Computational discovery of small open reading frames in Bacillus lehensis

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333

PubMed Central

Nishimura, Yuki; Kamikawa, Ryoma; Hashimoto, Tetsuo; Inagaki, Yuji

2014-01-01

Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5′ and 3′ termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a “free-standing,” IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames. PMID:25054084

Draft genome sequence of rice orange leaf phytoplasma from Guangdong, China

USDA-ARS?s Scientific Manuscript database

The genome of rice orange leaf phytoplasma strain LD1 from Luoding City, Guangdong, P. R. China, was sequenced. The draft LD1genome is 599,264 bp with GC content of 28.2%, 647 predicted open reading frames and 33 RNA genes....

Communicating Inequalities to Enhance Support for Obesity-Prevention Policies: The Role of Social Comparisons, Age Frames, and Emotion.

PubMed

Skurka, Chris

2017-11-28

With certain populations in the United States at higher risk for obesity than other populations, public health advocates have attempted to draw attention to these inequalities to galvanize support for obesity-mitigation policies. Yet research comparing different messages about social inequalities indicates that not all social comparisons are persuasive. Drawing on Weiner's (1986) theory of perceived responsibility and social motivation, I experimentally tested promising message frames about obesity disparities. Participants (N = 653) read one of six messages following a 3 (social comparison frame: geographic vs. racial vs. no-comparison) × 2 (age frame: child vs. adult) between-subjects design. Unexpectedly, geographic frames (rural/urban) indirectly decreased policy support relative to the control frame by way of increased counterarguing. Compared to adult frames about obesity inequalities, childhood frames evoked more sympathy and less internal attribution, which in turn positively predicted support for obesity-prevention policies. Practical and theoretical implications of these findings are discussed.

Page turning system

NASA Technical Reports Server (NTRS)

Kerley, James J. (Inventor); Eklund, Wayne D. (Inventor)

1992-01-01

A device for holding reading materials for use by readers without arm mobility is presented. The device is adapted to hold the reading materials in position for reading with the pages displayed to enable turning by use of a rubber tipped stick that is held in the mouth and has a pair of rectangular frames. The frames are for holding and positioning the reading materials opened in reading posture with the pages displayed at a substantially unobstructed sighting position for reading. The pair of rectangular frames are connected to one another by a hinge so the angle between the frames may be varied thereby varying the inclination of the reading material. A pair of bent spring mounted wires for holding opposing pages of the reading material open for reading without substantial visual interference of the pages is mounted to the base. The wires are also adjustable to the thickness of the reading material and have a variable friction adjustment. This enables the force of the wires against the pages to be varied and permits the reader to manipulate the pages with the stick.

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

PubMed

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 structure (ARC) are identical to portions of the deduced open reading frame of TIG-1 mRNA.

Popcorn Story Frames from a Multicultural Perspective.

ERIC Educational Resources Information Center

DiLella, Carol Ann

Popcorn story frames from a multicultural perspective are holistic outlines that in the reading/writing process facilitate comprehension for all cultures learning to read and write stories. Popcorn story frames are structured and modeled in a horizontal fashion just like popcorn pops in a horizontal fashion. The frames are designed for learners…

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-03-01

Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. © 2015 American Society of Plant Biologists. All rights reserved.

Correction of Dystrophin Expression in Cells From Duchenne Muscular Dystrophy Patients Through Genomic Excision of Exon 51 by Zinc Finger Nucleases

PubMed Central

Ousterout, David G; Kabadi, Ami M; Thakore, Pratiksha I; Perez-Pinera, Pablo; Brown, Matthew T; Majoros, William H; Reddy, Timothy E; Gersbach, Charles A

2015-01-01

Duchenne muscular dystrophy (DMD) is caused by genetic mutations that result in the absence of dystrophin protein expression. Oligonucleotide-induced exon skipping can restore the dystrophin reading frame and protein production. However, this requires continuous drug administration and may not generate complete skipping of the targeted exon. In this study, we apply genome editing with zinc finger nucleases (ZFNs) to permanently remove essential splicing sequences in exon 51 of the dystrophin gene and thereby exclude exon 51 from the resulting dystrophin transcript. This approach can restore the dystrophin reading frame in ~13% of DMD patient mutations. Transfection of two ZFNs targeted to sites flanking the exon 51 splice acceptor into DMD patient myoblasts led to deletion of this genomic sequence. A clonal population was isolated with this deletion and following differentiation we confirmed loss of exon 51 from the dystrophin mRNA transcript and restoration of dystrophin protein expression. Furthermore, transplantation of corrected cells into immunodeficient mice resulted in human dystrophin expression localized to the sarcolemmal membrane. Finally, we quantified ZFN toxicity in human cells and mutagenesis at predicted off-target sites. This study demonstrates a powerful method to restore the dystrophin reading frame and protein expression by permanently deleting exons. PMID:25492562

A genetic scale of reading frame coding.

PubMed

Michel, Christian J

2014-08-21

The reading frame coding (RFC) of codes (sets) of trinucleotides is a genetic concept which has been largely ignored during the last 50 years. A first objective is the definition of a new and simple statistical parameter PrRFC for analysing the probability (efficiency) of reading frame coding (RFC) of any trinucleotide code. A second objective is to reveal different classes and subclasses of trinucleotide codes involved in reading frame coding: the circular codes of 20 trinucleotides and the bijective genetic codes of 20 trinucleotides coding the 20 amino acids. This approach allows us to propose a genetic scale of reading frame coding which ranges from 1/3 with the random codes (RFC probability identical in the three frames) to 1 with the comma-free circular codes (RFC probability maximal in the reading frame and null in the two shifted frames). This genetic scale shows, in particular, the reading frame coding probabilities of the 12,964,440 circular codes (PrRFC=83.2% in average), the 216 C(3) self-complementary circular codes (PrRFC=84.1% in average) including the code X identified in eukaryotic and prokaryotic genes (PrRFC=81.3%) and the 339,738,624 bijective genetic codes (PrRFC=61.5% in average) including the 52 codes without permuted trinucleotides (PrRFC=66.0% in average). Otherwise, the reading frame coding probabilities of each trinucleotide code coding an amino acid with the universal genetic code are also determined. The four amino acids Gly, Lys, Phe and Pro are coded by codes (not circular) with RFC probabilities equal to 2/3, 1/2, 1/2 and 2/3, respectively. The amino acid Leu is coded by a circular code (not comma-free) with a RFC probability equal to 18/19. The 15 other amino acids are coded by comma-free circular codes, i.e. with RFC probabilities equal to 1. The identification of coding properties in some classes of trinucleotide codes studied here may bring new insights in the origin and evolution of the genetic code. Copyright © 2014 Elsevier Ltd. All rights reserved.

Complete Genome Sequence of the Mesoplasma florum W37 Strain

PubMed Central

Baby, Vincent; Matteau, Dominick; Knight, Thomas F.

2013-01-01

Mesoplasma florum is a small-genome fast-growing mollicute that is an attractive model for systems and synthetic genomics studies. We report the complete 825,824-bp genome sequence of a second representative of this species, M. florum strain W37, which contains 733 predicted open reading frames and 35 stable RNAs. PMID:24285658

Whole genome sequence of “Candidatus Profftella armatura” from Diaphorina citri in Guangdong, China

USDA-ARS?s Scientific Manuscript database

The genome of “Candidatus Profftella armatura” strain YCPA, a symbiont of Asian citrus psyllid, from Guangdong, China, was sequenced. The strain chromosome was 457,565 bp with 24.3% G+C content, 364 predicted open reading frames (ORFs), and 38 RNA genes. The strain also contains a 5,458 bp plasmid, ...

Genome Sequence of JangDynasty, a Newly Isolated Mycobacteriophage

PubMed Central

Jang, Casey; Kalaj, Nancy; Hwang, Brian; Hughes, Lorelei; Yang, Connie; Pak, Thomas; Kim, John; Han, Dong Yoon; Tedjakusnadi, Jason; Fernandez, Nicholas; Dean, Natasha; Muthiah, Arun; Sutter, Nathaniel B.

2018-01-01

ABSTRACT JangDynasty is a bacteriophage that infects Mycobacterium smegmatis mc2155. It has a genome length of 70,883 bp, with 124 predicted open reading frames (ORFs), 42 of which have known functions. JangDynasty belongs to cluster O, and like other cluster O phages, it is a siphovirus with a prolate capsid. PMID:29798914

Complete Genome Sequence of Pseudomonas aeruginosa Phage AAT-1

PubMed Central

Andrade-Domínguez, Andrés

2016-01-01

Aspects of the interaction between phages and animals are of interest and importance for medical applications. Here, we report the genome sequence of the lytic Pseudomonas phage AAT-1, isolated from mammalian serum. AAT-1 is a double-stranded DNA phage, with a genome of 57,599 bp, containing 76 predicted open reading frames. PMID:27563032

A draft genome sequence of “Candidatus Liberibacter asiaticus” from California, USA

USDA-ARS?s Scientific Manuscript database

The draft genome sequence of “Candidatus Liberibacter asiaticus” strain HHCA, collected from a lemon tree in California, USA, is reported. The HHCA strain has a genome size of 1,118,244 bp, with G+C content of 36.6%. The HHCA genome encodes 1,191 predicted open reading frames and 51 RNA genes....

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.

PubMed

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.

Determination of the complete genomic sequence and analysis of the gene products of the virus of Spring Viremia of Carp, a fish rhabdovirus.

PubMed

Hoffmann, Bernd; Schütze, Heike; Mettenleiter, Thomas C

2002-03-20

The complete genome of spring viremia of carp virus (SVCV) was cloned and the sequence of 11019 nucleotides was determined. It contains five open reading frames (ORF's) encoding for the nucleoprotein N; phosphoprotein P; matrix protein M; glycoprotein G; and the viral RNA dependent RNA polymerase L. Genes are organised in the order typical for rhabdoviruses: 3'-N-P-M-G-L-5'. The short leader and trailer regions of SVCV exhibit inverse complementarity and are similar to the respective 3' and 5' ends of the genome of vesicular stomatitis virus. To verify the predicted open reading frames proteins were expressed in bacteria and analysed with a polyclonal anti-SVCV serum. Furthermore, monospecific antisera against the distinct viral proteins were generated. Comparison of genome and protein confirm the assignment of SVCV to the genus Vesiculovirus.

Expression of a non-coding RNA in ectromelia virus is required for normal plaque formation.

PubMed

Esteban, David J; Upton, Chris; Bartow-McKenney, Casey; Buller, R Mark L; Chen, Nanhai G; Schriewer, Jill; Lefkowitz, Elliot J; Wang, Chunlin

2014-02-01

Poxviruses are dsDNA viruses with large genomes. Many genes in the genome remain uncharacterized, and recent studies have demonstrated that the poxvirus transcriptome includes numerous so-called anomalous transcripts not associated with open reading frames. Here, we characterize the expression and role of an apparently non-coding RNA in orthopoxviruses, which we call viral hairpin RNA (vhRNA). Using a bioinformatics approach, we predicted expression of a transcript not associated with an open reading frame that is likely to form a stem-loop structure due to the presence of a 21 nt palindromic sequence. Expression of the transcript as early as 2 h post-infection was confirmed by northern blot and analysis of publicly available vaccinia virus infected cell transcriptomes. The transcription start site was determined by RACE PCE and transcriptome analysis, and early and late promoter sequences were identified. Finally, to test the function of the transcript we generated an ectromelia virus knockout, which failed to form plaques in cell culture. The important role of the transcript in viral replication was further demonstrated using siRNA. Although the function of the transcript remains unknown, our work contributes to evidence of an increasingly complex poxvirus transcriptome, suggesting that transcripts such as vhRNA not associated with an annotated open reading frame can play an important role in viral replication.

The Saccharomyces cerevisiae LOS1 gene involved in pre-tRNA splicing encodes a nuclear protein that behaves as a component of the nuclear matrix.

PubMed

Shen, W C; Selvakumar, D; Stanford, D R; Hopper, A K

1993-09-15

Mutations of the Saccharomyces cerevisiae LOS1 gene cause the accumulation of end matured intron-containing pre-tRNAs at elevated temperatures. In an effort to decipher the role of the LOS1 protein in pre-tRNA splicing, we have analyzed the LOS1 gene and its protein product. The LOS1 gene is located on the left arm of chromosome XI and the order of genes in this area of the chromosome is .... URA1 ... SAC1 TRP3 UBA1 STE6 LOS1 .... FAS1..... The LOS1 open reading frame encodes a putative protein of 1100 amino acids that shows no significant homology to other genes. The LOS1 open reading frame was tagged with the influenza virus hemagglutinin epitope recognized by the 12CA5 antibody. The 12CA5 antibody recognizes an epitope-tagged protein of the size predicted by the LOS1 open reading frame. Using this antibody for indirect immunofluorescence and cell fractionation studies we show that the LOS1 protein is located in nuclei. Los1p cannot be extracted from nuclei by treatment with nucleases, salts, or Triton X-100. This insolubility suggests that Los1p is a component of the nucleoskeleton. We propose that LOS1 mutations may affect pre-tRNA processing via alteration of the nuclear matrix.

Open Reading Frame Phylogenetic Analysis on the Cloud

PubMed Central

2013-01-01

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

Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar

Treesearch

John Kuzio; Margot N. Pearson; Steve H. Harwood; C. Joel Funk; Jay T. Evans; James M. Slavicek; George F. Rohrmann

1999-01-01

The genome of the Lymantria dispar multinucleocapsid nucleopolyhedrovirus (LdMNPV) was sequenced and analyzed. It is composed of 161,046 bases with a G + C content of 57.5% and contains 163 putative open reading frames (ORFs) of ≥150 nucleotides. Homologs were found to 95 of the 155 genes predicted for the Autographa californica...

Whole genome sequence of “Candidatus Liberibacter asiaticus” from a huanglongbing-affected citrus tree in Central Florida

USDA-ARS?s Scientific Manuscript database

The draft genome sequence of “Candidatus Liberibacter asiaticus” strain FL17, isolated from an HLB-affected citrus tree in central Florida, was determined. The FL17 genome comprised 1,227,253 bp with a G+C content of 36.5%, 1,175 predicted open reading frames, and 53 RNA genes....

A draft whole genome sequence of “Candidatus Liberibacter asiaticus” strain TX2351 from Asian citrus psyllids in Texas, USA

USDA-ARS?s Scientific Manuscript database

The draft genome sequence of “Candidatus Liberibacter asiaticus” strain TX2351 collected from ACP in South Texas has been determined. The TX2351 genome is 1,252,043 bp in size with a 36.5% G+C content, encoding 1,184 predicted open reading frames and 51 RNA genes....

Genome Sequence of JangDynasty, a Newly Isolated Mycobacteriophage.

PubMed

Jang, Casey; Kalaj, Nancy; Hwang, Brian; Hughes, Lorelei; Yang, Connie; Pak, Thomas; Kim, John; Han, Dong Yoon; Tedjakusnadi, Jason; Fernandez, Nicholas; Dean, Natasha; Muthiah, Arun; Sutter, Nathaniel B; Diaz, Arturo

2018-05-24

JangDynasty is a bacteriophage that infects Mycobacterium smegmatis mc 2 155. It has a genome length of 70,883 bp, with 124 predicted open reading frames (ORFs), 42 of which have known functions. JangDynasty belongs to cluster O, and like other cluster O phages, it is a siphovirus with a prolate capsid. Copyright © 2018 Jang et al.

Homology between DNA polymerases of poxviruses, herpesviruses, and adenoviruses: nucleotide sequence of the vaccinia virus DNA polymerase gene.

PubMed Central

Earl, P L; Jones, E V; Moss, B

1986-01-01

A 5400-base-pair segment of the vaccinia virus genome was sequenced and an open reading frame of 938 codons was found precisely where the DNA polymerase had been mapped by transfer of a phosphonoacetate-resistance marker. A single nucleotide substitution changing glycine at position 347 to aspartic acid accounts for the drug resistance of the mutant vaccinia virus. The 5' end of the DNA polymerase mRNA was located 80 base pairs before the methionine codon initiating the open reading frame. Correspondence between the predicted Mr 108,577 polypeptide and the 110,000 purified enzyme indicates that little or no proteolytic processing occurs. Extensive homology, extending over 435 amino acids, was found upon comparing the DNA polymerase of vaccinia virus and DNA polymerase of Epstein-Barr virus. A highly conserved sequence of 14 amino acids in the carboxyl-terminal regions of the above DNA polymerases is also present at a similar location in adenovirus DNA polymerase. This structure, which is predicted to form a turn flanked by beta-pleated sheets, may form part of an essential binding or catalytic site that accounts for its presence in DNA polymerases of poxviruses, herpesviruses, and adenoviruses. Images PMID:3012524

Give blood today or save lives tomorrow: Matching decision and message construal level to maximize blood donation intentions.

PubMed

Czeizler, Amalia; Garbarino, Ellen

2017-01-01

The research extends construal theory by testing if a match between the temporal construal framing of a blood donation decision and a blood donation request leads to higher donation intentions than a mismatch. Results show participants considering future donation who read an abstract donation request have significantly higher donation intentions than those who read a concrete request. Conversely, participants considering donating today who read a concrete donation request have significantly higher donation intentions than those who read an abstract request. This study confirms the importance of matching the construal framing of the communication to the temporal framing of the decision.

Structural determinants of an internal ribosome entry site that direct translational reading frame selection

PubMed Central

Ren, Qian; Au, Hilda H.T.; Wang, Qing S.; Lee, Seonghoon; Jan, Eric

2014-01-01

The dicistrovirus intergenic internal ribosome entry site (IGR IRES) directly recruits the ribosome and initiates translation using a non-AUG codon. A subset of IGR IRESs initiates translation in either of two overlapping open reading frames (ORFs), resulting in expression of the 0 frame viral structural polyprotein and an overlapping +1 frame ORFx. A U–G base pair adjacent to the anticodon-like pseudoknot of the IRES directs +1 frame translation. Here, we show that the U-G base pair is not absolutely required for +1 frame translation. Extensive mutagenesis demonstrates that 0 and +1 frame translation can be uncoupled. Ribonucleic acid (RNA) structural probing analyses reveal that the mutant IRESs adopt distinct conformations. Toeprinting analysis suggests that the reading frame is selected at a step downstream of ribosome assembly. We propose a model whereby the IRES adopts conformations to occlude the 0 frame aminoacyl-tRNA thereby allowing delivery of the +1 frame aminoacyl-tRNA to the A site to initiate translation of ORFx. This study provides a new paradigm for programmed recoding mechanisms that increase the coding capacity of a viral genome. PMID:25038250

Developmental rearrangement of cyanobacterial nif genes: nucleotide sequence, open reading frames, and cytochrome P-450 homology of the Anabaena sp. strain PCC 7120 nifD element.

PubMed Central

Lammers, P J; McLaughlin, S; Papin, S; Trujillo-Provencio, C; Ryncarz, A J

1990-01-01

An 11-kbp DNA element of unknown function interrupts the nifD gene in vegetative cells of Anabaena sp. strain PCC 7120. In developing heterocysts the nifD element excises from the chromosome via site-specific recombination between short repeat sequences that flank the element. The nucleotide sequence of the nifH-proximal half of the element was determined to elucidate the genetic potential of the element. Four open reading frames with the same relative orientation as the nifD element-encoded xisA gene were identified in the sequenced region. Each of the open reading frames was preceded by a reasonable ribosome-binding site and had biased codon utilization preferences consistent with low levels of expression. Open reading frame 3 was highly homologous with three cytochrome P-450 omega-hydroxylase proteins and showed regional homology to functionally significant domains common to the cytochrome P-450 superfamily. The sequence encoding open reading frame 2 was the most highly conserved portion of the sequenced region based on heterologous hybridization experiments with three genera of heterocystous cyanobacteria. Images PMID:2123860

When 'fit' leads to fit, and when 'fit' leads to fat: how message framing and intrinsic vs. extrinsic exercise outcomes interact in promoting physical activity.

PubMed

Gallagher, Kristel M; Updegraff, John A

2011-07-01

A unique aspect of exercise is that people may choose to engage in it to achieve a variety of outcomes, ranging from extrinsic (appearance, health) to intrinsic (satisfaction, enjoyment). We examined how the impact of gain- vs. loss-framed messages depends on the type of outcome emphasised. Drawing from regulatory focus theory (Higgins, E.T. (1997). Beyond pleasure and pain. American Psychologist, 52, 1280-1300; Higgins, E.T. (2000). Making a good decision: Value from fit. American Psychologist, 55, 1217-1230), we predicted that gain-framed messages would 'fit' with intrinsic outcomes and loss-framed messages would 'fit' with extrinsic outcomes, but the effect of such fit on physical activity would depend on the participants' need for cognition (NC). We tested these hypotheses with a sample of 176 sedentary young adults who read an exercise message with randomly assigned frame (gain/loss) and outcome (intrinsic/extrinsic). Participants provided daily reports of exercise over the following week. The predicted interaction between frame, outcome and NC was found (p=0.001) such that a 'fit' message promoted somewhat, but not significantly, greater exercise for those with high NC, but a 'non-fit' message promoted significantly greater exercise for those with low NC. Furthermore, differences in physical activity were partially mediated by attitudes towards exercise. Findings shed light on how the outcomes and motivations associated with physical activity shape people's behavioural responses to framed health communications. © 2011 Taylor & Francis

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

PubMed

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.

Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection

PubMed Central

Au, Hilda H.; Cornilescu, Gabriel; Mouzakis, Kathryn D.; Ren, Qian; Burke, Jordan E.; Lee, Seonghoon; Butcher, Samuel E.; Jan, Eric

2015-01-01

The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and +1 frame translation, suggesting that the structure adopts distinct conformations that contribute to 0 or +1 frame translation. Using a reconstituted translation system, we show that ribosomes assembled on mutant IRESs that direct exclusive 0 or +1 frame translation lack reading frame fidelity. Finally, a nuclear magnetic resonance/small-angle X-ray scattering hybrid approach reveals that the PKI domain of the IAPV IRES adopts an RNA structure that resembles a complete tRNA. The tRNA shape-mimicry enables the viral IRES to gain access to the ribosome tRNA-binding sites and form intermolecular contacts with the ribosome that are necessary for initiating IRES translation in a specific reading frame. PMID:26554019

Promoting the Avoidance of High-Calorie Snacks: Priming Autonomy Moderates Message Framing Effects

PubMed Central

Pavey, Louisa; Churchill, Sue

2014-01-01

The beneficial effects of gain-framed vs. loss-framed messages promoting health protective behaviors have been found to be inconsistent, and consideration of potential moderating variables is essential if framed health promotion messages are to be effective. This research aimed to determine the influence of highlighting autonomy (choice and freedom) and heteronomy (coercion) on the avoidance of high-calorie snacks following reading gain-framed or loss-framed health messages. In Study 1 (N = 152) participants completed an autonomy, neutral, or heteronomy priming task, and read a gain-framed or loss-framed health message. In Study 2 (N = 242) participants read a gain-framed or loss-framed health message with embedded autonomy or heteronomy primes. In both studies, snacking intentions and behavior were recorded after seven days. In both studies, when autonomy was highlighted, the gain-framed message (compared to the loss-framed message) resulted in stronger intentions to avoid high-calorie snacks, and lower self-reported snack consumption after seven days. Study 2 demonstrated this effect occurred only for participants to whom the information was most relevant (BMI>25). The results suggest that messages promoting healthy dietary behavior may be more persuasive if the autonomy-supportive vs. coercive nature of the health information is matched to the message frame. Further research is needed to examine potential mediating processes. PMID:25078965

Promoting the avoidance of high-calorie snacks: priming autonomy moderates message framing effects.

PubMed

Pavey, Louisa; Churchill, Sue

2014-01-01

The beneficial effects of gain-framed vs. loss-framed messages promoting health protective behaviors have been found to be inconsistent, and consideration of potential moderating variables is essential if framed health promotion messages are to be effective. This research aimed to determine the influence of highlighting autonomy (choice and freedom) and heteronomy (coercion) on the avoidance of high-calorie snacks following reading gain-framed or loss-framed health messages. In Study 1 (N = 152) participants completed an autonomy, neutral, or heteronomy priming task, and read a gain-framed or loss-framed health message. In Study 2 (N = 242) participants read a gain-framed or loss-framed health message with embedded autonomy or heteronomy primes. In both studies, snacking intentions and behavior were recorded after seven days. In both studies, when autonomy was highlighted, the gain-framed message (compared to the loss-framed message) resulted in stronger intentions to avoid high-calorie snacks, and lower self-reported snack consumption after seven days. Study 2 demonstrated this effect occurred only for participants to whom the information was most relevant (BMI>25). The results suggest that messages promoting healthy dietary behavior may be more persuasive if the autonomy-supportive vs. coercive nature of the health information is matched to the message frame. Further research is needed to examine potential mediating processes.

ORF43 of Maize rayado fino virus is dispensable for systemic infection of maize and transmission by leafhoppers

USDA-ARS?s Scientific Manuscript database

Maize rayado fino virus (MRFV) possesses an open reading frame (ORF) encoding a protein with predicted mass of 43 kDa (ORF43) that has been postulated to be a viral movement protein. Using a clone of MRFV (pMRFV-US) from which infectious RNA can be produced, point mutations were introduced to eithe...

Draft Genome Sequence of the d-Xylose-Fermenting Yeast Spathaspora arborariae UFMG-HM19.1AT

PubMed Central

Lobo, Francisco P.; Gonçalves, Davi L.; Alves, Sergio L.; Gerber, Alexandra L.; de Vasconcelos, Ana Tereza R.; Basso, Luiz C.; Franco, Glória R.; Soares, Marco A.; Cadete, Raquel M.; Rosa, Carlos A.

2014-01-01

The draft genome sequence of the yeast Spathaspora arborariae UFMG-HM19.1AT (CBS 11463 = NRRL Y-48658) is presented here. The sequenced genome size is 12.7 Mb, consisting of 41 scaffolds containing a total of 5,625 predicted open reading frames, including many genes encoding enzymes and transporters involved in d-xylose fermentation. PMID:24435867

Draft genome sequence of Xylella fastidiosa supsp. multiplex strain Griffin-1 from Quercus rubra in Georgia

USDA-ARS?s Scientific Manuscript database

The draft genome sequence of Xylella fastidiosa subsp. multiplex Strain Griffin-1 isolated from a red oak tree (Quercus rubra) in Georgia, U.S.A. is reported. The bacterium has a genome size of 2,387,314 bp with 51.7% G+C content and comprises 2,903 predicted open reading frames (ORFs), and 50 RNA g...

Complete genome sequence of Flavobacterium psychrophilum strain CSF259-93 used to select rainbow trout for increased genetic resistance against bacterial cold water disease

USDA-ARS?s Scientific Manuscript database

The genome sequence of Flavobacterium psychrophilum strain CSF259-93, isolated from rainbow trout (Oncorhynchus mykiss), consists of a single circular genome of 2,900,735 bp and 2,701 predicted open reading frames (ORFs). Strain CSF259-93 has been used to select a line of rainbow trout with increase...

Complete Genome Sequence of Pseudomonas aeruginosa Phage AAT-1.

PubMed

Andrade-Domínguez, Andrés; Kolter, Roberto

2016-08-25

Aspects of the interaction between phages and animals are of interest and importance for medical applications. Here, we report the genome sequence of the lytic Pseudomonas phage AAT-1, isolated from mammalian serum. AAT-1 is a double-stranded DNA phage, with a genome of 57,599 bp, containing 76 predicted open reading frames. Copyright © 2016 Andrade-Domínguez and Kolter.

Popcorn Story Frames.

ERIC Educational Resources Information Center

DiLella, Carol Ann

This paper presents "popcorn story frames"--holistic outlines that facilitate comprehension when reading and writing stories, useful for outlining stories read and for creating outlines for original student stories--that are particularly useful for elementary and intermediate school students. "Popcorn" pops in a horizontal…

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

PubMed Central

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

URF6, Last Unidentified Reading Frame of Human mtDNA, Codes for an NADH Dehydrogenase Subunit

NASA Astrophysics Data System (ADS)

Chomyn, Anne; Cleeter, Michael W. J.; Ragan, C. Ian; Riley, Marcia; Doolittle, Russell F.; Attardi, Giuseppe

1986-10-01

The polypeptide encoded in URF6, the last unassigned reading frame of human mitochondrial DNA, has been identified with antibodies to peptides predicted from the DNA sequence. Antibodies prepared against highly purified respiratory chain NADH dehydrogenase from beef heart or against the cytoplasmically synthesized 49-kilodalton iron-sulfur subunit isolated from this enzyme complex, when added to a deoxycholate or a Triton X-100 mitochondrial lysate of HeLa cells, specifically precipitated the URF6 product together with the six other URF products previously identified as subunits of NADH dehydrogenase. These results strongly point to the URF6 product as being another subunit of this enzyme complex. Thus, almost 60% of the protein coding capacity of mammalian mitochondrial DNA is utilized for the assembly of the first enzyme complex of the respiratory chain. The absence of such information in yeast mitochondrial DNA dramatizes the variability in gene content of different mitochondrial genomes.

Physics of Non-Inertial Reference Frames

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

Kamalov, Timur F.

2010-12-22

Physics of non-inertial reference frames is a generalizing of Newton's laws to any reference frames. It is the system of general axioms for classical and quantum mechanics. The first, Kinematics Principle reads: the kinematic state of a body free of forces conserves and equal in absolute value to an invariant of the observer's reference frame. The second, Dynamics Principle extended Newton's second law to non-inertial reference frames and also contains additional variables there are higher derivatives of coordinates. Dynamics Principle reads: a force induces a change in the kinematic state of the body and is proportional to the rate ofmore » its change. It is mean that if the kinematic invariant of the reference frame is n-th derivative with respect the time, then the dynamics of a body being affected by the force F is described by the 2n-th differential equation. The third, Statics Principle reads: the sum of all forces acting a body at rest is equal to zero.« less

A Duchenne Muscular Dystrophy Gene Hot Spot Mutation in Dystrophin-Deficient Cavalier King Charles Spaniels Is Amenable to Exon 51 Skipping

PubMed Central

Walmsley, Gemma L.; Arechavala-Gomeza, Virginia; Fernandez-Fuente, Marta; Burke, Margaret M.; Nagel, Nicole; Holder, Angela; Stanley, Rachael; Chandler, Kate; Marks, Stanley L.; Muntoni, Francesco; Shelton, G. Diane; Piercy, Richard J.

2010-01-01

Background Duchenne muscular dystrophy (DMD), which afflicts 1 in 3500 boys, is one of the most common genetic disorders of children. This fatal degenerative condition is caused by an absence or deficiency of dystrophin in striated muscle. Most affected patients have inherited or spontaneous deletions in the dystrophin gene that disrupt the reading frame resulting in unstable truncated products. For these patients, restoration of the reading frame via antisense oligonucleotide-mediated exon skipping is a promising therapeutic approach. The major DMD deletion “hot spot” is found between exons 45 and 53, and skipping exon 51 in particular is predicted to ameliorate the dystrophic phenotype in the greatest number of patients. Currently the mdx mouse is the most widely used animal model of DMD, although its mild phenotype limits its suitability in clinical trials. The Golden Retriever muscular dystrophy (GRMD) model has a severe phenotype, but due to its large size, is expensive to use. Both these models have mutations in regions of the dystrophin gene distant from the commonly mutated DMD “hot spot”. Methodology/Principal Findings Here we describe the severe phenotype, histopathological findings, and molecular analysis of Cavalier King Charles Spaniels with dystrophin-deficient muscular dystrophy (CKCS-MD). The dogs harbour a missense mutation in the 5′ donor splice site of exon 50 that results in deletion of exon 50 in mRNA transcripts and a predicted premature truncation of the translated protein. Antisense oligonucleotide-mediated skipping of exon 51 in cultured myoblasts from an affected dog restored the reading frame and protein expression. Conclusions/Significance Given the small size of the breed, the amiable temperament and the nature of the mutation, we propose that CKCS-MD is a valuable new model for clinical trials of antisense oligonucleotide-induced exon skipping and other therapeutic approaches for DMD. PMID:20072625

Encrypting Digital Camera with Automatic Encryption Key Deletion

NASA Technical Reports Server (NTRS)

Oakley, Ernest C. (Inventor)

2007-01-01

A digital video camera includes an image sensor capable of producing a frame of video data representing an image viewed by the sensor, an image memory for storing video data such as previously recorded frame data in a video frame location of the image memory, a read circuit for fetching the previously recorded frame data, an encryption circuit having an encryption key input connected to receive the previously recorded frame data from the read circuit as an encryption key, an un-encrypted data input connected to receive the frame of video data from the image sensor and an encrypted data output port, and a write circuit for writing a frame of encrypted video data received from the encrypted data output port of the encryption circuit to the memory and overwriting the video frame location storing the previously recorded frame data.

The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames

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

Solovyev, V.V.; Salamov, A.A.; Lawrence, C.B.

1994-12-31

Discriminant analysis is applied to the problem of recognition 5`-, internal and 3`-exons in human DNA sequences. Specific recognition functions were developed for revealing exons of particular types. The method based on a splice site prediction algorithm that uses the linear Fisher discriminant to combine the information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotide in protein coding and nation regions. The accuracy of our splice site recognition function is about 97%. A discriminant function for 5`-exon prediction includes hexanucleotide composition of upstream region, triplet composition around the ATG codon, ORF codingmore » potential, donor splice site potential and composition of downstream introit region. For internal exon prediction, we combine in a discriminant function the characteristics describing the 5`- intron region, donor splice site, coding region, acceptor splice site and Y-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79% and a level of pseudoexon ORF prediction of 99.96%. The recognition quality computed at the level of individual nucleotides is 89%, for exon sequences and 98% for intron sequences. A discriminant function for 3`-exon prediction includes octanucleolide composition of upstream nation region, triplet composition around the stop codon, ORF coding potential, acceptor splice site potential and hexanucleotide composition of downstream region. We unite these three discriminant functions in exon predicting program FEX (find exons). FEX exactly predicts 70% of 1016 exons from the test of 181 complete genes with specificity 73%, and 89% exons are exactly or partially predicted. On the average, 85% of nucleotides were predicted accurately with specificity 91%.« less

Whole-Genome Sequence of "Candidatus Profftella armatura" from Diaphorina citri in Guangdong, China.

PubMed

Wu, F; Deng, X; Liang, G; Huang, J; Cen, Y; Chen, J

2015-11-05

The genome of "Candidatus Profftella armatura" strain YCPA from Diaphorina citri in Guangdong, China, was sequenced. The strain has a chromosome of 457,565 bp, 24.3% G+C content, 364 predicted open reading frames (ORFs), and 38 RNAs, and a plasmid, pYCPA54, of 5,458 bp with 23.9% G+C content and 5 ORFs. Copyright © 2015 Wu et al.

Complete Genome Sequence of EtG, the First Phage Sequenced from Erwinia tracheiphila.

PubMed

Andrade-Domínguez, Andrés; Kolter, Roberto; Shapiro, Lori R

2018-02-22

Erwinia tracheiphila is the causal agent of bacterial wilt of cucurbits. Here, we report the genome sequence of the temperate phage EtG, which was isolated from an E. tracheiphila -infected cucumber plant. Phage EtG has a linear 30,413-bp double-stranded DNA genome with cohesive ends and 45 predicted open reading frames. Copyright © 2018 Andrade-Domínguez et al.

Extensive frameshift at all AGG and CCC codons in the mitochondrial cytochrome c oxidase subunit 1 gene of Perkinsus marinus (Alveolata; Dinoflagellata).

PubMed

Masuda, Isao; Matsuzaki, Motomichi; Kita, Kiyoshi

2010-10-01

Diverse mitochondrial (mt) genetic systems have evolved independently of the more uniform nuclear system and often employ modified genetic codes. The organization and genetic system of dinoflagellate mt genomes are particularly unusual and remain an evolutionary enigma. We determined the sequence of full-length cytochrome c oxidase subunit 1 (cox1) mRNA of the earliest diverging dinoflagellate Perkinsus and show that this gene resides in the mt genome. Apparently, this mRNA is not translated in a single reading frame with standard codon usage. Our examination of the nucleotide sequence and three-frame translation of the mRNA suggest that the reading frame must be shifted 10 times, at every AGG and CCC codon, to yield a consensus COX1 protein. We suggest two possible mechanisms for these translational frameshifts: a ribosomal frameshift in which stalled ribosomes skip the first bases of these codons or specialized tRNAs recognizing non-triplet codons, AGGY and CCCCU. Regardless of the mechanism, active and efficient machinery would be required to tolerate the frameshifts predicted in Perkinsus mitochondria. To our knowledge, this is the first evidence of translational frameshifts in protist mitochondria and, by far, is the most extensive case in mitochondria.

PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse

PubMed Central

Reuter, Kerstin; Helms, Volkhard

2016-01-01

Translation of mRNA sequences into proteins typically starts at an AUG triplet. In rare cases, translation may also start at alternative non–AUG codons located in the annotated 5’ UTR which leads to an increased regulatory complexity. Since ribosome profiling detects translational start sites at the nucleotide level, the properties of these start sites can then be used for the statistical evaluation of functional open reading frames. We developed a linear regression approach to predict in–frame and out–of–frame translational start sites within the 5’ UTR from mRNA sequence information together with their translation initiation confidence. Predicted start codons comprise AUG as well as near–cognate codons. The underlying datasets are based on published translational start sites for human HEK293 and mouse embryonic stem cells that were derived by the original authors from ribosome profiling data. The average prediction accuracy of true vs. false start sites for HEK293 cells was 80%. When applied to mouse mRNA sequences, the same model predicted translation initiation sites observed in mouse ES cells with an accuracy of 76%. Moreover, we illustrate the effect of in silico mutations in the flanking sequence context of a start site on the predicted initiation confidence. Our new webservice PreTIS visualizes alternative start sites and their respective ORFs and predicts their ability to initiate translation. Solely, the mRNA sequence is required as input. PreTIS is accessible at http://service.bioinformatik.uni-saarland.de/pretis. PMID:27768687

Constructing high complexity synthetic libraries of long ORFs using in vitro selection

NASA Technical Reports Server (NTRS)

Cho, G.; Keefe, A. D.; Liu, R.; Wilson, D. S.; Szostak, J. W.

2000-01-01

We present a method that can significantly increase the complexity of protein libraries used for in vitro or in vivo protein selection experiments. Protein libraries are often encoded by chemically synthesized DNA, in which part of the open reading frame is randomized. There are, however, major obstacles associated with the chemical synthesis of long open reading frames, especially those containing random segments. Insertions and deletions that occur during chemical synthesis cause frameshifts, and stop codons in the random region will cause premature termination. These problems can together greatly reduce the number of full-length synthetic genes in the library. We describe a strategy in which smaller segments of the synthetic open reading frame are selected in vitro using mRNA display for the absence of frameshifts and stop codons. These smaller segments are then ligated together to form combinatorial libraries of long uninterrupted open reading frames. This process can increase the number of full-length open reading frames in libraries by up to two orders of magnitude, resulting in protein libraries with complexities of greater than 10(13). We have used this methodology to generate three types of displayed protein library: a completely random sequence library, a library of concatemerized oligopeptide cassettes with a propensity for forming amphipathic alpha-helical or beta-strand structures, and a library based on one of the most common enzymatic scaffolds, the alpha/beta (TIM) barrel. Copyright 2000 Academic Press.

Transcription-associated mutational pressure in the Parvovirus B19 genome: Reactivated genomes contribute to the variability of viral populations.

PubMed

Khrustalev, Vladislav Victorovich; Ermalovich, Marina Anatolyevna; Hübschen, Judith M; Khrustaleva, Tatyana Aleksandrovna

2017-12-21

In this study we used non-overlapping parts of the two long open reading frames coding for nonstructural (NS) and capsid (VP) proteins of all available sequences of the Parvovirus B19 subgenotype 1a genome and found out that the rates of A to G, C to T and A to T mutations are higher in the first long reading frame (NS) of the virus than in the second one (VP). This difference in mutational pressure directions for two parts of the same viral genome can be explained by the fact of transcription of just the first long reading frame during the lifelong latency in nonerythroid cells. Adenine deamination (producing A to G and A to T mutations) and cytosine deamination (producing C to T mutations) occur more frequently in transcriptional bubbles formed by DNA "plus" strand of the first open reading frame. These mutations can be inherited only in case of reactivation of the infectious virus due to the help of Adenovirus that allows latent Parvovirus B19 to start transcription of the second reading frame and then to replicate its genome by the rolling circle mechanism using the specific origin. Results of this study provide evidence that the genomes reactivated from latency make significant contributions to the variability of Parvovirus B19. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fear, anger, fruits, and veggies: interactive effects of emotion and message framing on health behavior.

PubMed

Gerend, Mary A; Maner, Jon K

2011-07-01

Message framing is a theoretically grounded health communication strategy designed to motivate action by emphasizing either the benefits of engaging in a particular behavior (gains) or the costs of failing to engage in the behavior (losses). This study investigated whether the effectiveness of a framed message depends on the emotional state of the message recipient. We examined effects of fear versus anger, emotions that frequently occur within the context of health decision-making. Undergraduate students (N = 133) were randomly assigned to complete a fear or anger induction task after which they read a gain- or loss-framed pamphlet promoting fruit and vegetable consumption. Fruit and vegetable intake (servings per day) subsequently was assessed over the following 2 weeks. As predicted, a significant frame by emotion interaction was observed, such that participants in the fear condition reported eating more servings of fruits and vegetables after exposure to a loss-framed message than to a gain-framed message. In contrast, participants in the anger condition reported eating (marginally) more servings of fruits and vegetables after exposure to a gain-framed message than to a loss-framed message. Greater increases in fruit and vegetable intake from baseline to follow-up were observed when the message frame was matched to the participant's emotional state. The effectiveness of framed health communications depends on the message recipient's current emotional state. Affective factors that are incidental to the behavior recommended in a health communication can affect the relative success of gain- and loss-framed appeals.

Memory T-Cell-Mediated Immune Responses Specific to an Alternative Core Protein in Hepatitis C Virus Infection

PubMed Central

Bain, Christine; Parroche, Peggy; Lavergne, Jean Pierre; Duverger, Blandine; Vieux, Claude; Dubois, Valérie; Komurian-Pradel, Florence; Trépo, Christian; Gebuhrer, Lucette; Paranhos-Baccala, Glaucia; Penin, François; Inchauspé, Geneviève

2004-01-01

In vitro studies have described the synthesis of an alternative reading frame form of the hepatitis C virus (HCV) core protein that was named F protein or ARFP (alternative reading frame protein) and includes a domain coded by the +1 open reading frame of the RNA core coding region. The expression of this protein in HCV-infected patients remains controversial. We have analyzed peripheral blood from 47 chronically or previously HCV-infected patients for the presence of T lymphocytes and antibodies specific to the ARFP. Anti-ARFP antibodies were detected in 41.6% of the patients infected with various HCV genotypes. Using a specific ARFP 99-amino-acid polypeptide as well as four ARFP predicted class I-restricted 9-mer peptides, we show that 20% of the patients display specific lymphocytes capable of producing gamma interferon, interleukin-10, or both cytokines. Patients harboring three different viral genotypes (1a, 1b, and 3) carried T lymphocytes reactive to genotype 1b-derived peptides. In longitudinal analysis of patients receiving therapy, both core and ARFP-specific T-cell- and B-cell-mediated responses were documented. The magnitude and kinetics of the HCV antigen-specific responses differed and were not linked with viremia or therapy outcome. These observations provide strong and new arguments in favor of the synthesis, during natural HCV infection, of an ARFP derived from the core sequence. Moreover, the present data provide the first demonstration of the presence of T-cell-mediated immune responses directed to this novel HCV antigen. PMID:15367612

Motivating Reading Comprehension: Concept-Oriented Reading Instruction

ERIC Educational Resources Information Center

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

2004-01-01

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

The Role of eIF4E Activity in Breast Cancer

DTIC Science & Technology

2010-08-01

ORF, open reading frame; qPCR, quantitative PCR; RACE, rapid amplification of cDNA ends; RT, reverse transcriptase ; uORF, upstream ORF; UTR...were also performed using template lacking RT ( reverse transcriptase ): products were either undetectable or greatly reduced (>30000-fold less product...have previously shown that a 5’UTR expressed from the human AXIN2 gene contains a sixty nucleotide sequence that is predicted to form a stable stem

The influence of visual and vestibular orientation cues in a clock reading task.

PubMed

Davidenko, Nicolas; Cheong, Yeram; Waterman, Amanda; Smith, Jacob; Anderson, Barrett; Harmon, Sarah

2018-05-23

We investigated how performance in the real-life perceptual task of analog clock reading is influenced by the clock's orientation with respect to egocentric, gravitational, and visual-environmental reference frames. In Experiment 1, we designed a simple clock-reading task and found that observers' reaction time to correctly tell the time depends systematically on the clock's orientation. In Experiment 2, we dissociated egocentric from environmental reference frames by having participants sit upright or lie sideways while performing the task. We found that both reference frames substantially contribute to response times in this task. In Experiment 3, we placed upright or rotated participants in an upright or rotated immersive virtual environment, which allowed us to further dissociate vestibular from visual cues to the environmental reference frame. We found evidence of environmental reference frame effects only when visual and vestibular cues were aligned. We discuss the implications for the design of remote and head-mounted displays. Copyright © 2018 Elsevier Inc. All rights reserved.

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

USDA-ARS?s Scientific Manuscript database

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

Framing effects reveal discrete lexical-semantic and sublexical procedures in reading: an fMRI study

PubMed Central

Danelli, Laura; Marelli, Marco; Berlingeri, Manuela; Tettamanti, Marco; Sberna, Maurizio; Paulesu, Eraldo; Luzzatti, Claudio

2015-01-01

According to the dual-route model, a printed string of letters can be processed by either a grapheme-to-phoneme conversion (GPC) route or a lexical-semantic route. Although meta-analyses of the imaging literature support the existence of distinct but interacting reading procedures, individual neuroimaging studies that explored neural correlates of reading yielded inconclusive results. We used a list-manipulation paradigm to provide a fresh empirical look at this issue and to isolate specific areas that underlie the two reading procedures. In a lexical condition, we embedded disyllabic Italian words (target stimuli) in lists of either loanwords or trisyllabic Italian words with unpredictable stress position. In a GPC condition, similar target stimuli were included within lists of pseudowords. The procedure was designed to induce participants to emphasize either the lexical-semantic or the GPC reading procedure, while controlling for possible linguistic confounds and keeping the reading task requirements stable across the two conditions. Thirty-three adults participated in the behavioral study, and 20 further adult participants were included in the fMRI study. At the behavioral level, we found sizeable effects of the framing manipulations that included slower voice onset times for stimuli in the pseudoword frames. At the functional anatomical level, the occipital and temporal regions, and the intraparietal sulcus were specifically activated when subjects were reading target words in a lexical frame. The inferior parietal and anterior fusiform cortex were specifically activated in the GPC condition. These patterns of activation represented a valid classifying model of fMRI images associated with target reading in both frames in the multi-voxel pattern analyses. Further activations were shared by the two procedures in the occipital and inferior parietal areas, in the premotor cortex, in the frontal regions and the left supplementary motor area. These regions are most likely involved in either early input or late output processes. PMID:26441712

Framing effects reveal discrete lexical-semantic and sublexical procedures in reading: an fMRI study.

PubMed

Danelli, Laura; Marelli, Marco; Berlingeri, Manuela; Tettamanti, Marco; Sberna, Maurizio; Paulesu, Eraldo; Luzzatti, Claudio

2015-01-01

According to the dual-route model, a printed string of letters can be processed by either a grapheme-to-phoneme conversion (GPC) route or a lexical-semantic route. Although meta-analyses of the imaging literature support the existence of distinct but interacting reading procedures, individual neuroimaging studies that explored neural correlates of reading yielded inconclusive results. We used a list-manipulation paradigm to provide a fresh empirical look at this issue and to isolate specific areas that underlie the two reading procedures. In a lexical condition, we embedded disyllabic Italian words (target stimuli) in lists of either loanwords or trisyllabic Italian words with unpredictable stress position. In a GPC condition, similar target stimuli were included within lists of pseudowords. The procedure was designed to induce participants to emphasize either the lexical-semantic or the GPC reading procedure, while controlling for possible linguistic confounds and keeping the reading task requirements stable across the two conditions. Thirty-three adults participated in the behavioral study, and 20 further adult participants were included in the fMRI study. At the behavioral level, we found sizeable effects of the framing manipulations that included slower voice onset times for stimuli in the pseudoword frames. At the functional anatomical level, the occipital and temporal regions, and the intraparietal sulcus were specifically activated when subjects were reading target words in a lexical frame. The inferior parietal and anterior fusiform cortex were specifically activated in the GPC condition. These patterns of activation represented a valid classifying model of fMRI images associated with target reading in both frames in the multi-voxel pattern analyses. Further activations were shared by the two procedures in the occipital and inferior parietal areas, in the premotor cortex, in the frontal regions and the left supplementary motor area. These regions are most likely involved in either early input or late output processes.

Phonological Constraints on the Assembly of Skeletal Structure in Reading

ERIC Educational Resources Information Center

Marom, Michal; Berent, Iris

2010-01-01

Linguistic research suggests that certain skeletal frames (e.g., CVC) are preferred to others (e.g., VCC). We examine whether such preferences constrain reading in the Stroop task. We demonstrate that CCVC nonwords facilitate naming the color "black" (/blaek/, a CCVC frame) relative to CVC controls. Conversely, CCVC items inhibit "red" (a CVC…

ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

PubMed

Büssow, Konrad; Hoffmann, Steve; Sievert, Volker

2002-12-19

Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. A Java program was developed for retrieval of protein and nucleic acid sequences and annotations from NCBI GenBank, using the XML sequence format. Annotations retrieved by ORFer include sequence name, organism and also the completeness of the sequence. The program has a graphical user interface, although it can be used in a non-interactive mode. For protein sequences, the program also extracts the open reading frame sequence, if available, and checks its correct translation. ORFer accepts user input in the form of single or lists of GenBank GI identifiers or accession numbers. It can be used to extract complete sets of open reading frames and protein sequences from any kind of GenBank sequence entry, including complete genomes or chromosomes. Sequences are either stored with their features in a relational database or can be exported as text files in Fasta or tabulator delimited format. The ORFer program is freely available at http://www.proteinstrukturfabrik.de/orfer. The ORFer program allows for fast retrieval of DNA sequences, protein sequences and their open reading frames and sequence annotations from GenBank. Furthermore, storage of sequences and features in a relational database is supported. Such a database can supplement a laboratory information system (LIMS) with appropriate sequence information.

Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene

PubMed Central

Firth, Andrew E

2008-01-01

Background The genus Orbivirus includes several species that infect livestock – including Bluetongue virus (BTV) and African horse sickness virus (AHSV). These viruses have linear dsRNA genomes divided into ten segments, all of which have previously been assumed to be monocistronic. Results Bioinformatic evidence is presented for a short overlapping coding sequence (CDS) in the Orbivirus genome segment 9, overlapping the VP6 cistron in the +1 reading frame. In BTV, a 77–79 codon AUG-initiated open reading frame (hereafter ORFX) is present in all 48 segment 9 sequences analysed. The pattern of base variations across the 48-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 VP6 reading frame are taken into account; MLOGD software). In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP6. The ORFX AUG codon has a strong Kozak context in all 48 sequences. Each has only one or two upstream AUG codons, always in the VP6 reading frame, and (with a single exception) always with weak or medium Kozak context. Thus, in BTV, ORFX may be translated via leaky scanning. A long (83–169 codon) ORF is present in a corresponding location and reading frame in all other Orbivirus species analysed except Saint Croix River virus (SCRV; the most divergent). Again, the pattern of base variations across sequence alignments indicates multiple coding in the VP6 and ORFX reading frames. Conclusion At ~9.5 kDa, the putative ORFX product in BTV is too small to appear on most published protein gels. Nonetheless, a review of past literature reveals a number of possible detections. We hope that presentation of this bioinformatic analysis will stimulate an attempt to experimentally verify the expression and functional role of ORFX, and hence lead to a greater understanding of the molecular biology of these important pathogens. PMID:18489030

What makes African American health disparities newsworthy? An experiment among journalists about story framing.

PubMed

Hinnant, Amanda; Oh, Hyun Jee; Caburnay, Charlene A; Kreuter, Matthew W

2011-12-01

News stories reporting race-specific health information commonly emphasize disparities between racial groups. But recent research suggests this focus on disparities has unintended effects on African American audiences, generating negative emotions and less interest in preventive behaviors (Nicholson RA, Kreuter MW, Lapka C et al. Unintended effects of emphasizing disparities in cancer communication to African-Americans. Cancer Epidemiol Biomarkers Prev 2008; 17: 2946-52). They found that black adults are more interested in cancer screening after reading about the progress African Americans have made in fighting cancer than after reading stories emphasizing disparities between blacks and whites. This study builds on past findings by (i) examining how health journalists judge the newsworthiness of stories that report race-specific health information by emphasizing disparities versus progress and (ii) determining whether these judgments can be changed by informing journalists of audience reactions to disparity versus progress framing. In a double-blind-randomized experiment, 175 health journalists read either a disparity- or progress-framed story on colon cancer, preceded by either an inoculation about audience effects of such framing or an unrelated (i.e. control) information stimuli. Journalists rated the disparity-frame story more favorably than the progress-frame story in every category of news values. However, the inoculation significantly increased positive reactions to the progress-frame story. Informing journalists of audience reactions to race-specific health information could influence how health news stories are framed.

The Role of elF4E Activity in Breast Cancer

DTIC Science & Technology

2011-08-01

protein; ORF, open reading frame; qPCR, quantitative PCR; RACE, rapid amplification of cDNA ends; RT, reverse transcriptase ; uORF, upstream ORF; UTR...Reactions were also performed using template lacking RT ( reverse transcriptase ): products were either undetectable or greatly reduced (>30000-fold less...that a 5’UTR expressed from the human AXIN2 gene contains a sixty nucleotide sequence that is predicted to form a stable stem-loop structure6. This

A low molecular weight protein tyrosine phosphatase from Synechocystis sp. strain PCC 6803: enzymatic characterization and identification of its potential substrates

PubMed Central

Mukhopadhyay, Archana; Kennelly, Peter J.

2011-01-01

The predicted protein product of open reading frame slr0328 from Synechocystis sp. PCC 6803, SynPTP, possesses significant amino acid sequence similarity with known low molecular weight protein tyrosine phosphatases (PTPs). To determine the functional properties of this hypothetical protein, open reading frame slr0328 was expressed in Escherichia coli. The purified recombinant protein, SynPTP, displayed its catalytic phosphatase activity towards several tyrosine, but not serine, phosphorylated exogenous protein substrates. The protein phosphatase activity of SynPTP was inhibited by sodium orthovanadate, a known inhibitor of tyrosine phosphatases, but not by okadaic acid, an inhibitor for many serine/threonine phosphatases. Kinetic analysis indicated that the Km and Vmax values for SynPTP towards p-nitrophenyl phosphate are similar to those of other known bacterial low molecular weight PTPs. Mutagenic alteration of the predicted catalytic cysteine of PTP, Cys7, to serine abolished enzyme activity. Using a combination of immunodetection, mass spectrometric analysis and mutagenically altered Cys7SerAsp125Ala-SynPTP, we identified PsaD (photosystem I subunit II), CpcD (phycocyanin rod linker protein) and phycocyanin-α and -β subunits as possible endogenous substrates of SynPTP in this cyanobacterium. These results indicate that SynPTP might be involved in the regulation of photosynthesis in Synechocystis sp. PCC 6803. PMID:21288886

Fear, Anger, Fruits, and Veggies: Interactive Effects of Emotion and Message Framing on Health Behavior

PubMed Central

Gerend, Mary A.; Maner, Jon K.

2010-01-01

Objective Message framing is a theoretically grounded health communication strategy designed to motivate action by emphasizing the benefits of engaging in a particular behavior (gains) or the costs of failing to engage in the behavior (losses). This study investigated whether the effectiveness of a framed message depends on the emotional state of the message recipient. We examined effects of fear versus anger, emotions that frequently occur within the context of health decision-making. Methods Undergraduate students (N = 133) were randomly assigned to complete a fear or anger induction task after which they read a gain- or loss-framed pamphlet promoting fruit and vegetable consumption. Fruit and vegetable intake (servings per day) was subsequently assessed over the following two weeks. Results As predicted, a significant frame by emotion interaction was observed, such that participants in the fear condition reported eating more servings of fruits and vegetables after exposure to a loss-framed message than to a gain-framed message. In contrast, participants in the anger condition reported eating (marginally) more servings of fruits and vegetables after exposure to a gain-framed message than to a loss-framed message. That is, greater increases in fruit and vegetable intake from baseline to follow-up were observed when frame was matched to participants’ emotional state than when it was mismatched. Conclusion The effectiveness of framed health communications depends on the message recipient’s current emotional state. Affective factors that are incidental to the behavior recommended in a health communication can affect the relative success of gain- and loss-framed appeals. PMID:21534679

CCC CGA is a weak translational recoding site in Escherichia coli.

PubMed

Shu, Ping; Dai, Huacheng; Mandecki, Wlodek; Goldman, Emanuel

2004-12-08

Previously published experiments had indicated unexpected expression of a control vector in which a beta-galactosidase reporter was in the +1 reading frame relative to the translation start. This control vector contained the codon pair CCC CGA in the zero reading frame, raising the possibility that ribosomes rephased on this sequence, with peptidyl-tRNA(Pro) pairing with CCC in the +1 frame. This putative rephasing might also be exacerbated by the rare CGA Arg codon in the second position due to increased vacancy of the ribosomal A-site. To test this hypothesis, a series of site-directed mutants was constructed, including mutations in both the first and second codons of this codon pair. The results show that interrupting the continuous run of C residues with synonymous codon changes essentially abolishes the frameshift. Further, changing the rare Arg codon to a common Arg codon also reduces the frequency of the frameshift. These results provide strong support for the hypothesis that CCC CGA in the zero frame is indeed a weak translational frameshift site in Escherichia coli, with a 1-2% efficiency. Because the vector sequence also contains another CCC triplet in the +1 reading frame starting within the next codon after the CGA, our data also support possible contribution to expression of a +7 nucleotide ribosome hop into the same +1 reading frame. We also confirm here a previous report that CCC UGA is a translational frameshift site, in these experiments, with about 5% efficiency.

Identification of a non-LTR retrotransposon from the gypsy moth

Treesearch

K.J. Garner; J.M. Slavicek

1999-01-01

A family of highly repetitive elements, named LDT1, has been identified in the gypsy moth, Lymantria dispar. The complete element is 5.4 kb in length and lacks long-terminal repeats, The element contains two open reading frames with a significant amino acid sequence similarity to several non-LTR retrotransposons. The first open reading frame contains...

Time and outcome framing in intertemporal tradeoffs.

PubMed

Scholten, Marc; Read, Daniel

2013-07-01

A robust anomaly in intertemporal choice is the delay-speedup asymmetry: Receipts are discounted more, and payments are discounted less, when delayed than when expedited over the same interval. We developed 2 versions of the tradeoff model (Scholten & Read, 2010) to address such situations, in which an outcome is expected at a given time but then its timing is changed. The outcome framing model generalizes the approach taken by the hyperbolic discounting model (Loewenstein & Prelec, 1992): Not obtaining a positive outcome when expected is a worse than expected state, to which people are over-responsive, or hypersensitive, and not incurring a negative outcome when expected is a better than expected state, to which people are under-responsive, or hyposensitive. The time framing model takes a new approach: Delaying a positive outcome or speeding up a negative one involves a loss of time to which people are hypersensitive, and speeding up a positive outcome or delaying a negative one involves a gain of time to which people are hyposensitive. We compare the models on their quantitative predictions of indifference data from matching and preference data from choice. The time framing model systematically outperforms the outcome framing model. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Regulation of hTERT Expression and Function in Newly Immortalized p53(+) Human Mammary Epithelial Cell Lines

DTIC Science & Technology

2008-06-01

proteins during embryogene- sis, neurodevelopment and cancer. Part of their function is through the repression of CKIs, including p16. Some functions...protein 2 Other AUTS2 autism susceptibility candidate 2 C1orf24 chromosome 1 open reading frame 24 C20orf97 chromosome 20 open reading frame 97

Regulation of hTERT Expression and Function in Newly Immortalized p53(+) Human Mammary Epithelial Cell Lines

DTIC Science & Technology

2007-06-01

embryogene- sis, neurodevelopment and cancer. Part of their function is through the repression of CKIs, including p16. Some functions have been attributed to...AUTS2 autism susceptibility candidate 2 C1orf24 chromosome 1 open reading frame 24 C20orf97 chromosome 20 open reading frame 97 DKFZP566B183

Characterization of the 5’- and 3’-terminal subgenomic RNAs produced by a capillovirus: evidence for a CP subgenomic RNA

USDA-ARS?s Scientific Manuscript database

The members of Capillovirus genus encode two overlapping open reading frames (ORFs): ORF1 encodes a large polyprotein containing the domains of replication-associated proteins plus a coat protein (CP), and ORF2 encodes a movement protein, located within ORF1 in a different reading frame. Organizatio...

Self-guide framing and persuasion: responsibly increasing message processing to ideal levels.

PubMed

Evans, Lisa M; Petty, Richard E

2003-03-01

The current research examines the effect that framing persuasive messages in terms of self-guides (ideal vs. ought) has on the attitudes and cognitive responses of individuals with chronic ideal versus ought self-guides. The strength of participants' ideal and ought self-guides and the magnitude of participants' ideal and ought self-discrepancies were measured using a computerized reaction time program. One week later, participants read a persuasive message about a fictional breakfast product, framed in terms of either ideals or oughts. Matching framing to stronger self-guide led to enhanced message processing activity, especially among individuals who were low in need for cognition. Individuals who read messages framed to match their stronger self-guides paid more attention to argument quality, as reflected in their attitudes and cognitive responses. Messages with self-guide framing that matched individuals' stronger self-discrepancies did not have this effect on processing.

The effect of message framing on breast self-examination attitudes, intentions, and behavior.

PubMed

Meyerowitz, B E; Chaiken, S

1987-03-01

In this study we tested the framing hypothesis that a pamphlet stressing the negative consequences of not performing breast self-examination (BSE) would be more persuasive than a pamphlet emphasizing BSE's positive consequences. College-aged female subjects were exposed to a loss-frame pamphlet, a gain-frame pamphlet, or a no-arguments pamphlet, or they received no pamphlet describing the importance of and the techniques for performing BSE. Attitudes toward BSE and intentions to perform BSE were assessed immediately after this intervention and again 4 months later. The follow-up also assessed subjects' postexperimental BSE behavior. Consistent with predictions, subjects who read a pamphlet with arguments framed in loss language manifested more positive BSE attitudes, intentions, and behaviors than did subjects in the other three conditions. The greater impact of the loss pamphlet could not be attributed to greater fear arousal, better memory for pamphlet content, greater perceived susceptibility to breast cancer, or stronger beliefs in BSE's efficacy on the part of the loss subjects. Only measures of perceived self-efficacy in performing BSE were differentially affected by the framing manipulation, with loss subjects reporting the greatest levels of self-confidence. The results are discussed in terms of prospect theory's framing postulate and a simpler negativity-bias conceptualization, and underlying mechanisms such as differential salience and vividness are considered. Clinical implications of the findings are also explored.

What makes African American health disparities newsworthy? An experiment among journalists about story framing

PubMed Central

Hinnant, Amanda; Oh, Hyun Jee; Caburnay, Charlene A.; Kreuter, Matthew W.

2011-01-01

News stories reporting race-specific health information commonly emphasize disparities between racial groups. But recent research suggests this focus on disparities has unintended effects on African American audiences, generating negative emotions and less interest in preventive behaviors (Nicholson RA, Kreuter MW, Lapka C et al. Unintended effects of emphasizing disparities in cancer communication to African-Americans. Cancer Epidemiol Biomarkers Prev 2008; 17: 2946–52). They found that black adults are more interested in cancer screening after reading about the progress African Americans have made in fighting cancer than after reading stories emphasizing disparities between blacks and whites. This study builds on past findings by (i) examining how health journalists judge the newsworthiness of stories that report race-specific health information by emphasizing disparities versus progress and (ii) determining whether these judgments can be changed by informing journalists of audience reactions to disparity versus progress framing. In a double-blind-randomized experiment, 175 health journalists read either a disparity- or progress-framed story on colon cancer, preceded by either an inoculation about audience effects of such framing or an unrelated (i.e. control) information stimuli. Journalists rated the disparity-frame story more favorably than the progress-frame story in every category of news values. However, the inoculation significantly increased positive reactions to the progress-frame story. Informing journalists of audience reactions to race-specific health information could influence how health news stories are framed. PMID:21911844

Cloning and identification of bacteriophage T4 gene 2 product gp2 and action of gp2 on infecting DNA in vivo.

PubMed Central

Lipinska, B; Rao, A S; Bolten, B M; Balakrishnan, R; Goldberg, E B

1989-01-01

We sequenced bacteriophage T4 genes 2 and 3 and the putative C-terminal portion of gene 50. They were found to have appropriate open reading frames directed counterclockwise on the T4 map. Mutations in genes 2 and 64 were shown to be in the same open reading frame, which we now call gene 2. This gene codes for a protein of 27,068 daltons. The open reading frame corresponding to gene 3 codes for a protein of 20,634 daltons. Appropriate bands on polyacrylamide gels were identified at 30 and 20 kilodaltons, respectively. We found that the product of the cloned gene 2 can protect T4 DNA double-stranded ends from exonuclease V action. Images PMID:2644202

Transient replication of BPV-1 requires two viral polypeptides encoded by the E1 and E2 open reading frames.

PubMed

Ustav, M; Stenlund, A

1991-02-01

Bovine papillomavirus (BPV) DNA is maintained as an episome with a constant copy number in transformed cells and is stably inherited. To study BPV replication we have developed a transient replication assay based on a highly efficient electroporation procedure. Using this assay we have determined that in the context of the viral genome two of the viral open reading frames, E1 and E2, are required for replication. Furthermore we show that when produced from expression vectors in the absence of other viral gene products, the full length E2 transactivator polypeptide and a 72 kd polypeptide encoded by the E1 open reading frame in its entirety, are both necessary and sufficient for replication BPV in C127 cells.

Using message framing to promote acceptance of the human papillomavirus vaccine.

PubMed

Gerend, Mary A; Shepherd, Janet E

2007-11-01

Use of message framing for encouraging vaccination, an increasingly common preventive health behavior, has received little empirical investigation. The authors examined the relative effectiveness of gain-versus loss-framed messages in promoting acceptance of a vaccine against human papillomavirus (HPV)-a virus responsible for virtually all cases of cervical cancer. Undergraduate women (N = 121) were randomly assigned to read a booklet describing the benefits of receiving (gain-framed message) or the costs of not receiving (loss-framed message) a prophylactic HPV vaccine. After reading the booklet, participants indicated their intent to obtain the HPV vaccine. A 5-item composite representing intentions to obtain the HPV vaccine. The effect of message framing on HPV vaccine acceptance was moderated by risky sexual behavior and approach avoidance motivation. A loss-framed message led to greater HPV vaccination intentions than a gain framed message but only among participants who had multiple sexual partners and participants who infrequently used condoms. The loss-frame advantage was also observed among participants high in avoidance motivation. Findings highlight characteristics of the message recipient that may affect the success of framed messages promoting vaccine acceptance. This study has practical implications for the development of health communications promoting vaccination.

The influence of message framing, intention to quit smoking, and nicotine dependence on the persuasiveness of smoking cessation messages.

PubMed

Moorman, Marjolein; van den Putte, Bas

2008-10-01

This study explores the combined effect of message framing, intention to quit smoking, and nicotine dependence on the persuasiveness of smoking cessation messages. Pre- and post-message measures of quit intention, attitude toward smoking cessation, and perceived behavioral control were taken in two separate waves from current cigarette smokers with varying levels of nicotine dependence (N=151). In the second wave, participants were randomly assigned to one of two groups. In the first group, participants read a smoking cessation message which emphasized the benefits of quitting (positive frame). In the second group participants read a message which emphasized the costs of not quitting (negative frame). Results show that smokers' intentions to quit smoking and their level of nicotine dependence jointly influence the persuasiveness of positive and negative message frames. When nicotine dependence and quitting intention are both high, a negative frame works best. Conversely, a positive frame is preferable when nicotine dependence or quitting intention is low. Smokers' level of processing is proposed as the underlying mechanism explaining the different effects of message frames.

QuickView video preview software of colon capsule endoscopy: reliability in presenting colorectal polyps as compared to normal mode reading.

PubMed

Farnbacher, Michael J; Krause, Horst H; Hagel, Alexander F; Raithel, Martin; Neurath, Markus F; Schneider, Thomas

2014-03-01

OBJECTIVE. Colon capsule endoscopy (CCE) proved to be highly sensitive in detection of colorectal polyps (CP). Major limitation is the time-consuming video reading. The aim of this prospective, double-center study was to assess the theoretical time-saving potential and its possible impact on the reliability of "QuickView" (QV), in the presentation of CP as compared to normal mode (NM). METHODS. During NM reading of 65 CCE videos (mean patient´s age 56 years), all frames showing CPs were collected and compared to the number of frames presented by QV at increasing QV settings (10, 20, ... 80%). Reliability of QV in presenting polyps <6 mm and ≥6 mm (significant polyp), and identifying patients for subsequent therapeutic colonoscopy, capsule egestion rate, cleansing level, and estimated time-saving potential were assessed. RESULTS. At a 30% QV setting, the QV video presented 89% of the significant polyps and 86% of any polyps with ≥1 frame (per-polyp analysis) identified in NM before. At a 10% QV setting, 98% of the 52 patients with significant polyps could be identified (per-patient analysis) by QV video analysis. Capsule excretion rate was 74% and colon cleanliness was adequate in 85%. QV´s presentation rate correlates to the QV setting, the polyp size, and the number of frames per finding. CONCLUSIONS. Depending on its setting, the reliability of QV in presenting CP as compared to NM reading is notable. However, if no significant polyp is presented by QV, NM reading must be performed afterwards. The reduction of frames to be analyzed in QV might speed up identification of candidates for therapeutic colonoscopy.

Transient replication of BPV-1 requires two viral polypeptides encoded by the E1 and E2 open reading frames.

PubMed Central

Ustav, M; Stenlund, A

1991-01-01

Bovine papillomavirus (BPV) DNA is maintained as an episome with a constant copy number in transformed cells and is stably inherited. To study BPV replication we have developed a transient replication assay based on a highly efficient electroporation procedure. Using this assay we have determined that in the context of the viral genome two of the viral open reading frames, E1 and E2, are required for replication. Furthermore we show that when produced from expression vectors in the absence of other viral gene products, the full length E2 transactivator polypeptide and a 72 kd polypeptide encoded by the E1 open reading frame in its entirety, are both necessary and sufficient for replication BPV in C127 cells. Images PMID:1846806

Evolution of vitamin B2 biosynthesis: structural and functional similarity between pyrimidine deaminases of eubacterial and plant origin.

PubMed

Fischer, Markus; Römisch, Werner; Saller, Sabine; Illarionov, Boris; Richter, Gerald; Rohdich, Felix; Eisenreich, Wolfgang; Bacher, Adelbert

2004-08-27

The Arabidopsis thaliana open reading frame At4g20960 predicts a protein whose N-terminal part is similar to the eubacterial 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate deaminase domain. A synthetic open reading frame specifying a pseudomature form of the plant enzyme directed the synthesis of a recombinant protein which was purified to apparent homogeneity and was shown by NMR spectroscopy to convert 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-ribosylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate at a rate of 0.9 micromol mg(-1) min(-1). The substrate and product of the enzyme are both subject to spontaneous anomerization of the ribosyl side chain as shown by (13)C NMR spectroscopy. The protein contains 1 eq of Zn(2+)/subunit. The deaminase activity could be assigned to the N-terminal section of the plant protein. The deaminase domains of plants and eubacteria share a high degree of similarity, in contrast to deaminases from fungi. These data show that the riboflavin biosynthesis in plants proceeds by the same reaction steps as in eubacteria, whereas fungi use a different pathway.

Efficient exon skipping of SGCG mutations mediated by phosphorodiamidate morpholino oligomers.

PubMed

Wyatt, Eugene J; Demonbreun, Alexis R; Kim, Ellis Y; Puckelwartz, Megan J; Vo, Andy H; Dellefave-Castillo, Lisa M; Gao, Quan Q; Vainzof, Mariz; Pavanello, Rita C M; Zatz, Mayana; McNally, Elizabeth M

2018-05-03

Exon skipping uses chemically modified antisense oligonucleotides to modulate RNA splicing. Therapeutically, exon skipping can bypass mutations and restore reading frame disruption by generating internally truncated, functional proteins to rescue the loss of native gene expression. Limb-girdle muscular dystrophy type 2C is caused by autosomal recessive mutations in the SGCG gene, which encodes the dystrophin-associated protein γ-sarcoglycan. The most common SGCG mutations disrupt the transcript reading frame abrogating γ-sarcoglycan protein expression. In order to treat most SGCG gene mutations, it is necessary to skip 4 exons in order to restore the SGCG transcript reading frame, creating an internally truncated protein referred to as Mini-Gamma. Using direct reprogramming of human cells with MyoD, myogenic cells were tested with 2 antisense oligonucleotide chemistries, 2'-O-methyl phosphorothioate oligonucleotides and vivo-phosphorodiamidate morpholino oligomers, to induce exon skipping. Treatment with vivo-phosphorodiamidate morpholino oligomers demonstrated efficient skipping of the targeted exons and corrected the mutant reading frame, resulting in the expression of a functional Mini-Gamma protein. Antisense-induced exon skipping of SGCG occurred in normal cells and those with multiple distinct SGCG mutations, including the most common 521ΔT mutation. These findings demonstrate a multiexon-skipping strategy applicable to the majority of limb-girdle muscular dystrophy 2C patients.

Transcription of TP0126, Treponema pallidum Putative OmpW Homolog, Is Regulated by the Length of a Homopolymeric Guanosine Repeat

PubMed Central

Brandt, Stephanie L.; Ke, Wujian; Reid, Tara B.; Molini, Barbara J.; Iverson-Cabral, Stefanie; Ciccarese, Giulia; Drago, Francesco; Lukehart, Sheila A.; Centurion-Lara, Arturo

2015-01-01

An effective mechanism for introduction of phenotypic diversity within a bacterial population exploits changes in the length of repetitive DNA elements located within gene promoters. This phenomenon, known as phase variation, causes rapid activation or silencing of gene expression and fosters bacterial adaptation to new or changing environments. Phase variation often occurs in surface-exposed proteins, and in Treponema pallidum subsp. pallidum, the syphilis agent, it was reported to affect transcription of three putative outer membrane protein (OMP)-encoding genes. When the T. pallidum subsp. pallidum Nichols strain genome was initially annotated, the TP0126 open reading frame was predicted to include a poly(G) tract and did not appear to have a predicted signal sequence that might suggest the possibility of its being an OMP. Here we show that the initial annotation was incorrect, that this poly(G) is instead located within the TP0126 promoter, and that it varies in length in vivo during experimental syphilis. Additionally, we show that TP0126 transcription is affected by changes in the poly(G) length consistent with regulation by phase variation. In silico analysis of the TP0126 open reading frame based on the experimentally identified transcriptional start site shortens this hypothetical protein by 69 amino acids, reveals a predicted cleavable signal peptide, and suggests structural homology with the OmpW family of porins. Circular dichroism of recombinant TP0126 supports structural homology to OmpW. Together with the evidence that TP0126 is fully conserved among T. pallidum subspecies and strains, these data suggest an important role for TP0126 in T. pallidum biology and syphilis pathogenesis. PMID:25802057

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

PubMed Central

Bowling, Bethany V.; Schultheis, Patrick J.

2015-01-01

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

Experimental Definition and Validation of Protein Coding Transcripts in Chlamydomonas reinhardtii

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

Kourosh Salehi-Ashtiani; Jason A. Papin

Algal fuel sources promise unsurpassed yields in a carbon neutral manner that minimizes resource competition between agriculture and fuel crops. Many challenges must be addressed before algal biofuels can be accepted as a component of the fossil fuel replacement strategy. One significant challenge is that the cost of algal fuel production must become competitive with existing fuel alternatives. Algal biofuel production presents the opportunity to fine-tune microbial metabolic machinery for an optimal blend of biomass constituents and desired fuel molecules. Genome-scale model-driven algal metabolic design promises to facilitate both goals by directing the utilization of metabolites in the complex, interconnectedmore » metabolic networks to optimize production of the compounds of interest. Using Chlamydomonas reinhardtii as a model, we developed a systems-level methodology bridging metabolic network reconstruction with annotation and experimental verification of enzyme encoding open reading frames. We reconstructed a genome-scale metabolic network for this alga and devised a novel light-modeling approach that enables quantitative growth prediction for a given light source, resolving wavelength and photon flux. We experimentally verified transcripts accounted for in the network and physiologically validated model function through simulation and generation of new experimental growth data, providing high confidence in network contents and predictive applications. The network offers insight into algal metabolism and potential for genetic engineering and efficient light source design, a pioneering resource for studying light-driven metabolism and quantitative systems biology. Our approach to generate a predictive metabolic model integrated with cloned open reading frames, provides a cost-effective platform to generate metabolic engineering resources. While the generated resources are specific to algal systems, the approach that we have developed is not specific to algae and can be readily expanded to other microbial systems as well as higher plants and animals.« less

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

PubMed

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

2016-02-01

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

Isolation, sequence analysis, and comparison of two plasmids (28 and 29 kilobases) from the biomining bacterium Leptospirillum ferrooxidans ATCC 49879.

PubMed

Coram, Nicolette J; van Zyl, Leonardo J; Rawlings, Douglas E

2005-11-01

Two plasmids, of 28,878 bp and 28,012 bp, were isolated from Leptospirillum ferrooxidans ATCC 49879. Altogether, a total of 67 open reading frames (ORFs) were identified on both plasmids, of which 32 had predicted products with high homology to proteins of known function, while 11 ORFs had predicted products with homology to previously identified proteins of unknown function. Twenty-four ORFs had products with no homologues in the GenBank/NCBI database. An analysis of the ORFs and other features of the two plasmids, the first to be isolated from a bacterium of the genus Leptospirillum, is presented.

Reading and TV; Proceedings of the Spring 1972 Rutgers University Reading Conference.

ERIC Educational Resources Information Center

Shew, Phillip, Ed.; Muscara, Sandra, Ed.

The perspectives of this document, which explores the relationships between television and reading instruction, are both theoretical and practical. Articles in the first section establish a frame of reference for evaluating the use of television in reading instruction, focusing particularly on the relationships among media and their import for…

Tobacco chloroplast tRNALys(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron

PubMed Central

Sugita, Mamoru; Shinozaki, Kazuo; Sugiura, Masahiro

1985-01-01

The nucleotide sequence of a tRNALys(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNAGly(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long. Images PMID:16593561

Tobacco chloroplast tRNA(UUU) gene contains a 2.5-kilobase-pair intron: An open reading frame and a conserved boundary sequence in the intron.

PubMed

Sugita, M; Shinozaki, K; Sugiura, M

1985-06-01

The nucleotide sequence of a tRNA(Lys)(UUU) gene on tobacco (Nicotiana tabacum) chloroplast DNA has been determined. This gene is located 215 base pairs upstream from the gene for the 32,000-dalton thylakoid membrane protein on the same DNA strand and has a 2526-base-pair intron in the anticodon loop. The intron boundary sequence does not follow the G-U/A-G rule but is similar to those of tobacco chloroplast split genes for tRNA(Gly)(UCC) and ribosomal proteins L2 and S12. The intron contains one major open reading frame of 509 codons. The codon usage in the open reading frame resembles those observed in the genes for tobacco chloroplast proteins so far analyzed. The primary transcript of this tRNA gene is 2.7 kilobases long.

When message-frame fits salient cultural-frame, messages feel more persuasive.

PubMed

Uskul, Ayse K; Oyserman, Daphna

2010-03-01

The present study examines the persuasive effects of tailored health messages comparing those tailored to match (versus not match) both chronic cultural frame and momentarily salient cultural frame. Evidence from two studies (Study 1: n = 72 European Americans; Study 2: n = 48 Asian Americans) supports the hypothesis that message persuasiveness increases when chronic cultural frame, health message tailoring and momentarily salient cultural frame all match. The hypothesis was tested using a message about health risks of caffeine consumption among individuals prescreened to be regular caffeine consumers. After being primed for individualism, European Americans who read a health message that focused on the personal self were more likely to accept the message-they found it more persuasive, believed they were more at risk and engaged in more message-congruent behaviour. These effects were also found among Asian Americans who were primed for collectivism and who read a health message that focused on relational obligations. The findings point to the importance of investigating the role of situational cues in persuasive effects of health messages and suggest that matching content to primed frame consistent with the chronic frame may be a way to know what to match messages to.

Complete nucleotide sequence of jasmine virus H, a new member of the family Tombusviridae.

PubMed

Zhuo, Tao; Zhu, Li-Juan; Lu, Cheng-Cong; Jiang, Chao-Yang; Chen, Zi-Yin; Zhang, Guangzhi; Wang, Zong-Hua; Jovel, Juan; Han, Yan-Hong

2018-03-01

Jasmine virus H (JaVH) is a novel virus associated with symptoms of yellow mosaic on jasmine. The JaVH genome is 3,867 nt in length with five open reading frames (ORFs) encoding a 27-kDa protein (ORF 1), an 87-kDa replicase protein (ORF 2), two centrally located movement proteins (ORF 3 and 4), and a 37-kDa capsid protein (ORF 5). Based on genomic and phylogenetic analysis, JaVH is predicted to be a member of the genus Pelarspovirus in the family Tombusviridae.

Structure and Expression of Genes for Flavivirus Immunogens.

DTIC Science & Technology

1985-09-01

the same order in YFV i.e., C-M-E-NSI--- NS3---NS5 and an open reading frame extends at least through the C-M-E-NS1 coding region, consistent with...been determined (Castle et al., 1985). Comparison of these results shows that 1) the six major JEV genes mapped thus far occur in the same order in YFV ...pre-M proteins and 3) the predicted structures of the E, NSI and ns2a proteins of JEV and YFV exhibit a high degree of relatedness. The E proteins

Identification of a New Human Adenovirus Protein Encoded by a Novel Late l-Strand Transcription Unit▿

PubMed Central

Tollefson, Ann E.; Ying, Baoling; Doronin, Konstantin; Sidor, Peter D.; Wold, William S. M.

2007-01-01

A short open reading frame named the “U exon,” located on the adenovirus (Ad) l-strand (for leftward transcription) between the early E3 region and the fiber gene, is conserved in mastadenoviruses. We have observed that Ad5 mutants with large deletions in E3 that infringe on the U exon display a mild growth defect, as well as an aberrant Ad E2 DNA-binding protein (DBP) intranuclear localization pattern and an apparent failure to organize replication centers during late infection. Mutants in which the U exon DNA is reconstructed have a reversed phenotype. Chow et al. (L. T. Chow et al., J. Mol. Biol. 134:265-303, 1979) described mRNAs initiating in the region of the U exon and spliced to downstream sequences in the late DBP mRNA leader and the DBP-coding region. We have cloned this mRNA (as cDNA) from Ad5 late mRNA; the predicted protein is 217 amino acids, initiating in the U exon and continuing in frame in the DBP leader and in the DBP-coding region but in a different reading frame from DBP. Polyclonal and monoclonal antibodies generated against the predicted U exon protein (UXP) showed that UXP is ∼24K in size by immunoblot and is a late protein. At 18 to 24 h postinfection, UXP is strongly associated with nucleoli and is found throughout the nucleus; later, UXP is associated with the periphery of replication centers, suggesting a function relevant to Ad DNA replication or RNA transcription. UXP is expressed by all four species C Ads. When expressed in transient transfections, UXP complements the aberrant DBP localization pattern of UXP-negative Ad5 mutants. Our data indicate that UXP is a previously unrecognized protein derived from a novel late l-strand transcription unit. PMID:17881437

Research on a Frame-Based Model of Reading Comprehension. Final Report.

ERIC Educational Resources Information Center

Goldstein, Ira

This report summarizes computational investigations of language comprehension based on Marvin Minsky's theory of frames, a recent advance in artifical intelligence theories about the representation of knowledge. The investigations discussed explored frame theory as a basis for text comprehension by implementing models of the theory and developing…

Integrating Cognitive Views into Psychometric Models for Reading Comprehension Assessment. Research Report. ETS RR-17-35

ERIC Educational Resources Information Center

Rahman, Taslima; Mislevy, Robert J.

2017-01-01

To demonstrate how methodologies for assessing reading comprehension can grow out of views of the construct suggested in the reading research literature, we constructed tasks and carried out psychometric analyses that were framed in accordance with 2 leading reading models. In estimating item difficulty and subsequently, examinee proficiency, an…

The role of language in suicide reporting: Investigating the influence of problematic suicide referents.

PubMed

Arendt, Florian; Scherr, Sebastian; Niederkrotenthaler, Thomas; Till, Benedikt

2018-02-14

Although suicide experts recommend using neutral suicide referents in news media reporting, this recommendation has not yet been tested empirically. This recommendation, based on the empirically yet untested assumption that problematic suicide referents carry meaning that is inappropriate from a prevention perspective, may lead to a different perspective on suicide, termed "framing effects." For example, in German-speaking countries, the neutral term Suizid (suicide) is recommended. Conversely, Freitod ("free death") and Selbstmord ("self-murder") convey associative meanings related to problematic concepts such as free will (Freitod) and crime/murder (Selbstmord), and are therefore not recommended. Using a web-based randomized controlled trial focused on German speakers (N = 451), we tested whether the news media's use of Suizid, Selbstmord, and Freitod elicits framing effects. Participants read identical news reports about suicide. Only the specific suicide referents varied depending on the experimental condition. Post-reading, participants wrote short summaries of the news reports, completed a word-fragment completion test and a questionnaire targeting suicide-related attitudes. We found that the news frame primed some frame-related concepts in the memory and also increased frame-related word choice. Importantly, we found that participants reading the free will-related Freitod frame showed greater attitudinal support for suicide among individuals suffering from incurable diseases. This study highlights the importance of how the news media write about suicide and supports the language recommendations put forward by suicide experts. Copyright © 2018 Elsevier Ltd. All rights reserved.

Pathogenic and multidrug-resistant Escherichia fergusonii from broiler chicken.

PubMed

Forgetta, V; Rempel, H; Malouin, F; Vaillancourt, R; Topp, E; Dewar, K; Diarra, M S

2012-02-01

An Escherichia spp. isolate, ECD-227, was previously identified from the broiler chicken as a phylogenetically divergent and multidrug-resistant Escherichia coli possessing numerous virulence genes. In this study, whole genome sequencing and comparative genome analysis was used to further characterize this isolate. The presence of known and putative antibiotic resistance and virulence open reading frames were determined by comparison to pathogenic (E. coli O157:H7 TW14359, APEC O1:K1:H7, and UPEC UTI89) and nonpathogenic species (E. coli K-12 MG1655 and Escherichia fergusonii ATCC 35469). The assembled genome size of 4.87 Mb was sequenced to 18-fold depth of coverage and predicted to contain 4,376 open reading frames. Phylogenetic analysis of 537 open reading frames present across 110 enteric bacterial species identifies ECD-227 to be E. fergusonii. The genome of ECD-227 contains 5 plasmids showing similarity to known E. coli and Salmonella enterica plasmids. The presence of virulence and antibiotic resistance genes were identified and localized to the chromosome and plasmids. The mutation in gyrA (S83L) involved in fluoroquinolone resistance was identified. The Salmonella-like plasmids harbor antibiotic resistance genes on a class I integron (aadA, qacEΔ-sul1, aac3-VI, and sulI) as well as numerous virulence genes (iucABCD, sitABCD, cib, traT). In addition to the genome analysis, the virulence of ECD-227 was evaluated in a 1-d-old chick model. In the virulence assay, ECD-227 was found to induce 18 to 30% mortality in 1-d-old chicks after 24 h and 48 h of infection, respectively. This study documents an avian multidrug-resistant and virulent E. fergusonii. The existence of several resistance genes to multiple classes of antibiotics indicates that infection caused by ECD-227 would be difficult to treat using antimicrobials currently available for poultry.

Scripture Reading Practices of Methodist Youth

ERIC Educational Resources Information Center

Rackley, Eric

2017-01-01

Framed as the "transaction" between readers and texts, this article examines the scripture reading practices of three Methodist youth. Data were generated through verbal protocols in which youth verbalized their thinking as they read self-selected passages from the Bible. Multiple rounds of inductive thematic analyses identified how the…

Hyper-active gap filling

PubMed Central

Omaki, Akira; Lau, Ellen F.; Davidson White, Imogen; Dakan, Myles L.; Apple, Aaron; Phillips, Colin

2015-01-01

Much work has demonstrated that speakers of verb-final languages are able to construct rich syntactic representations in advance of verb information. This may reflect general architectural properties of the language processor, or it may only reflect a language-specific adaptation to the demands of verb-finality. The present study addresses this issue by examining whether speakers of a verb-medial language (English) wait to consult verb transitivity information before constructing filler-gap dependencies, where internal arguments are fronted and hence precede the verb. This configuration makes it possible to investigate whether the parser actively makes representational commitments on the gap position before verb transitivity information becomes available. A key prediction of the view that rich pre-verbal structure building is a general architectural property is that speakers of verb-medial languages should predictively construct dependencies in advance of verb transitivity information, and therefore that disruption should be observed when the verb has intransitive subcategorization frames that are incompatible with the predicted structure. In three reading experiments (self-paced and eye-tracking) that manipulated verb transitivity, we found evidence for reading disruption when the verb was intransitive, although no such reading difficulty was observed when the critical verb was embedded inside a syntactic island structure, which blocks filler-gap dependency completion. These results are consistent with the hypothesis that in English, as in verb-final languages, information from preverbal noun phrases is sufficient to trigger active dependency completion without having access to verb transitivity information. PMID:25914658

Hyper-active gap filling.

PubMed

Omaki, Akira; Lau, Ellen F; Davidson White, Imogen; Dakan, Myles L; Apple, Aaron; Phillips, Colin

2015-01-01

Much work has demonstrated that speakers of verb-final languages are able to construct rich syntactic representations in advance of verb information. This may reflect general architectural properties of the language processor, or it may only reflect a language-specific adaptation to the demands of verb-finality. The present study addresses this issue by examining whether speakers of a verb-medial language (English) wait to consult verb transitivity information before constructing filler-gap dependencies, where internal arguments are fronted and hence precede the verb. This configuration makes it possible to investigate whether the parser actively makes representational commitments on the gap position before verb transitivity information becomes available. A key prediction of the view that rich pre-verbal structure building is a general architectural property is that speakers of verb-medial languages should predictively construct dependencies in advance of verb transitivity information, and therefore that disruption should be observed when the verb has intransitive subcategorization frames that are incompatible with the predicted structure. In three reading experiments (self-paced and eye-tracking) that manipulated verb transitivity, we found evidence for reading disruption when the verb was intransitive, although no such reading difficulty was observed when the critical verb was embedded inside a syntactic island structure, which blocks filler-gap dependency completion. These results are consistent with the hypothesis that in English, as in verb-final languages, information from preverbal noun phrases is sufficient to trigger active dependency completion without having access to verb transitivity information.

Creating Joint Attentional Frames and Pointing to Evidence in the Reading and Writing Process

ERIC Educational Resources Information Center

Unger, John A.; Liu, Rong; Scullion, Vicki A.

2015-01-01

This theory-into-practice paper integrates Tomasello's concept of Joint Attentional Frames and well-known ideas related to the work of Russian psychologist, Lev Vygotsky, with more recent ideas from social semiotics. Classroom procedures for incorporating student-created Joint Attentional Frames into literacy lessons are explained by links to…

Identification of the polypeptides encoded in the unassigned reading frames 2, 4, 4L, and 5 of human mitochondrial DNA.

PubMed Central

Mariottini, P; Chomyn, A; Riley, M; Cottrell, B; Doolittle, R F; Attardi, G

1986-01-01

In previous work, antibodies prepared against chemically synthesized peptides predicted from the DNA sequence were used to identify the polypeptides encoded in three of the eight unassigned reading frames (URFs) of human mitochondrial DNA (mtDNA). In the present study, this approach has been extended to other human mtDNA URFs. In particular, antibodies directed against the NH2-terminal octapeptide of the putative URF2 product specifically precipitated component 11 of the HeLa cell mitochondrial translation products, the reaction being inhibited by the specific peptide. Similarly, antibodies directed against the COOH-terminal nonapeptide of the putative URF4 product reacted specifically with components 4 and 5, and antibodies against a COOH-terminal heptapeptide of the presumptive URF4L product reacted specifically with component 26. Antibodies against the NH2-terminal heptapeptide of the putative product of URF5 reacted with component 1, but only to a marginal extent; however, the results of a trypsin fingerprinting analysis of component 1 point strongly to this component as being the authentic product of URF5. The polypeptide assignments to the mtDNA URFs analyzed here are supported by the relative electrophoretic mobilities of proteins 11, 4-5, 26, and 1, which are those expected for the molecular weights predicted from the DNA sequence for the products of URF2, URF4, URF4L, and URF5, respectively. With the present assignment, seven of the eight human mtDNA URFs have been shown to be expressed in HeLa cells. Images PMID:3456601

FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences.

PubMed

Schiex, Thomas; Gouzy, Jérôme; Moisan, Annick; de Oliveira, Yannick

2003-07-01

We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output. Its performances are evaluated on different bacterial genomes. The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms.

Writing through Visual Acts of Reading: Incorporating Visual Aesthetics in Integrated Writing and Reading Tasks

ERIC Educational Resources Information Center

Choo, Suzanne S.

2010-01-01

The English curriculum tends to be framed in relation to two unconscious boundaries based on the dichotomies between writing and reading as well as print and image. This paper re-envisions the curriculum as comprising a hybrid space where students are involved in composing texts that integrate writing and reading practices while also considering…

Reduction of capsule endoscopy reading times by unsupervised image mining.

PubMed

Iakovidis, D K; Tsevas, S; Polydorou, A

2010-09-01

The screening of the small intestine has become painless and easy with wireless capsule endoscopy (WCE) that is a revolutionary, relatively non-invasive imaging technique performed by a wireless swallowable endoscopic capsule transmitting thousands of video frames per examination. The average time required for the visual inspection of a full 8-h WCE video ranges from 45 to 120min, depending on the experience of the examiner. In this paper, we propose a novel approach to WCE reading time reduction by unsupervised mining of video frames. The proposed methodology is based on a data reduction algorithm which is applied according to a novel scheme for the extraction of representative video frames from a full length WCE video. It can be used either as a video summarization or as a video bookmarking tool, providing the comparative advantage of being general, unbounded by the finiteness of a training set. The number of frames extracted is controlled by a parameter that can be tuned automatically. Comprehensive experiments on real WCE videos indicate that a significant reduction in the reading times is feasible. In the case of the WCE videos used this reduction reached 85% without any loss of abnormalities.

SIELETERS: A Static Fourier Transform Infrared Imaging Spectrometer for Airborne Hyperspectral Measurements

DTIC Science & Technology

2009-10-01

cryostat and cooled at a temperature under 77K by a Stirling cryocooler , as represented on the following Figure 5 : Cryostat...Figure 5. Detector cryostat and cryocooler The read-out frequency of the detectors is adapted to the ground speed of the plane above...Cold shield Detector plane Cryocoole r Cryocoole r compresso r Fixed frame Roll frame Pitch frame Yaw frame SIELETERS: a Static Fourier

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

PubMed

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

2013-10-01

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

Genetic analysis of the agrocinopine catabolic region of Agrobacterium tumefaciens Ti plasmid pTiC58, which encodes genes required for opine and agrocin 84 transport.

PubMed Central

Hayman, G T; Beck von Bodman, S; Kim, H; Jiang, P; Farrand, S K

1993-01-01

The acc region, subcloned from pTiC58 of classical nopaline and agrocinopine A and B Agrobacterium tumefaciens C58, allowed agrobacteria to grow using agrocinopine B as the sole source of carbon and energy. acc is approximately 6 kb in size. It consists of at least five genes, accA through accE, as defined by complementation analysis using subcloned fragments and transposon insertion mutations of acc carried on different plasmids within the same cell. All five regions are required for agrocin 84 sensitivity, and at least four are required for agrocinopine and agrocin 84 uptake. The complementation results are consistent with the hypothesis that each of the five regions is separately transcribed. Maxicell experiments showed that the first of these genes, accA, encodes a 60-kDa protein. Analysis of osmotic shock fractions showed this protein to be located in the periplasm. The DNA sequence of the accA region revealed an open reading frame encoding a predicted polypeptide of 59,147 Da. The amino acid sequence encoded by this open reading frame is similar to the periplasmic binding proteins OppA and DppA of Escherichia coli and Salmonella typhimurium and OppA of Bacillus subtilis. Images PMID:8366042

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

PubMed Central

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

2013-01-01

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

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

PubMed Central

Untiveros, Milton; Olspert, Allan; Artola, Katrin

2016-01-01

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

Alternate promoter selection within a human cytomegalovirus immediate-early and early transcription unit (UL119-115) defines true late transcripts containing open reading frames for putative viral glycoproteins.

PubMed Central

Leatham, M P; Witte, P R; Stinski, M F

1991-01-01

The human cytomegalovirus open reading frames (ORFs) UL119 through UL115 (UL119-115) are located downstream of the immediate-early 1 and 2 transcription units. The promoter upstream of UL119 is active at all times after infection and drives the synthesis of a spliced 3.1-kb mRNA. The viral mRNA initiates in UL119, contains UL119-117 and UL116, and terminates just downstream of UL115. True late transcripts that are detected only after viral DNA synthesis originate from this transcription unit. True late mRNAs of 2.1 kb, containing ORFs UL116 and UL115, and 1.2 kb, containing ORF UL115 only, are synthesized. The true late viral mRNAs are 3' coterminal with the 3.1-kb mRNA. This transcription unit is an example of late promoters nested within an immediate-early-early transcription unit. The gene products of UL119-117, UL116, and UL115 are predicted to be glycoproteins. Efficient expression of the downstream ORFs at late times after infection may be related to alternate promoter usage and downstream cap site selection. Images PMID:1717716

Desire or Disease? Framing Obesity to Influence Attributions of Responsibility and Policy Support.

PubMed

McGlynn, Joseph; McGlone, Matthew S

2018-02-01

The way we describe health threats affects perceptions of severity and preferred solutions to reduce risk. Most people agree obesity is a problem, but differ in how they attribute responsibility for development and decline of the disease. We explored effects of message framing on attributions of responsibility and support for public obesity policies using a 3 × 2 factorial design. Participants read one of six versions of a health message describing the negative effects of obesity. Message frames influenced respondent attributions and their support for policies to reduce obesity. Those who read a message that assigned agency to the disease (e.g., Obesity causes health problems) endorsed genetics as the cause to a greater degree than those who read a semantically equivalent message that instead assigned agency to people (e.g., Obese people develop health problems). In contrast, assigning agency to people rather than to the disease prompted higher attributions of individual responsibility and support for public policies. Explicit message frames that directly connected responsibility for obesity to either individual or societal factors had no effect on respondent perceptions. Findings suggest explicit arguments may be less effective in shifting perceptions of health threats than arguments embedded in agentic message frames. The results demonstrate specific message features that influence how people attribute responsibility for the onset and solution of obesity.

Transposition of an intron in yeast mitochondria requires a protein encoded by that intron.

PubMed

Macreadie, I G; Scott, R M; Zinn, A R; Butow, R A

1985-06-01

The optional 1143 bp intron in the yeast mitochondrial 21S rRNA gene (omega +) is nearly quantitatively inserted in genetic crosses into 21S rRNA alleles that lack it (omega -). The intron contains an open reading frame that can encode a protein of 235 amino acids, but no function has been ascribed to this sequence. We previously found an in vivo double-strand break in omega - DNA at or close to the intron insertion site only in zygotes of omega + X omega - crosses that appears with the same kinetics as intron insertion. We now show that mutations in the intron open reading frame that would alter the translation product simultaneously inhibit nonreciprocal omega recombination and the in vivo double-strand break in omega - DNA. These results provide evidence that the open reading frame encodes a protein required for intron transposition and support the role of the double-strand break in the process.

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.

PubMed

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.

The nucleotide sequence of a segment of Trypanosoma brucei mitochondrial maxi-circle DNA that contains the gene for apocytochrome b and some unusual unassigned reading frames.

PubMed Central

Benne, R; De Vries, B F; Van den Burg, J; Klaver, B

1983-01-01

The nucleotide sequence of a 2.5-kb segment of the maxi-circle of Trypanosoma brucei mtDNA has been determined. The segment contains the gene for apocytochrome b, which displays about 25% homology at the amino acid level to the apocytochrome b gene from fungal and mammalian mtDNAs. Northern blot and S1 nuclease analyses have yielded accurate map positions of an RNA species in an area that coincides with the reading frame. The segment also contains two pairs of overlapping unassigned reading frames, which lack homology with any known mitochondrial gene or URF. The DNA sequence in these areas is AG-rich (70%), resulting in URFs with an unusually high level of glycine and charged amino acids (60%). They may not encode proteins, in spite of their size and the fact that abundant transcripts are mapped in these areas. Images PMID:6314266

Protein expression of preferred human codon-optimized Gaussia luciferase genes with an artificial open-reading frame in mammalian and bacterial cells.

PubMed

Inouye, Satoshi; Suzuki, Takahiro

2016-12-01

The protein expressions of three preferred human codon-optimized Gaussia luciferase genes (pGLuc, EpGLuc, and KpGLuc) were characterized in mammalian and bacterial cells by comparing them with those of wild-type Gaussia luciferase gene (wGLuc) and human codon-optimized Gaussia luciferase gene (hGLuc). Two synthetic genes of EpGLuc and KpGLuc containing the complete preferred human codons have an artificial open-reading frame; however, they had the similar protein expression levels to those of pGLuc and hGLuc in mammalian cells. In bacterial cells, the protein expressions of pGLuc, EpGLuc, and KpGLuc with approximately 65% GC content were the same and showed approximately 60% activities of wGLuc and hGLuc. The artificial open-reading frame in EpGLuc and KpGLuc did not affect the protein expression in mammalian and bacterial cells. Copyright © 2016 Elsevier Inc. All rights reserved.

Maternal Emotion Framing and Children's Social Behavior: The Role of Children's Feelings and Beliefs about Peers

ERIC Educational Resources Information Center

Meece, Darrell W.; Colwell, Malinda J.; Mize, Jacquelyn

2007-01-01

Children's feelings and beliefs about peer relationships were examined as a possible mediator between mothers' positive and negative emotional framing and children's (n = 46) behavior with peers. Mothers' emotion framing was assessed as they and their young children read a picture book depicting emotionally-laden content, but no printed text.…

Frameshifting in the p6 cDNA phage display system.

PubMed

Govarts, Cindy; Somers, Klaartje; Stinissen, Piet; Somers, Veerle

2010-12-20

Phage display is a powerful technique that enables easy identification of targets for any type of ligand. Targets are displayed at the phage surface as a fusion protein to one of the phage coat proteins. By means of a repeated process of affinity selection on a ligand, specific enrichment of displayed targets will occur. In our studies using C-terminal display of cDNA fragments to phage coat protein p6, we noticed the occasional enrichment of targets that do not contain an open reading frame. This event has previously been described in other phage display studies using N-terminal display of targets to phage coat proteins and was due to uncommon translational events like frameshifting. The aim of this study was to examine if C-terminal display of targets to p6 is also subjected to frameshifting. To this end, an enriched target not containing an open reading frame was selected and an E-tag was coupled at the C-terminus in order to measure target display at the surface of the phage. The tagged construct was subsequently expressed in 3 different reading frames and display of both target and E-tag measured to detect the occurrence of frameshifting. As a result, we were able to demonstrate display of the target both in the 0 and in the +1 reading frame indicating that frameshifting can also take place when C-terminal fusion to minor coat protein p6 is applied.

Reading "Salt and Pepper": Social Practices, Unfinished Narratives, and Critical Interpretations

ERIC Educational Resources Information Center

Anderson, Diane Downer

2008-01-01

In "Reading "Salt and Pepper"" Anderson examines a story written by three third grade girls and their insights about that story as they re-read it during its production and retrospectively, eight years later. Using a frame for understanding children's writing as social practice, the children's interviews, showing their multiple and sometimes…

Theory-based metrological traceability in education: A reading measurement network.

PubMed

Fisher, William P; Stenner, A Jackson

2016-10-01

Huge resources are invested in metrology and standards in the natural sciences, engineering, and across a wide range of commercial technologies. Significant positive returns of human, social, environmental, and economic value on these investments have been sustained for decades. Proven methods for calibrating test and survey instruments in linear units are readily available, as are data- and theory-based methods for equating those instruments to a shared unit. Using these methods, metrological traceability is obtained in a variety of commercially available elementary and secondary English and Spanish language reading education programs in the U.S., Canada, Mexico, and Australia. Given established historical patterns, widespread routine reproduction of predicted text-based and instructional effects expressed in a common language and shared frame of reference may lead to significant developments in theory and practice. Opportunities for systematic implementations of teacher-driven lean thinking and continuous quality improvement methods may be of particular interest and value.

Effects of competing news media frames of weight on antifat stigma, beliefs about weight and support for obesity-related public policies.

PubMed

Frederick, D A; Saguy, A C; Sandhu, G; Mann, T

2016-03-01

In the popular news media, public health officials routinely emphasize the health risks of obesity and portray weight as under personal control. These messages may increase support for policies designed to reduce rates of obesity, but can also increase antifat stigma. Less often, the media cover 'Health at Every Size' or 'Fat Rights' perspectives that may have the opposite effects. We investigated how exposure to different 'fat frames' shifts attitudes about weight and support for obesity policies. Across four experiments (n=2187), people read constructed news articles framing fatness as negative (unhealthy, controllable, acceptable to stigmatize) or positive (healthy, uncontrollable, unacceptable to stigmatize). Compared with people who read fat-positive frames, people who read fat-negative frames expressed more: belief in the health risks of being fat (d=0.95-1.22), belief weight is controllable (d=0.38-0.55), support for charging obese people more for health insurance (d=0.26-0.77), antifat prejudice (in three out of four experiments, d=0.28-0.39), willingness to discriminate against fat people (d=0.39-0.71) and less willingness to celebrate body size diversity (d=0.37-0.64). They were also less willing to say that women at the lower end of the obese range could be healthy at their weights. Effects on support for public policies, however, were generally small and/or nonsignificant. Compared with a control condition, exposure to fat-positive frames generally shifted attitudes more than fat-negative frames. In experiment 4, adding a message about the unacceptability of weight-based discrimination to unhealthy/controllable news articles only reduced antifat stigma on one of three measures compared with articles adding a discrimination-acceptable message. Exposure to different news frames of fat can shift beliefs about weight-related health risks and weight-based stigma. Shifting policy attitudes, however, is more challenging.

Large-scale, multi-genome analysis of alternate open reading frames in bacteria and archaea.

PubMed

Veloso, Felipe; Riadi, Gonzalo; Aliaga, Daniela; Lieph, Ryan; Holmes, David S

2005-01-01

Analysis of over 300,000 annotated genes in 105 bacterial and archaeal genomes reveals an unexpectedly high frequency of large (>300 nucleotides) alternate open reading frames (ORFs). Especially notable is the very high frequency of alternate ORFs in frames +3 and -1 (where the annotated gene is defined as frame +1). The occurrence of alternate ORFs is correlated with genomic G+C content and is strongly influenced by synonymous codon usage bias. The frequency of alternate ORFs in frame -1 is also influenced by the occurrence of codons encoding leucine and serine in frame +1. Although some alternate ORFs have been shown to encode proteins, many others are probably not expressed because they lack appropriate signals for transcription and translation. These latter can be mis-annotated by automatic gene finding programs leading to errors in public databases. Especially prone to mis-annotation is frame -1, because it exhibits a potential codon usage and theoretical capacity to encode proteins with an amino acid composition most similar to real genes. Some alternate ORFs are conserved across bacterial or archaeal species, and can give rise to misannotated "conserved hypothetical" genes, while others are unique to a genome and are misidentified as "hypothetical orphan" genes, contributing significantly to the orphan gene paradox.

I spy with my little eye: cognitive processing of framed physical activity messages.

PubMed

Bassett-Gunter, Rebecca L; Latimer-Cheung, Amy E; Martin Ginis, Kathleen A; Castelhano, Monica

2014-01-01

The primary purpose was to examine the relative cognitive processing of gain-framed versus loss-framed physical activity messages following exposure to health risk information. Guided by the Extended Parallel Process Model, the secondary purpose was to examine the relation between dwell time, message recall, and message-relevant thoughts, as well as perceived risk, personal relevance, and fear arousal. Baseline measures of perceived risk for inactivity-related disease and health problems were administered to 77 undergraduate students. Participants read population-specific health risk information while wearing a head-mounted eye tracker, which measured dwell time on message content. Perceived risk was then reassessed. Next, participants read PA messages while the eye tracker measured dwell time on message content. Immediately following message exposure, recall, thought-listing, fear arousal, and personal relevance were measured. Dwell time on gain-framed messages was significantly greater than loss-framed messages. However, message recall and thought-listing did not differ by message frame. Dwell time was not significantly related to recall or thought-listing. Consistent with the Extended Parallel Process Model, fear arousal was significantly related to recall, thought-listing, and personal relevance. In conclusion, gain-framed messages may evoke greater dwell time than loss-famed messages. However, dwell time alone may be insufficient for evoking further cognitive processing.

Do you want the good news or the bad news? Gain- versus loss-framed messages following health risk information: The effects on leisure time physical activity beliefs and cognitions.

PubMed

Bassett-Gunter, Rebecca L; Martin Ginis, Kathleen A; Latimer-Cheung, Amy E

2013-12-01

The primary purpose was to examine the relative effectiveness of chronic disease and psychological health risk information combined with gain- versus loss-framed leisure time physical activity (LTPA) messages for changing perceived personal risk, LTPA response efficacy (i.e., the belief that LTPA can effectively reduce risk), and LTPA intentions. A secondary purpose was to explore the relationship between message framing and cognitive processing. Baseline assessments of perceived risk for inactivity-related disease and psychological health problems, LTPA response efficacy, and intentions were measured among 96 individuals with spinal cord injury (SCI). Participants read population-specific information about the risk for inactivity-related disease and psychological health problems following SCI, and perceived risk was reassessed. Participants were then randomized to read LTPA response efficacy messages emphasizing the benefits of LTPA (gain framed) or the risks of inactivity (loss framed). Immediately following message exposure, cognitive processing (i.e., thought listing and message recall), LTPA response efficacy, and LTPA intentions were assessed. Changes in perceived risk were observed following exposure to health risk information. Changes in LTPA response efficacy and intentions were greater following loss-framed messages targeting psychological health compared with gain-framed messages. Greater cognitive processing was observed following loss-framed messages compared with gain-framed messages. Following exposure to psychological health risk information, loss-framed messages may be more effective than gain-framed messages for eliciting cognitive processing and changing LTPA beliefs and intentions.

The Practicality of Poetry: Using Sonnets to Improve Reading Ability

ERIC Educational Resources Information Center

Vallicelli, Arthur E.

2012-01-01

This dissertation examines the way in which sonnets improved reading comprehension through a case study. The study was conceptually framed around the ideas of the New Critics, who employed two particular fallacies to ensure the most accurate reading of literature. The purpose of the study was to see the potential benefits that could come from…

Parafoveal-on-Foveal Effects of Emotional Word Semantics in Reading Chinese Sentences: Evidence from Eye Movements

ERIC Educational Resources Information Center

Yan, Ming; Sommer, Werner

2015-01-01

Despite the well-known influence of emotional meaning on cognition, relatively less is known about its effects on reading behavior. We investigated whether fixation behavior during the reading of Chinese sentences is influenced by emotional word meaning in the parafovea. Two-character target words embedded into the same sentence frames provided…

Lenses on Reading: An Introduction to Theories and Models. Second Edition

ERIC Educational Resources Information Center

Tracey, Diane H.; Morrow, Lesley Mandel

2012-01-01

This widely adopted text explores key theories and models that frame reading instruction and research. Readers learn why theory matters in designing and implementing high-quality instruction and research; how to critically evaluate the assumptions and beliefs that guide their own work; and what can be gained by looking at reading through multiple…

Effects of Information Framing on Human Papillomavirus Vaccination

PubMed Central

Weiner, Judith L.; Kelly, Bridget J.; Hornik, Robert C.; Cappella, Joseph N.

2009-01-01

Abstract Background In June 2006, the first vaccine to prevent human papillomavirus (HPV) transmission was approved for use in females in the United States. Because the vaccine was approved for females as young as 9, its success depends on parents' and individuals' willingness to accept vaccination. Little is known about how attitudes toward this vaccine will be influenced by the way the vaccine is portrayed in the media or in public debate. Methods To assess the effects of information framing on intentions to vaccinate self or female children, if appropriate, 635 adults read one of three short descriptive paragraphs about the vaccine, each of which emphasized a different aspect of the vaccine. Participants were then asked about their intentions to vaccinate under cost or no-cost conditions. Results Women who read that the vaccine protects only against cervical cancer had significantly higher intentions to vaccinate themselves when the vaccine was available at little or no cost compared with women who read alternate versions of the descriptive paragraph, F(2,325) = 5.74, p = 0.004. Conclusions How the HPV vaccine is framed may affect vaccination intentions under certain conditions. Women may be more receptive to the vaccine if it is framed as a cervical cancer prevention tool rather than a sexually transmitted infection (STI) prevention tool. PMID:19183094

An Out-of-frame Overlapping Reading Frame in the Ataxin-1 Coding Sequence Encodes a Novel Ataxin-1 Interacting Protein*

PubMed Central

Bergeron, Danny; Lapointe, Catherine; Bissonnette, Cyntia; Tremblay, Guillaume; Motard, Julie; Roucou, Xavier

2013-01-01

Spinocerebellar ataxia type 1 is an autosomal dominant cerebellar ataxia associated with the expansion of a polyglutamine tract within the ataxin-1 (ATXN1) protein. Recent studies suggest that understanding the normal function of ATXN1 in cellular processes is essential to decipher the pathogenesis mechanisms in spinocerebellar ataxia type 1. We found an alternative translation initiation ATG codon in the +3 reading frame of human ATXN1 starting 30 nucleotides downstream of the initiation codon for ATXN1 and ending at nucleotide 587. This novel overlapping open reading frame (ORF) encodes a 21-kDa polypeptide termed Alt-ATXN1 (Alternative ATXN1) with a completely different amino acid sequence from ATXN1. We introduced a hemagglutinin tag in-frame with Alt-ATXN1 in ATXN1 cDNA and showed in cell culture the co-expression of both ATXN1 and Alt-ATXN1. Remarkably, Alt-ATXN1 colocalized and interacted with ATXN1 in nuclear inclusions. In contrast, in the absence of ATXN1 expression, Alt-ATXN1 displays a homogenous nucleoplasmic distribution. Alt-ATXN1 interacts with poly(A)+ RNA, and its nuclear localization is dependent on RNA transcription. Polyclonal antibodies raised against Alt-ATXN1 confirmed the expression of Alt-ATXN1 in human cerebellum expressing ATXN1. These results demonstrate that human ATXN1 gene is a dual coding sequence and that ATXN1 interacts with and controls the subcellular distribution of Alt-ATXN1. PMID:23760502

Mining of Novel Thermo-Stable Cellulolytic Genes from a Thermophilic Cellulose-Degrading Consortium by Metagenomics

PubMed Central

Xia, Yu; Ju, Feng; Fang, Herbert H. P.; Zhang, Tong

2013-01-01

In this study, metagenomics was applied to characterize the microbial community and to discover carbohydrate-active genes of an enriched thermophilic cellulose-degrading sludge. The 16S analysis showed that the sludge microbiome was dominated by genus of cellulolytic Clostridium and methanogenesis Methanothermobacter. In order to retrieve genes from the metagenome, de novo assembly of the 11,930,760 Illumina 100 bp paired-end reads (totally 1.2 Gb) was carried out. 75% of all reads was utilized in the de novo assembly. 31,499 ORFs (Open Reading Frame) with an average length of 852 bp were predicted from the assembly; and 64% of these ORFs were predicted to present full-length genes. Based on the Hidden Markol Model, 253 of the predicted thermo-stable genes were identified as putatively carbohydrate-active. Among them the relative dominance of GH9 (Glycoside Hydrolase) and corresponding CBM3 (Carbohydrate Binding Module) revealed a cellulosome-based attached metabolism of polysaccharide in the thermophilic sludge. The putative carbohydrate-active genes ranged from 20% to 100% amino acid sequence identity to known proteins in NCBI nr database, with half of them showed less than 50% similarity. In addition, the coverage of the genes (in terms of ORFs) identified in the sludge were developed into three clear trends (112×, 29× and 8×) in which 85% of the high coverage trend (112×) mainly consisted of phylum of Firmicutes while 49.3% of the 29× trend was affiliated to the phylum of Chloroflexi. PMID:23341999

Testing the effects of message framing, kernel state, and exercise guideline adherence on exercise intentions and resolve.

PubMed

de Bruijn, Gert-Jan; Out, Kim; Rhodes, Ryan E

2014-11-01

To study the effects of framed messages on exercise intention and resolve. Two (type of frame: gain or loss) × 2 (type of kernel state: desirable or undesirable outcome) post-test study. Participants were recruited online and questioned about their previous exercise behaviour and their exercise risk perception. After this, they were randomly allocated to one of four messages that were different in terms of positive or negative outcomes (type of frame) and in terms of attained or avoided outcomes (type of kernel state). After reading the message, participants indicated their intention and resolve to engage in sufficient exercise. No effects were found for intention. For resolve, there was a significant interaction between type of frame, type of kernel state, and exercise adherence. Those who did not adhere to the exercise guideline and read the loss-framed message with attained outcomes reported significantly higher resolve than all other participants. This study indicates the relevance of including attained outcomes in message framing exercise interventions as well as a focus on exercise resolve. What is already known on this subject? Message framing is commonly used to increase exercise intentions and behaviour. Meta-analyses do not provide consistent support for this theory. Very little attention has been paid to resolve and message factors on framing effects. What does this study add? Framed messages have an effect on exercise resolve, but not on intention. Loss-framed messages with attained outcomes are most persuasive for those who do not adhere to exercise guidelines. Exercise framing studies should include behavioural resolve next to intention. . © 2014 The British Psychological Society.

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

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

Hill, K.E.; Lloyd, R.S.; Read, R.

1991-03-11

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

Murder by the book: using crime fiction as a bibliotherapeutic resource.

PubMed

Brewster, Liz

2017-03-01

Crime is a popular genre of fiction, widely read but sometimes seen as 'throwaway'. Disregarding this type of fiction because it is seen as low quality does not take into account its value to readers. Reading has been established as a means of improving mental health and well-being-often known as bibliotherapy. This often focuses on fiction considered to have literary merit rather than genre fiction like crime. However, in framing therapeutic reading in this way, the impact of texts considered to have low cultural value such as crime has been concealed. Examining readers' responses as a starting point identifies some reasons why crime fiction fulfils a need. Readers in an empirical study spoke about the strong narrative as a distraction, the predictability as a comfort and the safe distance from events as a reassurance that left them feeling that reading crime fiction was a refuge from the world. In exploring readers' responses in relation to the academic literature, the paper argues that there is a need to think differently about how readers engage with texts and how they experience reading as therapeutic, with a role for fiction like crime. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Evaluation of Proposed Electroplated HGU-4/P Frames

DTIC Science & Technology

1975-02-01

READ INSTRUCTIONS BEFORE COMPLE11NG FORII RIECIPII!NT’S CAT AI.OCI NUMBIIR &. TYPE 0,. RIEPOA"T a Pl!lltiOD CoV•t~•o Final I. PERF’OAMINO ORG...rJ Nickel dermatitis Skin reaction Contact dermatitis Aviator frames Nickel-containing frames ZO. ABSTRACT (Contlnu• on rever•• aid• II n•c...Laboratory. Of the 18 subjects who wore the test frames for three months, one subject, an aviator, developed a mild dermatitis along the frontal and

A retrotransposable element from the mosquito Anopheles gambiae .

PubMed Central

Besansky, N J

1990-01-01

A family of middle repetitive elements from the African malaria vector Anopheles gambiae is described. Approximately 100 copies of the element, designated T1Ag, are dispersed in the genome. Full-length elements are 4.6 kilobase pairs in length, but truncation of the 5' end is common. Nucleotide sequences of one full-length, two 5'-truncated, and two 5' ends of T1Ag elements were determined and aligned to define a consensus sequence. Sequence analysis revealed two long, overlapping open reading frames followed by a polyadenylation signal, AATAAA, and a tail consisting of tandem repetitions of the motif TGAAA. No direct or inverted long terminal repeats (LTRs) were detected. The first open reading frame, 442 amino acids in length, includes a domain resembling that of nucleic acid-binding proteins. The second open reading frame, 975 amino acids long, resembles the reverse transcriptases of a category of retrotransposable elements without LTRs, variously termed class II retrotransposons, class III elements or non-LTR retrotransposons. Similarity at the sequence and structural levels places T1Ag in this category. Images PMID:1689457

RNA editing makes mistakes in plant mitochondria: editing loses sense in transcripts of a rps19 pseudogene and in creating stop codons in coxI and rps3 mRNAs of Oenothera.

PubMed Central

Schuster, W; Brennicke, A

1991-01-01

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

A versatile and efficient high-throughput cloning tool for structural biology.

PubMed

Geertsma, Eric R; Dutzler, Raimund

2011-04-19

Methods for the cloning of large numbers of open reading frames into expression vectors are of critical importance for challenging structural biology projects. Here we describe a system termed fragment exchange (FX) cloning that facilitates the high-throughput generation of expression constructs. The method is based on a class IIS restriction enzyme and negative selection markers. FX cloning combines attractive features of established recombination- and ligation-independent cloning methods: It allows the straightforward transfer of an open reading frame into a variety of expression vectors and is highly efficient and very economic in its use. In addition, FX cloning avoids the common but undesirable feature of significantly extending target open reading frames with cloning related sequences, as it leaves a minimal seam of only a single extra amino acid to either side of the protein. The method has proven to be very robust and suitable for all common pro- and eukaryotic expression systems. It considerably speeds up the generation of expression constructs compared to traditional methods and thus facilitates a broader expression screening.

Eye Movements when Reading Spaced and Unspaced Thai and English: A Comparison of Thai-English Bilinguals and English Monolinguals

ERIC Educational Resources Information Center

Winskel, Heather; Radach, Ralph; Luksaneeyanawin, Sudaporn

2009-01-01

The study investigated the eye movements of Thai-English bilinguals when reading both Thai and English with and without interword spaces, in comparison with English monolinguals. Thai is an alphabetic orthography without interword spaces. Participants read sentences with high and low frequency target words embedded in same sentence frames with and…

Korean Learners' Metacognition in Reading Using Think-Aloud Procedures with a Focus on Regulation of Cognition

ERIC Educational Resources Information Center

Kim, Hyang-Il; Cha, Kyung-Ae

2015-01-01

The primary goal of this study was to explore the changes that four Korean university students made in their regulation of cognition during reading processes. The students were trained using explicit reading strategy instruction based on the CALLA model. To this end, first, metacognition was framed and categorized by the definition from Baker and…

Understanding What Students Know: Evaluating Their Online Research and Reading Comprehension Skills

ERIC Educational Resources Information Center

Castek, Jill; Coiro, Julie

2015-01-01

This piece is framed by questions we are often asked when we talk about online reading assessments and instruction with teachers. We begin with some of the lessons we have learned in our own experiences with designing measures of online reading comprehension. Then we share our thoughts about key design considerations as well as some of the biggest…

Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei.

PubMed

Cassidy, Liam; Prasse, Daniela; Linke, Dennis; Schmitz, Ruth A; Tholey, Andreas

2016-10-07

The recent discovery of an increasing number of small open reading frames (sORF) creates the need for suitable analytical technologies for the comprehensive identification of the corresponding gene products. For biological and functional studies the knowledge of the entire set of proteins and sORF gene products is essential. Consequently in the present study we evaluated analytical approaches that will allow for simultaneous analysis of widest parts of the proteome together with the predicted sORF. We performed a full proteome analysis of the methane producing archaeon Methanosarcina mazei strain Gö1 cytosolic proteome using a high/low pH reversed phase LC-MS bottom-up approach. The second analytical approach was based on semi-top-down strategy, encompassing a separation at intact protein level using a GelFree system, followed by digestion and LC-MS analysis. A high overlap in identified proteins was found for both approaches yielding the most comprehensive coverage of the cytosolic proteome of this organism achieved so far. The application of the second approach in combination with an adjustment of the search criteria for database searches further led to a significant increase of sORF peptide identifications, finally allowing to detect and identify 28 sORF gene products.

The P gene of bovine parainfluenza virus 3 expresses all three reading frames from a single mRNA editing site.

PubMed Central

Pelet, T; Curran, J; Kolakofsky, D

1991-01-01

The P gene of bovine parainfluenza virus 3 (bPIV3) contains two downstream overlapping ORFs, called V and D. By comparison with the mRNA editing sites of other paramyxoviruses, two editing sites were predicted for bPIV3; site a to express the D protein, and site b to express the V protein. Examination of the bPIV3 mRNAs, however, indicates that site b is non-functional whereas site a operates frequently. Insertions at site a give rise to both V and D protein mRNAs, because a very broad distribution of Gs is added when insertions occur. This broad distribution is very different from the editing sites of Sendai virus or SV5, where predominantly one form of edited mRNA containing either a one or two G insertion respectively is created, to access the single overlapping ORF of these viruses. A model is proposed to explain how paramyxoviruses control the range of G insertions on that fraction of the mRNAs where insertions occur. The bPIV3 P gene is unique as far as we know, in that a sizeable portion of the gene expresses all 3 reading frames as protein. bPIV3 apparently does this from a single editing site by removing the constraints which control the number of slippage rounds which take place. Images PMID:1846805

Identification and analysis of proton-translocating pyrophosphatases in the methanogenic archaeon Methansarcina mazei.

PubMed

Bäumer, Sebastian; Lentes, Sabine; Gottschalk, Gerhard; Deppenmeier, Uwe

2002-03-01

Analysis of genome sequence data from the methanogenic archaeon Methanosarcina mazei Gö1 revealed the existence of two open reading frames encoding proton-translocating pyrophosphatases (PPases). These open reading frames are linked by a 750-bp intergenic region containing TC-rich stretches and are transcribed in opposite directions. The corresponding polypeptides are referred to as Mvp1 and Mvp2 and consist of 671 and 676 amino acids, respectively. Both enzymes represent extremely hydrophobic, integral membrane proteins with 15 predicted transmembrane segments and an overall amino acid sequence similarity of 50.1%. Multiple sequence alignments revealed that Mvp1 is closely related to eukaryotic PPases, whereas Mvp2 shows highest homologies to bacterial PPases. Northern blot experiments with RNA from methanol-grown cells harvested in the mid-log growth phase indicated that only Mvp2 was produced under these conditions. Analysis of washed membranes showed that Mvp2 had a specific activity of 0.34 U mg (protein)(-1). Proton translocation experiments with inverted membrane vesicles prepared from methanol-grown cells showed that hydrolysis of 1 mol of pyrophosphate was coupled to the translocation of about 1 mol of protons across the cytoplasmic membrane. Appropriate conditions for mvp1 expression could not be determined yet. The pyrophosphatases of M. mazei Gö1 represent the first examples of this enzyme class in methanogenic archaea and may be part of their energy-conserving system.

The Env-like open reading frame of the baculovirus-integrated retrotransposon TED encodes a retrovirus-like envelope protein.

PubMed

Ozers, M S; Friesen, P D

1996-12-15

TED is a 7.5-kbp member of the gypsy family of retrotransposons that was first identified by its integration within the baculovirus DNA genome. This lepidopteran (moth) transposon contains three retrovirus-like genes, including functional gag and pol that yield reverse transcriptase-containing virus-like particles. To identify and characterize the product(s) of the third env-like open reading frame, TED ORF3 was expressed in homologous lepidopteran cells by using a baculovirus vector, vENV. Immunoblots and immunoprecipitations with antiserum raised against a bacterial ORF3-fusion protein detected two ORF3-encoded proteins, p68env and gp75env. On the basis of selective incorporation of [3H]mannose and inhibition of modification by tunicamycin which blocks N-linked glycosylation, gp75env is a glycoprotein derived from core precursor p68env. As predicted by the presence of a transmembrane domain near the carboxyl terminus, both p68env and gp75env were associated with heavy membranes of vENV-infected cells. Thus, TED ORF3 encodes a membrane glycoprotein with properties characteristic of retroviral env proteins. These data are consistent with the hypothesis that TED is an invertebrate retrovirus. Moreover, TED integration within the baculovirus genome provides an example of retroelement-mediated acquisition of host genes that may contribute to virus evolution.

Translational and structural requirements of the early nodulin gene enod40, a short-open reading frame-containing RNA, for elicitation of a cell-specific growth response in the alfalfa root cortex.

PubMed

Sousa, C; Johansson, C; Charon, C; Manyani, H; Sautter, C; Kondorosi, A; Crespi, M

2001-01-01

A diversity of mRNAs containing only short open reading frames (sORF-RNAs; encoding less than 30 amino acids) have been shown to be induced in growth and differentiation processes. The early nodulin gene enod40, coding for a 0.7-kb sORF-RNA, is expressed in the nodule primordium developing in the root cortex of leguminous plants after infection by symbiotic bacteria. Ballistic microtargeting of this gene into Medicago roots induced division of cortical cells. Translation of two sORFs (I and II, 13 and 27 amino acids, respectively) present in the conserved 5' and 3' regions of enod40 was required for this biological activity. These sORFs may be translated in roots via a reinitiation mechanism. In vitro translation products starting from the ATG of sORF I were detectable by mutating enod40 to yield peptides larger than 38 amino acids. Deletion of a Medicago truncatula enod40 region between the sORFs, spanning a predicted RNA structure, did not affect their translation but resulted in significantly decreased biological activity. Our data reveal a complex regulation of enod40 action, pointing to a role of sORF-encoded peptides and structured RNA signals in developmental processes involving sORF-RNAs.

Nucleotide sequencing and characterization of the genes encoding benzene oxidation enzymes of Pseudomonas putida.

PubMed Central

Irie, S; Doi, S; Yorifuji, T; Takagi, M; Yano, K

1987-01-01

The nucleotide sequence of the genes from Pseudomonas putida encoding oxidation of benzene to catechol was determined. Five open reading frames were found in the sequence. Four corresponding protein molecules were detected by a DNA-directed in vitro translation system. Escherichia coli cells containing the fragment with the four open reading frames transformed benzene to cis-benzene glycol, which is an intermediate of the oxidation of benzene to catechol. The relation between the product of each cistron and the components of the benzene oxidation enzyme system is discussed. Images PMID:3667527

The calibration of read-out-streak photometry in the XMM-Newton Optical Monitor and the construction of a bright-source catalogue

NASA Astrophysics Data System (ADS)

Page, M. J.; Chan, N.; Breeveld, A. A.; Talavera, A.; Yershov, V.; Kennedy, T.; Kuin, N. P. M.; Hancock, B.; Smith, P. J.; Carter, M.

2017-04-01

The dynamic range of the XMM-Newton Optical Monitor (XMM-OM) is limited at the bright end by coincidence loss, the superposition of multiple photons in the individual frames recorded from its micro-channel-plate (MCP) intensified charge-coupled device (CCD) detector. One way to overcome this limitation is to use photons that arrive during the frame transfer of the CCD, forming vertical read-out streaks for bright sources. We calibrate these read-out streaks for photometry of bright sources observed with XMM-OM. The bright-source limit for read-out-streak photometry is set by the recharge time of the MCPs. For XMM-OM, we find that the MCP recharge time is 5.5 × 10-4 s. We determine that the effective bright limits for read-out-streak photometry with XMM-OM are approximately 1.5 mag brighter than the bright-source limits for normal aperture photometry in full-frame images. This translates into bright-source limits in Vega magnitudes of UVW2=7.1, UVM2=8.0, UVW1=9.4, U=10.5, B=11.5, V=10.2, and White=12.5 for data taken early in the mission. The limits brighten by up to 0.2 mag, depending on filter, over the course of the mission as the detector ages. The method is demonstrated by deriving UVW1 photometry for the symbiotic nova RR Telescopii, and the new photometry is used to constrain the e-folding time of its decaying ultraviolet (UV) emission. Using the read-out-streak method, we obtain photometry for 50 per cent of the missing UV source measurements in version 2.1 of the XMM-Newton Serendipitous UV Source Survey catalogue.

To Watch or to Read? The Respective Influence of Televised Political Debates and Media Debate Coverage on Citizen Learning

ERIC Educational Resources Information Center

Kunde, Meg

2017-01-01

Courses: Media and Politics, Political Communication, Political Rhetoric, Media Effects. Objective: By taking part in a classroom activity, students will explore how cognitive frames and media frames play a role in learning from political debates.

The in vivo use of alternate 3'-splice sites in group I introns.

PubMed

Sellem, C H; Belcour, L

1994-04-11

Alternative splicing of group I introns has been postulated as a possible mechanism that would ensure the translation of proteins encoded into intronic open reading frames, discontinuous with the upstream exon and lacking an initiation signal. Alternate splice sites were previously depicted according to secondary structures of several group I introns. We present here strong evidence that, in the case of Podospora anserina nad 1-i4 and cox1-i7 mitochondrial introns, alternative splicing events do occur in vivo. Indeed, by PCR experiments we have detected molecules whose sequence is precisely that expected if the predicted alternate 3'-splice sites were used.

Language use depending on news frame and immigrant origin.

PubMed

Fernández, Itziar; Igartua, Juan-José; Moral, Félix; Palacios, Elena; Acosta, Tania; Muñoz, Dolores

2013-01-01

The purpose of this study was to analyze the effect of the media on individuals' specific language use in relation to a news story on immigration: the influence of the news frame and group cue. Abstraction, complexity of language use, and negative affective language were evaluated. The 523 participants were randomly distributed to each of the four experimental conditions: news frame (crime versus economic contribution) by group cue (geographical origin of the immigrants involved: Moroccans versus Latin Americans). Through content analysis of the ideas and reflections that arose after the participants read the different news stories, using the Linguistic Category Model (LCM; Semin & Fiedler, 1991) to measure abstract language and the Linguistic Inquiry and Word Count (LIWC; Pennebaker, Booth, & Francis, 2007) to analyze complex language and negative affective language, it emerged that abstract language and negative affective language were more frequent in the participants assigned to the news frame on crime. Complex language was more commonly used when the news frame referred to the economic contribution of immigrants. Regression analyses showed the mediating role of attitude to immigration in the effects of news frame on negative affective language. The bootstrap method was used to assess the magnitude of the indirect effect. A significant mediator effect was also found through structural equation modeling. Analyses of covariance showed one interaction between news frame and group cue: Among those who read the news story in a frame linking immigration to crime and Moroccan origin, abstract language was more characteristic. The results are discussed from the theoretical perspective of framing.

Bijective transformation circular codes and nucleotide exchanging RNA transcription.

PubMed

Michel, Christian J; Seligmann, Hervé

2014-04-01

The C(3) self-complementary circular code X identified in genes of prokaryotes and eukaryotes is a set of 20 trinucleotides enabling reading frame retrieval and maintenance, i.e. a framing code (Arquès and Michel, 1996; Michel, 2012, 2013). Some mitochondrial RNAs correspond to DNA sequences when RNA transcription systematically exchanges between nucleotides (Seligmann, 2013a,b). We study here the 23 bijective transformation codes ΠX of X which may code nucleotide exchanging RNA transcription as suggested by this mitochondrial observation. The 23 bijective transformation codes ΠX are C(3) trinucleotide circular codes, seven of them are also self-complementary. Furthermore, several correlations are observed between the Reading Frame Retrieval (RFR) probability of bijective transformation codes ΠX and the different biological properties of ΠX related to their numbers of RNAs in GenBank's EST database, their polymerization rate, their number of amino acids and the chirality of amino acids they code. Results suggest that the circular code X with the functions of reading frame retrieval and maintenance in regular RNA transcription, may also have, through its bijective transformation codes ΠX, the same functions in nucleotide exchanging RNA transcription. Associations with properties such as amino acid chirality suggest that the RFR of X and its bijective transformations molded the origins of the genetic code's machinery. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

How to Communicate with a Machine: On Reading a Public Library's OPAC

ERIC Educational Resources Information Center

Saarti, Jarmo; Raivio, Jouko

2011-01-01

This article presents a reading of the user interface in one public library system. Its aim is to find out the frames and competences required and used in the communication between the computer and the patron. The authors see the computer as a text that is to be read by the user who wants to search for information from the library. The transition…

The Status of Exon Skipping as a Therapeutic Approach to Duchenne Muscular Dystrophy

PubMed Central

Lu, Qi-Long; Yokota, Toshifumi; Takeda, Shin'ichi; Garcia, Luis; Muntoni, Francesco; Partridge, Terence

2011-01-01

Duchenne muscular dystrophy (DMD) is associated with mutations in the dystrophin gene that disrupt the open reading frame whereas the milder Becker's form is associated with mutations which leave an in-frame mRNA transcript that can be translated into a protein that includes the N- and C- terminal functional domains. It has been shown that by excluding specific exons at, or adjacent to, frame-shifting mutations, open reading frame can be restored to an out-of-frame mRNA, leading to the production of a partially functional Becker-like dystrophin protein. Such targeted exclusion can be achieved by administration of oligonucleotides that are complementary to sequences that are crucial to normal splicing of the exon into the transcript. This principle has been validated in mouse and canine models of DMD with a number of variants of oligonucleotide analogue chemistries and by transduction with adeno-associated virus (AAV)-small nuclear RNA (snRNA) reagents encoding the antisense sequence. Two different oligonucleotide agents are now being investigated in human trials for splicing out of exon 51 with some early indications of success at the biochemical level. PMID:20978473

Reading Videogames as (Authorless) Literature

ERIC Educational Resources Information Center

Berger, Richard; McDougall, Julian

2013-01-01

This article presents the outcomes of research, funded by the Arts and Humanities Research Council in England and informed by work in the fields of new literacy research, gaming studies and the socio-cultural framing of education, for which the videogame "L. A. Noire" was studied within the orthodox framing of the English literature…

Analysis of genes involved in biosynthesis of the lantibiotic subtilin.

PubMed Central

Klein, C; Kaletta, C; Schnell, N; Entian, K D

1992-01-01

Lantibiotics are peptide-derived antibiotics with high antimicrobial activity against pathogenic gram-positive bacteria. They are ribosomally synthesized and posttranslationally modified (N. Schnell, K.-D. Entian, U. Schneider, F. Götz, H. Zähner, R. Kellner, and G. Jung, Nature [London] 333:276-278, 1988). The most important lantibiotics are subtilin and the food preservative nisin, which both have a very similar structure. By using a hybridization probe specific for the structural gene of subtilin, spaS, the DNA region adjacent to spaS was isolated from Bacillus subtilis. Sequence analysis of a 4.9-kb fragment revealed several open reading frames with the same orientation as spaS. Downstream of spaS, no reading frames were present on the isolated XbaI fragment. Upstream of spaS, three reading frames, spaB, spaC, and spaT, were identified which showed strong homology to genes identified near the structural gene of the lantibiotic epidermin. The SpaT protein derived from the spaT sequence was homologous to hemolysin B of Escherichia coli, which indicated its possible function in subtilin transport. Gene deletions within spaB and spaC revealed subtilin-negative mutants, whereas spaT gene disruption mutants still produced subtilin. Remarkably, the spaT mutant colonies revealed a clumpy surface morphology on solid media. After growth on liquid media, spaT mutant cells agglutinated in the mid-logarithmic growth phase, forming longitudinal 3- to 10-fold-enlarged cells which aggregated. Aggregate formation preceded subtilin production and cells lost their viability, possibly as a result of intracellular subtilin accumulation. Our results clearly proved that reading frames spaB and spaC are essential for subtilin biosynthesis whereas spaT mutants are probably deficient in subtilin transport. Images PMID:1539969

Genomewide Function Conservation and Phylogeny in the Herpesviridae

PubMed Central

Albà, M. Mar; Das, Rhiju; Orengo, Christine A.; Kellam, Paul

2001-01-01

The Herpesviridae are a large group of well-characterized double-stranded DNA viruses for which many complete genome sequences have been determined. We have extracted protein sequences from all predicted open reading frames of 19 herpesvirus genomes. Sequence comparison and protein sequence clustering methods have been used to construct herpesvirus protein homologous families. This resulted in 1692 proteins being clustered into 243 multiprotein families and 196 singleton proteins. Predicted functions were assigned to each homologous family based on genome annotation and published data and each family classified into seven broad functional groups. Phylogenetic profiles were constructed for each herpesvirus from the homologous protein families and used to determine conserved functions and genomewide phylogenetic trees. These trees agreed with molecular-sequence-derived trees and allowed greater insight into the phylogeny of ungulate and murine gammaherpesviruses. PMID:11156614

Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller’s organ, of the cattle tick, Rhipicephalus australis

PubMed Central

Munoz, Sergio; Guerrero, Felix D.; Kellogg, Anastasia; Heekin, Andrew M.

2017-01-01

The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller’s organ, located in the tick’s forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs) are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues. The two forelegs from adult R. australis were excised, RNA extracted, and pyrosequenced with 454 technology. Reads were assembled into unigenes and annotated by sequence similarity. Python scripts were written to find open reading frames (ORFs) from each unigene. These ORFs were analyzed by different GPCR prediction approaches based on sequence alignments, support vector machines, hidden Markov models, and principal component analysis. GPCRs consistently predicted by multiple methods were further studied by phylogenetic analysis and 3D homology modeling. From 4,782 assembled unigenes, 40,907 possible ORFs were predicted. Using Blastp, Pfam, GPCRpred, TMHMM, and PCA-GPCR, a basic set of 46 GPCR candidates were compiled and a phylogenetic tree was constructed. With further screening of tertiary structures predicted by RaptorX, 6 likely GPCRs emerged and the strongest candidate was classified by PCA-GPCR to be a GABAB receptor. PMID:28231302

Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller's organ, of the cattle tick, Rhipicephalus australis.

PubMed

Munoz, Sergio; Guerrero, Felix D; Kellogg, Anastasia; Heekin, Andrew M; Leung, Ming-Ying

2017-01-01

The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller's organ, located in the tick's forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs) are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues. The two forelegs from adult R. australis were excised, RNA extracted, and pyrosequenced with 454 technology. Reads were assembled into unigenes and annotated by sequence similarity. Python scripts were written to find open reading frames (ORFs) from each unigene. These ORFs were analyzed by different GPCR prediction approaches based on sequence alignments, support vector machines, hidden Markov models, and principal component analysis. GPCRs consistently predicted by multiple methods were further studied by phylogenetic analysis and 3D homology modeling. From 4,782 assembled unigenes, 40,907 possible ORFs were predicted. Using Blastp, Pfam, GPCRpred, TMHMM, and PCA-GPCR, a basic set of 46 GPCR candidates were compiled and a phylogenetic tree was constructed. With further screening of tertiary structures predicted by RaptorX, 6 likely GPCRs emerged and the strongest candidate was classified by PCA-GPCR to be a GABAB receptor.

Spectral characterisation and noise performance of Vanilla—an active pixel sensor

NASA Astrophysics Data System (ADS)

Blue, Andrew; Bates, R.; Bohndiek, S. E.; Clark, A.; Arvanitis, Costas D.; Greenshaw, T.; Laing, A.; Maneuski, D.; Turchetta, R.; O'Shea, V.

2008-06-01

This work will report on the characterisation of a new active pixel sensor, Vanilla. The Vanilla comprises of 512×512 (25μm 2) pixels. The sensor has a 12 bit digital output for full-frame mode, although it can also be readout in analogue mode, whereby it can also be read in a fully programmable region-of-interest (ROI) mode. In full frame, the sensor can operate at a readout rate of more than 100 frames per second (fps), while in ROI mode, the speed depends on the size, shape and number of ROIs. For example, an ROI of 6×6 pixels can be read at 20,000 fps in analogue mode. Using photon transfer curve (PTC) measurements allowed for the calculation of the read noise, shot noise, full-well capacity and camera gain constant of the sensor. Spectral response measurements detailed the quantum efficiency (QE) of the detector through the UV and visible region. Analysis of the ROI readout mode was also performed. Such measurements suggest that the Vanilla APS (active pixel sensor) will be suitable for a wide range of applications including particle physics and medical imaging.

Investigating the Syllabus as a Defining Document

ERIC Educational Resources Information Center

Bowers-Campbell, Joy

2015-01-01

The following study is part of a larger study exploring reading identity in students who were placed into a mandatory developmental reading class because of low scores on college placement exams. Sociocultural theories of learning framed the qualitative study. Although the larger study addressed two overarching questions related to reading…

Learning to Read: A Third Perspective

ERIC Educational Resources Information Center

Gregory, Eve

2016-01-01

How children learn to read is a controversial matter. Since the teaching of literacy has always been a major purpose of schooling, pedagogy and teaching methods have generally framed research and practice. Psychologists and linguists have played a major role in determining what we mean by "literacy learning". Although they disagree on…

Electronic clinical predictive thermometer using logarithm for temperature prediction

NASA Technical Reports Server (NTRS)

Cambridge, Vivien J. (Inventor); Koger, Thomas L. (Inventor); Nail, William L. (Inventor); Diaz, Patrick (Inventor)

1998-01-01

A thermometer that rapidly predicts body temperature based on the temperature signals received from a temperature sensing probe when it comes into contact with the body. The logarithms of the differences between the temperature signals in a selected time frame are determined. A line is fit through the logarithms and the slope of the line is used as a system time constant in predicting the final temperature of the body. The time constant in conjunction with predetermined additional constants are used to compute the predicted temperature. Data quality in the time frame is monitored and if unacceptable, a different time frame of temperature signals is selected for use in prediction. The processor switches to a monitor mode if data quality over a limited number of time frames is unacceptable. Determining the start time on which the measurement time frame for prediction is based is performed by summing the second derivatives of temperature signals over time frames. When the sum of second derivatives in a particular time frame exceeds a threshold, the start time is established.

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

PubMed

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

1996-06-15

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

Construction Cluster Volume I [Wood Structural Framing].

ERIC Educational Resources Information Center

Pennsylvania State Dept. of Justice, Harrisburg. Bureau of Correction.

The document is the first of a series, to be integrated with a G.E.D. program, containing instructional materials at the basic skills level for the construction cluster. It focuses on wood structural framing and contains 20 units: (1) occupational information; (2) blueprint reading; (3) using leveling instruments and laying out building lines; (4)…

The Influence of Negative Advertising Frames on Political Cynicism and Politician Accountability.

ERIC Educational Resources Information Center

Schenck-Hamlin, William J.; Procter, David E.; Rumsey, Deborah J.

2000-01-01

Examines the influence of negative political advertising frames on the thoughts and feelings undergraduate students generate in response to campaign advertising. Finds that participants were more likely to generate cynical comments and hold politicians accountable for the country's ills when reading candidate theme advertisements than ad hoc issue…

Technological Difficulties: A Theoretical Frame for Understanding the Non-Relativistic Permanence of Traditional Print Literacy in Elementary Education

ERIC Educational Resources Information Center

Hassett, Dawnene D.

2006-01-01

Currently, definitions of "science", "reading", and "literacy" in the US lend a seemingly nonrelativistic permanence to these terms, and render them resistant to critique. This paper offers a theoretical frame for critiquing this permanence, analysing why early-literacy instruction is tightly tied to traditional forms…

Kepler Fine Guidance Sensor Data

NASA Technical Reports Server (NTRS)

Van Cleve, Jeffrey; Campbell, Jennifer Roseanna

2017-01-01

The Kepler and K2 missions collected Fine Guidance Sensor (FGS) data in addition to the science data, as discussed in the Kepler Instrument Handbook (KIH, Van Cleve and Caldwell 2016). The FGS CCDs are frame transfer devices (KIH Table 7) located in the corners of the Kepler focal plane (KIH Figure 24), which are read out 10 times every second. The FGS data are being made available to the user community for scientific analysis as flux and centroid time series, along with a limited number of FGS full frame images which may be useful for constructing a World Coordinate System (WCS) or otherwise putting the time series data in context. This document will describe the data content and file format, and give example MATLAB scripts to read the time series. There are three file types delivered as the FGS data.1. Flux and Centroid (FLC) data: time series of star signal and centroid data. 2. Ancillary FGS Reference (AFR) data: catalog of information about the observed stars in the FLC data. 3. FGS Full-Frame Image (FGI) data: full-frame image snapshots of the FGS CCDs.

Clinical characterisation of Becker muscular dystrophy patients predicts favourable outcome in exon-skipping therapy.

PubMed

van den Bergen, J C; Schade van Westrum, S M; Dekker, L; van der Kooi, A J; de Visser, M; Wokke, B H A; Straathof, C S; Hulsker, M A; Aartsma-Rus, A; Verschuuren, J J; Ginjaar, H B

2014-01-01

Duchenne and Becker muscular dystrophy (DMD/BMD) are both caused by mutations in the DMD gene. Out-of-frame mutations in DMD lead to absence of the dystrophin protein, while in-frame BMD mutations cause production of internally deleted dystrophin. Clinically, patients with DMD loose ambulance around the age of 12, need ventilatory support at their late teens and die in their third or fourth decade due to pulmonary or cardiac failure. BMD has a more variable disease course. The disease course of patients with BMD with specific mutations could be very informative to predict the outcome of the exon-skipping therapy, aiming to restore the reading-frame in patients with DMD. Patients with BMD with a mutation equalling a DMD mutation after successful exon skipping were selected from the Dutch Dystrophinopathy Database. Information about disease course was gathered through a standardised questionnaire. Cardiac data were collected from medical correspondence and a previous study on cardiac function in BMD. Forty-eight patients were included, representing 11 different mutations. Median age of patients was 43 years (range 6-67). Nine patients were wheelchair users (26-56 years). Dilated cardiomyopathy was present in 7/36 patients. Only one patient used ventilatory support. Three patients had died at the age of 45, 50 and 76 years, respectively. This study provides mutation specific data on the course of disease in patients with BMD. It shows that the disease course of patients with BMD, with a mutation equalling a 'skipped' DMD mutation is relatively mild. This finding strongly supports the potential benefit of exon skipping in patients with DMD.

Identification, cloning, and sequencing of a fragment of Amsacta moorei entomopoxvirus DNA containing the spheroidin gene and three vaccinia virus-related open reading frames.

PubMed Central

Hall, R L; Moyer, R W

1991-01-01

Entomopoxvirus virions are frequently contained within crystalline occlusion bodies, which are composed of primarily a single protein, spheroidin, which is analogous to the polyhedrin protein of baculovirus. The spheroidin gene of Amsacta moorei entomopoxvirus was identified following the microsequencing of polypeptides generated from cyanogen bromide treatment of spheroidin and the subsequent synthesis of oligonucleotide hybridization probes. DNA sequencing of a 6.8-kb region of DNA containing the spheroidin gene showed that the spheroidin protein is derived from a 3.0-kb open reading frame potentially encoding a protein of 115 kDa. Three copies of the heptanucleotide, TTTTTNT, a sequence associated with early gene transcription in the vertebrate poxviruses, and four in-frame translational termination signals were found within 60 bp upstream of the putative spheroidin gene promoter (TAAATG). The spheroidin gene promoter region contains the sequence TAAATG, which is found in many late promoters of the vertebrate poxviruses and which serves as the site of transcriptional initiation, as shown by primer extension. Primer extension experiments also showed that spheroidin gene transcripts contain 5' poly(A) sequences typical of vertebrate poxvirus late transcripts. The 92 bases upstream of the initiating TAAATG are unusually A + T rich and contain only 7 G or C residues. An analysis of open reading frames around the spheroidin gene suggests that the colinear core of "essential genes" typical of the vertebrate poxviruses is absent in A. moorei entomopoxvirus. Images PMID:1942245

Living organ donation: the effect of message frame on an altruistic behaviour.

PubMed

McGregor, Lesley M; Ferguson, Eamonn; O'Carroll, Ronan E

2012-09-01

This experimental study investigates the impact of message frame and risk perceptions upon willingness to consider living organ donation. A 2 (gain vs. loss) by 2 (liver vs. kidney) by 2 (involved vs. not involved) between-group study was conducted. Eighty-seven participants completed a questionnaire after reading a vignette designed to invite participants to consider living kidney or liver donation. Within a gain frame scenario, willingness to donate was significantly higher when the risk of donating was lower. The results have important implications for the generalizability of framing theories and the promotion of living organ donation.

Differential Effects of Message Framing on Obesity Policy Support Between Democrats and Republicans.

PubMed

Lee, Tae Kyoung; Kim, Hye Kyung

2017-12-01

This study tests whether gain- and loss-framed messages about establishing obesity-reducing policies have different persuasive effects on Republicans and Democrats. In a randomized between-subject experiment, participants (N = 384) read a message emphasizing either benefits to a society by establishing policies aimed to reduce obesity (i.e., gain-framed message) or costs to a society that fails to establish those policies (i.e., loss-framed message). Results indicated that Democrats perceived the gain-framed message as more persuasive than the loss-framed message and the perceived argument strength fully mediated the framing effect on Democrats' policy support; however, there was no framing effect on perceived argument strength among Republicans. On the other hand, the gain-framed message led Republicans to attribute the cause of obesity less to the individual level compared to the loss-framed message and the no-message condition. We observed no framing difference among Democrats on causal attributions. Theoretical and practical implications of these findings are discussed.

Network-based H.264/AVC whole frame loss visibility model and frame dropping methods.

PubMed

Chang, Yueh-Lun; Lin, Ting-Lan; Cosman, Pamela C

2012-08-01

We examine the visual effect of whole frame loss by different decoders. Whole frame losses are introduced in H.264/AVC compressed videos which are then decoded by two different decoders with different common concealment effects: frame copy and frame interpolation. The videos are seen by human observers who respond to each glitch they spot. We found that about 39% of whole frame losses of B frames are not observed by any of the subjects, and over 58% of the B frame losses are observed by 20% or fewer of the subjects. Using simple predictive features which can be calculated inside a network node with no access to the original video and no pixel level reconstruction of the frame, we developed models which can predict the visibility of whole B frame losses. The models are then used in a router to predict the visual impact of a frame loss and perform intelligent frame dropping to relieve network congestion. Dropping frames based on their visual scores proves superior to random dropping of B frames.

Dystrophin quantification and clinical correlations in Becker muscular dystrophy: implications for clinical trials.

PubMed

Anthony, Karen; Cirak, Sebahattin; Torelli, Silvia; Tasca, Giorgio; Feng, Lucy; Arechavala-Gomeza, Virginia; Armaroli, Annarita; Guglieri, Michela; Straathof, Chiara S; Verschuuren, Jan J; Aartsma-Rus, Annemieke; Helderman-van den Enden, Paula; Bushby, Katherine; Straub, Volker; Sewry, Caroline; Ferlini, Alessandra; Ricci, Enzo; Morgan, Jennifer E; Muntoni, Francesco

2011-12-01

Duchenne muscular dystrophy is caused by mutations in the DMD gene that disrupt the open reading frame and prevent the full translation of its protein product, dystrophin. Restoration of the open reading frame and dystrophin production can be achieved by exon skipping using antisense oligonucleotides targeted to splicing elements. This approach aims to transform the Duchenne muscular dystrophy phenotype to that of the milder disorder, Becker muscular dystrophy, typically caused by in-frame dystrophin deletions that allow the production of an internally deleted but partially functional dystrophin. There is ongoing debate regarding the functional properties of the different internally deleted dystrophins produced by exon skipping for different mutations; more insight would be valuable to improve and better predict the outcome of exon skipping clinical trials. To this end, we have characterized the clinical phenotype of 17 patients with Becker muscular dystrophy harbouring in-frame deletions relevant to on-going or planned exon skipping clinical trials for Duchenne muscular dystrophy and correlated it to the levels of dystrophin, and dystrophin-associated protein expression. The cohort of 17 patients, selected exclusively on the basis of their genotype, included 4 asymptomatic, 12 mild and 1 severe patient. All patients had dystrophin levels of >40% of control and significantly higher dystrophin (P = 0.013), β-dystroglycan (P = 0.025) and neuronal nitric oxide synthase (P = 0.034) expression was observed in asymptomatic individuals versus symptomatic patients with Becker muscular dystrophy. Furthermore, grouping the patients by deletion, patients with Becker muscular dystrophy with deletions with an end-point of exon 51 (the skipping of which could rescue the largest group of Duchenne muscular dystrophy deletions) showed significantly higher dystrophin levels (P = 0.034) than those with deletions ending with exon 53. This is the first quantitative study on both dystrophin and dystrophin-associated protein expression in patients with Becker muscular dystrophy with deletions relevant for on-going exon skipping trials in Duchenne muscular dystrophy. Taken together, our results indicate that all varieties of internally deleted dystrophin assessed in this study have the functional capability to provide a substantial clinical benefit to patients with Duchenne muscular dystrophy.

Dystrophin quantification and clinical correlations in Becker muscular dystrophy: implications for clinical trials

PubMed Central

Anthony, Karen; Cirak, Sebahattin; Torelli, Silvia; Tasca, Giorgio; Feng, Lucy; Arechavala-Gomeza, Virginia; Armaroli, Annarita; Guglieri, Michela; Straathof, Chiara S.; Verschuuren, Jan J.; Aartsma-Rus, Annemieke; Helderman-van den Enden, Paula; Bushby, Katherine; Straub, Volker; Sewry, Caroline; Ferlini, Alessandra; Ricci, Enzo; Morgan, Jennifer E.

2011-01-01

Duchenne muscular dystrophy is caused by mutations in the DMD gene that disrupt the open reading frame and prevent the full translation of its protein product, dystrophin. Restoration of the open reading frame and dystrophin production can be achieved by exon skipping using antisense oligonucleotides targeted to splicing elements. This approach aims to transform the Duchenne muscular dystrophy phenotype to that of the milder disorder, Becker muscular dystrophy, typically caused by in-frame dystrophin deletions that allow the production of an internally deleted but partially functional dystrophin. There is ongoing debate regarding the functional properties of the different internally deleted dystrophins produced by exon skipping for different mutations; more insight would be valuable to improve and better predict the outcome of exon skipping clinical trials. To this end, we have characterized the clinical phenotype of 17 patients with Becker muscular dystrophy harbouring in-frame deletions relevant to on-going or planned exon skipping clinical trials for Duchenne muscular dystrophy and correlated it to the levels of dystrophin, and dystrophin-associated protein expression. The cohort of 17 patients, selected exclusively on the basis of their genotype, included 4 asymptomatic, 12 mild and 1 severe patient. All patients had dystrophin levels of >40% of control and significantly higher dystrophin (P = 0.013), β-dystroglycan (P = 0.025) and neuronal nitric oxide synthase (P = 0.034) expression was observed in asymptomatic individuals versus symptomatic patients with Becker muscular dystrophy. Furthermore, grouping the patients by deletion, patients with Becker muscular dystrophy with deletions with an end-point of exon 51 (the skipping of which could rescue the largest group of Duchenne muscular dystrophy deletions) showed significantly higher dystrophin levels (P = 0.034) than those with deletions ending with exon 53. This is the first quantitative study on both dystrophin and dystrophin-associated protein expression in patients with Becker muscular dystrophy with deletions relevant for on-going exon skipping trials in Duchenne muscular dystrophy. Taken together, our results indicate that all varieties of internally deleted dystrophin assessed in this study have the functional capability to provide a substantial clinical benefit to patients with Duchenne muscular dystrophy. PMID:22102647

Molecular Characterization of Mosquitocidal Toxin (Surface Layer Protein, SLP) from Bacillus cereus VCRC B540.

PubMed

Mani, Chinnasamy; Selvakumari, Jeyaperumal; Han, YeonSoo; Jo, YongHun; Thirugnanasambantham, Krishnaraj; Sundarapandian, Somaiah; Poopathi, Subbiah

2018-04-01

A marine Bacillus cereus (VCRC B540) with mosquitocidal effect was recently reported from red snapper fish (Lutjanus sanguineous) gut and surface layer protein (S-layer protein, SLP) was reported to be mosquito larvicidal factor. In this present study, the gene encoding the surface layer protein was amplified from the genomic DNA and functionally characterized. Amplification of SLP-encoding gene revealed 1,518 bp PCR product, and analysis of the sequence revealed the presence of 1482 bp open reading frame with coding capacity for a polypeptide of 493 amino acids. Phylogenetic analysis revealed with homology among closely related Bacillus cereus groups of organisms as well as Bacillus strains. Removal of nucleotides encoding signaling peptide revealed the functional cloning fragment of length 1398 bp. Theoretical molecular weight (51.7 kDa) and isoelectric point (5.99) of the deduced functional SLP protein were predicted using ProtParam. The amplified PCR product was cloned into a plasmid vector (pGEM-T), and the open reading frame free off signaling peptide was subsequently cloned inpET-28a(+) and expressed in Escherichia coli BL21 (DE3). The isopropyl-β-D-thiogalactopyranoside (IPTG)-induced recombinant SLP was confirmed using western blotting, and functional SLP revealed mosquito larvicidal property. Therefore, the major findings revealed that SLP is a factor responsible for mosquitocidal activity, and the molecular characterization of this toxin was extensively studied.

Characterization of the Tupaia rhabdovirus genome reveals a long open reading frame overlapping with P and a novel gene encoding a small hydrophobic protein.

PubMed

Springfeld, Christoph; Darai, Gholamreza; Cattaneo, Roberto

2005-06-01

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

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

PubMed Central

Springfeld, Christoph; Darai, Gholamreza; Cattaneo, Roberto

2005-01-01

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

Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates

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

Jackson, P.J.; Walthers, E.A.; Richmond, K.L.

1997-04-01

PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five Polymorphisms differed by the presence Of two to six copies of the 12-bp tandem repeat 5{prime}-CAATATCAACAA-3{prime}. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats aremore » generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations. 22 refs., 4 figs., 3 tabs.« less

Characterization and complete genome sequence of a panicovirus from Bermuda grass by high-throughput sequencing.

PubMed

Tahir, Muhammad N; Lockhart, Ben; Grinstead, Samuel; Mollov, Dimitre

2017-04-01

Bermuda grass samples were examined by transmission electron microscopy and 28-30 nm spherical virus particles were observed. Total RNA from these plants was subjected to high-throughput sequencing (HTS). The nearly full genome sequence of a panicovirus was identified from one HTS scaffold. Sanger sequencing was used to confirm the HTS results and complete the genome sequence of 4404 nt. This virus was provisionally named Bermuda grass latent virus (BGLV). Its predicted open reading frames follow the typical arrangement of the genus Panicovirus. Based on sequence comparisons and phylogenetic analyses BGLV differs from other viruses and therefore taxonomically it is a new member of the genus Panicovirus, family Tombusviridae.

Cloning and expression analysis of FaPR-1 gene in strawberry

NASA Astrophysics Data System (ADS)

Mo, Fan; Luo, Ya; Ge, Cong; Mo, Qin; Ling, Yajie; Luo, Shu; Tang, Haoru

2018-04-01

The FaPR-1 gene was cloned by RT-PCR from `Benihoppe' strawberry and its bioinformatics analysis was conducted. The results showed that the open reading frame was 483 bp encoding encoding l60 amino acids which protein molecular weight and theoretical isoelectricity were 17854.17 and 8.72 respectively. Subcellular localization prediction shows that this gene is located extracellularly. By comparing strawberry FaPR-l and other plant Pathogenesis-related protein, homology and phylogenetic tree construction showed that the homology with grapes, peach is relatively close. In the treatments of ABA, sucrose and the mixture of the two, the expression of FaPR-1 in strawberry fruit were significantly increased.

Genomic and Phylogenetic Characterization of Brazilian Yellow Fever Virus Strains

PubMed Central

Palacios, Gustavo; Cardoso, Jedson F.; Martins, Livia C.; Sousa, Edivaldo C.; de Lima, Clayton P. S.; Medeiros, Daniele B. A.; Savji, Nazir; Desai, Aaloki; Rodrigues, Sueli G.; Carvalho, Valeria L.; Lipkin, W. Ian

2012-01-01

Globally, yellow fever virus infects nearly 200,000 people, leading to 30,000 deaths annually. Although the virus is endemic to Latin America, only a single genome from this region has been sequenced. Here, we report 12 Brazilian yellow fever virus complete genomes, their genetic traits, phylogenetic characterization, and phylogeographic dynamics. Variable 3′ noncoding region (3′NCR) patterns and specific mutations throughout the open reading frame altered predicted secondary structures. Our findings suggest that whereas the introduction of yellow fever virus in Brazil led to genotype I-predominant dispersal throughout South and Central Americas, genotype II remained confined to Bolivia, Peru, and the western Brazilian Amazon. PMID:23015713

Complete nucleotide sequence of clematis chlorotic mottle virus, a new member of the family Tombusviridae.

PubMed

McLaughlin, Margaret; Lockhart, Ben; Jordan, Ramon; Denton, Geoff; Mollov, Dimitre

2017-05-01

Clematis chlorotic mottle virus (ClCMV) is a previously undescribed virus associated with symptoms of yellow mottling and veining, chlorotic ring spots, line pattern mosaics, and flower distortion and discoloration on ornamental Clematis. The ClCMV genome is 3,880 nt in length with five open reading frames (ORFs) encoding a 27-kDa protein (ORF 1), an 87-kDa replicase protein (ORF 2), two centrally located movement proteins (ORF 3 and 4), and a 37-kDa capsid protein (ORF 5). Based on morphological, genomic, and phylogenetic analysis, ClCMV is predicted to be a member of the genus Pelarspovirus in the family Tombusviridae.

"At a School Like This" Implementing Policy in a Kindergarten Reading Program

ERIC Educational Resources Information Center

Harris, Pauline

2010-01-01

This paper examines influences in a teacher's working context on policy implementation in a Kindergarten reading program. This exploration is based on a year's observations, interviews and artefact collection in the teacher's classroom; and is framed by Bernstein's notion of the pedagogic device (2000). Positioned between policy and the history of…

Indian and Bangladeshi Perspectives: Use of Metacognition and Framing in Postgraduate Study

ERIC Educational Resources Information Center

Bell, Joyce

2007-01-01

The importance of reading for academic study cannot be overemphasised. At the postgraduate level in particular, students are faced with complex text interpretation processes. International students, in addition, have to make a significant cultural/study shift; not only do they have to become accustomed to the reading of academic texts using…

Instructional Engineering Principles to Frame the Future of Reading Intervention Research and Practice

ERIC Educational Resources Information Center

Simmons, Deborah

2015-01-01

In this article, I outline thoughts regarding the complexities and possibilities of the next generation of reading intervention for students who do not benefit from typical instructional practices. I ground my recommendations in school-based research and observations conducted primarily in kindergarten through third grade and more recently in…

Development of the TACOM (Tank Automotive Command) Thermal Imaging Model (TTIM). Volume 1. Technical Guide and User’s Manual.

DTIC Science & Technology

1984-12-01

BLOCK DATA Default values for variables input by menus. LIBR Interface with frame I/O routines. SNSR Interface with sensor routines. ATMOS Interface with...Routines Included in Frame I/O Interface Routine Description LIBR Selects options for input or output to a data library. FRREAD Reads frame from file and/or...Layer", Journal of Applied Meteorology 20, pp. 242-249, March 1981. 15 L.J. Harding, Numerical Analysis and Applications Software Abstracts, Computing

A new open reading frame in the genome of the cyanobacterium Synechocystis sp. PCC 6803

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

Lysenko, E.S.; Ogarkova, O.A.; Tarasov, V.A.

1995-02-01

A new open reading frame ORF242, coding for a 26.47-kDa polypeptide, was found in a DNA fragment of the cyanobacterium Synechocystis 6803, transforming a photosynthetic mutant to photoautotrophy and having homology with plant chloroplast DNA. In the 5{prime} flanking region of ORF242, consensus sequences characteristic of a functioning gene were found. One copy of ORF242 is present in the Synechocystis 6803 genome. Insertion inactivation of ORF242 does not lead to a decrease in photosynthetic activity in cells of cyanobacteria but may influence the ratio between active complexes of photosystems I and II. 22 refs., 6 figs., 2 tabs.

The open reading frames in the 3' long terminal repeats of several mouse mammary tumor virus integrants encode V beta 3-specific superantigens

PubMed Central

1992-01-01

Mice expressing the minor lymphocyte stimulation antigens, Mls-1a, -2a, or -3a, singly on the B10.BR background have been generated. Mls phenotypes correlate with the integration of mouse mammary tumor viruses (MTV) in the mouse genome. The open reading frames within the 3' long terminal repeats of the integrated MTVs 1, 3, 6, and 13 encode V beta 3-specific superantigens. Sequence data for these viral superantigens is presented, indicating that it is the COOH-terminal portion of the viral superantigen that interacts with the T cell receptor V beta element. PMID:1309854

A novel helper phage enabling construction of genome-scale ORF-enriched phage display libraries.

PubMed

Gupta, Amita; Shrivastava, Nimisha; Grover, Payal; Singh, Ajay; Mathur, Kapil; Verma, Vaishali; Kaur, Charanpreet; Chaudhary, Vijay K

2013-01-01

Phagemid-based expression of cloned genes fused to the gIIIP coding sequence and rescue using helper phages, such as VCSM13, has been used extensively for constructing large antibody phage display libraries. However, for randomly primed cDNA and gene fragment libraries, this system encounters reading frame problems wherein only one of 18 phages display the translated foreign peptide/protein fused to phagemid-encoded gIIIP. The elimination of phages carrying out-of-frame inserts is vital in order to improve the quality of phage display libraries. In this study, we designed a novel helper phage, AGM13, which carries trypsin-sensitive sites within the linker regions of gIIIP. This renders the phage highly sensitive to trypsin digestion, which abolishes its infectivity. For open reading frame (ORF) selection, the phagemid-borne phages are rescued using AGM13, so that clones with in-frame inserts express fusion proteins with phagemid-encoded trypsin-resistant gIIIP, which becomes incorporated into the phages along with a few copies of AGM13-encoded trypsin-sensitive gIIIP. In contrast, clones with out-of-frame inserts produce phages carrying only AGM13-encoded trypsin-sensitive gIIIP. Trypsin treatment of the phage population renders the phages with out-of-frame inserts non-infectious, whereas phages carrying in-frame inserts remain fully infectious and can hence be enriched by infection. This strategy was applied efficiently at a genome scale to generate an ORF-enriched whole genome fragment library from Mycobacterium tuberculosis, in which nearly 100% of the clones carried in-frame inserts after selection. The ORF-enriched libraries were successfully used for identification of linear and conformational epitopes for monoclonal antibodies specific to mycobacterial proteins.

Physical activity advertisements that feature daily well-being improve autonomy and body image in overweight women but not men.

PubMed

Segar, Michelle L; Updegraff, John A; Zikmund-Fisher, Brian J; Richardson, Caroline R

2012-01-01

The reasons for exercising that are featured in health communications brand exercise and socialize individuals about why they should be physically active. Discovering which reasons for exercising are associated with high-quality motivation and behavioral regulation is essential to promoting physical activity and weight control that can be sustained over time. This study investigates whether framing physical activity in advertisements featuring distinct types of goals differentially influences body image and behavioral regulations based on self-determination theory among overweight and obese individuals. Using a three-arm randomized trial, overweight and obese women and men (aged 40-60 yr, n = 1690) read one of three ads framing physical activity as a way to achieve (1) better health, (2) weight loss, or (3) daily well-being. Framing effects were estimated in an ANOVA model with pairwise comparisons using the Bonferroni correction. This study showed that there are immediate framing effects on physical activity behavioral regulations and body image from reading a one-page advertisement about physical activity and that gender and BMI moderate these effects. Framing physical activity as a way to enhance daily well-being positively influenced participants' perceptions about the experience of being physically active and enhanced body image among overweight women, but not men. The experiment had less impact among the obese study participants compared to those who were overweight. These findings support a growing body of research suggesting that, compared to weight loss, framing physical activity for daily well-being is a better gain-frame message for overweight women in midlife.

Physical Activity Advertisements That Feature Daily Well-Being Improve Autonomy and Body Image in Overweight Women but Not Men

PubMed Central

Segar, Michelle L.; Updegraff, John A.; Zikmund-Fisher, Brian J.; Richardson, Caroline R.

2012-01-01

The reasons for exercising that are featured in health communications brand exercise and socialize individuals about why they should be physically active. Discovering which reasons for exercising are associated with high-quality motivation and behavioral regulation is essential to promoting physical activity and weight control that can be sustained over time. This study investigates whether framing physical activity in advertisements featuring distinct types of goals differentially influences body image and behavioral regulations based on self-determination theory among overweight and obese individuals. Using a three-arm randomized trial, overweight and obese women and men (aged 40–60 yr, n = 1690) read one of three ads framing physical activity as a way to achieve (1) better health, (2) weight loss, or (3) daily well-being. Framing effects were estimated in an ANOVA model with pairwise comparisons using the Bonferroni correction. This study showed that there are immediate framing effects on physical activity behavioral regulations and body image from reading a one-page advertisement about physical activity and that gender and BMI moderate these effects. Framing physical activity as a way to enhance daily well-being positively influenced participants' perceptions about the experience of being physically active and enhanced body image among overweight women, but not men. The experiment had less impact among the obese study participants compared to those who were overweight. These findings support a growing body of research suggesting that, compared to weight loss, framing physical activity for daily well-being is a better gain-frame message for overweight women in midlife. PMID:22701782

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

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

Chen, Lei

2008-01-01

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

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

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

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

2008-02-22

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

Interpreting the biological relevance of bioinformatic analyses with T-DNA sequence for protein allergenicity.

PubMed

Harper, B; McClain, S; Ganko, E W

2012-08-01

Global regulatory agencies require bioinformatic sequence analysis as part of their safety evaluation for transgenic crops. Analysis typically focuses on encoded proteins and adjacent endogenous flanking sequences. Recently, regulatory expectations have expanded to include all reading frames of the inserted DNA. The intent is to provide biologically relevant results that can be used in the overall assessment of safety. This paper evaluates the relevance of assessing the allergenic potential of all DNA reading frames found in common food genes using methods considered for the analysis of T-DNA sequences used in transgenic crops. FASTA and BLASTX algorithms were used to compare genes from maize, rice, soybean, cucumber, melon, watermelon, and tomato using international regulatory guidance. Results show that BLASTX for maize yielded 7254 alignments that exceeded allergen similarity thresholds and 210,772 alignments that matched eight or more consecutive amino acids with an allergen; other crops produced similar results. This analysis suggests that each nontransgenic crop has a much greater potential for allergenic risk than what has been observed clinically. We demonstrate that a meaningful safety assessment is unlikely to be provided by using methods with inherently high frequencies of false positive alignments when broadly applied to all reading frames of DNA sequence. Copyright © 2012 Elsevier Inc. All rights reserved.

A local duplication of the Melanocortin receptor 1 locus in Astyanax

PubMed Central

Gross, Joshua B.; Weagley, James; Stahl, Bethany A.; Ma, Li; Espinasa, Luis; McGaugh, Suzanne E.

2017-01-01

In this study, we report evidence of a novel duplication of Melanocortin receptor 1 (Mc1r) in the cavefish genome. This locus was discovered following the observation of excessive allelic diversity in a ~820 bp fragment of Mc1r amplified via degenerate PCR from a natural population of Astyanax aeneus fish from Guerrero, Mexico. The cavefish genome reveals the presence of two closely related Mc1r open reading frames separated by a 1.46 kb intergenic region. One open reading frame corresponds to the previously reported Mc1r receptor, and the other open reading frame (duplicate copy) is 975 bp in length, encoding a receptor of 325 amino acids. Sequence similarity analyses position both copies in the syntenic region of the single Mc1r locus in 16 representative craniate genomes spanning bony fish (including Astyanax) to mammals, suggesting we discovered tandem duplicates of this important gene. The two Mc1r copies share ~89% sequence similarity, and, within Astyanax, are more similar to one another compared to other melanocortin family members. Future studies will inform the precise functional significance of the duplicated Mc1r locus, and if this novel copy number variant may have adaptive significance for the Astyanax lineage. PMID:28738163

Mitochondrial Intronic Open Reading Frames in Podospora: Mobility and Consecutive Exonic Sequence Variations

PubMed Central

Sellem, C. H.; d'Aubenton-Carafa, Y.; Rossignol, M.; Belcour, L.

1996-01-01

The mitochondrial genome of 23 wild-type strains belonging to three different species of the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes. PMID:8725226

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

PubMed

Sellem, C H; d'Aubenton-Carafa, Y; Rossignol, M; Belcour, L

1996-06-01

The mitochondrial genome of 23 wild-type strains belonging to three different species of the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group 1 intronic ORFs are mobile elements and that their transfer, and concomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

CSAF Reading List 2013

Science.gov Websites

"Imperial Wild Eagles" of Japan and in turn won immortality as the Flying Tigers. One of --one of the first postwar films out of Hollywood to treat the war on emotionally complex terms. Framed release. Read More... Ordinance Group Loading GBU-24B Ordinance Group Loading GBU-24B by Douglas Smith

Image Processing In Laser-Beam-Steering Subsystem

NASA Technical Reports Server (NTRS)

Lesh, James R.; Ansari, Homayoon; Chen, Chien-Chung; Russell, Donald W.

1996-01-01

Conceptual design of image-processing circuitry developed for proposed tracking apparatus described in "Beam-Steering Subsystem For Laser Communication" (NPO-19069). In proposed system, desired frame rate achieved by "windowed" readout scheme in which only pixels containing and surrounding two spots read out and others skipped without being read. Image data processed rapidly and efficiently to achieve high frequency response.

Just Because It's Digital, Doesn't Mean It's Good: Evaluating Digital Picture Books

ERIC Educational Resources Information Center

McGeehan, Catherine; Chambers, Sandra; Nowakowski, Jessica

2018-01-01

At the current time, the reviews of digital picture books are not based on the reading comprehension process or framed in the context of how readers achieve critical reading comprehension. Rather these reviews, often completed by technology specialists, focus on features that are "attractive" and "entertaining" to readers…

Law and Justice CTE Program Offers a Hands-On Approach to Learning

ERIC Educational Resources Information Center

Klein, Jennifer

2013-01-01

Tom Washburn, founder of the Law and Justice Program in Fulton County Schools in Atlanta, Georgia, sees career and technical education (CTE) as a framework for gains in reading comprehension, public speaking, math and science. "It's a holistic approach to learning, framed by law and justice. Behind the scenes we're reading novels, improving…

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

USDA-ARS?s Scientific Manuscript database

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

Using Poetry as a Communication Multimodality to Encourage Reading Engagement of Selected African-American Learners: A Case Study

ERIC Educational Resources Information Center

Ward, Cherie A.

2015-01-01

This study examined the use of poetry as a multimodal communicative text to encourage reading engagement in selected African-American learners with mild intellectual disabilities. Framed by critical discourse theory, genre theory, and Gardner's theory of multiple intelligences, this investigation presented poetry as an alternative text…

Termination and read-through proteins encoded by genome segment 9 of Colorado tick fever virus.

PubMed

Mohd Jaafar, Fauziah; Attoui, Houssam; De Micco, Philippe; De Lamballerie, Xavier

2004-08-01

Genome segment 9 (Seg-9) of Colorado tick fever virus (CTFV) is 1884 bp long and contains a large open reading frame (ORF; 1845 nt in length overall), although a single in-frame stop codon (at nt 1052-1054) reduces the ORF coding capacity by approximately 40 %. However, analyses of highly conserved RNA sequences in the vicinity of the stop codon indicate that it belongs to a class of 'leaky terminators'. The third nucleotide positions in codons situated both before and after the stop codon, shows the highest variability, suggesting that both regions are translated during virus replication. This also suggests that the stop signal is functionally leaky, allowing read-through translation to occur. Indeed, both the truncated 'termination' protein and the full-length 'read-through' protein (VP9 and VP9', respectively) were detected in CTFV-infected cells, in cells transfected with a plasmid expressing only Seg-9 protein products, and in the in vitro translation products from undenatured Seg-9 ssRNA. The ratios of full-length and truncated proteins generated suggest that read-through may be down-regulated by other viral proteins. Western blot analysis of infected cells and purified CTFV showed that VP9 is a structural component of the virion, while VP9' is a non-structural protein.

Co-infection with human polyomavirus BK enhances gene expression and replication of human adenovirus.

PubMed

Bil-Lula, Iwona; Woźniak, Mieczysław

2018-03-26

Immunocompromised patients are susceptible to multiple viral infections. Relevant interactions between co-infecting viruses might result from viral regulatory genes which trans-activate or repress the expression of host cell genes as well as the genes of any co-infecting virus. The aim of the current study was to show that the replication of human adenovirus 5 is enhanced by co-infection with BK polyomavirus and is associated with increased expression of proteins including early region 4 open reading frame 1 and both the large tumor antigen and small tumor antigen. Clinical samples of whole blood and urine from 156 hematopoietic stem cell transplant recipients were tested. We also inoculated adenocarcinomic human alveolar basal epithelial cells with both human adenovirus 5 and BK polyomavirus to evaluate if co-infection of viruses affected their replication. Data showed that adenovirus load was significantly higher in the plasma (mean 7.5 x 10 3  ± 8.5 x 10 2 copies/ml) and urine (mean 1.9 x 10 3  ± 8.0 x 10 2 copies/ml) of samples from patients with co-infections, in comparison to samples from patients with isolated adenovirus infection. In vitro co-infection led to an increased (8.6 times) expression of the adenovirus early region 4 open reading frame gene 48 hours post-inoculation. The expression of the early region 4 open reading frame gene positively correlated with the expression of BK polyomavirus large tumor antigen (r = 0.90, p < 0.0001) and small tumor antigen (r = 0.83, p < 0.001) genes. The enhanced expression of the early region 4 open reading frame gene due to co-infection with BK polyomavirus was associated with enhanced adenovirus, but not BK polyomavirus, replication. The current study provides evidence that co-infection of adenovirus and BK polyomavirus contributes to enhanced adenovirus replication. Data obtained from this study may have significant importance in the clinical setting.

Human milk metagenome: a functional capacity analysis

PubMed Central

2013-01-01

Background Human milk contains a diverse population of bacteria that likely influences colonization of the infant gastrointestinal tract. Recent studies, however, have been limited to characterization of this microbial community by 16S rRNA analysis. In the present study, a metagenomic approach using Illumina sequencing of a pooled milk sample (ten donors) was employed to determine the genera of bacteria and the types of bacterial open reading frames in human milk that may influence bacterial establishment and stability in this primal food matrix. The human milk metagenome was also compared to that of breast-fed and formula-fed infants’ feces (n = 5, each) and mothers’ feces (n = 3) at the phylum level and at a functional level using open reading frame abundance. Additionally, immune-modulatory bacterial-DNA motifs were also searched for within human milk. Results The bacterial community in human milk contained over 360 prokaryotic genera, with sequences aligning predominantly to the phyla of Proteobacteria (65%) and Firmicutes (34%), and the genera of Pseudomonas (61.1%), Staphylococcus (33.4%) and Streptococcus (0.5%). From assembled human milk-derived contigs, 30,128 open reading frames were annotated and assigned to functional categories. When compared to the metagenome of infants’ and mothers’ feces, the human milk metagenome was less diverse at the phylum level, and contained more open reading frames associated with nitrogen metabolism, membrane transport and stress response (P < 0.05). The human milk metagenome also contained a similar occurrence of immune-modulatory DNA motifs to that of infants’ and mothers’ fecal metagenomes. Conclusions Our results further expand the complexity of the human milk metagenome and enforce the benefits of human milk ingestion on the microbial colonization of the infant gut and immunity. Discovery of immune-modulatory motifs in the metagenome of human milk indicates more exhaustive analyses of the functionality of the human milk metagenome are warranted. PMID:23705844

Bacterial genes involved in incorporation of nickel into a hydrogenase enzyme.

PubMed Central

Fu, C; Javedan, S; Moshiri, F; Maier, R J

1994-01-01

Nickel is an essential component of all H2-uptake hydrogenases. A fragment of DNA that complements a H2-uptake-deficient but nickel-cured mutant strain (JHK7) of Bradyrhizobium japonicum was isolated and sequenced. This 4.5-kb DNA fragment contains four open reading frames designated as ORF1, hupN, hupO, and hupP, which encode polypeptides with predicted masses of 17, 40, 19, and 63.5 kDa, respectively. The last three open reading frames (hupNOP) are most likely organized as an operon with a putative sigma 54-type promoter. Based on its hydropathy profile, HupN is predicted to be a transmembrane protein. It has 56% identity to the previously described HoxN (high-affinity nickel transport protein) of Alcaligenes eutrophus. A subclone (pJF23) containing the hupNOP genes excluding ORF1 completely complemented (in trans) strain JHK7 for hydrogenase activity in low nickel conditions. pJF26 containing only a functional hupN complemented the hydrogenase activity of mutant strain JHK7 to 30-55% of the wild-type level. Mutant strain JHK70, with a chromosomal deletion in hupP but with an intact hupNO, showed greater activities than pJF26-complemented JHK7 but still had lower activities than the wild type at all nickel levels tested. pJF25, containing the entire hupO and hupP, but without hupN (a portion of hupN was deleted), did not complement hydrogenase activity of mutant strain JHK7. The results suggest that the products of the hupNOP operon are all involved in nickel incorporation/metabolism into the hydrogenase apoprotein. Based on (previous) nickel transport studies of strain JHK7, the hupNOP genes appear not to be involved in nickel transport by whole cells. The deleterious effects on hydrogenase expression are most pronounced by lack of the HupN product. PMID:8197192

Nucleotide sequence of the gag gene and gag-pol junction of feline leukemia virus.

PubMed Central

Laprevotte, I; Hampe, A; Sherr, C J; Galibert, F

1984-01-01

The nucleotide sequence of the gag gene of feline leukemia virus and its flanking sequences were determined and compared with the corresponding sequences of two strains of feline sarcoma virus and with that of the Moloney strain of murine leukemia virus. A high degree of nucleotide sequence homology between the feline leukemia virus and murine leukemia virus gag genes was observed, suggesting that retroviruses of domestic cats and laboratory mice have a common, proximal evolutionary progenitor. The predicted structure of the complete feline leukemia virus gag gene precursor suggests that the translation of nonglycosylated and glycosylated gag gene polypeptides is initiated at two different AUG codons. These initiator codons fall in the same reading frame and are separated by a 222-base-pair segment which encodes an amino terminal signal peptide. The nucleotide sequence predicts the order of amino acids in each of the individual gag-coded proteins (p15, p12, p30, p10), all of which derive from the gag gene precursor. Stable stem-and-loop secondary structures are proposed for two regions of viral RNA. The first falls within sequences at the 5' end of the viral genome, together with adjacent palindromic sequences which may play a role in dimer linkage of RNA subunits. The second includes coding sequences at the gag-pol junction and is proposed to be involved in translation of the pol gene product. Sequence analysis of the latter region shows that the gag and pol genes are translated in different reading frames. Classical consensus splice donor and acceptor sequences could not be localized to regions which would permit synthesis of the expected gag-pol precursor protein. Alternatively, we suggest that the pol gene product (RNA-dependent DNA polymerase) could be translated by a frameshift suppressing mechanism which could involve cleavage modification of stems and loops in a manner similar to that observed in tRNA processing. PMID:6328019

Nucleotide sequence and genetic organization of barley stripe mosaic virus RNA gamma.

PubMed

Gustafson, G; Hunter, B; Hanau, R; Armour, S L; Jackson, A O

1987-06-01

The complete nucleotide sequences of RNA gamma from the Type and ND18 strains of barley stripe mosaic virus (BSMV) have been determined. The sequences are 3164 (Type) and 2791 (ND18) nucleotides in length. Both sequences contain a 5'-noncoding region (87 or 88 nucleotides) which is followed by a long open reading frame (ORF1). A 42-nucleotide intercistronic region separates ORF1 from a second, shorter open reading frame (ORF2) located near the 3'-end of the RNA. There is a high degree of homology between the Type and ND18 strains in the nucleotide sequence of ORF1. However, the Type strain contains a 366 nucleotide direct tandem repeat within ORF1 which is absent in the ND18 strain. Consequently, the predicted translation product of Type RNA gamma ORF1 (mol wt 87,312) is significantly larger than that of ND18 RNA gamma ORF1 (mol wt 74,011). The amino acid sequence of the ORF1 polypeptide contains homologies with putative RNA polymerases from other RNA viruses, suggesting that this protein may function in replication of the BSMV genome. The nucleotide sequence of RNA gamma ORF2 is nearly identical in the Type and ND18 strains. ORF2 codes for a polypeptide with a predicted molecular weight of 17,209 (Type) or 17,074 (ND18) which is known to be translated from a subgenomic (sg) RNA. The initiation point of this sgRNA has been mapped to a location 27 nucleotides upstream of the ORF2 initiation codon in the intercistronic region between ORF1 and ORF2. The sgRNA is not coterminal with the 3'-end of the genomic RNA, but instead contains heterogeneous poly(A) termini up to 150 nucleotides long (J. Stanley, R. Hanau, and A. O. Jackson, 1984, Virology 139, 375-383). In the genomic RNA gamma, ORF2 is followed by a short poly(A) tract and a 238-nucleotide tRNA-like structure.

Collaborative capacity, problem framing, and mutual trust in addressing the wildland fire social problem: An annotated reading list

Treesearch

Jeffrey J. Brooks; Alexander N. Bujak; Joseph G. Champ; Daniel R. Williams

2006-01-01

We reviewed, annotated, and organized recent social science research and developed a framework for addressing the wildland fire social problem. We annotated articles related to three topic areas or factors, which are critical for understanding collective action, particularly in the wildland-urban interface. These factors are collaborative capacity, problem framing, and...

Overlapping reading frames at the LYS5 locus in the yeast Yarrowia lipolytica.

PubMed Central

Xuan, J W; Fournier, P; Declerck, N; Chasles, M; Gaillardin, C

1990-01-01

Mutants affected at the LYS5 locus of Yarrowia lipolytica lack detectable dehydrogenase (SDH) activity. The LYS5 gene has previously been cloned, and we present here the sequence of the 2.5-kilobase-pair (kb) DNA fragment complementing the lys5 mutation. Two large antiparallel open reading frames (ORF1 and ORF2) were observed, flanked by potential transcription signals. Both ORFs appear to be transcribed, but several lines of evidence suggest that only ORF2 is translated and encodes SDH. (i) The global amino acid compositions of Saccharomyces cerevisiae SDH and of the putative ORF2 product are similar and that of ORF1 is dissimilar. (ii) An in-frame translational fusion of ORF2 with the Escherichia coli lacZ gene was introduced into yeast cells and resulted in a beta-galactosidase activity regulated similarly to SDH; no beta-galactosidase activity was obtained with an in-frame fusion of ORF1 with lacZ. (iii) The introduction of a stop codon at the beginning of ORF2 prevented SDH expression in yeast cells, whereas no phenotypic effect was observed when ORF1 translation was blocked. Images PMID:2388625

Schizophrenia in the News: The Role of News Frames in Shaping Online Reader Dialogue about Mental Illness.

PubMed

Gwarjanski, Anna Rae; Parrott, Scott

2018-08-01

A quantitative content analysis examined the portrayal of schizophrenia in eight of the most read online news publications in the United States. The analysis documented the prevalence of stigma frames, which communicate stereotypes concerning schizophrenia, and stigma-challenge frames, which contradict stereotypes, in 558 articles related to schizophrenia. The study also examined the relationship between media framing and reader commentary, including the likelihood of readers posting stigmatizing comments, stigma-challenging comments, and comments in which they disclosed personal experience with mental illness. Stigma frames were prevalent in the sample, suggesting the news media continue associating schizophrenia with violent and criminal behavior. Stigma frames stood greater chance of being accompanied by stigmatizing comments from readers when compared to stigma-challenging frames. Conversely, stigma-challenging frames stood greater chance of being accompanied by stigma-challenging comments from readers. Readers were more likely to disclose personal experience with mental illness when they encountered a stigma-challenging frame. Recommendations are made for journalists and health communicators.

Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes.

PubMed

Ohno, S

1984-01-01

Three outstanding properties uniquely qualify repeats of base oligomers as the primordial coding sequences of all polypeptide chains. First, when compared with randomly generated base sequences in general, they are more likely to have long open reading frames. Second, periodical polypeptide chains specified by such repeats are more likely to assume either alpha-helical or beta-sheet secondary structures than are polypeptide chains of random sequence. Third, provided that the number of bases in the oligomeric unit is not a multiple of 3, these internally repetitious coding sequences are impervious to randomly sustained base substitutions, deletions, and insertions. This is because the recurring periodicity of their polypeptide chains is given by three consecutive copies of the oligomeric unit translated in three different reading frames. Accordingly, when one reading frame is open, the other two are automatically open as well, all three being capable of coding for polypeptide chains of identical periodicity. Under this circumstance, a frame shift due to the deletion or insertion of a number of bases that is not a multiple of 3 fails to alter the down-stream amino acid sequence, and even a base change causing premature chain-termination can silence only one of the three potential coding units. Newly arisen coding sequences in modern organisms are oligomeric repeats, and most of the older genes retain various vestiges of their original internal repetitions. Some of the genes (e.g., oncogenes) have even inherited the property of being impervious to randomly sustained base changes.

Building an Experimental Setup to Characterize an H4RG-15

NASA Astrophysics Data System (ADS)

Hirata, Mickie; Hodapp, K.; Hall, Donald N. B.; Goebel, Sean B.; Jacobson, Shane M.

2018-01-01

The Teledyne Imaging Sensors H4RG-15 infrared detector is designed for the next era of extremely large telescopes. Characterization of individual H4RG-15 detectors are critical for future astronomical use. ULBcam, a former UH88 IR camera and remnant test dewar for H2RG characterization, was previously modified for H4RG-15 characterization. During the summer, this system was further upgraded with a baffle tube to a blackbody illumination source to allow controlled field illumination. This baffle tube, designed in OpenSCAD, was constructed in the IfA machine shop. Specific placements of the 50-micron aperture and scatter restrictive baffling was designed in Zemax. Four separate data sets were acquired to look into detector persistence, dark current, read noise, and charge gain. With the illumination source set at 450 K, ten ramps of 90/90 read frames were taken to pass saturation values. These tests were repeated at 500K to show results at over saturated conditions. Five ramps of 136/136 read frames were taken with a blank shutter applied. The persistence results showed expected results with signals settling from the third ramp. Dark current results showed higher than Teledyne stated values at 0.06 electrons/second, a factor of 6 higher than expected, which exposes systematic ULBcam dark testing capabilities. The read noise resulted with an expected value of 0.014 electrons. The charge gain showed 0.02 electrons/ADU where the expected value is 2 electrons/ADU. Data analysis using reference frame subtraction will be done for future work.

A multivariate prediction model for Rho-dependent termination of transcription.

PubMed

Nadiras, Cédric; Eveno, Eric; Schwartz, Annie; Figueroa-Bossi, Nara; Boudvillain, Marc

2018-06-21

Bacterial transcription termination proceeds via two main mechanisms triggered either by simple, well-conserved (intrinsic) nucleic acid motifs or by the motor protein Rho. Although bacterial genomes can harbor hundreds of termination signals of either type, only intrinsic terminators are reliably predicted. Computational tools to detect the more complex and diversiform Rho-dependent terminators are lacking. To tackle this issue, we devised a prediction method based on Orthogonal Projections to Latent Structures Discriminant Analysis [OPLS-DA] of a large set of in vitro termination data. Using previously uncharacterized genomic sequences for biochemical evaluation and OPLS-DA, we identified new Rho-dependent signals and quantitative sequence descriptors with significant predictive value. Most relevant descriptors specify features of transcript C>G skewness, secondary structure, and richness in regularly-spaced 5'CC/UC dinucleotides that are consistent with known principles for Rho-RNA interaction. Descriptors collectively warrant OPLS-DA predictions of Rho-dependent termination with a ∼85% success rate. Scanning of the Escherichia coli genome with the OPLS-DA model identifies significantly more termination-competent regions than anticipated from transcriptomics and predicts that regions intrinsically refractory to Rho are primarily located in open reading frames. Altogether, this work delineates features important for Rho activity and describes the first method able to predict Rho-dependent terminators in bacterial genomes.

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

PubMed

Behrens, R; Hayles, J; Nurse, P

2000-12-01

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

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

PubMed Central

Behrens, Ralf; Hayles, Jacky; Nurse, Paul

2000-01-01

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

Identification of a Mg2+-sensitive ORF in the 5′-leader of TRPM7 magnesium channel mRNA

PubMed Central

Nikonorova, Inna A.; Kornakov, Nikolay V.; Dmitriev, Sergey E.; Vassilenko, Konstantin S.; Ryazanov, Alexey G.

2014-01-01

TRPM7 is an essential and ubiquitous channel-kinase regulating cellular influx of Mg2+. Although TRPM7 mRNA is highly abundant, very small amount of the protein is detected in cells, suggesting post-transcriptional regulation of trpm7 gene expression. We found that TRPM7 mRNA 5′-leader contains two evolutionarily conserved upstream open reading frames that act together to drastically inhibit translation of the TRPM7 reading frame at high magnesium levels and ensure its optimal translation at low magnesium levels, when the activity of the channel-kinase is most required. The study provides the first example of magnesium channel synthesis being controlled by Mg2+ in higher eukaryotes. PMID:25326319

Reading at the Front: Books and Soldiers in the First World War

ERIC Educational Resources Information Center

Sutcliffe, Marcella P.

2016-01-01

This paper focuses on the reading and educational practices of common soldiers during the First World War. It argues that the question of how war libraries were imagined and constructed by civilians needs to be framed in the larger context of pre-war Edwardian debates surrounding the "value of books" in society. Indeed, it was within…

The Effects of Using a Combination of Story Frames and Retelling Strategies with Learning Disabled Students To Build Their Comprehension Ability.

ERIC Educational Resources Information Center

Kuldanek, Kelly

Reading is the foundation for literacy and comprehension is the foundation for education. Many learning disabled students struggle to understand what they have read and many instructional approaches in small group settings focus on decoding rather than on comprehension. Employing a dual strategic approach to facilitate comprehension enables…

"Drawing Is a Frame of Mind": An Evaluation of Students' Perceptions about Reading Instruction within a Response to Intervention Model

ERIC Educational Resources Information Center

Chapman, Lauren; Greenfield, Renee; Rinaldi, Claudia

2010-01-01

This investigation is part of a larger study examining the effects of a school-wide literacy reform effort through a multi-leveled system of instructional delivery. The research question addressed was, "How do students perceive reading instruction within their elementary language arts classroom?" Students' perceptions were analyzed through…

"What Do You Think?" Let Me Tell You: Discourse about Texts and the Literature Classroom

ERIC Educational Resources Information Center

Mason, Jessica; Giovanelli, Marcello

2017-01-01

This article examines the practice of studying texts in secondary school English lessons as a particular type of reading experience. Through a critical stylistic analysis of a popular edition of John Steinbeck's "Of Mice and Men", the article explores how reading the text is framed by educational editions, and how this might present the…

Framing the Genetics Curriculum for Social Justice: An Experimental Exploration of How the Biology Curriculum Influences Beliefs about Racial Difference

ERIC Educational Resources Information Center

Donovan, Brian M.

2016-01-01

This field experiment manipulated the racial framing of a reading on human genetic disease to explore whether racial terminology in the biology curriculum affects how adolescents explain and respond to the racial achievement gap in American education. Carried out in a public high school in the San Francisco Bay Area, students recruited for the…

Isolation and Genome Characterization of the Virulent Staphylococcus aureus Bacteriophage SA97

PubMed Central

Chang, Yoonjee; Shin, Hakdong; Lee, Ju-Hoon; Park, Chul Jong; Paik, Soon-Young; Ryu, Sangryeol

2015-01-01

A novel bacteriophage that infects S. aureus, SA97, was isolated and characterized. The phage SA97 belongs to the Siphoviridae family, and the cell wall teichoic acid (WTA) was found to be a host receptor of the phage SA97. Genome analysis revealed that SA97 contains 40,592 bp of DNA encoding 54 predicted open reading frames (ORFs), and none of these genes were related to virulence or drug resistance. Although a few genes associated with lysogen formation were detected in the phage SA97 genome, the phage SA97 produced neither lysogen nor transductant in S. aureus. These results suggest that the phage SA97 may be a promising candidate for controlling S. aureus. PMID:26437428

A Frameshift Mutation in the Cubilin Gene (CUBN) in Border Collies with Imerslund-Gräsbeck Syndrome (Selective Cobalamin Malabsorption)

PubMed Central

Owczarek-Lipska, Marta; Jagannathan, Vidhya; Drögemüller, Cord; Lutz, Sabina; Glanemann, Barbara

2013-01-01

Imerslund-Gräsbeck syndrome (IGS) or selective cobalamin malabsorption has been described in humans and dogs. IGS occurs in Border Collies and is inherited as a monogenic autosomal recessive trait in this breed. Using 7 IGS cases and 7 non-affected controls we mapped the causative mutation by genome-wide association and homozygosity mapping to a 3.53 Mb interval on chromosome 2. We re-sequenced the genome of one affected dog at ∼10× coverage and detected 17 non-synonymous variants in the critical interval. Two of these non-synonymous variants were in the cubilin gene (CUBN), which is known to play an essential role in cobalamin uptake from the ileum. We tested these two CUBN variants for association with IGS in larger cohorts of dogs and found that only one of them was perfectly associated with the phenotype. This variant, a single base pair deletion (c.8392delC), is predicted to cause a frameshift and premature stop codon in the CUBN gene. The resulting mutant open reading frame is 821 codons shorter than the wildtype open reading frame (p.Q2798Rfs*3). Interestingly, we observed an additional nonsense mutation in the MRC1 gene encoding the mannose receptor, C type 1, which was in perfect linkage disequilibrium with the CUBN frameshift mutation. Based on our genetic data and the known role of CUBN for cobalamin uptake we conclude that the identified CUBN frameshift mutation is most likely causative for IGS in Border Collies. PMID:23613799

Genomic analysis of the symbiotic marine crenarchaeon, Cenarchaeumsymbiosum

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

Hallam, Steven J.; Konstantinidis, Konstantinos T.; Brochier,Celine

2006-06-24

Crenarchaea are ubiquitous and abundant microbial constituents of soils, sediments, lakes and ocean waters, yet relatively little is known about their fundamental evolutionary, ecological, and physiological properties. To better describe the ubiquitous nonthermophilic Crenarchaea, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont, Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although synthetic, overlapping a- and b-type ribotypes harbored significant genetic variability. A single tiling path comprising the dominant a-type genotype was assembled, and used to explore the biological properties ofmore » C. symbiosum and its planktonic relatives. Out of a total of 2,066 predicted open reading frames, 36% were more highly conserved with other Archaea. The remainder partitioned between bacteria (18%), eukaryotes (1.5%) and viruses (0.1%). A total of 525 open reading frames were more highly conserved with sequences derived from marine environmental genomic surveys, most probably representing orthologous genes found in free-living planktonic Crenarchaea. The remaining genes partitioned between functional RNAs (2.4%), and hypotheticals (42%) with limited homology to known functional genes. The latter category likely contains genes specifically involved in mediated archaeal-sponge symbiosis. Phylogenetic analyses placed C. symbiosum as a basal crenarchaeon, sharing specific genomic features in common with either Crenarchaea, Euryarchaea, or both. The genome sequence of C. symbiosum reflect a unique and unusual evolutionary, physiological, and ecological history, one remarkably distinct from that of any other previously known microbial lineage.« less

Identification and analysis of proton-translocating pyrophosphatases in the methanogenic archaeon Methanosarcina mazei

PubMed Central

Bäumer, Sebastian; Lentes, Sabine; Gottschalk, Gerhard; Deppenmeier, Uwe

2002-01-01

Analysis of genome sequence data from the methanogenic archaeon Methanosarcina mazei Gö1 revealed the existence of two open reading frames encoding proton-translocating pyrophosphatases (PPases). These open reading frames are linked by a 750-bp intergenic region containing TC-rich stretches and are transcribed in opposite directions. The corresponding polypeptides are referred to as Mvp1 and Mvp2 and consist of 671 and 676 amino acids, respectively. Both enzymes represent extremely hydrophobic, integral membrane proteins with 15 predicted transmembrane segments and an overall amino acid sequence similarity of 50.1%. Multiple sequence alignments revealed that Mvp1 is closely related to eukaryotic PPases, whereas Mvp2 shows highest homologies to bacterial PPases. Northern blot experiments with RNA from methanol-grown cells harvested in the mid-log growth phase indicated that only Mvp2 was produced under these conditions. Analysis of washed membranes showed that Mvp2 had a specific activity of 0.34 U mg (protein)–1. Proton translocation experiments with inverted membrane vesicles prepared from methanol-grown cells showed that hydrolysis of 1 mol of pyrophosphate was coupled to the translocation of about 1 mol of protons across the cytoplasmic membrane. Appropriate conditions for mvp1 expression could not be determined yet. The pyrophosphatases of M. mazei Gö1 represent the first examples of this enzyme class in methanogenic archaea and may be part of their energy-conserving system. Abbreviations: DCCD, N,N′-dicyclohexylcarbodiimide; PPase, inorganic pyrophosphatase; PPi, inorganic pyrophosphate; Δp, proton motive force. PMID:15803653

deFUME: Dynamic exploration of functional metagenomic sequencing data.

PubMed

van der Helm, Eric; Geertz-Hansen, Henrik Marcus; Genee, Hans Jasper; Malla, Sailesh; Sommer, Morten Otto Alexander

2015-07-31

Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME.

Risky business: risk information and the moderating effect of message frame and past behaviour on women's perceptions of the Human Papillomavirus vaccine.

PubMed

Gainforth, Heather L; Latimer, Amy E

2012-09-01

The effect of response cost information, message framing and past behaviour on women's coping appraisal and motivation to be vaccinated against the Human Papillomavirus (HPV) were investigated using a 2 Frame × 2 Response Cost × 2 Pap Status design. Women (N = 286) read one of four messages about the vaccine. Women who received high-risk information perceived the vaccine as having higher response cost and were less motivated to be vaccinated compared to women who received low-risk information. The deleterious effects of risk information on specific aspects of women's coping appraisal may be mitigated by appropriately framed messages.

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

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

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

1996-06-01

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

Complete sequence of Tvv1, a family of Ty 1 copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking.

PubMed

Pelsy, F.; Merdinoglu, D.

2002-09-01

A chromosome-walking strategy was used to sequence and characterize retrotransposons in the grapevine genome. The reconstitution of a family of retroelements, named Tvv1, was achieved by six successive steps. These elements share a single, highly conserved open reading frame 4,153 nucleotides-long, putatively encoding the gag, pro, int, rt and rh proteins. Comparison of the Tvv1 open reading frame coding potential with those of drosophila copia and tobacco Tnt1, revealed that Tvv1 is closely related to Ty 1 copia-like retrotransposons. A highly variable untranslated leader region, upstream of the open reading frame, allowed us to differentiate Tvv1 variants, which represent a family of at least 28 copies, in varying sizes. This internal region is flanked by two long terminal repeats in direct orientation, sized between 149 and 157 bp. Among elements theoretically sized from 4,970 to 5,550 bp, we describe the full-length sequence of a reference element Tvv1-1, 5,343 nucleotides-long. The full-length sequence of Tvv1-1 compared to pea PDR1 shows a 53.3% identity. In addition, both elements contain long terminal repeats of nearly the same size in which the U5 region could be entirely absent. Therefore, we assume that Tvv1 and PDR1 could constitute a particular class of short LTRs retroelements.

Circular codes revisited: a statistical approach.

PubMed

Gonzalez, D L; Giannerini, S; Rosa, R

2011-04-21

In 1996 Arquès and Michel [1996. A complementary circular code in the protein coding genes. J. Theor. Biol. 182, 45-58] discovered the existence of a common circular code in eukaryote and prokaryote genomes. Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, C(3) maximal codes with respect to a large set of coding sequences. The results indicate that, on average, the code proposed by Arquès and Michel has the best covering capability but, still, there exists a great variability among sequences. Second, we focus on such code and explore the role played by the proportion of the bases by means of a hierarchy of permutation tests. The results show the existence of a sort of optimization mechanism such that coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization. Copyright © 2011 Elsevier Ltd. All rights reserved.

Frame prediction using recurrent convolutional encoder with residual learning

NASA Astrophysics Data System (ADS)

Yue, Boxuan; Liang, Jun

2018-05-01

The prediction for the frame of a video is difficult but in urgent need in auto-driving. Conventional methods can only predict some abstract trends of the region of interest. The boom of deep learning makes the prediction for frames possible. In this paper, we propose a novel recurrent convolutional encoder and DE convolutional decoder structure to predict frames. We introduce the residual learning in the convolution encoder structure to solve the gradient issues. The residual learning can transform the gradient back propagation to an identity mapping. It can reserve the whole gradient information and overcome the gradient issues in Recurrent Neural Networks (RNN) and Convolutional Neural Networks (CNN). Besides, compared with the branches in CNNs and the gated structures in RNNs, the residual learning can save the training time significantly. In the experiments, we use UCF101 dataset to train our networks, the predictions are compared with some state-of-the-art methods. The results show that our networks can predict frames fast and efficiently. Furthermore, our networks are used for the driving video to verify the practicability.

Vector adaptive predictive coder for speech and audio

NASA Technical Reports Server (NTRS)

Chen, Juin-Hwey (Inventor); Gersho, Allen (Inventor)

1990-01-01

A real-time vector adaptive predictive coder which approximates each vector of K speech samples by using each of M fixed vectors in a first codebook to excite a time-varying synthesis filter and picking the vector that minimizes distortion. Predictive analysis for each frame determines parameters used for computing from vectors in the first codebook zero-state response vectors that are stored at the same address (index) in a second codebook. Encoding of input speech vectors s.sub.n is then carried out using the second codebook. When the vector that minimizes distortion is found, its index is transmitted to a decoder which has a codebook identical to the first codebook of the decoder. There the index is used to read out a vector that is used to synthesize an output speech vector s.sub.n. The parameters used in the encoder are quantized, for example by using a table, and the indices are transmitted to the decoder where they are decoded to specify transfer characteristics of filters used in producing the vector s.sub.n from the receiver codebook vector selected by the vector index transmitted.

Behavioral frequency moderates the effects of message framing on HPV vaccine acceptability.

PubMed

Gerend, Mary A; Shepherd, Janet E; Monday, Kara A

2008-04-01

Research suggests that gain-framed messages are generally more effective than loss-framed messages at promoting preventive health behaviors. Virtually all previous studies, however, have examined prevention behaviors that require regular and repeated action to be effective. Little is known about the utility of message framing for promoting low-frequency prevention behaviors such as vaccination. Moreover, few studies have identified mediators of framing effects. We investigated whether behavioral frequency (operationalized as the number of shots required) moderated the effect of framed health messages on women's intentions to receive the human papillomavirus (HPV) vaccine. We also sought to identify mediators of framing effects. Undergraduate women (N = 237) were randomly assigned to read an HPV vaccination booklet that varied by message frame (gain vs. loss) and behavioral frequency (one shot vs. six shots). We observed a frame-by-frequency interaction such that the loss-framed message led to greater vaccination intentions than did the gain-framed message but only among participants in the one-shot condition. Perceived susceptibility to HPV infection mediated the observed framing effects. This study provides an important exception to the commonly observed gain-framed advantage for preventive health behaviors. Loss-framed appeals appear to be particularly effective in promoting interest in low-frequency prevention behaviors such as HPV vaccination.

Framing effect debiasing in medical decision making.

PubMed

Almashat, Sammy; Ayotte, Brian; Edelstein, Barry; Margrett, Jennifer

2008-04-01

Numerous studies have demonstrated the robustness of the framing effect in a variety of contexts. The present study investigated the effects of a debiasing procedure designed to prevent the framing effect for young adults who made decisions based on hypothetical medical decision-making vignettes. The debiasing technique involved participants listing advantages and disadvantages of each treatment prior to making a choice. One hundred and two undergraduate students read a set of three medical treatment vignettes that presented information in terms of different outcome probabilities under either debiasing or control conditions. The framing effect was demonstrated by the control group in two of the three vignettes. The debiasing group successfully avoided the framing effect for both of these vignettes. These results further support previous findings of the framing effect as well as an effective debiasing technique. This study improved upon previous framing debiasing studies by including a control group and personal medical scenarios, as well as demonstrating debiasing in a framing condition in which the framing effect was demonstrated without a debiasing procedure. The findings suggest a relatively simple manipulation may circumvent the use of decision-making heuristics in patients.

The Dangers of Test Preparation: What Students Learn (And Don't Learn) about Reading Comprehension from Test-Centric Literacy Instruction

ERIC Educational Resources Information Center

Davis, Dennis S.; Vehabovic, Nermin

2018-01-01

The authors offer guidance on recognizing and resisting test-centric instruction in reading comprehension. They posit that five practices indicate a test-centric view of comprehension: when the tested content is privileged, when the test becomes the text, when annotation requirements replace strategic thinking, when test items frame how students…

Collective Beer Brand Identity: A Semiotic Analysis of the Websites Representing Small and Medium Enterprises in the Brewing Industry of Western PA

ERIC Educational Resources Information Center

Cincotta, Dominic

2014-01-01

This research studies how brand identities, individually and communally, as read through websites are created among small and medium-sized enterprise breweries in western Pennsylvania. Content analysis through the frame of Kress and van Leeuwen was used as the basis for the codebook that reads each brand identity for the researcher. The…

Reading for Integration, Identifying Complementary Threshold Concepts: The ACRL "Framework" in Conversation with "Naming What We Know: Threshold Concepts of Writing"

ERIC Educational Resources Information Center

Johnson, Brittney; McCracken, I. Moriah

2016-01-01

In 2015, threshold concepts formed the foundation of two disciplinary documents: The "ACRL Framework for Information Literacy" (2015) and "Naming What We Know: Threshold Concepts of Writing Studies" (2015). While there is no consensus in the fields about the value of threshold concepts in teaching, reading the six Frames in the…

Enhancing Soundtracks From Old Movies

NASA Technical Reports Server (NTRS)

Frazer, Robert E.

1992-01-01

Proposed system enhances soundtracks of old movies. Signal on optical soundtrack of film digitized and processed to reduce noise and improve quality; timing signals added, and signal recorded on compact disk. Digital comparator and voltage-controlled oscillator synchronizes speed of film-drive motor and compact disk motor. Frame-coded detector reads binary frame-identifying marks on film. Digital comparator generates error signal if marks on film do not match those on compact disk.

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

PubMed

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.

Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences

PubMed Central

Groves, Benjamin; Kuchina, Anna; Rosenberg, Alexander B.; Jojic, Nebojsa; Fields, Stanley; Seelig, Georg

2017-01-01

Our ability to predict protein expression from DNA sequence alone remains poor, reflecting our limited understanding of cis-regulatory grammar and hampering the design of engineered genes for synthetic biology applications. Here, we generate a model that predicts the protein expression of the 5′ untranslated region (UTR) of mRNAs in the yeast Saccharomyces cerevisiae. We constructed a library of half a million 50-nucleotide-long random 5′ UTRs and assayed their activity in a massively parallel growth selection experiment. The resulting data allow us to quantify the impact on protein expression of Kozak sequence composition, upstream open reading frames (uORFs), and secondary structure. We trained a convolutional neural network (CNN) on the random library and showed that it performs well at predicting the protein expression of both a held-out set of the random 5′ UTRs as well as native S. cerevisiae 5′ UTRs. The model additionally was used to computationally evolve highly active 5′ UTRs. We confirmed experimentally that the great majority of the evolved sequences led to higher protein expression rates than the starting sequences, demonstrating the predictive power of this model. PMID:29097404

Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data.

PubMed

Rask, Thomas S; Petersen, Bent; Chen, Donald S; Day, Karen P; Pedersen, Anders Gorm

2016-04-22

Amplicon pyrosequencing targets a known genetic region and thus inherently produces reads highly anticipated to have certain features, such as conserved nucleotide sequence, and in the case of protein coding DNA, an open reading frame. Pyrosequencing errors, consisting mainly of nucleotide insertions and deletions, are on the other hand likely to disrupt open reading frames. Such an inverse relationship between errors and expectation based on prior knowledge can be used advantageously to guide the process known as basecalling, i.e. the inference of nucleotide sequence from raw sequencing data. The new basecalling method described here, named Multipass, implements a probabilistic framework for working with the raw flowgrams obtained by pyrosequencing. For each sequence variant Multipass calculates the likelihood and nucleotide sequence of several most likely sequences given the flowgram data. This probabilistic approach enables integration of basecalling into a larger model where other parameters can be incorporated, such as the likelihood for observing a full-length open reading frame at the targeted region. We apply the method to 454 amplicon pyrosequencing data obtained from a malaria virulence gene family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon sequencing data, particularly where extensive prior knowledge is available about the obtained sequences, for example in analysis of the immunoglobulin VDJ region where Multipass can be combined with a model for the known recombining germline genes. Multipass is available for Roche 454 data at http://www.cbs.dtu.dk/services/MultiPass-1.0 , and the concept can potentially be implemented for other sequencing technologies as well.

Case study of read-across predictions using a Generalized Read-Across (GenRA) Approach (10th World Congress)

EPA Science Inventory

We developed the Generalized Read-Across (GenRA) approach to facilitate automated, algorithmic read across predictions. GenRA uses in vitro bioactivity data in conjunction with chemical information to predict up to 574 different apical outcomes from repeat-dose toxicity studies. ...

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

PubMed

Whitford, Veronica; Titone, Debra

2014-01-01

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

The effects of social and health consequence framing on heavy drinking intentions among college students.

PubMed

Kingsbury, John H; Gibbons, Frederick X; Gerrard, Meg

2015-02-01

Many interventions targeting college student drinking have focused on negative health effects of drinking heavily; however, some research suggests that social factors may have a stronger influence on the drinking behaviour of young people. Moreover, few studies have examined message framing effects in the context of alcohol consumption. This study investigated the effects of social and health consequence framing on college students' intentions to engage in heavy drinking. This study used a 2 × 2 experimental design with an appended control condition. One hundred and twenty-four college students (74 women; M(age) = 18.9) participated in this study for course credit. Participants read vignettes that were ostensibly written by a recent graduate from the university, who described an episode of drinking in which he or she experienced either social or health consequences. These consequences were framed as either a gain (i.e., positive consequences of not drinking heavily) or a loss (i.e., negative consequences of drinking heavily). After reading the vignette, participants completed a measure of heavy drinking intentions. Regression analyses revealed that social consequences were associated with lower heavy drinking intentions when framed as a loss and that health consequences were associated with lower heavy drinking intentions when framed as a gain. These effects were stronger among those who reported higher (vs. lower) levels of previous drinking. Results suggest that interventions that focus on the negative health effects of heavy drinking may be improved by instead emphasizing the negative social consequences of drinking heavily and the positive health consequences of avoiding this behaviour. Statement of contribution What is already known on this subject? Previous studies have shown that gain frames are more effective than loss frames when highlighting the health consequences of health risk behaviours, such as heavy drinking. The heavy drinking behaviour of young people is influenced by social factors (e.g., perceived social consequences). However, little is known about framing effects for social consequences of heavy drinking. What does this study add? This study builds on previous research by demonstrating that a loss frame is more effective than a gain frame when highlighting the social consequences of health risk behaviour. Framing effects are strongest for those with more previous drinking experience. © 2014 The British Psychological Society.

Frames and knowledge in mixed media: how activation changes information intake.

PubMed

Veenstra, Aaron S; Sayre, Ben; Shah, Dhavan V; McLeod, Douglas M

2008-08-01

Many people consider strategic framing, the journalistic tendency to reduce politics to a game or competition focused on the tactical maneuvers of political actors, to be harmful to democracy because it erodes citizen interest in the democratic process. Our results demonstrate that this is not always the case. Testing the effects of textual strategic frames and video processing in a digital environment, we show that strategic frames may also provide a context that is more conducive to learning in mixed media news environments than that provided by value frames, those focused on the value conflict between principled policy opponents. Further analysis reveals that this effect is most clearly seen among people who read political blogs (i.e., those who are already active and interested in politics). Our data suggest that for individuals with cognitive networks built around ideological concerns, such as blog readers, value-framed messages provide cues to stop encoding new information, while strategically framed messages lead people to continue absorbing and learning in mixed media environments.

Data communications in a parallel active messaging interface of a parallel computer

DOEpatents

Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

2014-09-02

Eager send data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints that specify a client, a context, and a task, including receiving an eager send data communications instruction with transfer data disposed in a send buffer characterized by a read/write send buffer memory address in a read/write virtual address space of the origin endpoint; determining for the send buffer a read-only send buffer memory address in a read-only virtual address space, the read-only virtual address space shared by both the origin endpoint and the target endpoint, with all frames of physical memory mapped to pages of virtual memory in the read-only virtual address space; and communicating by the origin endpoint to the target endpoint an eager send message header that includes the read-only send buffer memory address.

Data communications in a parallel active messaging interface of a parallel computer

DOEpatents

Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

2014-09-16

Eager send data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints that specify a client, a context, and a task, including receiving an eager send data communications instruction with transfer data disposed in a send buffer characterized by a read/write send buffer memory address in a read/write virtual address space of the origin endpoint; determining for the send buffer a read-only send buffer memory address in a read-only virtual address space, the read-only virtual address space shared by both the origin endpoint and the target endpoint, with all frames of physical memory mapped to pages of virtual memory in the read-only virtual address space; and communicating by the origin endpoint to the target endpoint an eager send message header that includes the read-only send buffer memory address.

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

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

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

1993-09-01

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

TCOF1 gene encodes a putative nucleolar phosphoprotein that exhibits mutations in Treacher Collins Syndrome throughout its coding region.

PubMed

Wise, C A; Chiang, L C; Paznekas, W A; Sharma, M; Musy, M M; Ashley, J A; Lovett, M; Jabs, E W

1997-04-01

Treacher Collins Syndrome (TCS) is the most common of the human mandibulofacial dysostosis disorders. Recently, a partial TCOF1 cDNA was identified and shown to contain mutations in TCS families. Here we present the entire exon/intron genomic structure and the complete coding sequence of TCOF1. TCOF1 encodes a low complexity protein of 1,411 amino acids, whose predicted protein structure reveals repeated motifs that mirror the organization of its exons. These motifs are shared with nucleolar trafficking proteins in other species and are predicted to be highly phosphorylated by casein kinase. Consistent with this, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localization signals. Throughout the open reading frame, we detected an additional eight mutations in TCS families and several polymorphisms. We postulate that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development.

TCOF1 gene encodes a putative nucleolar phosphoprotein that exhibits mutations in Treacher Collins Syndrome throughout its coding region

PubMed Central

Wise, Carol A.; Chiang, Lydia C.; Paznekas, William A.; Sharma, Mridula; Musy, Maurice M.; Ashley, Jennifer A.; Lovett, Michael; Jabs, Ethylin W.

1997-01-01

Treacher Collins Syndrome (TCS) is the most common of the human mandibulofacial dysostosis disorders. Recently, a partial TCOF1 cDNA was identified and shown to contain mutations in TCS families. Here we present the entire exon/intron genomic structure and the complete coding sequence of TCOF1. TCOF1 encodes a low complexity protein of 1,411 amino acids, whose predicted protein structure reveals repeated motifs that mirror the organization of its exons. These motifs are shared with nucleolar trafficking proteins in other species and are predicted to be highly phosphorylated by casein kinase. Consistent with this, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localization signals. Throughout the open reading frame, we detected an additional eight mutations in TCS families and several polymorphisms. We postulate that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development. PMID:9096354

Construction and Screening of a Lentiviral Secretome Library.

PubMed

Liu, Tao; Jia, Panpan; Ma, Huailei; Reed, Sean A; Luo, Xiaozhou; Larman, H Benjamin; Schultz, Peter G

2017-06-22

Over 2,000 human proteins are predicted to be secreted, but the biological function of the many of these proteins is still unknown. Moreover, a number of these proteins may act as new therapeutic agents or be targets for the development of therapeutic antibodies. To further explore the extracellular proteome, we have developed a secretome-enriched open reading frame (ORF) library that can be readily screened for autocrine activity in cell-based phenotypic or reporter assays. Next-generation sequencing (NGS) and database analysis predict that the library contains approximately 900 ORFs encoding known secreted proteins (accounting for 77.8% of the library), as well as genes encoding potentially unknown secreted proteins. In a proof-of-principle study, human TF-1 cells were screened for proliferative factors, and the known cytokine GMCSF was identified as a dominant hit. This library offers a relatively low-cost and straightforward approach for functional autocrine screens of secreted proteins. Copyright © 2017 Elsevier Ltd. All rights reserved.

Redefining the genetics of Murine Gammaherpesvirus 68 via transcriptome-based annotation

PubMed Central

Johnson, L. Steven; Willert, Erin K.; Virgin, Herbert W.

2010-01-01

Summary Viral genetic studies often focus on large open reading frames (ORFs) identified during genome annotation (ORF-based annotation). Here we provide a tool and software set for defining gene expression by murine gammaherpesvirus 68 (γHV68) nucleotide-by-nucleotide across the 119,450 basepair (bp) genome. These tools allowed us to determine that viral RNA expression was significantly more complex than predicted from ORF-based annotation, including over 73,000 nucleotides of unexpected transcription within 30 expressed genomic regions (EGRs). Approximately 90% of this RNA expression was antisense to genomic regions containing known large ORFs. We verified the existence of novel transcripts in three EGRs using standard methods to validate the approach and determined which parts of the transcriptome depend on protein or viral DNA synthesis. This redefines the genetic map of γHV68, indicates that herpesviruses contain significantly more genetic complexity than predicted from ORF-based genome annotations, and provides new tools and approaches for viral genetic studies. PMID:20542255

In silico cloning and B/T cell epitope prediction of triosephosphate isomerase from Echinococcus granulosus.

PubMed

Wang, Fen; Ye, Bin

2016-10-01

Cystic echinococcosis is a worldwide zoonosis caused by Echinococcus granulosus. Because the methods of diagnosis and treatment for cystic echinococcosis were limited, it is still necessary to screen target proteins for the development of new anti-hydatidosis vaccine. In this study, the triosephosphate isomerase gene of E. granulosus was in silico cloned. The B cell and T cell epitopes were predicted by bioinformatics methods. The cDNA sequence of EgTIM was composition of 1094 base pairs, with an open reading frame of 753 base pairs. The deduced amino acid sequences were composed of 250 amino acids. Five cross-reactive epitopes, locating on 21aa-35aa, 43aa-57aa, 94aa-107aa, 115-129aa, and 164aa-183aa, could be expected to serve as candidate epitopes in the development of vaccine against E. granulosus. These results could provide bases for gene cloning, recombinant expression, and the designation of anti-hydatidosis vaccine.

Expression of the Pasteurella haemolytica leukotoxin is inhibited by a locus that encodes an ATP-binding cassette homolog.

PubMed Central

Highlander, S K; Wickersham, E A; Garza, O; Weinstock, G M

1993-01-01

Multicopy and single-copy chromosomal fusions between the Pasteurella haemolytica leukotoxin regulatory region and the Escherichia coli beta-galactosidase gene have been constructed. These fusions were used as reporters to identify and isolate regulators of leukotoxin expression from a P. haemolytica cosmid library. A cosmid clone, which inhibited leukotoxin expression from multicopy and single-copy protein fusions, was isolated and found to contain the complete leukotoxin gene cluster plus additional upstream sequences. The locus responsible for inhibition of expression from leukotoxin-beta-galactosidase fusions was mapped within these upstream sequences, by transposon mutagenesis with Tn5, and its DNA sequence was determined. The inhibitory activity was found to be associated with a predicted 440-amino-acid reading frame (lapA) that lies within a four-gene arginine transport locus. LapA is predicted to be the nucleotide-binding component of this transport system and shares homology with the Clp family of proteases. Images PMID:8359916

Message framing and color combination in the perception of medical information.

PubMed

Chien, Yu-Hung

2011-04-01

A 2 x 2 between-subjects design was used to examine the effects of message framing (gain vs loss) and color combination (red background with white characters vs white background with black characters) on 120 university students' perception of materials promoting the H1N1 flu vaccine and their willingness to receive the vaccine after they had read the materials. Each participant completed a 6-item questionnaire, and the results of an analysis of variance showed that participants rated vaccine information presented through loss-framed messages as having greater interest and leading to greater understanding. Loss-framed messages presented on a white background with black characters significantly increased the willingness of the participants to receive the vaccine.

Promoting the avoidance of high-calorie snacks. The role of temporal message framing and eating self-efficacy.

PubMed

Churchill, Susan; Good, Anna; Pavey, Louisa

2014-09-01

Message framing outcomes of healthy behaviours as occurring 'every day' vs. 'every year' can influence the temporal proximity and perceived likelihood of these outcomes. However, it is not known how pre-existing beliefs such as confidence in one's ability to perform health-related behaviour interact with such messages. The purpose of this research was to investigate whether eating self-efficacy moderates the effect of temporal framing (day-frame vs. year-frame) on snacking behaviour. Participants (N = 95) completed the short form of the Weight Efficacy Lifestyle Questionnaire (WEL-SF) and read either a day-framed or year-framed message about the health benefits associated with avoiding snacking. Consumption of snacks was reported 7 days later. For those with low levels of eating self-efficacy (WEL-SF score < 4.3 on a 7-point response scale), the year-framed message was associated with lower levels of snacking than the day-framed message. The current research identifies a key role for eating self-efficacy in shaping recipients' responses to temporally framed messages about the health benefits associated with the avoidance of snacking. Copyright © 2014 Elsevier Ltd. All rights reserved.

Message framing and parents' intentions to have their children vaccinated against HPV.

PubMed

Gainforth, Heather L; Cao, Wei; Latimer-Cheung, Amy E

2012-11-01

Framing a message in terms of the benefits of engaging in the behavior (gain frame), the costs of failing to engage in the behavior (loss frame), or both the benefits and the costs (mixed frame) can impact parents' decisions about their childrens' and adolescents' health. This study, investigated the effect of framed messages on parents' intentions to have their children vaccinated against human papillomavirus (HPV). The study employed a 2 (gender of the parent) × 2 (gender of the child) × 3 (message frame) between-groups, quasi-experimental design. A convenience sample of 367 parents with children in Grade 5, 6, or 7 who had at least one child who had not been vaccinated against HPV. Social-cognitive variables relating to intentions to vaccinate a child were assessed. Participants were randomly assigned to read one of three framed messages about the HPV vaccine (gain, loss, or mixed). Gain-framed messages seemed to persuade mothers of sons to speak to a doctor about the vaccine (p < .05). Framing effects were not significant for other outcomes. Findings provide preliminary evidence that certain vaccination messages may be more effective for different parent-child dyads. © 2012 Wiley Periodicals, Inc.

Reading skills of students with speech sound disorders at three stages of literacy development.

PubMed

Skebo, Crysten M; Lewis, Barbara A; Freebairn, Lisa A; Tag, Jessica; Avrich Ciesla, Allison; Stein, Catherine M

2013-10-01

The relationship between phonological awareness, overall language, vocabulary, and nonlinguistic cognitive skills to decoding and reading comprehension was examined for students at 3 stages of literacy development (i.e., early elementary school, middle school, and high school). Students with histories of speech sound disorders (SSD) with and without language impairment (LI) were compared to students without histories of SSD or LI (typical language; TL). In a cross-sectional design, students ages 7;0 (years;months) to 17;9 completed tests that measured reading, language, and nonlinguistic cognitive skills. For the TL group, phonological awareness predicted decoding at early elementary school, and overall language predicted reading comprehension at early elementary school and both decoding and reading comprehension at middle school and high school. For the SSD-only group, vocabulary predicted both decoding and reading comprehension at early elementary school, and overall language predicted both decoding and reading comprehension at middle school and decoding at high school. For the SSD and LI group, overall language predicted decoding at all 3 literacy stages and reading comprehension at early elementary school and middle school, and vocabulary predicted reading comprehension at high school. Although similar skills contribute to reading across the age span, the relative importance of these skills changes with children's literacy stages.

Reading Skills of Students With Speech Sound Disorders at Three Stages of Literacy Development

PubMed Central

Skebo, Crysten M.; Lewis, Barbara A.; Freebairn, Lisa A.; Tag, Jessica; Ciesla, Allison Avrich; Stein, Catherine M.

2015-01-01

Purpose The relationship between phonological awareness, overall language, vocabulary, and nonlinguistic cognitive skills to decoding and reading comprehension was examined for students at 3 stages of literacy development (i.e., early elementary school, middle school, and high school). Students with histories of speech sound disorders (SSD) with and without language impairment (LI) were compared to students without histories of SSD or LI (typical language; TL). Method In a cross-sectional design, students ages 7;0 (years; months) to 17;9 completed tests that measured reading, language, and nonlinguistic cognitive skills. Results For the TL group, phonological awareness predicted decoding at early elementary school, and overall language predicted reading comprehension at early elementary school and both decoding and reading comprehension at middle school and high school. For the SSD-only group, vocabulary predicted both decoding and reading comprehension at early elementary school, and overall language predicted both decoding and reading comprehension at middle school and decoding at high school. For the SSD and LI group, overall language predicted decoding at all 3 literacy stages and reading comprehension at early elementary school and middle school, and vocabulary predicted reading comprehension at high school. Conclusion Although similar skills contribute to reading across the age span, the relative importance of these skills changes with children’s literacy stages. PMID:23833280

Type 2 NADH Dehydrogenases in the Cyanobacterium Synechocystis sp. Strain PCC 6803 Are Involved in Regulation Rather Than Respiration

PubMed Central

Howitt, Crispin A.; Udall, Pacer K.; Vermaas, Wim F. J.

1999-01-01

Analysis of the genome of Synechocystis sp. strain PCC 6803 reveals three open reading frames (slr0851, slr1743, and sll1484) that may code for type 2 NAD(P)H dehydrogenases (NDH-2). The sequence similarity between the translated open reading frames and NDH-2s from other organisms is low, generally not exceeding 30% identity. However, NAD(P)H and flavin adenine dinucleotide binding motifs are conserved in all three putative NDH-2s in Synechocystis sp. strain PCC 6803. The three open reading frames were cloned, and deletion constructs were made for each. An expression construct containing one of the three open reading frames, slr1743, was able to functionally complement an Escherichia coli mutant lacking both NDH-1s and NDH-2s. Therefore, slr0851, slr1743, and sll1484 have been designated ndbA, ndbB, and ndbC, respectively. Strains that lacked one or more of the ndb genes were created in wild-type and photosystem (PS) I-less backgrounds. Deletion of ndb genes led to small changes in photoautotrophic growth rates and respiratory activities. Electron transfer rates into the plastoquinone pool in thylakoids in darkness were consistent with the presence of a small amount of NDH-2 activity in thylakoids. No difference was observed between wild-type and the Ndb-less strains in the banding patterns seen on native gels when stained for either NADH or NADPH dehydrogenase activity, indicating that the Ndb proteins do not accumulate to high levels. A striking phenotype of the PS I-less background strains lacking one or more of the NDH-2s is that they were able to grow at high light intensities that were lethal to the control strain but they retained normal PS II activity. We suggest that the Ndb proteins in Synechocystis sp. strain PCC 6803 are redox sensors and that they play a regulatory role responding to the redox state of the plastoquinone pool. PMID:10383967

Prediction and Stability of Reading Problems in Middle Childhood

ERIC Educational Resources Information Center

Ritchey, Kristen D.; Silverman, Rebecca D.; Schatschneider, Christopher; Speece, Deborah L.

2015-01-01

The longitudinal prediction of reading problems from fourth grade to sixth grade was investigated with a sample of 173 students. Reading problems at the end of sixth grade were defined by significantly below average performance (= 15th percentile) on reading factors defining word reading, fluency, and reading comprehension. Sixth grade poor reader…

Early Prediction of Reading Comprehension within the Simple View Framework

ERIC Educational Resources Information Center

Catts, Hugh W.; Herrera, Sarah; Nielsen, Diane Corcoran; Bridges, Mindy Sittner

2015-01-01

The simple view of reading proposes that reading comprehension is the product of word reading and language comprehension. In this study, we used the simple view framework to examine the early prediction of reading comprehension abilities. Using multiple measures for all constructs, we assessed word reading precursors (i.e., letter knowledge,…

A study on multiresolution lossless video coding using inter/intra frame adaptive prediction

NASA Astrophysics Data System (ADS)

Nakachi, Takayuki; Sawabe, Tomoko; Fujii, Tetsuro

2003-06-01

Lossless video coding is required in the fields of archiving and editing digital cinema or digital broadcasting contents. This paper combines a discrete wavelet transform and adaptive inter/intra-frame prediction in the wavelet transform domain to create multiresolution lossless video coding. The multiresolution structure offered by the wavelet transform facilitates interchange among several video source formats such as Super High Definition (SHD) images, HDTV, SDTV, and mobile applications. Adaptive inter/intra-frame prediction is an extension of JPEG-LS, a state-of-the-art lossless still image compression standard. Based on the image statistics of the wavelet transform domains in successive frames, inter/intra frame adaptive prediction is applied to the appropriate wavelet transform domain. This adaptation offers superior compression performance. This is achieved with low computational cost and no increase in additional information. Experiments on digital cinema test sequences confirm the effectiveness of the proposed algorithm.

Therapy for Duchenne muscular dystrophy: renewed optimism from genetic approaches.

PubMed

Fairclough, Rebecca J; Wood, Matthew J; Davies, Kay E

2013-06-01

Duchenne muscular dystrophy (DMD) is a devastating progressive disease for which there is currently no effective treatment except palliative therapy. There are several promising genetic approaches, including viral delivery of the missing dystrophin gene, read-through of translation stop codons, exon skipping to restore the reading frame and increased expression of the compensatory utrophin gene. The lessons learned from these approaches will be applicable to many other disorders.

EROS to universal tape conversion processor

NASA Technical Reports Server (NTRS)

Obrien, S. O. (Principal Investigator)

1980-01-01

The function of the EROS processor is to allow a user to select a specific area from a full frame LANDSAT image which is written on tape in the EROS format. The area of interest is read from the EROS formatted tape and converted to the JSC Universal format and written onto another tape. This tape can then be read by the IMDACS processing system and normal analysis can be performed.

Innovative multi-cantilever array sensor system with MOEMS read-out

NASA Astrophysics Data System (ADS)

Ivaldi, F.; Bieniek, T.; Janus, P.; Grabiec, P.; Majstrzyk, W.; Kopiec, D.; Gotszalk, T.

2016-11-01

Cantilever based sensor system are a well-established sensor family exploited in several every-day life applications as well as in high-end research areas. The very high sensitivity of such systems and the possibility to design and functionalize the cantilevers to create purpose built and highly selective sensors have increased the interest of the scientific community and the industry in further exploiting this promising sensors type. Optical deflection detection systems for cantilever sensors provide a reliable, flexible method for reading information from cantilevers with the highest sensitivity. However the need of using multi-cantilever arrays in several fields of application such as medicine, biology or safety related areas, make the optical method less suitable due to its structural complexity. Working in the frame of a the Joint Undertaking project Lab4MEMS II our group proposes a novel and innovative approach to solve this issue, by integrating a Micro-Opto-Electro-Mechanical-System (MOEMS) with dedicated optics, electronics and software with a MOEMS micro-mirror, ultimately developed in the frame of Lab4MEMSII. In this way we are able to present a closely packed, lightweight solution combining the advantages of standard optical read-out systems with the possibility of recording multiple read-outs from large cantilever arrays quasi simultaneously.

Response to Intervention as a Predictor of Long-Term Reading Outcomes in Children with Dyslexia.

PubMed

van der Kleij, Sanne W; Segers, Eliane; Groen, Margriet A; Verhoeven, Ludo

2017-08-01

The goal of this study was to investigate how growth during a phonics-based intervention, as well as reading levels at baseline testing, predicted long-term reading outcomes of children with dyslexia. Eighty Dutch children with dyslexia who had completed a 50-week phonics-based intervention in grade 4 were tested in grade 5 on both word and pseudoword (following regular Dutch orthographic patterns) reading efficiency and compared to 93 typical readers. In grade 5 the children with dyslexia were still significantly slower in word and pseudoword reading than their typically developing peers. Results showed that long-term pseudoword reading in the group with dyslexia was predicted by pseudoword reading at pretest and growth in pseudoword reading during the intervention, which was itself predicted by pseudoword reading at pretest. This was not the case for word reading. We found that long-term word reading was directly predicted from pretest word reading, and indirectly via pretest pseudoword reading, via growth in pseudoword and word reading. It can be concluded that pseudoword reading is not only a good indicator of severity of reading difficulties in children with dyslexia, it is also an indicator of who will profit from intervention in the long-term. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Genome analysis and identification of gelatinase encoded gene in Enterobacter aerogenes

NASA Astrophysics Data System (ADS)

Shahimi, Safiyyah; Mutalib, Sahilah Abdul; Khalid, Rozida Abdul; Repin, Rul Aisyah Mat; Lamri, Mohd Fadly; Bakar, Mohd Faizal Abu; Isa, Mohd Noor Mat

2016-11-01

In this study, bioinformatic analysis towards genome sequence of E. aerogenes was done to determine gene encoded for gelatinase. Enterobacter aerogenes was isolated from hot spring water and gelatinase species-specific bacterium to porcine and fish gelatin. This bacterium offers the possibility of enzymes production which is specific to both species gelatine, respectively. Enterobacter aerogenes was partially genome sequenced resulting in 5.0 mega basepair (Mbp) total size of sequence. From pre-process pipeline, 87.6 Mbp of total reads, 68.8 Mbp of total high quality reads and 78.58 percent of high quality percentage was determined. Genome assembly produced 120 contigs with 67.5% of contigs over 1 kilo base pair (kbp), 124856 bp of N50 contig length and 55.17 % of GC base content percentage. About 4705 protein gene was identified from protein prediction analysis. Two candidate genes selected have highest similarity identity percentage against gelatinase enzyme available in Swiss-Prot and NCBI online database. They were NODE_9_length_26866_cov_148.013245_12 containing 1029 base pair (bp) sequence with 342 amino acid sequence and NODE_24_length_155103_cov_177.082458_62 which containing 717 bp sequence with 238 amino acid sequence, respectively. Thus, two paired of primers (forward and reverse) were designed, based on the open reading frame (ORF) of selected genes. Genome analysis of E. aerogenes resulting genes encoded gelatinase were identified.

Identification of a novel homolog of the Drosophila staufen protein in the chromosome 8q13-q21.1 region.

PubMed

Buchner, G; Bassi, M T; Andolfi, G; Ballabio, A; Franco, B

1999-11-15

We report the identification of a new transcript homologous to the Drosophila staufen protein. This transcript, named STAU2 (HGMW-approved gene symbol and name), maps to the chromosome 8q13-q21 region. The full-length STAU2 cDNA is 4058 bp and contains an open reading frame of 479 amino acids. Analysis of the predicted protein product indicated the presence of three double-stranded RNA-binding domains. Best-fit analysis revealed a 48.5% similarity to the Drosophila protein and a 59.9% similarity to the recently described mammalian homolog hStau, indicating that at least two different transcripts with homologies to the fly protein are present in mammals. Copyright 1999 Academic Press.

Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

DOEpatents

Gardner, Shea N; Mariella, Jr., Raymond P; Christian, Allen T; Young, Jennifer A; Clague, David S

2013-06-25

A method of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths.

A tapeworm molecule manipulates vitellogenin expression in the beetle Tenebrio molitor

PubMed Central

Warr, E.; Meredith, J. M.; Nimmo, D. D.; Basu, S.; Hurd, H.; Eggleston, P.

2006-01-01

Metacestodes of Hymenolepis diminuta secrete a molecule that decreases vitellogenin (Vg) synthesis in the beetle host, Tenebrio molitor. The 5608 bp T. molitor Vg cDNA represents a single-copy gene encoding a single open reading frame of 1821 amino acids with a predicted molecular mass of 206 kDa. Northern blot analysis revealed detectable levels of transcripts only in adult females. In vivo, Vg mRNA abundance was significantly higher in fat bodies from infected females compared with control females at all but the earliest time point. In vitro, Vg mRNA abundance was significantly increased in fat bodies incubated with live stage I–II parasites. The apparent conflict between increased Vg mRNA abundance and decreased Vg protein in fat bodies from infected females is discussed. PMID:16907836

Hepatitis B virus genetic mutations and evolution in liver diseases

PubMed Central

Shen, Tao; Yan, Xin-Min

2014-01-01

Hepatitis B virus (HBV) belongs to the genus Orthohepadnavirus of the Hepadnaviridae family and is approximately 3.2 kb in length. Owing to a lack of proofreading capacity during reverse transcription and a high replication rate, HBV exhibits as quasispecies. To detect the genetic mutations of HBV, many methods with different sensitivities and throughputs were developed. According to documentary records, HBV mutation and evolution were important vial parameters in predicting disease progression and therapeutic outcome. In this review, we separately discussed the correlation between HBV genomic mutations in four open reading frames and liver disease progression. Since some of the results were controversial from different laboratories, it remains to be seen whether functional analyses will confirm their role in modifying the course of infection. PMID:24833874

Open Reading Frame E3-10.9K of Subspecies B1 Human Adenoviruses Encodes a Family of Late Orthologous Proteins That Vary in Their Predicted Structural Features and Subcellular Localization ▿

PubMed Central

Frietze, Kathryn M.; Campos, Samuel K.; Kajon, Adriana E.

2010-01-01

Subspecies B1 human adenoviruses (HAdV-B1s) are important causative agents of acute respiratory disease, but the molecular bases of their distinct pathobiology are still poorly understood. Marked differences in genetic content between HAdV-B1s and the well-characterized HAdV-Cs that may contribute to distinct pathogenic properties map to the E3 region. Between the highly conserved E3-19K and E3-10.4K/RIDα open reading frames (ORFs), and in the same location as the HAdV-C ADP/E3-11.6K ORF, HAdV-B1s carry ORFs E3-20.1K and E3-20.5K and a polymorphic third ORF, designated E3-10.9K, that varies in the size of its predicted product among HAdV-B1 serotypes and genomic variants. As an initial effort to define the function of the E3-10.9K ORF, we carried out a biochemical characterization of E3-10.9K-encoded orthologous proteins and investigated their expression in infected cells. Sequence-based predictions suggested that E3-10.9K orthologs with a hydrophobic domain are integral membrane proteins. Ectopically expressed, C-terminally tagged (with enhanced green fluorescent protein [EGFP]) E3-10.9K and E3-9K localized primarily to the plasma membrane, while E3-7.7K localized primarily to a juxtanuclear compartment that could not be identified. EGFP fusion proteins with a hydrophobic domain were N and O glycosylated. EGFP-tagged E3-4.8K, which lacked the hydrophobic domain, displayed diffuse cellular localization similar to that of the EGFP control. E3-10.9K transcripts from the major late promoter were detected at late time points postinfection. A C-terminally hemagglutinin-tagged version of E3-9K was detected by immunoprecipitation at late times postinfection in the membrane fraction of mutant virus-infected cells. These data suggest a role for ORF E3-10.9K-encoded proteins at late stages of HAdV-B1 replication, with potentially important functional implications for the documented ORF polymorphism. PMID:20739542

Word skipping: effects of word length, predictability, spelling and reading skill.

PubMed

Slattery, Timothy J; Yates, Mark

2017-08-31

Readers eyes often skip over words as they read. Skipping rates are largely determined by word length; short words are skipped more than long words. However, the predictability of a word in context also impacts skipping rates. Rayner, Slattery, Drieghe and Liversedge (2011) reported an effect of predictability on word skipping for even long words (10-13 characters) that extend beyond the word identification span. Recent research suggests that better readers and spellers have an enhanced perceptual span (Veldre & Andrews, 2014). We explored whether reading and spelling skill interact with word length and predictability to impact word skipping rates in a large sample (N=92) of average and poor adult readers. Participants read the items from Rayner et al. (2011) while their eye movements were recorded. Spelling skill (zSpell) was assessed using the dictation and recognition tasks developed by Sally Andrews and colleagues. Reading skill (zRead) was assessed from reading speed (words per minute) and accuracy of three 120 word passages each with 10 comprehension questions. We fit linear mixed models to the target gaze duration data and generalized linear mixed models to the target word skipping data. Target word gaze durations were significantly predicted by zRead while, the skipping likelihoods were significantly predicted by zSpell. Additionally, for gaze durations, zRead significantly interacted with word predictability as better readers relied less on context to support word processing. These effects are discussed in relation to the lexical quality hypothesis and eye movement models of reading.

Does mClass Reading 3D Predict Student Reading Proficiency on High-Stakes Assessments?

ERIC Educational Resources Information Center

Bowles, Amy S.

2015-01-01

This quantitative, correlational study investigated the relationship between the North Carolina End of Grade Assessment of Reading Comprehension (NCEOG) and mClass Reading 3D assessment in a North Carolina elementary school. It especially examined the degree to which mClass Reading 3D measures predict scores on the reading comprehension portion of…

Prediction and stability of reading problems in middle childhood.

PubMed

Ritchey, Kristen D; Silverman, Rebecca D; Schatschneider, Christopher; Speece, Deborah L

2015-01-01

The longitudinal prediction of reading problems from fourth grade to sixth grade was investigated with a sample of 173 students. Reading problems at the end of sixth grade were defined by significantly below average performance (≤ 15th percentile) on reading factors defining word reading, fluency, and reading comprehension. Sixth grade poor reader status was predicted by fall of fourth grade passage reading fluency, spelling fluency, and the number of reading problems identified by teachers. Reading fluency and spelling fluency were significant predictors in logistic regression equation that combined to yield a screening battery with an area under the curve of .91. These results suggest that brief assessments of reading and spelling fluency in fourth grade may be able to identify students in middle childhood who have a reading problem or who are at risk for experiencing reading problems in sixth grade. © Hammill Institute on Disabilities 2013.

Separating homeologs by phasing in the tetraploid wheat transcriptome.

PubMed

Krasileva, Ksenia V; Buffalo, Vince; Bailey, Paul; Pearce, Stephen; Ayling, Sarah; Tabbita, Facundo; Soria, Marcelo; Wang, Shichen; Akhunov, Eduard; Uauy, Cristobal; Dubcovsky, Jorge

2013-06-25

The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.

Separating homeologs by phasing in the tetraploid wheat transcriptome

PubMed Central

2013-01-01

Background The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. Results A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Conclusions Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies. PMID:23800085

Localization of the lysine epsilon-aminotransferase (lat) and delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase (pcbAB) genes from Streptomyces clavuligerus and production of lysine epsilon-aminotransferase activity in Escherichia coli.

PubMed Central

Tobin, M B; Kovacevic, S; Madduri, K; Hoskins, J A; Skatrud, P L; Vining, L C; Stuttard, C; Miller, J R

1991-01-01

Lysine epsilon-aminotransferase (LAT) in the beta-lactam-producing actinomycetes is considered to be the first step in the antibiotic biosynthetic pathway. Cloning of restriction fragments from Streptomyces clavuligerus, a beta-lactam producer, into Streptomyces lividans, a nonproducer that lacks LAT activity, led to the production of LAT in the host. DNA sequencing of restriction fragments containing the putative lat gene revealed a single open reading frame encoding a polypeptide with an approximately Mr 49,000. Expression of this coding sequence in Escherichia coli led to the production of LAT activity. Hence, LAT activity in S. clavuligerus is derived from a single polypeptide. A second open reading frame began immediately downstream from lat. Comparison of this partial sequence with the sequences of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D valine (ACV) synthetases from Penicillium chrysogenum and Cephalosporium acremonium and with nonribosomal peptide synthetases (gramicidin S and tyrocidine synthetases) found similarities among the open reading frames. Since mapping of the putative N and C termini of S. clavuligerus pcbAB suggests that the coding region occupies approximately 12 kbp and codes for a polypeptide related in size to the fungal ACV synthetases, the molecular characterization of the beta-lactam biosynthetic cluster between pcbC and cefE (approximately 25 kbp) is nearly complete. Images PMID:1917855

Analysis of genetic mutations in the 7a7b open reading frame of coronavirus of cheetahs (Acinonyx jubatus).

PubMed

Kennedy, Melissa A; Moore, Emily; Wilkes, Rebecca P; Citino, Scott B; Kania, Stephen A

2006-04-01

To analyze the 7a7b genes of the feline coronavirus (FCoV) of cheetahs, which are believed to play a role in virulence of this virus. Biologic samples collected during a 4-year period from 5 cheetahs at the same institution and at 1 time point from 4 cheetahs at different institutions. Samples were first screened for FCoV via a reverse transcription-PCR procedure involving primers that encompassed the 3'-untranslated region. Samples that yielded positive assay results were analyzed by use of primers that targeted the 7a7b open reading frames. The nucleotide sequences of the 7a7b amplification products were determined and analyzed. In most isolates, substantial deletional mutations in the 7a gene were detected that would result in aberrant or no expression of the 7a product because of altered reading frames. Although the 7b gene was also found to contain mutations, these were primarily point mutations resulting in minor amino acid changes. The coronavirus associated with 1 cheetah with feline infectious peritonitis had intact 7a and 7b genes. The data suggest that mutations arise readily in the 7a region and may remain stable in FCoV of cheetahs. In contrast, an intact 7b gene may be necessary for in vivo virus infection and replication. Persistent infection with FCoV in a cheetah population results in continued virus circulation and may lead to a quasispecies of virus variants.

Internet video telephony allows speech reading by deaf individuals and improves speech perception by cochlear implant users.

PubMed

Mantokoudis, Georgios; Dähler, Claudia; Dubach, Patrick; Kompis, Martin; Caversaccio, Marco D; Senn, Pascal

2013-01-01

To analyze speech reading through Internet video calls by profoundly hearing-impaired individuals and cochlear implant (CI) users. Speech reading skills of 14 deaf adults and 21 CI users were assessed using the Hochmair Schulz Moser (HSM) sentence test. We presented video simulations using different video resolutions (1280 × 720, 640 × 480, 320 × 240, 160 × 120 px), frame rates (30, 20, 10, 7, 5 frames per second (fps)), speech velocities (three different speakers), webcameras (Logitech Pro9000, C600 and C500) and image/sound delays (0-500 ms). All video simulations were presented with and without sound and in two screen sizes. Additionally, scores for live Skype™ video connection and live face-to-face communication were assessed. Higher frame rate (>7 fps), higher camera resolution (>640 × 480 px) and shorter picture/sound delay (<100 ms) were associated with increased speech perception scores. Scores were strongly dependent on the speaker but were not influenced by physical properties of the camera optics or the full screen mode. There is a significant median gain of +8.5%pts (p = 0.009) in speech perception for all 21 CI-users if visual cues are additionally shown. CI users with poor open set speech perception scores (n = 11) showed the greatest benefit under combined audio-visual presentation (median speech perception +11.8%pts, p = 0.032). Webcameras have the potential to improve telecommunication of hearing-impaired individuals.

The relative persuasiveness of gain-framed versus loss-Framed HIV testing message: evidence from a field experiment in northwest Ethiopia.

PubMed

Bekalu, Mesfin Awoke; Eggermont, Steven

2014-01-01

This study assessed the relative advantages of gain- versus loss-framed messages for promoting HIV testing among a sample of urban and rural residents in northwest Ethiopia. The authors randomly assigned 394 participants to read gain-framed (n = 196) or loss-framed (n = 198) HIV testing message prepared in a form of brochure. Experience with HIV testing, concern about and information needs on HIV/AIDS, and urbanity versus rurality significantly moderated the effects of framing on intention to test for HIV. A gain-frame advantage was found among urbanites, participants with high experience with HIV testing, and those with high concern about and information needs on HIV/AIDS, suggesting a more likely construal of HIV testing as a prevention behavior among these individuals. In contrast, a loss-frame advantage was found among ruralites and participants with low concern about and information needs on HIV/AIDS, suggesting a more likely construal of HIV testing as a detection behavior among such individuals. Moreover, gain- and loss-framing led to similar outcomes among individuals with low levels of experience with HIV testing, with a slight advantage for the loss-framed message. All of the framing effects obtained were of small to medium size.

Individualized Prediction of Reading Comprehension Ability Using Gray Matter Volume.

PubMed

Cui, Zaixu; Su, Mengmeng; Li, Liangjie; Shu, Hua; Gong, Gaolang

2018-05-01

Reading comprehension is a crucial reading skill for learning and putatively contains 2 key components: reading decoding and linguistic comprehension. Current understanding of the neural mechanism underlying these reading comprehension components is lacking, and whether and how neuroanatomical features can be used to predict these 2 skills remain largely unexplored. In the present study, we analyzed a large sample from the Human Connectome Project (HCP) dataset and successfully built multivariate predictive models for these 2 skills using whole-brain gray matter volume features. The results showed that these models effectively captured individual differences in these 2 skills and were able to significantly predict these components of reading comprehension for unseen individuals. The strict cross-validation using the HCP cohort and another independent cohort of children demonstrated the model generalizability. The identified gray matter regions contributing to the skill prediction consisted of a wide range of regions covering the putative reading, cerebellum, and subcortical systems. Interestingly, there were gender differences in the predictive models, with the female-specific model overestimating the males' abilities. Moreover, the identified contributing gray matter regions for the female-specific and male-specific models exhibited considerable differences, supporting a gender-dependent neuroanatomical substrate for reading comprehension.

Submillisecond X-ray photon correlation spectroscopy from a pixel array detector with fast dual gating and no readout dead-time

DOE PAGES

Zhang, Qingteng; Dufresne, Eric M.; Grybos, Pawel; ...

2016-04-19

Small-angle scattering X-ray photon correlation spectroscopy (XPCS) studies were performed using a novel photon-counting pixel array detector with dual counters for each pixel. Each counter can be read out independently from the other to ensure there is no readout dead-time between the neighboring frames. A maximum frame rate of 11.8 kHz was achieved. Results on test samples show good agreement with simple diffusion. Lastly, the potential of extending the time resolution of XPCS beyond the limit set by the detector frame rate using dual counters is also discussed.

Submillisecond X-ray photon correlation spectroscopy from a pixel array detector with fast dual gating and no readout dead-time

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

Zhang, Qingteng; Dufresne, Eric M.; Grybos, Pawel

Small-angle scattering X-ray photon correlation spectroscopy (XPCS) studies were performed using a novel photon-counting pixel array detector with dual counters for each pixel. Each counter can be read out independently from the other to ensure there is no readout dead-time between the neighboring frames. A maximum frame rate of 11.8 kHz was achieved. Results on test samples show good agreement with simple diffusion. Lastly, the potential of extending the time resolution of XPCS beyond the limit set by the detector frame rate using dual counters is also discussed.

Submillisecond X-ray photon correlation spectroscopy from a pixel array detector with fast dual gating and no readout dead-time.

PubMed

Zhang, Qingteng; Dufresne, Eric M; Grybos, Pawel; Kmon, Piotr; Maj, Piotr; Narayanan, Suresh; Deptuch, Grzegorz W; Szczygiel, Robert; Sandy, Alec

2016-05-01

Small-angle scattering X-ray photon correlation spectroscopy (XPCS) studies were performed using a novel photon-counting pixel array detector with dual counters for each pixel. Each counter can be read out independently from the other to ensure there is no readout dead-time between the neighboring frames. A maximum frame rate of 11.8 kHz was achieved. Results on test samples show good agreement with simple diffusion. The potential of extending the time resolution of XPCS beyond the limit set by the detector frame rate using dual counters is also discussed.

Implementing software based on relation frame theory to develop and increase relational cognitive skills

NASA Astrophysics Data System (ADS)

Presti, Giovambattista; Messina, Concetta; Mongelli, Francesca; Sireci, Maria Josè; Collotta, Mario

2017-11-01

Relational Frame Theory is a post-skinnerian theory of language and cognition based on more than thirty years of basic and applied research. It defines language and cognitive skills as an operant repertoire of responses to arbitrarily related stimuli specific, as far as is now known, of the human species. RFT has been proved useful in addressing cognitive barriers to human action in psychotherapy and also improving children skills in reading, IQ testing, and in metaphoric and categorical repertoires. We present a frame of action where RFT can be used in programming software to help autistic children to develop cognitive skills within a developmental vision.

Involvement of a Serpin serine protease inhibitor (OoSerpin) from mollusc Octopus ocellatus in antibacterial response.

PubMed

Wei, Xiumei; Xu, Jie; Yang, Jianmin; Liu, Xiangquan; Zhang, Ranran; Wang, Weijun; Yang, Jialong

2015-01-01

Serpin is an important member of serine protease inhibitors (SPIs), which is capable of regulating proteolytic events and involving in a variety of physiological processes. In present study, a Serpin homolog was identified from Octopus ocellatus (designated as OoSerpin). Full-length cDNA of OoSerpin was of 1735 bp, containing a 5' untranslated region of 214 bp, a 3' UTR of 282 bp, and an open reading frame of 1239 bp. The open reading frame encoded a polypeptide of 412 amino acids which has a predicted molecular weight of 46.5 kDa and an isoelectric point of 8.52. The OoSerpin protein shares 37% sequence identity with other Serpins from Mus musculus (NP_941373) and Ixodes scapularis (XP_002407493). The existence of a conserved SERPIN domain strongly suggested that OoSerpin was a member of the Serpin subfamily. Expression patterns of OoSerpin, both in tissues and towards bacterial stimulation, were then characterized. The mRNA of OoSerpin was constitutively expressed at different levels in all tested tissues of untreated O. ocellatus, including mantle (lowest), muscle, renal sac, gill, hemocyte, gonad, systemic heart, and hepatopancreas (highest). The transcriptional level of OoSerpin was significantly up-regulated (P<0.01) in O. ocellatus upon bacterial challenges with Vibrio anguillarum and Micrococcus luteus, indicating its involvement in the antibacterial immune response. Furthermore, rOoSerpin, the recombinant protein of OoSerpin, exhibited strong abilities to inhibit proteinase activities of trypsin and chymotrypsin as well as the growth of Escherichia coli. Our results demonstrate that OoSerpin is a potential antibacterial factor involved in the immune response of O. ocellatus against bacterial infection. Copyright © 2014 Elsevier Ltd. All rights reserved.

A novel gene whose expression in Medicago truncatula roots is suppressed in response to colonization by vesicular-arbuscular mycorrhizal (VAM) fungi and to phosphate nutrition.

PubMed

Burleigh, S H; Harrison, M J

1997-05-01

A cDNA clone (Mt4) was isolated as a result of a differential screen to identify genes showing altered expression during the interaction between Medicago truncatula and the vesicular-arbuscular mycorrhizal (VAM) fungus Glomus versiforme. Mt4 represents a M. truncatula mRNA that contains numerous short open reading frames, the two longest of which are predicted to encode polypeptides of 51 amino acids each. One of these open reading frames shares a short region of identity with a phosphate starvation-inducible gene from tomato. Mt4 gene expression is regulated in response to colonization by mycorrhizal fungi: transcripts were detected in non-colonized roots and levels decreased in both M. truncatula and M. sativa (alfalfa) roots after colonization by G. versiforme. Transcript levels also decreased during the incomplete interaction between G. versiforme and a M. sativa mycorrhizal minus (myc-) line, indicating that the down-regulation of this gene occurs early during the interaction between the fungus and its host plant. Phosphate levels in the nutrient media also affected the expression of the Mt4 gene: transcripts were present in the roots of plants grown under phosphate-deficient conditions, but were undetectable in the roots of plants grown under phosphate sufficient conditions. Furthermore, expression was only observed when plants were grown under nitrogen-sufficient conditions. Northern blot analyses indicate that Mt4 transcripts are present primarily in roots and barely detectable in stems or leaves. Thus, Mt4 represents a M. truncatula gene whose expression is regulated in response to both colonization by mycorrhizal fungi and to the phosphate status of the plant.

Nucleotide sequence of the gene for the Mr 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of Mr 38,950

PubMed Central

Zurawski, Gerard; Bohnert, Hans J.; Whitfeld, Paul R.; Bottomley, Warwick

1982-01-01

The gene for the so-called Mr 32,000 rapidly labeled photosystem II thylakoid membrane protein (here designated psbA) of spinach (Spinacia oleracea) chloroplasts is located on the chloroplast DNA in the large single-copy region immediately adjacent to one of the inverted repeat sequences. In this paper we show that the size of the mRNA for this protein is ≈ 1.25 kilobases and that the direction of transcription is towards the inverted repeat unit. The nucleotide sequence of the gene and its flanking regions is presented. The only large open reading frame in the sequence codes for a protein of Mr 38,950. The nucleotide sequence of psbA from Nicotiana debneyi also has been determined, and comparison of the sequences from the two species shows them to be highly conserved (>95% homology) throughout the entire reading frame. Conservation of the amino acid sequence is absolute, there being no changes in a total of 353 residues. This leads us to conclude that the primary translation product of psbA must be a protein of Mr 38,950. The protein is characterized by the complete absence of lysine residues and is relatively rich in hydrophobic amino acids, which tend to be clustered. Transcription of spinach psbA starts about 86 base pairs before the first ATG codon. Immediately upstream from this point there is a sequence typical of that found in E. coli promoters. An almost identical sequence occurs in the equivalent region of N. debneyi DNA. Images PMID:16593262

Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome

PubMed Central

Hücker, Sarah M.; Ardern, Zachary; Goldberg, Tatyana; Schafferhans, Andrea; Bernhofer, Michael; Vestergaard, Gisle; Nelson, Chase W.; Schloter, Michael; Rost, Burkhard; Scherer, Siegfried

2017-01-01

In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the translatome (RIBOseq) of the enteric pathogen Escherichia coli O157:H7 strain Sakai was determined at two optimal growth conditions and a severe stress condition combining low temperature and high osmotic pressure. All intergenic open reading frames potentially encoding a protein of ≥ 30 amino acids were investigated with regard to coverage by transcription and translation signals and their translatability expressed by the ribosomal coverage value. This led to discovery of 465 unique, putative novel genes not yet annotated in this E. coli strain, which are evenly distributed over both DNA strands of the genome. For 255 of the novel genes, annotated homologs in other bacteria were found, and a machine-learning algorithm, trained on small protein-coding E. coli genes, predicted that 89% of these translated open reading frames represent bona fide genes. The remaining 210 putative novel genes without annotated homologs were compared to the 255 novel genes with homologs and to 250 short annotated genes of this E. coli strain. All three groups turned out to be similar with respect to their translatability distribution, fractions of differentially regulated genes, secondary structure composition, and the distribution of evolutionary constraint, suggesting that both novel groups represent legitimate genes. However, the machine-learning algorithm only recognized a small fraction of the 210 genes without annotated homologs. It is possible that these genes represent a novel group of genes, which have unusual features dissimilar to the genes of the machine-learning algorithm training set. PMID:28902868

Decisional strategy determines whether frame influences treatment preferences for medical decisions.

PubMed

Woodhead, Erin L; Lynch, Elizabeth B; Edelstein, Barry A

2011-06-01

Decision makers are influenced by the frame of information such that preferences vary depending on whether survival or mortality data are presented. Research is inconsistent as to whether and how age impacts framing effects. This paper presents two studies that used qualitative analyses of think-aloud protocols to understand how the type of information used in the decision making process varies by frame and age. In Study 1, 40 older adults, age 65 to 89, and 40 younger adults, age 18 to 24, responded to a hypothetical lung cancer scenario in a within-subject design. Participants received both a survival and mortality frame. Qualitative analyses revealed that two main decisional strategies were used by all participants: one strategy reflected a data-driven decisional process, whereas the other reflected an experience-driven process. Age predicted decisional strategy, with older adults less likely to use a data-driven strategy. Frame interacted with strategy to predict treatment choice; only those using a data-driven strategy demonstrated framing effects. In Study 2, 61 older adults, age 65 to 98, and 63 younger adults, age 18 to 30, responded to the same scenarios as in Study 1 in a between-subject design. The results of Study 1 were replicated, with age significantly predicting decisional strategy and frame interacting with strategy to predict treatment choice. Findings suggest that framing effects may be more related to decisional strategy than to age. (c) 2011 APA, all rights reserved.

Examining Predictive Validity of Oral Reading Fluency Slope in Upper Elementary Grades Using Quantile Regression.

PubMed

Cho, Eunsoo; Capin, Philip; Roberts, Greg; Vaughn, Sharon

2017-07-01

Within multitiered instructional delivery models, progress monitoring is a key mechanism for determining whether a child demonstrates an adequate response to instruction. One measure commonly used to monitor the reading progress of students is oral reading fluency (ORF). This study examined the extent to which ORF slope predicts reading comprehension outcomes for fifth-grade struggling readers ( n = 102) participating in an intensive reading intervention. Quantile regression models showed that ORF slope significantly predicted performance on a sentence-level fluency and comprehension assessment, regardless of the students' reading skills, controlling for initial ORF performance. However, ORF slope was differentially predictive of a passage-level comprehension assessment based on students' reading skills when controlling for initial ORF status. Results showed that ORF explained unique variance for struggling readers whose posttest performance was at the upper quantiles at the end of the reading intervention, but slope was not a significant predictor of passage-level comprehension for students whose reading problems were the most difficult to remediate.

Automatic draft reading based on image processing

NASA Astrophysics Data System (ADS)

Tsujii, Takahiro; Yoshida, Hiromi; Iiguni, Youji

2016-10-01

In marine transportation, a draft survey is a means to determine the quantity of bulk cargo. Automatic draft reading based on computer image processing has been proposed. However, the conventional draft mark segmentation may fail when the video sequence has many other regions than draft marks and a hull, and the estimated waterline is inherently higher than the true one. To solve these problems, we propose an automatic draft reading method that uses morphological operations to detect draft marks and estimate the waterline for every frame with Canny edge detection and a robust estimation. Moreover, we emulate surveyors' draft reading process for getting the understanding of a shipper and a receiver. In an experiment in a towing tank, the draft reading error of the proposed method was <1 cm, showing the advantage of the proposed method. It is also shown that accurate draft reading has been achieved in a real-world scene.

DICE: An Object Oriented Programming Environment for Cooperative Engineering Design

DTIC Science & Technology

1989-03-20

environment called PARMENIDES /FRULEKIT; PARMENIDES /FRULEKIT supports programming in frames and rules and was developed in LISP at Carnegie-Mellon...the domain of building design and construction. The Blackboard in DICEY-BUILDER is represented as frames in PARMENIDES , while the KMs are implemented... PARMENIDES fo rart omat format d a b C /envelope BLACKBOAR D machine to machine (’BLACKBOARD l m message f il transfer message p read •d message format J

The Maximal C³ Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses.

PubMed

Michel, Christian J

2017-04-18

In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C 3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses. The method was based on the preferential occurrence of trinucleotides among the three frames at the gene population level. We extend here this definition at the gene level. This new statistical approach considers all the genes, i.e., of large and small lengths, with the same weight for searching the circular code X . As a consequence, the concept of circular code, in particular the reading frame retrieval, is directly associated to each gene. At the gene level, the circular code X is strengthened in the genes of bacteria, eukaryotes, plasmids, and viruses, and is now also identified in the genes of archaea. The genes of mitochondria and chloroplasts contain a subset of the circular code X . Finally, by studying viral genes, the circular code X was found in DNA genomes, RNA genomes, double-stranded genomes, and single-stranded genomes.

Dynamic Assessment of Reading Difficulties: Predictive and Incremental Validity on Attitude toward Reading and the Use of Dialogue/Participation Strategies in Classroom Activities.

PubMed

Navarro, Juan-José; Lara, Laura

2017-01-01

Dynamic Assessment (DA) has been shown to have more predictive value than conventional tests for academic performance. However, in relation to reading difficulties, further research is needed to determine the predictive validity of DA for specific aspects of the different processes involved in reading and the differential validity of DA for different subgroups of students with an academic disadvantage. This paper analyzes the implementation of a DA device that evaluates processes involved in reading (EDPL) among 60 students with reading comprehension difficulties between 9 and 16 years of age, of whom 20 have intellectual disabilities, 24 have reading-related learning disabilities, and 16 have socio-cultural disadvantages. We specifically analyze the predictive validity of the EDPL device over attitude toward reading, and the use of dialogue/participation strategies in reading activities in the classroom during the implementation stage. We also analyze if the EDPL device provides additional information to that obtained with a conventionally applied personal-social adjustment scale (APSL). Results showed that dynamic scores, obtained from the implementation of the EDPL device, significantly predict the studied variables. Moreover, dynamic scores showed a significant incremental validity in relation to predictions based on an APSL scale. In relation to differential validity, the results indicated the superior predictive validity for DA for students with intellectual disabilities and reading disabilities than for students with socio-cultural disadvantages. Furthermore, the role of metacognition and its relation to the processes of personal-social adjustment in explaining the results is discussed.

Dynamic Assessment of Reading Difficulties: Predictive and Incremental Validity on Attitude toward Reading and the Use of Dialogue/Participation Strategies in Classroom Activities

PubMed Central

Navarro, Juan-José; Lara, Laura

2017-01-01

Dynamic Assessment (DA) has been shown to have more predictive value than conventional tests for academic performance. However, in relation to reading difficulties, further research is needed to determine the predictive validity of DA for specific aspects of the different processes involved in reading and the differential validity of DA for different subgroups of students with an academic disadvantage. This paper analyzes the implementation of a DA device that evaluates processes involved in reading (EDPL) among 60 students with reading comprehension difficulties between 9 and 16 years of age, of whom 20 have intellectual disabilities, 24 have reading-related learning disabilities, and 16 have socio-cultural disadvantages. We specifically analyze the predictive validity of the EDPL device over attitude toward reading, and the use of dialogue/participation strategies in reading activities in the classroom during the implementation stage. We also analyze if the EDPL device provides additional information to that obtained with a conventionally applied personal-social adjustment scale (APSL). Results showed that dynamic scores, obtained from the implementation of the EDPL device, significantly predict the studied variables. Moreover, dynamic scores showed a significant incremental validity in relation to predictions based on an APSL scale. In relation to differential validity, the results indicated the superior predictive validity for DA for students with intellectual disabilities and reading disabilities than for students with socio-cultural disadvantages. Furthermore, the role of metacognition and its relation to the processes of personal-social adjustment in explaining the results is discussed. PMID:28243215

The Predictive Utility of DIBELS Reading Assessment for Reading Comprehension among Third Grade English Language Learners and English Speaking Children

ERIC Educational Resources Information Center

Scheffel, Debora; Lefly, Dianne; Houser, Janet

2012-01-01

The study addresses the extent to which subtests on the Dynamic Indicators of Basic Early Literacy Skills Reading Assessment (DIBELS; Good & Kaminski, 2002) predict student success on a measure of reading comprehension and if prediction is consistent for native and second English Language Learners. 2,649 elementary students were assessed on a…

Epidemiological survey of idiopathic scoliosis and sequence alignment analysis of multiple candidate genes.

PubMed

Yang, Tao; Jia, Quanzhang; Guo, Hong; Xu, Jianzhong; Bai, Yun; Yang, Kai; Luo, Fei; Zhang, Zehua; Hou, Tianyong

2012-06-01

To investigate the effects of genetic factors on idiopathic scoliosis (IS) and genetic modes through genetic epidemiological survey on IS in Chongqing City, China, and to determine whether SH3GL1, GADD45B, and FGF22 in the chromosome 19p13.3 are the pathogenic genes of IS through genetic sequence analysis. 214 nuclear families were investigated to analyse the age incidence, familial aggregation, and heritability. SH3GL1, GADD45B, and FGF22 were chosen as candidate genes for mutation screening in 56 IS patients of 214 families. The sequence alignment analysis was performed to determine mutations and predict the protein structure. The average age of onset of 10.8 years suggests that IS is a early onset disease. Incidences of IS in first-, second-, third-degree relatives and the overall incidence in families (5.68%) were also significantly higher than that of the general population (1.04%). The U test indicated a significant difference, suggesting that IS has a familial aggregation. The heritability of first-degree relatives (77.68 ±10.39%), second-degree relatives (69.89 ±3.14%), and third-degree relatives (62.14 ±11.92%) illustrated that genetic factors play an important role in IS pathogenesis. The incidence of first-degree relatives (10.01%), second-degree relatives (2.55%) and third-degree relatives (1.76%) illustrated that IS is not in simple accord with monogenic Mendel's law but manifests as traits of multifactorial hereditary diseases. Sequence alignment of exons of SH3GL1, GADD45B, and FGF22 showed 17 base mutations, of which 16 mutations do not induce open reading frame (ORF) shift or amino acid changes whereas one mutation (C→T)occurred in SH3GL1 results in formation of the termination codon, which induces variation of protein reading frame. Prediction analysis of protein sequence showed that the SH3GL1 mutant encoded a truncated protein, thus affecting the protein structure. IS is a multifactorial genetic disease and SH3GL1 may be one of the pathogenic genes for IS.

Pathway Evidence of How Musical Perception Predicts Word-Level Reading Ability in Children with Reading Difficulties

PubMed Central

Cogo-Moreira, Hugo; Brandão de Ávila, Clara Regina; Ploubidis, George B.; de Jesus Mari, Jair

2013-01-01

Objective To investigate whether specific domains of musical perception (temporal and melodic domains) predict the word-level reading skills of eight- to ten-year-old children (n = 235) with reading difficulties, normal quotient of intelligence, and no previous exposure to music education classes. Method A general-specific solution of the Montreal Battery of Evaluation of Amusia (MBEA), which underlies a musical perception construct and is constituted by three latent factors (the general, temporal, and the melodic domain), was regressed on word-level reading skills (rate of correct isolated words/non-words read per minute). Results General and melodic latent domains predicted word-level reading skills. PMID:24358358

Framing effects and risk-sensitive decision making.

PubMed

Mishra, Sandeep; Gregson, Margaux; Lalumière, Martin L

2012-02-01

Prospect theory suggests that people are risk-averse when facing gains, but risk-prone when facing losses, a pattern known as the framing effect. Although framing effects have been widely demonstrated, few studies have investigated framing effects under conditions of need. Risk-sensitivity theory predicts that decision makers should prefer high-risk options in situations of high need, when lower risk options are unlikely to meet those needs. In two experiments, we examined (1) whether framing effects occurred in behavioural tasks involving risky decision making from description and decision making from experience, (2) whether participants' risky decision making conformed to the predictions of risk-sensitivity theory, and (3) whether decision framing interacted with conditions of need to influence decision making under risk. The results suggest that under all circumstances, risky decision making conformed to the predictions of risk-sensitivity theory. Framing effects were at least partially demonstrable under all experimental conditions. Finally, negative frames interacted with situations of high need to produce particularly elevated levels of risky choice. Together, the results suggest that risk-sensitivity theory can augment prospect theory to explain choice under conditions of need. ©2011 The British Psychological Society.

Graphic organizers and their effects on the reading comprehension of students with LD: a synthesis of research.

PubMed

Kim, Ae-Hwa; Vaughn, Sharon; Wanzek, Jeanne; Wei, Shangjin

2004-01-01

Previous research studies examining the effects of graphic organizers on reading comprehension for students with learning disabilities (LD) are reviewed. An extensive search of the professional literature between 1963 and June 2001 yielded a total of 21 group design intervention studies that met the criteria for inclusion in the synthesis. Using graphic organizers (i.e., semantic organizers, framed outlines, cognitive maps with and without a mnemonic) was associated with improved reading comprehension overall for students with LD. Compared to standardized reading measures, researcher-developed comprehension measures were associated with higher effect sizes. Initial gains demonstrated when using graphic organizers were not revealed during later comprehension tasks or on new comprehension tasks.

Neural evidence for description dependent reward processing in the framing effect.

PubMed

Yu, Rongjun; Zhang, Ping

2014-01-01

Human decision making can be influenced by emotionally valenced contexts, known as the framing effect. We used event-related brain potentials to investigate how framing influences the encoding of reward. We found that the feedback related negativity (FRN), which indexes the "worse than expected" negative prediction error in the anterior cingulate cortex (ACC), was more negative for the negative frame than for the positive frame in the win domain. Consistent with previous findings that the FRN is not sensitive to "better than expected" positive prediction error, the FRN did not differentiate the positive and negative frame in the loss domain. Our results provide neural evidence that the description invariance principle which states that reward representation and decision making are not influenced by how options are presented is violated in the framing effect.

Predicting Intervention Effectiveness from Reading Accuracy and Rate Measures through the Instructional Hierarchy: Evidence for a Skill-by-Treatment Interaction

ERIC Educational Resources Information Center

Szadokierski, Isadora; Burns, Matthew K.; McComas, Jennifer J.

2017-01-01

The current study used the learning hierarchy/instructional hierarchy phases of acquisition and fluency to predict intervention effectiveness based on preintervention reading skills. Preintervention reading accuracy (percentage of words read correctly) and rate (number of words read correctly per minute) were assessed for 49 second- and…

Predicting Math Outcomes: Reading Predictors and Comorbidity

ERIC Educational Resources Information Center

Fletcher, Jack M.

2005-01-01

This commentary addresses issues concerning (a) the measurement of numbers, letters, and words versus cognitive processes in early screening batteries, and (b) comorbid associations of reading, math, and attention disorders. Based on reading prediction studies, assessments that include numbers should be most predictive of math outcomes. However,…

Features of Instructional Talk Predictive of Reading Comprehension

ERIC Educational Resources Information Center

Michener, Catherine J.; Patrick Proctor, C.; Silverman, Rebecca D.

2018-01-01

Increasingly, reading research has begun to address how students' linguistic environments may explain their reading achievement. In this exploratory analysis, we investigated how the rates of specific instructional talk moves predicted student reading comprehension achievement. Transcripts from third-, fourth-, and fifth-grade classrooms (teacher…

A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes.

PubMed

Liu, H X; Cartegni, L; Zhang, M Q; Krainer, A R

2001-01-01

Point mutations can generate defective and sometimes harmful proteins. The nonsense-mediated mRNA decay (NMD) pathway minimizes the potential damage caused by nonsense mutations. In-frame nonsense codons located at a minimum distance upstream of the last exon-exon junction are recognized as premature termination codons (PTCs), targeting the mRNA for degradation. Some nonsense mutations cause skipping of one or more exons, presumably during pre-mRNA splicing in the nucleus; this phenomenon is termed nonsense-mediated altered splicing (NAS), and its underlying mechanism is unclear. By analyzing NAS in BRCA1, we show here that inappropriate exon skipping can be reproduced in vitro, and results from disruption of a splicing enhancer in the coding sequence. Enhancers can be disrupted by single nonsense, missense and translationally silent point mutations, without recognition of an open reading frame as such. These results argue against a nuclear reading-frame scanning mechanism for NAS. Coding-region single-nucleotide polymorphisms (cSNPs) within exonic splicing enhancers or silencers may affect the patterns or efficiency of mRNA splicing, which may in turn cause phenotypic variability and variable penetrance of mutations elsewhere in a gene.

Executive functioning predicts reading, mathematics, and theory of mind during the elementary years.

PubMed

Cantin, Rachelle H; Gnaedinger, Emily K; Gallaway, Kristin C; Hesson-McInnis, Matthew S; Hund, Alycia M

2016-06-01

The goal of this study was to specify how executive functioning components predict reading, mathematics, and theory of mind performance during the elementary years. A sample of 93 7- to 10-year-old children completed measures of working memory, inhibition, flexibility, reading, mathematics, and theory of mind. Path analysis revealed that all three executive functioning components (working memory, inhibition, and flexibility) mediated age differences in reading comprehension, whereas age predicted mathematics and theory of mind directly. In addition, reading mediated the influence of executive functioning components on mathematics and theory of mind, except that flexibility also predicted mathematics directly. These findings provide important details about the development of executive functioning, reading, mathematics, and theory of mind during the elementary years. Copyright © 2016 Elsevier Inc. All rights reserved.

Promoting mammography screening among Chinese American women using a message-framing intervention.

PubMed

Sun, Yiyuan; Sarma, Elizabeth A; Moyer, Anne; Messina, Catherine R

2015-07-01

This study examined the role of women's perceptions about the relative pros versus cons (decisional balance) of mammography in moderating Chinese American women's responses to gain- and loss-framed messages that promote mammography. One hundred and forty-three Chinese American women who were currently nonadherent to guidelines for receiving annual screening mammograms were randomly assigned to read either a gain- or loss-framed culturally appropriate print brochure about mammography screening. Mammography screening was self-reported at a 2-month follow-up. Although there was not a main effect for message frame, the hypothesized interaction between message frame and decisional balance was significant, indicating that women who received a framed message that matched their decisional balance were significantly more likely to have obtained a mammogram by the follow-up than women who received a mismatched message. Results suggest that decisional balance, and more generally, perceptions about mammography, may be an important moderator of framing effects for mammography among Chinese American women. The match between message frame and decisional balance should be considered when attempting to encourage Chinese American women to receive mammography screening, as a match between the two may be most persuasive. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

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

Vieira, P.; De Waal-Malefyt, R.; Dang, M.N.

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 BCRFImore » may have conserved only a subset of hIL-10 activities.« less

Identification of the psaA Gene, Coding for Pneumococcal Surface Adhesin A, in Viridans Group Streptococci other than Streptococcus pneumoniae

PubMed Central

Jado, Isabel; Fenoll, Asunción; Casal, Julio; Pérez, Amalia

2001-01-01

The gene encoding the pneumococcal surface adhesin A (PsaA) protein has been identified in three different viridans group streptococcal species. Comparative studies of the psaA gene identified in different pneumococcal isolates by sequencing PCR products showed a high degree of conservation among these strains. PsaA is encoded by an open reading frame of 930 bp. The analysis of this fragment in Streptococcus mitis, Streptococcus oralis, and Streptococcus anginosus strains revealed a sequence identity of 95, 94, and 90%, respectively, to the corresponding open reading frame of the previously reported Streptococcus pneumoniae serotype 6B strain. Our results confirm that psaA is present and detectable in heterologous bacterial species. The possible implications of these results for the suitability and potential use of PsaA in the identification and diagnosis of pneumococcal diseases are discussed. PMID:11527799

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

PubMed

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

1996-09-01

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

Inexpensive Neutron Imaging Cameras Using CCDs for Astronomy

NASA Astrophysics Data System (ADS)

Hewat, A. W.

We have developed inexpensive neutron imaging cameras using CCDs originally designed for amateur astronomical observation. The low-light, high resolution requirements of such CCDs are similar to those for neutron imaging, except that noise as well as cost is reduced by using slower read-out electronics. For example, we use the same 2048x2048 pixel ;Kodak; KAI-4022 CCD as used in the high performance PCO-2000 CCD camera, but our electronics requires ∼5 sec for full-frame read-out, ten times slower than the PCO-2000. Since neutron exposures also require several seconds, this is not seen as a serious disadvantage for many applications. If higher frame rates are needed, the CCD unit on our camera can be easily swapped for a faster readout detector with similar chip size and resolution, such as the PCO-2000 or the sCMOS PCO.edge 4.2.

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

PubMed

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.

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

PubMed Central

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

1993-01-01

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

Evaluating noise performance of the IUCAA sidecar drive electronics controller (ISDEC) based system for TMT on-instrument wavefront sensing (OIWFS) application

NASA Astrophysics Data System (ADS)

Burse, Mahesh; Chattopadhyay, Sabyasachi; Ramaprakash, A. N.; Sinha, Sakya; Prabhudesai, Swapnil; Punnadi, Sujit; Chordia, Pravin; Kohok, Abhay

2016-07-01

As a part of a design study for the On-Instrument Low Order Wave-front Sensor (OIWFS) for the TMT Infra-Red Imaging Spectrograph (IRIS), we recently evaluated the noise performance of a detector control system consisting of IUCAA SIDECAR DRIVE ELECRONICS CONTROLLER (ISDEC), SIDECAR ASIC and HAWAII-2RG (H2RG) MUX. To understand and improve the performance of this system to serve as a near infrared wavefront sensor, we implemented new read out modes like multiple regions of interest with differential multi-accumulate readout schemes for the HAWAII-2RG (H2RG) detector. In this system, the firmware running in SIDECAR ASIC programs the detector for ROI readout, reads the detector, processes the detector output and writes the digitized data into its internal memory. ISDEC reads the digitized data from ASIC, performs the differential multi-accumulate operations and then sends the processed data to a PC over a USB interface. A special loopback board was designed and used to measure and reduce the noise from SIDECAR ASIC DC biases2. We were able to reduce the mean r.m.s read noise of this system down to 1-2 e. for any arbitrary window frame of 4x4 size at frame rates below about 200 Hz.

Graphics-Printing Program For The HP Paintjet Printer

NASA Technical Reports Server (NTRS)

Atkins, Victor R.

1993-01-01

IMPRINT utility computer program developed to print graphics specified in raster files by use of Hewlett-Packard Paintjet(TM) color printer. Reads bit-mapped images from files on UNIX-based graphics workstation and prints out three different types of images: wire-frame images, solid-color images, and gray-scale images. Wire-frame images are in continuous tone or, in case of low resolution, in random gray scale. In case of color images, IMPRINT also prints by use of default palette of solid colors. Written in C language.

User's manual for SYNC: A FORTRAN program for merging and time-synchronizing data

NASA Technical Reports Server (NTRS)

Maine, R. E.

1981-01-01

The FORTRAN 77 computer program SYNC for merging and time synchronizing data is described. The program SYNC reads one or more input files which contain either synchronous data frames or time-tagged data points, which can be compressed. The program decompresses and time synchronizes the data, correcting for any channel time skews. Interpolation and hold last value synchronization algorithms are available. The output from SYNC is a file of time synchronized data frames at any requested sample rate.

Characterization of the Basic Replicon of Rhodococcus Plasmid pSOX and Development of a Rhodococcus-Escherichia coli Shuttle Vector†

PubMed Central

Denis-Larose, Claude; Bergeron, Hélène; Labbé, Diane; Greer, Charles W.; Hawari, Jalal; Grossman, Matthew J.; Sankey, Bruce M.; Lau, Peter C. K.

1998-01-01

The replication region of a 100-kb desulfurization plasmid (pSOX) from Rhodococcus sp. strain X309 was localized to a 4-kb KpnI fragment, and its sequence was determined. The amino acid sequence of one of the predicted open reading frames (ORFs) was related to the putative replication (Rep) protein sequences of the mycobacterial pLR7 family of plasmids. Three of the five predicted ORF products were identified by radiolabelling with the Escherichia coli T7 polymerase/promoter system. In E. coli, the Rep protein of pSOX was apparently synthesized in a shortened form, 21.3 kDa instead of the predicted 41.3 kDa, as a result of an internal initiation. This situation is reminescent of that for some bacterial Rep proteins. A shuttle plasmid was constructed with the pSOX origin, pBluescript II KS−, and the chloramphenicol resistance (Cmr) gene from pRF29. This new shuttle plasmid was used to demonstrate expression of the Bacillus subtilis sacB gene in a strain of Rhodococcus, rendering it sensitive to the presence of sucrose. PMID:9797291

Strategic Processing and Predictive Inference Generation in L2 Reading

ERIC Educational Resources Information Center

Nahatame, Shingo

2014-01-01

Predictive inference is the anticipation of the likely consequences of events described in a text. This study investigated predictive inference generation during second language (L2) reading, with a focus on the effects of strategy instructions. In this experiment, Japanese university students read several short narrative passages designed to…

Neurobiological and memory models of risky decision making in adolescents versus young adults.

PubMed

Reyna, Valerie F; Estrada, Steven M; DeMarinis, Jessica A; Myers, Regina M; Stanisz, Janine M; Mills, Britain A

2011-09-01

Predictions of fuzzy-trace theory and neurobiological approaches are examined regarding risk taking in a classic decision-making task--the framing task--as well as in the context of real-life risk taking. We report the 1st study of framing effects in adolescents versus adults, varying risk and reward, and relate choices to individual differences, sexual behavior, and behavioral intentions. As predicted by fuzzy-trace theory, adolescents modulated risk taking according to risk and reward. Adults showed standard framing, reflecting greater emphasis on gist-based (qualitative) reasoning, but adolescents displayed reverse framing when potential gains for risk taking were high, reflecting greater emphasis on verbatim-based (quantitative) reasoning. Reverse framing signals a different way of thinking compared with standard framing (reverse framing also differs from simply choosing the risky option). Measures of verbatim- and gist-based reasoning about risk, sensation seeking, behavioral activation, and inhibition were used to extract dimensions of risk proneness: Sensation seeking increased and then decreased, whereas inhibition increased from early adolescence to young adulthood, predicted by neurobiological theories. Two additional dimensions, verbatim- and gist-based reasoning about risk, loaded separately and predicted unique variance in risk taking. Importantly, framing responses predicted real-life risk taking. Reasoning was the most consistent predictor of real-life risk taking: (a) Intentions to have sex, sexual behavior, and number of partners decreased when gist-based reasoning was triggered by retrieval cues in questions about perceived risk, whereas (b) intentions to have sex and number of partners increased when verbatim-based reasoning was triggered by different retrieval cues in questions about perceived risk. (c) 2011 APA, all rights reserved.

Improving transmembrane protein consensus topology prediction using inter-helical interaction.

PubMed

Wang, Han; Zhang, Chao; Shi, Xiaohu; Zhang, Li; Zhou, You

2012-11-01

Alpha helix transmembrane proteins (αTMPs) represent roughly 30% of all open reading frames (ORFs) in a typical genome and are involved in many critical biological processes. Due to the special physicochemical properties, it is hard to crystallize and obtain high resolution structures experimentally, thus, sequence-based topology prediction is highly desirable for the study of transmembrane proteins (TMPs), both in structure prediction and function prediction. Various model-based topology prediction methods have been developed, but the accuracy of those individual predictors remain poor due to the limitation of the methods or the features they used. Thus, the consensus topology prediction method becomes practical for high accuracy applications by combining the advances of the individual predictors. Here, based on the observation that inter-helical interactions are commonly found within the transmembrane helixes (TMHs) and strongly indicate the existence of them, we present a novel consensus topology prediction method for αTMPs, CNTOP, which incorporates four top leading individual topology predictors, and further improves the prediction accuracy by using the predicted inter-helical interactions. The method achieved 87% prediction accuracy based on a benchmark dataset and 78% accuracy based on a non-redundant dataset which is composed of polytopic αTMPs. Our method derives the highest topology accuracy than any other individual predictors and consensus predictors, at the same time, the TMHs are more accurately predicted in their length and locations, where both the false positives (FPs) and the false negatives (FNs) decreased dramatically. The CNTOP is available at: http://ccst.jlu.edu.cn/JCSB/cntop/CNTOP.html. Copyright © 2012 Elsevier B.V. All rights reserved.

Using Subjective and Objective Measures to Predict Level of Reading Fluency at the End of First Grade

ERIC Educational Resources Information Center

Morris, Darrell; Pennell, Ashley M.; Perney, Jan; Trathen, Woodrow

2018-01-01

This study compared reading rate to reading fluency (as measured by a rating scale). After listening to first graders read short passages, we assigned an overall fluency rating (low, average, or high) to each reading. We then used predictive discriminant analyses to determine which of five measures--accuracy, rate (objective); accuracy, phrasing,…

Effects of mora deletion, nonword repetition, rapid naming, and visual search performance on beginning reading in Japanese.

PubMed

Kobayashi, Maya Shiho; Haynes, Charles W; Macaruso, Paul; Hook, Pamela E; Kato, Junko

2005-06-01

This study examined the extent to which mora deletion (phonological analysis), nonword repetition (phonological memory), rapid automatized naming (RAN), and visual search abilities predict reading in Japanese kindergartners and first graders. Analogous abilities have been identified as important predictors of reading skills in alphabetic languages like English. In contrast to English, which is based on grapheme-phoneme relationships, the primary components of Japanese orthography are two syllabaries-hiragana and katakana (collectively termed "kana")-and a system of morphosyllabic symbols (kanji). Three RAN tasks (numbers, objects, syllabary symbols [hiragana]) were used with kindergartners, with an additional kanji RAN task included for first graders. Reading measures included accuracy and speed of passage reading for kindergartners and first graders, and reading comprehension for first graders. In kindergartners, hiragana RAN and number RAN were the only significant predictors of reading accuracy and speed. In first graders, kanji RAN and hiragana RAN predicted reading speed, whereas accuracy was predicted by mora deletion. Reading comprehension was predicted by kanji RAN, mora deletion, and nonword repetition. Although number RAN did not contribute unique variance to any reading measure, it correlated highly with kanji RAN. Implications of these findings for research and practice are discussed.

Reading and writing skills in young adults with spina bifida and hydrocephalus.

PubMed

Barnes, Marcia; Dennis, Maureen; Hetherington, Ross

2004-09-01

Reading and writing were studied in 31 young adults with spina bifida and hydrocephalus (SBH). Like children with this condition, young adults with SBH had better word decoding than reading comprehension, and, compared to population means, had lower scores on a test of writing fluency. Reading comprehension was predicted by word decoding and listening comprehension. Writing was predicted by fine motor finger function, verbal intelligence, and short-term and working memory. These findings are consistent with cognitive models of reading and writing. Writing, but not reading, was related to highest level of education achieved and writing fluency predicted several aspects of functional independence. Reading comprehension and writing remain deficient in adults with SBH and have consequences for educational attainments and functional independence.

Cloning and bioinformatics analysis of PDC genes from Hylocereus undatus

NASA Astrophysics Data System (ADS)

Wu, Yunli; Luo, Xian; Lu, Han; Shen, Yu; Yuan, Lei; Luo, Lan

2018-04-01

The cDNA of PDC1 and PDC2 were amplified from the seedling of Hylocereus undatus `Guangming 2' by the technique of RACE (rapid amplification of cDNA ends). The PDC1 and PDC2 had a length of 1191bp and 2046 bp, and an open reading frame that encoded a protein of 351 and 604 amino acids, respectively. PDC1 was similar to PDC2 in motif and domain, which indicated that the two protein was relatively conserved to some extent. The 3D structure prediction showed that both of the two proteins of PDC1 and PDC2 were homotetramers. Amino acid sequence comparisons suggested that PDC1 had high identity with Chenopodium quinoa PDC1 (88% identity), PDC2 had high identity with Beta vulgaris PDC2 (84% identity).

Characterisation of a novel enterobacteria phage, CAjan, isolated from rat faeces.

PubMed

Carstens, Alexander B; Kot, Witold; Lametsch, Rene; Neve, Horst; Hansen, Lars H

2016-08-01

In this study, we describe the isolation and characterisation of the novel enterobacteria phage CAjan. This phage belongs to the order Caudovirales and the family Siphoviridae. The phage possesses a linear, double-stranded DNA genome consisting of 59,670 bp with a G+C content of 44.7 % and 91 predicted open reading frames (ORFs). Putative functions were assigned to 39 of the ORFs (37.4 %). The phage structural genes were furthermore functionally characterised by LC MS/MS. CAjan, together with Escherichia phage Seurat and Escherichia phage slur01, represent a novel and genetically distinct clade of Siphoviridae phages that could be considered to constitute a new phage genus. Despite limited sequence similarity, the phages in this group share a number of other common features, including genome structure and the presence of queuosine biosynthesis genes.

Molecular characterization and expression of the M6 gene of grass carp hemorrhage virus (GCHV), an aquareovirus.

PubMed

Qiu, T; Lu, R H; Zhang, J; Zhu, Z Y

2001-07-01

The complete nucleotide sequence of M6 gene of grass carp hemorrhage virus (GCHV) was determined. It is 2039 nucleotides in length and contains a single large open reading frame that could encode a protein of 648 amino acids with predicted molecular mass of 68.7 kDa. Amino acid sequence comparison revealed that the protein encoded by GCHV M6 is closely related to the protein mu1 of mammalian reovirus. The M6 gene, encoding the major outer-capsid protein, was expressed using the pET fusion protein vector in Escherichia coli and detected by Western blotting using chicken anti-GCHV immunoglobulin (IgY). The result indicates that the protein encoded by M6 may share a putative Asn-42-Pro-43 proteolytic cleavage site with mu1.

Complete genomic sequence of the Lactobacillus temperate phage LF1.

PubMed

Yoon, Bo Hyun; Chang, Hyo Ihl

2011-10-01

Bacteriophage LF1, a newly isolated temperate phage from a mitomycin-C-induced lysate of wild type Lactobacillus fermentum, was found to contain a double-strand DNA of 42,606 base pairs (bp) with a G+C content of 45%. Bioinformatic analysis of the phage genome revealed 57 putative open reading frames (ORFs). The predicted protein products of ORFs were determined and described. According to morphological analysis by transmission electron microscopy (TEM), LF1 has an isometric head and a non-contractile tail, indicating that it belongs to the family Siphoviridae. The temperate phage LF1 has a good genetic mosaic relationship with ΦPYB5 in the packaging module. To our knowledge, this is first report of genomic sequencing and characterization of temperate phage LF1 from wild-type L. fermentum isolated from Kimchi in Korea.

Neural evidence for description dependent reward processing in the framing effect

PubMed Central

Yu, Rongjun; Zhang, Ping

2014-01-01

Human decision making can be influenced by emotionally valenced contexts, known as the framing effect. We used event-related brain potentials to investigate how framing influences the encoding of reward. We found that the feedback related negativity (FRN), which indexes the “worse than expected” negative prediction error in the anterior cingulate cortex (ACC), was more negative for the negative frame than for the positive frame in the win domain. Consistent with previous findings that the FRN is not sensitive to “better than expected” positive prediction error, the FRN did not differentiate the positive and negative frame in the loss domain. Our results provide neural evidence that the description invariance principle which states that reward representation and decision making are not influenced by how options are presented is violated in the framing effect. PMID:24733998

Framing From Experience: Cognitive Processes and Predictions of Risky Choice.

PubMed

Gonzalez, Cleotilde; Mehlhorn, Katja

2016-07-01

A framing bias shows risk aversion in problems framed as "gains" and risk seeking in problems framed as "losses," even when these are objectively equivalent and probabilities and outcomes values are explicitly provided. We test this framing bias in situations where decision makers rely on their own experience, sampling the problem's options (safe and risky) and seeing the outcomes before making a choice. In Experiment 1, we replicate the framing bias in description-based decisions and find risk indifference in gains and losses in experience-based decisions. Predictions of an Instance-Based Learning model suggest that objective probabilities as well as the number of samples taken are factors that contribute to the lack of framing effect. We test these two factors in Experiment 2 and find no framing effect when a few samples are taken but when large samples are taken, the framing effect appears regardless of the objective probability values. Implications of behavioral results and cognitive modeling are discussed. Copyright © 2015 Cognitive Science Society, Inc.

Predicting reading ability in teenagers who are deaf or hard of hearing: A longitudinal analysis of language and reading.

PubMed

Worsfold, Sarah; Mahon, Merle; Pimperton, Hannah; Stevenson, Jim; Kennedy, Colin

2018-06-01

Deaf and hard of hearing (D/HH) children and young people are known to show group-level deficits in spoken language and reading abilities relative to their hearing peers. However, there is little evidence on the longitudinal predictive relationships between language and reading in this population. To determine the extent to which differences in spoken language ability in childhood predict reading ability in D/HH adolescents. and procedures: Participants were drawn from a population-based cohort study and comprised 53 D/HH teenagers, who used spoken language, and a comparison group of 38 normally hearing teenagers. All had completed standardised measures of spoken language (expression and comprehension) and reading (accuracy and comprehension) at 6-10 and 13-19 years of age. and results: Forced entry stepwise regression showed that, after taking reading ability at age 8 years into account, language scores at age 8 years did not add significantly to the prediction of Reading Accuracy z-scores at age 17 years (change in R 2  = 0.01, p = .459) but did make a significant contribution to the prediction of Reading Comprehension z-scores at age 17 years (change in R 2  = 0.17, p < .001). and implications: In D/HH individuals who are spoken language users, expressive and receptive language skills in middle childhood predict reading comprehension ability in adolescence. Continued intervention to support language development beyond primary school has the potential to benefit reading comprehension and hence educational access for D/HH adolescents. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

PubMed

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.

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences

PubMed Central

Reinhardt, Josephine A.; Wanjiru, Betty M.; Brant, Alicia T.; Saelao, Perot; Begun, David J.; Jones, Corbin D.

2013-01-01

How non-coding DNA gives rise to new protein-coding genes (de novo genes) is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs), while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important. PMID:24146629

Identification and Cloning of gusA, Encoding a New β-Glucuronidase from Lactobacillus gasseri ADH†

PubMed Central

Russell, W. M.; Klaenhammer, T. R.

2001-01-01

The gusA gene, encoding a new β-glucuronidase enzyme, has been cloned from Lactobacillus gasseri ADH. This is the first report of a β-glucuronidase gene cloned from a bacterial source other than Escherichia coli. A plasmid library of L. gasseri chromosomal DNA was screened for complementation of an E. coli gus mutant. Two overlapping clones that restored β-glucuronidase activity in the mutant strain were sequenced and revealed three complete and two partial open reading frames. The largest open reading frame, spanning 1,797 bp, encodes a 597-amino-acid protein that shows 39% identity to β-glucuronidase (GusA) of E. coli K-12 (EC 3.2.1.31). The other two complete open reading frames, which are arranged to be separately transcribed, encode a putative bile salt hydrolase and a putative protein of unknown function with similarities to MerR-type regulatory proteins. Overexpression of GusA was achieved in a β-glucuronidase-negative L. gasseri strain by expressing the gusA gene, subcloned onto a low-copy-number shuttle vector, from the strong Lactobacillus P6 promoter. GusA was also expressed in E. coli from a pET expression system. Preliminary characterization of the GusA protein from crude cell extracts revealed that the enzyme was active across an acidic pH range and a broad temperature range. An analysis of other lactobacilli identified β-glucuronidase activity and gusA homologs in other L. gasseri isolates but not in other Lactobacillus species tested. PMID:11229918

Internet Video Telephony Allows Speech Reading by Deaf Individuals and Improves Speech Perception by Cochlear Implant Users

PubMed Central

Mantokoudis, Georgios; Dähler, Claudia; Dubach, Patrick; Kompis, Martin; Caversaccio, Marco D.; Senn, Pascal

2013-01-01

Objective To analyze speech reading through Internet video calls by profoundly hearing-impaired individuals and cochlear implant (CI) users. Methods Speech reading skills of 14 deaf adults and 21 CI users were assessed using the Hochmair Schulz Moser (HSM) sentence test. We presented video simulations using different video resolutions (1280×720, 640×480, 320×240, 160×120 px), frame rates (30, 20, 10, 7, 5 frames per second (fps)), speech velocities (three different speakers), webcameras (Logitech Pro9000, C600 and C500) and image/sound delays (0–500 ms). All video simulations were presented with and without sound and in two screen sizes. Additionally, scores for live Skype™ video connection and live face-to-face communication were assessed. Results Higher frame rate (>7 fps), higher camera resolution (>640×480 px) and shorter picture/sound delay (<100 ms) were associated with increased speech perception scores. Scores were strongly dependent on the speaker but were not influenced by physical properties of the camera optics or the full screen mode. There is a significant median gain of +8.5%pts (p = 0.009) in speech perception for all 21 CI-users if visual cues are additionally shown. CI users with poor open set speech perception scores (n = 11) showed the greatest benefit under combined audio-visual presentation (median speech perception +11.8%pts, p = 0.032). Conclusion Webcameras have the potential to improve telecommunication of hearing-impaired individuals. PMID:23359119

Identification of a second PAD1 in Brettanomyces bruxellensis LAMAP2480.

PubMed

González, Camila; Godoy, Liliana; Ganga, Ma Angélica

2017-02-01

Volatile phenols are aromatic compounds produced by some yeasts of the genus Brettanomyces as defense against the toxicity of hydroxycinnamic acids (p-coumaric acid, ferulic acid and caffeic acid). The origin of these compounds in winemaking involves the sequential action of two enzymes: coumarate decarboxylase and vinylphenol reductase. The first one converts hydroxycinnamic acids into hydroxystyrenes, which are then reduced to ethyl derivatives by vinylphenol reductase. Volatile phenols derived from p-coumaric acid (4-vinylphenol and 4-ethylphenol) have been described as the major contributors to self-defeating aromas associated with stable, gouache, wet mouse, etc., which generates large economic losses in the wine industry. The gene responsible for the production of 4-vinylphenol from p-coumaric acid has been identified as PAD1, which encodes a phenylacrylic acid decarboxylase. PAD1 has been described for many species, among them Candida albicans, Candida dubliniensis, Debaryomyces hansenii and Pichia anomala. In Brettanomyces bruxellensis LAMAP2480, a 666 bp reading frame (DbPAD) encodes a coumarate decarboxylase. Recent studies have reported the existence of a new reading frame belonging to DbPAD called DbPAD2 of 531 bp, which could encode a protein with similar enzymatic activity to PAD1. The present study confirmed that the transformation of Saccharomyces cerevisiae strain BY4722 with reading frame DbPAD2 under the control of the B. bruxellensis ACT1 promoter, encodes an enzyme with coumarate decarboxylase activity. This work has provided deeper insight into the origin of aroma defects in wine due to contamination by Brettanomyces spp.

Predicting True Reading Gains After Remedial Tutoring.

ERIC Educational Resources Information Center

Dahlke, Anita B.

Using selected student variables, an attempt was made to predict retarded readers' true reading gains after remedial tutoring. The independent variables consisted of IQ and subtest scores obtained on the Wechsler Intelligence Scale for Children (WISC), pretutoring reading levels on the individually administered Diagnostic Reading Scales test, age,…

Predicting Word Reading Ability: A Quantile Regression Study

ERIC Educational Resources Information Center

McIlraith, Autumn L.

2018-01-01

Predictors of early word reading are well established. However, it is unclear if these predictors hold for readers across a range of word reading abilities. This study used quantile regression to investigate predictive relationships at different points in the distribution of word reading. Quantile regression analyses used preschool and…

Accuracy of the DIBELS Oral Reading Fluency Measure for Predicting Third Grade Reading Comprehension Outcomes

ERIC Educational Resources Information Center

Roehrig, Alysia D.; Petscher, Yaacov; Nettles, Stephen M.; Hudson, Roxanne F.; Torgesen, Joseph K.

2008-01-01

We evaluated the validity of DIBELS ("Dynamic Indicators of Basic Early Literacy Skills") ORF ("Oral Reading Fluency") for predicting performance on the "Florida Comprehensive Assessment Test" (FCAT-SSS) and "Stanford Achievement Test" (SAT-10) reading comprehension measures. The usefulness of previously…

Reaction Time Variability Associated with Reading Skills in Poor Readers with ADHD

PubMed Central

Tamm, Leanne; Epstein, Jeffery N.; Denton, Carolyn A.; Vaughn, Aaron J.; Peugh, James; Willcutt, Erik G.

2014-01-01

Objective Linkages between neuropsychological functioning (i.e., response inhibition, processing speed, reaction time variability) and word reading have been documented among children with Attention-Deficit/Hyperactivity Disorder (ADHD) and children with Reading Disorders. However, associations between neuropsychological functioning and other aspects of reading (i.e., fluency, comprehension) have not been well-documented among children with comorbid ADHD and Reading Disorder. Method Children with ADHD and poor word reading (i.e., ≤25th percentile) completed a stop signal task (SST) and tests of word reading, reading fluency, and reading comprehension. Multivariate multiple regression was conducted predicting the reading skills from SST variables [i.e., mean reaction time (MRT), reaction time standard deviation (SDRT), and stop signal reaction time (SSRT)]. Results SDRT predicted word reading, reading fluency, and reading comprehension. MRT and SSRT were not associated with any reading skill. After including word reading in models predicting reading fluency and reading comprehension, the effects of SDRT were minimized. Discussion Reaction time variability (i.e., SDRT) reflects impairments in information processing and failure to maintain executive control. The pattern of results from this study suggest SDRT exerts its effects on reading fluency and reading comprehension through its effect on word reading (i.e., decoding) and that this relation may be related to observed deficits in higher-level elements of reading. PMID:24528537

Effective or ineffective: attribute framing and the human papillomavirus (HPV) vaccine.

PubMed

Bigman, Cabral A; Cappella, Joseph N; Hornik, Robert C

2010-12-01

To experimentally test whether presenting logically equivalent, but differently valenced effectiveness information (i.e. attribute framing) affects perceived effectiveness of the human papillomavirus (HPV) vaccine, vaccine-related intentions and policy opinions. A survey-based experiment (N=334) was fielded in August and September 2007 as part of a larger ongoing web-enabled monthly survey, the Annenberg National Health Communication Survey. Participants were randomly assigned to read a short passage about the HPV vaccine that framed vaccine effectiveness information in one of five ways. Afterward, they rated the vaccine and related opinion questions. Main statistical methods included ANOVA and t-tests. On average, respondents exposed to positive framing (70% effective) rated the HPV vaccine as more effective and were more supportive of vaccine mandate policy than those exposed to the negative frame (30% ineffective) or the control frame. Mixed valence frames showed some evidence for order effects; phrasing that ended by emphasizing vaccine ineffectiveness showed similar vaccine ratings to the negative frame. The experiment finds that logically equivalent information about vaccine effectiveness not only influences perceived effectiveness, but can in some cases influence support for policies mandating vaccine use. These framing effects should be considered when designing messages. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Effective or ineffective: Attribute framing and the human papillomavirus (HPV) vaccine

PubMed Central

Bigman, Cabral A.; Cappella, Joseph N.; Hornik, Robert C.

2010-01-01

Objectives To experimentally test whether presenting logically equivalent, but differently valenced effectiveness information (i.e. attribute framing) affects perceived effectiveness of the human papillomavirus (HPV) vaccine, vaccine related intentions and policy opinions. Method A survey-based experiment (N= 334) was fielded in August and September 2007 as part of a larger ongoing web-enabled monthly survey, the Annenberg National Health Communication Survey. Participants were randomly assigned to read a short passage about the HPV vaccine that framed vaccine effectiveness information in one of five ways. Afterward, they rated the vaccine and related opinion questions. Main statistical methods included ANOVA and t-tests. Results On average, respondents exposed to positive framing (70% effective) rated the HPV vaccine as more effective and were more supportive of vaccine mandate policy than those exposed to the negative frame (30% ineffective) or the control frame. Mixed valence frames showed some evidence for order effects; phrasing that ended by emphasizing vaccine ineffectiveness showed similar vaccine ratings to the negative frame. Conclusions The experiment finds that logically equivalent information about vaccine effectiveness not only influences perceived effectiveness, but can in some cases influence support for policies mandating vaccine use. Practice implications These framing effects should be considered when designing messages. PMID:20851560

A spatial reference frame model of Beijing based on spatial cognitive experiment

NASA Astrophysics Data System (ADS)

Zhang, Jie; Zhang, Jing; Liu, Yu

2006-10-01

Orientation relation in the spatial relation is very important in GIS. People can obtain orientation information by making use of map reading and the cognition of the surrounding environment, and then create the spatial reference frame. City is a kind of special spatial environment, a person with life experiences has some spatial knowledge about the city where he or she lives in. Based on the spatial knowledge of the city environment, people can position, navigate and understand the meaning embodied in the environment correctly. Beijing as a real geographic space, its layout is very special and can form a kind of new spatial reference frame. Based on the characteristics of the layout of Beijing city, this paper will introduce a new spatial reference frame of Beijing and use two psychological experiments to validate its cognitive plausibility.

Does message framing predict willingness to participate in a hypothetical HIV vaccine trial: an application of Prospect Theory.

PubMed

Evangeli, Michael; Kafaar, Zuhayr; Kagee, Ashraf; Swartz, Leslie; Bullemor-Day, Philippa

2013-01-01

It is vital that enough participants are willing to participate in clinical trials to test HIV vaccines adequately. It is, therefore, necessary to explore what affects peoples' willingness to participate (WTP) in such trials. Studies have only examined individual factors associated with WTP and not the effect of messages about trial participation on potential participants (e.g., whether losses or gains are emphasized, or whether the outcome is certain or uncertain). This study explores whether the effects of message framing on WTP in a hypothetical HIV vaccine trial are consistent with Prospect Theory. This theory suggests that people are fundamentally risk averse and that (1) under conditions of low risk and high certainty, gain-framed messages will be influential (2) under conditions of high risk and low certainty, loss-framed messages will be influential. This cross-sectional study recruited 283 HIV-negative students from a South African university who were given a questionnaire that contained matched certain gain-framed, certain loss-framed, uncertain gain-framed, and uncertain loss-framed statements based on common barriers and facilitators of WTP. Participants were asked to rate how likely each statement was to result in their participation in a hypothetical preventative HIV vaccine trial. Consistent with Prospect Theory predictions, for certain outcomes, gain-framed messages were more likely to result in WTP than loss-framed messages. Inconsistent with predictions, loss-framed message were not more likely to be related to WTP for uncertain outcomes than gain-framed messages. Older students were less likely to express their WTP across the different message frames. Recruitment for HIV vaccine trials should pay attention to how messages about the trial are presented to potential participants.

Predicting reading and mathematics from neural activity for feedback learning.

PubMed

Peters, Sabine; Van der Meulen, Mara; Zanolie, Kiki; Crone, Eveline A

2017-01-01

Although many studies use feedback learning paradigms to study the process of learning in laboratory settings, little is known about their relevance for real-world learning settings such as school. In a large developmental sample (N = 228, 8-25 years), we investigated whether performance and neural activity during a feedback learning task predicted reading and mathematics performance 2 years later. The results indicated that feedback learning performance predicted both reading and mathematics performance. Activity during feedback learning in left superior dorsolateral prefrontal cortex (DLPFC) predicted reading performance, whereas activity in presupplementary motor area/anterior cingulate cortex (pre-SMA/ACC) predicted mathematical performance. Moreover, left superior DLPFC and pre-SMA/ACC activity predicted unique variance in reading and mathematics ability over behavioral testing of feedback learning performance alone. These results provide valuable insights into the relationship between laboratory-based learning tasks and learning in school settings, and the value of neural assessments for prediction of school performance over behavioral testing alone. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Can Curriculum-Embedded Measures Predict the Later Reading Achievement of Kindergarteners at Risk of Reading Disability?

ERIC Educational Resources Information Center

Oslund, Eric L.; Simmons, Deborah C.; Hagan-Burke, Shanna; Kwok, Oi-Man; Simmons, Leslie E.; Taylor, Aaron B.; Coyne, Michael D.

2015-01-01

This study examined the changing role and longitudinal predictive validity of curriculum-embedded progress-monitoring measures (CEMs ) for kindergarten students receiving Tier 2 intervention and identified as at risk of developing reading difficulties. Multiple measures were examined to determine whether they could predict comprehensive latent…

Phylogenetic tree construction using trinucleotide usage profile (TUP).

PubMed

Chen, Si; Deng, Lih-Yuan; Bowman, Dale; Shiau, Jyh-Jen Horng; Wong, Tit-Yee; Madahian, Behrouz; Lu, Henry Horng-Shing

2016-10-06

It has been a challenging task to build a genome-wide phylogenetic tree for a large group of species containing a large number of genes with long nucleotides sequences. The most popular method, called feature frequency profile (FFP-k), finds the frequency distribution for all words of certain length k over the whole genome sequence using (overlapping) windows of the same length. For a satisfactory result, the recommended word length (k) ranges from 6 to 15 and it may not be a multiple of 3 (codon length). The total number of possible words needed for FFP-k can range from 4 6 =4096 to 4 15 . We propose a simple improvement over the popular FFP method using only a typical word length of 3. A new method, called Trinucleotide Usage Profile (TUP), is proposed based only on the (relative) frequency distribution using non-overlapping windows of length 3. The total number of possible words needed for TUP is 4 3 =64, which is much less than the total count for the recommended optimal "resolution" for FFP. To build a phylogenetic tree, we propose first representing each of the species by a TUP vector and then using an appropriate distance measure between pairs of the TUP vectors for the tree construction. In particular, we propose summarizing a DNA sequence by a matrix of three rows corresponding to three reading frames, recording the frequency distribution of the non-overlapping words of length 3 in each of the reading frame. We also provide a numerical measure for comparing trees constructed with various methods. Compared to the FFP method, our empirical study showed that the proposed TUP method is more capable of building phylogenetic trees with a stronger biological support. We further provide some justifications on this from the information theory viewpoint. Unlike the FFP method, the TUP method takes the advantage that the starting of the first reading frame is (usually) known. Without this information, the FFP method could only rely on the frequency distribution of overlapping words, which is the average (or mixture) of the frequency distributions of three possible reading frames. Consequently, we show (from the entropy viewpoint) that the FFP procedure could dilute important gene information and therefore provides less accurate classification.

High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps.

PubMed

Georges, Arthur; Li, Qiye; Lian, Jinmin; O'Meally, Denis; Deakin, Janine; Wang, Zongji; Zhang, Pei; Fujita, Matthew; Patel, Hardip R; Holleley, Clare E; Zhou, Yang; Zhang, Xiuwen; Matsubara, Kazumi; Waters, Paul; Graves, Jennifer A Marshall; Sarre, Stephen D; Zhang, Guojie

2015-01-01

The lizards of the family Agamidae are one of the most prominent elements of the Australian reptile fauna. Here, we present a genomic resource built on the basis of a wild-caught male ZZ central bearded dragon Pogona vitticeps. The genomic sequence for P. vitticeps, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (179X raw read depth) from 13 insert libraries ranging from 250 bp to 40 kbp. After filtering for low-quality and duplicated reads, 146 Gbp of data (83X) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % of single nucleotide polymorphisms plus sequence insertions or deletions) complicated assembly; nevertheless, 96.4 % of reads mapped back to the assembled scaffolds, indicating that the assembly included most of the sequenced genome. Length of the assembly was 1.8 Gbp in 545,310 scaffolds (69,852 longer than 300 bp), the longest being 14.68 Mbp. N50 was 2.29 Mbp. Genes were annotated on the basis of de novo prediction, similarity to the green anole Anolis carolinensis, Gallus gallus and Homo sapiens proteins, and P. vitticeps transcriptome sequence assemblies, to yield 19,406 protein-coding genes in the assembly, 63 % of which had intact open reading frames. Our assembly captured 99 % (246 of 248) of core CEGMA genes, with 93 % (231) being complete. The quality of the P. vitticeps assembly is comparable or superior to that of other published squamate genomes, and the annotated P. vitticeps genome can be accessed through a genome browser available at https://genomics.canberra.edu.au.

FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions

PubMed Central

Li, Hui; Xiao, Li; Zhang, Lili; Wu, Jiarui; Wei, Bin; Sun, Ninghui; Zhao, Yi

2018-01-01

smORFs are small open reading frames of less than 100 codons. Recent low throughput experiments showed a lot of smORF-encoded peptides (SEPs) played crucial rule in processes such as regulation of transcription or translation, transportation through membranes and the antimicrobial activity. In order to gather more functional SEPs, it is necessary to have access to genome-wide prediction tools to give profound directions for low throughput experiments. In this study, we put forward a functional smORF-encoded peptides predictor (FSPP) which tended to predict authentic SEPs and their functions in a high throughput method. FSPP used the overlap of detected SEPs from Ribo-seq and mass spectrometry as target objects. With the expression data on transcription and translation levels, FSPP built two co-expression networks. Combing co-location relations, FSPP constructed a compound network and then annotated SEPs with functions of adjacent nodes. Tested on 38 sequenced samples of 5 human cell lines, FSPP successfully predicted 856 out of 960 annotated proteins. Interestingly, FSPP also highlighted 568 functional SEPs from these samples. After comparison, the roles predicted by FSPP were consistent with known functions. These results suggest that FSPP is a reliable tool for the identification of functional small peptides. FSPP source code can be acquired at https://www.bioinfo.org/FSPP. PMID:29675032

Constructing Literacy in the Kindergarten: Task Structure, Collaboration, and Motivation

PubMed Central

Nolen, Susan Bobbitt

2009-01-01

This ethnographic study explores kindergarten children’s emergent motivation to read and write, its relation to their developing concepts of reading and writing (Guice & Johnston, 1994; Johnston, 1997; Turner, 1995), and to their teachers instructional goals and classroom norms. Teachers and students together constructed legitimate literate activity in their classrooms, and this construction framed the motivation of students who were at risk for developing learning disabilities in reading and writing. Specifically, the kinds of reading and writing activity that were sanctioned in each class and the role of student–student collaboration colored students’ views of the purposes of literacy and their own ability to learn. Findings extend our understanding of how young children’s literacy motivation influences, and is influenced by, their classroom literacy culture. Implications for early literacy instruction for children with learning disabilities, and for their continuing motivation to read and write, are discussed. PMID:19727336

RAN as a predictor of reading skills, and vice versa: results from a randomised reading intervention.

PubMed

Wolff, Ulrika

2014-07-01

Although phonemic awareness is a well-known factor predicting early reading development, there is also evidence that Rapid Automatized Naming (RAN) is an independent factor that contributes to early reading. The aim of this study is to examine phonemic awareness and RAN as predictors of reading speed, reading comprehension and spelling for children with reading difficulties. It also investigates a possible reciprocal relationship between RAN and reading skills, and the possibility of enhancing RAN by intervention. These issues are addressed by examining longitudinal data from a randomised reading intervention study carried out in Sweden for 9-year-old children with reading difficulties (N = 112). The intervention comprised three main elements: training of phonics, reading comprehension strategies and reading speed. The analysis of the data was carried out using structural equation modelling. The results demonstrated that after controlling for autoregressive effects and non-verbal IQ, RAN predicts reading speed whereas phonemic awareness predicts reading comprehension and spelling. RAN was significantly enhanced by training and a reciprocal relationship between reading speed and RAN was found. These findings contribute to support the view that both phonemic awareness and RAN independently influence early phases of reading, and that both are possible to enhance by training.

Effects of news frames on perceived risk, emotions, and learning.

PubMed

Otieno, Christine; Spada, Hans; Renkl, Alexander

2013-01-01

The media play a key role in forming opinions by influencing people´s understanding and perception of a topic. People gather information about topics of interest from the internet and print media, which employ various news frames to attract attention. One example of a common news frame is the human-interest frame, which emotionalizes and dramatizes information and often accentuates individual affectedness. Our study investigated effects of human-interest frames compared to a neutral-text condition with respect to perceived risk, emotions, and knowledge acquisition, and tested whether these effects can be "generalized" to common variants of the human-interest frame. Ninety-one participants read either one variant of the human-interest frame or a neutrally formulated version of a newspaper article describing the effects of invasive species in general and the Asian ladybug (an invasive species) in particular. The framing was achieved by varying the opening and concluding paragraphs (about invasive species), as well as the headline. The core text (about the Asian ladybug) was the same across all conditions. All outcome variables on framing effects referred to this common core text. We found that all versions of the human-interest frame increased perceived risk and the strength of negative emotions compared to the neutral text. Furthermore, participants in the human-interest frame condition displayed better (quantitative) learning outcomes but also biased knowledge, highlighting a potential dilemma: Human-interest frames may increase learning, but they also lead to a rather unbalanced view of the given topic on a "deeper level".

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

PubMed Central

2013-01-01

We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS. PMID:23320958

The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses

PubMed Central

Michel, Christian J.

2017-01-01

In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses. The method was based on the preferential occurrence of trinucleotides among the three frames at the gene population level. We extend here this definition at the gene level. This new statistical approach considers all the genes, i.e., of large and small lengths, with the same weight for searching the circular code X. As a consequence, the concept of circular code, in particular the reading frame retrieval, is directly associated to each gene. At the gene level, the circular code X is strengthened in the genes of bacteria, eukaryotes, plasmids, and viruses, and is now also identified in the genes of archaea. The genes of mitochondria and chloroplasts contain a subset of the circular code X. Finally, by studying viral genes, the circular code X was found in DNA genomes, RNA genomes, double-stranded genomes, and single-stranded genomes. PMID:28420220

Predicting Reading Growth with Event-Related Potentials: Thinking Differently about Indexing “Responsiveness”

PubMed Central

Lemons, Christopher J.; Key, Alexandra P.F.; Fuchs, Douglas; Yoder, Paul J.; Fuchs, Lynn S.; Compton, Donald L.; Williams, Susan M.; Bouton, Bobette

2009-01-01

The purpose of this study was to determine if event-related potential (ERP) data collected during three reading-related tasks (Letter Sound Matching, Nonword Rhyming, and Nonword Reading) could be used to predict short-term reading growth on a curriculum-based measure of word identification fluency over 19 weeks in a sample of 29 first-grade children. Results indicate that ERP responses to the Letter Sound Matching task were predictive of reading change and remained so after controlling for two previously validated behavioral predictors of reading, Rapid Letter Naming and Segmenting. ERP data for the other tasks were not correlated with reading change. The potential for cognitive neuroscience to enhance current methods of indexing responsiveness in a response-to-intervention (RTI) model is discussed. PMID:20514353

Unique Contributions of Maternal Reading Proficiency to Predicting Children's Preschool Receptive Vocabulary and Reading Proficiency

ERIC Educational Resources Information Center

Phillips, Linda M.; Norris, Stephen P.; Hayward, Denyse V.; Lovell, Meridith A.

2017-01-01

This study investigated whether mothers' measured reading proficiency and their educational level predict, over and above each other, their children's receptive vocabulary and reading proficiency when confounding factors of speaking a minority language, ethnicity, number of children in the family, and marital and employment status are controlled.…

Predicting Word Reading and Comprehension with Executive Function and Speed Measures across Development: A Latent Variable Analysis

ERIC Educational Resources Information Center

Christopher, Micaela E.; Miyake, Akira; Keenan, Janice M.; Pennington, Bruce; DeFries, John C.; Wadsworth, Sally J.; Willcutt, Erik; Olson, Richard K.

2012-01-01

The present study explored whether different executive control and speed measures (working memory, inhibition, processing speed, and naming speed) independently predict individual differences in word reading and reading comprehension. Although previous studies suggest these cognitive constructs are important for reading, the authors analyze the…

Relations Among Student Attention Behaviors, Teacher Practices, and Beginning Word Reading Skill

PubMed Central

Sáez, Leilani; Folsom, Jessica Sidler; Al Otaiba, Stephanie; Schatschneider, Christopher

2011-01-01

The role of student attention for predicting kindergarten word reading was investigated among 432 students. Using SWAN behavior rating scores, we conducted an exploratory factor analysis, which yielded three distinct factors that reflected selective attention. In this study, we focused on the role of one of these factors, which we labeled attention-memory behaviors, for predicting reading performance. Teacher ratings of attention predicted word reading above and beyond the contribution of phonological awareness and vocabulary knowledge. In addition, the relations between four teacher practices and attention ratings for predicting reading performance were examined. Using HLM, significant interactions between student attention and teacher practices observed during literacy instruction were found. In general, as ratings of attention improved, better kindergarten word reading performance was associated with high levels of classroom behavior management. However, by mid-year, better word reading performance was not associated with high levels of teacher task- orienting. A significant three-way interaction was also found among attention, individualized instruction, and teacher task re-directions. The role of regulating kindergarten student attention to support beginning word reading skill development is discussed. PMID:22207616

The Role of Metacognitive Reading Strategies, Metacognitive Study and Learning Strategies, and Behavioral Study and Learning Strategies in Predicting Academic Success in Students With and Without a History of Reading Difficulties.

PubMed

Chevalier, Thérèse M; Parrila, Rauno; Ritchie, Krista C; Deacon, S Hélène

2017-01-01

We examined the self-reported use of reading, study, and learning strategies in university students with a history of reading difficulties (HRD; n = 77) and with no history of reading difficulties (NRD; n = 295). We examined both between-groups differences in strategy use and strategy use as a predictive measure of academic success. Participants completed online questionnaires regarding reading history and strategy use. GPA and frequency of use of academic support services were also obtained for all students. University students with HRD reported a different profile of strategy use than their NRD peers, and self-reported strategy use was differentially predictive of GPA for students with HRD and NRD. For students with HRD, the use of metacognitive reading strategies and the use of study aids predicted academic success. Implications for university student services providers are discussed. © Hammill Institute on Disabilities 2015.

The Impact of Positive and Negative Affect and Issue Framing on Issue Interpretation and Risk Taking.

PubMed

Mittal; Ross

1998-12-01

Two studies examined the influence of transient affective states and issue framing on issue interpretation and risk taking within the context of strategic decision making. In Study 1, participants in whom transient positive or negative affective states were induced by reading a short story showed systematic differences in issue interpretation and risk taking in a strategic decision making context. Compared to negative mood participants, those in a positive mood were more likely to interpret the strategic issue as an opportunity and displayed lower levels of risk taking. Study 2 replicated and extended these results by crossing affective states with threat and opportunity frames. Results showed that framing an issue (as a threat or an opportunity) had a stronger impact on issue interpretation among negative affect participants than among positive affect participants. Affective states also moderated the impact of issue framing on risk taking: the effect of framing on risk-taking was stronger under negative rather than positive affect. These results are interpreted via information-processing and motivational effects of affect on a decision maker. Copyright 1998 Academic Press.

Characterization of a 512x512-pixel 8-output full-frame CCD for high-speed imaging

NASA Astrophysics Data System (ADS)

Graeve, Thorsten; Dereniak, Eustace L.

1993-01-01

The characterization of a 512 by 512 pixel, eight-output full frame CCD manufactured by English Electric Valve under part number CCD13 is discussed. This device is a high- resolution Silicon-based array designed for visible imaging applications at readout periods as low as two milliseconds. The characterization of the device includes mean-variance analysis to determine read noise and dynamic range, as well as charge transfer efficiency, MTF, and quantum efficiency measurements. Dark current and non-uniformity issues on a pixel-to-pixel basis and between individual outputs are also examined. The characterization of the device is restricted by hardware limitations to a one MHz pixel rate, corresponding to a 40 ms readout time. However, subsections of the device have been operated at up to an equivalent 100 frames per second. To maximize the frame rate, the CCD is illuminated by a synchronized strobe flash in between frame readouts. The effects of the strobe illumination on the imagery obtained from the device is discussed.

Genome-Wide Polygenic Scores Predict Reading Performance Throughout the School Years.

PubMed

Selzam, Saskia; Dale, Philip S; Wagner, Richard K; DeFries, John C; Cederlöf, Martin; O'Reilly, Paul F; Krapohl, Eva; Plomin, Robert

2017-07-04

It is now possible to create individual-specific genetic scores, called genome-wide polygenic scores (GPS). We used a GPS for years of education ( EduYears ) to predict reading performance assessed at UK National Curriculum Key Stages 1 (age 7), 2 (age 12) and 3 (age 14) and on reading tests administered at ages 7 and 12 in a UK sample of 5,825 unrelated individuals. EduYears GPS accounts for up to 5% of the variance in reading performance at age 14. GPS predictions remained significant after accounting for general cognitive ability and family socioeconomic status. Reading performance of children in the lowest and highest 12.5% of the EduYears GPS distribution differed by a mean growth in reading ability of approximately two school years. It seems certain that polygenic scores will be used to predict strengths and weaknesses in education.

Genome-Wide Polygenic Scores Predict Reading Performance Throughout the School Years

PubMed Central

Selzam, Saskia; Dale, Philip S.; Wagner, Richard K.; DeFries, John C.; Cederlöf, Martin; O’Reilly, Paul F.; Krapohl, Eva; Plomin, Robert

2017-01-01

ABSTRACT It is now possible to create individual-specific genetic scores, called genome-wide polygenic scores (GPS). We used a GPS for years of education (EduYears) to predict reading performance assessed at UK National Curriculum Key Stages 1 (age 7), 2 (age 12) and 3 (age 14) and on reading tests administered at ages 7 and 12 in a UK sample of 5,825 unrelated individuals. EduYears GPS accounts for up to 5% of the variance in reading performance at age 14. GPS predictions remained significant after accounting for general cognitive ability and family socioeconomic status. Reading performance of children in the lowest and highest 12.5% of the EduYears GPS distribution differed by a mean growth in reading ability of approximately two school years. It seems certain that polygenic scores will be used to predict strengths and weaknesses in education. PMID:28706435

Using Method of Instruction to Predict the Skills Supporting Initial Reading Development: Insight from a Synthetic Phonics Approach

ERIC Educational Resources Information Center

McGeown, Sarah P.; Medford, Emma

2014-01-01

This study examined the skills predicting early reading development when children were taught by a synthetic phonics approach. Eighty five children taught to read by systematic synthetic phonics were assessed on reading and cognitive assessments prior to reading instruction (average age 4 years, 7 months), 6 months later (5 years, 1 month), and 73…

Conversational Language Use as a Predictor of Early Reading Development: Language History as a Moderating Variable

PubMed Central

DeThorne, Laura Segebart; Petrill, Stephen A.; Schatschneider, Chris; Cutting, Laurie

2010-01-01

Purpose The present study examined the nature of concurrent and predictive associations between conversational language use and reading development during early school-age years. Method Language and reading data from 380 twins in the Western Reserve Reading Project were examined via phenotypic correlations and multilevel modeling on exploratory latent factors. Results In the concurrent prediction of children’s early reading abilities, a significant interaction emerged between children’s conversational language abilities and their history of reported language difficulties. Specifically, conversational language concurrently predicted reading development above and beyond variance accounted for by formal vocabulary scores, but only in children with a history of reported language difficulties. A similar trend was noted in predicting reading skills 1 year later, but the interaction was not statistically significant. Conclusions Findings suggest a more nuanced view of the association between spoken language and early reading than is commonly proposed. One possibility is that children with and without a history of reported language difficulties rely on different skills, or the same skills to differing degrees, when completing early reading-related tasks. Future studies should examine the causal link between conversational language and early reading specifically in children with a history of reported language difficulties. PMID:20150410

The Role of Visual Processing Speed in Reading Speed Development

PubMed Central

Lobier, Muriel; Dubois, Matthieu; Valdois, Sylviane

2013-01-01

A steady increase in reading speed is the hallmark of normal reading acquisition. However, little is known of the influence of visual attention capacity on children's reading speed. The number of distinct visual elements that can be simultaneously processed at a glance (dubbed the visual attention span), predicts single-word reading speed in both normal reading and dyslexic children. However, the exact processes that account for the relationship between the visual attention span and reading speed remain to be specified. We used the Theory of Visual Attention to estimate visual processing speed and visual short-term memory capacity from a multiple letter report task in eight and nine year old children. The visual attention span and text reading speed were also assessed. Results showed that visual processing speed and visual short term memory capacity predicted the visual attention span. Furthermore, visual processing speed predicted reading speed, but visual short term memory capacity did not. Finally, the visual attention span mediated the effect of visual processing speed on reading speed. These results suggest that visual attention capacity could constrain reading speed in elementary school children. PMID:23593117

The role of visual processing speed in reading speed development.

PubMed

Lobier, Muriel; Dubois, Matthieu; Valdois, Sylviane

2013-01-01

A steady increase in reading speed is the hallmark of normal reading acquisition. However, little is known of the influence of visual attention capacity on children's reading speed. The number of distinct visual elements that can be simultaneously processed at a glance (dubbed the visual attention span), predicts single-word reading speed in both normal reading and dyslexic children. However, the exact processes that account for the relationship between the visual attention span and reading speed remain to be specified. We used the Theory of Visual Attention to estimate visual processing speed and visual short-term memory capacity from a multiple letter report task in eight and nine year old children. The visual attention span and text reading speed were also assessed. Results showed that visual processing speed and visual short term memory capacity predicted the visual attention span. Furthermore, visual processing speed predicted reading speed, but visual short term memory capacity did not. Finally, the visual attention span mediated the effect of visual processing speed on reading speed. These results suggest that visual attention capacity could constrain reading speed in elementary school children.

Systematically evaluating read-across prediction and ...

EPA Pesticide Factsheets

Read-across is a popular data gap filling technique within category and analogue approaches for regulatory purposes. Acceptance of read-across remains an ongoing challenge with several efforts underway for identifying and addressing uncertainties. Here we demonstrate an algorithmic, automated approach to evaluate the utility of using in vitro bioactivity data (“bioactivity descriptors”, from EPA’s ToxCast program) in conjunction with chemical descriptor information to derive local validity domains (specific sets of nearest neighbors) to facilitate read-across for a number of in vivo repeated dose toxicity study types. Over 3400 different chemical structure descriptors were generated for a set of 976 chemicals and supplemented with the outcomes from 821 in vitro assays. The read-across prediction for a given chemical was based on the similarity weighted endpoint outcomes of its nearest neighbors. The approach enabled a performance baseline for read-across predictions of specific study outcomes to be established. Bioactivity descriptors were often found to be more predictive of in vivo toxicity outcomes than chemical descriptors or a combination of both. The approach shows promise as part of a screening assessment in the absence of prior knowledge. Future work will investigate to what extent encoding expert knowledge leads to an improvement in read-across prediction. Read-across is a popular data gap filling technique within category and analogue approaches

The Complex World of Adolescent Literacy: Myths, Motivations, and Mysteries

PubMed Central

Moje, Elizabeth Birr; Overby, Melanie; Tysvaer, Nicole; Morris, Karen

2009-01-01

In this article, Elizabeth Birr Moje, Melanie Overby, Nicole Tysvaer, and Karen Morris challenge some of the prevailing myths about adolescents and their choices related to reading. The reading practices of youth from one urban community are examined using mixed methods in an effort to define what, how often, and why adolescents choose to read. By focusing on what features of texts youth find motivating, the authors find that reading and writing frequently occur in a range of literacy contexts outside school. However, only reading novels on a regular basis outside of school is shown to have a positive relationship to academic achievement as measured by school grades. This article describes how adolescents read texts that are embedded in social networks, allowing them to build social capital. Conclusions are framed in terms of the mysteries that remain — namely, how to build on what motivates adolescents' literacy practices in order to both promote the building of their social selves and improve their academic outcomes. PMID:19756223

Influencing health decision-making: A study of colour and message framing.

PubMed

Voss, Raymond P; Corser, Ryan; McCormick, Michael; Jasper, John D

2018-07-01

Previous research has provided evidence that colour associations and frame can influence behavioural intentions to engage in vaccination behaviours. In this study, the extension of these effects to sunscreen application behaviours was investigated. Additional colours and the manner in which colour primes were employed were also explored. Two hundred and eighty-six college students were primed with either short wavelength colours (blue/purple) or long wavelength colours (red/orange) as part of goal framed sunscreen information pamphlets. Self-reported behavioural intentions to apply sunscreen, immediate affective reaction to stimuli material, anticipated affect towards sunscreen use, and perceived efficacy of preventing skin cancer were measured. Individuals with no prior intention to use sunscreen expressed greater behavioural intentions to do so after reading a positively framed sunscreen pamphlet that was designed using short wavelength colours. The negatively framed messages and those presented in long wavelength colours did not enhance persuasion. In accordance with the Unification Theory of Framing, a match between the representations of the target behaviour, the colour prime, and the frame resulted in the greatest amount of persuasion. Creating communications with representations that match the target behaviour could be a powerful tool to increase compliance.

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

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

Long, C.M.; Rohrmann, G.F.; Merrill, G.F., E-mail: merrillg@onid.orst.ed

2009-06-05

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 involvedmore » 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.« less

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

PubMed

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

2009-06-05

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.

Characterization of the alkaline/neutral invertase gene in Dendrobium officinale and its relationship with polysaccharide accumulation.

PubMed

Gao, F; Cao, X F; Si, J P; Chen, Z Y; Duan, C L

2016-05-06

Dendrobium officinale is one of the most well-known traditional Chinese medicines, and polysaccharide is its main active ingredient. Many studies have investigated the synthesis and accumulation mechanisms of polysaccharide, but until recently, little was known about the molecular mechanism of how polysaccharide is synthesized because no related genes have been cloned. In this study, we cloned an alkaline/neutral invertase gene from D. officinale (DoNI) by the rapid amplification of cDNA ends (RACE) method. DoNI was 2231 bp long and contained an open reading frame that predicted a 62.8-kDa polypeptide with 554-amino acid residues. An alkaline/neutral invertase conserved domain was predicted from this deduced amino acid sequence, and DoNI had a similar deduced amino acid sequence to Setaria italica and Oryza brachyantha. We also found that DoNI expression in different tissues was closely related to DoNI activity, and more importantly, polysaccharide level. Our results indicate that DoNI is associated with polysaccharide accumulation in D. officinale.

The tight-adhesion proteins TadGEF of Bradyrhizobium diazoefficiens USDA 110 are involved in cell adhesion and infectivity on soybean roots.

PubMed

Mongiardini, Elías J; Parisi, Gustavo D; Quelas, Juan I; Lodeiro, Aníbal R

2016-01-01

Adhesion of symbiotic bacteria to host plants is an essential early step of the infection process that leads to the beneficial interaction. In the Bradyrhizobium diazoefficiens-soybean symbiosis few molecular determinants of adhesion are known. Here we identified the tight-adhesion gene products TadGEF in the open-reading frames blr3941-blr3943 of the B. diazoefficiens USDA 110 complete genomic sequence. Predicted structure of TadG indicates a transmembrane domain and two extracytosolic domains, from which the C-terminal has an integrin fold. TadE and TadF are also predicted as bearing transmembrane segments. Mutants in tadG or the small cluster tadGEF were impaired in adhesion to soybean roots, and the root infection was delayed. However, nodule histology was not compromised by the mutations, indicating that these effects were restricted to the earliest contact of the B. diazoefficiens and root surfaces. Knowledge of preinfection determinants is important for development of inoculants that are applied to soybean crops worldwide. Copyright © 2015 Elsevier GmbH. All rights reserved.

The Academic Diligence Task (ADT): Assessing Individual Differences in Effort on Tedious but Important Schoolwork

PubMed Central

Galla, Brian M.; Plummer, Benjamin D.; White, Rachel E.; Meketon, David; D’Mello, Sidney K.; Duckworth, Angela L.

2014-01-01

The current study reports on the development and validation of the Academic Diligence Task (ADT), designed to assess the tendency to expend effort on academic tasks which are tedious in the moment but valued in the long-term. In this novel online task, students allocate their time between solving simple math problems (framed as beneficial for problem solving skills) and, alternatively, playing Tetris or watching entertaining videos. Using a large sample of high school seniors (N = 921), the ADT demonstrated convergent validity with self-report ratings of Big Five conscientiousness and its facets, self-control and grit, as well as discriminant validity from theoretically unrelated constructs, such as Big Five extraversion, openness, and emotional stability, test anxiety, life satisfaction, and positive and negative affect. The ADT also demonstrated incremental predictive validity for objectively measured GPA, standardized math and reading achievement test scores, high school graduation, and college enrollment, over and beyond demographics and intelligence. Collectively, findings suggest the feasibility of online behavioral measures to assess noncognitive individual differences that predict academic outcomes. PMID:25258470

The Academic Diligence Task (ADT): Assessing Individual Differences in Effort on Tedious but Important Schoolwork.

PubMed

Galla, Brian M; Plummer, Benjamin D; White, Rachel E; Meketon, David; D'Mello, Sidney K; Duckworth, Angela L

2014-10-01

The current study reports on the development and validation of the Academic Diligence Task (ADT), designed to assess the tendency to expend effort on academic tasks which are tedious in the moment but valued in the long-term. In this novel online task, students allocate their time between solving simple math problems (framed as beneficial for problem solving skills) and, alternatively, playing Tetris or watching entertaining videos. Using a large sample of high school seniors ( N = 921), the ADT demonstrated convergent validity with self-report ratings of Big Five conscientiousness and its facets, self-control and grit, as well as discriminant validity from theoretically unrelated constructs, such as Big Five extraversion, openness, and emotional stability, test anxiety, life satisfaction, and positive and negative affect. The ADT also demonstrated incremental predictive validity for objectively measured GPA, standardized math and reading achievement test scores, high school graduation, and college enrollment, over and beyond demographics and intelligence. Collectively, findings suggest the feasibility of online behavioral measures to assess noncognitive individual differences that predict academic outcomes.

Identification of poxvirus CD8+ T cell determinants to enable rational design and characterization of smallpox vaccines.

PubMed

Tscharke, David C; Karupiah, Gunasegaran; Zhou, Jie; Palmore, Tara; Irvine, Kari R; Haeryfar, S M Mansour; Williams, Shanicka; Sidney, John; Sette, Alessandro; Bennink, Jack R; Yewdell, Jonathan W

2005-01-03

The large size of poxvirus genomes has stymied attempts to identify determinants recognized by CD8+ T cells and greatly impeded development of mouse smallpox vaccination models. Here, we use a vaccinia virus (VACV) expression library containing each of the predicted 258 open reading frames to identify five peptide determinants that account for approximately half of the VACV-specific CD8+ T cell response in C57BL/6 mice. We show that the primary immunodominance hierarchy is greatly affected by the route of VACV infection and the poxvirus strain used. Modified vaccinia virus ankara (MVA), a candidate replacement smallpox vaccine, failed to induce responses to two of the defined determinants. This could not be predicted by genomic comparison of viruses and is not due strictly to limited MVA replication in mice. Several determinants are immunogenic in cowpox and ectromelia (mousepox) virus infections, and immunization with the immunodominant determinant provided significant protection against lethal mousepox. These findings have important implications for understanding poxvirus immunity in animal models and bench-marking immune responses to poxvirus vaccines in humans.

Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions.

PubMed

Fujii, Sota; Toda, Takushi; Kikuchi, Shunsuke; Suzuki, Ryutaro; Yokoyama, Koji; Tsuchida, Hiroko; Yano, Kentaro; Toriyama, Kinya

2011-06-01

Plant mitochondria contain a relatively large amount of genetic information, suggesting that their functional regulation may not be as straightforward as that of metazoans. We used a genomic tiling array to draw a transcriptomic atlas of Oryza sativa japonica (rice) mitochondria, which was predicted to be approximately 490-kb long. Whereas statistical analysis verified the transcription of all previously known functional genes such as the ones related to oxidative phosphorylation, a similar extent of RNA expression was frequently observed in the inter-genic regions where none of the previously annotated genes are located. The newly identified open reading frames (ORFs) predicted in these transcribed inter-genic regions were generally not conserved among flowering plant species, suggesting that these ORFs did not play a role in mitochondrial principal functions. We also identified two partial fragments of retrotransposon sequences as being transcribed in rice mitochondria. The present study indicated the previously unexpected complexity of plant mitochondrial RNA metabolism. Our transcriptomic data (Oryza sativa Mitochondrial rna Expression Server: OsMES) is publicly accessible at [http://bioinf.mind.meiji.ac.jp/cgi-bin/gbrowse/OsMes/#search].

Message frames interact with motivational systems to determine depth of message processing.

PubMed

Shen, Lijiang; Dillard, James Price

2009-09-01

Although several theoretical perspectives predict that negatively framed messages will be processed more deeply than positively framed messages, a recent meta-analysis found no such difference. In this article, the authors explore 2 explanations for this inconsistency. One possibility is methodological: the statistics used in the primary studies underestimated framing effects on depth of message processing because the data were maldistributed. The other is theoretical: the absence of a main effect is veridical, but framing interacts with individual differences that predispose individuals to greater or lesser depth of processing. Data from 2 experiments (Ns = 286 and 252) were analyzed via tobit regression, a technique designed to overcome the limitations of maldistributed data. One study showed the predicted main effect for framing, but the other did not. Both studies showed the anticipated interaction: Depth of processing correlated positively with a measure of the behavioral activation system in the advantage framing condition, whereas depth of processing correlated positively with the behavioral inhibition system in the disadvantage framing condition.

Quality of Education Predicts Performance on the Wide Range Achievement Test-4th Edition Word Reading Subtest

PubMed Central

Sayegh, Philip; Arentoft, Alyssa; Thaler, Nicholas S.; Dean, Andy C.; Thames, April D.

2014-01-01

The current study examined whether self-rated education quality predicts Wide Range Achievement Test-4th Edition (WRAT-4) Word Reading subtest and neurocognitive performance, and aimed to establish this subtest's construct validity as an educational quality measure. In a community-based adult sample (N = 106), we tested whether education quality both increased the prediction of Word Reading scores beyond demographic variables and predicted global neurocognitive functioning after adjusting for WRAT-4. As expected, race/ethnicity and education predicted WRAT-4 reading performance. Hierarchical regression revealed that when including education quality, the amount of WRAT-4's explained variance increased significantly, with race/ethnicity and both education quality and years as significant predictors. Finally, WRAT-4 scores, but not education quality, predicted neurocognitive performance. Results support WRAT-4 Word Reading as a valid proxy measure for education quality and a key predictor of neurocognitive performance. Future research should examine these findings in larger, more diverse samples to determine their robust nature. PMID:25404004

Cognitive Abilities Underlying Reading Accuracy, Fluency and Spelling Acquisition in Korean Hangul Learners from Grades 1 to 4: A Cross-Sectional Study.

PubMed

Park, Hyun-Rin; Uno, Akira

2015-08-01

The purpose of this cross-sectional study was to examine the cognitive abilities that predict reading and spelling performance in Korean children in Grades 1 to 4, depending on expertise and reading experience. As a result, visual cognition, phonological awareness, naming speed and receptive vocabulary significantly predicted reading accuracy in children in Grades 1 and 2, whereas visual cognition, phonological awareness and rapid naming speed did not predict reading accuracy in children in higher grades. For reading, fluency, phonological awareness, rapid naming speed and receptive vocabulary were crucial abilities in children in Grades 1 to 3, whereas phonological awareness was not a significant predictor in children in Grade 4. In spelling, reading ability and receptive vocabulary were the most important abilities for accurate Hangul spelling. The results suggested that the degree of cognitive abilities required for reading and spelling changed depending on expertise and reading experience. Copyright © 2015 John Wiley & Sons, Ltd.

The Relationships among Cognitive Correlates and Irregular Word, Non-Word, and Word Reading

ERIC Educational Resources Information Center

Abu-Hamour, Bashir; University, Mu'tah; Urso, Annmarie; Mather, Nancy

2012-01-01

This study explored four hypotheses: (a) the relationships among rapid automatized naming (RAN) and processing speed (PS) to irregular word, non-word, and word reading; (b) the predictive power of various RAN and PS measures, (c) the cognitive correlates that best predicted irregular word, non-word, and word reading, and (d) reading performance of…

Two Readiness Measures As Predictors Of First- And Third-Grade Reading Achievement

ERIC Educational Resources Information Center

Randel, Mildred A.; And Others

1977-01-01

Multiple-regression procedures were used to assess effectiveness of the ABC Inventory and the Metropolitan Readiness Test (MRT) in predicting first- and third-grade reading achievement. MRT performance accounted for 11 percent of the variance in first-grade SRA reading scores. In predicting third-grade reading, the MRT accounted for 26 percent of…

What Type of Vocabulary Knowledge Predicts Reading Comprehension: Word Meaning Recall or Word Meaning Recognition?

ERIC Educational Resources Information Center

Laufer, Batia; Aviad-Levitzky, Tami

2017-01-01

This study examined how well second language (L2) recall and recognition vocabulary tests correlated with a reading test, how well each vocabulary test discriminated between reading proficiency levels, and how accurate each test was in predicting reading proficiency when compared with corpus studies. A total of 116 college-level learners of…

Reading Is Your Thing (Even if You're Not a Reading Teacher)

ERIC Educational Resources Information Center

Zwiers, Jeff

2011-01-01

The activities described in this article, Prediction Path and Quotation Cafe, are adapted from the IRA book "Building Reading Comprehension Habits in Grades 6-12." They highlight the reading comprehension habit of making inferences and predictions, which can be used across content areas and grade levels. In creating this toolkit of activities, the…

Predicting Intervention Effectiveness from Oral Reading Accuracy and Rate Measures through the Learning Hierarchy/Instructional Hierarchy

ERIC Educational Resources Information Center

Szadokierski, Isadora Elisabeth

2012-01-01

The current study used the Learning Hierarchy/Instructional Hierarchy (LH/IH) to predict intervention effectiveness based on the reading skills of students who are developing reading fluency. Pre-intervention reading accuracy and rate were assessed for 49 second and third grade participants who then participated in a brief experimental analysis…

The Nucleotide Sequence and Spliced pol mRNA Levels of the Nonprimate Spumavirus Bovine Foamy Virus

PubMed Central

Holzschu, Donald L.; Delaney, Mari A.; Renshaw, Randall W.; Casey, James W.

1998-01-01

We have determined the complete nucleotide sequence of a replication-competent clone of bovine foamy virus (BFV) and have quantitated the amount of splice pol mRNA processed early in infection. The 544-amino-acid Gag protein precursor has little sequence similarity with its primate foamy virus homologs, but the putative nucleocapsid (NC) protein, like the primate NCs, contains the three glycine-arginine-rich regions that are postulated to bind genomic RNA during virion assembly. The BFV gag and pol open reading frames overlap, with pro and pol in the same translational frame. As with the human foamy virus (HFV) and feline foamy virus, we have detected a spliced pol mRNA by PCR. Quantitatively, this mRNA approximates the level of full-length genomic RNA early in infection. The integrase (IN) domain of reverse transcriptase does not contain the canonical HH-CC zinc finger motif present in all characterized retroviral INs, but it does contain a nearby histidine residue that could conceivably participate as a member of the zinc finger. The env gene encodes a protein that is over 40% identical in sequence to the HFV Env. By comparison, the Gag precursor of BFV is predicted to be only 28% identical to the HFV protein. PMID:9499074

Progressive addition spectacle lenses: Design preferences and head movements while reading

NASA Astrophysics Data System (ADS)

Preston, Julie Lynn

In a subjective preference study, two key progressive addition lens parameters, near zone width and corridor length, were varied in a double-masked, randomized, clinical trial of 49 patients. Each subject received a complete eye examination and a new frame. Each wore 6 pairs of lenses for one week at a time and completed questionnaires relating to vision, adaptation, and satisfaction. The preferred lens was identified from the three near zone width lenses and from the three corridor length lenses. Patient characteristics were analyzed for their effect on design preference. Satisfaction ratings following a brief experience with each design were compared to ratings after one week of wear in order to ascertain the predictability of initial impressions. One lens design appeared twice in the preference trial, providing an assessment of the repeatability of the rating instrument. The lens design with the widest near zone was rated significantly lower than the other near zone width designs for nearly every question relating to vision, adaptation, and satisfaction. This lens was also least preferred of all the designs. Preferences for corridor length were evenly distributed among the three designs. Of patient characteristics, years of progressive addition lens wear and gender significantly affected design preference in this population. Initial impressions were not predictive of satisfaction after a week of wear. The rating instrument was judged to have low repeatability. In the head movement portion of the study, 18 participants from the preference study wore the three near zone width designs while reading three paragraphs of varying print size. From a 20 second recording for each of three different paragraphs with each lens, measures of head rotation and posture were collected. The amplitude of head rotation was significantly affected by print size but not by lens design. The effective zone widths on the lenses scanned by the eyes and the locations of the reading levels were calculated from the head rotation and posture data. Effective zone widths were narrower than the contour plot widths for each condition.

A functional connectivity-based neuromarker of sustained attention generalizes to predict recall in a reading task.

PubMed

Jangraw, David C; Gonzalez-Castillo, Javier; Handwerker, Daniel A; Ghane, Merage; Rosenberg, Monica D; Panwar, Puja; Bandettini, Peter A

2018-02-01

Sustaining attention to the task at hand is a crucial part of everyday life, from following a lecture at school to maintaining focus while driving. Lapses in sustained attention are frequent and often problematic, with conditions such as attention deficit hyperactivity disorder affecting millions of people worldwide. Recent work has had some success in finding signatures of sustained attention in whole-brain functional connectivity (FC) measures during basic tasks, but since FC can be dynamic and task-dependent, it remains unclear how fully these signatures would generalize to a more complex and naturalistic scenario. To this end, we used a previously defined whole-brain FC network - a marker of attention that was derived from a sustained attention task - to predict the ability of participants to recall material during a free-viewing reading task. Though the predictive network was trained on a different task and set of participants, the strength of FC in the sustained attention network predicted reading recall significantly better than permutation tests where behavior was scrambled to simulate chance performance. To test the generalization of the method used to derive the sustained attention network, we applied the same method to our reading task data to find a new FC network whose strength specifically predicts reading recall. Even though the sustained attention network provided significant prediction of recall, the reading network was more predictive of recall accuracy. The new reading network's spatial distribution indicates that reading recall is highest when temporal pole regions have higher FC with left occipital regions and lower FC with bilateral supramarginal gyrus. Right cerebellar to right frontal connectivity is also indicative of poor reading recall. We examine these and other differences between the two predictive FC networks, providing new insight into the task-dependent nature of FC-based performance metrics. Published by Elsevier Inc.

Cellular Selenoprotein mRNA Tethering via Antisense Interactions with Ebola and HIV-1 mRNAs May Impact Host Selenium Biochemistry.

PubMed

Taylor, Ethan Will; Ruzicka, Jan A; Premadasa, Lakmini; Zhao, Lijun

2016-01-01

Regulation of protein expression by non-coding RNAs typically involves effects on mRNA degradation and/or ribosomal translation. The possibility of virus-host mRNA-mRNA antisense tethering interactions (ATI) as a gain-of-function strategy, via the capture of functional RNA motifs, has not been hitherto considered. We present evidence that ATIs may be exploited by certain RNA viruses in order to tether the mRNAs of host selenoproteins, potentially exploiting the proximity of a captured host selenocysteine insertion sequence (SECIS) element to enable the expression of virally-encoded selenoprotein modules, via translation of in-frame UGA stop codons as selenocysteine. Computational analysis predicts thermodynamically stable ATIs between several widely expressed mammalian selenoprotein mRNAs (e.g., isoforms of thioredoxin reductase) and specific Ebola virus mRNAs, and HIV-1 mRNA, which we demonstrate via DNA gel shift assays. The probable functional significance of these ATIs is further supported by the observation that, in both viruses, they are located in close proximity to highly conserved in-frame UGA stop codons at the 3' end of open reading frames that encode essential viral proteins (the HIV-1 nef protein and the Ebola nucleoprotein). Significantly, in HIV/AIDS patients, an inverse correlation between serum selenium and mortality has been repeatedly documented, and clinical benefits of selenium in the context of multi-micronutrient supplementation have been demonstrated in several well-controlled clinical trials. Hence, in the light of our findings, the possibility of a similar role for selenium in Ebola pathogenesis and treatment merits serious investigation.

Characterizing ground motions that collapse steel special moment-resisting frames or make them unrepairable

USGS Publications Warehouse

Olsen, Anna H.; Heaton, Thomas H.; Hall, John F.

2015-01-01

This work applies 64,765 simulated seismic ground motions to four models each of 6- or 20-story, steel special moment-resisting frame buildings. We consider two vector intensity measures and categorize the building response as “collapsed,” “unrepairable,” or “repairable.” We then propose regression models to predict the building responses from the intensity measures. The best models for “collapse” or “unrepairable” use peak ground displacement and velocity as intensity measures, and the best models predicting peak interstory drift ratio, given that the frame model is “repairable,” use spectral acceleration and epsilon (ϵ) as intensity measures. The more flexible frame is always more likely than the stiffer frame to “collapse” or be “unrepairable.” A frame with fracture-prone welds is substantially more susceptible to “collapse” or “unrepairable” damage than the equivalent frame with sound welds. The 20-story frames with fracture-prone welds are more vulnerable to P-delta instability and have a much higher probability of collapse than do any of the 6-story frames.

Predictive Validity of Curriculum-Embedded Measures on Outcomes of Kindergarteners Identified as At Risk for Reading Difficulty

ERIC Educational Resources Information Center

Oslund, Eric L.; Hagan-Burke, Shanna; Simmons, Deborah C.; Clemens, Nathan H.; Simmons, Leslie E.; Taylor, Aaron B.; Kwok, Oi-man; Coyne, Michael D.

2017-01-01

This study examined the predictive validity of formative assessments embedded in a Tier 2 intervention curriculum for kindergarten students identified as at risk for reading difficulty. We examined when (i.e., months during the school year) measures could predict reading outcomes gathered at the end of kindergarten and whether the predictive…

The Roles of Cognitive and Language Abilities in Predicting Decoding and Reading Comprehension: Comparisons of Dyslexia and Specific Language Impairment

ERIC Educational Resources Information Center

Lauterbach, Alexandra A.; Park, Yujeong; Lombardino, Linda J.

2017-01-01

This study aimed to (a) explore the roles of cognitive and language variables in predicting reading abilities of two groups of individuals with reading disabilities (i.e., dyslexia and specific language impairment) and (b) examine which variable(s) is the most predictive in differentiating two groups. Inclusion/exclusion criteria applied to…

The Design and Implementation of a Read Prediction Buffer

DTIC Science & Technology

1992-12-01

City, State, and ZIP Code) 7b ADDRESS (City, State. and ZIP Code) 8a. NAME OF FUNDING /SPONSORING 8b. OFFICE SYMBOL 9 PROCUREMENT INSTRUMENT... 9 E. THESIS STRUCTURE.. . .... ............... 9 II. READ PREDICTION ALGORITHM AND BUFFER DESIGN 10 A. THE READ PREDICTION ALGORITHM...29 Figure 9 . Basic Multiplexer Cell .... .......... .. 30 Figure 10. Block Diagram Simulation Labels ......... 38 viii I. INTRODUCTION A

Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

PubMed

Michel, Christian J; Ngoune, Viviane Nguefack; Poch, Olivier; Ripp, Raymond; Thompson, Julie D

2017-12-03

A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X, in the complete genome of the yeast Saccharomyces cerevisiae . Several properties of X motifs are identified by basic statistics (at the frequency level), and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R. We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae . We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae , but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions). This property is true for all cardinalities of X motifs (from 4 to 20) and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non-X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together, represent the first evidence for a significant enrichment of X motifs in the genes of an extant organism. They raise two hypotheses: the X motifs may be evolutionary relics of the primitive codes used for translation, or they may continue to play a functional role in the complex processes of genome decoding and protein synthesis.

Mapping From an Instrumented Glove to a Robot Hand

NASA Technical Reports Server (NTRS)

Goza, Michael

2005-01-01

An algorithm has been developed to solve the problem of mapping from (1) a glove instrumented with joint-angle sensors to (2) an anthropomorphic robot hand. Such a mapping is needed to generate control signals to make the robot hand mimic the configuration of the hand of a human attempting to control the robot. The mapping problem is complicated by uncertainties in sensor locations caused by variations in sizes and shapes of hands and variations in the fit of the glove. The present mapping algorithm is robust in the face of these uncertainties, largely because it includes a calibration sub-algorithm that inherently adapts the mapping to the specific hand and glove, without need for measuring the hand and without regard for goodness of fit. The algorithm utilizes a forward-kinematics model of the glove derived from documentation provided by the manufacturer of the glove. In this case, forward-kinematics model signifies a mathematical model of the glove fingertip positions as functions of the sensor readings. More specifically, given the sensor readings, the forward-kinematics model calculates the glove fingertip positions in a Cartesian reference frame nominally attached to the palm. The algorithm also utilizes an inverse-kinematics model of the robot hand. In this case, inverse-kinematics model signifies a mathematical model of the robot finger-joint angles as functions of the robot fingertip positions. Again, more specifically, the inverse-kinematics model calculates the finger-joint commands needed to place the fingertips at specified positions in a Cartesian reference frame that is attached to the palm of the robot hand and that nominally corresponds to the Cartesian reference frame attached to the palm of the glove. Initially, because of the aforementioned uncertainties, the glove fingertip positions calculated by the forwardkinematics model in the glove Cartesian reference frame cannot be expected to match the robot fingertip positions in the robot-hand Cartesian reference frame. A calibration must be performed to make the glove and robot-hand fingertip positions correspond more precisely. The calibration procedure involves a few simple hand poses designed to provide well-defined fingertip positions. One of the poses is a fist. In each of the other poses, a finger touches the thumb. The calibration subalgorithm uses the sensor readings from these poses to modify the kinematical models to make the two sets of fingertip positions agree more closely.

Culturally Framing Aboriginal Literacy and Learning.

ERIC Educational Resources Information Center

Antone, Eileen

2003-01-01

More than just the development of reading and writing skills, Aboriginal literacy is a wholistic concept, with spiritual, physical, mental, and emotional aspects, involving relationships between self, community, nation, and creation. Models are presented for incorporating traditional Aboriginal knowledge and methodologies into Aboriginal learning…

Patients with Mild Alzheimer's Disease Fail When Using Their Working Memory: Evidence from the Eye Tracking Technique.

PubMed

Fernández, Gerardo; Manes, Facundo; Politi, Luis E; Orozco, David; Schumacher, Marcela; Castro, Liliana; Agamennoni, Osvaldo; Rotstein, Nora P

2016-01-01

Patients with Alzheimer's disease (AD) develop progressive language, visuoperceptual, attentional, and oculomotor changes that can have an impact on their reading comprehension. However, few studies have examined reading behavior in AD, and none have examined the contribution of predictive cueing in reading performance. For this purpose we analyzed the eye movement behavior of 35 healthy readers (Controls) and 35 patients with probable AD during reading of regular and high-predictable sentences. The cloze predictability of words N - 1, and N + 1 exerted an influence on the reader's gaze duration. The predictabilities of preceding words in high-predictable sentences served as task-appropriate cues that were used by Control readers. In contrast, these effects were not present in AD patients. In Controls, changes in predictability significantly affected fixation duration along the sentence; noteworthy, these changes did not affect fixation durations in AD patients. Hence, only in healthy readers did predictability of upcoming words influence fixation durations via memory retrieval. Our results suggest that Controls used stored information of familiar texts for enhancing their reading performance and imply that contextual-word predictability, whose processing is proposed to require memory retrieval, only affected reading behavior in healthy subjects. In AD patients, this loss reveals impairments in brain areas such as those corresponding to working memory and memory retrieval. These findings might be relevant for expanding the options for the early detection and monitoring in the early stages of AD. Furthermore, evaluation of eye movements during reading could provide a new tool for measuring drug impact on patients' behavior.

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

PubMed

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

2015-08-01

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

Production and pathogenicity of hepatitis C virus core gene products

PubMed Central

Li, Hui-Chun; Ma, Hsin-Chieh; Yang, Chee-Hing; Lo, Shih-Yen

2014-01-01

Hepatitis C virus (HCV) is a major cause of chronic liver diseases, including steatosis, cirrhosis and hepatocellular carcinoma, and its infection is also associated with insulin resistance and type 2 diabetes mellitus. HCV, belonging to the Flaviviridae family, is a small enveloped virus whose positive-stranded RNA genome encoding a polyprotein. The HCV core protein is cleaved first at residue 191 by the host signal peptidase and further cleaved by the host signal peptide peptidase at about residue 177 to generate the mature core protein (a.a. 1-177) and the cleaved peptide (a.a. 178-191). Core protein could induce insulin resistance, steatosis and even hepatocellular carcinoma through various mechanisms. The peptide (a.a. 178-191) may play a role in the immune response. The polymorphism of this peptide is associated with the cellular lipid drop accumulation, contributing to steatosis development. In addition to the conventional open reading frame (ORF), in the +1 frame, an ORF overlaps with the core protein-coding sequence and encodes the alternative reading frame proteins (ARFP or core+1). ARFP/core+1/F protein could enhance hepatocyte growth and may regulate iron metabolism. In this review, we briefly summarized the current knowledge regarding the production of different core gene products and their roles in viral pathogenesis. PMID:24966583

Do Fathers' Home Reading Practices at Age 2 Predict Child Language and Literacy at Age 4?

PubMed

Quach, Jon; Sarkadi, Anna; Napiza, Natasha; Wake, Melissa; Loughman, Amy; Goldfeld, Sharon

2018-03-01

Maternal shared reading practices predict emergent literacy, but fathers' contributions are less certain. We examined whether fathers' shared home reading activities at 2 years predict language and emergent literacy at age 4 years, when controlling for maternal contributions; and whether this differentially benefits these outcomes in disadvantaged children. Two-parent families were recruited from 5 relatively disadvantaged communities for the universal Let's Read literacy promotion population-based trial (ISRCTN 04602902) in Melbourne, Australia. For exposure at 2 years, home reading practices were recorded via self-reported maternal and paternal StimQ-Toddler questionnaires and dichotomized at study median (high vs low). At 4 years, outcomes assessed included receptive and expressive language (Clinical Evaluation of Language Fundamentals 4) and emergent literacy (Sunderland Phonological Awareness Test-Revised). Linear regression, adjusted for mothers' home reading, was performed to assess 2-year-old vocabulary and communication skills and family disadvantage. Interaction of disadvantage (yes vs no) with high home reading by fathers and at least one parent was assessed. Data were available for 405 families (64.3%). High father reading at 2 years (reference: low) predicted better expressive (mean difference, 4.7; 95% confidence interval, 1.5 to 8.0) and receptive (mean difference, 5.0; 95% confidence interval, 1.8 to 8.2) language at 4 years (both P < .001), but not emergent literacy skills. Similar patterns were observed in families with at least one parent with high home reading. Fathers' reading did not differentially benefit outcomes in disadvantaged children. Fathers' involvement in reading at 2 years predicted better language but not emergent literacy at 4 years, and it did not protect against adverse effects of socioeconomic disadvantage. Copyright © 2018 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Does Growth in Working Memory Span or Executive Processes Predict Growth in Reading and Math in Children with Reading Disabilities?

ERIC Educational Resources Information Center

Jerman, Olga; Reynolds, Chandra; Swanson, H. Lee

2012-01-01

The present study investigated whether (a) growth patterns related to cognitive processing (working memory, updating, inhibition) differed in subgroups of children with reading disabilities (RD) and (b) growth in working memory (executive processing) predicted growth in other cognitive areas, such as reading and math. Seventy-three children (ages…

Learning disabled and average readers' working memory and comprehension: does metacognition play a role?

PubMed

Swanson, H L; Trahan, M

1996-09-01

The present study investigates (a) whether learning disabled readers' working memory deficits that underlie poor reading comprehension are related to a general system, and (b) whether metacognition contributes to comprehension beyond what is predicted by working memory and word knowledge. To this end, performance between learning and disabled (N = 60) and average readers (N = 60) was compared on the reading comprehension, reading rate, and vocabulary subtests of the Nelson Skills Reading Test, Sentence Span test composed of high and low imagery words, and a Metacognitive Questionnaire. As expected, differences between groups in working memory, vocabulary, and reading measures emerged, whereas ability groups were statistically comparable on the Metacognitive Questionnaire. A within-group analysis indicated that the correlation patterns between working memory, vocabulary, metacognition, and reading comprehension were not the same between ability groups. For predicting reading comprehension, the metacognitive questionnaire best predicted learning disabled readers' performance, whereas the working memory span measure that included low-imagery words best predicted average achieving readers' comprehension. Overall, the results suggest that the relationship between learning disabled readers' generalised working memory deficits and poor reading comprehension may be mediated by metacognition.

Relations among student attention behaviors, teacher practices, and beginning word reading skill.

PubMed

Sáez, Leilani; Folsom, Jessica Sidler; Al Otaiba, Stephanie; Schatschneider, Christopher

2012-01-01

The role of student attention for predicting kindergarten word reading was investigated among 432 students. Using Strengths and Weaknesses of ADHD Symptoms and Normal Behavior Rating Scale behavior rating scores, the authors conducted an exploratory factor analysis, which yielded three distinct factors that reflected selective attention. In this study, the authors focused on the role of one of these factors, which they labeled attention-memory, for predicting reading performance. Teacher ratings of attention-memory predicted word reading above and beyond the contribution of phonological awareness and vocabulary knowledge. In addition, the relations between four teacher practices and attention ratings for predicting reading performance were examined. Using hierarchical linear modeling, the authors found significant interactions between student attention and teacher practices observed during literacy instruction. In general, as ratings of attention improved, better kindergarten word reading performance was associated with high levels of classroom behavior management. However, better word reading performance was not associated with high levels of teacher task orienting. A significant three-way interaction was also found among attention, individualized instruction, and teacher task redirections. The role of regulating kindergarten student attention to support beginning word reading skill development is discussed.

Word reading skill predicts anticipation of upcoming spoken language input: a study of children developing proficiency in reading.

PubMed

Mani, Nivedita; Huettig, Falk

2014-10-01

Despite the efficiency with which language users typically process spoken language, a growing body of research finds substantial individual differences in both the speed and accuracy of spoken language processing potentially attributable to participants' literacy skills. Against this background, the current study took a look at the role of word reading skill in listeners' anticipation of upcoming spoken language input in children at the cusp of learning to read; if reading skills affect predictive language processing, then children at this stage of literacy acquisition should be most susceptible to the effects of reading skills on spoken language processing. We tested 8-year-olds on their prediction of upcoming spoken language input in an eye-tracking task. Although children, like in previous studies to date, were successfully able to anticipate upcoming spoken language input, there was a strong positive correlation between children's word reading skills (but not their pseudo-word reading and meta-phonological awareness or their spoken word recognition skills) and their prediction skills. We suggest that these findings are most compatible with the notion that the process of learning orthographic representations during reading acquisition sharpens pre-existing lexical representations, which in turn also supports anticipation of upcoming spoken words. Copyright © 2014 Elsevier Inc. All rights reserved.

An analysis of mobile genetic elements in three Plasmodium species and their potential impact on the nucleotide composition of the P. falciparum genome.

PubMed

Durand, Pierre M; Oelofse, Andries J; Coetzer, Theresa L

2006-11-04

The completed genome sequences of the malaria parasites P. falciparum, P. y. yoelii and P. vivax have revealed some unusual features. P. falciparum contains the most AT rich genome sequenced so far--over 90% in some regions. In comparison, P. y. yoelii is approximately 77% and P. vivax is approximately 55% AT rich. The evolutionary reasons for these findings are unknown. Mobile genetic elements have a considerable impact on genome evolution but a thorough investigation of these elements in Plasmodium has not been undertaken. We therefore performed a comprehensive genome analysis of these elements and their derivatives in the three Plasmodium species. Whole genome analysis was performed using bioinformatic methods. Forty potential protein encoding sequences with features of transposable elements were identified in P. vivax, eight in P. y. yoelii and only six in P. falciparum. Further investigation of the six open reading frames in P. falciparum revealed that only one is potentially an active mobile genetic element. Most of the open reading frames identified in all three species are hypothetical proteins. Some represent annotated host proteins such as the putative telomerase reverse transcriptase genes in P. y. yoelii and P. falciparum. One of the P. vivax open reading frames identified in this study demonstrates similarity to telomerase reverse transcriptase and we conclude it to be the orthologue of this gene. There is a divergence in the frequencies of mobile genetic elements in the three Plasmodium species investigated. Despite the limitations of whole genome analytical methods, it is tempting to speculate that mobile genetic elements might have been a driving force behind the compositional bias of the P. falciparum genome.

Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting.

PubMed

Fellner, Lea; Simon, Svenja; Scherling, Christian; Witting, Michael; Schober, Steffen; Polte, Christine; Schmitt-Kopplin, Philippe; Keim, Daniel A; Scherer, Siegfried; Neuhaus, Klaus

2015-12-18

Gene duplication is believed to be the classical way to form novel genes, but overprinting may be an important alternative. Overprinting allows entirely novel proteins to evolve de novo, i.e., formerly non-coding open reading frames within functional genes become expressed. Only three cases have been described for Escherichia coli. Here, a fourth example is presented. RNA sequencing revealed an open reading frame weakly transcribed in cow dung, coding for 101 residues and embedded completely in the -2 reading frame of citC in enterohemorrhagic E. coli. This gene is designated novel overlapping gene, nog1. The promoter region fused to gfp exhibits specific activities and 5' rapid amplification of cDNA ends indicated the transcriptional start 40-bp upstream of the start codon. nog1 was strand-specifically arrested in translation by a nonsense mutation silent in citC. This Nog1-mutant showed a phenotype in competitive growth against wild type in the presence of MgCl2. Small differences in metabolite concentrations were also found. Bioinformatic analyses propose Nog1 to be inner membrane-bound and to possess at least one membrane-spanning domain. A phylogenetic analysis suggests that the orphan gene nog1 arose by overprinting after Escherichia/Shigella separated from the other γ-proteobacteria. Since nog1 is of recent origin, non-essential, short, weakly expressed and only marginally involved in E. coli's central metabolism, we propose that this gene is in an initial stage of evolution. While we present specific experimental evidence for the existence of a fourth overlapping gene in enterohemorrhagic E. coli, we believe that this may be an initial finding only and overlapping genes in bacteria may be more common than is currently assumed by microbiologists.

Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins▿

PubMed Central

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

2010-01-01

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. PMID:20164235

Alternate Reading Frame Protein (F Protein) of Hepatitis C Virus: Paradoxical Effects of Activation and Apoptosis on Human Dendritic Cells Lead to Stimulation of T Cells

PubMed Central

Samrat, Subodh Kumar; Li, Wen; Singh, Shakti; Kumar, Rakesh; Agrawal, Babita

2014-01-01

Hepatitis C virus (HCV) leads to chronic infection in the majority of infected individuals due to lack, failure, or inefficiency of generated adaptive immune responses. In a minority of patients, acute infection is followed by viral clearance. The immune correlates of viral clearance are not clear yet but have been extensively investigated, suggesting that multispecific and multifunctional cellular immunity is involved. The generation of cellular immunity is highly dependent upon how antigen presenting cells (APCs) process and present various viral antigens. Various structural and non-structural HCV proteins derived from the open reading frame (ORF) have been implicated in modulation of dendritic cells (DCs) and APCs. Besides the major ORF proteins, the HCV core region also encodes an alternate reading frame protein (ARFP or F), whose function in viral pathogenesis is not clear. In the current studies, we sought to determine the role of HCV-derived ARFP in modulating dendritic cells and stimulation of T cell responses. Recombinant adenovirus vectors containing F or core protein derived from HCV (genotype 1a) were prepared and used to endogenously express these proteins in dendritic cells. We made an intriguing observation that endogenous expression of F protein in human DCs leads to contrasting effects on activation and apoptosis of DCs, allowing activated DCs to efficiently internalize apoptotic DCs. These in turn result in efficient ability of DCs to process and present antigen and to prime and stimulate F protein derived peptide-specific T cells from HCV-naive individuals. Taken together, our findings suggest important aspects of F protein in modulating DC function and stimulating T cell responses in humans. PMID:24475147

Recombinant expression of the alternate reading frame protein (ARFP) of hepatitis C virus genotype 4a (HCV-4a) and detection of ARFP and anti-ARFP antibodies in HCV-infected patients.

PubMed

Shehat, Michael G; Bahey-El-Din, Mohammed; Kassem, Mervat A; Farghaly, Faten A; Abdul-Rahman, Medhat H; Fanaki, Nourhan H

2015-08-01

HCV is a single-stranded RNA virus with a single open reading frame (ORF) that is translated into a polyprotein that is then processed to form 10 viral proteins. An additional eleventh viral protein, the alternative reading frame protein (ARFP), was discovered relatively recently. This protein results from a translational frameshift in the core region during the expression of the viral proteins. Recombinant expression of different forms of ARFP was previously done for HCV genotypes 1 and 2, and more recently, genotype 3. However, none of the previous studies addressed the expression of ARFP of HCV genotype 4a, which is responsible for 80 % of HCV infections in the Middle East and Africa. Moreover, the direct detection of the ARFP antigen in HCV-infected patients was never studied before for any HCV genotype. In the present study, recombinant ARFP derived from HCV genotype 4a was successfully expressed in E. coli and purified using metal affinity chromatography. The recombinant ARFP protein and anti-ARFP antibodies were used for detection of ARFP antigen in patients' sera, employing competitive enzyme-linked immunosorbent assay (ELISA) procedures. Furthermore, the recombinant antigen was also used to detect and quantify anti-ARFP antibodies in HCV-infected Egyptian patients at different stages of pegylated interferon/ribavirin therapy, using an ELISA assay. The ARFP antigen was detectable in 69.4 % of RNA-positive sera, indicating that ARFP antigen is produced during the natural course of HCV infection. In addition, significant levels of anti-ARFP antibodies were present in 41 % of the serum samples tested. The important diagnostic value of the recombinant ARFP antigen was also demonstrated.

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

PubMed Central

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

1988-01-01

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

Ribosomal scanning past the primary initiation codon as a mechanism for expression of CTL epitopes encoded in alternative reading frames

PubMed Central

1996-01-01

An increasing amount of evidence has shown that epitopes restricted to MHC class I molecules and recognized by CTL need not be encoded in a primary open reading frame (ORF). Such epitopes have been demonstrated after stop codons, in alternative reading frames (RF) and within introns. We have used a series of frameshifts (FS) introduced into the Influenza A/PR/8 /34 nucleoprotein (NP) gene to confirm the previous in vitro observations of cryptic epitope expression, and show that they are sufficiently expressed to prime immune responses in vivo. This presentation is not due to sub-dominant epitopes, transcription from cryptic promoters beyond the point of the FS, or internal initiation of translation. By introducing additional mutations to the construct exhibiting the most potent presentation, we have identified initiation codon readthrough (termed scanthrough here, where the scanning ribosome bypasses the conventional initiation codon, initiating translation further downstream) as the likely mechanism of epitope production. Further mutational analysis demonstrated that, while it should operate during the expression of wild-type (WT) protein, scanthrough does not provide a major source of processing substrate in our system. These findings suggest (i) that the full array of self- and pathogen-derived epitopes available during thymic selection and infection has not been fully appreciated and (ii) that cryptic epitope expression should be considered when the specificity of a CTL response cannot be identified or in therapeutic situations when conventional CTL targets are limited, as may be the case with latent viral infections and transformed cells. Finally, initiation codon readthrough provides a plausible explanation for the presentation of exocytic proteins by MHC class I molecules. PMID:8879204

MLPA based detection of mutations in the dystrophin gene of 180 Polish families with Duchenne/Becker muscular dystrophy.

PubMed

Zimowski, Janusz G; Massalska, Diana; Holding, Mariola; Jadczak, Sylwia; Fidziańska, Elżbieta; Lusakowska, Anna; Kostera-Pruszczyk, Anna; Kamińska, Anna; Zaremba, Jacek

2014-01-01

Duchenne/Becker muscular dystrophy (DMD/BMD) is a recessive, X-linked disorder caused by a mutation in the dystrophin gene. Deletions account for approximately 60-65% of mutations, duplications for 5-10%. The remaining cases are mainly point mutations. According to Monaco theory clinical form of the disease depends on maintaining or disrupting the reading frame. The purpose of the study was to determine frequency and location of deletions and duplications in the dystrophin gene, to determine the compliance between maintaining/disrupting the reading frame and clinical form of the disease and to check the effectiveness of MLPA (multiplex ligation-dependent probe amplification) in the detection of these mutations in hemizygous patients and heterozygous female carriers. The material is composed of combined results of molecular diagnosis carried out in years 2009-2012 in 180 unrelated patients referred with the diagnosis of DMD/BMD tested by use of MLPA. We identified 110 deletions, 22 duplication (in one patient two different duplications were detected) and 2 point mutations. Deletions involved mainly exons 45-54 and 3-21, whereas most duplications involved exons 3-18. The compliance with Monaco theory was 95% for deletions and 76% for duplications. Most of mutations in the dystrophin gene were localized in the hot spots - different for deletions and duplications. MLPA enabled their quick identification, exact localization and determination whether or not they maintained or disrupted the reading frame. MLPA was also effective in detection of deletions and duplications in female carriers. Copyright © 2014 Polish Neurological Society. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

Duchenne Muscular Dystrophy and Becker Muscular Dystrophy Confirmed by Multiplex Ligation-Dependent Probe Amplification: Genotype-Phenotype Correlation in a Large Cohort.

PubMed

Vengalil, Seena; Preethish-Kumar, Veeramani; Polavarapu, Kiran; Mahadevappa, Manjunath; Sekar, Deepha; Purushottam, Meera; Thomas, Priya Treesa; Nashi, Saraswathi; Nalini, Atchayaram

2017-01-01

Studies of cases of Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) confirmed by multiplex ligation-dependent probe amplification (MLPA) have determined the clinical characteristics, genotype, and relations between the reading frame and phenotype for different countries. This is the first such study from India. A retrospective genotype-phenotype analysis of 317 MLPA-confirmed patients with DMD or BMD who visited the neuromuscular clinic of a quaternary referral center in southern India. The 317 patients comprised 279 cases of DMD (88%), 32 of BMD (10.1%), and 6 of intermediate phenotype (1.9%). Deletions accounted for 91.8% of cases, with duplications causing the remaining 8.2%. There were 254 cases of DMD (91%) with deletions and 25 (9%) due to duplications, and 31 cases (96.8%) of BMD with deletions and 1 (3.2%) due to duplication. All six cases of intermediate type were due to deletions. The most-common mutation was a single-exon deletion. Deletions of six or fewer exons constituted 68.8% of cases. The deletion of exon 50 was the most common. The reading-frame rule held in 90% of DMD and 94% of BMD cases. A tendency toward a lower IQ and earlier wheelchair dependence was observed with distal exon deletions, though a significant correlation was not found. The reading-frame rule held in 90% to 94% of children, which is consistent with reports from other parts of the world. However, testing by MLPA is a limitation, and advanced sequencing methods including analysis of the structure of mutant dystrophin is needed for more-accurate assessments of the genotype-phenotype correlation.

Self-complementary circular codes in coding theory.

PubMed

Fimmel, Elena; Michel, Christian J; Starman, Martin; Strüngmann, Lutz

2018-04-01

Self-complementary circular codes are involved in pairing genetic processes. A maximal [Formula: see text] self-complementary circular code X of trinucleotides was identified in genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel in Life 7(20):1-16 2017, J Theor Biol 380:156-177, 2015; Arquès and Michel in J Theor Biol 182:45-58 1996). In this paper, self-complementary circular codes are investigated using the graph theory approach recently formulated in Fimmel et al. (Philos Trans R Soc A 374:20150058, 2016). A directed graph [Formula: see text] associated with any code X mirrors the properties of the code. In the present paper, we demonstrate a necessary condition for the self-complementarity of an arbitrary code X in terms of the graph theory. The same condition has been proven to be sufficient for codes which are circular and of large size [Formula: see text] trinucleotides, in particular for maximal circular codes ([Formula: see text] trinucleotides). For codes of small-size [Formula: see text] trinucleotides, some very rare counterexamples have been constructed. Furthermore, the length and the structure of the longest paths in the graphs associated with the self-complementary circular codes are investigated. It has been proven that the longest paths in such graphs determine the reading frame for the self-complementary circular codes. By applying this result, the reading frame in any arbitrary sequence of trinucleotides is retrieved after at most 15 nucleotides, i.e., 5 consecutive trinucleotides, from the circular code X identified in genes. Thus, an X motif of a length of at least 15 nucleotides in an arbitrary sequence of trinucleotides (not necessarily all of them belonging to X) uniquely defines the reading (correct) frame, an important criterion for analyzing the X motifs in genes in the future.

The Role of Metacognitive Reading Strategies, Metacognitive Study and Learning Strategies, and Behavioral Study and Learning Strategies in Predicting Academic Success in Students with and without a History of Reading Difficulties

ERIC Educational Resources Information Center

Chevalier, Thérèse M.; Parrila, Rauno; Ritchie, Krista C.; Deacon, S. Hélène

2017-01-01

We examined the self-reported use of reading, study, and learning strategies in university students with a history of reading difficulties (HRD; n = 77) and with no history of reading difficulties (NRD; n = 295). We examined both between-groups differences in strategy use and strategy use as a predictive measure of academic success. Participants…

Time will tell: A longitudinal investigation of brain-behavior relationships during reading development

DOE PAGES

Stites, Mallory C.; Laszlo, Sarah

2017-02-23

ERPs are a powerful tool for the study of reading, as they are both temporally precise and functionally specific. These are essential characteristics for studying a process that unfolds rapidly and consists of multiple, interactive subprocesses. In work with adults, clear, specific models exist linking components of the ERP with individual subprocesses of reading including orthographic decoding, phonological processing, and semantic access (e.g., Grainger & Holcomb, 2009). The relationships between ERP components and reading subprocesses are less clear in development; here, we address two questions regarding these relationships. First, we ask whether there are ERP markers that predict future readingmore » behaviors across a longitudinal year. Second, we ask whether any relationships observed between ERP components and reading behavior across time map onto the better-established relationships between ERPs and reading subprocesses in adults. To address these questions, we acquired ERPs from children engaging in a silent reading task and then, a year later, collected behavioral assessments of their reading ability. Finally, we find that ERPs collected in Year 1 do predict reading behaviors a year later. Further, we find that these relationships do conform, at least to some extent, to relationships between ERP components and reading subprocesses observed in adults, with, for example, N250 amplitude in Year 1 predicting phonological awareness in Year 2, and N400 amplitude in Year 1 predicting vocabulary in Year 2.« less

Time will tell: A longitudinal investigation of brain-behavior relationships during reading development

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

Stites, Mallory C.; Laszlo, Sarah

ERPs are a powerful tool for the study of reading, as they are both temporally precise and functionally specific. These are essential characteristics for studying a process that unfolds rapidly and consists of multiple, interactive subprocesses. In work with adults, clear, specific models exist linking components of the ERP with individual subprocesses of reading including orthographic decoding, phonological processing, and semantic access (e.g., Grainger & Holcomb, 2009). The relationships between ERP components and reading subprocesses are less clear in development; here, we address two questions regarding these relationships. First, we ask whether there are ERP markers that predict future readingmore » behaviors across a longitudinal year. Second, we ask whether any relationships observed between ERP components and reading behavior across time map onto the better-established relationships between ERPs and reading subprocesses in adults. To address these questions, we acquired ERPs from children engaging in a silent reading task and then, a year later, collected behavioral assessments of their reading ability. Finally, we find that ERPs collected in Year 1 do predict reading behaviors a year later. Further, we find that these relationships do conform, at least to some extent, to relationships between ERP components and reading subprocesses observed in adults, with, for example, N250 amplitude in Year 1 predicting phonological awareness in Year 2, and N400 amplitude in Year 1 predicting vocabulary in Year 2.« less

Moderation of phenotypic severity in dystrophic and junctional forms of epidermolysis bullosa through in-frame skipping of exons containing non-sense or frameshift mutations.

PubMed

McGrath, J A; Ashton, G H; Mellerio, J E; Salas-Alanis, J C; Swensson, O; McMillan, J R; Eady, R A

1999-09-01

Non-sense mutations on both alleles of either the type VII collagen gene (COL7A1) or the genes encoding laminin 5 (LAMA3, LAMB3, or LAMC2) usually result in clinically severe forms of recessive dystrophic or junctional epidermolysis bullosa, respectively. In this study we assessed two unrelated families whose mutations in genomic DNA predicted severe recessive dystrophic epidermolysis bullosa or junctional epidermolysis bullosa phenotypes but in whom the manifestations were milder than expected. The recessive dystrophic epidermolysis bullosa patients had a homozygous single base-pair frameshift mutation in exon 19 of COL7A1 (2470insG). Clinically, there was generalized blistering but only mild scarring. Skin biopsy revealed positive type VII collagen immunoreactivity and recognizable anchoring fibrils. The junctional epidermolysis bullosa patients were compound heterozygotes for a frameshift/non-sense combination of mutations in exons 3 and 17 of LAMB3 (29insC/Q834X). These patients did not have the lethal form of junctional epidermolysis bullosa but, as adults, displayed the milder generalized atrophic benign epidermolysis bullosa variant. There was undetectable laminin 5 staining at the dermal-epidermal junction using an antibody to the beta3 chain, but faintly positive alpha3 and gamma2 chain labeling, and there was variable hypoplasia of hemidesmosomes. To explain the milder recessive dystrophic epidermolysis bullosa and junctional epidermolysis bullosa phenotypes in these families, reverse transcription-polymerase chain reaction, using RNA extracted from frozen skin, was able to provide evidence for some rescue of mutant mRNA transcripts with restoration of the open- reading frame. In the recessive dystrophic epidermolysis bullosa patients, transcripts containing in-frame skipping of exon 19 of COL7A1 in the cDNA were detected, and in the junctional epidermolysis bullosa patients transcripts with in-frame skipping of exon 17 of LAMB3 were identified. The truncated proteins encoded by these transcripts are expected to lack certain critical domains involved in cell-matrix attachment, but may still be able to contribute to adhesion thereby moderating the severity of the skin blistering. This study shows the limitations in predicting phenotype in epidermolysis bullosa solely based on mutation analysis of genomic DNA and emphasizes the importance of immunohistochemistry, electron microscopy, and mRNA assessment as parallel investigations.

Boosting Contextual Information for Deep Neural Network Based Voice Activity Detection

DTIC Science & Technology

2015-02-01

multi-resolution stacking (MRS), which is a stack of ensemble classifiers. Each classifier in a building block inputs the concatenation of the predictions ...a base classifier in MRS, named boosted deep neural network (bDNN). bDNN first generates multiple base predictions from different contexts of a single...frame by only one DNN and then aggregates the base predictions for a better prediction of the frame, and it is different from computationally

Reduce Manual Curation by Combining Gene Predictions from Multiple Annotation Engines, a Case Study of Start Codon Prediction

PubMed Central

Ederveen, Thomas H. A.; Overmars, Lex; van Hijum, Sacha A. F. T.

2013-01-01

Nowadays, prokaryotic genomes are sequenced faster than the capacity to manually curate gene annotations. Automated genome annotation engines provide users a straight-forward and complete solution for predicting ORF coordinates and function. For many labs, the use of AGEs is therefore essential to decrease the time necessary for annotating a given prokaryotic genome. However, it is not uncommon for AGEs to provide different and sometimes conflicting predictions. Combining multiple AGEs might allow for more accurate predictions. Here we analyzed the ab initio open reading frame (ORF) calling performance of different AGEs based on curated genome annotations of eight strains from different bacterial species with GC% ranging from 35–52%. We present a case study which demonstrates a novel way of comparative genome annotation, using combinations of AGEs in a pre-defined order (or path) to predict ORF start codons. The order of AGE combinations is from high to low specificity, where the specificity is based on the eight genome annotations. For each AGE combination we are able to derive a so-called projected confidence value, which is the average specificity of ORF start codon prediction based on the eight genomes. The projected confidence enables estimating likeliness of a correct prediction for a particular ORF start codon by a particular AGE combination, pinpointing ORFs notoriously difficult to predict start codons. We correctly predict start codons for 90.5±4.8% of the genes in a genome (based on the eight genomes) with an accuracy of 81.1±7.6%. Our consensus-path methodology allows a marked improvement over majority voting (9.7±4.4%) and with an optimal path ORF start prediction sensitivity is gained while maintaining a high specificity. PMID:23675487

Effects of News Frames on Perceived Risk, Emotions, and Learning

PubMed Central

Otieno, Christine; Spada, Hans; Renkl, Alexander

2013-01-01

The media play a key role in forming opinions by influencing people´s understanding and perception of a topic. People gather information about topics of interest from the internet and print media, which employ various news frames to attract attention. One example of a common news frame is the human-interest frame, which emotionalizes and dramatizes information and often accentuates individual affectedness. Our study investigated effects of human-interest frames compared to a neutral-text condition with respect to perceived risk, emotions, and knowledge acquisition, and tested whether these effects can be "generalized" to common variants of the human-interest frame. Ninety-one participants read either one variant of the human-interest frame or a neutrally formulated version of a newspaper article describing the effects of invasive species in general and the Asian ladybug (an invasive species) in particular. The framing was achieved by varying the opening and concluding paragraphs (about invasive species), as well as the headline. The core text (about the Asian ladybug) was the same across all conditions. All outcome variables on framing effects referred to this common core text. We found that all versions of the human-interest frame increased perceived risk and the strength of negative emotions compared to the neutral text. Furthermore, participants in the human-interest frame condition displayed better (quantitative) learning outcomes but also biased knowledge, highlighting a potential dilemma: Human-interest frames may increase learning, but they also lead to a rather unbalanced view of the given topic on a “deeper level”. PMID:24223999

In silico prediction of the G-protein coupled receptors expressed during the metamorphic molt of Sagmariasus verreauxi (Crustacea: Decapoda) by mining transcriptomic data: RNA-seq to repertoire.

PubMed

Buckley, Sean J; Fitzgibbon, Quinn P; Smith, Gregory G; Ventura, Tomer

2016-03-01

Against a backdrop of food insecurity, the farming of decapod crustaceans is a rapidly expanding and globally significant source of food protein. Sagmariasus verreauxi spiny lobster, the subject of this study, are decapods of underdeveloped aquaculture potential. Crustacean neuropeptide G-protein coupled receptors (GPCRs) mediate endocrine pathways that are integral to animal fecundity, growth and survival. The potential use of novel biotechnologies to enhance GPCR-mediated physiology may assist in improving the health and productivity of farmed decapod populations. This study catalogues the GPCRs expressed in the early developmental stages, as well as adult tissues, with a view to illuminating key neuropeptide receptors. De novo assembled contiguous sequences generated from transcriptomic reads of metamorphic and post metamorphic S. verreauxi were filtered for seven transmembrane domains, and used as a reference for iterative re-mapping. Subsequent putative GPCR open reading frames (ORFs) were BLAST annotated, categorised, and compared to published orthologues based on phylogenetic analysis. A total of 85 GPCRs were digitally predicted, that represented each of the four arthropod subfamilies. They generally displayed low-level and non-differential metamorphic expression with few exceptions that we examined using RT-PCR and qPCR. Two putative CHH-like neuropeptide receptors were annotated. Three dimensional structural modelling suggests that these receptors exhibit a conserved extracellular ligand binding pocket, providing support to the notion that these receptors co-evolved with their ligands across Decapoda. This perhaps narrows the search for means to increase productivity of farmed decapod populations. Copyright © 2016 Elsevier Inc. All rights reserved.

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

ERIC Educational Resources Information Center

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

2015-01-01

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

Detection of novel divergent arenaviruses in boid snakes with inclusion body disease in The Netherlands.

PubMed

Bodewes, R; Kik, M J L; Raj, V Stalin; Schapendonk, C M E; Haagmans, B L; Smits, S L; Osterhaus, A D M E

2013-06-01

Arenaviruses are bi-segmented negative-stranded RNA viruses, which were until recently only detected in rodents and humans. Now highly divergent arenaviruses have been identified in boid snakes with inclusion body disease (IBD). Here, we describe the identification of a new species and variants of the highly divergent arenaviruses, which were detected in tissues of captive boid snakes with IBD in The Netherlands by next-generation sequencing. Phylogenetic analysis of the complete sequence of the open reading frames of the four predicted proteins of one of the detected viruses revealed that this virus was most closely related to the recently identified Golden Gate virus, while considerable sequence differences were observed between the highly divergent arenaviruses detected in this study. These findings add to the recent identification of the highly divergent arenaviruses in boid snakes with IBD in the United States and indicate that these viruses also circulate among boid snakes in Europe.

Cloning and characterization of a Candida albicans gene homologous to fructose-1,6-bisphosphatase genes.

PubMed

De la Rosa, J M; Ruíz, T; Rodríguez, L

2000-12-01

By sequencing of the DNA adjacent to the Candida albicans SEC61 gene, an open reading frame encoding a polypeptide of 331 amino acids was found. The predicted protein showed a strong homology with the fructose-1,6-bisphosphatase [FbPase] from other organisms, and conserved regions included the catalytic motif found in all known FbPases. Although the cloned gene did not complement the growth failure of a Saccharomyces cerevisiae fbp1 mutant in media with gluconeogenic carbon sources, it was transcribed in the transformants in a fashion that indicates a partial repression by glucose. A similar control on the transcription of this gene and on FbPase activity was found in wild-type C. albicans, where the cloned gene (CaFBP1) was shown to be localized in a single chromosomal locus in the genome.

Molecular cloning and characterization of an SRCAP chromatin remodeling homologue in Toxoplasma gondii.

PubMed

Sullivan, William J; Monroy, M Alexandra; Bohne, Wolfgang; Nallani, Karuna C; Chrivia, John; Yaciuk, Peter; Smith, Charles K; Queener, Sherry F

2003-05-01

We have identified and mapped a gene in Toxoplasma gondii that encodes a homologue of SRCAP (Snf2-related CBP activator protein), a member of the SNF/SWI family of chromatin remodeling factors. The genomic locus (TgSRCAP) is present as a single copy and contains 16 introns. The predicted cDNA contains an open reading frame of 8,775 bp and encodes a protein of 2,924 amino acids. We have identified additional SRCAP-like sequences in Apicomplexa for comparison by screening genomic databases. An analysis of SRCAP homologues between species reveals signature features that may be indicative of SRCAP members. Expression of mRNA encoding TgSRCAP is upregulated when tachyzoite (invasive form) parasites are induced to differentiate into bradyzoites (encysted form) in vitro. Recombinant TgSRCAP protein is functionally equivalent to the human homologue, being capable of increasing transcription mediated by CREB.

Identification of the mpl gene encoding UDP-N-acetylmuramate: L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase in Escherichia coli and its role in recycling of cell wall peptidoglycan.

PubMed Central

Mengin-Lecreulx, D; van Heijenoort, J; Park, J T

1996-01-01

A gene, mpl, encoding UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelat e ligase was recognized by its amino acid sequence homology with murC as the open reading frame yjfG present at 96 min on the Escherichia coli map. The existence of such an enzymatic activity was predicted from studies indicating that reutilization of the intact tripeptide L-alanyl-gamma-D-glutamyl-meso-diaminopimelate occurred and accounted for well over 30% of new cell wall synthesis. Murein tripeptide ligase activity could be demonstrated in crude extracts, and greatly increased activity was produced when the gene was cloned and expressed under control of the trc promoter. A null mutant totally lacked activity but was viable, showing that the enzyme is not essential for growth. PMID:8808921

Bioinformatics analysis of the phytoene synthase gene in cabbage (Brassica oleracea var. capitata)

NASA Astrophysics Data System (ADS)

Sun, Bo; Jiang, Min; Xue, Shengling; Zheng, Aihong; Zhang, Fen; Tang, Haoru

2018-04-01

Phytoene Synthase (PSY) is an important enzyme in carotenoid biosynthesis. Here, the Brassica oleracea var. capitata PSY (BocPSY) gene sequences were obtained from Brassica database (BRAD), and preformed for bioinformatics analysis. The BocPSY1, BocPSY2 and BocPSY3 genes mapped to chromosomes 2,3 and 9, and contains an open reading frame of 1,248 bp, 1,266 bp and 1,275 bp that encodes a 415, 421, 424 amino acid protein, respectively. Subcellular localization predicted all BocPSY genes were in the chloroplast. The conserved domain of the BocPSY protein is PLN02632. Homology analysis indicates that the levels of identity among BocPSYs were all more than 85%, and the PSY protein is apparently conserved during plant evolution. The findings of the present study provide a molecular basis for the elucidation of PSY gene function in cabbage.

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

PubMed

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.

Nucleotide sequence of a complementary DNA encoding pea cytosolic copper/zinc superoxide dismutase. [Pisum sativum L

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

White, D.A.; Zilinskas, B.A.

1991-08-01

The authors now report the nucleotide sequence of the cytosolic Cu/Zn SOD cloned from a {lambda}gt11 cDNA library constructed from mRNA extracted from leaves of 7- to 10-d pea seedlings (Pisum sativum L.). The clone was isolated using a 22-base synthetic oligonucleotide complementary to the amino acid sequence CGIIGLQG. This sequence, found at the protein's carboxy terminus, is highly conserved among plant cytosolic Cu/Zn SODs but not chloroplastic Cu/Zn SODs. The 738-base pair sequence contains an open reading frame specifying 152 codons and a predicted M{sub r} of 18,024 D. The deduced amino acid sequence is highly homologous (79-82% identity)more » with the sequences of other known plant cytosolic Cu/Zn SODs but less highly conserved (63-65%) when compared with several chloroplastic Cu/Zn SODs including pea (10).« less

Light-frame wall and floor systems : analysis and performance

Treesearch

G. Sherwood; R. C. Moody

1989-01-01

This report describes methods of predicting the performance of light-frame wood structures with emphasis on floor and wall systems. Methods of predicting structural performance, fire safety, and environmental concerns including thermal, moisture, and acoustic performance are addressed in the three major sections.

Test Framing Generates a Stability Bias for Predictions of Learning by Causing People to Discount their Learning Beliefs

PubMed Central

Ariel, Robert; Hines, Jarrod C.; Hertzog, Christopher

2014-01-01

People estimate minimal changes in learning when making predictions of learning (POLs) for future study opportunities despite later showing increased performance and an awareness of that increase (Kornell & Bjork, 2009). This phenomenon is conceptualized as a stability bias in judgments about learning. We investigated the malleability of this effect, and whether it reflected people’s underlying beliefs about learning. We manipulated prediction framing to emphasize the role of testing vs. studying on memory and directly measured beliefs about multi-trial study effects on learning by having participants construct predicted learning curves before and after the experiment. Mean POLs were more sensitive to the number of study-test opportunities when performance was framed in terms of study benefits rather than testing benefits and POLs reflected pre-existing beliefs about learning. The stability bias is partially due to framing and reflects discounted beliefs about learning benefits rather than inherent belief in the stability of performance. PMID:25067885

Test Framing Generates a Stability Bias for Predictions of Learning by Causing People to Discount their Learning Beliefs.

PubMed

Ariel, Robert; Hines, Jarrod C; Hertzog, Christopher

2014-08-01

People estimate minimal changes in learning when making predictions of learning (POLs) for future study opportunities despite later showing increased performance and an awareness of that increase (Kornell & Bjork, 2009). This phenomenon is conceptualized as a stability bias in judgments about learning. We investigated the malleability of this effect, and whether it reflected people's underlying beliefs about learning. We manipulated prediction framing to emphasize the role of testing vs. studying on memory and directly measured beliefs about multi-trial study effects on learning by having participants construct predicted learning curves before and after the experiment. Mean POLs were more sensitive to the number of study-test opportunities when performance was framed in terms of study benefits rather than testing benefits and POLs reflected pre-existing beliefs about learning. The stability bias is partially due to framing and reflects discounted beliefs about learning benefits rather than inherent belief in the stability of performance.

Predicting reading outcomes with progress monitoring slopes among middle grade students

PubMed Central

Tolar, Tammy D.; Barth, Amy E.; Fletcher, Jack M.; Francis, David J.; Vaughn, Sharon

2013-01-01

Effective implementation of response-to-intervention (RTI) frameworks depends on efficient tools for monitoring progress. Evaluations of growth (i.e., slope) may be less efficient than evaluations of status at a single time point, especially if slopes do not add to predictions of outcomes over status. We examined progress monitoring slope validity for predicting reading outcomes among middle school students by evaluating latent growth models for different progress monitoring measure-outcome combinations. We used multi-group modeling to evaluate the effects of reading ability, reading intervention, and progress monitoring administration condition on slope validity. Slope validity was greatest when progress monitoring was aligned with the outcome (i.e., word reading fluency slope was used to predict fluency outcomes in contrast to comprehension outcomes), but effects varied across administration conditions (viz., repeated reading of familiar vs. novel passages). Unless the progress monitoring measure is highly aligned with outcome, slope may be an inefficient method for evaluating progress in an RTI context. PMID:24659899

Vasculature-Specific Adenovirus Vectors for Gene Therapy of Prostate Cancer

DTIC Science & Technology

2007-02-01

reporter gene. To this end, a recombinant replication-deficient retrovirus vector containing an open reading frame of Renilla luciferase (hRLuc...dual-mode reporter gene ( Renilla luciferase and green fluorescent protein) has been designed and produced in a pan- tropic configuration. • Dual

Curriculum Guide Construction Cluster.

ERIC Educational Resources Information Center

Kline, Ken

As part of a model construction cluster curriculum development project, this guide was developed and implemented in the Beaverton (Oregon) School District. The curriculum guide contains 16 units covering the following topics: introduction to construction jobs; safety and first aid; blueprint readings; basic mathematics; site work; framing; roofing…

Complete genome sequence of a new maize-associated cytorhabdovirus

USDA-ARS?s Scientific Manuscript database

A new 11,877 nt cytorhabdovirus sequence with 6 open reading frames has been identified in a maize sample. It shares 50 and 51% genome-wide nucleotide sequence identity with northern cereal mosaic cytorhabdovirus (NCMV) and barley yellow striate mosaic cytorhabdovirus (BYSMV), respectively....

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

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

Panning, B.; Smiley, J.R.

1993-06-01

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

[Organization and expression of poliovirus genome].

PubMed

Vevcherenko, S G

1984-01-01

In the present paper on the basis of analysis of literary data it is postulated that along with the AUG codon at N743 there exists a second initiation codon in the poliovirus RNA (the AUG codon at N586). The translation initiated at N586 can be transferred to the phase of the major reading frame by removing the small hairpin N732-N744 formed near the first initiation site, or by removing the small region N739-N745. In the first case at the boundary between the hypothetical leader peptide encoded by the 5'-terminus of the long, open reading frame of the spliced poliovirus RNA and the capsid protein VP4 must be the Gln-Gly proteolytic cleavage signal, and in the second case--the Tyr-Gly signal. In both cases the leader peptide can be chipped off by the virus specific proteinase. It is supposed that the exon-intronic structure of the poliovirus genome is needed for coordination of translation and transcription during the poliovirus reproduction cycle.

ORF phage display to identify cellular proteins with different functions.

PubMed

Li, Wei

2012-09-01

Open reading frame (ORF) phage display is a new branch of phage display aimed at improving its efficiency to identify cellular proteins with specific binding or functional activities. Despite the success of phage display with antibody libraries and random peptide libraries, phage display with cDNA libraries of cellular proteins identifies a high percentage of non-ORF clones encoding unnatural short peptides with minimal biological implications. This is mainly because of the uncontrollable reading frames of cellular proteins in conventional cDNA libraries. ORF phage display solves this problem by eliminating non-ORF clones to generate ORF cDNA libraries. Here I summarize the procedures of ORF phage display, discuss the factors influencing its efficiency, present examples of its versatile applications, and highlight evidence of its capability of identifying biologically relevant cellular proteins. ORF phage display coupled with different selection strategies is capable of delineating diverse functions of cellular proteins with unique advantages. Copyright © 2012 Elsevier Inc. All rights reserved.

Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci.

PubMed

Mills, D A; McKay, L L; Dunny, G M

1996-06-01

Analysis of a region involved in the conjugative transfer of the lactococcal conjugative element pRS01 has revealed a bacteria] group II intron. Splicing of this lactococcal intron (designated Ll.ltrB) in vivo resulted in the ligation of two exon messages (ltrBE1 and ltrBE2) which encoded a putative conjugative relaxase essential for the transfer of pRS01. Like many group II introns, the Ll.ltrB intron possessed an open reading frame (ltrA) with homology to reverse transcriptases. Remarkably, sequence analysis of ltrA suggested a greater similarity to open reading frames encoded by eukaryotic mitochondrial group II introns than to those identified to date from other bacteria. Several insertional mutations within ltrA resulted in plasmids exhibiting a conjugative transfer-deficient phenotype. These results provide the first direct evidence for splicing of a prokaryotic group II intron in vivo and suggest that conjugative transfer is a mechanism for group II intron dissemination in bacteria.

The genome organisation and taxonomy of Sugarcane striate mosaic associated virus.

PubMed

Thompson, N; Randles, J W

2001-08-01

Sugarcane striate mosaic associated virus (SCSMaV) has slightly flexuous 950 nm x 15 nm filamentous particles and is associated with sugarcane striate mosaic disease in central Queensland, Australia. We report the full sequence of its RNA genome, which comprises 5 open reading frames representing the polymerase, movement function proteins encoded in a triple gene block and coat protein. Phylogenetic analyses based on either the full nucleotide sequence, the polymerase protein, or the coat protein all placed SCSMaV in an intermediate position between the genera Foveavirus and Carlavirus, but outside both genera. In addition, the absence of a sixth open reading frame excludes it from the genus Carlavirus, and the coat protein is approximately half the size of the type member for the genus Foveavirus. Although SCSMaV was most closely allied to Cherry green ring mottle virus by genome analysis, the two viruses are morphologically and biologically dissimilar. SCSMaV may therefore represent a new plant virus taxon.

Spliced RNA of woodchuck hepatitis virus.

PubMed

Ogston, C W; Razman, D G

1992-07-01

Polymerase chain reaction was used to investigate RNA splicing in liver of woodchucks infected with woodchuck hepatitis virus (WHV). Two spliced species were detected, and the splice junctions were sequenced. The larger spliced RNA has an intron of 1300 nucleotides, and the smaller spliced sequence shows an additional downstream intron of 1104 nucleotides. We did not detect singly spliced sequences from which the smaller intron alone was removed. Control experiments showed that spliced sequences are present in both RNA and DNA in infected liver, showing that the viral reverse transcriptase can use spliced RNA as template. Spliced sequences were detected also in virion DNA prepared from serum. The upstream intron produces a reading frame that fuses the core to the polymerase polypeptide, while the downstream intron causes an inframe deletion in the polymerase open reading frame. Whereas the splicing patterns in WHV are superficially similar to those reported recently in hepatitis B virus, we detected no obvious homology in the coding capacity of spliced RNAs from these two viruses.

Generating an Open Reading Frame (ORF) Entry Clone and Destination Clone.

PubMed

Reece-Hoyes, John S; Walhout, Albertha J M

2018-01-02

This protocol describes using the Gateway recombinatorial cloning system to create an Entry clone carrying an open reading frame (ORF) and then to transfer the ORF into a Destination vector. In this example, BP recombination is used to clone an ORF from a cDNA source into the Donor vector pDONR 221. The ORF from the resulting Entry clone is then transferred into the Destination vector pDEST-15; the product (the Destination clone) will express the ORF as an amino-terminal GST-fusion. The technique can be used as a guide for cloning any other DNA fragment of interest-a promoter sequence or 3' untranslated region (UTR), for example-with substitutions of different genetic material such as genomic DNA, att sites, and vectors as required. The series of constructions and transformations requires 9-15 d, not including time that may be required for sequence confirmation, if desired/necessary. © 2018 Cold Spring Harbor Laboratory Press.

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

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

White, Richard A.; Brown, Joseph M.; Colby, Sean M.

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based onmore » majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.« less

Singled out as the effect to be explained: implications for collective self-esteem.

PubMed

Bruckmüller, Susanne

2013-02-01

The description and explanation of intergroup differences tend to be framed in terms of how nonnormative (untypical and/or stigmatized) groups differ from normative groups rather than vice versa. Three experiments examined how this affects group members' collective self-esteem. Single participants felt worse about being single when they read (Study 1) or wrote (Study 2) about how singles differ from coupled people than when they read or wrote about how coupled people differ from singles-although they mentioned more positive aspects of being single under the former comparative framing. In Study 3, left-handed participants indicated lower private collective self-esteem after writing about how left-handers differ from right-handers than after writing about how right-handers differ from left-handers. Thus, regardless of the specific characteristics that the comparison focused on, being marked as different and having to explain one's group identity negatively affected members of nonnormative, but not members of normative groups.

Differentiation of mycoplasmalike organisms (MLOs) in European fruit trees by PCR using specific primers derived from the sequence of a chromosomal fragment of the apple proliferation MLO.

PubMed Central

Jarausch, W; Saillard, C; Dosba, F; Bové, J M

1994-01-01

A 1.8-kb chromosomal DNA fragment of the mycoplasmalike organism (MLO) associated with apple proliferation was sequenced. Three putative open reading frames were observed on this fragment. The protein encoded by open reading frame 2 shows significant homologies with bacterial nitroreductases. From the nucleotide sequence four primer pairs for PCR were chosen to specifically amplify DNA from MLOs associated with European diseases of fruit trees. Primer pairs specific for (i) Malus-affecting MLOs, (ii) Malus- and Prunus-affecting MLOs, and (iii) Malus-, Prunus-, and Pyrus-affecting MLOs were obtained. Restriction enzyme analysis of the amplification products revealed restriction fragment length polymorphisms between Malus-, Prunus, and Pyrus-affecting MLOs as well as between different isolates of the apple proliferation MLO. No amplification with either primer pair could be obtained with DNA from 12 different MLOs experimentally maintained in periwinkle. Images PMID:7916180

The assisted prediction modelling frame with hybridisation and ensemble for business risk forecasting and an implementation

NASA Astrophysics Data System (ADS)

Li, Hui; Hong, Lu-Yao; Zhou, Qing; Yu, Hai-Jie

2015-08-01

The business failure of numerous companies results in financial crises. The high social costs associated with such crises have made people to search for effective tools for business risk prediction, among which, support vector machine is very effective. Several modelling means, including single-technique modelling, hybrid modelling, and ensemble modelling, have been suggested in forecasting business risk with support vector machine. However, existing literature seldom focuses on the general modelling frame for business risk prediction, and seldom investigates performance differences among different modelling means. We reviewed researches on forecasting business risk with support vector machine, proposed the general assisted prediction modelling frame with hybridisation and ensemble (APMF-WHAE), and finally, investigated the use of principal components analysis, support vector machine, random sampling, and group decision, under the general frame in forecasting business risk. Under the APMF-WHAE frame with support vector machine as the base predictive model, four specific predictive models were produced, namely, pure support vector machine, a hybrid support vector machine involved with principal components analysis, a support vector machine ensemble involved with random sampling and group decision, and an ensemble of hybrid support vector machine using group decision to integrate various hybrid support vector machines on variables produced from principle components analysis and samples from random sampling. The experimental results indicate that hybrid support vector machine and ensemble of hybrid support vector machines were able to produce dominating performance than pure support vector machine and support vector machine ensemble.

Classification Accuracy of Oral Reading Fluency and Maze in Predicting Performance on Large-Scale Reading Assessments

ERIC Educational Resources Information Center

Decker, Dawn M.; Hixson, Michael D.; Shaw, Amber; Johnson, Gloria

2014-01-01

The purpose of this study was to examine whether using a multiple-measure framework yielded better classification accuracy than oral reading fluency (ORF) or maze alone in predicting pass/fail rates for middle-school students on a large-scale reading assessment. Participants were 178 students in Grades 7 and 8 from a Midwestern school district.…

The Prediction of Reading Levels between Second and Third Grade Limited English Proficient Students in a Bilingual Program

ERIC Educational Resources Information Center

Moses, Britani Creel

2010-01-01

The purpose of this study was to predict the third grade English reading TAKS scores while considering the same students' native language, Spanish, reading level as assessed by a state-approved reading assessment, the Evaluacion del desarrollo de la lectura (EDL), from the end of the second grade year. In addition, this study was been designed to…

Anterior Insula Activity Predicts the Influence of Positively-Framed Messages on Decision Making

PubMed Central

Krawitz, Adam; Fukunaga, Rena; Brown, Joshua W.

2010-01-01

The neural mechanisms underlying the influence of persuasive messages on decision making are largely unknown. We address this using event-related functional magnetic resonance imaging to investigate how informative messages alter risk appraisal during choice. Participants performed the Iowa Gambling Task while viewing a positively-framed, negatively-framed, or control message about the options. Right anterior insula correlated with improvement in choice behavior due to the positively-framed, but not the negatively-framed, message. With the positively-framed message there was increased activation proportional to message effectiveness when less-preferred options were chosen, consistent with a role in the prediction of adverse outcomes. In addition, dorsomedial and left dorsolateral prefrontal cortex correlated with overall decision quality regardless of message type. The dorsomedial region mediated the relationship between right anterior insula and decision quality with the positively-framed messages. These findings suggest a network of frontal brain regions that integrate informative messages into the evaluation of options during decision-making. PMID:20805540

Design, Fabrication and Test of Composite Curved Frames for Helicopter Fuselage Structure

NASA Technical Reports Server (NTRS)

Lowry, D. W.; Krebs, N. E.; Dobyns, A. L.

1984-01-01

Aspects of curved beam effects and their importance in designing composite frame structures are discussed. The curved beam effect induces radial flange loadings which in turn causes flange curling. This curling increases the axial flange stresses and induces transverse bending. These effects are more important in composite structures due to their general inability to redistribute stresses by general yielding, such as in metal structures. A detailed finite element analysis was conducted and used in the design of composite curved frame specimens. Five specimens were statically tested and compared with predicted and test strains. The curved frame effects must be accurately accounted for to avoid premature fracture; finite element methods can accurately predict most of the stresses and no elastic relief from curved beam effects occurred in the composite frames tested. Finite element studies are presented for comparative curved beam effects on composite and metal frames.

Prohibitin-2 gene reveals sex-related differences in the salmon louse Caligus rogercresseyi.

PubMed

Farlora, Rodolfo; Nuñez-Acuña, Gustavo; Gallardo-Escárate, Cristian

2015-06-10

Prohibitins are evolutionarily conserved proteins present in multiple cellular compartments, and are involved in diverse cellular processes, including steroid hormone transcription and gametogenesis. In the present study, we report for the first time the characterization of the prohibitin-2 (Phb2) gene in the sea lice Caligus rogercresseyi. The CrPhb2 cDNA showed a total length of 1406 bp, which contained a predicted open reading frame (ORF) of 894 base pairs (bp) encoding for 298 amino acids. Multiple sequence alignments of prohibitin proteins from other arthropods revealed a high degree of amino acid sequence conservation. In silico Illumina read counts and RT-qPCR analyses showed a sex-dependent differential expression, with mRNA levels exhibiting a 1.7-fold (RT-qPCR) increase in adult females compared with adult males. A total of nine single nucleotide polymorphisms (SNPs) were identified, three were located in the 5' UTR of the Phb2 messenger and six in the ORF, but no mutations associated with sex were found. These results contribute to expand the present knowledge of the reproduction-related genes in C. rogercresseyi, and may be useful in future experiments aimed at controlling the impacts of sea lice in fish farming. Copyright © 2015 Elsevier B.V. All rights reserved.

Eye Movements during Silent and Oral Reading in a Regular Orthography: Basic Characteristics and Correlations with Childhood Cognitive Abilities and Adolescent Reading Skills

PubMed Central

Krieber, Magdalena; Bartl-Pokorny, Katrin D.; Pokorny, Florian B.; Zhang, Dajie; Landerl, Karin; Körner, Christof; Pernkopf, Franz; Pock, Thomas; Einspieler, Christa; Marschik, Peter B.

2017-01-01

The present study aimed to define differences between silent and oral reading with respect to spatial and temporal eye movement parameters. Eye movements of 22 German-speaking adolescents (14 females; mean age = 13;6 years;months) were recorded while reading an age-appropriate text silently and orally. Preschool cognitive abilities were assessed at the participants’ age of 5;7 (years;months) using the Kaufman Assessment Battery for Children. The participants’ reading speed and reading comprehension at the age of 13;6 (years;months) were determined using a standardized inventory to evaluate silent reading skills in German readers (Lesegeschwindigkeits- und -verständnistest für Klassen 6–12). The results show that (i) reading mode significantly influenced both spatial and temporal characteristics of eye movement patterns; (ii) articulation decreased the consistency of intraindividual reading performances with regard to a significant number of eye movement parameters; (iii) reading skills predicted the majority of eye movement parameters during silent reading, but influenced only a restricted number of eye movement parameters when reading orally; (iv) differences with respect to a subset of eye movement parameters increased with reading skills; (v) an overall preschool cognitive performance score predicted reading skills at the age of 13;6 (years;months), but not eye movement patterns during either silent or oral reading. However, we found a few significant correlations between preschool performances on subscales of sequential and simultaneous processing and eye movement parameters for both reading modes. Overall, the findings suggest that eye movement patterns depend on the reading mode. Preschool cognitive abilities were more closely related to eye movement patterns of oral than silent reading, while reading skills predicted eye movement patterns during silent reading, but less so during oral reading. PMID:28151950

Building Scientific Confidence in the Development and ...

EPA Pesticide Factsheets

Read-across remains a popular data gap filling technique within category and analogue approaches for regulatory purposes. Acceptance of read-across is an ongoing challenge with several efforts underway for identifying and addressing uncertainties. Here we demonstrate an algorithmic approach to facilitate read-across using ToxCast in vitro bioactivity data in conjunction with chemical descriptor information to predict in vivo outcomes in guideline testing studies from ToxRefDB. Over 3400 different chemical structure descriptors were generated for a set of 976 chemicals and supplemented with the outcomes from 821 in vitro assays. The read-across prediction for a given chemical was based on the similarity weighted endpoint outcomes of its nearest neighbors calculated using in vitro bioactivity and chemical structure descriptors, called GenRA. GenRA is based on a computational approach for: (i) defining local validity domains using chemical and bioactivity descriptors, (ii) systematically deriving endpoint read-across predictions within these domains using similarity weighted activity of nearest neighbours, (iii) objectively evaluating predicted performance using tested chemicals, and (iv) assigning read-across predictions to untested chemicals along with estimates of uncertainty. We found in vitro bioactivity descriptors were often found to be more predictive of in vivo toxicity outcomes than chemical structure descriptors. We believe GenRA is an important first st

On forward inferences of fast and slow readers. An eye movement study

PubMed Central

Hawelka, Stefan; Schuster, Sarah; Gagl, Benjamin; Hutzler, Florian

2015-01-01

Unimpaired readers process words incredibly fast and hence it was assumed that top-down processing, such as predicting upcoming words, would be too slow to play an appreciable role in reading. This runs counter the major postulate of the predictive coding framework that our brain continually predicts probable upcoming sensory events. This means, it may generate predictions about the probable upcoming word during reading (dubbed forward inferences). Trying to asses these contradictory assumptions, we evaluated the effect of the predictability of words in sentences on eye movement control during silent reading. Participants were a group of fluent (i.e., fast) and a group of speed-impaired (i.e., slow) readers. The findings indicate that fast readers generate forward inferences, whereas speed-impaired readers do so to a reduced extent - indicating a significant role of predictive coding for fluent reading. PMID:25678030

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

ERIC Educational Resources Information Center

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…

Radical framing effects in the ultimatum game: the impact of explicit culturally transmitted frames on economic decision-making

PubMed Central

Lightner, Aaron D.

2017-01-01

Many studies have documented framing effects in economic games. These studies, however, have tended to use minimal framing cues (e.g. a single sentence labelling the frame), and the frames did not involve unambiguous offer expectations. Results often did not differ substantially from those in the unframed games. Here we test the hypothesis that, in contrast to the modal offer in the unframed ultimatum game (UG) (e.g. 60% to the proposer and 40% to the responder), offers in a UG explicitly framed either as a currency exchange or a windfall will closely conform to expectations for the frame and diverge substantially from the modal offer. Participants recruited from MTurk were randomized into one of two conditions. In the control condition, participants played a standard UG. In the treatment conditions, players were provided a vignette explicitly describing the frame with their roles: some were customers and bankers in a currency exchange, and others were in a windfall scenario. We predicted (i) that modal offers in the currency exchange would involve an asymmetric split where greater than 80% went to customers and less than 20% went to bankers, and (ii) that variation in windfall offers would converge onto a 50–50 split with significantly less variation than the control condition. Our first prediction was confirmed with substantial effect sizes (d = 1.09 and d = −2.04), whereas we found no evidence for our second prediction. The first result provides further evidence that it is difficult to draw firm conclusions about economic decision-making from decontextualized games. PMID:29308218

Radical framing effects in the ultimatum game: the impact of explicit culturally transmitted frames on economic decision-making.

PubMed

Lightner, Aaron D; Barclay, Pat; Hagen, Edward H

2017-12-01

Many studies have documented framing effects in economic games. These studies, however, have tended to use minimal framing cues (e.g. a single sentence labelling the frame), and the frames did not involve unambiguous offer expectations. Results often did not differ substantially from those in the unframed games. Here we test the hypothesis that, in contrast to the modal offer in the unframed ultimatum game (UG) (e.g. 60% to the proposer and 40% to the responder), offers in a UG explicitly framed either as a currency exchange or a windfall will closely conform to expectations for the frame and diverge substantially from the modal offer. Participants recruited from MTurk were randomized into one of two conditions. In the control condition, participants played a standard UG. In the treatment conditions, players were provided a vignette explicitly describing the frame with their roles: some were customers and bankers in a currency exchange, and others were in a windfall scenario. We predicted (i) that modal offers in the currency exchange would involve an asymmetric split where greater than 80% went to customers and less than 20% went to bankers, and (ii) that variation in windfall offers would converge onto a 50-50 split with significantly less variation than the control condition. Our first prediction was confirmed with substantial effect sizes ( d  = 1.09 and d  = -2.04), whereas we found no evidence for our second prediction. The first result provides further evidence that it is difficult to draw firm conclusions about economic decision-making from decontextualized games.

A School Policy for Reading.

ERIC Educational Resources Information Center

Medwell, Jane

1992-01-01

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

Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data--The Case of the Grass Aegilops tauschii Complex Genome.

PubMed

Budak, Hikmet; Kantar, Melda

2015-07-01

MicroRNAs (miRNAs) are small, endogenous, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. As high-throughput next generation sequencing (NGS) and Big Data rapidly accumulate for various species, efforts for in silico identification of miRNAs intensify. Surprisingly, the effect of the input genomics sequence on the robustness of miRNA prediction was not evaluated in detail to date. In the present study, we performed a homology-based miRNA and isomiRNA prediction of the 5D chromosome of bread wheat progenitor, Aegilops tauschii, using two distinct sequence data sets as input: (1) raw sequence reads obtained from 454-GS FLX Titanium sequencing platform and (2) an assembly constructed from these reads. We also compared this method with a number of available plant sequence datasets. We report here the identification of 62 and 22 miRNAs from raw reads and the assembly, respectively, of which 16 were predicted with high confidence from both datasets. While raw reads promoted sensitivity with the high number of miRNAs predicted, 55% (12 out of 22) of the assembly-based predictions were supported by previous observations, bringing specificity forward compared to the read-based predictions, of which only 37% were supported. Importantly, raw reads could identify several repeat-related miRNAs that could not be detected with the assembly. However, raw reads could not capture 6 miRNAs, for which the stem-loops could only be covered by the relatively longer sequences from the assembly. In summary, the comparison of miRNA datasets obtained by these two strategies revealed that utilization of raw reads, as well as assemblies for in silico prediction, have distinct advantages and disadvantages. Consideration of these important nuances can benefit future miRNA identification efforts in the current age of NGS and Big Data driven life sciences innovation.

A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing.

PubMed

Thomas, Sean; Martinez, L L Isadora Trejo; Westenberger, Scott J; Sturm, Nancy R

2007-05-24

The structurally complex network of minicircles and maxicircles comprising the mitochondrial DNA of kinetoplastids mirrors the complexity of the RNA editing process that is required for faithful expression of encrypted maxicircle genes. Although a few of the guide RNAs that direct this editing process have been discovered on maxicircles, guide RNAs are mostly found on the minicircles. The nuclear and maxicircle genomes have been sequenced and assembled for Trypanosoma cruzi, the causative agent of Chagas disease, however the complement of 1.4-kb minicircles, carrying four guide RNA genes per molecule in this parasite, has been less thoroughly characterised. Fifty-four CL Brener and 53 Esmeraldo strain minicircle sequence reads were extracted from T. cruzi whole genome shotgun sequencing data. With these sequences and all published T. cruzi minicircle sequences, 108 unique guide RNAs from all known T. cruzi minicircle sequences and two guide RNAs from the CL Brener maxicircle were predicted using a local alignment algorithm and mapped onto predicted or experimentally determined sequences of edited maxicircle open reading frames. For half of the sequences no statistically significant guide RNA could be assigned. Likely positions of these unidentified gRNAs in T. cruzi minicircle sequences are estimated using a simple Hidden Markov Model. With the local alignment predictions as a standard, the HMM had an ~85% chance of correctly identifying at least 20 nucleotides of guide RNA from a given minicircle sequence. Inter-minicircle recombination was documented. Variable regions contain species-specific areas of distinct nucleotide preference. Two maxicircle guide RNA genes were found. The identification of new minicircle sequences and the further characterization of all published minicircles are presented, including the first observation of recombination between minicircles. Extrapolation suggests a level of 4% recombinants in the population, supporting a relatively high recombination rate that may serve to minimize the persistence of gRNA pseudogenes. Characteristic nucleotide preferences observed within variable regions provide potential clues regarding the transcription and maturation of T. cruzi guide RNAs. Based on these preferences, a method of predicting T. cruzi guide RNAs using only primary minicircle sequence data was created.

Identification of human short introns

PubMed Central

Abebrese, Emmanuel L.; Arnold, Zachary R.; Armstrong, Katharine; Burns, Lindsay; Day, R. Thomas; Hsu, Daniel G.; Jarrell, Katherine; Luo, Yi; Mugayo, Daphine

2017-01-01

Canonical pre-mRNA splicing requires snRNPs and associated splicing factors to excise conserved intronic sequences, with a minimum intron length required for efficient splicing. Non-canonical splicing–intron excision without the spliceosome–has been documented; most notably, some tRNAs and the XBP1 mRNA contain short introns that are not removed by the spliceosome. There have been some efforts to identify additional short introns, but little is known about how many short introns are processed from mRNAs. Here, we report an approach to identify RNA short introns from RNA-Seq data, discriminating against small genomic deletions. We identify hundreds of short introns conserved among multiple human cell lines. These short introns are often alternatively spliced and are found in a variety of RNAs–both mRNAs and lncRNAs. Short intron splicing efficiency is increased by secondary structure, and we detect both canonical and non-canonical short introns. In many cases, splicing of these short introns from mRNAs is predicted to alter the reading frame and change protein output. Our findings imply that standard gene prediction models which often assume a lower limit for intron size fail to predict short introns effectively. We conclude that short introns are abundant in the human transcriptome, and short intron splicing represents an added layer to mRNA regulation. PMID:28520720

Framing obesity a disease: Indirect effects of affect and controllability beliefs on weight bias.

PubMed

Nutter, Sarah; Alberga, Angela S; MacInnis, Cara; Ellard, John H; Russell-Mayhew, Shelly

2018-05-24

Obesity has been declared a disease by the American and Canadian Medical Associations. Although these declarations sparked much debate as to the impact of framing obesity as a disease on weight bias, strong empirical research is needed to examine this impact. The current study examined the impact of framing obesity a disease on weight bias, focusing on moderating and mediating processes. A sample of 309 participants living in the United States or Canada was recruited from Crowdflower. Participants completed measures of demographics, ideology, general attitudes, and previous contact quality and quantity with people living with obesity. Participants then read one of three articles as part of an experimental manipulation framing obesity as a disease, obesity not as a disease, and a control article unrelated to obesity. Post-manipulation included measures of affect, disgust, empathy, blame, and weight bias. Orthogonal contrasts were used to compare the obesity-disease condition to the obesity-not-disease condition and control condition. The manipulation had a direct effect on affect (emotions), such that affect toward individuals with obesity was more positive in the obesity-disease condition than the obesity-not-disease and control condition combined. Exploration of moderating effects revealed that both the belief in a just world and weight satisfaction moderated the relationship between the obesity-disease manipulation and blame for obesity. Two models of indirect effects on weight bias were also examined, which demonstrated that the obesity-disease manipulation predicted less weight bias through more positive affect (model 1) as well as less weight bias through decreased blame among individuals high in belief in a just world (model 2). This study further highlights the complex effects of declaring obesity a disease, uncovering a new direction for future research into the role of affect as well as indirect effects of characterising obesity a disease on weight bias.

Ease of imagination, message framing, and physical activity messages.

PubMed

Berry, Tanya R; Carson, Valerie

2010-02-01

The purpose of this research was to replicate a study that examined how message framing and ease of imagination interact to influence attitudes towards the prevention of heart disease through physical activity and a healthy diet. Changes were made such that only physical activity behaviour was profiled and assessed as a moderating variable. It was hypothesized that gain-framed messages would positively influence attitudes with hard to imagine symptoms, that loss-framed messages would positively influence attitudes with easy to imagine symptoms and exercise frequency would moderate the findings. This study employed a 2 (easy or hard to imagine symptoms) by 2 (gain- or loss-framed) Solomon square design whereby participants, half of whom completed a pre-test, were randomly assigned to one of four conditions: easy to imagine/gain-framed, hard to imagine/gain-framed, easy to imagine/loss-framed, or hard to imagine/loss-framed. Participants included adults over the age of 55 years (N=57) and undergraduate students (18-22 years; N=118). They were described either hard to imagine or easy to imagine symptoms of heart disease and diabetes and asked to imagine them. Participants then read either a gain- or loss-framed physical activity message followed by post-test questionnaires that assessed attitudes, exercise frequency, and demographics. Regression analyses showed no significant framing effects but significant effects for ease of imagination and exercise frequency as a moderating variable. This study failed to replicate the original research findings but showed that participants who exercised the least and were in the hard to imagine condition had the worst attitudes towards physical activity.

Culture, health, and bigotry: How exposure to cultural accounts of fatness shape attitudes about health risk, health policies, and weight-based prejudice.

PubMed

Frederick, David A; Saguy, Abigail C; Gruys, Kjerstin

2016-09-01

We conducted three experiments to examine how cultural frames shape attitudes about health, focusing on obesity, which is considered a public health crisis and is imbued with symbolic meaning. College students (Ns = 99, 114, and 293) read news articles that presented high body weight according to one or more of the following frames: 1) public health crisis; 2) personal responsibility; 3) health at every size (HAES); or 4) fat rights. Compared to people who read the HAES and Fat Rights articles, those who read the Public Health Crisis and Personal Responsibility articles expressed more belief in the health risks of being fat (ds = 1.28 to 1.79), belief that fat people should pay more for insurance (ds = 0.53 to 0.71), anti-fat prejudice (ds = 0.61 to 0.69), willingness to discriminate against fat people (ds = 0.41 to 0.59), and less willingness to celebrate body-size diversity (ds = 0.77 to 1.07). They were less willing to say women at the lower end of the obese range could be healthy. Exposure to these articles increased support for price-raising policies to curb obesity but not support for redistributive or compensatory policies. In Experiment 3, in comparison to a control condition, exposure to HAES or Fat Rights frames significantly reduced beliefs in the risks of obesity and support for charging fat people more for insurance. However, only people exposed to the Fat Rights frame expressed fewer anti-fat attitudes and more willingness to celebrate body-size diversity. Our findings suggest that simply disseminating information that people can be both fat and healthy will not suffice to reduce prejudice. Given that anti-fat stigma is a health risk and barrier to collective solidarity, fat rights viewpoints can buffer against the negative consequences of anti-fat stigma and promote a culture of health by fostering empathy and social justice. Copyright © 2015 Elsevier Ltd. All rights reserved.

Contextual predictability enhances reading performance in patients with schizophrenia.

PubMed

Fernández, Gerardo; Guinjoan, Salvador; Sapognikoff, Marcelo; Orozco, David; Agamennoni, Osvaldo

2016-07-30

In the present work we analyzed fixation duration in 40 healthy individuals and 18 patients with chronic, stable SZ during reading of regular sentences and proverbs. While they read, their eye movements were recorded. We used lineal mixed models to analyze fixation durations. The predictability of words N-1, N, and N+1 exerted a strong influence on controls and SZ patients. The influence of the predictabilities of preceding, current, and upcoming words on SZ was clearly reduced for proverbs in comparison to regular sentences. Both controls and SZ readers were able to use highly predictable fixated words for an easier reading. Our results suggest that SZ readers might compensate attentional and working memory deficiencies by using stored information of familiar texts for enhancing their reading performance. The predictabilities of words in proverbs serve as task-appropriate cues that are used by SZ readers. To the best of our knowledge, this is the first study using eyetracking for measuring how patients with SZ process well-defined words embedded in regular sentences and proverbs. Evaluation of the resulting changes in fixation durations might provide a useful tool for understanding how SZ patients could enhance their reading performance. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Predicting Reading and Interpreting I. Q. Differences

ERIC Educational Resources Information Center

Miller, Wallace D.

1973-01-01

The purposes of this study were to determine which of the tests, PPVT, SIT, or Lorge-Thorndike (LT), may be the most useful to the classroom teacher in predicting reading achievement, for use in reading expectancy formulas, and for analyzing I.Q. scores obtained on different tests. (Author/RK)

Predicting Third Grade Reading Success from Kindergarten Phonological Awareness

ERIC Educational Resources Information Center

Robinson, Stephanie J.

2013-01-01

Although phonological awareness (PA) is an essential preliteracy skill with well-established predictive validity for elementary school reading success, previous research indicates that PA intervention does not demonstrate long term effects on reading. The theory of automaticity was the underlying foundation used to understand the importance of…

Transcriptional analysis of Penaeus stylirostris densovirus genes

USDA-ARS?s Scientific Manuscript database

Penaeus stylirostris densovirus (PstDNV) genome contains three open reading frames (ORFs), left, middle, and right, which encode a non-structural (NS) protein, an unknown protein, and a capsid protein (CP), respectively. Transcription mapping revealed that P2, P11 and P61 promoters transcribe the le...

CCR study: evidence for benefit of TARP vaccine for men with early stage prostate cancer | Center for Cancer Research

Cancer.gov

Results from a pilot clinical trial found that TARP, or T-cell receptor gamma chain alternate reading frame protein, vaccination slowed prostate-specific antigen (PSA) rise in the majority of patients with early stage prostate cancer.

Problem-Solving Test: Attenuation--A Mechanism to Regulate Bacterial Tryptophan Biosynthesis

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2010-01-01

Terms to be familiar with before you start to solve the test: tryptophan, transcription unit, operon, "trp" repressor, corepressor, operator, promoter, palindrome, initiation, elongation, and termination of transcription, open reading frame, coupled transcription/translation, chromosome-polysome complex. (Contains 2 figures and 1 footnote.)