A 21.7 kb DNA segment on the left arm of yeast chromosome XIV carries WHI3, GCR2, SPX18, SPX19, an homologue to the heat shock gene SSB1 and 8 new open reading frames of unknown function.

Science.gov (United States)

Jonniaux, J L; Coster, F; Purnelle, B; Goffeau, A

1994-12-01

We report the amino acid sequence of 13 open reading frames (ORF > 299 bp) located on a 21.7 kb DNA segment from the left arm of chromosome XIV of Saccharomyces cerevisiae. Five open reading frames had been entirely or partially sequenced previously: WHI3, GCR2, SPX19, SPX18 and a heat shock gene similar to SSB1. The products of 8 other ORFs are new putative proteins among which N1394 is probably a membrane protein. N1346 contains a leucine zipper pattern and the corresponding ORF presents an HAP (global regulator of respiratory genes) upstream activating sequence in the promoting region. N1386 shares homologies with the DNA structure-specific recognition protein family SSRPs and the corresponding ORF is preceded by an MCB (MluI cell cycle box) upstream activating factor.

Yeast Interacting Proteins Database: YCL046W, YGL115W [Yeast Interacting Proteins Database

Lifescience Database Archive (English)

Full Text Available YCL046W - Dubious open reading frame unlikely to encode a protein, based on availab...ading frame unlikely to encode a protein, based on available experimental and comparative sequence data; par

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

Science.gov (United States)

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…

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

Energy Technology Data Exchange (ETDEWEB)

Kim, Kyoung Mi; Cho, Hana [School of Life Sciences and Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of); Kim, Yoon Ki, E-mail: yk-kim@korea.ac.kr [School of Life Sciences and Biotechnology, Korea University, Seoul 136-701 (Korea, Republic of)

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.

Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples.

Science.gov (United States)

Grant, Susan; Grant, William D; Cowan, Don A; Jones, Brian E; Ma, Yanhe; Ventosa, Antonio; Heaphy, Shaun

2006-01-01

Here we describe the application of metagenomic technologies to construct cDNA libraries from RNA isolated from environmental samples. RNAlater (Ambion) was shown to stabilize RNA in environmental samples for periods of at least 3 months at -20 degrees C. Protocols for library construction were established on total RNA extracted from Acanthamoeba polyphaga trophozoites. The methodology was then used on algal mats from geothermal hot springs in Tengchong county, Yunnan Province, People's Republic of China, and activated sludge from a sewage treatment plant in Leicestershire, United Kingdom. The Tenchong libraries were dominated by RNA from prokaryotes, reflecting the mainly prokaryote microbial composition. The majority of these clones resulted from rRNA; only a few appeared to be derived from mRNA. In contrast, many clones from the activated sludge library had significant similarity to eukaryote mRNA-encoded protein sequences. A library was also made using polyadenylated RNA isolated from total RNA from activated sludge; many more clones in this library were related to eukaryotic mRNA sequences and proteins. Open reading frames (ORFs) up to 378 amino acids in size could be identified. Some resembled known proteins over their full length, e.g., 36% match to cystatin, 49% match to ribosomal protein L32, 63% match to ribosomal protein S16, 70% to CPC2 protein. The methodology described here permits the polyadenylated transcriptome to be isolated from environmental samples with no knowledge of the identity of the microorganisms in the sample or the necessity to culture them. It has many uses, including the identification of novel eukaryotic ORFs encoding proteins and enzymes.

Identification of immunogenic and virulence-associated Campylobacter jejuni proteins

DEFF Research Database (Denmark)

Nielsen, Lene Nørby; Luijkx, Thomas A.; Vegge, Christina Skovgaard

2012-01-01

With the aim of identifying proteins important for host interaction and virulence, we have screened an expression library of NCTC 11168 Campylobacter jejuni genes for highly immunogenic proteins. A commercial C. jejuni open reading frame (ORF) library consisting of more than 1,600 genes was trans......With the aim of identifying proteins important for host interaction and virulence, we have screened an expression library of NCTC 11168 Campylobacter jejuni genes for highly immunogenic proteins. A commercial C. jejuni open reading frame (ORF) library consisting of more than 1,600 genes...

Adenovirus type 9 E4 open reading frame 1 encodes a transforming protein required for the production of mammary tumors in rats.

OpenAIRE

Javier, R T

1994-01-01

The E4 region of human adenovirus type 9 (Ad9) transforms established rat embryo fibroblasts and encodes an essential determinant for the production of estrogen-dependent mammary tumors in rats. Testing of the seven Ad9 E4 open reading frames (ORFs) individually for transformation of the established rat embryo fibroblast cell line CREF indicated that only Ad9 E4 ORF1 possessed a significant ability to generate transformed foci on these cells. In contrast, the E4 ORF1 sequences from human Ad5 ...

Virtual knotting in proteins and other open curves

Science.gov (United States)

Alexander, Keith; Taylor, Alexander; Dennis, Mark

Long filaments naturally knot, from string to long-chain molecules. Knotting in a filament affects its properties, and may be very stable or disappear under slight manipulation. Knotting has been identified in protein backbones for which these mechanical constraints are of fundamental importance to their function, although they are open curves in which knots are not mathematically well defined; knotting can only be identified by closing the ends of the chain. We introduce a new method for resolving knotting in open curves using virtual knots, a wider class of topological objects that do not use a classical closure, capturing the topological ambiguity of open curves. Having analysed all proteins in the Protein Data Bank by this new scheme, we recover and extend previous knotting results, and identify topological interest in some new cases. The statistics of virtual knots in proteins are compared with those of Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important. This work was supported by the Leverhulme Trust Programme Grant ``Scientific Properties of Complex Knots'' and the EPSRC.

DNA vaccination of pigs with open reading frame 1-7 of PRRS virus

DEFF Research Database (Denmark)

Barfoed, Annette Malene; Blixenkrone-Møller, Merete; Jensen, Merethe Holm

2004-01-01

We cloned all open reading frames of a Danish isolate of porcine reproductive and respiratory syndrome (PRRS) virus in DNA vaccination vectors. Pigs were vaccinated using a gene gun with each single construct (ORF1, ORF2, ORF3, ORF4, ORF5, ORF6, or ORF7) or combinations thereof. Vaccination...

Serological diagnosis of Strongylus vulgaris infection: use of a recombinant protein

DEFF Research Database (Denmark)

Andersen, Ulla Vestergaard; Howe, Daniel K.; Olsen, Susanne Nautrup

, an immunoreactive cDNA clone was subcloned into E. coli and the plasmid sequenced, the open reading frame encoding the mature protein was cloned into a pET22b expression vector and expressed as a His-tagged recombinant protein in BL21 expression cells. The recombinant protein was used in an indirect enzyme....... vulgaris (n=9) reacted against the recombinant protein, expressed as optic density (OD) readings of >24 % of a positive control, while sera from negative horses had OD readings

Protein adsorption onto nanozeolite: effect of micropore openings.

Science.gov (United States)

Wu, Jiamin; Li, Xiang; Yan, Yueer; Hu, Yuanyuan; Zhang, Yahong; Tang, Yi

2013-09-15

A clear and deep understanding of protein adsorption on porous surfaces is desirable for the reasonable design and applications of porous materials. In this study, the effect of surface micropores on protein adsorption was systematically investigated by comparing adsorption behavior of cytochrome c (Cyto-c) and Candida antarctica Lipase B (CALB) on porous and non-porous nanozeolites silicalite-1 and Beta. It was found that micropore openings on the surface of nanozeolites played a key role in determining adsorption affinity, conformations, and activities of proteins. Both Cyto-c and CALB showed higher affinity to porous nanozeolites than to non-porous ones, resulting in greater conformational change of proteins on porous surfaces which in turn affected their bio-catalytic performance. The activity of Cyto-c improved while that of CALB decreased on porous nanozeolites. Recognition of certain amino acid residues or size-matching secondary structures by micropore openings on the surface of nanozeolites was proposed to be the reason. Moreover, the pore opening effect of porous nanozeolites on protein behavior could be altered by changing protein coverage on them. This study gives a novel insight into the interaction between proteins and microporous materials, which will help to guide the rational fabrication and bio-applications of porous materials in the future. Copyright © 2013 Elsevier Inc. All rights reserved.

Euglena gracilis chloroplast DNA: analysis of a 1.6 kb intron of the psb C gene containing an open reading frame of 458 codons.

Science.gov (United States)

Montandon, P E; Vasserot, A; Stutz, E

1986-01-01

We retrieved a 1.6 kbp intron separating two exons of the psb C gene which codes for the 44 kDa reaction center protein of photosystem II. This intron is 3 to 4 times the size of all previously sequenced Euglena gracilis chloroplast introns. It contains an open reading frame of 458 codons potentially coding for a basic protein of 54 kDa of yet unknown function. The intron boundaries follow consensus sequences established for chloroplast introns related to class II and nuclear pre-mRNA introns. Its 3'-terminal segment has structural features similar to class II mitochondrial introns with an invariant base A as possible branch point for lariat formation.

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

Science.gov (United States)

Huson, Daniel H; Tappu, Rewati; Bazinet, Adam L; Xie, Chao; Cummings, Michael P; Nieselt, Kay; Williams, Rohan

2017-01-25

Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes. We present a new method for performing gene-centric assembly, called protein-alignment-guided assembly, and provide an implementation in our metagenome analysis tool MEGAN. Genes are assembled on the fly, based on the alignment of all reads against a protein reference database such as NCBI-nr. Specifically, the user selects a gene family based on a classification such as KEGG and all reads binned to that gene family are assembled. Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered. Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way.

Adenovirus E4 open reading frame 4-induced dephosphorylation inhibits E1A activation of the E2 promoter and E2F-1-mediated transactivation independently of the retinoblastoma tumor suppressor protein

DEFF Research Database (Denmark)

Mannervik, M; Fan, S; Ström, A C

1999-01-01

of the viral E4 open reading frame 4 (E4-ORF4) protein. This effect does not to require the retinoblastoma protein that previously has been shown to regulate E2F activity. The inhibitory activity of E4-ORF4 appears to be specific because E4-ORF4 had little effect on, for example, E4-ORF6/7 transactivation......Previous studies have shown that the cell cycle-regulated E2F transcription factor is subjected to both positive and negative control by phosphorylation. Here we show that in transient transfection experiments, adenovirus E1A activation of the viral E2 promoter is abrogated by coexpression...... of the E2 promoter. We further show that the repressive effect of E4-ORF4 on E2 transcription works mainly through the E2F DNA-binding sites in the E2 promoter. In agreement with this, we find that E4-ORF4 inhibits E2F-1/DP-1-mediated transactivation. We also show that E4-ORF4 inhibits E2 mRNA expression...

Observing Protein & Energy Nutrition (OPEN) Study

Science.gov (United States)

The Observing Protein and Energy Nutrition (OPEN) Study was designed to assess dietary measurement error by comparing results from self-reported dietary intake data with four dietary biomarkers: doubly labeled water and urinary nitrogen, sodium, and potassium.

Specific Increase of Protein Levels by Enhancing Translation Using Antisense Oligonucleotides Targeting Upstream Open Frames.

Science.gov (United States)

Liang, Xue-Hai; Shen, Wen; Crooke, Stanley T

2017-01-01

A number of diseases are caused by low levels of key proteins; therefore, increasing the amount of specific proteins in human bodies is of therapeutic interest. Protein expression is downregulated by some structural or sequence elements present in the 5' UTR of mRNAs, such as upstream open reading frames (uORF). Translation initiation from uORF(s) reduces translation from the downstream primary ORF encoding the main protein product in the same mRNA, leading to a less efficient protein expression. Therefore, it is possible to use antisense oligonucleotides (ASOs) to specifically inhibit translation of the uORF by base-pairing with the uAUG region of the mRNA, redirecting translation machinery to initiate from the primary AUG site. Here we review the recent findings that translation of specific mRNAs can be enhanced using ASOs targeting uORF regions. Appropriately designed and optimized ASOs are highly specific, and they act in a sequence- and position-dependent manner, with very minor off-target effects. Protein levels can be increased using this approach in different types of human and mouse cells, and, importantly, also in mice. Since uORFs are present in around half of human mRNAs, the uORF-targeting ASOs may thus have valuable potential as research tools and as therapeutics to increase the levels of proteins for a variety of genes.

Molecular typing of methicillin-resistant Staphylococcus aureus: Comparison of PCR-based open reading frame typing, multilocus sequence typing, and Staphylococcus protein A gene typing.

Science.gov (United States)

Ogihara, Shinji; Saito, Ryoichi; Sawabe, Etsuko; Kozakai, Takahiro; Shima, Mari; Aiso, Yoshibumi; Fujie, Toshihide; Nukui, Yoko; Koike, Ryuji; Hagihara, Michio; Tohda, Shuji

2018-04-01

The recently developed PCR-based open reading frame typing (POT) method is a useful molecular typing tool. Here, we evaluated the performance of POT for molecular typing of methicillin-resistant Staphylococcus aureus (MRSA) isolates and compared its performance to those of multilocus sequence typing (MLST) and Staphylococcus protein A gene typing (spa typing). Thirty-seven MRSA isolates were collected between July 2012 and May 2015. MLST, spa typing, and POT were performed, and their discriminatory powers were evaluated using Simpson's index analysis. The MRSA isolates were classified into 11, 18, and 33 types by MLST, spa typing, and POT, respectively. The predominant strains identified by MLST, spa typing, and POT were ST8 and ST764, t002, and 93-191-127, respectively. The discriminatory power of MLST, spa typing, and POT was 0.853, 0.875, and 0.992, respectively, indicating that POT had the highest discriminatory power. Moreover, the results of MLST and spa were available after 2 days, whereas that of POT was available in 5 h. Furthermore, POT is rapid and easy to perform and interpret. Therefore, POT is a superior molecular typing tool for monitoring nosocomial transmission of MRSA. Copyright © 2017 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Expression, purification and biochemical characterization of a single-stranded DNA binding protein from Herbaspirillum seropedicae.

Science.gov (United States)

Vernal, Javier; Serpa, Viviane I; Tavares, Carolina; Souza, Emanuel M; Pedrosa, Fábio O; Terenzi, Hernán

2007-05-01

An open reading frame encoding a protein similar in size and sequence to the Escherichia coli single-stranded DNA binding protein (SSB protein) was identified in the Herbaspirillum seropedicae genome. This open reading frame was cloned into the expression plasmid pET14b. The SSB protein from H. seropedicae, named Hs_SSB, was overexpressed in E. coli strain BL21(DE3) and purified to homogeneity. Mass spectrometry data confirmed the identity of this protein. The apparent molecular mass of the native Hs_SSB was estimated by gel filtration, suggesting that the native protein is a tetramer made up of four similar subunits. The purified protein binds to single-stranded DNA (ssDNA) in a similar manner to other SSB proteins. The production of this recombinant protein in good yield opens up the possibility of obtaining its 3D-structure and will help further investigations into DNA metabolism.

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

Science.gov (United States)

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.

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

OpenAIRE

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 asso...

Streamlined sign-out of capillary protein electrophoresis using middleware and an open-source macro application.

Science.gov (United States)

Mathur, Gagan; Haugen, Thomas H; Davis, Scott L; Krasowski, Matthew D

2014-01-01

Interfacing of clinical laboratory instruments with the laboratory information system (LIS) via "middleware" software is increasingly common. Our clinical laboratory implemented capillary electrophoresis using a Sebia(®) Capillarys-2™ (Norcross, GA, USA) instrument for serum and urine protein electrophoresis. Using Data Innovations Instrument Manager, an interface was established with the LIS (Cerner) that allowed for bi-directional transmission of numeric data. However, the text of the interpretive pathology report was not properly transferred. To reduce manual effort and possibility for error in text data transfer, we developed scripts in AutoHotkey, a free, open-source macro-creation and automation software utility. Scripts were written to create macros that automated mouse and key strokes. The scripts retrieve the specimen accession number, capture user input text, and insert the text interpretation in the correct patient record in the desired format. The scripts accurately and precisely transfer narrative interpretation into the LIS. Combined with bar-code reading by the electrophoresis instrument, the scripts transfer data efficiently to the correct patient record. In addition, the AutoHotKey script automated repetitive key strokes required for manual entry into the LIS, making protein electrophoresis sign-out easier to learn and faster to use by the pathology residents. Scripts allow for either preliminary verification by residents or final sign-out by the attending pathologist. Using the open-source AutoHotKey software, we successfully improved the transfer of text data between capillary electrophoresis software and the LIS. The use of open-source software tools should not be overlooked as tools to improve interfacing of laboratory instruments.

Streamlined sign-out of capillary protein electrophoresis using middleware and an open-source macro application

Directory of Open Access Journals (Sweden)

Gagan Mathur

2014-01-01

Full Text Available Background: Interfacing of clinical laboratory instruments with the laboratory information system (LIS via "middleware" software is increasingly common. Our clinical laboratory implemented capillary electrophoresis using a Sebia; Capillarys-2™ (Norcross, GA, USA instrument for serum and urine protein electrophoresis. Using Data Innovations Instrument Manager, an interface was established with the LIS (Cerner that allowed for bi-directional transmission of numeric data. However, the text of the interpretive pathology report was not properly transferred. To reduce manual effort and possibility for error in text data transfer, we developed scripts in AutoHotkey, a free, open-source macro-creation and automation software utility. Materials and Methods: Scripts were written to create macros that automated mouse and key strokes. The scripts retrieve the specimen accession number, capture user input text, and insert the text interpretation in the correct patient record in the desired format. Results: The scripts accurately and precisely transfer narrative interpretation into the LIS. Combined with bar-code reading by the electrophoresis instrument, the scripts transfer data efficiently to the correct patient record. In addition, the AutoHotKey script automated repetitive key strokes required for manual entry into the LIS, making protein electrophoresis sign-out easier to learn and faster to use by the pathology residents. Scripts allow for either preliminary verification by residents or final sign-out by the attending pathologist. Conclusions: Using the open-source AutoHotKey software, we successfully improved the transfer of text data between capillary electrophoresis software and the LIS. The use of open-source software tools should not be overlooked as tools to improve interfacing of laboratory instruments.

Open Oncology Notes: A Qualitative Study of Oncology Patients' Experiences Reading Their Cancer Care Notes.

Science.gov (United States)

Kayastha, Neha; Pollak, Kathryn I; LeBlanc, Thomas W

2018-04-01

Electronic medical records increasingly allow patients access to clinician notes. Although most believe that open notes benefits patients, some suggest negative consequences. Little is known about the experiences of patients with cancer reading their medical notes; thus we aimed to describe this qualitatively. We interviewed 20 adults with metastatic or incurable cancer receiving cancer treatment. The semistructured qualitative interviews included four segments: assessing their overall experience reading notes, discussing how notes affected their cancer care experiences, reading a real note with the interviewer, and making suggestions for improvement. We used a constant comparison approach to analyze these qualitative data. We found four themes. Patients reported that notes resulted in the following: (1) increased comprehension; (2) ameliorated uncertainty, relieved anxiety, and facilitated control; (3) increased trust; and (4) for a subset of patients, increased anxiety. Patients described increased comprehension because notes refreshed their memory and clarified their understanding of visits. This helped mitigate the unfamiliarity of cancer, addressing uncertainty and relieving anxiety. Notes facilitated control, empowering patients to ask clinicians more questions. The transparency of notes also increased trust in clinicians. For a subset of patients, however, notes were emotionally difficult to read and raised concerns. Patients identified medical jargon and repetition in notes as areas for improvement. Most patients thought that reading notes improved their care experiences. A small subset of patients experienced increased distress. As reading notes becomes a routine part of the patient experience, physicians might want to elicit and address concerns that arise from notes, thereby further engaging patients in their care.

OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

Directory of Open Access Journals (Sweden)

Johnson Helen L

2008-01-01

Full Text Available Abstract Background Information extraction (IE efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a diverse literature. Here we report on the design, implementation and several evaluations of OpenDMAP, an ontology-driven, integrated concept analysis system. It significantly advances the state of the art in information extraction by leveraging knowledge in ontological resources, integrating diverse text processing applications, and using an expanded pattern language that allows the mixing of syntactic and semantic elements and variable ordering. Results OpenDMAP information extraction systems were produced for extracting protein transport assertions (transport, protein-protein interaction assertions (interaction and assertions that a gene is expressed in a cell type (expression. Evaluations were performed on each system, resulting in F-scores ranging from .26 – .72 (precision .39 – .85, recall .16 – .85. Additionally, each of these systems was run over all abstracts in MEDLINE, producing a total of 72,460 transport instances, 265,795 interaction instances and 176,153 expression instances. Conclusion OpenDMAP advances the performance standards for extracting protein-protein interaction predications from the full texts of biomedical research articles. Furthermore, this level of performance appears to generalize to other information extraction tasks, including extracting information about predicates of more than two arguments. The output of the information extraction system is always constructed from elements of an ontology, ensuring that the knowledge representation is grounded with respect to a carefully constructed model of reality. The results of these efforts can be used to increase the efficiency of manual curation efforts and to provide additional features in systems that integrate multiple sources for

Drosophila Nora virus capsid proteins differ from those of other picorna-like viruses.

Science.gov (United States)

Ekström, Jens-Ola; Habayeb, Mazen S; Srivastava, Vaibhav; Kieselbach, Thomas; Wingsle, Gunnar; Hultmark, Dan

2011-09-01

The recently discovered Nora virus from Drosophila melanogaster is a single-stranded RNA virus. Its published genomic sequence encodes a typical picorna-like cassette of replicative enzymes, but no capsid proteins similar to those in other picorna-like viruses. We have now done additional sequencing at the termini of the viral genome, extending it by 455 nucleotides at the 5' end, but no more coding sequence was found. The completeness of the final 12,333-nucleotide sequence was verified by the production of infectious virus from the cloned genome. To identify the capsid proteins, we purified Nora virus particles and analyzed their proteins by mass spectrometry. Our results show that the capsid is built from three major proteins, VP4A, B and C, encoded in the fourth open reading frame of the viral genome. The viral particles also contain traces of a protein from the third open reading frame, VP3. VP4A and B are not closely related to other picorna-like virus capsid proteins in sequence, but may form similar jelly roll folds. VP4C differs from the others and is predicted to have an essentially α-helical conformation. In a related virus, identified from EST database sequences from Nasonia parasitoid wasps, VP4C is encoded in a separate open reading frame, separated from VP4A and B by a frame-shift. This opens a possibility that VP4C is produced in non-equimolar quantities. Altogether, our results suggest that the Nora virus capsid has a different protein organization compared to the order Picornavirales. Copyright © 2011 Elsevier B.V. All rights reserved.

Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion.

Science.gov (United States)

Cohrs, Randall J; Lee, Katherine S; Beach, Addilynn; Sanford, Bridget; Baird, Nicholas L; Como, Christina; Graybill, Chiharu; Jones, Dallas; Tekeste, Eden; Ballard, Mitchell; Chen, Xiaomi; Yalacki, David; Frietze, Seth; Jones, Kenneth; Lenac Rovis, Tihana; Jonjić, Stipan; Haas, Jürgen; Gilden, Don

2017-10-15

The neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture. IMPORTANCE Viruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiple in vitro passages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture. Copyright © 2017 American Society for Microbiology.

The virion-associated open reading frame 49 of murine gammaherpesvirus 68 promotes viral replication both in vitro and in vivo as a derepressor of RTA.

Science.gov (United States)

Noh, Cheol-Woo; Cho, Hye-Jeong; Kang, Hye-Ri; Jin, Hyun Yong; Lee, Shaoying; Deng, Hongyu; Wu, Ting-Ting; Arumugaswami, Vaithilingaraja; Sun, Ren; Song, Moon Jung

2012-01-01

Replication and transcription activator (RTA), an immediate-early gene, is a key molecular switch to evoke lytic replication of gammaherpesviruses. Open reading frame 49 (ORF49) is conserved among gammaherpesviruses and shown to cooperate with RTA in regulating virus lytic replication. Here we show a molecular mechanism and in vivo functions of murine gammaherpesvirus 68 (MHV-68 or γHV-68) ORF49. MHV-68 ORF49 was transcribed and translated as a late gene. The ORF49 protein was associated with a virion, interacting with the ORF64 large tegument protein and the ORF25 capsid protein. Moreover, ORF49 directly bound to RTA and its negative cellular regulator, poly(ADP-ribose) polymerase-1 (PARP-1), and disrupted the interactions of RTA and PARP-1. Productive replication of an ORF49-deficient mutant virus (49S) was attenuated in vivo as well as in vitro. Likewise, latent infection was also impaired in the spleen of 49S-infected mice. Taken together, our results suggest that the virion-associated ORF49 protein may promote virus replication both in vitro and in vivo by providing an optimal environment in the early phase of virus infection as a derepressor of RTA.

Molecular characterization of a heme-binding protein of Bacteroides fragilis BE1.

OpenAIRE

Otto, B R; Kusters, J G; Luirink, J; de Graaf, F K; Oudega, B

1996-01-01

An iron-repressible 44-kDa outer membrane protein plays a crucial role in the acquisition of heme by the anaerobic bacterium Bacteroides fragilis. The DNA sequence of the gene encoding the 44-kDa protein (hupA) was determined. The hupA gene encodes a protein of 431 amino acid residues with a calculated molecular mass of 48,189 Da. The hupA gene is preceded by an open reading frame of 480 bp that probably encodes a protein with a calculated molecular mass of 18,073 Da. hupA and this open readi...

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

Science.gov (United States)

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…

Polydopamine-coated open tubular column for the separation of proteins by capillary electrochromatography.

Science.gov (United States)

Xiao, Xing; Wang, Wentao; Chen, Jia; Jia, Li

2015-08-01

The separation and determination of proteins in food is an important aspect in food industry. Inspired by the self-polymerization of dopamine under alkaline conditions and the natural adhesive properties of polydopamine, in this paper, a simple and economical method was developed for the preparation of polydopamine-coated open tubular column, in which ammonium persulfate was used as the source of oxygen to induce and facilitate the polymerization of dopamine to form polydopamine. In comparison with a naked fused-silica capillary, the direction and magnitude of the electro-osmotic flow of the as-prepared polydopamine-coated open tubular column could be manipulated by varying the pH values of background solutions due to the existence of amine and phenolic hydroxyl groups on polydopamine coating. The surface morphology of the polydopamine-coated open tubular column was studied by scanning electron microscopy, and the thickness of polydopamine coating was 106 nm. The performance of the polydopamine-coated open tubular column was validated by analysis of proteins. The relative standard deviations of migration times of proteins representing run-to-run, day-to-day, and column-to-column were less than 3.5%. In addition, the feasibility of the polydopamine-coated open tubular column for real samples was verified by the separation of proteins in chicken egg white and pure milk. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conserved-peptide upstream open reading frames (CPuORFs are associated with regulatory genes in angiosperms

Directory of Open Access Journals (Sweden)

Richard A Jorgensen

2012-08-01

Full Text Available Upstream open reading frames (uORFs are common in eukaryotic transcripts, but those that encode conserved peptides (CPuORFs occur in less than 1% of transcripts. The peptides encoded by three plant CPuORF families are known to control translation of the downstream ORF in response to a small signal molecule (sucrose, polyamines and phosphocholine. In flowering plants, transcription factors are statistically over-represented among genes that possess CPuORFs, and in general it appeared that many CPuORF genes also had other regulatory functions, though the significance of this suggestion was uncertain (Hayden and Jorgensen, 2007. Five years later the literature provides much more information on the functions of many CPuORF genes. Here we reassess the functions of 27 known CPuORF gene families and find that 22 of these families play a variety of different regulatory roles, from transcriptional control to protein turnover, and from small signal molecules to signal transduction kinases. Clearly then, there is indeed a strong association of CPuORFs with regulatory genes. In addition, 16 of these families play key roles in a variety of different biological processes. Most strikingly, the core sucrose response network includes three different CPuORFs, creating the potential for sophisticated balancing of the network in response to three different molecular inputs. We propose that the function of most CPuORFs is to modulate translation of a downstream major ORF (mORF in response to a signal molecule recognized by the conserved peptide and that because the mORFs of CPuORF genes generally encode regulatory proteins, many of them centrally important in the biology of plants, CPuORFs play key roles in balancing such regulatory networks.

Long interspersed element-1 protein expression is a hallmark of many human cancers.

Science.gov (United States)

Rodić, Nemanja; Sharma, Reema; Sharma, Rajni; Zampella, John; Dai, Lixin; Taylor, Martin S; Hruban, Ralph H; Iacobuzio-Donahue, Christine A; Maitra, Anirban; Torbenson, Michael S; Goggins, Michael; Shih, Ie-Ming; Duffield, Amy S; Montgomery, Elizabeth A; Gabrielson, Edward; Netto, George J; Lotan, Tamara L; De Marzo, Angelo M; Westra, William; Binder, Zev A; Orr, Brent A; Gallia, Gary L; Eberhart, Charles G; Boeke, Jef D; Harris, Chris R; Burns, Kathleen H

2014-05-01

Cancers comprise a heterogeneous group of human diseases. Unifying characteristics include unchecked abilities of tumor cells to proliferate and spread anatomically, and the presence of clonal advantageous genetic changes. However, universal and highly specific tumor markers are unknown. Herein, we report widespread long interspersed element-1 (LINE-1) repeat expression in human cancers. We show that nearly half of all human cancers are immunoreactive for a LINE-1-encoded protein. LINE-1 protein expression is a common feature of many types of high-grade malignant cancers, is rarely detected in early stages of tumorigenesis, and is absent from normal somatic tissues. Studies have shown that LINE-1 contributes to genetic changes in cancers, with somatic LINE-1 insertions seen in selected types of human cancers, particularly colon cancer. We sought to correlate this observation with expression of the LINE-1-encoded protein, open reading frame 1 protein, and found that LINE-1 open reading frame 1 protein is a surprisingly broad, yet highly tumor-specific, antigen. Copyright © 2014 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

cDNA cloning and mRNA expression of heat shock protein 70 gene ...

African Journals Online (AJOL)

In this study, the full-length heat shock protein 70 of Tegillarca granosa was cloned from cDNA library by rapid amplification of cDNA end (RACE). The open reading frame (ORF) of heat shock protein 70 was 1968 bp, and it encoded a protein of 655 amino acids with a predicted molecular weight of 71.48 kDa and an ...

An upstream open reading frame controls translation of var2csa, a gene implicated in placental malaria.

Directory of Open Access Journals (Sweden)

Borko Amulic

2009-01-01

Full Text Available Malaria, caused by the parasite Plasmodium falciparum, is responsible for substantial morbidity, mortality and economic losses in tropical regions of the world. Pregnant women are exceptionally vulnerable to severe consequences of the infection, due to the specific adhesion of parasite-infected erythrocytes in the placenta. This adhesion is mediated by a unique variant of PfEMP1, a parasite encoded, hyper-variable antigen placed on the surface of infected cells. This variant, called VAR2CSA, binds to chondroitin sulfate A on syncytiotrophoblasts in the intervillous space of placentas. VAR2CSA appears to only be expressed in the presence of a placenta, suggesting that its expression is actively repressed in men, children or non-pregnant women; however, the mechanism of repression is not understood. Using cultured parasite lines and reporter gene constructs, we show that the gene encoding VAR2CSA contains a small upstream open reading frame that acts to repress translation of the resulting mRNA, revealing a novel form of gene regulation in malaria parasites. The mechanism underlying this translational repression is reversible, allowing high levels of protein translation upon selection, thus potentially enabling parasites to upregulate expression of this variant antigen in the presence of the appropriate host tissue.

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

Science.gov (United States)

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

2013-10-01

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

Tomato golden mosaic virus open reading frame AL4 is genetically distinct from its C4 analogue in monopartite geminiviruses.

Science.gov (United States)

Pooma, W; Petty, I T

1996-08-01

Tomato golden mosaic virus (TGMV) is a bipartite geminivirus with six well-characterized genes. An additional open reading frame (ORF), AL4, lies within the essential AL1 gene. Recent studies of monopartite, dicot-infecting geminiviruses have revealed that mutations in their analogous C4 ORFs have host-specific effects on infectivity, symptomatology, virus movement and/or viral DNA accumulation. We have investigated whether TGMV has a similar host-specific requirement for AL4. The phenotypes of three TGMV al4 mutants were determined in a range of hosts, which included species that revealed c4 mutant phenotypes for monopartite geminiviruses. Each TGMV al4 mutant was indistinguishable from wild-type TGMV in all hosts tested. Additional analyses of double mutants revealed no evidence for functional redundancy between AL4 and the AL3, or AR1 genes. In contrast to the putative C4 proteins of monpartite geminiviruses, TGMV AL4, if it is expressed, is either non-functional, or functionally redundant with an essential TGMV gene product.

Identification and validation of novel small proteins in Pseudomonas putida

DEFF Research Database (Denmark)

Yang, Xiaochen; Ingemann Jensen, Sheila; Wulff, Tune

2016-01-01

Small proteins of fifty amino acids or less have been understudied due to difficulties that impede their annotation and detection. In order to obtain information on small open reading frames (sORFs) in P. putida, bioinformatic and proteomic approaches were used to identify putative small open...... reading frames (sORFs) in the well-characterized strain KT2440. A plasmid-based system was established for sORF validation, enabling expression of C-terminal sequential peptide affinity (SPA) tagged variants and their detection via protein immunoblotting. Out of 22 tested putative sORFs, the expression...... of fourteen sORFs was confirmed, where all except one are novel. All of the validated sORFs except one are located adjacent to annotated genes on the same strand and three are in close proximity to genes with known functions. These include an ABC transporter operon and the two transcriptional regulators Fis...

Identification of endogenous retroviral reading frames in the human genome

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Wiuf Carsten

2004-10-01

Full Text Available Abstract Background Human endogenous retroviruses (HERVs comprise a large class of repetitive retroelements. Most HERVs are ancient and invaded our genome at least 25 million years ago, except for the evolutionary young HERV-K group. The far majority of the encoded genes are degenerate due to mutational decay and only a few non-HERV-K loci are known to retain intact reading frames. Additional intact HERV genes may exist, since retroviral reading frames have not been systematically annotated on a genome-wide scale. Results By clustering of hits from multiple BLAST searches using known retroviral sequences we have mapped 1.1% of the human genome as retrovirus related. The coding potential of all identified HERV regions were analyzed by annotating viral open reading frames (vORFs and we report 7836 loci as verified by protein homology criteria. Among 59 intact or almost-intact viral polyproteins scattered around the human genome we have found 29 envelope genes including two novel gammaretroviral types. One encodes a protein similar to a recently discovered zebrafish retrovirus (ZFERV while another shows partial, C-terminal, homology to Syncytin (HERV-W/FRD. Conclusions This compilation of HERV sequences and their coding potential provide a useful tool for pursuing functional analysis such as RNA expression profiling and effects of viral proteins, which may, in turn, reveal a role for HERVs in human health and disease. All data are publicly available through a database at http://www.retrosearch.dk.

Identification and characterization of a novel Chlamydia trachomatis reticulate body protein

DEFF Research Database (Denmark)

Shaw, Allan C; Larsen, Martin Røssel; Roepstorff, Peter

2002-01-01

The genome of the obligate intracellular bacterium Chlamydia trachomatis comprises 894 genes predicted by computer-based analysis. As part of a large-scale proteome analysis of C. trachomatis, a small abundant protein encoded by a previously unrecognized novel 204-bp open reading frame was identi...... cycle. The protein is rapidly degraded and is only present in reticulate or intermediate bodies, suggesting a possible function in the intracellular stage of C. trachomatis development. We have termed the protein '7-kDa reticulate body protein'....

Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus , family

Directory of Open Access Journals (Sweden)

Aneta Gubala

2017-07-01

Full Text Available Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector.

Genome-wide screens for expressed hypothetical proteins

DEFF Research Database (Denmark)

Madsen, Claus Desler; Durhuus, Jon Ambæk; Rasmussen, Lene Juel

2012-01-01

A hypothetical protein (HP) is defined as a protein that is predicted to be expressed from an open reading frame, but for which there is no experimental evidence of translation. HPs constitute a substantial fraction of proteomes of human as well as of other organisms. With the general belief that...... that the majority of HPs are the product of pseudogenes, it is essential to have a tool with the ability of pinpointing the minority of HPs with a high probability of being expressed....

The Reading Environment; Proceedings of the Annual Reading Conference (8th, Terre Haute, Indiana, June 15-16, 1978).

Science.gov (United States)

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

The papers presented in this annual reading conference report focus on various aspects of the topic, "The Reading Environment." The opening address advocates establishing reading programs that correspond to the developmental stages of individual children--programs that consider the needs of the whole child. The other papers delivered at the…

Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins.

Science.gov (United States)

Plant, Ewan P; Rakauskaite, Rasa; Taylor, Deborah R; Dinman, Jonathan D

2010-05-01

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed -1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the -1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a "golden mean" model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins.

Close connections between open science and open-source software

Directory of Open Access Journals (Sweden)

YouHua Chen

2014-09-01

Full Text Available Open science is increasingly gaining attention in recent years. In this mini-review, we briefly discuss and summarize the reasons of introducing open science into academic publications for scientists. We argue that open-source software (like R and Python software can be the universal and important platforms for doing open science because of their appealing features: open source, easy-reading document, commonly used in various scientific disciplines like statistics, chemistry and biology. At last, the challenges and future perspectives of performing open science are discussed.

A novel glutamine-rich putative transcriptional adaptor protein (TIG-1), preferentially expressed in placental and bone-marrow tissues.

Science.gov (United States)

Abraham, S; Solomon, W B

2000-09-19

We used a subtractive hybridization protocol to identify novel expressed sequence tags (ESTs) corresponding to mRNAs whose expression was induced upon exposure of the human leukemia cell line K562 to the phorbol ester 12-O-tetradecanolyphorbol-13-acetate (TPA). The complete open reading frame of one of the novel ESTs, named TIG-1, was obtained by screening K562 cell and placental cDNA libraries. The deduced open reading frame of the TIG-1 cDNA encodes for a glutamine repeat-rich protein with a predicted molecular weight of 63kDa. The predicted open reading frame also contains a consensus bipartite nuclear localization signal, though no specific DNA-binding domain is found. The corresponding TIG-1 mRNA is ubiquitously expressed. Placental tissue expresses the TIG-1 mRNA 200 times more than the lowest expressing tissues such as kidney and lung. There is also preferential TIG-1 mRNA expression in cells of bone-marrow lineage.In-vitro transcription/translation of the TIG-1 cDNA yielded a polypeptide with an apparent molecular weight of 97kDa. Using polyclonal antibodies obtained from a rabbit immunized with the carboxy-terminal portion of bacterially expressed TIG-1 protein, a polypeptide with molecular weight of 97kDa was identified by Western blot analyses of protein lysates obtained from K562 cells. Cotransfection assays of K562 cells, using a GAL4-TIG-1 fusion gene and GAL4 operator-CAT, indicate that the TIG-1 protein may have transcriptional regulatory activity when tethered to DNA. We hypothesize that this novel glutamine-rich protein participates in a protein complex that regulates gene transcription. It has been demonstrated by Naar et al. (Naar, A.M., Beaurang, P.A., Zhou, S., Abraham, S., Solomon, W.B., Tjian, R., 1999, Composite co-activator ARC mediates chromatin-directed transcriptional activation. Nature 398, 828-830) that the amino acid sequences of peptide fragments obtained from a polypeptide found in a complex of proteins that alters chromatin

Apologies for Blanks or Laments for Dumbness: Tina Darragh’s Opposable Dumbs as Open Source and/or Open Content

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Mark Leahy

2016-04-01

Full Text Available This essay engages in a reading of Tina Darragh’s publication 'Opposable Dumbs'  (2010. This reading is carried out in pursuit of a number of critical and theoretical questions, that include asking what sort of text this is, and how we might read it. The essay considers how Darragh’s work connects to the debate around open source and free software, and to the politics and poetics of that debate. Taking up the call for creative responses in Darragh’s anti-rights or inverted copyright statement, the writing takes a route through the text that parallels some of Darragh’s strategies as a writer. This creative reading is linked to a reading of Stephen Voyce’s essay on open source poetics (2011, with some reference to a wider discourse around FLOSS, creative commons, and copyleft strategies. This essay proposes Darragh’s work as a case study for Voyce’s proposals, and suggests that her practice may in fact go further than he proposes in moving from a position of ‘open source’ to one of ‘open content.’

Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus Hapavirus, family Rhabdoviridae.

Science.gov (United States)

Gubala, Aneta; Walsh, Susan; McAllister, Jane; Weir, Richard; Davis, Steven; Melville, Lorna; Mitchell, Ian; Bulach, Dieter; Gauci, Penny; Skvortsov, Alex; Boyle, David

2017-01-01

Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector.

Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus Hapavirus, family Rhabdoviridae

Science.gov (United States)

Gubala, Aneta; Walsh, Susan; McAllister, Jane; Weir, Richard; Davis, Steven; Melville, Lorna; Mitchell, Ian; Bulach, Dieter; Gauci, Penny; Skvortsov, Alex; Boyle, David

2017-01-01

Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector. PMID:28747815

Cloning and expression analysis of a blue copperbinding protein ...

African Journals Online (AJOL)

Adifferentially expressed fragment EST145 was isolated by suppression subtractive hybridization (SSH) method. Using EST145 as the probe, a blue copper-binding protein gene designated as DvBCB was screened from Dasypyrum villosum cDNA Library. The DvBCB gene was 845 bp in length with an open reading frame ...

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

Directory of Open Access Journals (Sweden)

Soares Ademilson EE

2004-11-01

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

Nucleotide sequence of a cDNA for branched chain acyltransferase with analysis of the deduced protein structure

International Nuclear Information System (INIS)

Hummel, K.B.; Litwer, S.; Bradford, A.P.; Aitken, A.; Danner, D.J.; Yeaman, S.J.

1988-01-01

Nucleotide sequence was determined for a 1.6-kilobase human cDNA putative for the branched chain acyltransferase protein of the branched chain α-ketoacid dehydrogenase complex. Translation of the sequence reveals an open reading frame encoding a 315-amino acid protein of molecular weight 35,759 followed by 560 bases of 3'-untranslated sequence. Three repeats of the polyadenylation signal hexamer ATTAAA are present prior to the polyadenylate tail. Within the open reading frame is a 10-amino acid fragment which matches exactly the amino acid sequence around the lipoate-lysine residue in bovine kidney branched chain acyltransferase, thus confirming the identity of the cDNA. Analysis of the deduced protein structure for the human branched chain acyltransferase revealed an organization into domains similar to that reported for the acyltransferase proteins of the pyruvate and α-ketoglutarate dehydrogenase complexes. This similarity in organization suggests that a more detailed analysis of the proteins will be required to explain the individual substrate and multienzyme complex specificity shown by these acyltransferases

ADOPT Open Access

CERN Multimedia

2007-01-01

Are you writing a theoretical paper? An experimental one? Or one about instrumentation? You can publish it in Open Access. Now. Read how... You might have heard about Open Access, the next big thing in scientific publishing. The idea is to make the results of your (publicly funded) research free to read for everyone out there ... not only those lucky ones who work in places where libraries can afford to purchase the expensive subscriptions to scientific journals. CERN, DESY and other particle physics institutes have accepted an offer by one of the leading journals in High Energy Physics, JHEP: our libraries will pay a special subscription fee, and, in exchange, all articles with at least one author from our institutes will be published in Open Access. Anyone, anywhere and anytime will be able to read them, without any financial barrier! If you are writing an instrumentation paper, you can submit it to JINST and benefit from the same offer. This is a major step forward in the planned conversion of existi...

Selfish DNA in protein-coding genes of Rickettsia.

Science.gov (United States)

Ogata, H; Audic, S; Barbe, V; Artiguenave, F; Fournier, P E; Raoult, D; Claverie, J M

2000-10-13

Rickettsia conorii, the aetiological agent of Mediterranean spotted fever, is an intracellular bacterium transmitted by ticks. Preliminary analyses of the nearly complete genome sequence of R. conorii have revealed 44 occurrences of a previously undescribed palindromic repeat (150 base pairs long) throughout the genome. Unexpectedly, this repeat was found inserted in-frame within 19 different R. conorii open reading frames likely to encode functional proteins. We found the same repeat in proteins of other Rickettsia species. The finding of a mobile element inserted in many unrelated genes suggests the potential role of selfish DNA in the creation of new protein sequences.

Molecular cloning, functional expression, and tissue distribution of a novel human gap junction-forming protein, connexin-31.9. Interaction with zona occludens protein-1

NARCIS (Netherlands)

Nielsen, Peter A; Beahm, Derek L; Giepmans, Ben N G; Baruch, Amos; Hall, James E; Kumar, Nalin M

2002-01-01

A novel human connexin gene (GJA11) was cloned from a genomic library. The open reading frame encoded a hypothetical protein of 294 amino acid residues with a predicted molecular mass of 31,933, hence referred to as connexin-31.9 (Cx31.9) or alpha 11 connexin. A clone in GenBank containing the

The Protein Data Bank archive as an open data resource

Science.gov (United States)

Berman, Helen M.; Kleywegt, Gerard J.; Nakamura, Haruki; Markley, John L.

2014-10-01

The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012). An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources in biology.

Classification of Dutch and German avian reoviruses by sequencing the sigma-C protein.

NARCIS (Netherlands)

Kant, A.; Balk, F.R.M.; Born, L.; Roozelaar, van D.; Heijmans, J.; Gielkens, A.; Huurne, ter A.A.H.M.

2003-01-01

We have amplified, cloned and sequenced (part of) the open reading frame of the S1 segment encoding the ¿ C protein of avian reoviruses isolated from chickens with different disease conditions in Germany and The Netherlands during 1980 up to 2000. These avian reoviruses were analysed

Translational control of Nrf2 within the open reading frame

International Nuclear Information System (INIS)

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

2013-01-01

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

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

Science.gov (United States)

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…

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

Directory of Open Access Journals (Sweden)

Tracy G Cassels

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

Death of a dogma: eukaryotic mRNAs can code for more than one protein.

Science.gov (United States)

Mouilleron, Hélène; Delcourt, Vivian; Roucou, Xavier

2016-01-08

mRNAs carry the genetic information that is translated by ribosomes. The traditional view of a mature eukaryotic mRNA is a molecule with three main regions, the 5' UTR, the protein coding open reading frame (ORF) or coding sequence (CDS), and the 3' UTR. This concept assumes that ribosomes translate one ORF only, generally the longest one, and produce one protein. As a result, in the early days of genomics and bioinformatics, one CDS was associated with each protein-coding gene. This fundamental concept of a single CDS is being challenged by increasing experimental evidence indicating that annotated proteins are not the only proteins translated from mRNAs. In particular, mass spectrometry (MS)-based proteomics and ribosome profiling have detected productive translation of alternative open reading frames. In several cases, the alternative and annotated proteins interact. Thus, the expression of two or more proteins translated from the same mRNA may offer a mechanism to ensure the co-expression of proteins which have functional interactions. Translational mechanisms already described in eukaryotic cells indicate that the cellular machinery is able to translate different CDSs from a single viral or cellular mRNA. In addition to summarizing data showing that the protein coding potential of eukaryotic mRNAs has been underestimated, this review aims to challenge the single translated CDS dogma. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Patients' Positive and Negative Responses to Reading Mental Health Clinical Notes Online.

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Denneson, Lauren M; Chen, Jason I; Pisciotta, Maura; Tuepker, Anais; Dobscha, Steven K

2018-05-01

This study describes responses to OpenNotes, clinical notes available online, among patients receiving mental health care and explores whether responses vary by patient demographic or clinical characteristics. Survey data from 178 veterans receiving mental health treatment at a large Veterans Affairs medical center included patient-reported health self-efficacy, health knowledge, alliance with clinicians, and negative emotional responses after reading OpenNotes. Health care data were extracted from the patient care database. Reading OpenNotes helped many participants feel in control of their health care (49%) and have more trust in clinicians (45%), although a few (8%) frequently felt upset after reading their notes. In multivariate models, posttraumatic stress disorder was associated with increased patient-clinician alliance (p=.046) but also with negative emotional responses (p<.01). Patients receiving mental health care frequently reported benefits from reading OpenNotes, yet some experienced negative responses.

Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans

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Pupko Tal

2008-10-01

Full Text Available Abstract Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM that originated from the rsp-2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM motif. Reviewers This article was reviewed by Dan Graur and William Martin. For the full reviews, please go to the Reviewers' Reports section.

RAD6 gene of Saccharomyces cerevisiae encodes a protein containing a tract of 13 consecutive aspartates

International Nuclear Information System (INIS)

Reynolds, P.; Weber, S.; Prakash, L.

1985-01-01

The RAD6 gene of Saccharomyces cerevisiae is required for postreplication repair of UV-damaged DNA, for induced mutagenesis, and for sporulation. The authors have mapped the transcripts and determined the nucleotide sequence of the cloned RAD6 gene. The RAD6 gene encodes two transcripts of 0.98 and 0.86 kilobases which differ only in their 3' termini. The transcribed region contains an open reading frame of 516 nucleotides. The rad6-1 and rad6-3 mutant alleles, which the authors have cloned and sequenced, introduce amber and ochre nonsense mutations, respectively into the open reading frame, proving that it encodes the RAD6 protein. The RAD6 protein predicted by the nucleotide sequence is 172 amino acids long, has a molecular weight of 19,704, and contains 23.3% acidic and 11.6% basic residues. Its most striking feature is the highly acidic carboxyl terminus: 20 of the 23 terminal amino acids are acidic, including 13 consecutive aspartates. RAD6 protein thus resembles high mobility group proteins HMG-1 and HMG-2, which each contain a carboxyl-proximal tract of acidic amino acids. 48 references, 6 figures

Cloning and expression of a small heat shock protein gene ...

African Journals Online (AJOL)

The cDNA sequence of this gene is 920 bp in size (GenBank: HM132040) and contains an open reading frame (ORF) of 636 bp, which was predicted to encode a protein with 211 amino acid residues. The phylogenetic tree showed that CaHSP24 was quite similar to mitochondrial sHSPs from other plants but was distantly ...

A novel, mouse mammary tumor virus encoded protein with Rev-like properties

International Nuclear Information System (INIS)

Indik, Stanislav; Guenzburg, Walter H.; Salmons, Brian; Rouault, Francoise

2005-01-01

We have identified a novel, multiple spliced, subgenomic mRNA species in MMTV producing cells of different origin containing an open reading frame encoding a 39-kDa Rev-like protein, Rem (regulator of expression of MMTV). An EGFP-Rem fusion protein is shown to be predominantly in the nucleolus. Further leptomycin B inhibits the nuclear export of nonspliced MMTV transcripts, implicating Rem in nuclear export by the Crm1 pathway in MMTV. Rem is thus reminiscent of the Rec protein from the related endogenous human retrovirus, HERV-K

Clock domain crossing modules for OCP-style read/write interfaces

DEFF Research Database (Denmark)

Herlev, Mathias; Sparsø, Jens

The open core protocol (OCP) is an openly licensed, configurable, and scalable interface protocol for on-chip subsystem communications. The protocol defines read and write transactions from a master towards a slave across a point-to-point connection and the protocol assumes a single common clock....... This paper presents the design of two OCP clock domain crossing interface modules, that can be used to construct systems with multiple clock domains. One module (called OCPio) supports a single word read-write interface and the other module (called OCPburst) supports a four word burst read-write interface......-style read-write transaction interfaces. An OCP interface typically has control signals related to both the master issuing a read or write request and the slave producing a response. If all these control signals are passed across the clock domain boundary and synchronized it may add significant latency...

Viewing Reading Recovery as a Restructuring Phenomenon

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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.…

Investigation of the Effect of Using a Novel as an Extensive Reading on Students’ Attitudes and Reading Ability

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Shima Ghiabi

2014-07-01

Full Text Available The present study aims at investigating learners’ perceptions on the use of a novel as an extensive reading in a college EFL reading course. For this purpose, fifty Iranian EFL students read and received instructions on an unabridged short novel in addition to, their text book for one semester. Three questionnaires were used to measure students’ attitudes toward novel-reading, students’ confidence in novel reading ability and students’ perceptions toward using a novel as an auxiliary material, prior to and after reading the novel. In addition, three open questions were offered to obtain benefits and obstacles of the novel reading. T-test analysis were used and findings revealed that there was a significant improvement after reading the novel in students’ attitudes, confidence, interest and their novel-reading ability. However, they suggested reading the novels according to the theme that they preferred. The result of this study are of pedagogic significance to EFL teaching in that they indicated how well a novel was received in an EFL Advanced reading class.

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).

Science.gov (United States)

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…

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

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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…

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

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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

Annotation and Curation of Uncharacterized proteins- Challenges

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Johny eIjaq

2015-03-01

Full Text Available Hypothetical Proteins are the proteins that are predicted to be expressed from an open reading frame (ORF, constituting a substantial fraction of proteomes in both prokaryotes and eukaryotes. Genome projects have led to the identification of many therapeutic targets, the putative function of the protein and their interactions. In this review we have enlisted various methods. Annotation linked to structural and functional prediction of hypothetical proteins assist in the discovery of new structures and functions serving as markers and pharmacological targets for drug designing, discovery and screening. Mass spectrometry is an analytical technique for validating protein characterisation. Matrix-assisted laser desorption ionization–mass spectrometry (MALDI-MS is an efficient analytical method. Microarrays and Protein expression profiles help understanding the biological systems through a systems-wide study of proteins and their interactions with other proteins and non-proteinaceous molecules to control complex processes in cells and tissues and even whole organism. Next generation sequencing technology accelerates multiple areas of genomics research.

Prediction of Protein-Protein Interactions by NanoLuc-Based Protein-Fragment Complementation Assay | Office of Cancer Genomics

Science.gov (United States)

The CTD2 Center at Emory has developed a new NanoLuc®-based protein-fragment complementation assay (NanoPCA) which allows the detection of novel protein-protein interactions (PPI). NanoPCA allows the study of PPI dynamics with reversible interactions.  Read the abstract. Experimental Approaches Read the detailed Experimetnal Approaches. 

A transthyretin-related protein is functionally expressed in Herbaspirillum seropedicae.

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Matiollo, Camila; Vernal, Javier; Ecco, Gabriela; Bertoldo, Jean Borges; Razzera, Guilherme; de Souza, Emanuel M; Pedrosa, Fábio O; Terenzi, Hernán

2009-10-02

Transthyretin-related proteins (TRPs) constitute a family of proteins structurally related to transthyretin (TTR) and are found in a large range of bacterial, fungal, plant, invertebrate, and vertebrate species. However, it was recently recognized that both prokaryotic and eukaryotic members of this family are not functionally related to transthyretins. TRPs are in fact involved in the purine catabolic pathway and function as hydroxyisourate hydrolases. An open reading frame encoding a protein similar to the Escherichia coli TRP was identified in Herbaspirillum seropedicae genome (Hs_TRP). It was cloned, overexpressed in E. coli, and purified to homogeneity. Mass spectrometry data confirmed the identity of this protein, and circular dichroism spectrum indicated a predominance of beta-sheet structure, as expected for a TRP. We have demonstrated that Hs_TRP is a 5-hydroxyisourate hydrolase and by site-directed mutagenesis the importance of three conserved catalytic residues for Hs_TRP activity was further confirmed. The production of large quantities of this recombinant protein opens up the possibility of obtaining its 3D-structure and will help further investigations into purine catabolism.

Predicting functional upstream open reading frames in Saccharomyces cerevisiae

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Kristiansson Erik

2009-12-01

Full Text Available Abstract Background Some upstream open reading frames (uORFs regulate gene expression (i.e., they are functional and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not yet fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of experimentally verified functional uORFs are needed. Unfortunately, wet-experiments to verify that uORFs are functional are expensive. Results In this paper, a new computational approach to predicting functional uORFs in the yeast Saccharomyces cerevisiae is presented. Our approach is based on inductive logic programming and makes use of a novel combination of knowledge about biological conservation, Gene Ontology annotations and genes' responses to different conditions. Our method results in a set of simple and informative hypotheses with an estimated sensitivity of 76%. The hypotheses predict 301 further genes to have 398 novel functional uORFs. Three (RPC11, TPK1, and FOL1 of these 301 genes have been hypothesised, following wet-experiments, by a related study to have functional uORFs. A comparison with another related study suggests that eleven of the predicted functional uORFs from genes LDB17, HEM3, CIN8, BCK2, PMC1, FAS1, APP1, ACC1, CKA2, SUR1, and ATH1 are strong candidates for wet-lab experimental studies. Conclusions Learning based prediction of functional uORFs can be done with a high sensitivity. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help to elucidate the regulatory roles of uORFs.

Nurturing a lexical legacy: reading experience is critical for the development of word reading skill

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Nation, Kate

2017-12-01

The scientific study of reading has taught us much about the beginnings of reading in childhood, with clear evidence that the gateway to reading opens when children are able to decode, or `sound out' written words. Similarly, there is a large evidence base charting the cognitive processes that characterise skilled word recognition in adults. Less understood is how children develop word reading expertise. Once basic reading skills are in place, what factors are critical for children to move from novice to expert? This paper outlines the role of reading experience in this transition. Encountering individual words in text provides opportunities for children to refine their knowledge about how spelling represents spoken language. Alongside this, however, reading experience provides much more than repeated exposure to individual words in isolation. According to the lexical legacy perspective, outlined in this paper, experiencing words in diverse and meaningful language environments is critical for the development of word reading skill. At its heart is the idea that reading provides exposure to words in many different contexts, episodes and experiences which, over time, sum to a rich and nuanced database about their lexical history within an individual's experience. These rich and diverse encounters bring about local variation at the word level: a lexical legacy that is measurable during word reading behaviour, even in skilled adults.

Myocardial ischemic preconditioning upregulated protein 1(Mipu1):zinc finger protein 667 - a multifunctional KRAB/C{sub 2}H{sub 2} zinc finger protein

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Han, D.; Zhang, C. [Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, Post-doctoral Mobile Stations for Basic Medicine, University of South China, Hengyang City, Hunan Province (China); Fan, W.J. [Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, Post-doctoral Mobile Stations for Basic Medicine, University of South China, Hengyang City, Hunan Province (China); The Second Affiliated Hospital, University of South China, Hengyang City, Hunan Province (China); Pan, W.J.; Feng, D.M.; Qu, S.L.; Jiang, Z.S. [Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, Post-doctoral Mobile Stations for Basic Medicine, University of South China, Hengyang City, Hunan Province (China)

2014-10-31

Myocardial ischemic preconditioning upregulated protein 1 (Mipu1) is a newly discovered upregulated gene produced in rats during the myocardial ischemic preconditioning process. Mipu1 cDNA contains a 1824-base pair open reading frame and encodes a 608 amino acid protein with an N-terminal Krüppel-associated box (KRAB) domain and classical zinc finger C{sub 2}H{sub 2} motifs in the C-terminus. Mipu1 protein is located in the cell nucleus. Recent studies found that Mipu1 has a protective effect on the ischemia-reperfusion injury of heart, brain, and other organs. As a nuclear factor, Mipu1 may perform its protective function through directly transcribing and repressing the expression of proapoptotic genes to repress cell apoptosis. In addition, Mipu1 also plays an important role in regulating the gene expression of downstream inflammatory mediators by inhibiting the activation of activator protein-1 and serum response element.

Identification of the gene encoding the 65-kilodalton DNA-binding protein of herpes simplex virus type 1

International Nuclear Information System (INIS)

Parris, D.S.; Cross, A.; Orr, A.; Frame, M.C.; Murphy, M.; McGeoch, D.J.; Marsden, H.S.; Haarr, L.

1988-01-01

Hybrid arrest of in vitro translation was used to localize the region of the herpes simplex virus type 1 genome encoding the 65-kilodalton DNA-binding protein (65K DBP ) to between genome coordinates 0.592 and 0.649. Knowledge of the DNA sequence of this region allowed us to identify three open reading frames as likely candidates for the gene encoding 65K DBP . Two independent approaches were used to determine which of these three open reading frames encoded the protein. For the first approach a monoclonal antibody, MAb 6898, which reacted specifically with 65K DBP , was isolated. This antibody was used, with the techniques of hybrid arrest of in vitro translation and in vitro translation of selected mRNA, to identify the gene encoding 65K DBP . The second approach involved preparation of antisera directed against oligopeptides corresponding to regions of the predicted amino acid sequence of this gene. These antisera reacted specifically with 65K DBP , thus confirming the gene assignment

Put reading first: Positive effects of direct instruction and scaffolding ...

African Journals Online (AJOL)

Put reading first: Positive effects of direct instruction and scaffolding for ESL learners struggling with reading. ... are intended to open up for debate a topic of critical importance to the country's education system. ... AJOL African Journals Online.

Cultural Awareness and Reading. Proceedings of the Annual Reading Conference (12th, Terre Haute, Indiana, June 17-18, 1982).

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Gibbs, Vanita M., Comp.; Pabst, Robert L., Comp.

Reflecting the expertise of the speakers and providing a rich resource of information within the conference theme, the articles in these proceedings explore the relationship between cultural awareness and reading. The proceedings begin with a copy of the conference program and opening remarks by the conference cochair. Following an opening address…

Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes

DEFF Research Database (Denmark)

Peng, Xu; Brügger, Kim; Shen, Biao

2003-01-01

terminally modified and corresponds to SSO454, an open reading frame of previously unassigned function. It binds specifically to DNA fragments carrying double and single repeat sequences, binding on one side of the repeat structure, and producing an opening of the opposite side of the DNA structure. It also...... recognizes both main families of repeat sequences in S. solfataricus. The recombinant protein, expressed in Escherichia coli, showed the same binding properties to the SRSR repeat as the native one. The SSO454 protein exhibits a tripartite internal repeat structure which yields a good sequence match...... with a helix-turn-helix DNA-binding motif. Although this putative motif is shared by other archaeal proteins, orthologs of SSO454 were only detected in species within the Sulfolobus genus and in the closely related Acidianus genus. We infer that the genus-specific protein induces an opening of the structure...

The Effect of a Specialized Dyslexia Font, Opendyslexic, on Reading Rate and Accuracy

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Wery, Jessica J.; Diliberto, Jennifer A.

2017-01-01

A single-subject alternating treatment design was used to investigate the extent to which a specialized dyslexia font, OpenDyslexic, impacted reading rate or accuracy compared to two commonly used fonts when used with elementary students identified as having dyslexia. OpenDyslexic was compared to Arial and Times New Roman in three reading tasks:…

Teacher's current practices of teaching reading and grade four ...

African Journals Online (AJOL)

This study examined the practices and challenges of teaching reading strategies and ... Twelve grade 4 students were selected using simple random sampling ... The quantitative data disclosed lower student scores, while the qualitative data ... By Country · List All Titles · Free To Read Titles This Journal is Open Access.

Reading: A Motivating and Interactive Process

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Santoyo Brigitte

2000-08-01

Full Text Available This research was primarily intended for those who are professionally concerned with the teaching of a foreign language, and especially for those who consider reading to be one of the most important sources for developing comprehension and production processes. We wanted our students to develop reading strategies by means of meaningful and motivating stories. Meaningful, because interesting stories encourage them to improve, and motivating, because they open the doors to multiple possibilities, thereby reinforcing other abilities.

Reading Quizzes Improve Exam Scores for Community College Students

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Pape-Lindstrom, Pamela; Eddy, Sarah; Freeman, Scott

2018-01-01

To test the hypothesis that adding course structure may encourage self-regulated learning skills resulting in an increase in student exam performance in the community college setting, we added daily preclass online, open-book reading quizzes to an introductory biology course. We compared three control terms without reading quizzes and three…

Crystal structure of Homo sapiens protein LOC79017

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Bae, Euiyoung; Bingman, Craig A.; Aceti, David J.; Phillips, Jr., George N. (UW)

2010-02-08

LOC79017 (MW 21.0 kDa, residues 1-188) was annotated as a hypothetical protein encoded by Homo sapiens chromosome 7 open reading frame 24. It was selected as a target by the Center for Eukaryotic Structural Genomics (CESG) because it did not share more than 30% sequence identity with any protein for which the three-dimensional structure is known. The biological function of the protein has not been established yet. Parts of LOC79017 were identified as members of uncharacterized Pfam families (residues 1-95 as PB006073 and residues 104-180 as PB031696). BLAST searches revealed homologues of LOC79017 in many eukaryotes, but none of them have been functionally characterized. Here, we report the crystal structure of H. sapiens protein LOC79017 (UniGene code Hs.530024, UniProt code O75223, CESG target number go.35223).

Poly(norepinephrine)-coated open tubular column for the separation of proteins and recombination human erythropoietin by capillary electrochromatography.

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Xiao, Xue; Zhang, Yamin; Wu, Jia; Jia, Li

2017-12-01

Recombinant human erythropoietin is an important therapeutic protein with high economic interest due to the benefits provided by its clinical use for the treatment of anemias associated with chronic renal failure and chemotherapy. In this work, a poly(norepinephrine)-coated open tubular column was successfully prepared based on the self-polymerization of norepinephrine under mild alkaline condition, the favorable film forming and easy adhesive properties of poly(norepinephrine). The poly(norepinephrine) coating was characterized by scanning electron microscopy and measurement of the electro-osmotic flow. The thickness of the coating was about 431 nm. The electrochromatographic performance of the poly(norepinephrine)-coated open tubular column was evaluated by separation of proteins. Some basic and acidic proteins including two variants of bovine serum albumin and two variants of β-lactoglobulin achieved separation in the poly(norepinephrine)-coated open tubular column. More importantly, the column demonstrated separation ability for the glycoforms of recombinant human erythropoietin. In addition, the column demonstrated good repeatability with the run-to-run, day-to-day, and column-to-column relative standard deviations of migration times of proteins less than 3.40%. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Measuring College Students' Reading Comprehension Ability Using Cloze Tests

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

2011-01-01

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

A High Five for ChemistryOpen.

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Peralta, David; Ortúzar, Natalia

2016-02-01

Fabulous at five! When ChemistryOpen was launched in 2011, it was the first society-owned general chemistry journal to publish open-access articles exclusively. Five years down the line, it has featured excellent work in all fields of chemistry, leading to an impressive first full impact factor of 3.25. In this Editorial, read about how ChemistryOpen has grown over the past five years and made its mark as a high-quality open-access journal with impact.

Cell transformation mediated by the Epstein-Barr virus G protein-coupled receptor BILF1 is dependent on constitutive signaling

DEFF Research Database (Denmark)

Lyngaa, Rikke Birgitte; Nørregaard, K.; Kristensen, Martin

2010-01-01

Epstein-Barr virus (EBV) open reading frame BILF1 encodes a seven trans-membrane (TM) G protein-coupled receptor that signals with high constitutive activity through G alpha(i) (Beisser et al., 2005; Paulsen et al., 2005). In this paper, the transforming potential of BILF1 is investigated in vitro...

Efficient identification of phosphatidylserine-binding proteins by ORF phage display

International Nuclear Information System (INIS)

Caberoy, Nora B.; Zhou, Yixiong; Alvarado, Gabriela; Fan, Xianqun; Li, Wei

2009-01-01

To efficiently elucidate the biological roles of phosphatidylserine (PS), we developed open-reading-frame (ORF) phage display to identify PS-binding proteins. The procedure of phage panning was optimized with a phage clone expressing MFG-E8, a well-known PS-binding protein. Three rounds of phage panning with ORF phage display cDNA library resulted in ∼300-fold enrichment in PS-binding activity. A total of 17 PS-binding phage clones were identified. Unlike phage display with conventional cDNA libraries, all 17 PS-binding clones were ORFs encoding 13 real proteins. Sequence analysis revealed that all identified PS-specific phage clones had dimeric basic amino acid residues. GST fusion proteins were expressed for 3 PS-binding proteins and verified for their binding activity to PS liposomes, but not phosphatidylcholine liposomes. These results elucidated previously unknown PS-binding proteins and demonstrated that ORF phage display is a versatile technology capable of efficiently identifying binding proteins for non-protein molecules like PS.

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

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

2007-12-01

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

The CPT1C 5'UTR contains a repressing upstream open reading frame that is regulated by cellular energy availability and AMPK.

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Ines Lohse

Full Text Available BACKGROUND: Translational control is utilized as a means of regulating gene expression in many species. In most cases, posttranscriptional regulatory mechanisms play an important role in stress response pathways and can lead to dysfunctional physiology if blocked by mutations. Carnitine Palmitoyltransferase 1 C (CPT1C, the brain-specific member of the CPT 1 family, has previously been shown to be involved in regulating metabolism in situations of energy surplus. PRINCIPAL FINDINGS: Sequence analysis of the CPT1C mRNA revealed that it contains an upstream open reading frame (uORF in the 5' UTR of its mRNA. Using CPT1C 5' UTR/luciferase constructs, we investigated the role of the uORF in translational regulation. The results presented here show that translation from the CPT1C main open reading frame (mORF is repressed by the presence of the uORF, that this repression is relieved in response to specific stress stimuli, namely glucose deprivation and palmitate-BSA treatment, and that AMPK inhibition can relieve this uORF-dependent repression. SIGNIFICANCE: The fact that the mORF regulation is relieved in response to a specific set of stress stimuli rather than general stress response, hints at an involvement of CPT1C in cellular energy-sensing pathways and provides further evidence for a role of CPT1C in hypothalamic regulation of energy homeostasis.

Role of protein sulfation in vasodilation induced by minoxidil sulfate, a K+ channel opener

International Nuclear Information System (INIS)

Meisheri, K.D.; Oleynek, J.J.; Puddington, L.

1991-01-01

Evidence from contractile, radioisotope ion flux and electrophysiological studies suggest that minoxidil sulfate (MNXS) acts as a K+ channel opener in vascular smooth muscle. This study was designed to examine possible biochemical mechanisms by which MNXS exerts such an effect. Experiments performed in the isolated rabbit mesenteric artery (RMA) showed that MNXS, 5 microM, but not the parent compound minoxidil, was a potent vasodilator. Whereas the relaxant effects of an another K+ channel opener vasodilator, BRL-34915 (cromakalim), were removed by washing with physiological saline solution, the effects of MNXS persisted after repeated washout attempts. Furthermore, after an initial exposure of segments of intact RMA to [35S] MNXS, greater than 30% of the radiolabel was retained 2 hr after removal of the drug. In contrast, retention of radiolabel was not detected with either [3H]MNXS (label on the piperidine ring of MNXS) or [3H]minoxidil (each less than 3% after a 2-hr washout). These data suggested that the sulfate moiety from MNXS was closely associated with the vascular tissue. To determine if proteins were the acceptors of sulfate from MNXS, intact RMAs were incubated with [35S]MNXS, and then 35S-labeled proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and analyzed by fluorography. Preferential labeling of a 116 kD protein was detected by 2 and 5 min of treatment. A 43 kD protein (resembling actin) also showed significant labeling. A similar profile of 35S-labeled proteins was observed in [35S] MNXS-treated A7r5 rat aortic smooth muscle cells, suggesting that the majority of proteins labeled by [35S]MNXS in intact RMA were components of smooth muscle cells

A novel Hsp70 of the yeast ER lumen is required for the efficient translocation of a number of protein precursors.

OpenAIRE

Craven, R A; Egerton, M; Stirling, C J

1996-01-01

The yeast genome sequencing project predicts an open reading frame (YKL073) that would encode a novel member of the Hsp70 family of molecular chaperones. We report that this 881 codon reading frame represents a functional gene expressing a 113-119 kDa glycoprotein localized within the lumen of the endoplasmic reticulum (ER). We therefore propose to designate this gene LHS1 (Lumenal Hsp Seventy). Our studies indicate that LHS1 is regulated by the unfolded protein response pathway, as evidenced...

Foot-and-mouth disease virus capsid proteins; analysis of protein processing, assembly and utility as vaccines

DEFF Research Database (Denmark)

Belsham, Graham

Foot-and-mouth disease (FMD) remains one of the most economically important infectious diseases of production animals globally. The infection is caused by foot-and-mouth disease virus (FMDV), a member of the picornavirus family. The positive sense RNA genome of the virus includes a single, large......, open reading frame that encodes a polyprotein. The intact polyprotein is never observed as it is processed, both during and after translation, to 15 different mature proteins plus a variety of precursors. The FMDV capsid protein precursor, P1-2A, is cleaved by the virus encoded 3C protease (3Cpro......) to generate VP0, VP3, VP1 and the peptide 2A. Sixty copies of each of the capsid proteins “self-assemble” into empty capsid particles or with the RNA genome into infectious viruses. These particles normally lack 2A but it is possible to construct and isolate mutant FMDVs in which the cleavage of the VP1/2A...

How Reading Volume Affects both Reading Fluency and Reading Achievement

Directory of Open Access Journals (Sweden)

Richard L. ALLINGTON

2014-10-01

Full Text Available 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 about 15 minutes of reading activity daily. The remaining 75 minute of reading lessons is filled with many other activities such as completing workbook pages or responding to low-level literal questions about what has been read. Studies designed to enhance the volume of reading that children do during their reading lessons demonstrate one way to enhance reading development. Repeated readings have been widely used in fostering reading fluency but wide reading options seem to work faster and more broadly in developing reading proficiencies, including oral reading fluency.

Targets of DNA-binding proteins in bacterial promoter regions present enhanced probabilities for spontaneous thermal openings

International Nuclear Information System (INIS)

Apostolaki, Angeliki; Kalosakas, George

2011-01-01

We mapped promoter regions of double-stranded DNA with respect to the probabilities of appearance of relatively large bubble openings exclusively due to thermal fluctuations at physiological temperatures. We analyzed five well-studied promoter regions of procaryotic type and found a spatial correlation between the binding sites of transcription factors and the position of peaks in the probability pattern of large thermal openings. Other distinct peaks of the calculated patterns correlate with potential binding sites of DNA-binding proteins. These results suggest that a DNA molecule would more frequently expose the bases that participate in contacts with proteins, which would probably enhance the probability of the latter to reach their targets. It also stands for using this method as a means to analyze DNA sequences based on their intrinsic thermal properties

Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids.

Science.gov (United States)

Dorier, Julien; Goundaroulis, Dimos; Benedetti, Fabrizio; Stasiak, Andrzej

2018-05-02

The backbone of most proteins forms an open curve. To study their entanglement, a common strategy consists in searching for the presence of knots in their backbones using topological invariants. However, this approach requires to close the curve into a loop, which alters the geometry of curve. Knoto-ID allows evaluating the entanglement of open curves without the need to close them, using the recent concept of knotoids which is a generalization of the classical knot theory to open curves. Knoto-ID can analyse the global topology of the full chain as well as the local topology by exhaustively studying all subchains or only determining the knotted core. Knoto-ID permits to localize topologically non-trivial protein folds that are not detected by informatics tools detecting knotted protein folds. Knoto-ID is written in C ++ and includes R (www.R-project.org) scripts to generate plots of projections maps, fingerprint matrices and disk matrices. Knoto-ID is distributed under the GNU General Public License (GPL), version 2 or any later version and is available at https://github.com/sib-swiss/Knoto-ID. A binary distribution for Mac OS X, Linux and Windows with detailed user guide and examples can be obtained from https://www.vital-it.ch/software/Knoto-ID. julien.dorier@sib.swiss.

Designing legible fonts for distance reading

DEFF Research Database (Denmark)

Beier, Sofie

2016-01-01

This chapter reviews existing knowledge on distance legibility of fonts, and finds that for optimal distance reading, letters and numbers benefit from relative wide shapes, open inner counters and a large x-height; fonts should further be widely spaced, and the weight should not be too heavy or t...

The Protein Interaction Network of Bacteriophage Lambda with Its Host, Escherichia coli

Science.gov (United States)

Blasche, Sonja; Wuchty, Stefan; Rajagopala, Seesandra V.

2013-01-01

Although most of the 73 open reading frames (ORFs) in bacteriophage λ have been investigated intensively, the function of many genes in host-phage interactions remains poorly understood. Using yeast two-hybrid screens of all lambda ORFs for interactions with its host Escherichia coli, we determined a raw data set of 631 host-phage interactions resulting in a set of 62 high-confidence interactions after multiple rounds of retesting. These links suggest novel regulatory interactions between the E. coli transcriptional network and lambda proteins. Targeted host proteins and genes required for lambda infection are enriched among highly connected proteins, suggesting that bacteriophages resemble interaction patterns of human viruses. Lambda tail proteins interact with both bacterial fimbrial proteins and E. coli proteins homologous to other phage proteins. Lambda appears to dramatically differ from other phages, such as T7, because of its unusually large number of modified and processed proteins, which reduces the number of host-virus interactions detectable by yeast two-hybrid screens. PMID:24049175

Nanocapillaries for Open Tubular Chromatographic Separations of Proteins in Femtoliter to Picoliter Samples

Science.gov (United States)

Wang, Xiayan; Cheng, Chang; Wang, Shili; Zhao, Meiping; Dasgupta, Purnendu K.; Liu, Shaorong

2009-01-01

We have recently examined the potential of bare nanocapillaries for free solution DNA separations and demonstrated efficiencies exceeding 106 theoretical plates/m. In the present work, we demonstrate the use of bare and hydroxypropylcellulose (HPC) coated open tubular nanocapillaries for protein separations. Using 1.5 μm inner diameter (i.d.) capillary columns, hydrodynamically injecting femto to picoliter (fL-pL) volumes of fluorescent or fluorescent dye labeled protein samples, utilizing a pneumatically pressurized chamber containing 1.0 mM sodium tetraborate solution eluent (typ. 200 psi) as the pump and performing on-column detection using a simple laser-induced fluorescence detector, we demonstrate efficiencies of close to a million theoretical plates/m while generating single digit μL volumes of waste for a complete chromatographic run. We achieve baseline resolution for a protein mixture consisting of transferrin, α-lactalbumin, insulin, and α -2-macroglobulin. PMID:19663450

Open Admissions: A Bibliography for Research and Application.

Science.gov (United States)

Shrier, Irene; Lavin, David E.

This bibliography presents materials for research and application of open admissions policies in higher education. Sections cover: open admissions; factors influencing high school graduates to attend college; disadvantaged and minority students; precollege and special programs; English and reading skills; general compensatory programs; dropouts;…

Automated mass correction and data interpretation for protein open-access liquid chromatography-mass spectrometry.

Science.gov (United States)

Wagner, Craig D; Hall, John T; White, Wendy L; Miller, Luke A D; Williams, Jon D

2007-02-01

Characterization of recombinant protein purification fractions and final products by liquid chromatography-mass spectrometry (LC/MS) are requested more frequently each year. A protein open-access (OA) LC/MS system was developed in our laboratory to meet this demand. This paper compares the system that we originally implemented in our facilities in 2003 to the one now in use, and discusses, in more detail, recent enhancements that have improved its robustness, reliability, and data reporting capabilities. The system utilizes instruments equipped with reversed-phase chromatography and an orthogonal accelerated time-of-flight mass spectrometer fitted with an electrospray source. Sample analysis requests are accomplished using a simple form on a web-enabled laboratory information management system (LIMS). This distributed form is accessible from any intranet-connected company desktop computer. Automated data acquisition and processing are performed using a combination of in-house (OA-Self Service, OA-Monitor, and OA-Analysis Engine) and vendor-supplied programs (AutoLynx, and OpenLynx) located on acquisition computers and off-line processing workstations. Analysis results are then reported via the same web-based LIMS. Also presented are solutions to problems not addressed on commercially available, small-molecule OA-LC/MS systems. These include automated transforming of mass-to-charge (m/z) spectra to mass spectra and automated data interpretation that considers minor variants to the protein sequence-such as common post-translational modifications (PTMs). Currently, our protein OA-LC/MS platform runs on five LC/MS instruments located in three separate GlaxoSmithKline R&D sites in the US and UK. To date, more than 8000 protein OA-LC/MS samples have been analyzed. With these user friendly and highly automated OA systems in place, mass spectrometry plays a key role in assessing the quality of recombinant proteins, either produced at our facilities or bought from external

Reading apps for children: Readability from the design perspective

Science.gov (United States)

Mohammed, Wasan Abdulwahab; Husni, Husniza

2017-10-01

Electronic reading for young children opens new avenues especially with the advance of modern reading devices. The readability of mobile learning applications has received extensive attention by the designers and developers. The reason for such concern is due to its importance in determining usability related issues especially in the design context for children. In many cases, children find it difficult to interact with mobile reading apps. This is because apps for reading and for entertainment require different features. As such, this study sets out three objectives: 1) to evaluate five reading apps for young children from design perspectives; 2) to examine the readability for current existing mobile apps for reading and 3) to propose and evaluate mobile apps UI guideline for readability. Readability indices, observation and interview were conducted on 6 - 8 years old students. The obtained result showed that certain reading apps provide better reading experience for children than others. Some of the reasons are mostly related to the design characteristics embedded within the app. In addition, the use of animation was found to stimulate children reading experience as it is believed to offer the interactivity elements to gain their interest and willingness to read. These findings are believed to provide the recommendations and insights for designers of reading apps for children.

Reading Profiles in Multi-Site Data With Missingness.

Science.gov (United States)

Eckert, Mark A; Vaden, Kenneth I; Gebregziabher, Mulugeta

2018-01-01

Children with reading disability exhibit varied deficits in reading and cognitive abilities that contribute to their reading comprehension problems. Some children exhibit primary deficits in phonological processing, while others can exhibit deficits in oral language and executive functions that affect comprehension. This behavioral heterogeneity is problematic when missing data prevent the characterization of different reading profiles, which often occurs in retrospective data sharing initiatives without coordinated data collection. Here we show that reading profiles can be reliably identified based on Random Forest classification of incomplete behavioral datasets, after the missForest method is used to multiply impute missing values. Results from simulation analyses showed that reading profiles could be accurately classified across degrees of missingness (e.g., ∼5% classification error for 30% missingness across the sample). The application of missForest to a real multi-site dataset with missingness ( n = 924) showed that reading disability profiles significantly and consistently differed in reading and cognitive abilities for cases with and without missing data. The results of validation analyses indicated that the reading profiles (cases with and without missing data) exhibited significant differences for an independent set of behavioral variables that were not used to classify reading profiles. Together, the results show how multiple imputation can be applied to the classification of cases with missing data and can increase the integrity of results from multi-site open access datasets.

Reading Profiles in Multi-Site Data With Missingness

Directory of Open Access Journals (Sweden)

Mark A. Eckert

2018-05-01

Full Text Available Children with reading disability exhibit varied deficits in reading and cognitive abilities that contribute to their reading comprehension problems. Some children exhibit primary deficits in phonological processing, while others can exhibit deficits in oral language and executive functions that affect comprehension. This behavioral heterogeneity is problematic when missing data prevent the characterization of different reading profiles, which often occurs in retrospective data sharing initiatives without coordinated data collection. Here we show that reading profiles can be reliably identified based on Random Forest classification of incomplete behavioral datasets, after the missForest method is used to multiply impute missing values. Results from simulation analyses showed that reading profiles could be accurately classified across degrees of missingness (e.g., ∼5% classification error for 30% missingness across the sample. The application of missForest to a real multi-site dataset with missingness (n = 924 showed that reading disability profiles significantly and consistently differed in reading and cognitive abilities for cases with and without missing data. The results of validation analyses indicated that the reading profiles (cases with and without missing data exhibited significant differences for an independent set of behavioral variables that were not used to classify reading profiles. Together, the results show how multiple imputation can be applied to the classification of cases with missing data and can increase the integrity of results from multi-site open access datasets.

Toward a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

Energy Technology Data Exchange (ETDEWEB)

Chhabra, S.R.; Joachimiak, M.P.; Petzold, C.J.; Zane, G.M.; Price, M.N.; Gaucher, S.; Reveco, S.A.; Fok, V.; Johanson, A.R.; Batth, T.S.; Singer, M.; Chandonia, J.M.; Joyner, D.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Singh, A.K.; Keasling, J.D.

2011-05-01

Protein–protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study E. coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio 5 vulgaris Hildenborough, a model anaerobe and sulfate reducer. In this paper we present the first attempt to identify protein-protein interactions in an obligate anaerobic bacterium. We used suicide vector-assisted chromosomal modification of 12 open reading frames encoded by this sulfate reducer to append an eight amino acid affinity tag to the carboxy-terminus of the chosen proteins. Three biological replicates of the 10 ‘pulled-down’ proteins were separated and analyzed using liquid chromatography-mass spectrometry. Replicate agreement ranged between 35% and 69%. An interaction network among 12 bait and 90 prey proteins was reconstructed based on 134 bait-prey interactions computationally identified to be of high confidence. We discuss the biological significance of several unique metabolic features of D. vulgaris revealed by this protein-protein interaction data 15 and protein modifications that were observed. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.

Comparative Membrane Proteomics Reveals a Nonannotated E. coli Heat Shock Protein.

Science.gov (United States)

Yuan, Peijia; D'Lima, Nadia G; Slavoff, Sarah A

2018-01-09

Recent advances in proteomics and genomics have enabled discovery of thousands of previously nonannotated small open reading frames (smORFs) in genomes across evolutionary space. Furthermore, quantitative mass spectrometry has recently been applied to analysis of regulated smORF expression. However, bottom-up proteomics has remained relatively insensitive to membrane proteins, suggesting they may have been underdetected in previous studies. In this report, we add biochemical membrane protein enrichment to our previously developed label-free quantitative proteomics protocol, revealing a never-before-identified heat shock protein in Escherichia coli K12. This putative smORF-encoded heat shock protein, GndA, is likely to be ∼36-55 amino acids in length and contains a predicted transmembrane helix. We validate heat shock-regulated expression of the gndA smORF and demonstrate that a GndA-GFP fusion protein cofractionates with the cell membrane. Quantitative membrane proteomics therefore has the ability to reveal nonannotated small proteins that may play roles in bacterial stress responses.

Bible reading in Africa: the shaping of a reformed perspective

Directory of Open Access Journals (Sweden)

B. Wielenga

2010-07-01

Full Text Available In this article I try to develop a reformed perspective on Bible reading in Africa by ordinary readers. I explore the concept of ordinary readers in the context of recent hermeneutical discus-sions, and of the differences between their mode of reading and that of biblical scholars against the background ofthe reality of the oral or semi-literate cultures of Africa. A reformed perspec-tive, with its emphasis on the church as locus for Bible reading under the operation of the Holy Spirit, opens up a way forward out of the dilemma between ordinary and professional Bible reading. A reformed perspective can also clear the way for a gender-sensitive reading of the Bible in a continent where most Bible readers are women. This requires from those who read the Bible together an attitude of humility.

Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis

Directory of Open Access Journals (Sweden)

Eroukova Veronika

2008-12-01

Full Text Available Abstract Background Functional genomics has received considerable attention in the post-genomic era, as it aims to identify function(s for different genes. One way to study gene function is to investigate the alterations in the responses of deletion mutants to different stimuli. Here we investigate the genetic profile of yeast non-essential gene deletion array (yGDA, ~4700 strains for increased sensitivity to paromomycin, which targets the process of protein synthesis. Results As expected, our analysis indicated that the majority of deletion strains (134 with increased sensitivity to paromomycin, are involved in protein biosynthesis. The remaining strains can be divided into smaller functional categories: metabolism (45, cellular component biogenesis and organization (28, DNA maintenance (21, transport (20, others (38 and unknown (39. These may represent minor cellular target sites (side-effects for paromomycin. They may also represent novel links to protein synthesis. One of these strains carries a deletion for a previously uncharacterized ORF, YBR261C, that we term TAE1 for Translation Associated Element 1. Our focused follow-up experiments indicated that deletion of TAE1 alters the ribosomal profile of the mutant cells. Also, gene deletion strain for TAE1 has defects in both translation efficiency and fidelity. Miniaturized synthetic genetic array analysis further indicates that TAE1 genetically interacts with 16 ribosomal protein genes. Phenotypic suppression analysis using TAE1 overexpression also links TAE1 to protein synthesis. Conclusion We show that a previously uncharacterized ORF, YBR261C, affects the process of protein synthesis and reaffirm that large-scale genetic profile analysis can be a useful tool to study novel gene function(s.

Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis.

Science.gov (United States)

Alamgir, Md; Eroukova, Veronika; Jessulat, Matthew; Xu, Jianhua; Golshani, Ashkan

2008-12-03

Functional genomics has received considerable attention in the post-genomic era, as it aims to identify function(s) for different genes. One way to study gene function is to investigate the alterations in the responses of deletion mutants to different stimuli. Here we investigate the genetic profile of yeast non-essential gene deletion array (yGDA, approximately 4700 strains) for increased sensitivity to paromomycin, which targets the process of protein synthesis. As expected, our analysis indicated that the majority of deletion strains (134) with increased sensitivity to paromomycin, are involved in protein biosynthesis. The remaining strains can be divided into smaller functional categories: metabolism (45), cellular component biogenesis and organization (28), DNA maintenance (21), transport (20), others (38) and unknown (39). These may represent minor cellular target sites (side-effects) for paromomycin. They may also represent novel links to protein synthesis. One of these strains carries a deletion for a previously uncharacterized ORF, YBR261C, that we term TAE1 for Translation Associated Element 1. Our focused follow-up experiments indicated that deletion of TAE1 alters the ribosomal profile of the mutant cells. Also, gene deletion strain for TAE1 has defects in both translation efficiency and fidelity. Miniaturized synthetic genetic array analysis further indicates that TAE1 genetically interacts with 16 ribosomal protein genes. Phenotypic suppression analysis using TAE1 overexpression also links TAE1 to protein synthesis. We show that a previously uncharacterized ORF, YBR261C, affects the process of protein synthesis and reaffirm that large-scale genetic profile analysis can be a useful tool to study novel gene function(s).

Cloning and tissue distribution of rat hear fatty acid binding protein mRNA: identical forms in heart and skeletal muscle

International Nuclear Information System (INIS)

Claffey, K.P.; Herrera, V.L.; Brecher, P.; Ruiz-Opazo, N.

1987-01-01

A fatty acid binding protein (FABP) as been identified and characterized in rat heart, but the function and regulation of this protein are unclear. In this study the cDNA for rat heart FABP was cloned from a λ gt11 library. Sequencing of the cDNA showed an open reading frame coding for a protein with 133 amino acids and a calculated size of 14,776 daltons. Several differences were found between the sequence determined from the cDNA and that reported previously by protein sequencing techniques. Northern blot analysis using rat heart FABP cDNA as a probe established the presence of an abundant mRNA in rat heart about 0.85 kilobases in length. This mRNA was detected, but was not abundant, in fetal heart tissue. Tissue distribution studies showed a similar mRNA species in red, but not white, skeletal muscle. In general, the mRNA tissue distribution was similar to that of the protein detected by Western immunoblot analysis, suggesting that heart FABP expression may be regulated at the transcriptional level. S1 nuclease mapping studies confirmed that the mRNA hybridized to rat heart FABP cDNA was identical in heart and red skeletal muscle throughout the entire open reading frame. The structural differences between heart FABP and other members of this multigene family may be related to the functional requirements of oxidative muscle for fatty acids as a fuel source

Cloning and tissue distribution of rat hear fatty acid binding protein mRNA: identical forms in heart and skeletal muscle

Energy Technology Data Exchange (ETDEWEB)

Claffey, K.P.; Herrera, V.L.; Brecher, P.; Ruiz-Opazo, N.

1987-12-01

A fatty acid binding protein (FABP) as been identified and characterized in rat heart, but the function and regulation of this protein are unclear. In this study the cDNA for rat heart FABP was cloned from a lambda gt11 library. Sequencing of the cDNA showed an open reading frame coding for a protein with 133 amino acids and a calculated size of 14,776 daltons. Several differences were found between the sequence determined from the cDNA and that reported previously by protein sequencing techniques. Northern blot analysis using rat heart FABP cDNA as a probe established the presence of an abundant mRNA in rat heart about 0.85 kilobases in length. This mRNA was detected, but was not abundant, in fetal heart tissue. Tissue distribution studies showed a similar mRNA species in red, but not white, skeletal muscle. In general, the mRNA tissue distribution was similar to that of the protein detected by Western immunoblot analysis, suggesting that heart FABP expression may be regulated at the transcriptional level. S1 nuclease mapping studies confirmed that the mRNA hybridized to rat heart FABP cDNA was identical in heart and red skeletal muscle throughout the entire open reading frame. The structural differences between heart FABP and other members of this multigene family may be related to the functional requirements of oxidative muscle for fatty acids as a fuel source.

libgapmis: extending short-read alignments.

Science.gov (United States)

Alachiotis, Nikolaos; Berger, Simon; Flouri, Tomáš; Pissis, Solon P; Stamatakis, Alexandros

2013-01-01

show that libgapmis is better-suited and more efficient than existing algorithms for this task. The importance of our contribution is underlined by the fact that the provided functions may be seamlessly integrated into any short-read alignment pipeline. The open-source code of libgapmis is available at http://www.exelixis-lab.org/gapmis.

Fusion protein gene nucleotide sequence similarities, shared antigenic sites and phylogenetic analysis suggest that phocid distemper virus 2 and canine distemper virus belong to the same virus entity.

NARCIS (Netherlands)

I.K.G. Visser (Ilona); R.W.J. van der Heijden (Roger); M.W.G. van de Bildt (Marco); M.J.H. Kenter (Marcel); C. Örvell; A.D.M.E. Osterhaus (Albert)

1993-01-01

textabstractNucleotide sequencing of the fusion protein (F) gene of phocid distemper virus-2 (PDV-2), recently isolated from Baikal seals (Phoca sibirica), revealed an open reading frame (nucleotides 84 to 2075) with two potential in-frame ATG translation initiation codons. We suggest that the

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

Science.gov (United States)

Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

ProDaMa: an open source Python library to generate protein structure datasets.

Science.gov (United States)

Armano, Giuliano; Manconi, Andrea

2009-10-02

The huge difference between the number of known sequences and known tertiary structures has justified the use of automated methods for protein analysis. Although a general methodology to solve these problems has not been yet devised, researchers are engaged in developing more accurate techniques and algorithms whose training plays a relevant role in determining their performance. From this perspective, particular importance is given to the training data used in experiments, and researchers are often engaged in the generation of specialized datasets that meet their requirements. To facilitate the task of generating specialized datasets we devised and implemented ProDaMa, an open source Python library than provides classes for retrieving, organizing, updating, analyzing, and filtering protein data. ProDaMa has been used to generate specialized datasets useful for secondary structure prediction and to develop a collaborative web application aimed at generating and sharing protein structure datasets. The library, the related database, and the documentation are freely available at the URL http://iasc.diee.unica.it/prodama.

Federal Reading Rooms for Risk Management Plans (RMP)

Science.gov (United States)

Reading Rooms, listed here by state, are open to the public by either appointment or walk-in. You may access Off-Site Consequence Analysis (scenarios) portions of RMPs, and take notes but not remove or reproduce materials.

Business models in open innovation and commercialization - a dynamic approach

NARCIS (Netherlands)

Vanhaverbeke, W.P.M.; Picot, A; Doeblin, S.

2009-01-01

This afternoon I will talk about business models because in open innovation they play a crucial role. If you have read the books of Henry Chesbrough or other authors on open innovation, you know that business models are important in explaining the phenomenon of open innovation. Moreover, they are

Molecular comparison of the structural proteins encoding gene clusters of two related Lactobacillus delbrueckii bacteriophages.

Science.gov (United States)

Vasala, A; Dupont, L; Baumann, M; Ritzenthaler, P; Alatossava, T

1993-01-01

Virulent phage LL-H and temperate phage mv4 are two related bacteriophages of Lactobacillus delbrueckii. The gene clusters encoding structural proteins of these two phages have been sequenced and further analyzed. Six open reading frames (ORF-1 to ORF-6) were detected. Protein sequencing and Western immunoblotting experiments confirmed that ORF-3 (g34) encoded the main capsid protein Gp34. The presence of a putative late promoter in front of the phage LL-H g34 gene was suggested by primer extension experiments. Comparative sequence analysis between phage LL-H and phage mv4 revealed striking similarities in the structure and organization of this gene cluster, suggesting that the genes encoding phage structural proteins belong to a highly conservative module. Images PMID:8497043

Literary text reading and conversation: beyond ethnomethodology boundaries

Directory of Open Access Journals (Sweden)

Viviana Suárez Galvis

2014-01-01

Full Text Available This article leaves aside ethnomethodological approaches to conversation, and aims at opening the debate about the need of conceiving it under the light of pedagogical principles that position it as a propitious discursive gender to express the emotional, aesthetics, thoughtful, and intellectual meetings embodied while reading literary texts. Such interest arose from a research centered on finding the existing relationships between conversation and construction of aesthetical-literary experiences. The results show that students get a pleasant feeling when giving sense to what they read, and this encourages them to share with others their significant experiences when reading, allowing the internal process of meaning construction and the dialogic strengthening of the experiences to be connected.

A plant virus movement protein forms ringlike complexes with the major nucleolar protein, fibrillarin, in vitro.

Science.gov (United States)

Canetta, Elisabetta; Kim, Sang Hyon; Kalinina, Natalia O; Shaw, Jane; Adya, Ashok K; Gillespie, Trudi; Brown, John W S; Taliansky, Michael

2008-02-29

Fibrillarin, one of the major proteins of the nucleolus, has methyltransferase activity directing 2'-O-ribose methylation of rRNA and snRNAs and is required for rRNA processing. The ability of the plant umbravirus, groundnut rosette virus, to move long distances through the phloem, the specialized plant vascular system, has been shown to strictly depend on the interaction of one of its proteins, the ORF3 protein (protein encoded by open reading frame 3), with fibrillarin. This interaction is essential for several stages in the groundnut rosette virus life cycle such as nucleolar import of the ORF3 protein via Cajal bodies, relocalization of some fibrillarin from the nucleolus to cytoplasm, and assembly of cytoplasmic umbraviral ribonucleoprotein particles that are themselves required for the long-distance spread of the virus and systemic infection. Here, using atomic force microscopy, we determine the architecture of these complexes as single-layered ringlike structures with a diameter of 18-22 nm and a height of 2.0+/-0.4 nm, which consist of several (n=6-8) distinct protein granules. We also estimate the molar ratio of fibrillarin to ORF3 protein in the complexes as approximately 1:1. Based on these data, we propose a model of the structural organization of fibrillarin-ORF3 protein complexes and discuss potential mechanistic and functional implications that may also apply to other viruses.

MDMA enhances "mind reading" of positive emotions and impairs "mind reading" of negative emotions.

Science.gov (United States)

Hysek, Cédric M; Domes, Gregor; Liechti, Matthias E

2012-07-01

3,4-Methylenedioxymethamphetamine (MDMA, ecstasy) increases sociability. The prosocial effects of MDMA may result from the release of the "social hormone" oxytocin and associated alterations in the processing of socioemotional stimuli. We investigated the effects of MDMA (125 mg) on the ability to infer the mental states of others from social cues of the eye region in the Reading the Mind in the Eyes Test. The study included 48 healthy volunteers (24 men, 24 women) and used a double-blind, placebo-controlled, within-subjects design. A choice reaction time test was used to exclude impairments in psychomotor function. We also measured circulating oxytocin and cortisol levels and subjective drug effects. MDMA differentially affected mind reading depending on the emotional valence of the stimuli. MDMA enhanced the accuracy of mental state decoding for positive stimuli (e.g., friendly), impaired mind reading for negative stimuli (e.g., hostile), and had no effect on mind reading for neutral stimuli (e.g., reflective). MDMA did not affect psychomotor performance, increased circulating oxytocin and cortisol levels, and produced subjective prosocial effects, including feelings of being more open, talkative, and closer to others. The shift in the ability to correctly read socioemotional information toward stimuli associated with positive emotional valence, together with the prosocial feelings elicited by MDMA, may enhance social approach behavior and sociability when MDMA is used recreationally and facilitate therapeutic relationships in MDMA-assisted psychotherapeutic settings.

A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2

Directory of Open Access Journals (Sweden)

Sylvie Lalonde

2010-09-01

Full Text Available Interactions between membrane proteins and the soluble fraction are essential for signal transduction and for regulating nutrient transport. To gain insights into the membrane-based interactome, 3,852 open reading frames (ORFs out of a target list of 8,383 representing membrane and signaling proteins from Arabidopsis thaliana were cloned into a Gateway compatible vector. The mating-based split-ubiquitin system was used to screen for potential protein-protein interactions (pPPIs among 490 Arabidopsis ORFs. A binary robotic screen between 142 receptor-like kinases, 72 transporters, 57 soluble protein kinases and phosphatases, 40 glycosyltransferases, 95 proteins of various functions and 89 proteins with unknown function detected 387 out of 90,370 possible PPIs. A secondary screen confirmed 343 (of 387 pPPIs between 179 proteins, yielding a scale-free network (r2=0.863. Eighty of 142 transmembrane receptor-like kinases (RLK tested positive, identifying three homomers, 63 heteromers and 80 pPPIs with other proteins. Thirty-one out of 142 RLK interactors (including RLKs had previously been found to be phosphorylated; thus interactors may be substrates for respective RLKs. None of the pPPIs described here had been reported in the major interactome databases, including potential interactors of G protein-coupled receptors, phospholipase C, and AMT ammonium transporters. Two RLKs found as putative interactors of AMT1;1 were independently confirmed using a split luciferase assay in Arabidopsis protoplasts. These RLKs may be involved in ammonium-dependent phosphorylation of the C-terminus and regulation of ammonium uptake activity. The robotic screening method established here will enable a systematic analysis of membrane protein interactions in fungi, plants and metazoa.

A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli

Directory of Open Access Journals (Sweden)

Adi Oron-Gottesman

2016-11-01

Full Text Available Escherichia coli mazEF is an extensively studied stress-induced toxin-antitoxin (TA system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM, composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant. This in-frame ACA cleavage of MazF seems to depend on MazF binding to an extracellular-death-factor (EDF-like element in ribosomal protein bS1 (bacterial S1, apparently causing MazF to be part of STM ribosomes. Furthermore, due to the in-frame MazF cleavage of ACAs under stress, a bias occurs in the reading of the genetic code causing the amino acid threonine to be encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA.

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

Directory of Open Access Journals (Sweden)

Konrad J Karczewski

Full Text Available The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping, a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Cloning, production, and purification of proteins for a medium-scale structural genomics project.

Science.gov (United States)

Quevillon-Cheruel, Sophie; Collinet, Bruno; Trésaugues, Lionel; Minard, Philippe; Henckes, Gilles; Aufrère, Robert; Blondeau, Karine; Zhou, Cong-Zhao; Liger, Dominique; Bettache, Nabila; Poupon, Anne; Aboulfath, Ilham; Leulliot, Nicolas; Janin, Joël; van Tilbeurgh, Herman

2007-01-01

The South-Paris Yeast Structural Genomics Pilot Project (http://www.genomics.eu.org) aims at systematically expressing, purifying, and determining the three-dimensional structures of Saccharomyces cerevisiae proteins. We have already cloned 240 yeast open reading frames in the Escherichia coli pET system. Eighty-two percent of the targets can be expressed in E. coli, and 61% yield soluble protein. We have currently purified 58 proteins. Twelve X-ray structures have been solved, six are in progress, and six other proteins gave crystals. In this chapter, we present the general experimental flowchart applied for this project. One of the main difficulties encountered in this pilot project was the low solubility of a great number of target proteins. We have developed parallel strategies to recover these proteins from inclusion bodies, including refolding, coexpression with chaperones, and an in vitro expression system. A limited proteolysis protocol, developed to localize flexible regions in proteins that could hinder crystallization, is also described.

Providing Information about Reading Lists via a Dashboard Interface

Directory of Open Access Journals (Sweden)

Dr Jason Cooper

2013-01-01

Full Text Available As developers of the open source LORLS Resource/Reading List Management System we have developed a dashboard to better support academic staffs’ understanding of how their students use reading lists. This dashboard provides both graphical and tabulated information drawn from LORLS and the Aleph Integrated Library System. Development of the dashboard required changes to back-end functionality of LORLS such as logging views of reading lists and caching of loan data. Changes to the front end included the use of HTML5 canvas elements to generate pie charts and line graphs. Recently launched to academic staff at Loughborough University, the dashboard has already garnered much praise. It is hoped that further development of the dashboard will provide even more support for academics in the compilation of their reading lists.

Identification and characterization of a novel non-structural protein of bluetongue virus.

Directory of Open Access Journals (Sweden)

Maxime Ratinier

2011-12-01

Full Text Available Bluetongue virus (BTV is the causative agent of a major disease of livestock (bluetongue. For over two decades, it has been widely accepted that the 10 segments of the dsRNA genome of BTV encode for 7 structural and 3 non-structural proteins. The non-structural proteins (NS1, NS2, NS3/NS3a play different key roles during the viral replication cycle. In this study we show that BTV expresses a fourth non-structural protein (that we designated NS4 encoded by an open reading frame in segment 9 overlapping the open reading frame encoding VP6. NS4 is 77-79 amino acid residues in length and highly conserved among several BTV serotypes/strains. NS4 was expressed early post-infection and localized in the nucleoli of BTV infected cells. By reverse genetics, we showed that NS4 is dispensable for BTV replication in vitro, both in mammalian and insect cells, and does not affect viral virulence in murine models of bluetongue infection. Interestingly, NS4 conferred a replication advantage to BTV-8, but not to BTV-1, in cells in an interferon (IFN-induced antiviral state. However, the BTV-1 NS4 conferred a replication advantage both to a BTV-8 reassortant containing the entire segment 9 of BTV-1 and to a BTV-8 mutant with the NS4 identical to the homologous BTV-1 protein. Collectively, this study suggests that NS4 plays an important role in virus-host interaction and is one of the mechanisms played, at least by BTV-8, to counteract the antiviral response of the host. In addition, the distinct nucleolar localization of NS4, being expressed by a virus that replicates exclusively in the cytoplasm, offers new avenues to investigate the multiple roles played by the nucleolus in the biology of the cell.

Identifying New Small Proteins in Escherichia coli.

Science.gov (United States)

VanOrsdel, Caitlin E; Kelly, John P; Burke, Brittany N; Lein, Christina D; Oufiero, Christopher E; Sanchez, Joseph F; Wimmers, Larry E; Hearn, David J; Abuikhdair, Fatimeh J; Barnhart, Kathryn R; Duley, Michelle L; Ernst, Sarah E G; Kenerson, Briana A; Serafin, Aubrey J; Hemm, Matthew R

2018-04-12

The number of small proteins (SPs) encoded in the Escherichia coli genome is unknown, as current bioinformatics and biochemical techniques make short gene and small protein identification challenging. One method of small protein identification involves adding an epitope tag to the 3' end of a short open reading frame (sORF) on the chromosome, with synthesis confirmed by immunoblot assays. In this study, this strategy was used to identify new E. coli small proteins, tagging 80 sORFs in the E. coli genome, and assayed for protein synthesis. The selected sORFs represent diverse sequence characteristics, including degrees of sORF conservation, predicted transmembrane domains, sORF direction with respect to flanking genes, ribosome binding site (RBS) prediction, and ribosome profiling results. Of 80 sORFs, 36 resulted in encoded synthesized proteins-a 45% success rate. Modeling of detected versus non-detected small proteins analysis showed predictions based on RBS prediction, transcription data, and ribosome profiling had statistically-significant correlation with protein synthesis; however, there was no correlation between current sORF annotation and protein synthesis. These results suggest substantial numbers of small proteins remain undiscovered in E. coli, and existing bioinformatics techniques must continue to improve to facilitate identification. © 2018 The Authors. Proteomics Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, Towson University.

A transposase strategy for creating libraries of circularly permuted proteins.

Science.gov (United States)

Mehta, Manan M; Liu, Shirley; Silberg, Jonathan J

2012-05-01

A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions.

Gardenia jasminoides Encodes an Inhibitor-2 Protein for Protein Phosphatase Type 1

Science.gov (United States)

Gao, Lan; Li, Hao-Ming

2017-08-01

Protein phosphatase-1 (PP1) regulates diverse, essential cellular processes such as cell cycle progression, protein synthesis, muscle contraction, carbohydrate metabolism, transcription and neuronal signaling. Inhibitor-2 (I-2) can inhibit the activity of PP1 and has been found in diverse organisms. In this work, a Gardenia jasminoides fruit cDNA library was constructed, and the GjI-2 cDNA was isolated from the cDNA library by sequencing method. The GjI-2 cDNA contains a predicted 543 bp open reading frame that encodes 180 amino acids. The bioinformatics analysis suggested that the GjI-2 has conserved PP1c binding motif, and contains a conserved phosphorylation site, which is important in regulation of its activity. The three-dimensional model structure of GjI-2 was buite, its similar with the structure of I-2 from mouse. The results suggest that GjI-2 has relatively conserved RVxF, FxxR/KxR/K and HYNE motif, and these motifs are involved in interaction with PP1.

Open3DALIGN

DEFF Research Database (Denmark)

Tosco, Paolo; Balle, Thomas

2011-01-01

Description Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If Py......MOL is installed on the system while Open3DALIGN is being operated interactively, the setup of alignments can be followed in real time on PyMOL's viewport. A typical workflow could be the following: 1.A dataset is imported as SDF file 2.Optionally, for each compound of the dataset a quenched molecular dynamics...... (QMD) conformational search is carried out to find the most stable conformers in a user-defined energy range from the global minimum 3.One or more template compounds are chosen, then the whole dataset is best-aligned to the template(s). The alignment is a performed rigidly, using for each compound...

A sensitive short read homology search tool for paired-end read sequencing data.

Science.gov (United States)

Techa-Angkoon, Prapaporn; Sun, Yanni; Lei, Jikai

2017-10-16

Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenomic data, profile homology search is widely adopted in integrated pipelines for functional analysis. While the state-of-the-art tool HMMER has achieved high sensitivity and accuracy in domain annotation, the sensitivity of HMMER on short reads declines rapidly. The low sensitivity on short read homology search can lead to inaccurate domain composition and abundance computation. Our experimental results showed that half of the reads were missed by HMMER for a RNA-Seq dataset. Thus, there is a need for better methods to improve the homology search performance for short reads. We introduce a profile homology search tool named Short-Pair that is designed for short paired-end reads. By using an approximate Bayesian approach employing distribution of fragment lengths and alignment scores, Short-Pair can retrieve the missing end and determine true domains. In particular, Short-Pair increases the accuracy in aligning short reads that are part of remote homologs. We applied Short-Pair to a RNA-Seq dataset and a metagenomic dataset and quantified its sensitivity and accuracy on homology search. The experimental results show that Short-Pair can achieve better overall performance than the state-of-the-art methodology of profile homology search. Short-Pair is best used for next-generation sequencing (NGS) data that lack reference genomes. It provides a complementary paired-end read homology search tool to HMMER. The source code is freely available at https://sourceforge.net/projects/short-pair/ .

Human herpesvirus 6B U19 protein is a PML-regulated transcriptional activator that localizes to nuclear foci in a PML-independent manner

DEFF Research Database (Denmark)

Kofod-Olsen, Emil; Ross-Hansen, Katrine; Mikkelsen, Jacob Giehm

2008-01-01

Human herpesvirus 6B (HHV-6B) contains an IE-B domain spanning open reading frames U16/17-U19, based on homology with human cytomegalovirus. Here, the protein product, U19, of the HHV-6B U19 gene is identified as a 47 kDa transcriptional activator. HHV-6B infection or overexpression of U19...

ProDaMa: an open source Python library to generate protein structure datasets

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Manconi Andrea

2009-10-01

Full Text Available Abstract Background The huge difference between the number of known sequences and known tertiary structures has justified the use of automated methods for protein analysis. Although a general methodology to solve these problems has not been yet devised, researchers are engaged in developing more accurate techniques and algorithms whose training plays a relevant role in determining their performance. From this perspective, particular importance is given to the training data used in experiments, and researchers are often engaged in the generation of specialized datasets that meet their requirements. Findings To facilitate the task of generating specialized datasets we devised and implemented ProDaMa, an open source Python library than provides classes for retrieving, organizing, updating, analyzing, and filtering protein data. Conclusion ProDaMa has been used to generate specialized datasets useful for secondary structure prediction and to develop a collaborative web application aimed at generating and sharing protein structure datasets. The library, the related database, and the documentation are freely available at the URL http://iasc.diee.unica.it/prodama.

Developing reading literacy by reading badge

OpenAIRE

Rejc, Blanka

2017-01-01

Reading is a fundamental activity of our society and is present in all areas of a person’s life. Authors who deal with reading define reading with different definitions, some of them I also presented in my master’s degree thesis. The ways of reading, typology of readers and knowledge of different reading models are only some of the important theoretical facts that serve as a basis for the research and defining reading. Reading motivation is an important motivational factor, which encourages a...

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

Science.gov (United States)

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…

A Vision for Open Cyber-Scholarly Infrastructures

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Costantino Thanos

2016-05-01

Full Text Available The characteristics of modern science, i.e., data-intensive, multidisciplinary, open, and heavily dependent on Internet technologies, entail the creation of a linked scholarly record that is online and open. Instrumental in making this vision happen is the development of the next generation of Open Cyber-Scholarly Infrastructures (OCIs, i.e., enablers of an open, evolvable, and extensible scholarly ecosystem. The paper delineates the evolving scenario of the modern scholarly record and describes the functionality of future OCIs as well as the radical changes in scholarly practices including new reading, learning, and information-seeking practices enabled by OCIs.

Do reading and spelling share a lexicon?

Science.gov (United States)

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. Copyright © 2016 Elsevier Inc. All rights reserved.

Presence of potential allergy-related linear epitopes in novel proteins from conventional crops and the implication for the safety assessment of these crops with respect to the current testing of genetically modified crops

NARCIS (Netherlands)

Kleter, G.A.; Peijnenburg, A.A.C.M.

2003-01-01

Mitochondria of cytoplasmic male sterile crop plants contain novel, chimeric open reading frames. In addition, a number of crops carry endogenous double-stranded ribonucleic acid (dsRNA). In this study, the novel proteins encoded by these genetic components were screened for the presence of

I read, you read, we read: the history of reading in Slovenia

Directory of Open Access Journals (Sweden)

Anja Dular

2013-03-01

Full Text Available ABSTRACTPurpose: The aim of the article is to research reading habits in Slovenia in the period between 16th and 19th century and to find similarities with Austria and other European countries of that time.Methodology/approach: For the purpose of the analysis different resources were used – study books, catechisms, prayer books and manuals. We were focused on introductions in which readers are advised how to read, explaining to whom the work is intended and emphasizing the importance of meditation on the texts.Results: Historically the laud reading was prefered, as to continue the folk tradition. However, the 16th century texts were transmitted by women while the folk tradition was narrated by males. In the 18th century the higher level of literacy and greater book production and availability caused that the books were not a privilege of a few. At that time more texts were intended for silent, individual reading. Interestingly, the authors emphasized the importance of meditation on the texts, too. It was also advised when to read – it wasrecommedend to read in leisure time on Sundays, and on holidays. The role of books was also to breakaway with the reality and to forget everyday problems. Due to the overproduction of books in the 17th centrury it was concerned that books are misleading the crowds. The church considered the reading of books as inappropriate, and criticized fiction, novels and adventure stories mostly read by women.Research limitation: The study is based on Slovenian texts only, although the foreign literature, especially in German, was generally available, too.Originality/practical implications: The study is fullfiling the gap in the history of reading in Slovenia.

Developmental, Component-Based Model of Reading Fluency: An Investigation of Predictors of Word-Reading Fluency, Text-Reading Fluency, and Reading Comprehension.

Science.gov (United States)

Kim, Young-Suk Grace

2015-01-01

The primary goal was to expand our understanding of text reading fluency (efficiency or automaticity)-how its relation to other constructs (e.g., word reading fluency and reading comprehension) changes over time and how it is different from word reading fluency and reading comprehension. We examined (1) developmentally changing relations among word reading fluency, listening comprehension, text reading fluency, and reading comprehension; (2) the relation of reading comprehension to text reading fluency; (3) unique emergent literacy predictors (i.e., phonological awareness, orthographic awareness, morphological awareness, letter name knowledge, vocabulary) of text reading fluency vs. word reading fluency; and (4) unique language and cognitive predictors (e.g., vocabulary, grammatical knowledge, theory of mind) of text reading fluency vs. reading comprehension. These questions were addressed using longitudinal data (two timepoints; Mean age = 5;24 & 6;08) from Korean-speaking children ( N = 143). Results showed that listening comprehension was related to text reading fluency at time 2, but not at time 1. At both times text reading fluency was related to reading comprehension, and reading comprehension was related to text reading fluency over and above word reading fluency and listening comprehension. Orthographic awareness was related to text reading fluency over and above other emergent literacy skills and word reading fluency. Vocabulary and grammatical knowledge were independently related to text reading fluency and reading comprehension whereas theory of mind was related to reading comprehension, but not text reading fluency. These results reveal developmental nature of relations and mechanism of text reading fluency in reading development.

RNA sequence determinants of a coupled termination-reinitiation strategy for downstream open reading frame translation in Helminthosporium victoriae virus 190S and other victoriviruses (Family Totiviridae).

Science.gov (United States)

Li, Hua; Havens, Wendy M; Nibert, Max L; Ghabrial, Said A

2011-07-01

The genome-length, dicistronic mRNA of the double-stranded RNA fungal virus Helminthosporium victoriae virus 190S (genus Victorivirus, family Totiviridae) contains two long open reading frames (ORFs) that overlap in the tetranucleotide AUGA. Translation of the downstream ORF, which encodes the RNA-dependent RNA polymerase (RdRp), has been proposed to depend on ribosomal reinitiation following termination of the upstream ORF, which encodes the capsid protein. In the current study, we examined the RNA sequence determinants for RdRp translation in this virus and demonstrated that a coupled termination-reinitiation (stop-restart) strategy is indeed used. Signals for termination-reinitiation are found within a 32-nucleotide stretch of RNA immediately upstream of the AUGA motif, including a predicted pseudoknot structure. The close proximity in which this predicted structure is followed by the upstream ORF's stop codon appears to be especially important for promoting translation of the downstream ORF. The normal strong preferences for an AUG start codon and the canonical sequence context to favor translation initiation appear somewhat relaxed for the downstream ORF. Similar sequence motifs and predicted RNA structures in other victoriviruses suggest that they all share a related stop-restart strategy for RdRp translation. Members of the genus Victorivirus thus provide new and unique opportunities for exploring the molecular mechanisms of translational coupling, which remain only partly understood in this and other systems.

Does Extensive Reading Promote Reading Speed?

Science.gov (United States)

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 without…

Open Access: there is something you can do…

CERN Multimedia

Jens Vigen

2014-01-01

Since the very beginning, CERN has put a lot of emphasis on the fact that its scientific output should be accessible to everyone. Today, on average, around 10% of articles are published Open Access worldwide. However, that figure is much lower when the proceedings of conferences, including those held at CERN, are taken into account.   The CERN Convention reads: “…and the results of its experimental and theoretical work shall be published or otherwise made generally available”. There is little doubt that if this had been written today, it would have explicitly mentioned that our results should be published Open Access. This is indeed what has happened as CERN has moved into the LHC era: a little known fact is that all LHC physics results have been published Open Access and can be read in their final form by anybody with an Internet connection. Most importantly, this information can be re-used thanks to Creative Commons licenses, which is not the case for conventional...

Transcription initiation complex structures elucidate DNA opening.

Science.gov (United States)

Plaschka, C; Hantsche, M; Dienemann, C; Burzinski, C; Plitzko, J; Cramer, P

2016-05-19

Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.

Expression and RNA Interference of Ribosomal Protein L5 Gene in Nilaparvata lugens (Hemiptera: Delphacidae).

Science.gov (United States)

Zhu, Jiajun; Hao, Peiying; Lu, Chaofeng; Ma, Yan; Feng, Yalin; Yu, Xiaoping

2017-05-01

The ribosomal proteins play important roles in the growth and development of organisms. This study aimed to explore the function of NlRPL5 (GenBank KX379234), a ribosomal protein L5 gene, in the brown planthopper Nilaparvata lugens. The open reading frame of NlRPL5 was cloned from N. lugens based on a previous transcriptome analysis. The results revealed that the open reading frame of NlRPL5 is of 900 bp, encoding 299 amino acid residues. The reverse transcription quantitative PCR results suggested that the expression of NlRPL5 gene was stronger in gravid females, but was relatively low in nymphs, males, and newly emerged females. The expression level of NlRPL5 in the ovary was about twofolds of that in the head, thorax, or fat body. RNAi of dsNlRPL5 resulted in a significant reduction of mRNA levels, ∼50% decrease in comparison with the dsGFP control at day 6. Treatment of dsNlRPL5 significantly restricted the ovarian development, and decreased the number of eggs laid on the rice (Oryza sativa) plants. This study provided a new clue for further study on the function and regulation mechanism of NlRPL5 in N. lugens. © The Author 2017. Published by Oxford University Press on behalf of the Entomological Society of America.

Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLalphas/ALEX Relay.

Directory of Open Access Journals (Sweden)

2005-08-01

Full Text Available XLalphas and ALEX are structurally unrelated mammalian proteins translated from alternative overlapping reading frames of a single transcript. Not only are they encoded by the same locus, but a specific XLalphas/ALEX interaction is essential for G-protein signaling in neuroendocrine cells. A disruption of this interaction leads to abnormal human phenotypes, including mental retardation and growth deficiency. The region of overlap between the two reading frames evolves at a remarkable speed: the divergence between human and mouse ALEX polypeptides makes them virtually unalignable. To trace the evolution of this puzzling locus, we sequenced it in apes, Old World monkeys, and a New World monkey. We show that the overlap between the two reading frames and the physical interaction between the two proteins force the locus to evolve in an unprecedented way. Namely, to maintain two overlapping protein-coding regions the locus is forced to have high GC content, which significantly elevates its intrinsic evolutionary rate. However, the two encoded proteins cannot afford to change too quickly relative to each other as this may impair their interaction and lead to severe physiological consequences. As a result XLalphas and ALEX evolve in an oscillating fashion constantly balancing the rates of amino acid replacements. This is the first example of a rapidly evolving locus encoding interacting proteins via overlapping reading frames, with a possible link to the origin of species-specific neurological differences.

TEACHER CANDIDATES’ VIEWS ON E-BOOKS AND SCREEN READING

Directory of Open Access Journals (Sweden)

Nevin AKKAYA

2015-08-01

Full Text Available Today, it is a necessity to make use of information technologies in creating, distributing and accessing information resources. The electronic resources as products of the developing information technologies include bibliographical text databases, e-journals, e-books, open achieves and web sites. Today, Many printed material can be accesssed by electronically in readers. Furthermore, e-books have been increasingly preferred as a mode of reading because of its advantages such as portability, storage and rich content. Individuals who want to sustain their development on this mode of reading prefer screen reading. Because reading has become a necessity because of the developing information technologies. This study aimed to examine the views of students studying Turkish language teaching at an education faculty on e-books and screen reading. Action research, one of the qualitative research design, was used during the research. Data were analyzed by content analysis. Whereas 40.7% of the ones who have taken part in this study have expressed not knowing anything about e-books, 57.8% of the participants have claimed they have knowledge about the issue of e-books. 55.3% of the participants consider that e-books contribute to the habit of reading. 73% of the participants have expressed that they have no knowledge about screen reading.

Concurrent and Accurate Short Read Mapping on Multicore Processors.

Science.gov (United States)

Martínez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina, Sergio; Castillo, Maribel; Dopazo, Joaquín; Quintana-Ortí, Enrique S

2015-01-01

We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at http://www.opencb.org, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.

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

Energy Technology Data Exchange (ETDEWEB)

Vieira, P.; De Waal-Malefyt, R.; Dang, M.N.; Johnson, K.E.; Kastelein, R.; Fiorentino, D.F.; DeVries, J.E.; Roncarolo, M.G.; Mosmann, T.R.; Moore, K.W. (DNAX Research Inst. of Molecular and Cellular Biology, Palo Alto, CA (United States))

1991-02-15

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

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

International Nuclear Information System (INIS)

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

1991-01-01

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

Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome.

Directory of Open Access Journals (Sweden)

Albrecht von Brunn

2007-05-01

Full Text Available The severe acute respiratory syndrome coronavirus (SARS-CoV genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. The functions of a large number of viral ORFs are poorly understood or unknown. In order to gain more insight into functions and modes of action and interaction of the different proteins, we cloned the viral ORFeome and performed a genome-wide analysis for intraviral protein interactions and for intracellular localization. 900 pairwise interactions were tested by yeast-two-hybrid matrix analysis, and more than 65 positive non-redundant interactions, including six self interactions, were identified. About 38% of interactions were subsequently confirmed by CoIP in mammalian cells. Nsp2, nsp8 and ORF9b showed a wide range of interactions with other viral proteins. Nsp8 interacts with replicase proteins nsp2, nsp5, nsp6, nsp7, nsp8, nsp9, nsp12, nsp13 and nsp14, indicating a crucial role as a major player within the replication complex machinery. It was shown by others that nsp8 is essential for viral replication in vitro, whereas nsp2 is not. We show that also accessory protein ORF9b does not play a pivotal role for viral replication, as it can be deleted from the virus displaying normal plaque sizes and growth characteristics in Vero cells. However, it can be expected to be important for the virus-host interplay and for pathogenicity, due to its large number of interactions, by enhancing the global stability of the SARS proteome network, or play some unrealized role in regulating protein-protein interactions. The interactions identified provide valuable material for future studies.

Molecular cloning and chromosome mapping of the human gene encoding protein phosphotyrosyl phosphatase 1B

International Nuclear Information System (INIS)

Brown-Shimer, S.; Johnson, K.A.; Bruskin, A.; Green, N.R.; Hill, D.E.; Lawrence, J.B.; Johnson, C.

1990-01-01

The inactivation of growth suppressor genes appears to play a major role in the malignant process. To assess whether protein phosphotyrosyl phosphatases function as growth suppressors, the authors have isolated a cDNA clone encoding human protein phosphotyrosyl phosphatase 1B for structural and functional characterization. The translation product deduced from the 1,305-nucleotide open reading frame predicts a protein containing 435 amino acids and having a molecular mass of 49,966 Da. The amino-terminal 321 amino acids deduced from the cDNA sequence are identical to the empirically determined sequence of protein phosphotyrosyl phosphatase 1B. A genomic clone has been isolated and used in an in situ hybridization to banded metaphase chromosomes to determine that the gene encoding protein phosphotyrosyl phosphatase 1B maps as a single-copy gene to the long arm of chromosome 20 in the region q13.1-q13.2

Developmental, Component-Based Model of Reading Fluency: An Investigation of Predictors of Word-Reading Fluency, Text-Reading Fluency, and Reading Comprehension

OpenAIRE

Kim, Young-Suk Grace

2015-01-01

The primary goal was to expand our understanding of text reading fluency (efficiency or automaticity)—how its relation to other constructs (e.g., word reading fluency and reading comprehension) changes over time and how it is different from word reading fluency and reading comprehension. We examined (1) developmentally changing relations among word reading fluency, listening comprehension, text reading fluency, and reading comprehension; (2) the relation of reading comprehension to text readi...

Resolution of Holliday junctions in Escherichia coli: identification of the ruvC gene product as a 19-kilodalton protein.

Science.gov (United States)

Sharples, G J; Lloyd, R G

1991-12-01

The ruvC gene of Escherichia coli specifies a nuclease that resolves Holliday junction intermediates in genetic recombination (B. Connolly, C.A. Parsons, F.E. Benson, H.J. Dunderdale, G.J. Sharples, R.G. Lloyd, and S.C. West, Proc. Natl. Acad, Sci. USA 88:6063-6067, 1991). The gene was located between aspS and the ruvAB operon by DNA sequencing and deletion analysis of ruvC plasmids and was shown to encode a protein of 18,747 Da. Analysis of the DNA flanking ruvC indicated that the gene is transcribed independently of the LexA-regulated ruvAB operon and is not under direct SOS control. ruvC lies downstream of an open reading frame, orf-33, for a protein which migrates during sodium dodecyl sulfate-polyacrylamide gel electrophoresis as a 33-kDa polypeptide. These two genes probably form an operon. However, expression of ruvC was found to be very poor relative to that of orf-33. A double ribosomal frameshift between these genes is proposed as a possible reason for the low level of RuvC. Two further open reading frames of unknown function were identified, one on either side of the orf-33-ruvC operon.

The nonstructural protein 8 (nsp8) of the SARS coronavirus interacts with its ORF6 accessory protein

International Nuclear Information System (INIS)

Kumar, Purnima; Gunalan, Vithiagaran; Liu Boping; Chow, Vincent T.K.; Druce, Julian; Birch, Chris; Catton, Mike; Fielding, Burtram C.; Tan, Yee-Joo; Lal, Sunil K.

2007-01-01

Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) caused a severe outbreak in several regions of the world in 2003. The SARS-CoV genome is predicted to contain 14 functional open reading frames (ORFs). The first ORF (1a and 1b) encodes a large polyprotein that is cleaved into nonstructural proteins (nsp). The other ORFs encode for four structural proteins (spike, membrane, nucleocapsid and envelope) as well as eight SARS-CoV-specific accessory proteins (3a, 3b, 6, 7a, 7b, 8a, 8b and 9b). In this report we have cloned the predicted nsp8 gene and the ORF6 gene of the SARS-CoV and studied their abilities to interact with each other. We expressed the two proteins as fusion proteins in the yeast two-hybrid system to demonstrate protein-protein interactions and tested the same using a yeast genetic cross. Further the strength of the interaction was measured by challenging growth of the positive interaction clones on increasing gradients of 2-amino trizole. The interaction was then verified by expressing both proteins separately in-vitro in a coupled-transcription translation system and by coimmunoprecipitation in mammalian cells. Finally, colocalization experiments were performed in SARS-CoV infected Vero E6 mammalian cells to confirm the nsp8-ORF6 interaction. To the best of our knowledge, this is the first report of the interaction between a SARS-CoV accessory protein and nsp8 and our findings suggest that ORF6 protein may play a role in virus replication

Developmental relations between reading comprehension and reading strategies

OpenAIRE

Muijselaar, M.M.L.; Swart, N.M.; Steenbeek-Planting, E.G.; Droop, W.; Verhoeven, L.T.W.; Jong, P.F. de

2017-01-01

We examined the developmental relations between knowledge of reading strategies and reading comprehension in a longitudinal study of 312 Dutch children from the beginning of fourth grade to the end of fifth grade. Measures for reading comprehension, reading strategies, reading fluency, vocabulary, and working memory were administered. A structural equation model was constructed to estimate the unique relations between reading strategies and reading comprehension, while controlling for reading...

LightNVM: The Linux Open-Channel SSD Subsystem

DEFF Research Database (Denmark)

Bjørling, Matias; Gonzalez, Javier; Bonnet, Philippe

2017-01-01

resource utilization. We propose that SSD management trade-offs should be handled through Open-Channel SSDs, a new class of SSDs, that give hosts control over their internals. We present our experience building LightNVM, the Linux Open-Channel SSD subsystem. We introduce a new Physical Page Ad- dress I...... to limit read latency variability and that it can be customized to achieve predictable I/O latencies....

I read. You read? Challenges and possibilities in working with literary literacy

Directory of Open Access Journals (Sweden)

Sayonara Abrantes de Oliveira

2017-07-01

Full Text Available This article is the result of a project linked to the Institutional Program of Scientific Initiation Scholarships for Higher Education (PIBIC-EM. The program’s objective was to analyze the contributing factors for the process of reading literacy training in order to verify how young people make their choices of literary texts, as well as know the difficulties and facilities they face in contact with these genres. To do so, we used the quantitative qualitative research through the application of a questionnaire, consisting of open questions, and applied to the students of the Integrated in Information Technology and Integrated Technician in the Environment of the Federal Institute of Education, Science and Technology of Paraíba (IFPB/campus Sousa courses. We also analyzed the perceptions derived from the observations of the Reader Club of the same campus, in an attempt to verify how the intervention of activities that mediate literary literacy favors the stimulus to the reading formation. Based on the data analysis, we observed that the student's distance element from reading is the lack of incentive, that is, the construction of an atmosphere that surrounds him, both in the classroom and in the other environments that welcome him. To overcome this, it is necessary for the teacher to have a theoretical-methodological apparatus guiding in his classes, since mediation favors literary literacy, having as support the Receptional Method and a conception of reading that articulates the interactional to the discursive, helping in the organization and selection of texts, in order to achieve the objectives of the formation of the reader.

Open access and beyond

Directory of Open Access Journals (Sweden)

Das Chhaya

2006-09-01

Full Text Available Abstract 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.

Cloning and expression of the coding regions of the heat shock proteins HSP10 and HSP16 from Piscirickettsia salmonis

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VIVIAN WILHELM

2003-01-01

Full Text Available The genes encoding the heat shock proteins HSP10 and HSP16 of the salmon pathogen Piscirickettsia salmonis have been isolated and sequenced. The HSP10 coding sequence is located in an open reading frame of 291 base pairs encoding 96 aminoacids. The HSP16 coding region was isolated as a 471 base pair fragment encoding a protein of 156 aminoacids. The deduced aminoacid sequences of both proteins show a significant homology to the respective protein from other prokaryotic organisms. Both proteins were expressed in E. coli as fusion proteins with thioredoxin and purified by chromatography on Ni-column. A rabbit serum against P. salmonis total proteins reacts with the recombinant HSP10 and HSP16 proteins. Similar reactivity was determined by ELISA using serum from salmon infected with P. salmonis. The possibility of formulating a vaccine containing these two proteins is discussed

Teaching Reading

Science.gov (United States)

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…

Slow Reading: Reading along "Lectio" Lines

Science.gov (United States)

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…

The Impact of Open Licensing on the Early Reader Ecosystem

Science.gov (United States)

Butcher, Neil; Hoosen, Sarah; Levey, Lisbeth; Moore, Derek

2016-01-01

The Impact of Open Licensing on the Early Reader Ecosystem examines how to use open licensing to promote quality learning resources for young children that are relevant and interesting. Research in early reading tends to focus on traditional publishing value and supply chains, without taking much consideration of new approaches and solutions…

A Study on Strategies for Teaching Speaking and Reading Comprehension Skills

OpenAIRE

AHMAD; Prof. Dr.I Ketut Seken,MA; Dra. Luh Putu Artini, MA., Ph.D

2013-01-01

The central intention of this study was to analyze the English teachers’ strategies in teaching speaking and reading comprehension skills in SMPN 1 Selong. It was conducted to get detailed information about the students’ responses toward their teachers’ strategies in teaching speaking and reading comprehension skills. This study employed a qualitative research design. Necessary data were gathered using open-ended question, classroom observation, interview, and questionnaire. The result ...

Discovery and annotation of small proteins using genomics, proteomics and computational approaches

Energy Technology Data Exchange (ETDEWEB)

Yang, Xiaohan; Tschaplinski, Timothy J.; Hurst, Gregory B.; Jawdy, Sara; Abraham, Paul E.; Lankford, Patricia K.; Adams, Rachel M.; Shah, Manesh B.; Hettich, Robert L.; Lindquist, Erika; Kalluri, Udaya C.; Gunter, Lee E.; Pennacchio, Christa; Tuskan, Gerald A.

2011-03-02

Small proteins (10 200 amino acids aa in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained 2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences. We identified an initial set of 12,852 sORFs encoding proteins of 10 200 aa in length. Three computational approaches were then used to enrich for bona fide protein-coding sORFs from the initial sORF set: (1) codingpotential prediction, (2) evolutionary conservation between P. deltoides and other plant species, and (3) gene family clustering within P. deltoides. As a result, a high-confidence sORF candidate set containing 1469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set. In the high-confidence sORF candidate set, known protein domains were identified in 1282 genes (higher-confidence sORF candidate set), out of which 611 genes, designated as highest-confidence candidate sORF set, were supported by proteomics data. Of the 611 highest-confidence candidate sORF genes, 56 were new to the current Populus genome annotation. This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available.

An Integrated Framework Advancing Membrane Protein Modeling and Design.

Directory of Open Access Journals (Sweden)

Rebecca F Alford

2015-09-01

Full Text Available Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1 prediction of free energy changes upon mutation; (2 high-resolution structural refinement; (3 protein-protein docking; and (4 assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design.

The Relationship between SES and Reading Comprehension in Chinese: A Mediation Model

Directory of Open Access Journals (Sweden)

Yahua Cheng

2017-04-01

Full Text Available An increasing body of research provides evidence that socioeconomic status (SES was significantly related to children’s reading development; however, the psychological mechanism underlying the association between them remained an open question. The present study is designed to test the hypothesized three-path effect of vocabulary knowledge and morphological awareness as mediators between SES and sentence reading comprehension in Chinese first-graders. Results of mediation model showed that SES exerted its effect on sentence reading comprehension through the indirect path via the simple mediating effect of morphological awareness and the three-path mediating effect of vocabulary knowledge and morphological awareness. The findings highlight a previously unidentified mechanism of the relationship between SES and reading comprehension in Chinese young children.

Characterisation of Structural Proteins from Chronic Bee Paralysis Virus (CBPV Using Mass Spectrometry

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Aurore Chevin

2015-06-01

Full Text Available Chronic bee paralysis virus (CBPV is the etiological agent of chronic paralysis, an infectious and contagious disease in adult honeybees. CBPV is a positive single-stranded RNA virus which contains two major viral RNA fragments. RNA 1 (3674 nt and RNA 2 (2305 nt encode three and four putative open reading frames (ORFs, respectively. RNA 1 is thought to encode the viral RNA-dependent RNA polymerase (RdRp since the amino acid sequence derived from ORF 3 shares similarities with the RdRP of families Nodaviridae and Tombusviridae. The genomic organization of CBPV and in silico analyses have suggested that RNA 1 encodes non-structural proteins, while RNA 2 encodes structural proteins, which are probably encoded by ORFs 2 and 3. In this study, purified CBPV particles were used to characterize virion proteins by mass spectrometry. Several polypeptides corresponding to proteins encoded by ORF 2 and 3 on RNA 2 were detected. Their role in the formation of the viral capsid is discussed.

CO2 dose–response functions for wheat grain, protein and mineral yield based on FACE and open-top chamber experiments

International Nuclear Information System (INIS)

Pleijel, Håkan; Högy, Petra

2015-01-01

Data from three Swedish open-top chamber and four German FACE experiments were combined to derive response functions for elevated CO 2 (eCO 2 ) effects on Cd, Zn, Mn, protein, grain yield, grain mass and grain number of wheat. Grain yield and grain number were increased by ∼6% and ∼7%, respectively, per 100 ppm CO 2 ; the former effect was linked to plant nitrogen status. Grain mass was not influenced by eCO 2 , whereas Cd concentration was reduced. Unlike Zn, Mn and protein, effects on Cd yield were not related to effects on grain yield. Yields of Mn, Zn and (weakly) protein were positively affected by eCO 2 . For protein, grain yield, grain mass and grain number, the results were consistent among the FACE and OTC experiments. A key conclusion was that yields of essential nutrients were enhanced (Mn > Zn > protein), although less than grain yield, which would not be expected from a simple dilution model. - Highlights: • Grain yield and grain number were positively affected by 6–7% per 100 ppm CO 2 . • Yield stimulation by CO 2 was influenced by plant nitrogen status. • Cd concentration was reduced by elevated CO 2 . • Yields of Zn, Mn and protein were stimulated by CO 2 , but less than grain yield. • A simple dilution model did not explain effects on Zn, Mn and protein. - Yields of Zn, Mn and protein were stimulated less by elevated CO 2 than grain yield, while Cd yield and grain mass were unaffected, in wheat exposed in FACE and open-top chambers

Cohesion: An Overview for the Teacher of Reading. Revised.

Science.gov (United States)

Chapman, L. John

Pronouns, substitutes, elipses, conjunctions, synonyms, antonyms, superordinates and subordinates, and part-whole relations all provide cohesive ties that help a reader understand text. A study at Britain's Open University (England) has revealed the way in which the perception of cohesive ties is achieved as children's reading ability grows.…

Reading comprehension and reading related abilities in adolescents with reading disabilities and attention-deficit/hyperactivity disorder.

Science.gov (United States)

Ghelani, Karen; Sidhu, Robindra; Jain, Umesh; Tannock, Rosemary

2004-11-01

Reading comprehension is a very complex task that requires different cognitive processes and reading abilities over the life span. There are fewer studies of reading comprehension relative to investigations of word reading abilities. Reading comprehension difficulties, however, have been identified in two common and frequently overlapping childhood disorders: reading disability (RD) and attention-deficit/hyperactivity disorder (ADHD). The nature of reading comprehension difficulties in these groups remains unclear. The performance of four groups of adolescents (RD, ADHD, comorbid ADHD and RD, and normal controls) was compared on reading comprehension tasks as well as on reading rate and accuracy tasks. Adolescents with RD showed difficulties across most reading tasks, although their comprehension scores were average. Adolescents with ADHD exhibited adequate single word reading abilities. Subtle difficulties were observed, however, on measures of text reading rate and accuracy as well as on silent reading comprehension, but scores remained in the average range. The comorbid group demonstrated similar difficulties to the RD group on word reading accuracy and on reading rate but experienced problems on only silent reading comprehension. Implications for reading interventions are outlined, as well as the clinical relevance for diagnosis.

OPEN about obesity

DEFF Research Database (Denmark)

Lissner, L; Troiano, R P; Midthune, D

2007-01-01

energy and protein recovery biomarkers as reference measures. POPULATION AND METHODS: This report employs data from the Observing Protein and Energy Nutrition (OPEN) study. Analyses are based on stratified samples of 211 (57 obese) men and 179 (50 obese) women who completed 24-h recalls (24HR), food...

The Explicit Instruction of Reading Strategies: Directed Reading Thinking Activity vs. Guided Reading Strategies

Directory of Open Access Journals (Sweden)

Mohammad Mehdi Yazdani

2015-05-01

Full Text Available Investigating the efficiencies and deficiencies of reading strategies is one of the noticeable issues in the related theory and research in reading comprehension instruction. This study was to examine the impact of Directed Reading Thinking Activity (DRTA and Guided Reading (GR on reading comprehension. Sixty three Iranian students of grade one in Shahed high school in the city of Bojnourd took part in the study. They were assigned in three groups, one control and two experimental groups. The instruction lasted for ten weeks. This study utilized a pretest posttest control group in quantitative quasi- experimental design. The same reading comprehension test was administered as pre-test and post-test. The results were twofold: First, the instruction of learning strategies could foster reading comprehension skill. Second, while the explicit instruction of both strategies could improve the students' reading comprehension skill, Directed Reading Thinking Activity had a more significant positive effect than Guided Reading.

Developmental Relations Between Reading Comprehension and Reading Strategies

NARCIS (Netherlands)

Muijselaar, M.; Swart, N.M.; Steenbeek-Planting, E.G,.; Droop, M.; Verhoeven, L.; de Jong, P.F.

2017-01-01

We examined the developmental relations between knowledge of reading strategies and reading comprehension in a longitudinal study of 312 Dutch children from the beginning of fourth grade to the end of fifth grade. Measures for reading comprehension, reading strategies, reading fluency, vocabulary,

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

Science.gov (United States)

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

2016-01-01

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

Balancing Open Access with Academic Standards: Implications for Community College Faculty

Science.gov (United States)

Gabbard, Anita; Mupinga, Davison M.

2013-01-01

Community colleges act as the gateway for students to higher education. Many of these colleges realize this mission through open-door policies where students lacking in basic reading, writing, and mathematics skills can enroll. But, this open-access policy often creates challenges when meeting academic standards. Based on data collected from…

Characterization of the expression and immunogenicity of the ns4b protein of human coronavirus 229E

DEFF Research Database (Denmark)

Chagnon, F; Lamarre, A; Lachance, C

1998-01-01

to demonstrate the expression of ns4b in HCV-229E-infected cells using flow cytometry. Given a previously reported contiguous five amino acid shared region between ns4b and myelin basic protein, a purified recombinant histidine-tagged ns4b protein and (or) human myelin basic protein were injected into mice......Sequencing of complementary DNAs prepared from various coronaviruses has revealed open reading frames encoding putative proteins that are yet to be characterized and are so far only described as nonstructural (ns). As a first step in the elucidation of its function, we characterized the expression...... and immunogenicity of the ns4b gene product from strain 229E of human coronavirus (HCV-229E), a respiratory virus with a neurotropic potential. The gene was cloned and expressed in bacteria. A fusion protein of ns4b with maltose-binding protein was injected into rabbits to generate specific antibodies that were used...

OpenDrift - an open source framework for ocean trajectory modeling

Science.gov (United States)

Dagestad, Knut-Frode; Breivik, Øyvind; Ådlandsvik, Bjørn

2016-04-01

We will present a new, open source tool for modeling the trajectories and fate of particles or substances (Lagrangian Elements) drifting in the ocean, or even in the atmosphere. The software is named OpenDrift, and has been developed at Norwegian Meteorological Institute in cooperation with Institute of Marine Research. OpenDrift is a generic framework written in Python, and is openly available at https://github.com/knutfrode/opendrift/. The framework is modular with respect to three aspects: (1) obtaining input data, (2) the transport/morphological processes, and (3) exporting of results to file. Modularity is achieved through well defined interfaces between components, and use of a consistent vocabulary (CF conventions) for naming of variables. Modular input implies that it is not necessary to preprocess input data (e.g. currents, wind and waves from Eulerian models) to a particular file format. Instead "reader modules" can be written/used to obtain data directly from any original source, including files or through web based protocols (e.g. OPeNDAP/Thredds). Modularity of processes implies that a model developer may focus on the geophysical processes relevant for the application of interest, without needing to consider technical tasks such as reading, reprojecting, and colocating input data, rotation and scaling of vectors and model output. We will show a few example applications of using OpenDrift for predicting drifters, oil spills, and search and rescue objects.

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

Directory of Open Access Journals (Sweden)

Nicholas T. Ingolia

2014-09-01

Full Text Available Ribosome profiling suggests that ribosomes occupy many regions of the transcriptome thought to be noncoding, including 5′ UTRs and long noncoding RNAs (lncRNAs. Apparent ribosome footprints outside of protein-coding regions raise the possibility of artifacts unrelated to translation, particularly when they occupy multiple, overlapping open reading frames (ORFs. Here, we show hallmarks of translation in these footprints: copurification with the large ribosomal subunit, response to drugs targeting elongation, trinucleotide periodicity, and initiation at early AUGs. We develop a metric for distinguishing between 80S footprints and nonribosomal sources using footprint size distributions, which validates the vast majority of footprints outside of coding regions. We present evidence for polypeptide production beyond annotated genes, including the induction of immune responses following human cytomegalovirus (HCMV infection. Translation is pervasive on cytosolic transcripts outside of conserved reading frames, and direct detection of this expanded universe of translated products enables efforts at understanding how cells manage and exploit its consequences.

Differential protein expression in tears of patients with primary open angle and pseudoexfoliative glaucoma.

Science.gov (United States)

Pieragostino, Damiana; Bucci, Sonia; Agnifili, Luca; Fasanella, Vincenzo; D'Aguanno, Simona; Mastropasqua, Alessandra; Ciancaglini, Marco; Mastropasqua, Leonardo; Di Ilio, Carmine; Sacchetta, Paolo; Urbani, Andrea; Del Boccio, Piero

2012-04-01

Primary open angle (POAG) and pseudoexfoliative glaucoma (PXG) are the most common primary and secondary forms of glaucoma, respectively. Even though the patho-physiology, aqueous humor composition, risk factors, clinical features, therapy and drug induced ocular surface changes in POAG and PXG have been widely studied, to date information concerning tear protein characterization is lacking. Tears are a source of nourishment for ocular surface tissues and a vehicle to remove local waste products, metabolized drugs and inflammatory mediators produced in several ophthalmic diseases. In glaucoma, the proteomic definition of tears may provide insights concerning patho-physiology of the disease and ocular surface modifications induced by topical therapy. Our study aimed at characterizing protein patterns in tears of patients with medically controlled POAG and PXG. A comparative tears proteomic analysis by label-free LC-MS(E) highlighted differences in the expression of several proteins in the two glaucoma sub-types and control subjects, highlighting inflammation pathways expressed in both diseases. Results were independently reconfirmed by SDS-PAGE and linear MALDI-TOF MS, validating altered levels of Lysozyme C, Lipocalin-1, Protein S100, Immunoglobulins and Prolactin Inducible Protein. Moreover, we found a differential pattern of phosphorylated Cystatin-S that distinguishes the two pathologies. The most relevant results suggest that in both pathologies there may be active inflammation pathways related to the disease and/or induced by therapy. We show, for the first time, tear protein patterns expressed under controlled intraocular pressure conditions in POAG and PXG subjects. These findings could help in the understanding of molecular machinery underlying these ophthalmologic diseases, resulting in early diagnosis and more specific therapy.

Critical Pedagogy Principles in Teaching EFL Reading

Directory of Open Access Journals (Sweden)

Slamet Wahyudi Yulianto

2015-12-01

Full Text Available This study attempts to reveal how the use of critical pedagogy principles in teaching English as a Foreign Language (EFL reading facilitates students to think critically. Additionally, it investigates and elaborates the benefits and challenges of using critical pedagogy principles in teaching EFL reading. The three critical pedagogy principles used in this study were dialogic education, democratic classroom, and reading the world and the word. Critical thinking skills and dispositions expected to be performed by the participants were analysis and evaluation skills, open-mindedness, and making reasoned decision. This is a case study design which was conducted in the form of teaching program. The teaching program which consisted of eight meetings was given to 59 EFL sophomores in the Reading in Professional Context class at a private teacher education in Bandung. Data in the form of classroom talks and activities and students‟ responses as well as their critical thinking skills self-assessment were collected by using video recordings, observation notes, interview guideline, students‟ learning journals, and questionnaires. It is revealed that the teaching program has facilitated students to think critically by providing four categories of activity. They are (1 offering problematic topics and reading materials that are linked to the students‟ lives, (2 encouraging students to read between the lines, (3 distributing classroom power, and (4 creating space for students‟ voices to be heard. Meanwhile, there are two benefits of the teaching program, namely (1 language development and (2 new knowledge as well as experience acquisition. However, there are three major challenges in conducting the teaching program that are (1 the lack of classroom-friendly authentic controversial reading materials, (2 the passive culture, and (3 the unpredictable classroom.

Child-centered reading intervention: See, talk, dictate, read, write!

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Muhammet BAŞTUĞ

2016-06-01

Full Text Available Poor reading achievement of children in elementary schools has been one of the major concerns in education. The aim of this study is to examine the effectiveness of a child-centered reading intervention in eliminating the reading problems of a student with poor reading achievement. The research was conducted with a student having difficulty in reading. A reading intervention was designed that targeted multiple areas of reading and aimed to improve reading skills through the use of multiple strategies. This intervention is child-centered and includes visual aids, talking, dictating, reading and writing stages. The study was performed in 35 sessions consisting of stages of a single sentence (5 sessions, two sentences (5 sessions, three sentences (20 sessions and the text stage (5 sessions. The intervention sessions were audio-taped. These recordings and the written responses to the reading comprehension questions provided the data for analysis. The findings on the reading intervention revealed positive outcomes. The student exhibited certain improvements at the levels of reading, reading rate and reading comprehension. These results were discussed in the literature and the findings suggest that child-centered reading strategies such as talking, dictating and writing should be the main focus of instruction for students with low reading literacy achievement to enable these students to meet the demands of the curriculum.

IMPROVING STUDENTS’ READING COMPREHENSION THROUGH IINTERACTIVE READ-ALOUD TECHNIQUE

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Edi Santoso

2015-10-01

Full Text Available Abstract: The present study, entitled Improving Students’ Reading Comprehension through Interactive Read-Aloud, attempts to unlock problems found in teaching and reading comprehension through interactive read-aloud in a Senior High School of Sport (SMAN Olah Raga Lampung, in Metro. The findings revealed that students’ reading comprehension improved through interactive read-aloud. The improvement can be seen from the increase of test results, meaning construction, and motivation. The process of reading activities showed that the teacher’s gesture and body language, 20 questions, explain and guess activities were proven to help the students construct meaning from the given texts. In addition, interactive read-aloud is effective to boost students’ motivation to comprehend the texts.   Key words: Reading comprehension, interactive read-aloud.

Reading faster

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Paul Nation

2009-12-01

Full Text Available 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 reading fluency, and suggests how the development of fluency can become part of a reading programme.

Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene

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Atkins John F

2008-05-01

Full Text Available Abstract Members of the genus Cypovirus (family Reoviridae are common pathogens of insects. These viruses have linear dsRNA genomes divided into 10–11 segments, which have generally been assumed to be monocistronic. Here, bioinformatic evidence is presented for a short overlapping coding sequence (CDS in the cypovirus genome segment encoding the major core capsid protein VP1, overlapping the 5'-terminal region of the VP1 ORF in the +1 reading frame. In Cypovirus type 1 (CPV-1, a 62-codon AUG-initiated open reading frame (hereafter ORFX is present in all four available segment 1 sequences. The pattern of base variations across the sequence alignment indicates that ORFX is subject to functional constraints at the amino acid level (even when the constraints due to coding in the overlapping VP1 reading frame are taken into account; MLOGD software. In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP1. The genomic location of ORFX is consistent with translation via leaky scanning. A 62–64 codon AUG-initiated ORF is present in a corresponding location and reading frame in other available cypovirus sequences (2 CPV-14, 1 CPV-15 and an 87-codon ORFX homologue may also be present in Aedes pseudoscutellaris reovirus. The ORFX amino acid sequences are hydrophilic and basic, with between 12 and 16 Arg/Lys residues in each though, at 7.5–10.2 kDa, the putative ORFX product is too small to appear on typical published protein gels.

The mitochondrial gene encoding ribosomal protein S12 has been translocated to the nuclear genome in Oenothera.

Science.gov (United States)

Grohmann, L; Brennicke, A; Schuster, W

1992-01-01

The Oenothera mitochondrial genome contains only a gene fragment for ribosomal protein S12 (rps12), while other plants encode a functional gene in the mitochondrion. The complete Oenothera rps12 gene is located in the nucleus. The transit sequence necessary to target this protein to the mitochondrion is encoded by a 5'-extension of the open reading frame. Comparison of the amino acid sequence encoded by the nuclear gene with the polypeptides encoded by edited mitochondrial cDNA and genomic sequences of other plants suggests that gene transfer between mitochondrion and nucleus started from edited mitochondrial RNA molecules. Mechanisms and requirements of gene transfer and activation are discussed. Images PMID:1454526

An integrated protein localization and interaction map for Potato yellow dwarf virus, type species of the genus Nucleorhabdovirus

International Nuclear Information System (INIS)

Bandyopadhyay, Anindya; Kopperud, Kristin; Anderson, Gavin; Martin, Kathleen; Goodin, Michael

2010-01-01

The genome of Potato yellow dwarf virus (PYDV; Nucleorhabdovirus type species) was determined to be 12,875 nucleotides (nt). The antigenome is organized into seven open reading frames (ORFs) ordered 3'-N-X-P-Y-M-G-L-5', which likely encode the nucleocapsid, phospho, movement, matrix, glyco and RNA-dependent RNA polymerase proteins, respectively, except for X, which is of unknown function. The ORFs are flanked by a 3' leader RNA of 149 nt and a 5' trailer RNA of 97 nt, and are separated by conserved intergenic junctions. Phylogenetic analyses indicated that PYDV is closely related to other leafhopper-transmitted rhabdoviruses. Functional protein assays were used to determine the subcellular localization of PYDV proteins. Surprisingly, the M protein was able to induce the intranuclear accumulation of the inner nuclear membrane in the absence of any other viral protein. Finally, bimolecular fluorescence complementation was used to generate the most comprehensive protein interaction map for a plant-adapted rhabdovirus to date.

Identification and characterization of the pseudorabies virus UL43 protein

International Nuclear Information System (INIS)

Klupp, Barbara G.; Altenschmidt, Jan; Granzow, Harald; Fuchs, Walter; Mettenleiter, Thomas C.

2005-01-01

Among the least characterized herpesvirus membrane proteins are the homologs of UL43 of herpes simplex virus 1 (HSV-1). To identify and characterize the UL43 protein of pseudorabies virus (PrV), part of the open reading frame was expressed in Escherichia coli and used for immunization of a rabbit. The antiserum recognized in Western blots a 34-kDa protein in lysates of PrV infected cells and purified virions, demonstrating that the UL43 protein is a virion component. In indirect immunofluorescence analysis, the antiserum labeled vesicular structures in PrV infected cells which also contained glycoprotein B. To functionally analyze UL43, a deletion mutant was constructed lacking amino acids 23-332 of the 373aa protein. This mutant was only slightly impaired in replication as assayed by one-step growth kinetics, measurement of plaque sizes, and electron microscopy. Interestingly, the PrV UL43 protein was able to inhibit fusion induced by PrV glycoproteins in a transient expression-fusion assay to a similar extent as gM. Double mutant viruses lacking, in addition to UL43, the multiply membrane spanning glycoproteins K or M did not show a phenotype beyond that observed in the gK and gM single deletion mutants

Reading visual braille with a retinal prosthesis.

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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.

Promoting preschool reading

OpenAIRE

Istenič, Vesna

2013-01-01

The thesis titled Promoting preschool reading consists of a theoretiral and an empirical part. In the theoretical part I wrote about reading, the importance of reading, types of reading, about reading motivation, promoting reading motivation, internal and external motivation, influence of reading motivation on the child's reading activity, reading and familial literacy, the role of adults in promotion reading literacy, reading to a child and promoting reading in pre-school years, where I ...

Gypsy transposition correlates with the production of a retroviral envelope-like protein under the tissue-specific control of the Drosophila flamenco gene.

OpenAIRE

Pélisson, A; Song, S U; Prud'homme, N; Smith, P A; Bucheton, A; Corces, V G

1994-01-01

Gypsy displays striking similarities to vertebrate retroviruses, including the presence of a yet uncharacterized additional open reading frame (ORF3) and the recent evidence for infectivity. It is mobilized with high frequency in the germline of the progeny of females homozygous for the flamenco permissive mutation. We report the characterization of a gypsy subgenomic ORF3 RNA encoding typical retroviral envelope proteins. In females, env expression is strongly repressed by one copy of the no...

Low power test architecture for dynamic read destructive fault detection in SRAM

Science.gov (United States)

Takher, Vikram Singh; Choudhary, Rahul Raj

2018-06-01

Dynamic Read Destructive Fault (dRDF) is the outcome of resistive open defects in the core cells of static random-access memories (SRAMs). The sensitisation of dRDF involves either performing multiple read operations or creation of number of read equivalent stress (RES), on the core cell under test. Though the creation of RES is preferred over the performing multiple read operation on the core cell, cell dissipates more power during RES than during the read or write operation. This paper focuses on the reduction in power dissipation by optimisation of number of RESs, which are required to sensitise the dRDF during test mode of operation of SRAM. The novel pre-charge architecture has been proposed in order to reduce the power dissipation by limiting the number of RESs to an optimised number of two. The proposed low power architecture is simulated and analysed which shows reduction in power dissipation by reducing the number of RESs up to 18.18%.

Sequence and expression pattern of a novel human orphan G-protein-coupled receptor, GPRC5B, a family C receptor with a short amino-terminal domain

DEFF Research Database (Denmark)

Bräuner-Osborne, Hans; Krogsgaard-Larsen, P

2000-01-01

Query of GenBank with the amino acid sequence of human metabotropic glutamate receptor subtype 2 (mGluR2) identified a predicted gene product of unknown function on BAC clone CIT987SK-A-69G12 (located on chromosome band 16p12) as a homologous protein. The transcript, entitled GPRC5B, was cloned f...... from an expressed sequence tag clone that contained the entire open reading frame of the transcript encoding a protein of 395 amino acids. Analysis of the protein sequence reveal that GPRC5B contains a signal peptide and seven transmembrane alpha-helices, which is a hallmark of G...

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

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Seung Bum Park

Full Text Available 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.

Parents' reading-related knowledge and children's reading acquisition.

Science.gov (United States)

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

2011-12-01

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 knowledge, print exposure, storybook reading, and general cultural knowledge. Children were tested on measures of letter-word knowledge, sound awareness, receptive vocabulary, oral expression, and mathematical skill. Parent reading-related knowledge showed significant positive links with child letter-word knowledge and sound awareness, but showed no correlations with child measures of mathematical skill or vocabulary. Furthermore, parent reading-related knowledge was not associated with parents' own print exposure or cultural knowledge, indicating that knowledge about English word structure may be separate from other cognitive skills. Implications are discussed in terms of improving parent reading-related knowledge to promote child literacy.

Why should I read? - A cross-cultural investigation into adolescents' reading socialisation and reading attitude

Science.gov (United States)

Broeder, Peter; Stokmans, Mia

2013-06-01

While reading behaviour of adolescents is a frequent object of research, most studies in this field are restricted to a single country. This study investigates reading as a leisure-time activity across social groups from three regions differing in reading tradition as well as in the facilities available for reading. The authors analyse the reading behaviour of a total of 2,173 adolescents in the Netherlands, in Beijing (China), and in Cape Town (South Africa). Taking Icek Ajzen's Theory of Planned Behaviour as a starting point, the authors adjusted it to model the three most important determinants of reading behaviour, namely (1) reading attitude; (2) subjective norms (implicit and explicit social pressure to read); and (3) perceived behavioural control, which includes reading proficiency and appropriateness of the available books (book supply). While they found the adjusted model to fit the Dutch and Beijing situation quite well, it appeared to be inappropriate for the Cape Town situation. Despite considerable cultural and situational differences between the Netherlands and Beijing, the results show a similar pattern for these two environments. The most important determinants turn out to be: the hedonic reading attitude, the implicit norm of family and friends, the attractiveness of the available choice of books, and the perceived reading proficiency.

Self-processing 2A-polyproteins--a system for co-ordinate expression of multiple proteins in transgenic plants.

Science.gov (United States)

Halpin, C; Cooke, S E; Barakate, A; El Amrani, A; Ryan, M D

1999-02-01

Achieving co-ordinate, high-level and stable expression of multiple transgenes in plants is currently difficult. Expression levels are notoriously variable and influenced by factors that act independently on transgenes at different genetic loci. Instability of expression due to loss, re-arrangement or silencing of transgenes may occur, and is exacerbated by increasing numbers of transgenic loci and repeated use of homologous sequences. Even linking two or more genes within a T-DNA does not necessarily result in co-ordinate expression. Linking proteins in a single open reading frame--a polyprotein--is a strategy for co-ordinate expression used by many viruses. After translation, polyproteins are processed into constituent polypeptides, usually by proteinases encoded within the polyprotein itself. However, in foot-and-mouth disease virus (FMDV), a sequence (2A) of just 16-20 amino acids appears to have the unique capability to mediate cleavage at its own C-terminus by an apparently enzyme-independent, novel type of reaction. This sequence can also mediate cleavage in a heterologous protein context in a range of eukaryotic expression systems. We have constructed a plasmid in which the 2A sequence is inserted between the reporter genes chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS), maintaining a single open reading frame. Here we report that expression of this construct in wheatgerm lysate and transgenic plants results in efficient cleavage of the polyprotein and co-ordinate expression of active CAT and GUS. Self-processing polyproteins using the FMDV 2A sequence could therefore provide a system for ensuring co-ordinated, stable expression of multiple introduced proteins in plant cells.

Improving reading comprehension in reading and listening settings: the effect of two training programmes focusing on metacognition and working memory.

Science.gov (United States)

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

2014-06-01

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 comprehension must necessarily be based on processing written material or whether, as suggested in a recent study by Clarke et al. (2010, Psychol. Sci., 21, 1106), a programme based on verbal language could also be effective. The study examined the feasibility of improving text comprehension in school children by comparing the efficacy of two training programmes, both involving metacognition and WM, but one based on listening comprehension, the other on reading comprehension. The study involved a sample of 159 pupils attending eight classes in the fourth and fifth grades (age range 9-11 years). The listening and reading programmes focused on the same abilities/processes strictly related to text comprehension, and particularly metacognitive knowledge and control, WM (per se and in terms of integrating information in a text). The training programmes were implemented by school teachers as part of the class's normal school activities, under the supervision of experts. Their efficacy was compared with the results obtained in an active control group that completed standard text comprehension activities. Our results showed that both the training programmes focusing on specific text comprehension skills were effective in improving the children's achievement, but training in reading comprehension generated greater gains than the listening comprehension programme. Our study suggests that activities focusing specifically on metacognition and WM could foster text comprehension, but the potential benefit is influenced by the training modality, that is, the Reading group obtained greater and longer-lasting improvements than the Active control or

Genetic characterization of complete open reading frame of glycoprotein C gene of bovine herpesvirus 1

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Saurabh Majumder

2013-10-01

Full Text Available Aim: To characterize one of the major glycoprotein genes viz., glycoprotein C (gC; UL44, unique long region 44 of bovineherpesvirus 1(BoHV1 of Indian origin at genetic and phylogenetic level.Materials and Methods: A bovine herpesvirus 1 isolate viz., (BoHV1/IBR 216 II/ 1976/ India maintained at Division ofVirology, IVRI, Mukteswar was used for the current study. The DNA was extracted using commercial kit and the completeORF of gC gene was amplified, cloned, and sequenced by conventional Sanger sequencing method. The sequence wasgenetically and phylogenetically analysed using various bioinformatic tools. The sequence was submitted in the Genbankwith accession number Kc756965.Results: The complete ORF of gC gene was amplified and sequenced. It showed 100% sequence homology with referencecooper strain of BoHV1 and divergence varied from 0% to 2.7% with other isolates of BoHV1. The isolate under study haddivergence of 9.2%, 13%, 26.6%, and 9.2% with BoHV5 (Bovine herpesvirus 5, CvHV1 (Cervid herpesvirus 1, CpHV1(Caprine herpesvirus 1, and BuHV1 (Bubaline herpesvirus 1, respectively.Conclusion: This is the first genetic characterization of complete open reading frame (ORF of glycoprotein C gene (UL44 ofIndian isolate of BoHV1. The gC gene of BoHV1 is highly conserved among all BoHV1 isolates and it can be used as a targetfor designing diagnostic primers for the specific detection of BoHV1.

An Electronic open-quotes Barn Bookclose quotes

International Nuclear Information System (INIS)

James, J.Z.

1996-01-01

Electronic publication of a comprehensive compilation of neutron cross sections - an open-quotes electronic barn bookclose quotes - can be of immense value to the practicing nuclear engineer, as well as in nuclear education and training. This paper describes such a publication. The files are published on compact disk-read-only memory (CD-ROM), with automatic updating over the Internet. The current version stores the curves graphically, but a future version will take better advantage of the interactive capabilities of electronic publishing by drawing the curves from ACE files open-quotes on the fly.close quotes

Long-read sequencing data analysis for yeasts.

Science.gov (United States)

Yue, Jia-Xing; Liti, Gianni

2018-06-01

Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here, we present a modular computational framework named long-read sequencing data analysis for yeasts (LRSDAY), the first one-stop solution that streamlines this process. Starting from the raw sequencing reads, LRSDAY can produce chromosome-level genome assembly and comprehensive genome annotation in a highly automated manner with minimal manual intervention, which is not possible using any alternative tool available to date. The annotated genomic features include centromeres, protein-coding genes, tRNAs, transposable elements (TEs), and telomere-associated elements. Although tailored for S. cerevisiae, we designed LRSDAY to be highly modular and customizable, making it adaptable to virtually any eukaryotic organism. When applying LRSDAY to an S. cerevisiae strain, it takes ∼41 h to generate a complete and well-annotated genome from ∼100× Pacific Biosciences (PacBio) running the basic workflow with four threads. Basic experience working within the Linux command-line environment is recommended for carrying out the analysis using LRSDAY.

EST mining identifies proteins putatively secreted by the anthracnose pathogen Colletotrichum truncatum

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Vandenberg Albert

2011-06-01

Full Text Available Abstract Background Colletotrichum truncatum is a haploid, hemibiotrophic, ascomycete fungal pathogen that causes anthracnose disease on many economically important leguminous crops. This pathogen exploits sequential biotrophic- and necrotrophic- infection strategies to colonize the host. Transition from biotrophy to a destructive necrotrophic phase called the biotrophy-necrotrophy switch is critical in symptom development. C. truncatum likely secretes an arsenal of proteins that are implicated in maintaining a compatible interaction with its host. Some of them might be transition specific. Results A directional cDNA library was constructed from mRNA isolated from infected Lens culinaris leaflet tissues displaying the biotrophy-necrotrophy switch of C. truncatum and 5000 expressed sequence tags (ESTs with an average read of > 600 bp from the 5-prime end were generated. Nearly 39% of the ESTs were predicted to encode proteins of fungal origin and among these, 162 ESTs were predicted to contain N-terminal signal peptides (SPs in their deduced open reading frames (ORFs. The 162 sequences could be assembled into 122 tentative unigenes comprising 32 contigs and 90 singletons. Sequence analyses of unigenes revealed four potential groups: hydrolases, cell envelope associated proteins (CEAPs, candidate effectors and other proteins. Eleven candidate effector genes were identified based on features common to characterized fungal effectors, i.e. they encode small, soluble (lack of transmembrane domain, cysteine-rich proteins with a putative SP. For a selected subset of CEAPs and candidate effectors, semiquantitative RT-PCR showed that these transcripts were either expressed constitutively in both in vitro and in planta or induced during plant infection. Using potato virus X (PVX based transient expression assays, we showed that one of the candidate effectors, i. e. contig 8 that encodes a cerato-platanin (CP domain containing protein, unlike CP proteins

Effect of Kanji and Kana reading on cerebral blood flow patterns measured by PET

International Nuclear Information System (INIS)

Kiyosawa, Motohiro; Itoh, Masatoshi; Nakagawa, Youichi; Kobayashi, Naoki; Tamai, Makoto.

1995-01-01

To investigate the respective functions of pathways in processing visual information from different types of symbols, by positron emission tomography (PET) we examined the effect on cerebral blood flow (CBF) of reading the Japanese morphogram (kanji) versus the syllabogram (kana). Nine Japanese men were presented with three visual conditions in random order 2 minutes before the scan: eyes open controls, kanji morphogram reading, and kana syllabogram reading. Three words written in kanji or kana were shown, and subjects were instructed to read them silently and to identify the word unrelated logically to the other two. The reading and analyzing tasks activated wide areas of vision-related cortices. The comparison of the kanji and kana readings showed higher metabolism, with the former only in the posterior part of the primary visual cortex. Most of the CBF increases were common for both stimuli, although the patterns of these increases differed slightly. The correlation matrix of CBF change in the left hemisphere showed a ventral connection in kanji reading and a dorsal connection in kana reading. Our results suggest there is a functional differentiation in the brain between patterned and sequential perception when reading Japanese morphograms and syllabograms. (author)

A Survey of Protein Structures from Archaeal Viruses

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Nikki Dellas

2013-01-01

Full Text Available Viruses that infect the third domain of life, Archaea, are a newly emerging field of interest. To date, all characterized archaeal viruses infect archaea that thrive in extreme conditions, such as halophilic, hyperthermophilic, and methanogenic environments. Viruses in general, especially those replicating in extreme environments, contain highly mosaic genomes with open reading frames (ORFs whose sequences are often dissimilar to all other known ORFs. It has been estimated that approximately 85% of virally encoded ORFs do not match known sequences in the nucleic acid databases, and this percentage is even higher for archaeal viruses (typically 90%–100%. This statistic suggests that either virus genomes represent a larger segment of sequence space and/or that viruses encode genes of novel fold and/or function. Because the overall three-dimensional fold of a protein evolves more slowly than its sequence, efforts have been geared toward structural characterization of proteins encoded by archaeal viruses in order to gain insight into their potential functions. In this short review, we provide multiple examples where structural characterization of archaeal viral proteins has indeed provided significant functional and evolutionary insight.

Comparison of reading speed with 3 different log-scaled reading charts.

Science.gov (United States)

Buari, Noor Halilah; Chen, Ai-Hong; Musa, Nuraini

2014-01-01

A reading chart that resembles real reading conditions is important to evaluate the quality of life in terms of reading performance. The purpose of this study was to compare the reading speed of UiTM Malay related words (UiTM-Mrw) reading chart with MNread Acuity Chart and Colenbrander Reading Chart. Fifty subjects with normal sight were randomly recruited through randomized sampling in this study (mean age=22.98±1.65 years). Subjects were asked to read three different near charts aloud and as quickly as possible at random sequence. The charts were the UiTM-Mrw Reading Chart, MNread Acuity Chart and Colenbrander Reading Chart, respectively. The time taken to read each chart was recorded and any errors while reading were noted. Reading performance was quantified in terms of reading speed as words per minute (wpm). The mean reading speed for UiTM-Mrw Reading Chart, MNread Acuity Chart and Colenbrander Reading Chart was 200±30wpm, 196±28wpm and 194±31wpm, respectively. Comparison of reading speed between UiTM-Mrw Reading Chart and MNread Acuity Chart showed no significant difference (t=-0.73, p=0.72). The same happened with the reading speed between UiTM-Mrw Reading Chart and Colenbrander Reading Chart (t=-0.97, p=0.55). Bland and Altman plot showed good agreement between reading speed of UiTM-Mrw Reading Chart with MNread Acuity Chart with the Colenbrander Reading Chart. UiTM-Mrw Reading Chart in Malay language is highly comparable with standardized charts and can be used for evaluating reading speed. Copyright © 2013 Spanish General Council of Optometry. Published by Elsevier Espana. All rights reserved.

PyFolding: Open-Source Graphing, Simulation, and Analysis of the Biophysical Properties of Proteins.

Science.gov (United States)

Lowe, Alan R; Perez-Riba, Albert; Itzhaki, Laura S; Main, Ewan R G

2018-02-06

For many years, curve-fitting software has been heavily utilized to fit simple models to various types of biophysical data. Although such software packages are easy to use for simple functions, they are often expensive and present substantial impediments to applying more complex models or for the analysis of large data sets. One field that is reliant on such data analysis is the thermodynamics and kinetics of protein folding. Over the past decade, increasingly sophisticated analytical models have been generated, but without simple tools to enable routine analysis. Consequently, users have needed to generate their own tools or otherwise find willing collaborators. Here we present PyFolding, a free, open-source, and extensible Python framework for graphing, analysis, and simulation of the biophysical properties of proteins. To demonstrate the utility of PyFolding, we have used it to analyze and model experimental protein folding and thermodynamic data. Examples include: 1) multiphase kinetic folding fitted to linked equations, 2) global fitting of multiple data sets, and 3) analysis of repeat protein thermodynamics with Ising model variants. Moreover, we demonstrate how PyFolding is easily extensible to novel functionality beyond applications in protein folding via the addition of new models. Example scripts to perform these and other operations are supplied with the software, and we encourage users to contribute notebooks and models to create a community resource. Finally, we show that PyFolding can be used in conjunction with Jupyter notebooks as an easy way to share methods and analysis for publication and among research teams. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Expression and localization of a novel phosducin-like protein from amphioxus Branchiostoma belcheri

Science.gov (United States)

Saren, Gaowa; Zhao, Yonggang

2009-05-01

A full length amphioxus cDNA, encoding a novel phosducin-like protein ( Amphi-PhLP), was identified for the first time from the gut cDNA library of Branchiostoma belcheri. It is comprised of 1 550 bp and an open reading frame (ORF) of 241 amino acids, with a predicted molecular mass of approximately 28 kDa. In situ hybridization histochemistry revealed a tissue-specific expression pattern of Amphi-PhLP with the high levels in the ovary, and at a lower level in the hind gut and testis, hepatic caecum, gill, endostyle, and epipharyngeal groove, while it was absent in the muscle, neural tube and notochord. In the Chinese Hamster Ovary (CHO) cells transfected with the expression plasmid pEGFP-N1/ Amphi-PhLP, the fusion protein was targeted in the cytoplasm of CHO cells, suggesting that Amphi-PhLP is a cytosolic protein. This work may provide a framework for further understanding of the physiological function of Amphi-PhLP in B. belcheri.

Extended region of nodulation genes in Rhizobium meliloti 1021. II. Nucleotide sequence, transcription start sites and protein products

International Nuclear Information System (INIS)

Fisher, R.F.; Swanson, J.A.; Mulligan, J.T.; Long, S.R.

1987-01-01

The authors have established the DNA sequence and analyzed the transcription and translation products of a series of putative nodulation (nod) genes in Rhizobium meliloti strain 1021. Four loci have been designated nodF, nodE, nodG and nodH. The correlation of transposon insertion positions with phenotypes and open reading frames was confirmed by sequencing the insertion junctions of the transposons. The protein products of these nod genes were visualized by in vitro expression of cloned DNA segments in a R. meliloti transcription-translation system. In addition, the sequence for nodG was substantiated by creating translational fusions in all three reading frames at several points in the sequence; the resulting fusions were expressed in vitro in both E. coli and R. meliloti transcription-translation systems. A DNA segment bearing several open reading frames downstream of nodG corresponds to the putative nod gene mutated in strain nod-216. The transcription start sites of nodF and nodH were mapped by primer extension of RNA from cells induced with the plant flavone, luteolin. Initiation of transcription occurs approximately 25 bp downstream from the conserved sequence designated the nod box, suggesting that this conserved sequence acts as an upstream regulator of inducible nod gene expression. Its distance from the transcription start site is more suggestive of an activator binding site rather than an RNA polymerase binding site

Characterization of Hemagglutinin Negative Botulinum Progenitor Toxins

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Suzanne R. Kalb

2017-06-01

Full Text Available Botulism is a disease involving intoxication with botulinum neurotoxins (BoNTs, toxic proteins produced by Clostridium botulinum and other clostridia. The 150 kDa neurotoxin is produced in conjunction with other proteins to form the botulinum progenitor toxin complex (PTC, alternating in size from 300 kDa to 500 kDa. These progenitor complexes can be classified into hemagglutinin positive or hemagglutinin negative, depending on the ability of some of the neurotoxin-associated proteins (NAPs to cause hemagglutination. The hemagglutinin positive progenitor toxin complex consists of BoNT, nontoxic non-hemagglutinin (NTNH, and three hemagglutinin proteins; HA-70, HA-33, and HA-17. Hemagglutinin negative progenitor toxin complexes contain BoNT and NTNH as the minimally functional PTC (M-PTC, but not the three hemagglutinin proteins. Interestingly, the genome of hemagglutinin negative progenitor toxin complexes comprises open reading frames (orfs which encode for three proteins, but the existence of these proteins has not yet been extensively demonstrated. In this work, we demonstrate that these three proteins exist and form part of the PTC for hemagglutinin negative complexes. Several hemagglutinin negative strains producing BoNT/A, /E, and /F were found to contain the three open reading frame proteins. Additionally, several BoNT/A-containing bivalent strains were examined, and NAPs from both genes, including the open reading frame proteins, were associated with BoNT/A. The open reading frame encoded proteins are more easily removed from the botulinum complex than the hemagglutinin proteins, but are present in several BoNT/A and /F toxin preparations. These are not easily removed from the BoNT/E complex, however, and are present even in commercially-available purified BoNT/E complex.

Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

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Robert C. Edgar

2017-10-01

Full Text Available Next-generation sequencing of 16S ribosomal RNA is widely used to survey microbial communities. Sequences are typically assigned to Operational Taxonomic Units (OTUs. Closed- and open-reference OTU assignment matches reads to a reference database at 97% identity (closed, then clusters unmatched reads using a de novo method (open. Implementations of these methods in the QIIME package were tested on several mock community datasets with 20 strains using different sequencing technologies and primers. Richness (number of reported OTUs was often greatly exaggerated, with hundreds or thousands of OTUs generated on Illumina datasets. Between-sample diversity was also found to be highly exaggerated in many cases, with weighted Jaccard distances between identical mock samples often close to one, indicating very low similarity. Non-overlapping hyper-variable regions in 70% of species were assigned to different OTUs. On mock communities with Illumina V4 reads, 56% to 88% of predicted genus names were false positives. Biological inferences obtained using these methods are therefore not reliable.

The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties

International Nuclear Information System (INIS)

Lee, Changhee; Yoo, Dongwan

2006-01-01

The small envelope (E) protein of porcine reproductive and respiratory syndrome virus (PRRSV) is a hydrophobic 73 amino acid protein encoded in the internal open reading frame (ORF) of the bicistronic mRNA2. As a first step towards understanding the biological role of E protein during PRRSV replication, E gene expression was blocked in a full-length infectious clone by mutating the ATG translational initiation to GTG, such that the full-length mutant genomic clone was unable to synthesize the E protein. DNA transfection of PRRSV-susceptible cells with the E gene knocked-out genomic clone showed the absence of virus infectivity. P129-ΔE-transfected cells however produced virion particles in the culture supernatant, and these particles contained viral genomic RNA, demonstrating that the E protein is essential for PRRSV infection but dispensable for virion assembly. Electron microscopy suggests that the P129-ΔE virions assembled in the absence of E had a similar appearance to the wild-type particles. Strand-specific RT-PCR demonstrated that the E protein-negative, non-infectious P129-ΔE virus particles were able to enter cells but further steps of replication were interrupted. The entry of PRRSV has been suggested to be via receptor-mediated endocytosis, and lysomotropic basic compounds and known ion-channel blocking agents both inhibited PRRSV replication effectively during the uncoating process. The expression of E protein in Escherichia coli-mediated cell growth arrests and increased the membrane permeability. Cross-linking experiments in cells infected with PRRSV or transfected with E gene showed that the E protein was able to form homo-oligomers. Taken together, our data suggest that the PRRSV E protein is likely an ion-channel protein embedded in the viral envelope and facilitates uncoating of virus and release of the genome in the cytoplasm

Reflections on protein splicing: structures, functions and mechanisms

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Anraku, Yasuhiro; Satow, Yoshinori

2009-01-01

Twenty years ago, evidence that one gene produces two enzymes via protein splicing emerged from structural and expression studies of the VMA1 gene in Saccharomyces cerevisiae. VMA1 consists of a single open reading frame and contains two independent genetic information for Vma1p (a catalytic 70-kDa subunit of the vacuolar H+-ATPase) and VDE (a 50-kDa DNA endonuclease) as an in-frame spliced insert in the gene. Protein splicing is a posttranslational cellular process, in which an intervening polypeptide termed as the VMA1 intein is self-catalytically excised out from a nascent 120-kDa VMA1 precursor and two flanking polypeptides of the N- and C-exteins are ligated to produce the mature Vma1p. Subsequent studies have demonstrated that protein splicing is not unique to the VMA1 precursor and there are many operons in nature, which implement genetic information editing at protein level. To elucidate its structure-directed chemical mechanisms, a series of biochemical and crystal structural studies has been carried out with the use of various VMA1 recombinants. This article summarizes a VDE-mediated self-catalytic mechanism for protein splicing that is triggered and terminated solely via thiazolidine intermediates with tetrahedral configurations formed within the splicing sites where proton ingress and egress are driven by balanced protonation and deprotonation. PMID:19907126

Development open source microcontroller based temperature data logger

Science.gov (United States)

Abdullah, M. H.; Che Ghani, S. A.; Zaulkafilai, Z.; Tajuddin, S. N.

2017-10-01

This article discusses the development stages in designing, prototyping, testing and deploying a portable open source microcontroller based temperature data logger for use in rough industrial environment. The 5V powered prototype of data logger is equipped with open source Arduino microcontroller for integrating multiple thermocouple sensors with their module, secure digital (SD) card storage, liquid crystal display (LCD), real time clock and electronic enclosure made of acrylic. The program for the function of the datalogger is programmed so that 8 readings from the thermocouples can be acquired within 3 s interval and displayed on the LCD simultaneously. The recorded temperature readings at four different points on both hydrodistillation show similar profile pattern and highest yield of extracted oil was achieved on hydrodistillation 2 at 0.004%. From the obtained results, this study achieved the objective of developing an inexpensive, portable and robust eight channels temperature measuring module with capabilities to monitor and store real time data.

Functional analysis of virion host shutoff protein of pseudorabies virus

International Nuclear Information System (INIS)

Lin, H.-W.; Chang, Y.-Y.; Wong, M.-L.; Lin, J.-W.; Chang, T.-J.

2004-01-01

During lytic infection, the virion host shutoff (vhs) protein of alphaherpesviruses causes the degradation of mRNAs nonspecifically. In this work, we cloned the vhs gene (UL41 open reading frame) of pseudorabies virus (PRV; TNL strain) by PCR, and its nucleotide sequences were determined. The PCR product of vhs gene was subcloned into the prokaryotic pET32b expression vector, and production of the recombinant vhs protein was examined by SDS-PAGE. Result of Western blotting demonstrated that our recombinant vhs protein reacted with antiserum against a synthetic peptide of 17 amino acids of the vhs protein. After purification with nickel-chelate affinity chromatography, the purified recombinant vhs protein exhibited in vitro ribonuclease activity as expected. We further cloned the vhs gene into eukaryotic expression vectors and investigated the intracellular function of vhs protein by DNA transfection. By transient trasfection and CAT assay, we found the CAT activity was reduced in the presence of vhs, indicating that degradation of mRNA of the CAT gene was caused by the vhs. Furthermore, our results showed that the plaque formation of pseudorabies virus was blocked by exogenous vhs. Taken together, we have cloned the vhs gene of pseudorabies virus (TNL strain) and conducted functional analysis of the recombinant vhs protein in vitro as well as in vivo

Photometry Using Kepler "Superstamps" of Open Clusters NGC 6791 & NGC 6819

Science.gov (United States)

Kuehn, Charles A.; Drury, Jason A.; Bellamy, Beau R.; Stello, Dennis; Bedding, Timothy R.; Reed, Mike; Quick, Breanna

2015-09-01

The Kepler space telescope has proven to be a gold mine for the study of variable stars. Usually, Kepler only reads out a handful of pixels around each pre-selected target star, omitting a large number of stars in the Kepler field. Fortunately, for the open clusters NGC 6791 and NGC 6819, Kepler also read out larger "superstamps" which contained complete images of the central region of each cluster. These cluster images can be used to study additional stars in the open clusters that were not originally on Kepler's target list. We discuss our work on using two photometric techniques to analyze these superstamps and present sample results from this project to demonstrate the value of this technique for a wide variety of variable stars.

Nuclear localization signal regulates porcine circovirus type 2 capsid protein nuclear export through phosphorylation.

Science.gov (United States)

Hou, Qiang; Hou, Shaohua; Chen, Qing; Jia, Hong; Xin, Ting; Jiang, Yitong; Guo, Xiaoyu; Zhu, Hongfei

2018-02-15

The open reading frame 2 (ORF2) of Porcine circovirus type 2 (PCV2) encodes the major Capsid (Cap) protein, which self-assembles into virus-like particle (VLP) of similar morphology to the PCV2 virion and accumulates in the nucleus through the N-terminal arginine-rich nuclear localization signal (NLS). In this study, PCV2 Cap protein and its derivates were expressed via the baculovirus expression system, and the cellular localization of the recombinant proteins were investigated using anti-Cap mAb by imaging flow cytometry. Analysis of subcellular localization of Cap protein and its variants demonstrated that NLS mediated Cap protein nuclear export as well as nuclear import, and a phosphorylation site (S17) was identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the NLS domain to regulate Cap protein nuclear export. Phosphorylation of NLS regulating the PCV2 Cap protein nuclear export was also demonstrated in PK15 cells by fluorescence microscopy. Moreover, the influence of Rep and Rep' protein on Cap protein subcellular localization was investigated in PK15 cells. Phosphorylation of NLS regulating Cap protein nuclear export provides more detailed knowledge of the PCV2 viral life cycle. Copyright © 2018 Elsevier B.V. All rights reserved.

What oral text reading fluency can reveal about reading comprehension

NARCIS (Netherlands)

Veenendaal, N.J.; Groen, M.A.; Verhoeven, L.T.W.

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

An ankyrin-like protein with transmembrane domains is specifically lost after oncogenic transformation of human fibroblasts.

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Jaquemar, D; Schenker, T; Trueb, B

1999-03-12

We have identified a novel transformation-sensitive mRNA, which is present in cultured fibroblasts but is lacking in SV40 transformed cells as well as in many mesenchymal tumor cell lines. The corresponding gene is located on human chromosome 8 in band 8q13. The open reading frame of the mRNA encodes a protein of 1119 amino acids forming two distinct domains. The N-terminal domain consists of 18 repeats that are related to the cytoskeletal protein ankyrin. The C-terminal domain contains six putative transmembrane segments that resemble many ion channels. This overall structure is reminiscent of TRP-like proteins that function as store-operated calcium channels. The novel protein with an Mr of 130 kDa is expressed at a very low level in human fibroblasts and at a moderate level in liposarcoma cells. Overexpression in eukaryotic cells appears to interfere with normal growth, suggesting that it might play a direct or indirect role in signal transduction and growth control.

Pteros: fast and easy to use open-source C++ library for molecular analysis.

Science.gov (United States)

Yesylevskyy, Semen O

2012-07-15

An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from http://sourceforge.net/projects/pteros/. Copyright © 2012 Wiley Periodicals, Inc.

Biochemical Characterization of Bovine Brain Myristoyl-CoA:Protein N-Myristoyltransferase Type 2

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Ponniah Selvakumar

2009-01-01

Full Text Available Protein N-myristoylation is a lipidic modification which refers to the covalent attachment of myristate, a 14-carbon saturated fatty acid, to the N-terminal glycine residue of a number of mammalian, viral, and fungal proteins. In this paper, we have cloned the gene coding for myristoyl-CoA:protein N-myristoyltransferase (NMT from Bos tarus brain. The open reading frame codes for a 410-amino-acid protein and overexpressed in Escherichia coli. Kinetic studies suggested that bovine brain NMT2 and human NMT1 show significant differences in their peptide substrate specificities. The metal ion Ca2+ had stimulatory effects on NMT2 activity while Mn2+ and Zn2+ inhibited the enzyme activity. In addition, NMT2 activity was inhibited by various organic solvents and other detergents while NMT1 had a stimulatory effect. Biochemical characterization suggested that both forms of NMT have unique characteristics. Further analysis towards functional role NMT2 will lead the development of therapeutic target for the progression of various diseases such as cancer, cardiovascular diseases, and neurodegenerative diseases.

Processing and Memory of Central versus Peripheral Information as a Function of Reading Goals: Evidence from Eye-Movements

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Yeari, Menahem; van den Broek, Paul; Oudega, Marja

2015-01-01

The present study examined the effect of reading goals on the processing and memory of central and peripheral textual information. Using eye-tracking methodology, we compared the effect of four common reading goals--entertainment, presentation, studying for a close-ended (multiple-choice) questions test, and studying for an open-ended questions…

READ-EVAL-PRINT in Parallel and Asynchronous Proof-checking

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Makarius Wenzel

2013-07-01

Full Text Available The LCF tradition of interactive theorem proving, which was started by Milner in the 1970-ies, appears to be tied to the classic READ-EVAL-PRINT-LOOP of sequential and synchronous evaluation of prover commands. We break up this loop and retrofit the read-eval-print phases into a model of parallel and asynchronous proof processing. Thus we explain some key concepts of the Isabelle/Scala approach to prover interaction and integration, and the Isabelle/jEdit Prover IDE as front-end technology. We hope to open up the scientific discussion about non-trivial interaction models for ITP systems again, and help getting other old-school proof assistants on a similar track.

A novel member of the split betaalphabeta fold: Solution structure of the hypothetical protein YML108W from Saccharomyces cerevisiae

International Nuclear Information System (INIS)

Pineda-Lucena, Antonio; Liao, Jack; Cort, John R.; Yee, Adelinda; Kennedy, Michael A.; Edwards, Aled M.

2003-05-01

As part of the Northeast Structural Genomics Consortium pilot project focused on small eukaryotic proteins and protein domains, we have determined the NMR structure of the protein encoded by open reading frame YML108W from Saccharomyces cerevisiae. YML108W belongs to one of the numerous structural proteomics targets whose biological function is unknown. Moreover, this protein does not have sequence similarity to any other protein. The NMR structure of YML108W consists of a four-stranded b-sheet with strand order 2143 and two a-helices, with an overall topology of bbabba. Strand b1 runs parallel to b4, and b2:b1 and b4:b3 pairs are arranged in an antiparallel fashion. While this fold belongs to the split bab family, it appears to be unique among this family; it is a novel arrangement of secondary structure, thereby expanding the universe of protein folds

Open notes: doctors and patients signing on.

Science.gov (United States)

Delbanco, Tom; Walker, Jan; Darer, Jonathan D; Elmore, Joann G; Feldman, Henry J; Leveille, Suzanne G; Ralston, James D; Ross, Stephen E; Vodicka, Elisabeth; Weber, Valerie D

2010-07-20

Few patients read their doctors' notes, despite having the legal right to do so. As information technology makes medical records more accessible and society calls for greater transparency, patients' interest in reading their doctors' notes may increase. Inviting patients to review these notes could improve understanding of their health, foster productive communication, stimulate shared decision making, and ultimately lead to better outcomes. Yet, easy access to doctors' notes could have negative consequences, such as confusing or worrying patients and complicating rather than improving patient-doctor communication. To gain evidence about the feasibility, benefits, and harms of providing patients ready access to electronic doctors' notes, a team of physicians and nurses have embarked on a demonstration and evaluation of a project called OpenNotes. The authors describe the intervention and share what they learned from conversations with doctors and patients during the planning stages. The team anticipates that "open notes" will spread and suggests that over time, if drafted collaboratively and signed by both doctors and patients, they might evolve to become contracts for care.

The Effects of Extensive Reading on Reading Comprehension, Reading Rate, and Vocabulary Acquisition

Science.gov (United States)

Suk, Namhee

2017-01-01

Several empirical studies and syntheses of extensive reading have concluded that extensive reading has positive impacts on language learning in second- and foreign-language settings. However, many of the studies contained methodological or curricular limitations, raising questions about the asserted positive effects of extensive reading. The…

Structure of Human Pancreatic Lipase-Related Protein 2 with the Lid in an Open Conformation

Energy Technology Data Exchange (ETDEWEB)

Eydoux, Cecilia; Spinelli, Silvia; Davis, Tara L.; Walker, John R.; Seitova, Alma; Dhe-Paganon, Sirano; De Caro, Alain; Cambillau, Christian; Carriere, Frederic (CNRS-UMR); (Toronto)

2008-10-02

Access to the active site of pancreatic lipase (PL) is controlled by a surface loop, the lid, which normally undergoes conformational changes only upon addition of lipids or amphiphiles. Structures of PL with their lids in the open and functional conformation have required cocrystallization with amphiphiles. Here we report two crystal structures of wild-type and unglycosylated human pancreatic lipase-related protein 2 (HPLRP2) with the lid in an open conformation in the absence of amphiphiles. These structures solved independently are strikingly similar, with some residues of the lid being poorly defined in the electron-density map. The open conformation of the lid is however different from that previously observed in classical liganded PL, suggesting different kinetic properties for HPLRP2. Here we show that the HPLRP2 is directly inhibited by E600, does not present interfacial activation, and acts preferentially on substrates forming monomers or small aggregates (micelles) dispersed in solution like monoglycerides, phospholipids and galactolipids, whereas classical PL displays reverse properties and a high specificity for unsoluble substrates like triglycerides and diglycerides forming oil-in-water interfaces. These biochemical properties imply that the lid of HPLRP2 is likely to spontaneously adopt in solution the open conformation observed in the crystal structure. This open conformation generates a large cavity capable of accommodating the digalactose polar head of galactolipids, similar to that previously observed in the active site of the guinea pig PLRP2, but absent from the classical PL. Most of the structural and kinetic properties of HPLRP2 were found to be different from those of rat PLRP2, the structure of which was previously obtained with the lid in a closed conformation. Our findings illustrate the essential role of the lid in determining the substrate specificity and the mechanism of action of lipases.

Enhancing academic reading skills through extensive reading ...

African Journals Online (AJOL)

Abstract. The current study explores the feasibility of an extensive reading programme in the context of a low-income country (Mozambique), as well as the influence of extensive reading on academic reading. The programme took over 4 months and was conducted among 30 students majoring in Journalism at the Eduardo ...

Isolation, expression analysis and characterization of EgNDL, a NDR-like protein in oil palm (Elaeis guineensis Jacq.

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Kedsirin Ruttajorn

2016-06-01

Full Text Available A novel cDNA of a SF21-like protein or NDR-like protein (EgNDL from Elaeis guineensis Jacq. is 1,044 bp in length and encodes a putative protein with a 347-amino-acid open reading frame. The EgNDL showed 93% identity to the pollenspecific SF21-like protein of Phoenix dactylifera and also showed 79% identity to the NDL protein of Theobroma cacao. Expression analysis of the EgNDL gene in various tissues showed that EgNDL was expressed in the anthers, pistils, mesocarp and leaves. The high expression of EgNDL among three oil palm varieties was significantly expressed in Pisifera (P<0.05, which is commonly used as a male parent in crosses. Computational tools were used to predict the protein and concluded that EgNDL is a putative membrane protein that may function in a signal transduction pathway during pollen development. In this context, knowledge regarding EgNDL and its potential role in plant developmental processes will benefit oil palm breeding programs.

Rhythm, Rhyme, and Reason; Proceedings of the Annual Reading Conference (9th, Terre Haute, Indiana, June 14, 1979).

Science.gov (United States)

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

Part of a series on selected aspects of curriculum development, this monograph contains reading conference proceedings that include an opening address by author Marguerite Henry in which she shares personal experiences in her evolution as a writer and six papers on remedial reading and language arts. The first paper describes the neurological…

Signaling system in Porphyromonas gingivalis based on a LuxS protein.

Science.gov (United States)

Chung, W O; Park, Y; Lamont, R J; McNab, R; Barbieri, B; Demuth, D R

2001-07-01

The luxS gene of quorum-sensing Vibrio harveyi is required for type 2 autoinducer production. We identified a Porphyromonas gingivalis open reading frame encoding a predicted peptide of 161 aa that shares 29% identity with the amino acid sequence of the LuxS protein of V. harveyi. Conditioned medium from a late-log-phase P. gingivalis culture induced the luciferase operon of V. harveyi, but that from a luxS insertional mutant did not. In P. gingivalis, the expression of luxS mRNA was environmentally controlled and varied according to the cell density and the osmolarity of the culture medium. In addition, differential display PCR showed that the inactivation of P. gingivalis luxS resulted in up-regulation of a hemin acquisition protein and an arginine-specific protease and reduced expression of a hemin-regulated protein, a TonB homologue, and an excinuclease. The data suggest that the luxS gene in P. gingivalis may function to control the expression of genes involved in the acquisition of hemin.

Sulfolobus turreted icosahedral virus c92 protein responsible for the formation of pyramid-like cellular lysis structures.

Science.gov (United States)

Snyder, Jamie C; Brumfield, Susan K; Peng, Nan; She, Qunxin; Young, Mark J

2011-07-01

Host cells infected by Sulfolobus turreted icosahedral virus (STIV) have been shown to produce unusual pyramid-like structures on the cell surface. These structures represent a virus-induced lysis mechanism that is present in Archaea and appears to be distinct from the holin/endolysin system described for DNA bacteriophages. This study investigated the STIV gene products required for pyramid formation in its host Sulfolobus solfataricus. Overexpression of STIV open reading frame (ORF) c92 in S. solfataricus alone is sufficient to produce the pyramid-like lysis structures in cells. Gene disruption of c92 within STIV demonstrates that c92 is an essential protein for virus replication. Immunolocalization of c92 shows that the protein is localized to the cellular membranes forming the pyramid-like structures.

Reading: Time

NARCIS (Netherlands)

Annemarie Wennekers; Frank Huysmans; Jos de Haan

2018-01-01

Original title: Lees:Tijd The amount of time that Dutch people spend reading has been declining steadily since the 1950s. This decline in reading time contrasts starkly with the positive personal and social benefits that can be derived from reading, according to lots of research. The Reading:

Open ISEmeter: An open hardware high-impedance interface for potentiometric detection

International Nuclear Information System (INIS)

Salvador, C.; Carbajo, J.; Mozo, J. D.; Mesa, M. S.; Durán, E.; Alvarez, J. L.

2016-01-01

In this work, a new open hardware interface based on Arduino to read electromotive force (emf) from potentiometric detectors is presented. The interface has been fully designed with the open code philosophy and all documentation will be accessible on web. The paper describes a comprehensive project including the electronic design, the firmware loaded on Arduino, and the Java-coded graphical user interface to load data in a computer (PC or Mac) for processing. The prototype was tested by measuring the calibration curve of a detector. As detection element, an active poly(vinyl chloride)-based membrane was used, doped with cetyltrimethylammonium dodecylsulphate (CTA"+-DS"−). The experimental measures of emf indicate Nernstian behaviour with the CTA"+ content of test solutions, as it was described in the literature, proving the validity of the developed prototype. A comparative analysis of performance was made by using the same chemical detector but changing the measurement instrumentation.

Dialogic Reading Aloud to Promote Extensive Reading

Science.gov (United States)

Jacobs, George M.

2016-01-01

How can teachers motivate students to read extensively in a second language? One strategy is for teachers to read aloud to students to promote the joys of reading generally, to build students' language skills and to introduce students to specific authors, book series, genres, websites, etc. This article begins by discussing why teachers might want…

An investigation of Chinese university EFL learner’s foreign language reading anxiety, reading strategy use and reading comprehension performance

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Zhongshe Lu

2015-01-01

Full Text Available The present study explored the interrelations between foreign language (FL reading anxiety, FL reading strategy use and their interactive effect on FL reading comprehension performance at the tertiary level in China. Analyses of the survey data collected from 1702 university students yielded the following results: (a Both Foreign Language Reading Anxiety Scale (FLRAS and Foreign Language Reading Strategy Use Scale (FLRSUS had important subcomponents, (b more than half of the students generally did not feel anxious when reading English, and were confident in and satisfied with their English reading proficiency. Meanwhile, (c more than half of them moderately used different types of reading strategies such as planning, checking and confirming, predicting and assessing, when reading English, (d compared with their female peers, male students felt significantly more anxious when facing reading activities, less satisfied with their English reading proficiency, and used specific analyzing and planning strategies significantly less often during a reading activity, (e FLRAS was significantly inversely related to FLRSUS, and both were significantly correlated with the students’ FL reading comprehension performance, and (f FLRAS (overall FL reading anxiety, FLRAS1 (general anxiety about FL reading, and FLRSUS2 (predicting strategies were good predictors of FL reading comprehension performance. Based on the findings, some implications are discussed.

Genes of the unfolded protein response pathway harbor risk alleles for primary open angle glaucoma.

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Mary Anna Carbone

Full Text Available The statistical power of genome-wide association (GWA studies to detect risk alleles for human diseases is limited by the unfavorable ratio of SNPs to study subjects. This multiple testing problem can be surmounted with very large population sizes when common alleles of large effects give rise to disease status. However, GWA approaches fall short when many rare alleles may give rise to a common disease, or when the number of subjects that can be recruited is limited. Here, we demonstrate that this multiple testing problem can be overcome by a comparative genomics approach in which an initial genome-wide screen in a genetically amenable model organism is used to identify human orthologues that may harbor risk alleles for adult-onset primary open angle glaucoma (POAG. Glaucoma is a major cause of blindness, which affects over 60 million people worldwide. Several genes have been associated with juvenile onset glaucoma, but genetic factors that predispose to adult onset primary open angle glaucoma (POAG remain largely unknown. Previous genome-wide analysis in a Drosophila ocular hypertension model identified transcripts with altered regulation and showed induction of the unfolded protein response (UPR upon overexpression of transgenic human glaucoma-associated myocilin (MYOC. We selected 16 orthologous genes with 62 polymorphic markers and identified in two independent human populations two genes of the UPR that harbor POAG risk alleles, BIRC6 and PDIA5. Thus, effectiveness of the UPR in response to accumulation of misfolded or aggregated proteins may contribute to the pathogenesis of POAG and provide targets for early therapeutic intervention.

Genes of the unfolded protein response pathway harbor risk alleles for primary open angle glaucoma.

Science.gov (United States)

Carbone, Mary Anna; Chen, Yuhong; Hughes, Guy A; Weinreb, Robert N; Zabriskie, Norman A; Zhang, Kang; Anholt, Robert R H

2011-01-01

The statistical power of genome-wide association (GWA) studies to detect risk alleles for human diseases is limited by the unfavorable ratio of SNPs to study subjects. This multiple testing problem can be surmounted with very large population sizes when common alleles of large effects give rise to disease status. However, GWA approaches fall short when many rare alleles may give rise to a common disease, or when the number of subjects that can be recruited is limited. Here, we demonstrate that this multiple testing problem can be overcome by a comparative genomics approach in which an initial genome-wide screen in a genetically amenable model organism is used to identify human orthologues that may harbor risk alleles for adult-onset primary open angle glaucoma (POAG). Glaucoma is a major cause of blindness, which affects over 60 million people worldwide. Several genes have been associated with juvenile onset glaucoma, but genetic factors that predispose to adult onset primary open angle glaucoma (POAG) remain largely unknown. Previous genome-wide analysis in a Drosophila ocular hypertension model identified transcripts with altered regulation and showed induction of the unfolded protein response (UPR) upon overexpression of transgenic human glaucoma-associated myocilin (MYOC). We selected 16 orthologous genes with 62 polymorphic markers and identified in two independent human populations two genes of the UPR that harbor POAG risk alleles, BIRC6 and PDIA5. Thus, effectiveness of the UPR in response to accumulation of misfolded or aggregated proteins may contribute to the pathogenesis of POAG and provide targets for early therapeutic intervention.

Readings in artificial intelligence and databases

CERN Document Server

Mylopoulos, John

1988-01-01

The interaction of database and AI technologies is crucial to such applications as data mining, active databases, and knowledge-based expert systems. This volume collects the primary readings on the interactions, actual and potential, between these two fields. The editors have chosen articles to balance significant early research and the best and most comprehensive articles from the 1980s. An in-depth introduction discusses basic research motivations, giving a survey of the history, concepts, and terminology of the interaction. Major themes, approaches and results, open issues and future

The Habit of Reading: A Neglected Dimension of Adult Reading Instruction.

Science.gov (United States)

Fink, Katherine T.; Devine, Thomas G.

1993-01-01

Less competent adult readers have not developed the habit of reading. Ways to cultivate adult reading habits include relevant material, environment saturated with reading material, reading aloud to adults, having them read to children, sustained silent reading, modeling, book sharing, author conferences, and recognition. (SK)

Leptospiral outer membrane protein LipL41 is not essential for acute leptospirosis but requires a small chaperone protein, lep, for stable expression.

Science.gov (United States)

King, Amy M; Bartpho, Thanatchaporn; Sermswan, Rasana W; Bulach, Dieter M; Eshghi, Azad; Picardeau, Mathieu; Adler, Ben; Murray, Gerald L

2013-08-01

Leptospirosis is a worldwide zoonosis caused by pathogenic Leptospira spp., but knowledge of leptospiral pathogenesis remains limited. However, the development of mutagenesis systems has allowed the investigation of putative virulence factors and their involvement in leptospirosis. LipL41 is the third most abundant lipoprotein found in the outer membranes of pathogenic leptospires and has been considered a putative virulence factor. LipL41 is encoded on the large chromosome 28 bp upstream of a small open reading frame encoding a hypothetical protein of unknown function. This gene was named lep, for LipL41 expression partner. In this study, lipL41 was found to be cotranscribed with lep. Two transposon mutants were characterized: a lipL41 mutant and a lep mutant. In the lep mutant, LipL41 protein levels were reduced by approximately 90%. Lep was shown through cross-linking and coexpression experiments to bind to LipL41. Lep is proposed to be a molecular chaperone essential for the stable expression of LipL41. The roles of LipL41 and Lep in the pathogenesis of Leptospira interrogans were investigated; surprisingly, neither of these two unique proteins was essential for acute leptospirosis.

Miraculous Readings: Using Fantasy Novels about Reading to Reflect on Reading the Bible

Science.gov (United States)

Dalton, Russell W.

2009-01-01

This article reflects on the vivid images of reading presented in several popular fantasy novels, including "The Spiderwick Chronicles," "The Great Good Thing," and "The Neverending Story." It suggests that these images can be used to help children, youth, and adults reflect on the nature of reading and the potential power of reading sacred texts.…

The conserved baculovirus protein p33 (Ac92) is a flavin adenine dinucleotide-linked sulfhydryl oxidase

International Nuclear Information System (INIS)

Long, C.M.; Rohrmann, G.F.; Merrill, G.F.

2009-01-01

Open reading frame 92 of the Autographa californica baculovirus (Ac92) is one of about 30 core genes present in all sequenced baculovirus genomes. Computer analyses predicted that the Ac92 encoded protein (called p33) and several of its baculovirus orthologs were related to a family of flavin adenine dinucleotide (FAD)-linked sulfhydryl oxidases. Alignment of these proteins indicated that, although they were highly diverse, a number of amino acids in common with the Erv1p/Alrp family of sulfhydryl oxidases are present. Some of these conserved amino acids are predicted to stack against the isoalloxazine and adenine components of FAD, whereas others are involved in electron transfer. To investigate this relationship, Ac92 was expressed in bacteria as a His-tagged fusion protein, purified, and characterized both spectrophotometrically and for its enzymatic activity. The purified protein was found to have the color (yellow) and absorption spectrum consistent with it being a FAD-containing protein. Furthermore, it was demonstrated to have sulfhydryl oxidase activity using dithiothreitol and thioredoxin as substrates.

Reading Every Single Day: A Journey to Authentic Reading

Science.gov (United States)

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'…

Reading Comics

Science.gov (United States)

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…

Reading Processes of University Students with Dyslexia - An Examination of the Relationship between Oral Reading and Reading Comprehension.

Science.gov (United States)

Pedersen, Henriette Folkmann; Fusaroli, Riccardo; Lauridsen, Lene Louise; Parrila, Rauno

2016-11-01

The purpose of this study was to examine the quality of oral reading and how it relates to reading comprehension in students with dyslexia. A group of Danish university students with dyslexia (n = 16) and a comparison group of students with no history of reading problems (n = 16) were assessed on their oral reading performance when reading a complex text. Along with reading speed, we measured not only the number and quality of reading errors but also the extent and semantic nature of the self-corrections during reading. The reading comprehension was measured through aided text retellings. The results showed that, as a group, the dyslexics performed poorer on most measures, but there were notable within-group differences in the reading behaviours and little association between how well university students with dyslexia read aloud and comprehended the text. These findings suggest that many dyslexics in higher education tend to focus their attention on one subcomponent of the reading process, for example, decoding or comprehension, because engaging in both simultaneously may be too demanding for them. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Exegetical analyses and spiritual readings of the story of the ...

African Journals Online (AJOL)

The fourth reading is an intertextual one, which shows how the quotation of Gen 18:14 becomes an expression of one of the specific topics relating to the spirituality of the Gospel of Luke. The conclusion is that it is not the use of a specific method that is decisive for spirituality, but rather the openness of the researcher.

The open society and its enemies

CERN Document Server

Popper, Karl Raimund

2003-01-01

Written in political exile during the Second World War and first published in 1945, Karl Popper's The Open Society and Its Enemies is one of the most influential books of the twentieth century. Hailed by Bertrand Russell as a 'vigorous and profound defence of democracy', its now legendary attack on the philosophies of Plato, Hegel and Marx exposed the dangers inherent in centrally planned political systems. Popper's highly accessible style, his erudite and lucid explanations of the thought of great philosophers and the recent resurgence of totalitarian regimes around the world are just three of the reasons for the enduring popularity of The Open Society and Its Enemies, and for why it demands to be read both today and in years to come. This is the second of two volumes of The Open Society and Its Enemies.

Cellular Dewetting: Opening of Macroapertures in Endothelial Cells

Science.gov (United States)

Gonzalez-Rodriguez, David; Maddugoda, Madhavi P.; Stefani, Caroline; Janel, Sebastien; Lafont, Frank; Cuvelier, Damien; Lemichez, Emmanuel; Brochard-Wyart, Françoise

2012-05-01

Pathogenic bacteria can cross from blood vessels to host tissues by opening transendothelial cell macroapertures (TEMs). To induce TEM opening, bacteria intoxicate endothelial cells with proteins that disrupt the contractile cytoskeletal network. Cell membrane tension is no longer resisted by contractile fibers, leading to the opening of TEMs. Here we model the opening of TEMs as a new form of dewetting. While liquid dewetting is irreversible, we show that cellular dewetting is transient. Our model predicts the minimum radius for hole nucleation, the maximum TEM size, and the dynamics of TEM opening, in good agreement with experimental data. The physical model is then coupled with biological experimental data to reveal that the protein missing in metastasis (MIM) controls the line tension at the rim of the TEM and opposes its opening.

Reading fluency: implications for the assessment of children with reading disabilities.

Science.gov (United States)

Meisinger, Elizabeth B; Bloom, Juliana S; Hynd, George W

2010-06-01

The current investigation explored the diagnostic utility of reading fluency measures in the identification of children with reading disabilities. Participants were 50 children referred to a university-based clinic because of suspected reading problems and/or a prior diagnosis of dyslexia, where children completed a battery of standardized intellectual, reading achievement, and processing measures. Within this clinical sample, a group of children were identified that exhibited specific deficits in their reading fluency skills with concurrent deficits in rapid naming speed and reading comprehension. This group of children would not have been identified as having a reading disability according to assessment of single word reading skills alone, suggesting that it is essential to assess reading fluency in addition to word reading because failure to do so may result in the under-identification of children with reading disabilities.

"Read the Text, as if!"The Reading Retention Strategy

Science.gov (United States)

Divoll, Kent; Browning, Sandra

2013-01-01

Students do not always read what is expected in college courses (Berry, Cook, Hill, & Stevens, 2010; Phillips & Phillips, 2007; Sikorski et al., 2002) or they read to cram for an exam or quiz (Clump, Bauer, & Bradley, 2004). The Reading Retention Strategy (RRS) is designed to motivate students to read and assist students in…

Do reading additions improve reading in pre-presbyopes with low vision?

Science.gov (United States)

Alabdulkader, Balsam; Leat, Susan

2012-09-01

This study compared three different methods of determining a reading addition and the possible improvement on reading performance in children and young adults with low vision. Twenty-eight participants with low vision, aged 8 to 32 years, took part in the study. Reading additions were determined with (a) a modified Nott dynamic retinoscopy, (b) a subjective method, and (c) an age-based formula. Reading performance was assessed with MNREAD-style reading charts at 12.5 cm, with and without each reading addition in random order. Outcome measures were reading speed, critical print size, MNREAD threshold, and the area under the reading speed curve. For the whole group, there was no significant improvement in reading performance with any of the additions. When participants with normal accommodation at 12.5 cm were excluded, the area under the reading speed curve was significantly greater with all reading additions compared with no addition (p = 0.031, 0.028, and 0.028, respectively). Also, the reading acuity threshold was significantly better with all reading additions compared with no addition (p = 0.014, 0.030, and 0.036, respectively). Distance and near visual acuity, age, and contrast sensitivity did not predict improvement with a reading addition. All, but one, of the participants who showed a significant improvement in reading with an addition had reduced accommodation. A reading addition may improve reading performance for young people with low vision and should be considered as part of a low vision assessment, particularly when accommodation is reduced.

Readings in artificial intelligence and software engineering

CERN Document Server

Rich, Charles

1986-01-01

Readings in Artificial Intelligence and Software Engineering covers the main techniques and application of artificial intelligence and software engineering. The ultimate goal of artificial intelligence applied to software engineering is automatic programming. Automatic programming would allow a user to simply say what is wanted and have a program produced completely automatically. This book is organized into 11 parts encompassing 34 chapters that specifically tackle the topics of deductive synthesis, program transformations, program verification, and programming tutors. The opening parts p

Maternal Reading Self-Efficacy Associated with Perceived Barriers to Reading

Directory of Open Access Journals (Sweden)

Joyce Lin

2015-01-01

Full Text Available Although early reading practices impact a host of child literacy, language, and school outcomes, many parents do not read to their young children. One possible explanation for this lack of early literacy practices is mothers’ feelings about their ability to successfully read to their children. A series of multiple regressions were used to explore whether new mothers’ reading self-efficacy predicted their perceived barriers to reading to their 18-month-old children. Findings suggest that self-efficacy buffers against mother-centered (e.g., too tired, child-centered (e.g., toddler fussy, and structural (e.g., environmental distractions barriers to reading. Given the importance of early literacy and that not all mothers read to their toddlers, increasing reading self-efficacy may offer a way to reduce perceived barriers to early literacy practices.

Reading Strategies Used by Iranian EFL Learners While Reading Academic Texts

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Vida Yousefian

2015-11-01

Full Text Available The major aim of this study was to explore the nature and frequency of the reading strategies used by the EFL learners while reading academic texts. Normally, students tend to read all the information provided in reading materials. This study explores whether learners use reading strategies to assist them in reading comprehension. There was a sample of 45 English language (EFL learners from Islamic Azad University, Falavarjan Branch. The instrument utilized in this study was a survey questionnaire with 30 items including 13 global reading strategies, 8 problem solving strategies and 9 support reading strategies. The survey was going to signify how much EFL learners use each of these strategies while reading academic texts. The findings indicated that the participants used global reading strategies more (44.5% than problem solving strategies (29.0% and support reading strategies (26.5%. The results of the present study will let the instructors improve the reading strategies which are not used by EFL learners frequently. It also helps learners to promote the ability of using reading strategies and utilize the strategies in an appropriate and effective way.

The 75-kilodalton cytoplasmic Chlamydia trachomatis L2 polypeptide is a DnaK-like protein

DEFF Research Database (Denmark)

Birkelund, Svend; Lundemose, AG; Christiansen, Gunna

1990-01-01

,980-base-pair open reading frame revealed 94% homology with a 75-kilodalton protein from C. trachomatis serovar D and 57% homology with the DnaK proteins of E. coli and of Bacillus megaterium, while amino acid homology with human heat shock protein 70 (hsp70) was 42%. The promoter region was identified......The gene coding for the 75-kilodalton cytoplasmic Chlamydia trachomatis L2 polypeptide has been cloned in Escherichia coli, and the nucleotide sequence has been determined. The cloned DNA fragment contained the coding region as well as the putative promoter. The deduced amino acid sequence of the 1...... by computer search and by primer extension of mRNA synthesized in recombinant E. coli. The promoter region which differed from the putative promoter region in serovar D was shown to be a mixed promoter type in which the -10 region showed a regular TATA box configuration while the -35 region showed high...

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.

Science.gov (United States)

Bachman, John A; Gyori, Benjamin M; Sorger, Peter K

2018-06-28

For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers, a process known as named entity linking or "grounding." Correct grounding is essential for resolving relationships among mined information, curated interaction databases, and biological datasets. The accuracy of this process is largely dependent on the availability of machine-readable resources associating synonyms and abbreviations commonly found in biomedical literature with uniform identifiers. In a task involving automated reading of ∼215,000 articles using the REACH event extraction software we found that grounding was disproportionately inaccurate for multi-protein families (e.g., "AKT") and complexes with multiple subunits (e.g."NF- κB"). To address this problem we constructed FamPlex, a manually curated resource defining protein families and complexes as they are commonly encountered in biomedical text. In FamPlex the gene-level constituents of families and complexes are defined in a flexible format allowing for multi-level, hierarchical membership. To create FamPlex, text strings corresponding to entities were identified empirically from literature and linked manually to uniform identifiers; these identifiers were also mapped to equivalent entries in multiple related databases. FamPlex also includes curated prefix and suffix patterns that improve named entity recognition and event extraction. Evaluation of REACH extractions on a test corpus of ∼54,000 articles showed that FamPlex significantly increased grounding accuracy for families and complexes (from 15 to 71%). The hierarchical organization of entities in FamPlex also made it possible to integrate otherwise unconnected mechanistic information across families, subfamilies, and individual proteins. Applications of FamPlex to the TRIPS/DRUM reading system and the Biocreative VI Bioentity

Davies, Florence (1995. Introducing Reading. Davies, Florence (1995. Introducing Reading.

Directory of Open Access Journals (Sweden)

Sonia Maria Gomes Ferreira

2008-04-01

Full Text Available Arising at a time of unprecedented growth of interest in fostering critical thinking, Introducing Reading offers a clear introduction and thorough account of contemporary developments in the field of reading. While overtly focusing on the special demands of social and human aspects of the reading practice, the issues raised have crucial resonance in the sphere of critical reading. Explicitly addressed to teachers of mother tongue and foreign language contexts, the book claims to elaborate on aspects of reading which have received meager attention to date: individual readers engaged in different real-world reading tasks, the social contexts where such readers engage and interact with texts, and the nature and variety of texts, here regarded as “participants” in the interaction between reader and writer. To this extent, the book successfully reaches the ambitious aim of “socializing and humanizing reading and the teaching of reading” (p. xi. Arising at a time of unprecedented growth of interest in fostering critical thinking, Introducing Reading offers a clear introduction and thorough account of contemporary developments in the field of reading. While overtly focusing on the special demands of social and human aspects of the reading practice, the issues raised have crucial resonance in the sphere of critical reading. Explicitly addressed to teachers of mother tongue and foreign language contexts, the book claims to elaborate on aspects of reading which have received meager attention to date: individual readers engaged in different real-world reading tasks, the social contexts where such readers engage and interact with texts, and the nature and variety of texts, here regarded as “participants” in the interaction between reader and writer. To this extent, the book successfully reaches the ambitious aim of “socializing and humanizing reading and the teaching of reading” (p. xi.

Open ISEmeter: An open hardware high-impedance interface for potentiometric detection

Energy Technology Data Exchange (ETDEWEB)

Salvador, C.; Carbajo, J.; Mozo, J. D., E-mail: jdaniel.mozo@diq.uhu.es [Applied Electrochemistry Laboratory, Faculty of Experimental Sciences, University of Huelva, Av. 3 de Marzo s/n., 21007 Huelva (Spain); Mesa, M. S.; Durán, E. [Department of Electronics Engineering, Computers and Automatic, ETSI, University of Huelva, Campus de La Rabida, 21810 Huelva (Spain); Alvarez, J. L. [Department of Information Technologies, ETSI, University of Huelva, Campus de La Rabida, 21810 Huelva (Spain)

2016-05-15

In this work, a new open hardware interface based on Arduino to read electromotive force (emf) from potentiometric detectors is presented. The interface has been fully designed with the open code philosophy and all documentation will be accessible on web. The paper describes a comprehensive project including the electronic design, the firmware loaded on Arduino, and the Java-coded graphical user interface to load data in a computer (PC or Mac) for processing. The prototype was tested by measuring the calibration curve of a detector. As detection element, an active poly(vinyl chloride)-based membrane was used, doped with cetyltrimethylammonium dodecylsulphate (CTA{sup +}-DS{sup −}). The experimental measures of emf indicate Nernstian behaviour with the CTA{sup +} content of test solutions, as it was described in the literature, proving the validity of the developed prototype. A comparative analysis of performance was made by using the same chemical detector but changing the measurement instrumentation.

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

Science.gov (United States)

Maldonado, Michele

2012-01-01

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

Motivational reading on education, meaningful reading realisation

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Adriana Qafa

2017-07-01

Full Text Available In this study I will present some ideas on today’s educational practice for motivation, the realization of the meaningful reading. There is a special place for the methodical ranking of the reading process, starting in school. Main requests of this reading, consist of the deep meaning of the subject, exploration of the idea, and other elements of the subject, implementation of the technique’s rules of the expressive reading, such as breathing, voice, diction, intonation, spelling, stoppages, logical emphasizes, emotional expressions, temper, timber, gesticulations, and mimic. There is also highlighted the fact that the used method comes from the pupils’ results and depends on the capability and level of the teacher, from the programming’s scale, the tools that are put into disposition, the age and the level of the pupils, and from the environment that the teacher creates during courses. At the end there are some practical guidelines for the realization of the expressive reading in the literature subject.

Translational read-through of a nonsense mutation causing Bartter syndrome.

Science.gov (United States)

Cho, Hee Yeon; Lee, Beom Hee; Cheong, Hae Il

2013-06-01

Bartter syndrome (BS) is classified into 5 genotypes according to underlying mutant genes and BS III is caused by loss-of-function mutations in the CLCNKB gene encoding for basolateral ClC-Kb. BS III is the most common genotype in Korean patients with BS and W610X is the most common CLCNKB mutation in Korean BS III. In this study, we tested the hypothesis that the CLCNKB W610X mutation can be rescued in vitro using aminoglycoside antibiotics, which are known to induce translational read-through of a nonsense mutation. The CLCNKB cDNA was cloned into a eukaryotic expression vector and the W610X nonsense mutation was generated by site-directed mutagenesis. Cultured polarized MDCK cells were transfected with the vectors, and the read-through was induced using an aminoglycoside derivative, G418. Cellular expression of the target protein was monitored via immunohistochemistry. While cells transfected with the mutant CLCNKB failed to express ClC-Kb, G418 treatment of the cells induced the full-length protein expression, which was localized to the basolateral plasma membranes. It is demonstrated that the W610X mutation in CLCNKB can be a good candidate for trial of translational read-through induction as a therapeutic modality.

Word Reading Efficiency, Text Reading Fluency, and Reading Comprehension among Chinese Learners of English

Science.gov (United States)

Jiang, Xiangying; Sawaki, Yasuyo; Sabatini, John

2012-01-01

This study examined the relationship among word reading efficiency, text reading fluency, and reading comprehension for adult English as a Foreign Language (EFL) learners. Data from 185 adult Chinese EFL learners preparing to take the Test-of-English-as-a-Foreign-Language[TM] (TOEFL[R]) were analyzed in this study. The participants completed a…

TOOL: The Open Opinion Layer

OpenAIRE

Masum, Hassan

2002-01-01

Shared opinions drive society: what we read, how we vote, and where we shop are all heavily influenced by the choices of others. However, the cost in time and money to systematically share opinions remains high, while the actual performance history of opinion generators is often not tracked. This article explores the development of a distributed open opinion layer, which is given the generic name of TOOL. Similar to the evolution of network protocols as an underlying layer for many comput...

Galectin-1 Is an Interactive Protein of Selenoprotein M in the Brain

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Qiong Liu

2013-11-01

Full Text Available Selenium, an essential trace element for human health, mainly exerts its biological function through selenoproteins. Selenoprotein M (SelM is one of the highly expressed selenoproteins in the brain, but its biological effect and molecular mechanism remain unclear. Thus, the interactive protein of SelM was investigated in this paper to guide further study. In order to avoid protein translational stop, the selenocysteine-encoding UGA inside the open reading frame of SelM was site-directly changed to the cysteine-encoding UGC to generate the SelM' mutant. Meanwhile, its N terminal transmembrane signal peptide was also cut off. This truncated SelM' was used to screen a human fetal brain cDNA library by the yeast two-hybrid system. A new interactive protein of SelM' was found to be galectin-1 (Gal-1. This protein-protein interaction was further verified by the results of fluorescence resonance energy transfer techniques, glutathione S-transferase pull-down and co-immunoprecipitation assays. As Gal-1 plays important roles in preventing neurodegeneration and promoting neuroprotection in the brain, the interaction between SelM' and Gal-1 displays a new direction for studying the biological function of SelM in the human brain.

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

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Richard Wilton

2015-03-01

Full Text Available When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU hardware.We followed this approach in implementing a read aligner called Arioc that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found. We then carried out a read-by-read comparison of Arioc’s reported alignments with the alignments found by several leading read aligners. With simulated reads, Arioc has comparable or better accuracy than the other read aligners we tested. With human sequencing reads, Arioc demonstrates significantly greater throughput than the other aligners we evaluated across a wide range of sensitivity settings. The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license.

Developing New Reading Assessments to Promote Beginning Reading in Singapore

Science.gov (United States)

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…

Photometry Using Kepler “Superstamps” of Open Clusters NGC 6791 & NGC 6819

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Kuehn Charles A.

2015-01-01

Full Text Available The Kepler space telescope has proven to be a gold mine for the study of variable stars. Usually, Kepler only reads out a handful of pixels around each pre-selected target star, omitting a large number of stars in the Kepler field. Fortunately, for the open clusters NGC 6791 and NGC 6819, Kepler also read out larger “superstamps” which contained complete images of the central region of each cluster. These cluster images can be used to study additional stars in the open clusters that were not originally on Kepler’s target list. We discuss our work on using two photometric techniques to analyze these superstamps and present sample results from this project to demonstrate the value of this technique for a wide variety of variable stars.

Mussel glue protein has an open conformation.

Science.gov (United States)

Williams, T; Marumo, K; Waite, J H; Henkens, R W

1989-03-01

Both native glue protein from marine mussels and a synthetic nonhydroxylated analog were analyzed by far-uv CD under a variety of conditions. Analysis of the CD spectra using various models strongly suggest a primarily random coil structure for both forms of the protein, a fact also supported by the absence of spectral change for the glue protein upon dilution into 6 M guanidine hydrochloride. The nonhydroxylated analog, which consists of 20 repeats of the peptide sequence Ala-Lys-Pro-Ser-Tyr-Pro-Pro-Thr-Tyr-Lys, was further characterized by enzyme modification using mushroom tyrosinase. Enzymatic hydroxylation of tyrosines was found to be best fit by a model containing two rate constants, 5.6 (+/- 0.6) X 10(-3) and 7.2 (+/- 0.3) X 10(-2) min-1. At equilibrium, HPLC analysis of digests showed nearly 100% conversion of Tyr-9 and only 15 to 35% conversion of Tyr-5. The Chou and Fasman rules for predicting structure were applied to the repeat sequence listed above. The rules predict the absence of alpha helix and beta pleated sheets in the structure of this peptide. On the other hand, beta turns are predicted to be present with Tyr-5 being in the region of highest probability. These data suggest that the protein in solution has only a small amount of secondary structure.

In Silico screening for functional candidates amongst hypothetical proteins

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Sanderhoff May

2009-09-01

Full Text Available Abstract Background The definition of a hypothetical protein is a protein that is predicted to be expressed from an open reading frame, but for which there is no experimental evidence of translation. Hypothetical proteins constitute a substantial fraction of proteomes of human as well as of other eukaryotes. With the general belief that the majority of hypothetical proteins are the product of pseudogenes, it is essential to have a tool with the ability of pinpointing the minority of hypothetical proteins with a high probability of being expressed. Results Here, we present an in silico selection strategy where eukaryotic hypothetical proteins are sorted according to two criteria that can be reliably identified in silico: the presence of subcellular targeting signals and presence of characterized protein domains. To validate the selection strategy we applied it on a database of human hypothetical proteins dating to 2006 and compared the proteins predicted to be expressed by our selecting strategy, with their status in 2008. For the comparison we focused on mitochondrial proteins, since considerable amounts of research have focused on this field in between 2006 and 2008. Therefore, many proteins, defined as hypothetical in 2006, have later been characterized as mitochondrial. Conclusion Among the total amount of human proteins hypothetical in 2006, 21% have later been experimentally characterized and 6% of those have been shown to have a role in a mitochondrial context. In contrast, among the selected hypothetical proteins from the 2006 dataset, predicted by our strategy to have a mitochondrial role, 53-62% have later been experimentally characterized, and 85% of these have actually been assigned a role in mitochondria by 2008. Therefore our in silico selection strategy can be used to select the most promising candidates for subsequent in vitro and in vivo analyses.

The development of PISA reading competence in secondary education

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Jovanović Vitomir

2016-01-01

Full Text Available The aim of the paper is to provide a contribution to answering the question about the most important predictors of progress in reading competence achieved by students after two years of secondary education, as well as whether the set of predictors of progress is different from the set of predictors of achievement in reading literacy test and school achievement measured via school grades. The students from the sample for the PISA 2009 study conducted in Serbia were tested again after two years by the PISA reading literacy test, quasi longitudinally, measuring achievement correlates at another time point. The realised sample included 20 secondary schools and 446 students. We selected fourteen predictors that, according to the studies so far, proved to have highest correlations with school achievement. The results have shown that the predictors explain only 13% of variance of the progress in reading literacy test (R=.36; R2=.13; F =12.97; p<.05 although they explain 49% of variance of achievement at it (R=.70; R2 197,18 =.49; F257,18 =12.97; p<.001. This opens up the issue of the importance of early learning for progress in reading competence. In both the first and the second analysis, the strongest predictor was the autonomous form of extrinsic motivation which, according to the self-determination theory, speaks about the importance of learning for future life and career. A somewhat different set of used predictors predicted school achievement measured via school grades. Using metacognitive strategies is not an important predictor of school achievement while it is the predictor of achievement in the reading literacy test. Together with the findings pointing towards the lower than expected correlation between achievement in reading literacy and school achievement (r=.39; p<0.001 and generally low progress of Serbia at this test compared to the estimated progress of the OECD countries, these results give grounds for the conclusion that our

Reading the Stories of Teaching and Learning—ISSOTL 2016 Opening Keynote

Directory of Open Access Journals (Sweden)

Karen Manarin

2017-03-01

This article includes an embedded audio file from YouTube. To listen to the file linked from within the PDF, download the PDF and click the links. If you stay within the preview page, you'll have to right-click the links and open them in a new window.

Short read sequence typing (SRST: multi-locus sequence types from short reads

Directory of Open Access Journals (Sweden)

Inouye Michael

2012-07-01

software tool for accurate assignment of sequence types using short read data. Several uses for the tool are demonstrated, including quality control for high-throughput sequencing projects, plasmid MLST and analysis of genomic data during outbreak investigation. SRST is open-source, requires Python, BWA and SamTools, and is available from http://srst.sourceforge.net.

Large-scale identification of odorant-binding proteins and chemosensory proteins from expressed sequence tags in insects

Science.gov (United States)

2009-01-01

Background Insect odorant binding proteins (OBPs) and chemosensory proteins (CSPs) play an important role in chemical communication of insects. Gene discovery of these proteins is a time-consuming task. In recent years, expressed sequence tags (ESTs) of many insect species have accumulated, thus providing a useful resource for gene discovery. Results We have developed a computational pipeline to identify OBP and CSP genes from insect ESTs. In total, 752,841 insect ESTs were examined from 54 species covering eight Orders of Insecta. From these ESTs, 142 OBPs and 177 CSPs were identified, of which 117 OBPs and 129 CSPs are new. The complete open reading frames (ORFs) of 88 OBPs and 123 CSPs were obtained by electronic elongation. We randomly chose 26 OBPs from eight species of insects, and 21 CSPs from four species for RT-PCR validation. Twenty two OBPs and 16 CSPs were confirmed by RT-PCR, proving the efficiency and reliability of the algorithm. Together with all family members obtained from the NCBI (OBPs) or the UniProtKB (CSPs), 850 OBPs and 237 CSPs were analyzed for their structural characteristics and evolutionary relationship. Conclusions A large number of new OBPs and CSPs were found, providing the basis for deeper understanding of these proteins. In addition, the conserved motif and evolutionary analysis provide some new insights into the evolution of insect OBPs and CSPs. Motif pattern fine-tune the functions of OBPs and CSPs, leading to the minor difference in binding sex pheromone or plant volatiles in different insect Orders. PMID:20034407

Reading Speed as a Constraint of Accuracy of Self-Perception of Reading Skill

Science.gov (United States)

Kwon, Heekyung; Linderholm, Tracy

2015-01-01

We hypothesised that college students take reading speed into consideration when evaluating their own reading skill, even if reading speed does not reliably predict actual reading skill. To test this hypothesis, we measured self-perception of reading skill, self-perception of reading speed, actual reading skill and actual reading speed to…

Exploring Students' Reading Profiles to Guide a Reading Intervention Programme

Science.gov (United States)

Boakye, Naomi A. N. Y.

2017-01-01

There have been a number of studies on reading interventions to improve students' reading proficiency, yet the majority of these interventions are undertaken with the assumption that students' reading challenges are obvious and generic in nature. The interventions do not take into consideration the diversity in students' reading backgrounds and…

compomics-utilities: an open-source Java library for computational proteomics.

Science.gov (United States)

Barsnes, Harald; Vaudel, Marc; Colaert, Niklaas; Helsens, Kenny; Sickmann, Albert; Berven, Frode S; Martens, Lennart

2011-03-08

The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

compomics-utilities: an open-source Java library for computational proteomics

Directory of Open Access Journals (Sweden)

Helsens Kenny

2011-03-01

Full Text Available Abstract Background The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. Results In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. Conclusions As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.

Editorial - Open Access and accessing openness

Directory of Open Access Journals (Sweden)

Yngve Nordkvelle

2008-12-01

Full Text Available Seminar.net enters it’s fourth year, and has reached a state of maturity in a number of meanings: it receives manuscripts from all continents, the articles are read from 134 countries, of which India represents the highest number of readers, a number of articles have been read by more than 10 000 interested persons, and the frequency of issues is now three per year, and will reach four by next year. Interested parties now approach us in order to learn about our policies and practices.It takes time to become established and influential in the sense that articles are cited and referred to in prestigious publications. Still, the most prestigious publications are on paper. Many countries now embark on a policy that rewards researchers that publish in international journals, preferably in English. National languages are rendered less significant. In the UK, the research assessment exercise (RAE, and several other countries with a publication or citation based reward system in research, tend to favour quantitative dimensions at the expense of the quality of the publication. International publishing houses are huge profit-making companies that over years have increased their profit rates, charging increasingly economically pressured higher education institution with high subscription rates. With the advent of electronic publishing their position is severely challenged. It has been noted that the most significant publication of the last couple of decades was an electronic publication: Tim Berners Lee published the protocol for the World Wide Web in 1990. It was never refereed, nor was controlled by appointed gatekeepers of the “establishment”. The number of Open Access publications is rising every day, and the number of e-journals for academic publishing is reaching higher and higher numbers. In a recent case The Faculty of Arts and Sciences at Harvard University decided, that Harvard employees must publish all their material simultaneously on the

Changes in protein patterns and in vivo protein synthesis during senescence of hibiscus petals

International Nuclear Information System (INIS)

Woodson, W.R.; Handa, A.K.

1986-01-01

Changes in proteins associated with senescence of the flowers of Hibiscus rosa-sinensis was studied using SDS-PAGE. Total extractable protein from petals decreased with senescence. Changes were noted in patterns of proteins from aging petals. Flower opening and senescence was associated with appearance and disappearance of several polypeptides. One new polypeptide with an apparent mw of 41 kd was first seen the day of flower opening and increased to over 9% of the total protein content of senescent petal tissue. Protein synthesis during aging was investigated by following uptake and incorporation of 3 H-leucine into TCA-insoluble fraction of petal discs. Protein synthesis, as evidenced by the percent of label incorporated into the TCA-insoluble fraction, was greatest (32%) the day before flower opening. Senescent petal tissue incorporated 4% of label taken up into protein. Proteins were separated by SDS-PAGE and labelled polypeptides identified by fluorography. In presenescent petal tissue, radioactivity was distributed among several major polypeptides. In senescent tissue, much of the radioactivity was concentrated in the 41 kd polypeptide

Connected text reading and differences in text reading fluency in adult readers.

Directory of Open Access Journals (Sweden)

Sebastian Wallot

Full Text Available The process of connected text reading has received very little attention in contemporary cognitive psychology. This lack of attention is in parts due to a research tradition that emphasizes the role of basic lexical constituents, which can be studied in isolated words or sentences. However, this lack of attention is in parts also due to the lack of statistical analysis techniques, which accommodate interdependent time series. In this study, we investigate text reading performance with traditional and nonlinear analysis techniques and show how outcomes from multiple analyses can used to create a more detailed picture of the process of text reading. Specifically, we investigate reading performance of groups of literate adult readers that differ in reading fluency during a self-paced text reading task. Our results indicate that classical metrics of reading (such as word frequency do not capture text reading very well, and that classical measures of reading fluency (such as average reading time distinguish relatively poorly between participant groups. Nonlinear analyses of distribution tails and reading time fluctuations provide more fine-grained information about the reading process and reading fluency.

The role of speech prosody and text reading prosody in children's reading comprehension.

Science.gov (United States)

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

2014-12-01

Text reading prosody has been associated with reading comprehension. However, text reading prosody is a reading-dependent measure that relies heavily on decoding skills. Investigation of the contribution of speech prosody - which is independent from reading skills - in addition to text reading prosody, to reading comprehension could provide more insight into the general role of prosody in reading comprehension. The current study investigates how much variance in reading comprehension scores is explained by speech prosody and text reading prosody, after controlling for decoding, vocabulary, and syntactic awareness. A battery of reading and language assessments was performed by 106 Dutch fourth-grade primary school children. Speech prosody was assessed using a storytelling task and text reading prosody by oral text reading performance. Decoding skills, vocabulary, syntactic awareness, and reading comprehension were assessed using standardized tests. Hierarchical regression analyses showed that text reading prosody explained 6% of variance and that speech prosody explained 8% of variance in reading comprehension scores, after controlling for decoding, vocabulary, and syntactic awareness. Phrasing was the significant factor in both speech and text reading. When added in consecutive order, phrasing in speech added 5% variance to phrasing in reading. In contrast, phrasing in reading added only 3% variance to phrasing in speech. The variance that speech prosody explained in reading comprehension scores should not be neglected. Speech prosody seems to facilitate the construction of meaning in written language. © 2014 The British Psychological Society.

Idea Sharing: The Use of Read-Share-Act to Promote Extensive Reading

Science.gov (United States)

Charumanee, Nisakorn

2014-01-01

Nisakorn Charumanee believes that a reading teacher has an active role in cultivating reading culture or reading habit and in activating students to "want" to read. One way to do this is to integrate extensive reading into the classroom (Day and Bamford, 1998; Bamford and Day, 2004) where extensive reading can be enhanced if the teacher…

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

Science.gov (United States)

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…

4 Massive Open Online Courses and How They Work

Science.gov (United States)

Gose, Ben

2012-01-01

Massive open online courses (MOOC's) are the latest development in online education. Over the past decade, millions of students have taken free online versions of existing courses at well-known universities like the Massachusetts Institute of Technology, but such courses often offered little more than reading lists and lecture notes. MOOC's are…

The Assessment of Reading Comprehension Difficulties for Reading Intervention

Science.gov (United States)

Woolley, Gary

2008-01-01

There are many environmental and personal factors that contribute to reading success. Reading comprehension is a complex interaction of language, sensory perception, memory, and motivational aspects. However, most existing assessment tools have not adequately reflected the complex nature of reading comprehension. Good assessment requires a…

Open access and the humanities contexts, controversies and the future

CERN Document Server

Eve, Martin Paul

2014-01-01

If you work in a university, you are almost certain to have heard the term 'open access' in the past couple of years. You may also have heard either that it is the utopian answer to all the problems of research dissemination or perhaps that it marks the beginning of an apocalyptic new era of 'pay-to-say' publishing. In this book, Martin Paul Eve sets out the histories, contexts and controversies for open access, specifically in the humanities. Broaching practical elements alongside economic histories, open licensing, monographs and funder policies, this book is a must-read for both those new to ideas about open-access scholarly communications and those with an already keen interest in the latest developments for the humanities.

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

Science.gov (United States)

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

2014-01-01

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

To read or not to read

NARCIS (Netherlands)

Mol, Suzanne Elizabeth

2010-01-01

There is a widely held belief that reading (story)books makes us smarter and helps promote success in life. Does scientific evidence support this notion? The three meta-analyses in this thesis comprise 146 studies between 1988 and 2010 (N=10,308 participants) that addressed the role of book reading

Teachers’ beliefs about reading and use of reading strategies

OpenAIRE

VASILIKA RRAKU

2014-01-01

The aim of this article is to place the focus on teachers’ beliefs about reading and reading strategies to the purpose of emphasizing the im portance of reading strategies in the reading process. The method of study is analytic analysis of teachers’ beliefs obtained through ques tionnaires delivered to 18 English language teachers of elementary, secondary and high level education in the region of Saranda in lbania. The results of the study pointed to a great concordance between teach ers’ bel...

Teaching Vocabulary and Reading in An College:A Literature Review

Institute of Scientific and Technical Information of China (English)

华一君

2016-01-01

This paper is structured into three parts: 1) a description of the of English competence of“self-taught”students in Open College of Guangdong University of Foreign Studies;2) a systematic literature review on relevant topics to explain and provide guidance to see into the problems;3) a summary of research findings and inspiration from the literature review and tenta-tive suggestions for reading learning and teaching.

Science Language Accommodation in Elementary School Read-Alouds

Science.gov (United States)

Glass, Rory; Oliveira, Alandeom W.

2014-03-01

This study examines the pedagogical functions of accommodation (i.e. provision of simplified science speech) in science read-aloud sessions facilitated by five elementary teachers. We conceive of read-alouds as communicative events wherein teachers, faced with the task of orally delivering a science text of relatively high linguistic complexity, open up an alternate channel of communication, namely oral discussion. By doing so, teachers grant students access to a simplified linguistic input, a strategy designed to promote student comprehension of the textual contents of children's science books. It was found that nearly half (46%) of the read-aloud time was allotted to discussions with an increased percentage of less sophisticated words and reduced use of more sophisticated vocabulary than found in the books through communicative strategies such as simplified rewording, simplified definition, and simplified questioning. Further, aloud reading of more linguistically complex books required longer periods of discussion and an increased degree of teacher oral input and accommodation. We also found evidence of reversed simplification (i.e. sophistication), leading to student uptake of scientific language. The main significance of this study is that it reveals that teacher talk serves two often competing pedagogical functions (accessible communication of scientific information to students and promotion of student acquisition of the specialized language of science). It also underscores the importance of giving analytical consideration to the simplification-sophistication dimension of science classroom discourse as well as the potential of computer-based analysis of classroom discourse to inform science teaching.

A comparative analysis of minimally invasive and open spine surgery patient education resources.

Science.gov (United States)

Agarwal, Nitin; Feghhi, Daniel P; Gupta, Raghav; Hansberry, David R; Quinn, John C; Heary, Robert F; Goldstein, Ira M

2014-09-01

The Internet has become a widespread source for disseminating health information to large numbers of people. Such is the case for spine surgery as well. Given the complexity of spinal surgeries, an important point to consider is whether these resources are easily read and understood by most Americans. The average national reading grade level has been estimated to be at about the 7th grade. In the present study the authors strove to assess the readability of open spine surgery resources and minimally invasive spine surgery resources to offer suggestions to help improve the readability of patient resources. Online patient education resources were downloaded in 2013 from 50 resources representing either traditional open back surgery or minimally invasive spine surgery. Each resource was assessed using 10 scales from Readability Studio Professional Edition version 2012.1. Patient education resources representing traditional open back surgery or minimally invasive spine surgery were all found to be written at a level well above the recommended 6th grade level. In general, minimally invasive spine surgery materials were written at a higher grade level. The readability of patient education resources from spine surgery websites exceeds the average reading ability of an American adult. Revisions may be warranted to increase quality and patient comprehension of these resources to effectively reach a greater patient population.

Protein sensing by nanofluidic crystal and its signal enhancement

Science.gov (United States)

Sang, Jianming; Du, Hongtan; Wang, Wei; Chu, Ming; Wang, Yuedan; Li, Haichao; Alice Zhang, Haixia; Wu, Wengang; Li, Zhihong

2013-01-01

Nanofluidics has a unique property that ionic conductance across a nanometer-sized confined space is strongly affected by the space surface charge density, which can be utilized to construct electrical read-out biosensor. Based on this principle, this work demonstrated a novel protein sensor along with a sandwich signal enhancement approach. Nanoparticles with designed aptamer onside are assembled in a suspended micropore to form a 3-dimensional network of nanometer-sized interstices, named as nanofluidic crystal hereafter, as the basic sensing unit. Proteins captured by aptamers will change the surface charge density of nanoparticles and thereby can be detected by monitoring the ionic conductance across this nanofluidic crystal. Another aptamer can further enlarge the variations of the surface charge density by forming a sandwich structure (capturing aptamer/protein/signal enhancement aptamer) and the read-out conductance as well. The preliminary experimental results indicated that human α-thrombin was successfully detected by the corresponding aptamer modified nanofluidic crystal with the limit of detection of 5 nM (0.18 μg/ml) and the read-out signal was enhanced up to 3 folds by using another thrombin aptamer. Being easy to graft probe, facile and low-cost to prepare the nano-device, and having an electrical read-out, the present nanofluidic crystal scheme is a promising and universal strategy for protein sensing. PMID:24404017

A filtering method to generate high quality short reads using illumina paired-end technology.

Science.gov (United States)

Eren, A Murat; Vineis, Joseph H; Morrison, Hilary G; Sogin, Mitchell L

2013-01-01

Consensus between independent reads improves the accuracy of genome and transcriptome analyses, however lack of consensus between very similar sequences in metagenomic studies can and often does represent natural variation of biological significance. The common use of machine-assigned quality scores on next generation platforms does not necessarily correlate with accuracy. Here, we describe using the overlap of paired-end, short sequence reads to identify error-prone reads in marker gene analyses and their contribution to spurious OTUs following clustering analysis using QIIME. Our approach can also reduce error in shotgun sequencing data generated from libraries with small, tightly constrained insert sizes. The open-source implementation of this algorithm in Python programming language with user instructions can be obtained from https://github.com/meren/illumina-utils.

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.

Science.gov (United States)

Quintales, Luis; Soriano, Ignacio; Vázquez, Enrique; Segurado, Mónica; Antequera, Francisco

2015-04-01

Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition.

Multicultural Reading

Science.gov (United States)

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…

TEACHER CANDIDATES’ VIEWS ON E-BOOKS AND SCREEN READING

OpenAIRE

Nevin AKKAYA

2015-01-01

Today, it is a necessity to make use of information technologies in creating, distributing and accessing information resources. The electronic resources as products of the developing information technologies include bibliographical text databases, e-journals, e-books, open achieves and web sites. Today, Many printed material can be accesssed by electronically in readers. Furthermore, e-books have been increasingly preferred as a mode of reading because of its advantages such as portability, s...

SchemaOnRead: A Package for Schema-on-Read in R

Energy Technology Data Exchange (ETDEWEB)

North, Michael J.

2016-08-01

Schema-on-read is an agile approach to data storage and retrieval that defers investments in data organization until production queries need to be run by working with data directly in native form. Schema-on-read functions have been implemented in a wide range of analytical systems, most notably Hadoop. SchemaOnRead is a CRAN package that uses R’s flexible data representations to provide transparent and convenient support for the schema-on-read paradigm in R. The schema-on- read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info, Pajek network, R network, HTML, SPSS, Systat, and Stata files. The provided tools can be used as-is or easily adapted to implement customized schema-on-read tool chains in R. This paper’s contribution is that it introduces and describes SchemaOnRead, the first R package specifically focused on providing explicit schema-on-read support in R.

Examining Associations between Reading Motivation and Inference Generation beyond Reading Comprehension Skill

Science.gov (United States)

Clinton, Virginia

2015-01-01

The purpose of this study was to examine the associations between reading motivation and inference generation while reading. Undergraduate participants (N = 69) read two science articles while thinking aloud, completed a standardized reading comprehension assessment, and self reported their habitual reading motivation. Findings indicate that…

Earth observation open science and innovation

CERN Document Server

Aubrecht, Christoph

2018-01-01

This book is published open access under a CC BY 4.0 license. Over  the  past  decades,  rapid developments in digital and sensing technologies, such  as the Cloud, Web and Internet of Things, have dramatically changed the way we live and work. The digital transformation is revolutionizing our ability to monitor our planet and transforming the  way we access, process and exploit Earth Observation data from satellites. This book reviews these megatrends and their implications for the Earth Observation community as well as the wider data economy. It provides insight into new paradigms of Open Science and Innovation applied to space data, which are characterized by openness, access to large volume of complex data, wide availability of new community tools, new techniques for big data analytics such as Artificial Intelligence, unprecedented level of computing power, and new types of collaboration among researchers, innovators, entrepreneurs and citizen scientists. In addition, this book aims to provide reade...

Reading Amount as a Mediator of the Effects of Intrinsic and Extrinsic Reading Motivation on Reading Comprehension

Science.gov (United States)

Schaffner, Ellen; Schiefele, Ulrich; Ulferts, Hannah

2013-01-01

This study examined the role of reading amount as a mediator of the effects of intrinsic and extrinsic reading motivation on higher order reading comprehension (comprised of paragraph-and passage-level comprehension) in a sample of 159 fifth-grade elementary students. A positive association between intrinsic reading motivation and reading amount…

The relationship between different measures of oral reading fluency and reading comprehension in second-grade students who evidence different oral reading fluency difficulties.

Science.gov (United States)

Wise, Justin C; Sevcik, Rose A; Morris, Robin D; Lovett, Maureen W; Wolf, Maryanne; Kuhn, Melanie; Meisinger, Beth; Schwanenflugel, Paula

2010-07-01

The purpose of this study was to examine whether different measures of oral reading fluency relate differentially to reading comprehension performance in two samples of second-grade students: (a) students who evidenced difficulties with nonsense-word oral reading fluency, real-word oral reading fluency, and oral reading fluency of connected text (ORFD), and (b) students who evidenced difficulties only with oral reading fluency of connected text (CTD). Participants (ORFD, n = 146 and CTD, n = 949) were second-grade students who were recruited for participation in different reading intervention studies. Data analyzed were from measures of nonsense-word oral reading fluency, real-word oral reading fluency, oral reading fluency of connected text, and reading comprehension that were collected at the pre-intervention time point. Correlational and path analyses indicated that real-word oral reading fluency was the strongest predictor of reading comprehension performance in both samples and across average and poor reading comprehension abilities. Results of this study indicate that real-word oral reading fluency was the strongest predictor of reading comprehension and suggest that real-word oral reading fluency may be an efficient method for identifying potential reading comprehension difficulties.

Reading motivation, reading amount, and text comprehension in deaf and hearing adults.

Science.gov (United States)

Parault, Susan J; Williams, Heather M

2010-01-01

The purpose of this study is to examine the relationship between the variables of reading motivation, reading amount, and text comprehension in deaf and hearing adults. Research has shown that less than 50% of deaf students leave high school reading at or above a fourth-grade level (Allen, 1994). Our question is, how does this affect the levels of reading motivation and amount of reading in which deaf adults engage? Assessments of 30 hearing and 24 deaf adults showed that deaf participants reported significantly higher levels of reading motivation despite having been found to read at less than a sixth-grade level. No significant difference in the amount of reading between hearing and deaf adults was found. Amount of reading for personal reasons was found to be the best predictor of text comprehension in the deaf participants, and intrinsic motivation was found to be the best predictor of amount of reading in the deaf participants.

An investigation of Chinese university EFL learner’s foreign language reading anxiety, reading strategy use and reading comprehension performance

OpenAIRE

Zhongshe Lu; Meihua Liu

2015-01-01

The present study explored the interrelations between foreign language (FL) reading anxiety, FL reading strategy use and their interactive effect on FL reading comprehension performance at the tertiary level in China. Analyses of the survey data collected from 1702 university students yielded the following results: (a) Both Foreign Language Reading Anxiety Scale (FLRAS) and Foreign Language Reading Strategy Use Scale (FLRSUS) had important subcomponents, (b) more than half of the stu...

Neural Signatures of the Reading-Writing Connection: Greater Involvement of Writing in Chinese Reading than English Reading.

Science.gov (United States)

Cao, Fan; Perfetti, Charles A

2016-01-01

Research on cross-linguistic comparisons of the neural correlates of reading has consistently found that the left middle frontal gyrus (MFG) is more involved in Chinese than in English. However, there is a lack of consensus on the interpretation of the language difference. Because this region has been found to be involved in writing, we hypothesize that reading Chinese characters involves this writing region to a greater degree because Chinese speakers learn to read by repeatedly writing the characters. To test this hypothesis, we recruited English L1 learners of Chinese, who performed a reading task and a writing task in each language. The English L1 sample had learned some Chinese characters through character-writing and others through phonological learning, allowing a test of writing-on-reading effect. We found that the left MFG was more activated in Chinese than English regardless of task, and more activated in writing than in reading regardless of language. Furthermore, we found that this region was more activated for reading Chinese characters learned by character-writing than those learned by phonological learning. A major conclusion is that writing regions are also activated in reading, and that this reading-writing connection is modulated by the learning experience. We replicated the main findings in a group of native Chinese speakers, which excluded the possibility that the language differences observed in the English L1 participants were due to different language proficiency level.

Neural Signatures of the Reading-Writing Connection: Greater Involvement of Writing in Chinese Reading than English Reading.

Directory of Open Access Journals (Sweden)

Fan Cao

Full Text Available Research on cross-linguistic comparisons of the neural correlates of reading has consistently found that the left middle frontal gyrus (MFG is more involved in Chinese than in English. However, there is a lack of consensus on the interpretation of the language difference. Because this region has been found to be involved in writing, we hypothesize that reading Chinese characters involves this writing region to a greater degree because Chinese speakers learn to read by repeatedly writing the characters. To test this hypothesis, we recruited English L1 learners of Chinese, who performed a reading task and a writing task in each language. The English L1 sample had learned some Chinese characters through character-writing and others through phonological learning, allowing a test of writing-on-reading effect. We found that the left MFG was more activated in Chinese than English regardless of task, and more activated in writing than in reading regardless of language. Furthermore, we found that this region was more activated for reading Chinese characters learned by character-writing than those learned by phonological learning. A major conclusion is that writing regions are also activated in reading, and that this reading-writing connection is modulated by the learning experience. We replicated the main findings in a group of native Chinese speakers, which excluded the possibility that the language differences observed in the English L1 participants were due to different language proficiency level.

Isolation and expression of the genes coding for the membrane bound transglycosylase B (MltB and the transferrin binding protein B (TbpB of the salmon pathogen Piscirickettsia salmonis

Directory of Open Access Journals (Sweden)

VIVIAN WILHELM

2004-01-01

Full Text Available We have isolated and sequenced the genes encoding the membrane bound transglycosylase B (MltB and the transferring binding protein B (TbpB of the salmon pathogen Piscirickettsia salmonis. The results of the sequence revealed two open reading frames that encode proteins with calculated molecular weights of 38,830 and 85,140. The deduced aminoacid sequences of both proteins show a significant homology to the respective protein from phylogenetically related microorganisms. Partial sequences coding the amino and carboxyl regions of MltB and a sequence of 761 base pairs encoding the amino region of TbpB have been expressed in E. coli. The strong humoral response elicited by these proteins in mouse confirmed the immunogenic properties of the recombinant proteins. A similar response was elicited by both proteins when injected intraperitoneally in Atlantic salmon. The present data indicates that these proteins are good candidates to be used in formulations to study the protective immunity of salmon to infection by P. salmonis.

Analysis of the Sarcocystis neurona microneme protein SnMIC10: protein characteristics and expression during intracellular development.

Science.gov (United States)

Hoane, Jessica S; Carruthers, Vernon B; Striepen, Boris; Morrison, David P; Entzeroth, Rolf; Howe, Daniel K

2003-07-01

Sarcocystis neurona, an apicomplexan parasite, is the primary causative agent of equine protozoal myeloencephalitis. Like other members of the Apicomplexa, S. neurona zoites possess secretory organelles that contain proteins necessary for host cell invasion and intracellular survival. From a collection of S. neurona expressed sequence tags, we identified a sequence encoding a putative microneme protein based on similarity to Toxoplasma gondii MIC10 (TgMIC10). Pairwise sequence alignments of SnMIC10 to TgMIC10 and NcMIC10 from Neospora caninum revealed approximately 33% identity to both orthologues. The open reading frame of the S. neurona gene encodes a 255 amino acid protein with a predicted 39-residue signal peptide. Like TgMIC10 and NcMIC10, SnMIC10 is predicted to be hydrophilic, highly alpha-helical in structure, and devoid of identifiable adhesive domains. Antibodies raised against recombinant SnMIC10 recognised a protein band with an apparent molecular weight of 24 kDa in Western blots of S. neurona merozoites, consistent with the size predicted for SnMIC10. In vitro secretion assays demonstrated that this protein is secreted by extracellular merozoites in a temperature-dependent manner. Indirect immunofluorescence analysis of SnMIC10 showed a polar labelling pattern, which is consistent with the apical position of the micronemes, and immunoelectron microscopy provided definitive localisation of the protein to these secretory organelles. Further analysis of SnMIC10 in intracellular parasites revealed that expression of this protein is temporally regulated during endopolygeny, supporting the view that micronemes are only needed during host cell invasion. Collectively, the data indicate that SnMIC10 is a microneme protein that is part of the excreted/secreted antigen fraction of S. neurona. Identification and characterisation of additional S. neurona microneme antigens and comparisons to orthologues in other Apicomplexa could provide further insight into the

Reading Approach Use Effectiveness And EFL Reading Comprehension In University Muhammadiyah Of Parepare

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Baharuddin

2017-10-01

Full Text Available This study investigated Indonesian EFL learners approach of two reading approaches cognitive and metacognitive their perceived contact on effectiveness and the association between reading approach and effectiveness on their English reading comprehension. Fifty-Three English-major freshmen from University Muhammadiyah of Parepare participated in these lessons. Two principal questions were addressed 1 what is the most frequent use of reading approach reported by individual students 2 Is there any significant association between reading approach and effectiveness on their English reading comprehension To examine the effects of approach instruction on students reading performance a qualitative interview technique and quantitative research methods including a paired-sample t-test and Person Product Moment Correlation were used to estimate the relationship between reading approach use and effectiveness on students reading accomplishment. Significance showed that the most frequent use of reading approach was found to be metacognitive approach followed by the cognitive approach. In addition there was a significant positive connection between reading approach and effectiveness on their English reading comprehension. Reading approach on the other hand was unrelated to reading achievement. Results of interview findings were analyzed to explore in-depth in sequence about the condition of approach used. The implications of these findings for implementing effective reading strategy instruction are discussed.

Pupil's motivation in the 3. grades for required reading and The Reading Badge

OpenAIRE

Logar, Renata

2013-01-01

Reading is extremely important for pupils and their development. The pupil with reading habits riches his vocabulary and gaining knowledge. On the other hand the pupil through reading entry into the world of imagination and stories. Major role in motivating students to read have parents and teachers. In this graduation thesis I was interested in how third grade teachers motivate their pupils to read. In doing so, I was focused mainly to reading for required reading and The Reading Badge. ...

COLLABORATIVE STRATEGIC READING IMPLEMENTATION TO IMPROVE STUDENTS’ READING COMPREHENSION

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Desy Olivia Riani

2013-01-01

Full Text Available This collaborative action research is aimed to find out whether or not the implementation of Collaborative Strategic Reading (CSR improves students' reading comprehension and also to identify students' attitude towards the implementation of CSR. CSR is reading strategy that employs four strategies namely Preview, Click and Clunk, Get the Gist and Wrap Up during students’ cooperative learning. A class of eleventh grade students of a public senior high school in Majalengka, West Java, Indonesia is participated as the participant of the study. The required data were collected through the use of questionnaire, observation checklist, and reading test. The data from the questionnaire indicated that 82% students had positive attitude toward the implementation of CSR. They feel that CSR improves their motivation in learning English and CSR brings more fun to the process of learning. Moreover, it was found from observation data that the students were actively participated during CSR implementation and they were motivated when comprehending a text by means CSR strategy. Finally, the study proved that CSR improved students’ reading comprehension. Students’ mean score of reading test in the beginning of the study was 67, meanwhile, after applying CSR as reading strategy, their mean scores improved to 88.

Iowa City Reads! The Reading Event Worth Shouting About.

Science.gov (United States)

Donham van Deusen, Jean; Langhorne, Mary Jo

1997-01-01

Describes the Community Reading Month (CRM) initiative in Iowa City, Iowa; its goals are to promote the value of reading and to build a sense of community. Topics include the development of CRM, increased reading scores of Iowa City's elementary school students, activities for people of all ages, and planning and evaluation. (AEF)

A macrophage inflammatory protein homolog encoded by guinea pig cytomegalovirus signals via CC chemokine receptor 1

International Nuclear Information System (INIS)

Penfold, Mark; Miao Zhenhua; Wang Yu; Haggerty, Shannon; Schleiss, Mark R.

2003-01-01

Cytomegaloviruses encode homologs of cellular immune effector proteins, including chemokines (CKs) and CK receptor-like G protein-coupled receptors (GPCRs). Sequence of the guinea pig cytomegalovirus (GPCMV) genome identified an open reading frame (ORF) which predicted a 101 amino acid (aa) protein with homology to the macrophage inflammatory protein (MIP) subfamily of CC (β) CKs, designated GPCMV-MIP. To assess functionality of this CK, recombinant GPCMV-MIP was expressed in HEK293 cells and assayed for its ability to bind to and functionally interact with a variety of GPCRs. Specific signaling was observed with the hCCR1 receptor, which could be blocked with hMIP -1α in competition experiments. Migration assays revealed that GPCMV-MIP was able to induce chemotaxis in hCCR1-L1.2 cells. Antisera raised against a GST-MIP fusion protein immunoprecipitated species of ∼12 and 10 kDa from GPCMV-inoculated tissue culture lysates, and convalescent antiserum from GPCMV-infected animals was immunoreactive with GST-MIP by ELISA assay. These results represent the first substantive in vitro characterization of a functional CC CK encoded by a cytomegalovirus

Reading Self-Efficacy Predicts Word Reading But Not Comprehension in Both Girls and Boys.

Science.gov (United States)

Carroll, Julia M; Fox, Amy C

2016-01-01

The relationship between cognitive skills and reading has been well-established. However, the role of motivational factors such as self-efficacy in reading progress is less clear. In particular, it is not clear how self-efficacy relates to word level reading versus comprehension, and whether this differs in boys and girls. This study examines the relationship between self-efficacy, word reading and reading comprehension across the range of reading abilities after controlling for reading-related cognitive factors. One hundred and seventy nine children (86 males and 93 females) between 8 and 11 years old completed a self-report measure of reading self-efficacy together with measures of reading comprehension and word reading, working memory, auditory short-term memory, phonological awareness, and vocabulary. Boys and girls showed similar levels of attainment and reading self-efficacy. Reading self-efficacy was associated with word reading, but not with reading comprehension in either boys or girls. It is argued that this may reflect important differences between reading self-efficacy and more general measures of reading motivation and engagement. Reading self-efficacy is an element of reading motivation that is closely associated with a child's perceived attainments in reading and is less susceptible to the gender differences seen in broader measures.

Reading Self-Efficacy Predicts Word Reading But Not Comprehension in Both Girls and Boys

Science.gov (United States)

Carroll, Julia M.; Fox, Amy C.

2017-01-01

The relationship between cognitive skills and reading has been well-established. However, the role of motivational factors such as self-efficacy in reading progress is less clear. In particular, it is not clear how self-efficacy relates to word level reading versus comprehension, and whether this differs in boys and girls. This study examines the relationship between self-efficacy, word reading and reading comprehension across the range of reading abilities after controlling for reading-related cognitive factors. One hundred and seventy nine children (86 males and 93 females) between 8 and 11 years old completed a self-report measure of reading self-efficacy together with measures of reading comprehension and word reading, working memory, auditory short-term memory, phonological awareness, and vocabulary. Boys and girls showed similar levels of attainment and reading self-efficacy. Reading self-efficacy was associated with word reading, but not with reading comprehension in either boys or girls. It is argued that this may reflect important differences between reading self-efficacy and more general measures of reading motivation and engagement. Reading self-efficacy is an element of reading motivation that is closely associated with a child’s perceived attainments in reading and is less susceptible to the gender differences seen in broader measures. PMID:28144223

Metacognitive Reading Strategies, Motivation, and Reading Comprehension Performance of Saudi EFL Students

Science.gov (United States)

Meniado, Joel C.

2016-01-01

Metacognitive reading strategies and reading motivation play a significant role in enhancing reading comprehension. In an attempt to prove the foregoing claim in a context where there is no strong culture for reading, this study tries to find out if there is indeed a relationship between and among metacognitive reading strategies, reading…

Reading Fluency and Students with Reading Disabilities: How Fast Is Fast Enough to Promote Reading Comprehension?

Science.gov (United States)

O'Connor, Rollanda E.

2018-01-01

The goal of improving reading rate and fluency is to positively impact reading comprehension; however, it is unclear how fast students with learning disabilities (LD) need to read to reap this benefit. The purpose of this research was to identify the point of diminishing return for students who were dysfluent readers. Participants included 337…

TRIM45, a novel human RBCC/TRIM protein, inhibits transcriptional activities of ElK-1 and AP-1

International Nuclear Information System (INIS)

Wang Yuequn; Li Yongqing; Qi Xinzhu; Yuan Wuzhou; Ai Jianping; Zhu Chuanbing; Cao Lei; Yang Hong; Liu Fang; Wu Xiushan; Liu Mingyao

2004-01-01

The tripartite motif (TRIM) proteins play important roles in a variety of cellular functions including cell proliferation, differentiation, development, oncogenesis, and apoptosis. In this study, we report the identification and characterization of the human tripartite motif-containing protein 45 (TRIM45), a novel member of the TRIM family, from a human embryonic heart cDNA library. TRIM45 has a predicted 580 amino acid open reading frame, encoding a putative 64-kDa protein. The N-terminal region harbors a RING finger, two B-boxes, and a predicted α-helical coiled-coil domain, which together form the RBCC/TRIM motif found in a large family of proteins, whereas the C-terminal region contains a filamin-type immunoglobulin (IG-FLMN) domain. Northern blot analysis indicates that TRIM45 is expressed in a variety of human adult and embryonic tissues. In the cell, TRIM45 protein is expressed both in cytoplasm and in cell nucleus. Overexpression of TRIM45 in COS-7 cells inhibits the transcriptional activities of ElK-1 and AP-1. These results suggest that TRIM45 may act as a new transcriptional repressor in mitogen-activated protein kinase signaling pathway

Translational profiling of B cells infected with the Epstein-Barr virus reveals 5' leader ribosome recruitment through upstream open reading frames.

Science.gov (United States)

Bencun, Maja; Klinke, Olaf; Hotz-Wagenblatt, Agnes; Klaus, Severina; Tsai, Ming-Han; Poirey, Remy; Delecluse, Henri-Jacques

2018-04-06

The Epstein-Barr virus (EBV) genome encodes several hundred transcripts. We have used ribosome profiling to characterize viral translation in infected cells and map new translation initiation sites. We show here that EBV transcripts are translated with highly variable efficiency, owing to variable transcription and translation rates, variable ribosome recruitment to the leader region and coverage by monosomes versus polysomes. Some transcripts were hardly translated, others mainly carried monosomes, showed ribosome accumulation in leader regions and most likely represent non-coding RNAs. A similar process was visible for a subset of lytic genes including the key transactivators BZLF1 and BRLF1 in cells infected with weakly replicating EBV strains. This suggests that ribosome trapping, particularly in the leader region, represents a new checkpoint for the repression of lytic replication. We could identify 25 upstream open reading frames (uORFs) located upstream of coding transcripts that displayed 5' leader ribosome trapping, six of which were located in the leader region shared by many latent transcripts. These uORFs repressed viral translation and are likely to play an important role in the regulation of EBV translation.

The Relationship between Strategic Reading Instruction, Student Learning of L2-Based Reading Strategies and L2 Reading Achievement

Science.gov (United States)

Akkakoson, Songyut

2013-01-01

This study investigates the relationship between strategic reading instruction, the process of learning second language-based reading strategies and English reading achievement for Thai university students of science and technology. In a course in reading general English texts for 16?weeks, 82 students were taught using a strategies-based approach…

Reading Societies and their Social Exclusivity: Dalmatia in the First Half of the 19th century

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Jelena Lakuš

2009-04-01

Full Text Available Reading societies, known as the gabinetto di lettura, or the casino, appeared in Dalmatia in the middle of the 18th century modelled on their Western European, North Italian and Austrian counterparts. They became centres of social and cultural life in the region. However, their number was very small in comparison with other Central and Western European countries. In spite of that, their statutes can serve a historian as very fertile and useful historical sources. First of all, they can reveal the importance given to books and reading as well as changing attitude towards reading in the course of time. They can also indicate social structure of the reading circles as well as the interaction and communication among the members. In addition, they can reveal the participation of women in social and cultural life, internal functioning of the society, etc. Based on the statutes of several reading societies of the 19th century, this work suggests several important issues. First, it shows that in the first half of the 19th century the membership of these societies was still select and prestigious, acquired by position on the social scale. In other words, reading societies were still confined to very narrow social circles of the educated. Although in Western parts of Europe the reading public became more heterogeneous and open, in Dalmatia reading still preserved its exclusive features. Second, the work also suggests that what some historians of book and reading called the ”reading revolution” or ”revolution in reading” occurred in Dalmatia much later, and even then mostly in urban areas. Some changes in reading habits occurred in the region, albeit to a limited extent and with less influence on society as a whole. Third, the work also demonstrates that from the 1840s reading acquired a new dimension, becoming open to the more social strata and gradually losing its exclusive character. The reading societies, lending libraries and other cultural

Expression of a hantavirus N protein and its efficacy as antigen in immune assays

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L.T.M. Figueiredo

2008-07-01

Full Text Available Hantavirus cardiopulmonary syndrome (HCPS has been recognized as an important public heath problem. Five hantaviruses associated with HCPS are currently known in Brazil: Juquitiba, Araraquara, Laguna Negra-like, Castelo dos Sonhos, and Anajatuba viruses. The laboratory diagnosis of HCPS is routinely carried out by the detection of anti-hantavirus IgM and/or IgG antibodies. The present study describes the expression of the N protein of a hantavirus detected in the blood sample of an HCPS patient. The entire S segment of the virus was amplified and found to be 1858 nucleotides long, with an open reading frame of 1287 nucleotides that encodes a protein of 429 amino acids. The nucleotide sequence described here showed a high identity with the N protein gene of Araraquara virus. The entire N protein was expressed using the vector pET200D and the Escherichia coli BL21 strain. The expression of the recombinant protein was confirmed by the detection of a 52-kDa protein by Western blot using a pool of human sera obtained from HCPS patients, and by specific IgG detection in five serum samples of HCPS patients tested by ELISA. These results suggest that the recombinant N protein could be used as an antigen for the serological screening of hantavirus infection.

The Effect of Modified Collaborative Strategic Reading on EFL Learners' Reading Anxiety

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Shabnam Abbasnezhad

2016-12-01

Full Text Available The present study was an attempt to investigate the effectiveness of reading instructional approach called MCSR- Modified Collaborative Strategic Reading on reducing intermediate EFL learner's reading anxiety. Based on a pretest-posttest design, MCSR was implemented with 64 EFL learners at intermediate level. They received EFL reading instruction according to MCSR over two and a half months. A questionnaire called English as a Foreign Language Reading Anxiety Inventory EFLRAI was group-administered atthepretest and the posttest. Quantitative results indicated that participating students demonstrated significant gains in reducing reading anxiety. This study highlighted our understanding by considering the effectiveness of MCSR program and also it elaborated the effects of using strategies like MCSR in overcoming the big problem of reading anxiety among EFL learners as non-native students. And teachers changed the focus of attention from using traditional methods for teaching the essential skill of reading to modern programs like MCSR in order to remove their students' anxiety and stress in reading.

The Effect of Baby Books on Mothers’ Reading Beliefs and Reading Practices

Science.gov (United States)

Auger, Anamarie; Reich, Stephanie M.; Penner, Emily K.

2014-01-01

The impact of a baby book intervention on promoting positive reading beliefs and increasing reading frequency for low-income, new mothers (n = 167) was examined. The Baby Books Project randomly assigned low-income, first-time mothers to one of three study conditions, receiving educational books, non-educational books, or no books, during pregnancy and over the first year of parenthood. Home-based data collection occurred through pregnancy until 18 months post-partum. Mothers who received free baby books had higher beliefs about the importance of reading, the value of having resources to support reading, and the importance of verbal participation during reading. The results showed that providing any type of baby books to mothers positively influenced maternal reading beliefs, but did not increase infant-mother reading practices. Maternal reading beliefs across all three groups were significantly associated with self-reported reading frequency when children were at least 12 months of age. PMID:25264394

Specificities and pH profiles of adenine and hypoxanthine-guanine-xanthine phosphoribosyltransferases (nucleotide synthases) of the thermoacidophile archaeon Sulfolobus solfataricus

DEFF Research Database (Denmark)

Hansen, Michael Riis; Jensen, Kristine Steen; Rasmussen, Mads Skytte

2014-01-01

Two open reading frames in the genome of Sulfolobus solfataricus (SSO2341 and SSO2424) were cloned and expressed in E. coli. The protein products were purified and their enzymatic activity characterized. Although SSO2341 was annotated as a gene (gpT-1) encoding a 6-oxopurine...... phosphoribosyltransferase (PRTase), the protein product turned out to be a PRTase highly specific for adenine and we suggest that the reading frame should be renamed apT. The other reading frame SSO2424 (gpT-2) proved to be a true 6-oxopurine PRTase active with hypoxanthine, xanthine and guanine as substrates, and we.......5, while maximal activity with xanthine was observed at pH 7.5. We discuss likely reasons why SSO2341 in S. solfataricus and similar open reading frames in other Crenarchaeota could not be identified as genes encoding APRTase....

TPA-inducible proteins may account for sensitivity to promotion of transformation

International Nuclear Information System (INIS)

Hirano, K.; Smith, B.; Colburn, N.H.

1986-01-01

The preneoplastic JB6 mouse epidermal cell system includes cell lines sensitive (P + ) or resistant (P - ) to tumor promoter induced neoplastic transformation. The authors investigated whether a difference in TPA-inducible proteins may explain this differential sensitivity. The synthesis of a 39 Kd cytoplasmic protein (Major Excreted Protein) was TPA-inducible, but to a similar extent in both P + and P - cells. TPA stimulated phosphorylation but not synthesis of the previously described stress protein pp80 in both P + and P - cells from 1 to 5 hr after treatment. Pulse labelling of P + and P - cells with 35 S-methionine revealed a TPA dependent P + specific transient increase in the synthesis of 58Kd protein. Induction was observed at 1 hr, and returned to basal levels by 4 hr and 20 hr, in nuclear and cytoplasmic fractions, respectively. This protein is not phosphorylated in response to TPA treatment. P + cells differ from P - cells in one or more genes that specify sensitivity to promotion of transformation, designated pro genes. Antibodies to three peptides representing the pro-1 open reading frame were used in immunoprecipitation and Western blotting to isolate the pro-1 gene product. A 43 Kd protein was immunologically responsive to the pro-1 peptide antibodies, and showed an increased signal 40 min after TPA treatment. Since the predicted molecular weight of a pro-1 gene product is only 7 Kd, the possibility of a modification of the protein by poly(ADP-ribosylation) or glycosylation is being investigated

Rcount: simple and flexible RNA-Seq read counting.

Science.gov (United States)

Schmid, Marc W; Grossniklaus, Ueli

2015-02-01

Analysis of differential gene expression by RNA sequencing (RNA-Seq) is frequently done using feature counts, i.e. the number of reads mapping to a gene. However, commonly used count algorithms (e.g. HTSeq) do not address the problem of reads aligning with multiple locations in the genome (multireads) or reads aligning with positions where two or more genes overlap (ambiguous reads). Rcount specifically addresses these issues. Furthermore, Rcount allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA-coding genes) or to add flanking regions. Rcount provides a fast and easy-to-use graphical user interface requiring no command line or programming skills. It is implemented in C++ using the SeqAn (www.seqan.de) and the Qt libraries (qt-project.org). Source code and 64 bit binaries for (Ubuntu) Linux, Windows (7) and MacOSX are released under the GPLv3 license and are freely available on github.com/MWSchmid/Rcount. marcschmid@gmx.ch Test data, genome annotation files, useful Python and R scripts and a step-by-step user guide (including run-time and memory usage tests) are available on github.com/MWSchmid/Rcount. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Molecular cloning and protein structure of a human blood group Rh polypeptide

International Nuclear Information System (INIS)

Cherif-Zahar, B.; Bloy, C.; Le Van Kim, C.; Blanchard, D.; Bailly, P.; Hermand, P.; Salmon, C.; Cartron, J.P.; Colin, Y.

1990-01-01

cDNA clones encoding a human blood group Rh polypeptide were isolated from a human bone marrow cDNA library by using a polymerase chain reaction-amplified DNA fragment encoding the known common N-terminal region of the Rh proteins. The entire primary structure of the Rh polypeptide has been deduced from the nucleotide sequence of a 1384-base-pair-long cDNA clone. Translation of the open reading frame indicates that the Rh protein is composed of 417 amino acids, including the initiator methionine, which is removed in the mature protein, lacks a cleavable N-terminal sequence, and has no consensus site for potential N-glycosylation. The predicted molecular mass of the protein is 45,500, while that estimated for the Rh protein analyzed in NaDodSO 4 /polyacrylamide gels is in the range of 30,000-32,000. These findings suggest either that the hydrophobic Rh protein behaves abnormally on NaDodSO 4 gels or that the Rh mRNA may encode a precursor protein, which is further matured by a proteolytic cleavage of the C-terminal region of the polypeptide. Hydropathy analysis and secondary structure predictions suggest the presence of 13 membrane-spanning domains, indicating that the Rh polypeptide is highly hydrophobic and deeply buried within the phospholipid bilayer. These results suggest that the expression of the Rh gene(s) might be restricted to tissues or cell lines expressing erythroid characters

Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information

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Siyu Han

2016-01-01

Full Text Available More and more studies have demonstrated that long noncoding RNAs (lncRNAs play critical roles in diversity of biological process and are also associated with various types of disease. How to rapidly identify lncRNAs and messenger RNA is the fundamental step to uncover the function of lncRNAs identification. Here, we present a novel method for rapid identification of lncRNAs utilizing sequence intrinsic composition features and open reading frame information based on support vector machine model, named as Lncident (LncRNAs identification. The 10-fold cross-validation and ROC curve are used to evaluate the performance of Lncident. The main advantage of Lncident is high speed without the loss of accuracy. Compared with the exiting popular tools, Lncident outperforms Coding-Potential Calculator, Coding-Potential Assessment Tool, Coding-Noncoding Index, and PLEK. Lncident is also much faster than Coding-Potential Calculator and Coding-Noncoding Index. Lncident presents an outstanding performance on microorganism, which offers a great application prospect to the analysis of microorganism. In addition, Lncident can be trained by users’ own collected data. Furthermore, R package and web server are simultaneously developed in order to maximize the convenience for the users. The R package “Lncident” can be easily installed on multiple operating system platforms, as long as R is supported.

Protein Coexpression Using FMDV 2A: Effect of “Linker” Residues

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Ekaterina Minskaia

2013-01-01

Full Text Available Many biomedical applications absolutely require, or are substantially enhanced by, coexpression of multiple proteins from a single vector. Foot-and-mouth disease virus 2A (F2A and “2A-like” sequences (e.g., Thosea asigna virus 2A; T2A are used widely for this purpose since multiple proteins can be coexpressed by linking open reading frames (ORFs to form a single cistron. The activity of F2A “cleavage” may, however, be compromised by both the use of shorter versions of F2A and the sequences (derived from multiple-purpose cloning sites used to link F2A to the upstream protein. To characterise these effects, different lengths of F2A and T2A were inserted between green and cherry fluorescent proteins. Mutations were introduced in the linker region immediately upstream of both F2A- and T2A-based constructs and activities determined using both cell-free translation systems and transfected cells. In shorter versions of F2A, activity may be affected by both the C-terminal sequence of the protein upstream and, equally strikingly, the residues immediately upstream introduced during cloning. Mutations significantly improved activity for shorter versions of F2A but could decrease activity in the case of T2A. These data will aid the design of cloning strategies for the co-expression of multiple proteins in biomedical/biotechnological applications.

READING OPEN EDUCATION IN THE AGE OF MANKIND: REPRODUCTION OF MEANING IN THE DERRIDEAN SENSE

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Gulfem GURSES

2017-01-01

Full Text Available The rapid change in the communication technologies plays a significant role in the transformation processes of societies. The studies studying the industrial revolution in two phases inform us that the first phase of the revolution involved a revolution in machinery while the second phase saw a revolution in technology. Fast forwarding to the twentieth century, however, one of the areas that has been affected greatly from the said technological revolution is education. The structural changes in education are essential for a new educational process that is consistent with a heterogeneous student population and independent of time and space. In this respect, the new education system in information age has been come to be called open and distance education. In the 21st century, when the information age gave way to the human age, we see learner oriented education system. Putting the learner at the center of the educational process, this particular system puts an end to binary opposition between the subject and object. Having aimed at identifying students’ perception of open and distance education system -being the educational technology of the twenty first century-, the present study has been conducted with 69 students that were presently enrolled to the Anadolu University Faculty of Open Education and entitled to the certificate of honor. A metaphor analysis method was employed within the scope of this study. In order to evaluate the students’ perception of open education system, this study adopted a "phenomenological method" as its qualitative research method as it seemed to be more suited to its purpose. In order to identify the students' perception of open education system, they were given a semi structured questionnaire form that contained the following statement “Open Education is like ………… Because it is ………………” and asked to convey their thoughts by focusing exclusively on a single metaphor. The answers from the

A filtering method to generate high quality short reads using illumina paired-end technology.

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A Murat Eren

Full Text Available Consensus between independent reads improves the accuracy of genome and transcriptome analyses, however lack of consensus between very similar sequences in metagenomic studies can and often does represent natural variation of biological significance. The common use of machine-assigned quality scores on next generation platforms does not necessarily correlate with accuracy. Here, we describe using the overlap of paired-end, short sequence reads to identify error-prone reads in marker gene analyses and their contribution to spurious OTUs following clustering analysis using QIIME. Our approach can also reduce error in shotgun sequencing data generated from libraries with small, tightly constrained insert sizes. The open-source implementation of this algorithm in Python programming language with user instructions can be obtained from https://github.com/meren/illumina-utils.

Pre-reading activities in EFL/ESL reading textbooks and Turkish preparatory school teachers' attitudes toward pre-reading activities

OpenAIRE

Jecksembieyva, Nurgaisha

1993-01-01

Ankara : Faculty of Humanities and Letters and the Institute of Economics and Social Sciences of Bilkent University, 1993. Thesis (Master's) -- -Bilkent University, 1993. Includes bibliographical references leaves 35-40. The main focus of this study was to investigate pre-reading activities in EFL/ESL reading textbooks and to determine teachers' attitudes toward pre-reading activities. Fifteen reading textbooks for EFL/ESL students for different proficiency levels (beginning, interm...

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

OpenAIRE

Karczewski, Konrad J.; Fernald, Guy Haskin; Martin, Alicia R.; Snyder, Michael; Tatonetti, Nicholas P.; Dudley, Joel T.

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technic...

The Saccharomyces cerevisiae RAD18 gene encodes a protein that contains potential zinc finger domains for nucleic acid binding and a putative nucleotide binding sequence

Energy Technology Data Exchange (ETDEWEB)

Jones, J.S.; Prakash, L. (Univ. of Rochester School of Medicine, NY (USA)); Weber, S. (Kodak Research Park, Rochester, NY (USA))

1988-07-25

The RAD18 gene of Saccharomyces cerevisiae is required for postreplication repair of UV damaged DNA. The authors have isolated the RAD18 gene, determined its nucleotide sequence and examined if deletion mutations of this gene show different or more pronounced phenotypic effects than the previously described point mutations. The RAD18 gene open reading frame encodes a protein of 487 amino acids, with a calculated molecular weight of 55,512. The RAD18 protein contains three potential zinc finger domains for nucleic acid binding, and a putative nucleotide binding sequence that is present in many proteins that bind and hydrolyze ATP. The DNA binding and nucleotide binding activities could enable the RAD18 protein to bind damaged sites in the template DNA with high affinity. Alternatively, or in addition, RAD18 protein may be a transcriptional regulator. The RAD18 deletion mutation resembles the previously described point mutations in its effects on viability, DNA repair, UV mutagenesis, and sporulation.

Development of a Case-based Reading Curriculum and Its Effect on Resident Reading.

Science.gov (United States)

Messman, Anne M; Walker, Ian

2018-01-01

Textbook reading plays a foundational role in a resident's knowledge base. Many residency programs place residents on identical reading schedules, regardless of the clinical work or rotation the resident is doing. We sought to develop a reading curriculum that takes into account the clinical work a resident is doing so their reading curriculum corresponds with their clinical work. Preliminary data suggests an increased amount of resident reading and an increased interest in reading as a result of this change to their reading curriculum.

Molecular characterization of a peritrophic membrane protein from the silkworm, Bombyx mori.

Science.gov (United States)

Hu, Xiaolong; Chen, Lin; Yang, Rui; Xiang, Xingwei; Wu, Xiaofeng

2013-02-01

The peritrophic membrane lines the gut of most insects at one or more stages of their life cycles. It facilitates the digestive processes in the guts and protects from invasion by pathogens or food particles. In the current study, a novel PM protein, designated as BmMtch, was identified from the silkworm, Bombyx mori. The open reading frame of BmMtch is 888 bp in length, encoding 295 amino acid residues consisting of two domains (Mito_carr domains) and three transmembrane regions. They are localized on the 11th chromosome as single copy with one exon only. Quantitative real time PCR analysis (qRT-PCR) revealed that BmMtch was mainly expressed in larval fat bodies, Malpighian tubules, testis and ovaries, and could be detected through all stages of the life cycle of silkworm. Immuno-fluorescence analysis indicated that BmMtch was localized within the goblet cell of larval midgut. Western blotting analysis showed that BmMtch were detected in total proteins of PM and larval midgut. The characteristics of BmMtch indicated that BmMtch represents a novel member of insect PM proteins, without chitin-binding domains.

Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses.

Science.gov (United States)

Evgen'ev, M B; Corces, V G; Lankenau, D H

1992-06-05

We have determined the DNA structure of the Ulysses transposable element of Drosophila virilis and found that this transposon is 10,653 bp and is flanked by two unusually large direct repeats 2136 bp long. Ulysses shows the characteristic organization of LTR-containing retrotransposons, with matrix and capsid protein domains encoded in the first open reading frame. In addition, Ulysses contains protease, reverse transcriptase, RNase H and integrase domains encoded in the second open reading frame. Ulysses lacks a third open reading frame present in some retrotransposons that could encode an env-like protein. A dendrogram analysis based on multiple alignments of the protease, reverse transcriptase, RNase H, integrase and tRNA primer binding site of all known Drosophila LTR-containing retrotransposon sequences establishes a phylogenetic relationship of Ulysses to other retrotransposons and suggests that Ulysses belongs to a new family of this type of elements.

Influence of Acculturation on Parents' Readings of and Expectations for Physical Education

Science.gov (United States)

George, Meredith; Cutner-Smith, Matthew D.

2018-01-01

Purpose: The purpose of this study was to examine the influence of acculturation on parents' readings of and expectations for physical education. Method: Participants were 39 parents of pupils enrolled at one public middle school. Data were collected with an open-ended questionnaire and follow-up formal interviews. They were analyzed using…

Analysis of protein-protein interaction networks by means of annotated graph mining algorithms

NARCIS (Netherlands)

Rahmani, Hossein

2012-01-01

This thesis discusses solutions to several open problems in Protein-Protein Interaction (PPI) networks with the aid of Knowledge Discovery. PPI networks are usually represented as undirected graphs, with nodes corresponding to proteins and edges representing interactions among protein pairs. A large

Development of a Case-based Reading Curriculum and Its Effect on Resident Reading

Directory of Open Access Journals (Sweden)

Anne M. Messman

2017-12-01

Full Text Available Textbook reading plays a foundational role in a resident’s knowledge base. Many residency programs place residents on identical reading schedules, regardless of the clinical work or rotation the resident is doing. We sought to develop a reading curriculum that takes into account the clinical work a resident is doing so their reading curriculum corresponds with their clinical work. Preliminary data suggests an increased amount of resident reading and an increased interest in reading as a result of this change to their reading curriculum.

Reading Comprehension Strategies

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Unal Ulker

2017-12-01

Full Text Available The academic success of the university students greatly depends on the mastery of an academic reading skill. However, students as well as teachers, take the learning of this skill for granted, as they tend to presuppose that reading skill is acquired as a part of their secondary education. As a result, most first-year students employ non university strategies to read academic texts, which leads to a surface approach to reading and prevents students from a better understanding of the material. This paper will discuss the strategies that involve students in taking a deep approach to reading academic texts.

Early reading intervention by means of a multicomponent reading game

NARCIS (Netherlands)

Ven, M.A.M. van de; Leeuw, L.C. de; Weerdenburg, M.W.C. van; Steenbeek-Planting, E.G.

2017-01-01

This study examined the effects of an intervention with a multicomponent reading game on the development of reading skills in 60 Dutch primary school children with special educational needs. The game contains evidence-based reading exercises and is based on principles of applied gaming. Using a

Reading-Related Causal Attributions for Success and Failure: Dynamic Links With Reading Skill.

Science.gov (United States)

Frijters, Jan C; Tsujimoto, Kimberley C; Boada, Richard; Gottwald, Stephanie; Hill, Dina; Jacobson, Lisa A; Lovett, Maureen W; Mahone, E Mark; Willcutt, Erik G; Wolf, Maryanne; Bosson-Heenan, Joan; Gruen, Jeffrey R

2018-01-01

The present study investigated the relation among reading skills and attributions, naming speed, and phonological awareness across a wide range of reading skill. Participants were 1,105 school-age children and youths from two understudied populations: African Americans and Hispanic Americans. Individual assessments of children ranging in age from 8 to 15 years were conducted for reading outcomes, cognitive and linguistic predictors of reading, and attributions for success and failure in reading situations. Quantile regressions were formulated to estimate these relations across the full skill span of each outcome. Reading-related attributions predicted contextual word recognition, sight word and decoding fluency, and comprehension skills. Attributions to ability in success situations were positively related to each outcome across the full span. On three reading outcomes, this relation strengthened at higher skill levels. Attributions to effort in success situations were consistently and negatively related to all reading outcomes. The results provide evidence that the strength of the relation between reading and attributions varies according to reading skill levels, with the strongest evidence for ability-based attributions in situations of reading success.

Photoelectrochemical Complexes of Fucoxanthin-Chlorophyll Protein for Bio-Photovoltaic Conversion with a High Open-Circuit Photovoltage.

Science.gov (United States)

Zhang, Tianning; Liu, Cheng; Dong, Wenjing; Wang, Wenda; Sun, Yan; Chen, Xin; Yang, Chunhong; Dai, Ning

2017-12-05

Open-circuit photovoltage (V oc ) is among the critical parameters for achieving an efficient light-to-charge conversion in existing solar photovoltaic devices. Natural photosynthesis exploits light-harvesting chlorophyll (Chl) protein complexes to transfer sunlight energy efficiently. We describe the exploitation of photosynthetic fucoxanthin-chlorophyll protein (FCP) complexes for realizing photoelectrochemical cells with a high V oc . An antenna-dependent photocurrent response and a V oc up to 0.72 V are observed and demonstrated in the bio-photovoltaic devices fabricated with photosynthetic FCP complexes and TiO 2 nanostructures. Such high V oc is determined by fucoxanthin in FCP complexes, and is rarely found in photoelectrochemical cells with other natural light-harvesting antenna. We think that the FCP-based bio-photovoltaic conversion will provide an opportunity to fabricate environmental benign photoelectrochemical cells with high V oc , and also help improve the understanding of the essential physics behind the light-to-charge conversion in photosynthetic complexes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transcriptome profiling of fully open flowers in a frost-tolerant almond genotype in response to freezing stress.

Science.gov (United States)

Hosseinpour, Batool; Sepahvand, Sadegh; Kamali Aliabad, Kazem; Bakhtiarizadeh, MohammadReza; Imani, Ali; Assareh, Reza; Salami, Seyed Alireza

2018-02-01

Spring frost is a major limiting abiotic stress for the cultivation of almonds [Prunus dulcis (Mill.)] in Mediterranean areas or the Middle East. Spring frost, in particular, damages almond fully open flowers, resulting to significant reduction in yield. Little is known about the genetic factors expressed after frost stress in Prunus spp. as well as in almond fully open flowers. Here, we provide the molecular signature of pistils of fully open flowers from a frost-tolerant almond genotype. The level of frost tolerance in this genotype was determined for all three flowering stages and was confirmed by comparing it to two other cultivars using several physiological analyses. Afterwards, comprehensive expression profiling of genes expressed in fully open flowers was performed after being exposed to frost temperatures (during post-thaw period). Clean reads, 27,104,070 and 32,730,772, were obtained for non-frost-treated and frost-treated (FT) libraries, respectively. A total of 62.24 Mb was assembled, generating 50,896 unigenes and 66,906 transcripts. Therefore, 863 upregulated genes and 555 downregulated genes were identified in the FT library. Functional annotation showed that most of the upregulated genes were related to various biological processes involved in responding to abiotic stress. For the first time, a highly expressed cold-shock protein was identified in the reproductive organ of fruit trees. The expression of six genes was validated by RT-PCR. As the first comprehensive analysis of open flowers in a frost-tolerant almond genotype, this study represents a key step toward the molecular breeding of fruit tree species for frost tolerance.

Integration of open access literature into the RCSB Protein Data Bank using BioLit

Directory of Open Access Journals (Sweden)

Bourne Philip E

2010-04-01

Full Text Available Abstract Background Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright restriction, this distinction between database and literature is blurring. To exploit this opportunity we present the integration of open access literature with the RCSB Protein Data Bank (PDB. Results BioLit provides an enhanced view of articles with markup of semantic data and links to biological databases, based on the content of the article. For example, words matching to existing biological ontologies are highlighted and database identifiers are linked to their database of origin. Among other functions, it identifies PDB IDs that are mentioned in the open access literature, by parsing the full text for all research articles in PubMed Central (PMC and exposing the results as simple XML Web Services. Here, we integrate BioLit results with the RCSB PDB website by using these services to find PDB IDs that are mentioned in research articles and subsequently retrieving abstract, figures, and text excerpts for those articles. A new RCSB PDB literature view permits browsing through the figures and abstracts of the articles that mention a given structure. The BioLit Web Services that are providing the underlying data are publicly accessible. A client library is provided that supports querying these services (Java. Conclusions The integration between literature and websites, as demonstrated here with the RCSB PDB, provides a broader view for how a given structure has been analyzed and used. This approach detects the mention of a PDB structure even if it is not formally cited in the paper. Other structures related through the same literature references can also be identified, possibly providing new scientific insight. To our

The Importance of Metacognitive Reading Strategy Awareness in Reading Comprehension

Science.gov (United States)

Ahmadi, Mohammad Reza; Ismail, Hairul Nizam; Abdullah, Muhammad Kamarul Kabilan

2013-01-01

Metacognitive reading strategy awareness plays a significant role in reading comprehension and educational process. In spite of its importance, metacognitive strategy has long been the ignored skill in English language teaching, research, learning, and assessment. This lack of good metacognitive reading strategy skill is exacerbated by the central…

Cloning and characterization of a gene encoding Rac/Rop-like monomeric guanosine 5'-triphosphate-binding protein from Scoparia dulcis.

Science.gov (United States)

Mitamura, Toshiaki; Shite, Masato; Yamamura, Yoshimi; Kurosaki, Fumiya

2009-06-01

A cDNA clone, designated Sd-racrop (969 bp), was isolated from seedlings of Scoparia dulcis. This gene contains an open reading frame encoding the protein of 197 amino acid residues with high homology to Rac/Rop small guanosine 5'-triphosphate-binding proteins from various plant sources. In Southern hybridization analysis, the restriction digests prepared from genomic DNA of S. dulcis showed a main signal together with a few weakly hybridized bands. The transcriptional level of Sd-racrop showed a transient decrease by exposure of the leaf tissues of S. dulcis to the ethylene-generating reagent 2-chloroethylphosphonic acid. However, an appreciable increase in gene expression was reproducibly observed upon treatment of the plant with methyl jasmonate. These results suggest that the Sd-racrop product plays roles in ethylene- and methyl jasmonate-induced responses of S. dulcis accompanying the change in the transcriptional level, however, the cellular events mediated by this protein toward these external stimuli would be regulated by various mechanisms.

How do children read words? A focus on reading processes

NARCIS (Netherlands)

van den Boer, M.

2014-01-01

Being able to read is very important in our literate society. Many studies, therefore, have examined children’s reading skills to improve our understanding of reading development. In general, there have been two types of studies. On the one hand, there is a line of research that focuses on the

ELL High School Students' Metacognitive Awareness of Reading Strategy Use and Reading Proficiency

Science.gov (United States)

Hong-Nam, Kay

2014-01-01

This study investigated the metacognitive awareness and reading strategies use of high school-­aged English language learners (ELLs) and the relationship between ELL reading strategy use and reading proficiency as measured by a standardized reading test and self-­rated reading proficiency. Results reveal that participants reported moderate use of…

Rearing a reading habit

OpenAIRE

Sridhar, M. S.

2009-01-01

Discusses the importance and ways of inculcating reading habit in children at the right age, describes the five reading phases in children along with interest and the material to satiate the need, explains how four deterministic factors affect the reading habit of children, enlists motivations that are behind the reading process with tips to improve reading habit of children.

Effects of Listening While Reading (LWR on Swahili Reading Fluency and Comprehension

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Filipo Lubua

2016-10-01

Full Text Available A number of studies have examined the contribution of technology in teaching such languages as English, French, and Spanish, among many others. Contrarily, most LCTL’s, have received very little attention. This study investigates if listening while reading (LWR may expedite Swahili reading fluency and comprehension. The study employed the iBook Author tool to create weekly mediated and interactive reading texts, with comprehension exercises, which were eventually used to collect descriptive and qualitative data from four Elementary Swahili students. Participants participated in a seven week reading program, which provided them with some kind of directed self-learning, and met with the instructor for at least 30 minutes every week for observation and more reading activities. The teacher recorded their reading scores, and a number of themes on how LWR influenced reading fluency and comprehension are discussed here. It shows that participants have a positive attitude towards LWR and they suggest it for all the reading classes.

Preliteracy signatures of poor-reading abilities in resting-state EEG

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Giuseppina eSchiavone

2014-09-01

Full Text Available The hereditary character of dyslexia suggests the presence of putative underlying neural anomalies already in preliterate age. Here, we investigated whether early neurophysiological correlates of future reading difficulties—a hallmark of dyslexia—could be identified in the resting-state EEG of preliterate children. The children in this study were recruited at birth and classified on the basis of parents’ performance on reading tests to be at-risk of becoming poor readers (n = 48 or not (n = 14. Eyes-open rest EEG was measured at the age of 3 years, and the at-risk children were divided into fluent readers (n = 24 and non-fluent readers (n = 24 after reading assessment at their third grade of school. We found that fluent readers and non-fluent readers differed in normalized spectral amplitude. Non-fluent readers were characterized by lower amplitude in the delta-1 frequency band (0.5–2 Hz and higher amplitude in the alpha-1 band (6–8 Hz in multiple scalp regions compared to control and at-risk fluent readers. Interestingly, across groups these EEG biomarkers correlated with several behavioral test scores measured in the third grade. Specifically, the performance on reading fluency, phonological and orthographic tasks and rapid automatized naming task correlated positively with delta-1 and negatively with alpha-1. Together, our results suggest that combining family-risk status, neurophysiological testing and behavioral test scores in a longitudinal setting may help uncover physiological mechanisms implicated with neurodevelopmental disorders such as the predisposition to reading disabilities.

Deletion of the Vaccinia Virus I2 Protein Interrupts Virion Morphogenesis, Leading to Retention of the Scaffold Protein and Mislocalization of Membrane-Associated Entry Proteins.

Science.gov (United States)

Hyun, Seong-In; Weisberg, Andrea; Moss, Bernard

2017-08-01

The I2L open reading frame of vaccinia virus (VACV) encodes a conserved 72-amino-acid protein with a putative C-terminal transmembrane domain. Previous studies with a tetracycline-inducible mutant demonstrated that I2-deficient virions are defective in cell entry. The purpose of the present study was to determine the step of replication or entry that is affected by loss of the I2 protein. Fluorescence microscopy experiments showed that I2 colocalized with a major membrane protein of immature and mature virions. We generated a cell line that constitutively expressed I2 and allowed construction of the VACV I2L deletion mutant vΔI2. As anticipated, vΔI2 was unable to replicate in cells that did not express I2. Unexpectedly, morphogenesis was interrupted at a stage after immature virion formation, resulting in the accumulation of dense spherical particles instead of brick-shaped mature virions with well-defined core structures. The abnormal particles retained the D13 scaffold protein of immature virions, were severely deficient in the transmembrane proteins that comprise the entry fusion complex (EFC), and had increased amounts of unprocessed membrane and core proteins. Total lysates of cells infected with vΔI2 also had diminished EFC proteins due to instability attributed to their hydrophobicity and failure to be inserted into viral membranes. A similar instability of EFC proteins had previously been found with unrelated mutants blocked earlier in morphogenesis that also accumulated viral membranes retaining the D13 scaffold. We concluded that I2 is required for virion morphogenesis, release of the D13 scaffold, and the association of EFC proteins with viral membranes. IMPORTANCE Poxviruses comprise a large family that infect vertebrates and invertebrates, cause disease in both in humans and in wild and domesticated animals, and are being engineered as vectors for vaccines and cancer therapy. In addition, investigations of poxviruses have provided insights into

Reading Fluency Instruction for Students at Risk for Reading Failure

Science.gov (United States)

Ring, Jeremiah J.; Barefoot, Lexie C.; Avrit, Karen J.; Brown, Sasha A.; Black, Jeffrey L.

2013-01-01

The important role of reading fluency in the comprehension and motivation of readers is well documented. Two reading rate intervention programs were compared in a cluster-randomized clinical trial of students who were considered at-risk for reading failure. One program focused instruction at the word level; the second program focused instruction…

Early Reading Intervention by Means of a Multicomponent Reading Game

Science.gov (United States)

van de Ven, M.; de Leeuw, L.; van Weerdenburg, M.; Steenbeek-Planting, E. G.

2017-01-01

This study examined the effects of an intervention with a multicomponent reading game on the development of reading skills in 60 Dutch primary school children with special educational needs. The game contains evidence-based reading exercises and is based on principles of applied gaming. Using a multiple baseline approach, we tested children's…

STUDENTS’ READING PRACTICES AND ENVIRONMENTS

Directory of Open Access Journals (Sweden)

Aiza Johari

2013-07-01

Full Text Available Abstract: The challenges of reading are indeed apparent in most teaching and learning processes in ESL classrooms. As a result, this study is conducted to resolve the issues of students who seem to find reading to be unbearable. Many of them have limited ability to read well and hence, possess insufficient reading habits to become competent readers, particularly out-of-school context. Besides, poor home literacy environments also contribute to their shortcomings in reading. The main objectives of this study are to identify the students’ reasons for reading as well as to find out their home reading environments (reading backgrounds and habits; reading attitudes and motivation; reading exposure and supports. To identify these, questionnaires were distributed to 120 secondary school students (Form 4: 16 years old from one of the urban schools in Sarawak, Malaysia. The findings indicate that the students read to gain information and knowledge though many chose reading as a hobby as their last choice in explaining their motives of reading. Besides, they preferred non-academic reading materials, mainly lighter forms reading materials such as comics, story books and magazines. Though the students acknowledged the importance of reading in their daily lives, their average reading habits, attitude, motivation, exposure and support within the home domain had suggested otherwise. They mainly read for instrumental purposes while reading for pleasure seemed not to be given priority. Besides, the respondents acknowledge that their parents and themselves did not read much at home. As an implication, it is vital for students to improve their reading perceptions, abilities and practices to achieve personal, societal and national progress. On a final note, parents’ early and continuous efforts to be involved in their children’s literacy events in an out-of-school context are believed to be vital to inculcate positive reading environments, habits and culture

A neutron image plate quasi-Laue diffractometer for protein crystallography

Energy Technology Data Exchange (ETDEWEB)

Cipriani, F.; Castagna, J.C.; Wilkinson, C. [European Molecular Biology Laboratory, Grenoble (France)] [and others

1994-12-31

An instrument which is based on image plate technology has been constructed to perform cold neutron Laue crystallography on protein structures. The crystal is mounted at the center of a cylindrical detector which is 400mm long and has a circumference of 1000mm, with gadolinium oxide-containing image plates mounted on its exterior surface. Laue images registered on the plate are read out by rotating the drum and translating a laser read head parallel to the cylinder axis, giving a pixel size of 200{mu}m x 200{mu}m and a total read time of 5 minutes. Preliminary results indicate that it should be possible to obtain a complete data set from a protein crystal to atomic resolution in about two weeks.

Measuring adult literacy students' reading skills using the Gray Oral Reading Test.

Science.gov (United States)

Greenberg, Daphne; Pae, Hye Kyeong; Morris, Robin D; Calhoon, Mary Beth; Nanda, Alice O

2009-12-01

There are not enough reading tests standardized on adults who have very low literacy skills, and therefore tests standardized on children are frequently administered. This study addressed the complexities and problems of using a test normed on children to measure the reading comprehension skills of 193 adults who read at approximately third through fifth grade reading grade equivalency levels. Findings are reported from an analysis of the administration of Form A of the Gray Oral Reading Tests-Fourth Edition (Wiederholt & Bryant, 2001a, b). Results indicated that educators and researchers should be very cautious when interpreting test results of adults who have difficulty reading when children's norm-referenced tests are administered.

Open Access to Research Data Accessing, using and publishing collections of textual data in digital literary studies

OpenAIRE

Schöch, Christof

2015-01-01

Introduction What is open access to research data? Related issues A closer look What can you do with open research data? What is required from research data? Do resources fulfil these requirements? Why is getting access good, but giving access better? Current issues Some challenges Main hindrance: Legal issues Conclusions Recommended readings

Molecular cloning, sequence analysis and homology modeling of the first caudata amphibian antifreeze-like protein in axolotl (Ambystoma mexicanum).

Science.gov (United States)

Zhang, Songyan; Gao, Jiuxiang; Lu, Yiling; Cai, Shasha; Qiao, Xue; Wang, Yipeng; Yu, Haining

2013-08-01

Antifreeze proteins (AFPs) refer to a class of polypeptides that are produced by certain vertebrates, plants, fungi, and bacteria and which permit their survival in subzero environments. In this study, we report the molecular cloning, sequence analysis and three-dimensional structure of the axolotl antifreeze-like protein (AFLP) by homology modeling of the first caudate amphibian AFLP. We constructed a full-length spleen cDNA library of axolotl (Ambystoma mexicanum). An EST having highest similarity (∼42%) with freeze-responsive liver protein Li16 from Rana sylvatica was identified, and the full-length cDNA was subsequently obtained by RACE-PCR. The axolotl antifreeze-like protein sequence represents an open reading frame for a putative signal peptide and the mature protein composed of 93 amino acids. The calculated molecular mass and the theoretical isoelectric point (pl) of this mature protein were 10128.6 Da and 8.97, respectively. The molecular characterization of this gene and its deduced protein were further performed by detailed bioinformatics analysis. The three-dimensional structure of current AFLP was predicted by homology modeling, and the conserved residues required for functionality were identified. The homology model constructed could be of use for effective drug design. This is the first report of an antifreeze-like protein identified from a caudate amphibian.

Ribosomal protein S14 transcripts are edited in Oenothera mitochondria.

Science.gov (United States)

Schuster, W; Unseld, M; Wissinger, B; Brennicke, A

1990-01-01

The gene encoding ribosomal protein S14 (rps14) in Oenothera mitochondria is located upstream of the cytochrome b gene (cob). Sequence analysis of independently derived cDNA clones covering the entire rps14 coding region shows two nucleotides edited from the genomic DNA to the mRNA derived sequences by C to U modifications. A third editing event occurs four nucleotides upstream of the AUG initiation codon and improves a potential ribosome binding site. A CGG codon specifying arginine in a position conserved in evolution between chloroplasts and E. coli as a UGG tryptophan codon is not edited in any of the cDNAs analysed. An inverted repeat 3' of an unidentified open reading frame is located upstream of the rps14 gene. The inverted repeat sequence is highly conserved at analogous regions in other Oenothera mitochondrial loci. Images PMID:2326162

Cloning, purification and preliminary crystallographic studies of the 2AB protein from hepatitis A virus

International Nuclear Information System (INIS)

Garriga, Damià; Vives-Adrián, Laia; Buxaderas, Mònica; Ferreira-da-Silva, Frederico; Almeida, Bruno; Macedo-Ribeiro, Sandra; Pereira, Pedro José Barbosa; Verdaguer, Núria

2011-01-01

The 2AB protein derived from the nonstructural P2 region of hepatitis A virus has been cloned, purified and crystallized. The preliminary characterization of native and selenomethionine-derivative crystals is reported. The Picornaviridae family contains a large number of human pathogens such as rhinovirus, poliovirus and hepatitis A virus (HAV). Hepatitis A is an infectious disease that causes liver inflammation. It is highly endemic in developing countries with poor sanitation, where infections often occur in children. As in other picornaviruses, the genome of HAV contains one open reading frame encoding a single polyprotein that is subsequently processed by viral proteinases to originate mature viral proteins during and after the translation process. In the polyprotein, the N-terminal P1 region generates the four capsid proteins, while the C-terminal P2 and P3 regions contain the enzymes, precursors and accessory proteins essential for polyprotein processing and virus replication. Here, the first crystals of protein 2AB of HAV are reported. The crystals belonged to space group P4 1 or P4 3 , with unit-cell parameters a = b = 90.42, c = 73.43 Å, and contained two molecules in the asymmetric unit. Native and selenomethionine-derivative crystals diffracted to 2.7 and 3.2 Å resolution, respectively

Reading: United States.

Science.gov (United States)

Weber, Rose-Marie

1983-01-01

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

Identification of Bombyx mori bidensovirus VD1-ORF4 reveals a novel protein associated with viral structural component.

Science.gov (United States)

Li, Guohui; Hu, Zhaoyang; Guo, Xuli; Li, Guangtian; Tang, Qi; Wang, Peng; Chen, Keping; Yao, Qin

2013-06-01

Bombyx mori bidensovirus (BmBDV) VD1-ORF4 (open reading frame 4, ORF4) consists of 3,318 nucleotides, which codes for a predicted 1,105-amino acid protein containing a conserved DNA polymerase motif. However, its functions in viral propagation remain unknown. In the current study, the transcription of VD1-ORF4 was examined from 6 to 96 h postinfection (p.i.) by RT-PCR, 5'-RACE revealed the transcription initiation site of BmBDV ORF4 to be -16 nucleotides upstream from the start codon, and 3'-RACE revealed the transcription termination site of VD1-ORF4 to be +7 nucleotides downstream from termination codon. Three different proteins were examined in the extracts of BmBDV-infected silkworms midguts by Western blot using raised antibodies against VD1-ORF4 deduced amino acid, and a specific protein band about 53 kDa was further detected in purified virions using the same antibodies. Taken together, BmBDV VD1-ORF4 codes for three or more proteins during the viral life cycle, one of which is a 53 kDa protein and confirmed to be a component of BmBDV virion.

Reading Disabilities and PASS Reading Enhancement Programme

Science.gov (United States)

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…

The Effect of Collaborative Strategic Reading on Grade Six Students’ Reading Achievement

Directory of Open Access Journals (Sweden)

Siti Tamah

2016-01-01

Full Text Available One of the language skills to master by Indonesian EFL learners is reading. In order to assist learners comprehend reading texts, teachers are challenged to apply various teaching strategies. As this paper focuses on teaching reading, two teaching strategies dealing with reading instruction are compared. To be specific, in this paper the writers conduct a study to find the difference between Collaborative Strategic Reading (CSR and teacher-centered teaching strategy (by applying skimming and scanning. This study was a quasi experimental, which was conducted upon the sixth graders of an elementary school. The finding showed that reading achievements of the students who are taught using CSR and teacher-centered teaching strategy are not significantly different. Nevertheless, this study using Cohen’s d formula finds that CSR gave a small effect on students’ reading achievement.

Quantitative and functional characterization of the hyper-conserved protein of Prochlorococcus and marine Synechococcus.

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Caroline E Whidden

Full Text Available A large fraction of any bacterial genome consists of hypothetical protein-coding open reading frames (ORFs. While most of these ORFs are present only in one or a few sequenced genomes, a few are conserved, often across large phylogenetic distances. Such conservation provides clues to likely uncharacterized cellular functions that need to be elucidated. Marine cyanobacteria from the Prochlorococcus/marine Synechococcus clade are dominant bacteria in oceanic waters and are significant contributors to global primary production. A Hyper Conserved Protein (PSHCP of unknown function is 100% conserved at the amino acid level in genomes of Prochlorococcus/marine Synechococcus, but lacks homologs outside of this clade. In this study we investigated Prochlorococcus marinus strains MED4 and MIT 9313 and Synechococcus sp. strain WH 8102 for the transcription of the PSHCP gene using RT-Q-PCR, for the presence of the protein product through quantitative immunoblotting, and for the protein's binding partners in a pull down assay. Significant transcription of the gene was detected in all strains. The PSHCP protein content varied between 8±1 fmol and 26±9 fmol per ug total protein, depending on the strain. The 50 S ribosomal protein L2, the Photosystem I protein PsaD and the Ycf48-like protein were found associated with the PSHCP protein in all strains and not appreciably or at all in control experiments. We hypothesize that PSHCP is a protein associated with the ribosome, and is possibly involved in photosystem assembly.

Proteins analysed as virtual knots

Science.gov (United States)

Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.

2017-02-01

Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

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Morley Chris

2008-03-01

Full Text Available Abstract Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Results Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Conclusion Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.

L2 Reading in Thailand: Vocational College Students' Application of Reading Strategies to Their Reading of English Texts

Science.gov (United States)

Kasemsap, Bharani; Lee, Hugo Yu-Hsiu

2015-01-01

This study aims to explore the application of reading strategies to the reading of English texts by Thai vocational college students. Data were collected via questionnaire surveys, think-aloud experiments and semi-structured interviews. The research results reveal different typologies of reading strategies adopted by lower and higher level English…

The Effect of Background Music While Silent Reading on EFL Learners’ Reading Comprehension

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sakineh sahebdel

2014-05-01

Full Text Available This study attempted to determine the effect of background music while silent reading on Iranian EFL learners’ reading comprehension. The participants were 57 Iranian EFL learners between the ages of 14 and 16 in two 3rd grade high schoolclasses at pre-intermediate proficiency level. Before treatment,both experimental and control groups took a reading comprehension pretest. In the experimental group, the researchers played Mozart sonatas as background music and asked them to read the passage silently and then answer the reading comprehension questions. In the control group, the procedure was the same, but no music was played while silent reading by the students. After ten sessions, the students of both groups were asked to answer another independent but parallel form of reading section of PET as their post-test. The independent samples t-testresultsindicated that the experimental group outperformed the control group in reading comprehension posttest, and listening to background music while silent reading had a significantly positive effect on Iranian EFL learners’ reading comprehension. The results of the present study have implications for EFL students, teachers, and teacher educators as well as syllabus designers and materials developers.

Reading Journal as A Way to Improve Students’ Comprehension toward A Textbook Reading Material

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Menik Winiharti

2014-11-01

Full Text Available Reading journal is one way to record students’ independent learning based on text they read. This study was conducted to find out the students’ level of reading comprehension through some notes written in the reading journal, the extent to which the activity of writing reading journals improved students’ reading comprehension, whether the students got benefit from reading journal. There were 104 respondents coming from four different departments in Bina Nusantara University were asked to read a text related to the subject they learned in a certain session. Then they were assigned to write a journal that records the things they had read. When this task was finished, the lecturer ran a quiz containing related questions to check whether they really understood the content of the text. Afterwards, students were to fill in a questionnaire regarding their opinion on the impact of the reading journal toward their reading comprehension. The findings indicate that more than half of the participants appear to understand the material well, and the task plays a certain role in improving students’ understanding. The most crucial thing is that most students think they get benefit by writing the reading journal.

An Open Access future? Report from the eurocancercoms project

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Kenney, R; Warden, R

2011-01-01

In March 2011, as part of the background research to the FP7 Eurocancercoms project, the European Association for Cancer Research (EACR) conducted an online survey of its members working in Europe to discover their experiences of and attitudes to the issues surrounding academic publishing and Open Access. This paper presents the results from this survey and compares them to the results from a much larger survey on the same topic from the Study of Open Access Publishing (SOAP). The responses from both surveys show very positive attitudes to the Open Access publishing route; perhaps the most challenging statistic from the EACR survey is that 88% of respondents believe that publicly funded research should be made available to be read and used without access barriers As a conclusion and invitation to further discussion, this paper also contributes to the debate around subscription and Open Access publishing, supporting the case for accelerating the progress towards Open Access publishing of cancer research articles as a particularly supportive way of assisting all researchers to make unhindered progress with their work. PMID:22276063

Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data.

Science.gov (United States)

Barre, Arnaud; Armand, Stéphane

2014-04-01

C3D file format is widely used in the biomechanical field by companies and laboratories to store motion capture systems data. However, few software packages can visualize and modify the integrality of the data in the C3D file. Our objective was to develop an open-source and multi-platform framework to read, write, modify and visualize data from any motion analysis systems using standard (C3D) and proprietary file formats (used by many companies producing motion capture systems). The Biomechanical ToolKit (BTK) was developed to provide cost-effective and efficient tools for the biomechanical community to easily deal with motion analysis data. A large panel of operations is available to read, modify and process data through C++ API, bindings for high-level languages (Matlab, Octave, and Python), and standalone application (Mokka). All these tools are open-source and cross-platform and run on all major operating systems (Windows, Linux, MacOS X). Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

SchemaOnRead Manual

Energy Technology Data Exchange (ETDEWEB)

North, Michael J. [Argonne National Lab. (ANL), Argonne, IL (United States)

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.

501 reading comprehension questions

CERN Document Server

2014-01-01

This updated edition offers the most extensive and varied practice for all types of questions students might face on standardized and in-class tests. With this guide, students will learn to develop expert reading strategies, understand how to read faster and with greater comprehension, overcome reading anxiety, and increase appreciation of reading for pleasure. This book's step-by-step approach provides graduated coverage that moves from the basics to more advanced reading.

Sequence of a cDNA encoding turtle high mobility group 1 protein.

Science.gov (United States)

Zheng, Jifang; Hu, Bi; Wu, Duansheng

2005-07-01

In order to understand sequence information about turtle HMG1 gene, a cDNA encoding HMG1 protein of the Chinese soft-shell turtle (Pelodiscus sinensis) was amplified by RT-PCR from kidney total RNA, and was cloned, sequenced and analyzed. The results revealed that the open reading frame (ORF) of turtle HMG1 cDNA is 606 bp long. The ORF codifies 202 amino acid residues, from which two DNA-binding domains and one polyacidic region are derived. The DNA-binding domains share higher amino acid identity with homologues sequences of chicken (96.5%) and mammalian (74%) than homologues sequence of rainbow trout (67%). The polyacidic region shows 84.6% amino acid homology with the equivalent region of chicken HMG1 cDNA. Turtle HMG1 protein contains 3 Cys residues located at completely conserved positions. Conservation in sequence and structure suggests that the functions of turtle HMG1 cDNA may be highly conserved during evolution. To our knowledge, this is the first report of HMG1 cDNA sequence in any reptilian.

ye movement parameters while reading show cognitive processes of structural analysis of written speech

Directory of Open Access Journals (Sweden)

Latanov, Alexander V.

2016-06-01

Full Text Available This paper gives an overview of the published data on eye movement parameters while reading sentences in different languages with both local and global syntactic ambiguity. A locally ambiguous sentence contains a syntactically problematic phrase that leads to only one interpretation, while a globally ambiguous sentence has more than one distinct interpretation. In the first case the ambiguity persists only to the end of the sentence, when it is successfully resolved; in the second case the ambiguity is still present after reading the whole sentence. The obvious difficulty in analyzing the structure of locally and globally ambiguous sentences leads to increased reading time compared with unambiguous sentences. The syntactic ambiguity increases two major parameters: the fixation duration when reading words critical for interpreting the sentence, and the frequency of regressive saccades to reread those words. The reading time for critical words, disambiguating the local ambiguity, depends on the principle of early/late closure (i.e., high/low attachment: preferring a recurrent pattern to associate the critical word with a distant or closer word, respectively (as determined by its position in the sentence, and differs across languages. The first study of eye movement parameters in reading globally syntactic ambiguous sentences in the Russian language is reported in this paper. Our findings open up the prospects of quantitative studies of syntactic disambiguation in Slavonic and Romano-Germanic languages.

Psychometric Research in Reading.

Science.gov (United States)

Davis, Frederick B.

This review of psychometric research in reading analyzes the factors which seem related to reading comprehension skills. Experimental analysis of reading comprehension by L. E. Thorndike revealed two major components: knowledge of word meanings and verbal reasoning abilities. Subsequent analysis of experimental studies of reading comprehension…

An Open Letter to President Barack Obama from C. Frederick Risinger

Science.gov (United States)

Risinger, C. Frederick

2010-01-01

This article presents an open letter to President Barack Obama written by the author to express his concerns about the increasing emphasis on mathematics and science education along with the continued emphasis on reading/language arts while a fourth major curriculum area--social studies--is being marginalized by lack of funding and reduced…

Critical reading and critical thinking Critical reading and critical thinking

Directory of Open Access Journals (Sweden)

Loni Kreis Taglieber

2008-04-01

Full Text Available The purpose of this paper is to provide, for L1 and L2 reading and writing teachers, a brief overview of the literature about critical reading and higher level thinking skills. The teaching of these skills is still neglected in some language classes in Brazil, be it in L1 or in L2 classes. Thus, this paper may also serve as a resource guide for L1 and/or L2 reading and writing teachers who want to incorporate critical reading and thinking into their classes. In modern society, even in everyday life people frequently need to deal with complicated public and political issues, make decisions, and solve problems. In order to do this efficiently and effectively, citizens must be able to evaluate critically what they see, hear, and read. Also, with the huge amount of printed material available in all areas in this age of “information explosion” it is easy to feel overwhelmed. But often the information piled up on people’s desks and in their minds is of no use due to the enormous amount of it. The purpose of this paper is to provide, for L1 and L2 reading and writing teachers, a brief overview of the literature about critical reading and higher level thinking skills. The teaching of these skills is still neglected in some language classes in Brazil, be it in L1 or in L2 classes. Thus, this paper may also serve as a resource guide for L1 and/or L2 reading and writing teachers who want to incorporate critical reading and thinking into their classes. In modern society, even in everyday life people frequently need to deal with complicated public and political issues, make decisions, and solve problems. In order to do this efficiently and effectively, citizens must be able to evaluate critically what they see, hear, and read. Also, with the huge amount of printed material available in all areas in this age of “information explosion” it is easy to feel overwhelmed. But often the information piled up on people’s desks and in their minds is of

Tula hantavirus isolate with the full-length ORF for nonstructural protein NSs survives for more consequent passages in interferon-competent cells than the isolate having truncated NSs ORF.

Science.gov (United States)

Jääskeläinen, Kirsi M; Plyusnina, Angelina; Lundkvist, Ake; Vaheri, Antti; Plyusnin, Alexander

2008-01-11

The competitiveness of two Tula hantavirus (TULV) isolates, TULV/Lodz and TULV/Moravia, was evaluated in interferon (IFN) -competent and IFN-deficient cells. The two isolates differ in the length of the open reading frame (ORF) encoding the nonstructural protein NSs, which has previously been shown to inhibit IFN response in infected cells. In IFN-deficient Vero E6 cells both TULV isolates survived equally well. In contrast, in IFN-competent MRC5 cells TULV/Lodz isolate, that possesses the NSs ORF for the full-length protein of 90 aa, survived for more consequent passages than TULV/Moravia isolate, which contains the ORF for truncated NSs protein (66-67 aa). Our data show that expression of a full-length NSs protein is beneficial for the virus survival and competitiveness in IFN-competent cells and not essential in IFN-deficient cells. These results suggest that the N-terminal aa residues are important for the full activity of the NSs protein.

ZNF328, a novel human zinc-finger protein, suppresses transcriptional activities of SRE and AP-1

International Nuclear Information System (INIS)

Ou Ying; Wang Shenqiu; Cai Zhenyu; Wang Yuequn; Wang Canding; Li Yongqing; Li Fang; Yuan Wuzhou; Liu Bisheng; Wu Xiushan; Liu Mingyao

2005-01-01

The zinc finger proteins containing the Kruppel-associated box domain (KRAB-ZFPs) are the single largest class of transcription factors in human genome. Many of the KRAB-ZFPs are involved in cardiac development or cardiovascular diseases. Here, we have identified a novel human KRAB zinc finger gene, named ZNF328, from the human fetal heart cDNA library. The complete sequence of ZNF328 cDNA contains a 2376-bp open reading frame (ORF) and encodes a 792 amino acid protein with an N-terminal KRAB domain and classical zinc finger C 2 H 2 motifs in the C-terminus. Northern blot analysis indicates that the protein is expressed in most of the examined human adult and embryonic tissues. ZNF328 is a transcription suppressor when fused to Gal-4 DNA-binding domain and cotransfected with VP-16. Overexpression of ZNF328 in COS-7 cells inhibits the transcriptional activities of SRE and AP-1. Deletion analysis with a series of truncated fusion proteins indicates that the KRAB motif is a basal repression domain when cotransfected with VP-16. Similar results were obtained when the truncated fusion proteins were assayed for the transcriptional activities of SRE and AP-1. These results suggest that ZNF328 protein may act as a transcriptional repressor in mitogen-activated protein kinase (MAPK) signaling pathway to mediate cellular functions

Reading and Empathy

Science.gov (United States)

McCreary, John J.; Marchant, Gregory J.

2017-01-01

The relationship between reading and empathy was explored. Controlling for GPA and gender, reading variables were hypothesized as related to empathy; the relationship was expected to differ for males and females. For the complete sample, affective components were related to GPA but not reading. Perspective taking was related to reading…

Reading Big Words: Instructional Practices to Promote Multisyllabic Word Reading Fluency

Science.gov (United States)

Toste, Jessica R.; Williams, Kelly J.; Capin, Philip

2017-01-01

Poorly developed word recognition skills are the most pervasive and debilitating source of reading challenges for students with learning disabilities (LD). With a notable decrease in word reading instruction in the upper elementary grades, struggling readers receive fewer instructional opportunities to develop proficient word reading skills, yet…

The identification of point mutations in Duchenne muscular dystrophy patients by using reverse-transcription PCR and the protein truncation test

Energy Technology Data Exchange (ETDEWEB)

Gardner, R.J.; Bobrow, M.; Roberts, R.G. [St. Thomas`s Hospitals, London (United Kingdom)

1995-08-01

The protein truncation test (PTT) is a mutation-detection method that monitors the integrity of the open reading frame (ORF). More than 60% of cases of Duchenne muscular dystrophy (DMD) result from gross frameshifting deletions in the dystrophin gene that are detectable by multiplex PCR system. It has become apparent that virtually all of the remaining DMD mutations also disrupt the translational reading frame, making the PTT a logical next step toward a comprehensive strategy for the identification of all DMD mutations. We report here a pilot study involving 22 patients and describe the mutations characterized. These constitute 12 point mutations or small insertions/deletions and 4 gross rearrangements. We also have a remaining five patients in whom there does not appear to be mutation in the ORF. We believe that reverse-transcription-PCR/PTT is an efficient method by which to screen for small mutations in DMD patients with no deletion. 29 refs., 2 figs., 3 tabs.

Inward open characterization of EmrD transporter with molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Tan, Xianwei [School of Life Sciences, Tsinghua University, Beijing 100084 (China); Wang, Boxiong, E-mail: boxiong_wang@yahoo.com [Department of Precision Instrument, Tsinghua University, Beijing 100084 (China)

2016-06-10

EmrD is a member of the multidrug resistance exporter family. Up to now, little is known about the structural dynamics that underline the function of the EmrD protein in inward-facing open state and how the EmrD transits from an occluded state to an inward open state. For the first time the article applied the AT simulation to investigate the membrane transporter protein EmrD, and described the dynamic features of the whole protein, the domain, the helices, and the amino acid residues during an inward-open process from its occluded state. The gradual inward-open process is different from the current model of rigid-body domain motion in alternating-access mechanism. Simulation results show that the EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. In addition, it is observed that the helices exposed to the surrounding membrane show a higher level of flexibility than the other regions, and the protonated E227 plays a key role in the transition from the occluded to the open state. -- Highlights: •This study described the dynamic features of the whole EmrD protein, during an inward-open process from its occluded state. •The EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. •The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. •The protonated E227 plays a key role in the transition from the occluded to the open state.

Inward open characterization of EmrD transporter with molecular dynamics simulation

International Nuclear Information System (INIS)

Tan, Xianwei; Wang, Boxiong

2016-01-01

EmrD is a member of the multidrug resistance exporter family. Up to now, little is known about the structural dynamics that underline the function of the EmrD protein in inward-facing open state and how the EmrD transits from an occluded state to an inward open state. For the first time the article applied the AT simulation to investigate the membrane transporter protein EmrD, and described the dynamic features of the whole protein, the domain, the helices, and the amino acid residues during an inward-open process from its occluded state. The gradual inward-open process is different from the current model of rigid-body domain motion in alternating-access mechanism. Simulation results show that the EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. In addition, it is observed that the helices exposed to the surrounding membrane show a higher level of flexibility than the other regions, and the protonated E227 plays a key role in the transition from the occluded to the open state. -- Highlights: •This study described the dynamic features of the whole EmrD protein, during an inward-open process from its occluded state. •The EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. •The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. •The protonated E227 plays a key role in the transition from the occluded to the open state.

Theme: Parents and Reading.

Science.gov (United States)

Jund, Suzanne, Ed.

1977-01-01

This journal issue concentrates on the theme "Parents and Reading." It presents articles on sharing books with young children, using public relations in a reading program, guiding preschool learning, assessing language readiness, working with reading problems, and teaching reading readiness in Wisconsin kindergartens. Resources and a review of…

Effects of reading goals on reading comprehension, reading rate, and allocation of working memory in children and adolescents with spina bifida meningomyelocele

Science.gov (United States)

ENGLISH, LIANNE; BARNES, MARCIA A.; FLETCHER, JACK M.; DENNIS, MAUREEN; RAGHUBAR, KIMBERLY P.

2011-01-01

Spina bifida meningomyelocele (SBM) is a neurodevelopmental disorder associated with intact word decoding and deficient text and discourse comprehension. This study investigated the ability to adjust reading in accordance with specified reading goals in 79 children and adolescents with SBM (9–19 years of age) and 39 controls (8–17 years of age). Both groups demonstrated slower reading times and enhanced comprehension when reading to study or to come up with a title than when reading for specific information or for entertainment. For both groups, verbal working memory contributed to comprehension performance in those reading conditions hypothesized to require more cognitive effort. Despite their sensitivity to the goals of reading, the group with SBM answered fewer comprehension questions correctly across all reading goal conditions. The results are discussed in relation to the hypothesized cognitive underpinnings of comprehension deficits in SBM and to current models of text comprehension. PMID:20338082

Effects of reading goals on reading comprehension, reading rate, and allocation of working memory in children and adolescents with spina bifida meningomyelocele.

Science.gov (United States)

English, Lianne; Barnes, Marcia A; Fletcher, Jack M; Dennis, Maureen; Raghubar, Kimberly P

2010-05-01

Spina bifida meningomyelocele (SBM) is a neurodevelopmental disorder associated with intact word decoding and deficient text and discourse comprehension. This study investigated the ability to adjust reading in accordance with specified reading goals in 79 children and adolescents with SBM (9-19 years of age) and 39 controls (8-17 years of age). Both groups demonstrated slower reading times and enhanced comprehension when reading to study or to come up with a title than when reading for specific information or for entertainment. For both groups, verbal working memory contributed to comprehension performance in those reading conditions hypothesized to require more cognitive effort. Despite their sensitivity to the goals of reading, the group with SBM answered fewer comprehension questions correctly across all reading goal conditions. The results are discussed in relation to the hypothesized cognitive underpinnings of comprehension deficits in SBM and to current models of text comprehension.

The Severe Acute Respiratory Syndrome (SARS-coronavirus 3a protein may function as a modulator of the trafficking properties of the spike protein

Directory of Open Access Journals (Sweden)

Tan Yee-Joo

2005-02-01

Full Text Available Abstract Background A recent publication reported that a tyrosine-dependent sorting signal, present in cytoplasmic tail of the spike protein of most coronaviruses, mediates the intracellular retention of the spike protein. This motif is missing from the spike protein of the severe acute respiratory syndrome-coronavirus (SARS-CoV, resulting in high level of surface expression of the spike protein when it is expressed on its own in vitro. Presentation of the hypothesis It has been shown that the severe acute respiratory syndrome-coronavirus genome contains open reading frames that encode for proteins with no homologue in other coronaviruses. One of them is the 3a protein, which is expressed during infection in vitro and in vivo. The 3a protein, which contains a tyrosine-dependent sorting signal in its cytoplasmic domain, is expressed on the cell surface and can undergo internalization. In addition, 3a can bind to the spike protein and through this interaction, it may be able to cause the spike protein to become internalized, resulting in a decrease in its surface expression. Testing the hypothesis The effects of 3a on the internalization of cell surface spike protein can be examined biochemically and the significance of the interplay between these two viral proteins during viral infection can be studied using reverse genetics methodology. Implication of the hypothesis If this hypothesis is proven, it will indicate that the severe acute respiratory syndrome-coronavirus modulates the surface expression of the spike protein via a different mechanism from other coronaviruses. The interaction between 3a and S, which are expressed from separate subgenomic RNA, would be important for controlling the trafficking properties of S. The cell surface expression of S in infected cells significantly impacts viral assembly, viral spread and viral pathogenesis. Modulation by this unique pathway could confer certain advantages during the replication of the severe

Reading disorders and dyslexia.

Science.gov (United States)

Hulme, Charles; Snowling, Margaret J

2016-12-01

We review current knowledge about the nature of reading development and disorders, distinguishing between the processes involved in learning to decode print, and the processes involved in reading comprehension. Children with decoding difficulties/dyslexia experience deficits in phoneme awareness, letter-sound knowledge and rapid automatized naming in the preschool years and beyond. These phonological/language difficulties appear to be proximal causes of the problems in learning to decode print in dyslexia. We review data from a prospective study of children at high risk of dyslexia to show that being at family risk of dyslexia is a primary risk factor for poor reading and children with persistent language difficulties at school entry are more likely to develop reading problems. Early oral language difficulties are strong predictors of later difficulties in reading comprehension. There are two distinct forms of reading disorder in children: dyslexia (a difficulty in learning to translate print into speech) and reading comprehension impairment. Both forms of reading problem appear to be predominantly caused by deficits in underlying oral language skills. Implications for screening and for the delivery of robust interventions for language and reading are discussed.

Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants.

Science.gov (United States)

Butkiewicz, Mariusz; Haines, Jonathan L; Bush, William S

2017-05-15

Reading frame altering genomic variants can impact gene expression levels and the structure of protein products, thus potentially inducing disease phenotypes. Current annotation approaches report the impact of such variants in the context of altered DNA sequence only; attributes of the resulting transcript, reading frame and translated protein product are not reported. To remedy this shortcoming, we present a new genetic annotation approach termed Codon Consequence Scanner (COCOS). Implemented as an Ensembl variant effect predictor (VEP) plugin, COCOS captures amino acid sequence alterations stemming from variants that produce an altered reading frame, such as stop-lost variants and small insertions and deletions (InDels). To highlight its significance, COCOS was applied to data from the 1000 Genomes Project. Transcripts affected by stop-lost variants introduce a median of 15 amino acids, while InDels have a more extensive impact with a median of 66 amino acids being incorporated. Captured sequence alterations are written out in FASTA format and can be further analyzed for impact on the underlying protein structure. COCOS is available to all users on github: https://github.com/butkiem/COCOS. mariusz.butkiewicz@case.edu. © The Author 2017. Published by Oxford University Press.