid with the universal genetic code are also determined. The four amino acids Gly, Lys, Phe and Pro are coded by codes (not circular) with RFC probabilities equal to 2/3, 1/2, 1/2 and 2/3, respectively. The amino acid Leu is coded by a circular code (not comma-free) with a RFC probability equal to 18/19. The 15 other amino acids are coded by comma-free circular codes, i.e. with RFC probabilities equal to 1. The identification of coding properties in some classes of trinucleotide codes studied here may bring new insights in the origin and evolution of the genetic code. PMID:24698943

  16. Interruptions disrupt reading comprehension.

    PubMed

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

    2015-06-01

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

  17. 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

  18. Reading, Writing, and Running.

    ERIC Educational Resources Information Center

    Detherage, Jim

    1980-01-01

    Describes an English course that capitalizes on the popularity of running, integrating running with reading and writing activities. Notes the positive results of this interdisciplinary approach. Provides samples of student writings. (RL)

  19. 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

  20. 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)

  1. 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)

  2. 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.

  3. A School Reading Policy.

    ERIC Educational Resources Information Center

    Dawson, Alan

    1978-01-01

    Defines a school-based reading policy and explores the issues involved in setting up a program, including awareness and use of school resources, recording student progress, evaluation, parental involvement, and classroom organization and teaching methods. (FL)

  4. The "Enigma" Reading Program.

    ERIC Educational Resources Information Center

    Sachs, Frances Greenberg; Banas, Norma

    1985-01-01

    Approaches are discussed for constructing and implementing the ENIGMA (Engineering Individual Growth Through Manipulative Associations) reading program, a language-based activity using teacher-made puzzles and stories in a manipulative-associative manner. (CL)

  5. Reading Improvement Through Art

    ERIC Educational Resources Information Center

    Corwin, Sylvia K.

    1977-01-01

    A team of enthusiastic, dedicated teachers proved that for problem readers in today's high schools, in a setting where trained reading teachers collaborated with studio teachers, the visual arts can be an important tool for learning. (Author)

  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. Reading-Boxing Class

    ERIC Educational Resources Information Center

    Kravitz, Richard; Shapiro, Marvin

    1969-01-01

    The physical education department of the Pennsylvania Advancement School of Philadelphia has established a reading and communication skill project that uses the appeal of sports to help students improve their basic skills. (Author)

  8. Developmental reading disorder

    MedlinePlus

    ... people with DRD have normal or above-average intelligence. DRD may appear with other problems. These can ... causes of learning and reading disabilities, such as: Emotional disorders Intellectual disability Brain diseases Certain cultural and ...

  9. 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…

  10. 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…

  11. 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…

  12. 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…

  13. 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…

  14. Parents' Reading-Related Knowledge and Children's Reading Acquisition

    ERIC Educational Resources Information Center

    Ladd, Megan; Martin-Chang, Sandra; Levesque, Kyle

    2011-01-01

    Teacher reading-related knowledge (phonological awareness and phonics knowledge) predicts student reading, however little is known about the reading-related knowledge of parents. Participants comprised 70 dyads (children from kindergarten and grade 1 and their parents). Parents were administered a questionnaire tapping into reading-related…

  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. A Developmental Path to Reading: Reading the Signs.

    ERIC Educational Resources Information Center

    Mitchell, Kevin, Ed.

    2000-01-01

    This issue focuses on the developmental path that children typically take when learning to read. The purpose is to help parents take steps to ensure that their children will make the transition from learning to read to reading to learn by the end of third grade. An introductory section includes two articles: "Parents, Children, and Reading" (Carol…

  17. Reading Motivation and Reading Engagement: Clarifying Commingled Conceptions

    ERIC Educational Resources Information Center

    Unrau, Norman J.; Quirk, Matthew

    2014-01-01

    The constructs of motivation for reading and reading engagement have frequently become blurred and ambiguous in both research and discussions of practice. To address this commingling of constructs, the authors provide a concise review of the literature on motivation for reading and reading engagement and illustrate the blurring of those concepts…

  18. 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"…

  19. 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'…

  20. 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…

  1. 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,"…

  2. READING MANUAL, A GUIDEBOOK FOR ILLINOIS WORKSHOPS IN READING REMEDIATION.

    ERIC Educational Resources Information Center

    COVEY, CATHERINE

    THE IMPORTANCE OF ADAPTING READING INSTRUCTION TO EACH CHILD'S NEEDS IS STRESSED IN THIS HANDBOOK FOR TEACHERS OF REMEDIAL READING. INFORMATION IS ORGANIZED AROUND SIX TOPICS--(1) THE NATURE OF THE READING PROCESS, (2) CRITERIA FOR A GOOD ELEMENTARY READING PROGRAM, (3) REMEDIAL READERS, THE SYMPTOMS AND CAUSES (PHYSICAL, INTELLECTUAL,…

  3. 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…

  4. 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…

  5. 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…

  6. Reading Networks at Rest

    PubMed Central

    Kelly, Clare; Shehzad, Zarrar; Penesetti, Deepak; Castellanos, F. Xavier; Milham, Michael P.

    2010-01-01

    Resting-state functional connectivity (RSFC) approaches offer a novel tool to delineate distinct functional networks in the brain. In the present functional magnetic resonance imaging (fMRI) study, we elucidated patterns of RSFC associated with 6 regions of interest selected primarily from a meta-analysis on word reading (Bolger DJ, Perfetti CA, Schneider W. 2005. Cross-cultural effect on the brain revisited: universal structures plus writing system variation. Hum Brain Mapp. 25: 92–104). In 25 native adult readers of English, patterns of positive RSFC were consistent with patterns of task-based activity and functional connectivity associated with word reading. Moreover, conjunction analyses highlighted the posterior left inferior frontal gyrus and the posterior left middle temporal gyrus (post-LMTG) as potentially important loci of functional interaction among 5 of the 6 reading networks. The significance of the post-LMTG has typically been unappreciated in task-based studies on unimpaired readers but is frequently reported to be a locus of hypoactivity in dyslexic readers and exhibits intervention-induced changes of activity in dyslexic children. Finally, patterns of negative RSFC included not only regions of the so-called default mode network but also regions involved in effortful controlled processes, which may not be required once reading becomes automatized. In conclusion, the current study supports the utility of resting-state fMRI for investigating reading networks and has direct relevance for the understanding of reading disorders such as dyslexia. PMID:20139150

  7. Binocular advantages in reading.

    PubMed

    Jainta, Stephanie; Blythe, Hazel I; Liversedge, Simon P

    2014-03-01

    Reading, an essential skill for successful function in today's society, is a complex psychological process involving vision, memory, and language comprehension. Variability in fixation durations during reading reflects the ease of text comprehension, and increased word frequency results in reduced fixation times. Critically, readers not only process the fixated foveal word but also preprocess the parafoveal word to its right, thereby facilitating subsequent foveal processing. Typically, text is presented binocularly, and the oculomotor control system precisely coordinates the two frontally positioned eyes online. Binocular, compared to monocular, visual processing typically leads to superior performance, termed the "binocular advantage"; few studies have investigated the binocular advantage in reading. We used saccade-contingent display change methodology to demonstrate the benefit of binocular relative to monocular text presentation for both parafoveal and foveal lexical processing during reading. Our results demonstrate that denial of a unified visual signal derived from binocular inputs provides a cost to the efficiency of reading, particularly in relation to high-frequency words. Our findings fit neatly with current computational models of eye movement control during reading, wherein successful word identification is a primary determinant of saccade initiation. PMID:24530062

  8. Identification of Open Stomata1-Interacting Proteins Reveals Interactions with Sucrose Non-fermenting1-Related Protein Kinases2 and with Type 2A Protein Phosphatases That Function in Abscisic Acid Responses1[OPEN

    PubMed Central

    Waadt, Rainer; Manalansan, Bianca; Rauniyar, Navin; Munemasa, Shintaro; Booker, Matthew A.; Brandt, Benjamin; Waadt, Christian; Nusinow, Dmitri A.; Kay, Steve A.; Kunz, Hans-Henning; Schumacher, Karin; DeLong, Alison; Yates, John R.; Schroeder, Julian I.

    2015-01-01

    The plant hormone abscisic acid (ABA) controls growth and development and regulates plant water status through an established signaling pathway. In the presence of ABA, pyrabactin resistance/regulatory component of ABA receptor proteins inhibit type 2C protein phosphatases (PP2Cs). This, in turn, enables the activation of Sucrose Nonfermenting1-Related Protein Kinases2 (SnRK2). Open Stomata1 (OST1)/SnRK2.6/SRK2E is a major SnRK2-type protein kinase responsible for mediating ABA responses. Arabidopsis (Arabidopsis thaliana) expressing an epitope-tagged OST1 in the recessive ost1-3 mutant background was used for the copurification and identification of OST1-interacting proteins after osmotic stress and ABA treatments. These analyses, which were confirmed using bimolecular fluorescence complementation and coimmunoprecipitation, unexpectedly revealed homo- and heteromerization of OST1 with SnRK2.2, SnRK2.3, OST1, and SnRK2.8. Furthermore, several OST1-complexed proteins were identified as type 2A protein phosphatase (PP2A) subunits and as proteins involved in lipid and galactolipid metabolism. More detailed analyses suggested an interaction network between ABA-activated SnRK2-type protein kinases and several PP2A-type protein phosphatase regulatory subunits. pp2a double mutants exhibited a reduced sensitivity to ABA during seed germination and stomatal closure and an enhanced ABA sensitivity in root growth regulation. These analyses add PP2A-type protein phosphatases as another class of protein phosphatases to the interaction network of SnRK2-type protein kinases. PMID:26175513

  9. 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…

  10. Woodcock Diagnostic Reading Battery (WDRB).

    ERIC Educational Resources Information Center

    Simon, Janet

    1999-01-01

    This article describes the Woodcock Diagnostic Reading Battery, an instrument designed to assess the abilities and achievements of individuals ages 4 through 90 in the areas of basic reading skills, reading comprehension, phonological awareness, oral language comprehension, and reading aptitude. Its administration, standardization, reliability,…

  11. Focus on Reading. New Edition.

    ERIC Educational Resources Information Center

    Hood, Susan; Solomon, Nicky; Burns, Anne

    The handbook is designed as an introductory text on reading instruction for teachers of English as a Second Language. The first chapter explores the nature of reading through a series of activities that help identify the kind of knowledge one draws on and the strategies one uses in reading. Chapter 2 reviews key theories of reading that have…

  12. 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…

  13. DEVELOPING HIGH SCHOOL READING PROGRAMS.

    ERIC Educational Resources Information Center

    DAWSON, MILDRED A.

    FORTY-FOUR REPRINTS CONCERNING HIGH SCHOOL READING PROGRAMS SELECTED FROM "THE READING TEACHER" AND THE "JOURNAL OF READING" AND THE PROCEEDINGS OF THE INTERNATIONAL READING ASSOCIATION ARE PRESENTED. THE CRITERIA FOR SELECTION WERE CONSISTENCY WITH ACCEPTED CURRICULAR AND INSTRUCTIONAL PRINCIPLES, CURRENT APPROPRIATENESS, DUPLICATION, AND…

  14. 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…

  15. 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;…

  16. 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…

  17. 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…

  18. Paired Reading: Psycholinguistics in Practice.

    ERIC Educational Resources Information Center

    Barrett, James Martin

    1987-01-01

    Contends that children need to learn phonic skills, not necessarily through early direct teaching, but through reading experience. Suggests using Paired Reading, which is validated by psycholinguistic reading theory and provides opportunities to learn to read from context and use innate syntactic and semantic knowledge. (SKC)

  19. Effective interventions for reading disability.

    PubMed

    Williams, M C; Lecluyse, K; Rock-Faucheux, A

    1992-06-01

    A simple, readily accessible, and inexpensive intervention which produces immediate improvements in the reading comprehension abilities of reading-disabled children has been found. The intervention consists of colored overlays, or overlays which reduce the contrast of printed materials. This intervention produces reading comprehension gains in approximately 80 percent of the reading-disabled children tested. PMID:1378860

  20. 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"…

  1. Student Accountability: Guided Reading Kidstations

    ERIC Educational Resources Information Center

    Guastello, E. Francine; Lenz, Claire

    2005-01-01

    Guided reading is a major component of a comprehensive or balanced reading program. Most teachers understand the value of guided reading in the classroom but have difficulty managing effective implementation. They often ask, "What will the other students be doing when I am working with a guided reading group, and how do I manage all the children…

  2. Reading in the Geography Curriculum.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    To become an efficient reader of subject matter in geography, students need to have adequate background information to read the ensuing content. Vocabulary considerations thoroughly enter into the reading act. A major problem for the teacher when students read geographical content is to develop meaning. To assist students in reading and…

  3. 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),…

  4. Early Reading and Concrete Operations.

    ERIC Educational Resources Information Center

    Polk, Cindy L. Howes; Goldstein, David

    1980-01-01

    Indicated that early readers are more likely to be advanced in cognitive development than are nonearly-reading peers. After one year of formal reading instruction, early readers maintained their advantage in reading achievement. Measures of concrete operations were found to predict reading achievement for early and nonearly readers. (Author/DB)

  5. 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…

  6. The Role of Independent Reading in a "Balanced" Reading Program: Re-Thinking California's Reading Initiative.

    ERIC Educational Resources Information Center

    Jonson, Kathleen F.

    1998-01-01

    Notes that California undertook a new commitment to improve the basic reading skills of its elementary students; lists several components of this commitment, the "California Reading Initiative." Describes the state's definition of a balanced and comprehensive approach to reading. Argues that independent reading is a crucial component and should…

  7. Reading to Learn and Reading to Integrate: New Tasks for Reading Comprehension Tests?

    ERIC Educational Resources Information Center

    Trites, Latricia; McGroarty, Mary

    2005-01-01

    To address the concern that most traditional reading comprehension tests only measure basic comprehension, this study designed measures to assess more complex reading tasks: Reading to Learn and Reading to Integrate. The new measures were taken by 251 participants: 105 undergraduate native speakers of English, 106 undergraduate nonnative speakers,…

  8. 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.…

  9. 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,…

  10. 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,…

  11. 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…

  12. Reading Visual Braille with a Retinal Prosthesis

    PubMed Central

    Lauritzen, Thomas Z.; Harris, Jordan; Mohand-Said, Saddek; Sahel, Jose A.; Dorn, Jessy D.; McClure, Kelly; Greenberg, Robert J.

    2012-01-01

    Retinal prostheses, which restore partial vision to patients blinded by outer retinal degeneration, are currently in clinical trial. The Argus II retinal prosthesis system was recently awarded CE approval for commercial use in Europe. While retinal prosthesis users have achieved remarkable visual improvement to the point of reading letters and short sentences, the reading process is still fairly cumbersome. This study investigates the possibility of using an epiretinal prosthesis to stimulate visual braille as a sensory substitution for reading written letters and words. The Argus II retinal prosthesis system, used in this study, includes a 10 × 6 electrode array implanted epiretinally, a tiny video camera mounted on a pair of glasses, and a wearable computer that processes the video and determines the stimulation current of each electrode in real time. In the braille reading system, individual letters are created by a subset of dots from a 3 by 2 array of six dots. For the visual braille experiment, a grid of six electrodes was chosen out of the 10 × 6 Argus II array. Groups of these electrodes were then directly stimulated (bypassing the camera) to create visual percepts of individual braille letters. Experiments were performed in a single subject. Single letters were stimulated in an alternative forced choice (AFC) paradigm, and short 2–4-letter words were stimulated (one letter at a time) in an open-choice reading paradigm. The subject correctly identified 89% of single letters, 80% of 2-letter, 60% of 3-letter, and 70% of 4-letter words. This work suggests that text can successfully be stimulated and read as visual braille in retinal prosthesis patients. PMID:23189036

  13. A Vision of Reading.

    PubMed

    Grainger, Jonathan; Dufau, Stéphane; Ziegler, Johannes C

    2016-03-01

    Different fields of research within the cognitive sciences have investigated basic processes in reading, but progress has been hampered by limited cross-fertilization. We propose a theoretical framework aimed at facilitating integration of findings obtained via these different approaches with respect to the impact of visual factors on reading. We describe a specialized system for parallel letter processing that assigns letter identities to different locations along the horizontal meridian within the limits imposed by visual acuity and crowding. Spatial attention is used to set up this system during reading development, and difficulty in doing so has repercussions in terms of efficient translation of the orthographic code into its phonological counterpart, and fast access to semantics from print. PMID:26809725

  14. Oral Language and Reading; Proceedings of the Annual Reading Conference of the Department of Elementary Education at Indiana State University (3rd, Terre Haute, June 14-15, 1973).

    ERIC Educational Resources Information Center

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

    This pamphlet is a collection of the speeches given at the Third Annual Reading Conference at Indiana State University, Terre Haute. The theme of the conference was "Oral Language and Reading." The contents include: "Official Program"; opening remarks, "They Led and Followed," by William G. McCarthy; opening address, "Strategies for Reading…

  15. Drugstore Reading Glasses

    NASA Astrophysics Data System (ADS)

    Erlichson, Herman

    2006-03-01

    The occasion for this paper was my reading of a paper in the February 2005 issue of TPT. As one gets older the near point of the eye begins to recede.2 This is called presbyopia.3 An alternative to purchasing glasses from an optometrist is to purchase an inexpensive pair of reading glasses in a pharmacy. The pharmacy has these glasses ordered by diopters corresponding to the strength of the lens needed for a particular presbyopic eye. The glasses are, of course, not available for myopic eyes.

  16. SchemaOnRead Manual

    SciTech Connect

    North, Michael J.

    2015-09-30

    SchemaOnRead provides tools for implementing schema-on-read including a single function call (e.g., schemaOnRead("filename")) that reads text (TXT), comma separated value (CSV), raster image (BMP, PNG, GIF, TIFF, and JPG), R data (RDS), HDF5, NetCDF, spreadsheet (XLS, XLSX, ODS, and DIF), Weka Attribute-Relation File Format (ARFF), Epi Info (REC), Pajek network (PAJ), R network (NET), Hypertext Markup Language (HTML), SPSS (SAV), Systat (SYS), and Stata (DTA) files. It also recursively reads folders (e.g., schemaOnRead("folder")), returning a nested list of the contained elements.

  17. Vocabulary Assistance before and during Reading

    ERIC Educational Resources Information Center

    Alessi, Stephen; Dwyer, Angelique

    2008-01-01

    Intermediate learners of Spanish read a Spanish newspaper article with vocabulary assistance either before reading, while reading, both, or without any such assistance. Reading performance was significantly better for students receiving vocabulary assistance during reading, but not for those receiving it before reading. Reading time of the…

  18. A Read-Aloud for Science (Read It Aloud).

    ERIC Educational Resources Information Center

    Richardson, Judy S.; Breen, Margaret

    1996-01-01

    Recommends a young adult read-aloud selection for science classes on endangered species. Describes listening, writing, discussing, investigating, and debating activities capitalizing on this read-aloud. (SR)

  19. Children with Reading Disorders--I. Efficacy of Reading Remediation.

    ERIC Educational Resources Information Center

    Gittelman, Rachel; Feingold, Ingrid

    1983-01-01

    The efficacy of reading remediation, which emphasizes phonic decoding, was examined in 61 children (ages 7 through 13 years) with pure reading disorders. Comparisons between pre- and post intervention data clearly support the efficacy of remediation. (MP)

  20. Reading improvement in English- and Hebrew-speaking children with reading difficulties after reading acceleration training.

    PubMed

    Horowitz-Kraus, Tzipi; Cicchino, Nicole; Amiel, Merav; Holland, Scott K; Breznitz, Zvia

    2014-10-01

    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. Results of pre- and post-testing of reading abilities point to a significant main effect of the test, demonstrating improvements in silent contextual reading speed, reading comprehension, and speed of processing in both Hebrew and English training groups as compared to their performance before the intervention. This study indicates that the Reading Acceleration Program might be an effective program for improving reading abilities in children, independent of language. PMID:24919641