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

Allan, Christopher M.; Awad, Agape M.; Johnson, Jarrett S.

Coenzyme Q (Q or ubiquinone) is a redox active lipid composed of a fully substituted benzoquinone ring and a polyisoprenoid tail and is required for mitochondrial electron transport. In the yeast Saccharomyces cerevisiae, Q is synthesized by the products of 11 known genes, COQ1–COQ9, YAH1, and ARH1. The function of some of the Coq proteins remains unknown, and several steps in the Q biosynthetic pathway are not fully characterized. Several of the Coq proteins are associated in a macromolecular complex on the matrix face of the inner mitochondrial membrane, and this complex is required for efficient Q synthesis. In thismore » paper, we further characterize this complex via immunoblotting and proteomic analysis of tandem affinity-purified tagged Coq proteins. We show that Coq8, a putative kinase required for the stability of the Q biosynthetic complex, is associated with a Coq6-containing complex. Additionally Q 6 and late stage Q biosynthetic intermediates were also found to co-purify with the complex. A mitochondrial protein of unknown function, encoded by the YLR290C open reading frame, is also identified as a constituent of the complex and is shown to be required for efficient de novo Q biosynthesis. Finally, given its effect on Q synthesis and its association with the biosynthetic complex, we propose that the open reading frame YLR290C be designated COQ11.« less

Design and construction of a first-generation high-throughput integrated robotic molecular biology platform for bioenergy applications.

PubMed

Hughes, Stephen R; Butt, Tauseef R; Bartolett, Scott; Riedmuller, Steven B; Farrelly, Philip

2011-08-01

The molecular biological techniques for plasmid-based assembly and cloning of gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. High-throughput integrated robotic molecular biology platforms that have the capacity to rapidly clone and express heterologous gene open reading frames in bacteria and yeast and to screen large numbers of expressed proteins for optimized function are an important technology for improving microbial strains for biofuel production. The process involves the production of full-length complementary DNA libraries as a source of plasmid-based clones to express the desired proteins in active form for determination of their functions. Proteins that were identified by high-throughput screening as having desired characteristics are overexpressed in microbes to enable them to perform functions that will allow more cost-effective and sustainable production of biofuels. Because the plasmid libraries are composed of several thousand unique genes, automation of the process is essential. This review describes the design and implementation of an automated integrated programmable robotic workcell capable of producing complementary DNA libraries, colony picking, isolating plasmid DNA, transforming yeast and bacteria, expressing protein, and performing appropriate functional assays. These operations will allow tailoring microbial strains to use renewable feedstocks for production of biofuels, bioderived chemicals, fertilizers, and other coproducts for profitable and sustainable biorefineries. Published by Elsevier Inc.

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

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

Predicted secondary structure similarity in the absence of primary amino acid sequence homology: hepatitis B virus open reading frames.

PubMed Central

Schaeffer, E; Sninsky, J J

1984-01-01

Proteins that are related evolutionarily may have diverged at the level of primary amino acid sequence while maintaining similar secondary structures. Computer analysis has been used to compare the open reading frames of the hepatitis B virus to those of the woodchuck hepatitis virus at the level of amino acid sequence, and to predict the relative hydrophilic character and the secondary structure of putative polypeptides. Similarity is seen at the levels of relative hydrophilicity and secondary structure, in the absence of sequence homology. These data reinforce the proposal that these open reading frames encode viral proteins. Computer analysis of this type can be more generally used to establish structural similarities between proteins that do not share obvious sequence homology as well as to assess whether an open reading frame is fortuitous or codes for a protein. PMID:6585835

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.

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…

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

The type II pullulanase of Thermococcus hydrothermalis: molecular characterization of the gene and expression of the catalytic domain.

PubMed

Erra-Pujada, M; Debeire, P; Duchiron, F; O'Donohue, M J

1999-05-01

The gene encoding a hyperthermostable type II pullulanase produced by Thermococcus hydrothermalis (Th-Apu) has been isolated. Analysis of a total of 5.2 kb of genomic DNA has revealed the presence of three open reading frames, one of which (apuA) encodes the pullulanase. This enzyme is composed of 1,339 amino acid residues and exhibits a multidomain structure. In addition to a typical N-terminal signal peptide, Th-Apu possesses a catalytic domain, a domain bearing S-layer homology-like motifs, a Thr-rich region, and a potential C-terminal transmembrane domain. The presence of these noncatalytic domains suggests that Th-Apu may be anchored to the cell surface and be O glycosylated.

The Type II Pullulanase of Thermococcus hydrothermalis: Molecular Characterization of the Gene and Expression of the Catalytic Domain

PubMed Central

Erra-Pujada, Marta; Debeire, Philippe; Duchiron, Francis; O’Donohue, Michael J.

1999-01-01

The gene encoding a hyperthermostable type II pullulanase produced by Thermococcus hydrothermalis (Th-Apu) has been isolated. Analysis of a total of 5.2 kb of genomic DNA has revealed the presence of three open reading frames, one of which (apuA) encodes the pullulanase. This enzyme is composed of 1,339 amino acid residues and exhibits a multidomain structure. In addition to a typical N-terminal signal peptide, Th-Apu possesses a catalytic domain, a domain bearing S-layer homology-like motifs, a Thr-rich region, and a potential C-terminal transmembrane domain. The presence of these noncatalytic domains suggests that Th-Apu may be anchored to the cell surface and be O glycosylated. PMID:10322035

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.

Stem and Derivational-Suffix Processing during Reading by French Second and Third Graders

ERIC Educational Resources Information Center

Cole, Pascale; Bouton, Sophie; Leuwers, Christel; Casalis, Severine; Sprenger-Charolles, Liliane

2012-01-01

Morphological processing by French children was investigated in two experiments. The first showed that second and third graders read pseudowords such as "chat-ure" ("cat-ish") composed of an illegally combined real stem and real derivational suffix faster and more accurately than they read matched pseudowords composed of a pseudostem and a real…

The mitochondnal genome of Aspergillus nidulans contains reading frames homologous to the human URFs 1 and 4.

PubMed Central

Brown, T A; Davies, R W; Ray, J A; Waring, R B; Scazzocchio, C

1983-01-01

A 2830-bp segment of the mitochondrial genome of the fungus Aspergillus nidulans was sequenced and shown to contain two unidentified reading frames (URFs). These reading frames are 352 and 488 codons in length, and would specify unmodified proteins of mol. wts. 39,000 and 54,000, respectively. The derived amino acid sequences indicate that these genes are equivalent to the human mitochondrial URFs 1 and 4, with 39% amino acid homology for URF1 and 26% for URF4. Both URFs were shown by secondary structure predictions to code for predominantly beta-sheeted proteins with strong structural conservation between the fungal and human homologues. Counterparts of mammalian URFs have not previously been identified in non-mammalian genomes, and the discovery that A. nidulans possesses reading frames so closely homologous with URF1 and URF4 shows that these genes are of general functional importance in the mitochondria of diverse species. PMID:11894959

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.

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

Identification of Coq11, a New Coenzyme Q Biosynthetic Protein in the CoQ-Synthome in Saccharomyces cerevisiae*

PubMed Central

Allan, Christopher M.; Awad, Agape M.; Johnson, Jarrett S.; Shirasaki, Dyna I.; Wang, Charles; Blaby-Haas, Crysten E.; Merchant, Sabeeha S.; Loo, Joseph A.; Clarke, Catherine F.

2015-01-01

Coenzyme Q (Q or ubiquinone) is a redox active lipid composed of a fully substituted benzoquinone ring and a polyisoprenoid tail and is required for mitochondrial electron transport. In the yeast Saccharomyces cerevisiae, Q is synthesized by the products of 11 known genes, COQ1–COQ9, YAH1, and ARH1. The function of some of the Coq proteins remains unknown, and several steps in the Q biosynthetic pathway are not fully characterized. Several of the Coq proteins are associated in a macromolecular complex on the matrix face of the inner mitochondrial membrane, and this complex is required for efficient Q synthesis. Here, we further characterize this complex via immunoblotting and proteomic analysis of tandem affinity-purified tagged Coq proteins. We show that Coq8, a putative kinase required for the stability of the Q biosynthetic complex, is associated with a Coq6-containing complex. Additionally Q6 and late stage Q biosynthetic intermediates were also found to co-purify with the complex. A mitochondrial protein of unknown function, encoded by the YLR290C open reading frame, is also identified as a constituent of the complex and is shown to be required for efficient de novo Q biosynthesis. Given its effect on Q synthesis and its association with the biosynthetic complex, we propose that the open reading frame YLR290C be designated COQ11. PMID:25631044

Mrp--a new auxiliary gene essential for optimal expression of methicillin resistance in Staphylococcus aureus.

PubMed

Wu, S W; De Lencastre, H

1999-01-01

Screening of a library of Tn551 insertional mutants selected for reduction in the methicillin resistance level of the parental Staphylococcus aureus strain COL resulted in the isolation of mutant RUSA266 in which the minimal inhibitory concentration (MIC) of the parent was reduced from 1,600 to 1.5 micrograms/mL. Cloning and sequencing of the vicinity of the insertion site omega 726 identified an open reading frame (orf1365) encoding a very large polypeptide of more than 1,365 amino acids. A unique feature of the deduced amino acid sequence was the presence of multiple tandem repeats of 75 amino acids in the polypeptide, reminiscent of the structure of high-molecular-weight cell-surface proteins EF* and Emb identified in some streptococcal strains. Mutant RUSA266 with the inactivated gene, which we shall provisionally refer to as mrp (for multiple repeat polypeptide), produced a peptidoglycan with altered muropeptide composition, and both the reduced antibiotic resistance and the altered cell wall composition were co-transduced in back-crosses into the parental strain COL. Additional sequencing upstream of mrp has revealed that this gene was part of a five-gene cluster occupying a 9.2-kb region of the staphylococcal chromosome and was composed of glmM (directly upstream of mrp), two open reading frames orf310 and orf269 coding for two hypothetical proteins, and the gene encoding the staphylococcal arginase (arg). Transcriptional analysis demonstrated that the five genes in the cluster were transcribed together.

Identification of Coq11, a New Coenzyme Q Biosynthetic Protein in the CoQ-Synthome in Saccharomyces cerevisiae

DOE PAGES

Allan, Christopher M.; Awad, Agape M.; Johnson, Jarrett S.; ...

2015-01-28

Coenzyme Q (Q or ubiquinone) is a redox active lipid composed of a fully substituted benzoquinone ring and a polyisoprenoid tail and is required for mitochondrial electron transport. In the yeast Saccharomyces cerevisiae, Q is synthesized by the products of 11 known genes, COQ1–COQ9, YAH1, and ARH1. The function of some of the Coq proteins remains unknown, and several steps in the Q biosynthetic pathway are not fully characterized. Several of the Coq proteins are associated in a macromolecular complex on the matrix face of the inner mitochondrial membrane, and this complex is required for efficient Q synthesis. In thismore » paper, we further characterize this complex via immunoblotting and proteomic analysis of tandem affinity-purified tagged Coq proteins. We show that Coq8, a putative kinase required for the stability of the Q biosynthetic complex, is associated with a Coq6-containing complex. Additionally Q 6 and late stage Q biosynthetic intermediates were also found to co-purify with the complex. A mitochondrial protein of unknown function, encoded by the YLR290C open reading frame, is also identified as a constituent of the complex and is shown to be required for efficient de novo Q biosynthesis. Finally, given its effect on Q synthesis and its association with the biosynthetic complex, we propose that the open reading frame YLR290C be designated COQ11.« less

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 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.

Updated optical read/write memory system components

NASA Technical Reports Server (NTRS)

1973-01-01

The fabrication of an updated block data composer and holographic storage array for a breadboard holographic read/write memory system is described. System considerations such as transform optics and controlled aberration lens design are described along with the block data composer, photoplastic recording materials, and material development.

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.

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...

Cloning and characterization of an alternatively spliced gene in proximal Xq28 deleted in two patients with intersexual genitalia and myotubular myopathy

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

Laporte, J.; Hu, Ling-Jia; Kretz, C.

1997-05-01

We have identified a novel human gene that is entirely deleted in two boys with abnormal genital development and myotubular myopathy (MTM1). The gene, F18, is located in proximal Xq28, approximately 80 kb centromeric to the recently isolated MTM1 gene. Northern analysis of mRNA showed a ubiquitous pattern and suggested high levels of expression in skeletal muscle, brain, and heart. A transcript of 4.6 kb was detected in a range of tissues, and additional alternate forms of 3.8 and 2.6 kb were present in placenta and pancreas, respectively. The gene extends over 100 kb and is composed of at leastmore » seven exons, of which two are non-coding. Sequence analysis of a 4.6-kb cDNA contig revealed two overlapping open reading frames (ORFs) that encode putative proteins of 701 and 424 amino acids, respectively. Two alternative spliced transcripts affecting the large open reading frame were identified that, together with the Northern blot results, suggest that distinct proteins are derived from the gene. No significant homology to other known proteins was detected, but segments of the first ORF encode polyglutamine tracts and proline-rich domains, which are frequently observed in DNA-binding proteins. The F18 gene is a strong candidate for being implicated in the intersexual genitalia present in the two MTM1-deleted patients. The gene also serves as a candidate for other disorders that map to proximal Xq28. 15 refs., 3 figs., 1 tab.« less

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...

Identification of the initiation site of poliovirus polyprotein synthesis

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

Dorner, A.J.; Dorner, L.F.; Larsen, G.R.

1982-06-01

The complete nucleotide sequence of poliovirus RNA has a long open reading frame capable of encoding the precursor polyprotein NCVPOO. The first AUG codon in this reading frame is located 743 nucleotides from the 5' end of the RNA and is preceded by eight AUG codons in all three reading frames. Because all proteins that map at the amino terminus of the polyprotein (P1-1a, VPO, and VP4) are blocked at their amino termini and previous studies of ribosome binding have been inconclusive, direct identification of the initiation site of protein synthesis was difficult. We separated and identified all of themore » tryptic peptides of capsid protein VP4 and correlated these peptides with the amino acid sequence predicted to follow the AUG codon at nucleotide 743. Our data indicate that VP4 begins with a blocked glycine that is encoded immediately after the AUG codon at nucleotide 743. An S1 nuclease analysis of poliovirus mRNA failed to reveal a splice in the 5' region. We concluded that synthesis of poliovirus polyprotein is initiated at nucleotide 743, the first AUG codon in the long open reading frame.« less

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.

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

Molecular characterization of African orthobunyaviruses.

PubMed

Yandoko, E Nakouné; Gribaldo, S; Finance, C; Le Faou, A; Rihn, B H

2007-06-01

The genus Orthobunyavirus is composed of segmented, negative-sense RNA viruses that are responsible for mild to severe human diseases. To date, no molecular studies of bunyaviruses in the genus Orthobunyavirus from central Africa have been reported, and their classification relies on serological testing. Four new primer pairs for RT-PCR amplification and sequencing of the complete genomic small (S) RNA segments of 10 orthobunyaviruses isolated from the Central African Republic and pertaining to five different serogroups have been designed and evaluated. Phylogenetic analysis showed that these 10 viruses belong to the Bunyamwera serogroup. The S segment sequences differ from those of the Bunyamwera virus reference strain by 5-15 % at the nucleotide level, and both overlapping reading frames, encoding the nucleocapsid (N) and non-structural (NS) proteins, were evident in sequenced genomes. This study should improve diagnosis and surveillance of African bunyaviruses.

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.

The organisation and interviral homologies of genes at the 3' end of tobacco rattle virus RNA1

PubMed Central

Boccara, Martine; Hamilton, William D. O.; Baulcombe, David C.

1986-01-01

The RNA1 of tobacco rattle virus (TRV) has been cloned as cDNA and the nucleotide sequence determined of 2 kb from the 3'-terminal region. The sequence contains three long open reading frames. One of these starts 5' of the cDNA and probably corresponds to the carboxy-terminal sequence of a 170-K protein encoded on RNA1. The deduced protein sequence from this reading frame shows homology with the putative replicases of tobacco mosaic virus (TMV) and tricornaviruses. The location of the second open reading frame, which encodes a 29-K polypeptide, was shown by Northern blot analysis to coincide with a 1.6-kb subgenomic RNA. The validity of this reading frame was confirmed by showing that the cDNA extending over this region could be transcribed and translated in vitro to produce a polypeptide of the predicted size which co-migrates in electrophoresis with a translation product of authentic viral RNA. The sequence of this 29-K polypeptide showed homology with two regions in the 30-K protein of TMV. This homology includes positions in the TMV 30-K protein where mutations have been identified which affect the transport of virus between cells. The third open reading frame encodes a potential 16-K protein and was shown by Northern blot hybridisation to be contained within the region of a 0.7-kb subgenomic RNA which is found in cellular RNA of infected cells but not virus particles. The many similarities between TRV and TMV in viral morphology, gene organisation and sequence suggest that these two viral groups may share a common viral ancestor. ImagesFig. 2.Fig. 3. PMID:16453668

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.

HORN-6 special-purpose clustered computing system for electroholography.

PubMed

Ichihashi, Yasuyuki; Nakayama, Hirotaka; Ito, Tomoyoshi; Masuda, Nobuyuki; Shimobaba, Tomoyoshi; Shiraki, Atsushi; Sugie, Takashige

2009-08-03

We developed the HORN-6 special-purpose computer for holography. We designed and constructed the HORN-6 board to handle an object image composed of one million points and constructed a cluster system composed of 16 HORN-6 boards. Using this HORN-6 cluster system, we succeeded in creating a computer-generated hologram of a three-dimensional image composed of 1,000,000 points at a rate of 1 frame per second, and a computer-generated hologram of an image composed of 100,000 points at a rate of 10 frames per second, which is near video rate, when the size of a computer-generated hologram is 1,920 x 1,080. The calculation speed is approximately 4,600 times faster than that of a personal computer with an Intel 3.4-GHz Pentium 4 CPU.

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

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.

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…

The Eight Frame Colored Squiggle Technique

ERIC Educational Resources Information Center

Steinhardt, Lenore

2006-01-01

In this art therapy adaptation of the squiggle technique, the client draws eight colored squiggles on a paper folded into eight frames and then develops them into images utilizing a full range of color. The client is encouraged to write titles on each frame and use them to compose a story. This technique often stimulates emergence of meaningful…

Framing new research in science literacy and language use: Authenticity, multiple discourses, and the Third Space

NASA Astrophysics Data System (ADS)

Wallace, Carolyn S.

2004-11-01

This article presents a theoretical framework in the form of a model on which to base research in scientific literacy and language use. The assumption guiding the framework is that scientific literacy is comprised of the abilities to think metacognitively, to read and write scientific texts, and to apply the elements of a scientific argument. The framework is composed of three theoretical constructs: authenticity, multiple discourses, and Bhabha's Third Space. Some of the implications of the framework are that students need opportunities to (a) use scientific language in everyday situations; (b) negotiate readily among the many discourse genres of science; and (c) collaborate with teachers and peers on the meaning of scientific language. These ideas are illustrated with data excerpts from contemporary research studies. A set of potential research issues for the future is posed at the end of the article.

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.

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…

Frames and counter-frames giving meaning to dementia: a framing analysis of media content.

PubMed

Van Gorp, Baldwin; Vercruysse, Tom

2012-04-01

Media tend to reinforce the stigmatization of dementia as one of the most dreaded diseases in western society, which may have repercussions on the quality of life of those with the illness. The persons with dementia, but also those around them become imbued with the idea that life comes to an end as soon as the diagnosis is pronounced. The aim of this paper is to understand the dominant images related to dementia by means of an inductive framing analysis. The sample is composed of newspaper articles from six Belgian newspapers (2008-2010) and a convenience sample of popular images of the condition in movies, documentaries, literature and health care communications. The results demonstrate that the most dominant frame postulates that a human being is composed of two distinct parts: a material body and an immaterial mind. If this frame is used, the person with dementia ends up with no identity, which is in opposition to the Western ideals of personal self-fulfilment and individualism. For each dominant frame an alternative counter-frame is defined. It is concluded that the relative absence of counter-frames confirms the negative image of dementia. The inventory might be a help for caregivers and other professionals who want to evaluate their communication strategy. It is discussed that a more resolute use of counter-frames in communication about dementia might mitigate the stigma that surrounds dementia. Copyright © 2012 Elsevier Ltd. All rights reserved.

Relationship of word- and sentence-level working memory to reading and writing in second, fourth, and sixth grade.

PubMed

Berninger, Virginia W; Abbott, Robert D; Swanson, H Lee; Lovitt, Dan; Trivedi, Pam; Lin, Shin-Ju Cindy; Gould, Laura; Youngstrom, Marci; Shimada, Shirley; Amtmann, Dagmar

2010-04-01

The purpose of this study was to evaluate the contribution of working memory at the word and sentence levels of language to reading and writing outcomes. Measures of working memory at the word and sentence levels, reading and writing, were administered to 2nd (N = 122), 4th (N = 222), and 6th (N = 105) graders. Structural equation modeling was used to evaluate whether the 2 predictor working memory factors contributed unique variance beyond their shared covariance to each of 5 outcome factors: handwriting, spelling, composing, word reading, and reading comprehension. At each grade level, except for handwriting and composing in 6th grade, the word-level working memory factor contributed unique variance to each reading and writing outcome. The text-level working memory factor contributed unique variance to reading comprehension in 4th and 6th grade. The clinical significance of these findings for assessment and intervention is discussed.

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.

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…

From Autos To Stereos. A Collection of Readings.

ERIC Educational Resources Information Center

Ferri, Kathy

Designed to provide materials which the high school teacher can use to teach some of the basic reading skills or as supplementary reading material, this guide is composed of thirty-five articles of general interest which are vocationally oriented, followed by exercises designed to test comprehension and to teach reading concepts. The articles have…

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…

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

Clinical predictors of the optimal spectacle correction for comfort performing desktop tasks.

PubMed

Leffler, Christopher T; Davenport, Byrd; Rentz, Jodi; Miller, Amy; Benson, William

2008-11-01

The best strategy for spectacle correction of presbyopia for near tasks has not been determined. Thirty volunteers over the age of 40 years were tested for subjective accommodative amplitude, pupillary size, fusional vergence, interpupillary distance, arm length, preferred working distance, near and far visual acuity and preferred reading correction in the phoropter and trial frames. Subjects performed near tasks (reading, writing and counting change) using various spectacle correction strengths. Predictors of the correction maximising near task comfort were determined by multivariable linear regression. The mean age was 54.9 years (range 43 to 71) and 40 per cent had diabetes. Significant predictors of the most comfortable addition in univariate analyses were age (p<0.001), interpupillary distance (p=0.02), fusional vergence amplitude (p=0.02), distance visual acuity in the worse eye (p=0.01), vision at 40 cm in the worse eye with distance correction (p=0.01), duration of diabetes (p=0.01), and the preferred correction to read at 40 cm with the phoropter (p=0.002) or trial frames (p<0.001). Target distance selected wearing trial frames (in dioptres), arm length, and accommodative amplitude were not significant predictors (p>0.15). The preferred addition wearing trial frames holding a reading target at a distance selected by the patient was the only independent predictor. Excluding this variable, distance visual acuity was predictive independent of age or near vision wearing distance correction. The distance selected for task performance was predicted by vision wearing distance correction at near and at distance. Multivariable linear regression can be used to generate tables based on distance visual acuity and age or near vision wearing distance correction to determine tentative near spectacle addition. Final spectacle correction for desktop tasks can be estimated by subjective refraction with trial frames.

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.

The Reciprocal Relations between Morphological Processes and Reading

ERIC Educational Resources Information Center

Kruk, Richard S.; Bergman, Krista

2013-01-01

Reciprocal relations between emerging morphological processes and reading skills were examined in a longitudinal study tracking children from Grade 1 through Grade 3. The aim was to examine predictive relationships between productive morphological processing involving composing and decomposing of inflections and derivations, reading ability for…

Implementing PCRP: Fact or Fiction? Communication Skills.

ERIC Educational Resources Information Center

Rosecky, Marion

The Pennsylvania Comprehensive Reading/Communication Arts Plan (PCRP) is a language arts curriculum providing four critical experiences that all students need in order to become competent in reading, writing, listening, and speaking: responding to literature, sustained silent reading, oral and written composing, and investigating and mastering…

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.

Logical Structure and the Composing Process.

ERIC Educational Resources Information Center

Russow, Lilly-Marlene

An important aspect of the composing process is the element of organization--the coherent development of ideas and considerations of relevance. Most investigations of this aspect have focused on prewriting behavior or on "heuristics,""frames," or other approaches that presuppose that organization is something imposed from the…

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…

The Effect of Reading Comprehension and Problem Solving Strategies on Classifying Elementary 4th Grade Students with High and Low Problem Solving Success

ERIC Educational Resources Information Center

Ulu, Mustafa

2017-01-01

In this study, the effect of fluent reading (speed, reading accuracy percentage, prosodic reading), comprehension (literal comprehension, inferential comprehension) and problem solving strategies on classifying students with high and low problem solving success was researched. The sampling of the research is composed of 279 students at elementary…

Annotated A.B.E. Bibliography.

ERIC Educational Resources Information Center

Anderson, Ethel E., Comp.

Based on lists submitted by practitioners working in the 0 to grade 9 levels of English-speaking adult basic education (ABE) in Canada, this annotated bibliography is composed of 283 items currently in use. Six categories are included: (1) reading, which covers reading systems, instructional material, phonics, and independent reading; (2) language…

Perspectives: Readings on Contemporary American Government.

ERIC Educational Resources Information Center

Close Up Foundation, Arlington, VA.

This document is composed of readings and activities concerning the government of the United States. The main topics addressed are: the Constitution, the Presidency, the Congress, the Judiciary, the bureaucracy, interest groups, the media, and the people. Each section begins with an introductory reading, followed by essays from prominent citizens…

Comprehension Tools for Teachers: Reading for Understanding from Prekindergarten through Fourth Grade

ERIC Educational Resources Information Center

Connor, Carol McDonald; Phillips, Beth M.; Kaschak, Michael; Apel, Kenn; Kim, Young-Suk; Al Otaiba, Stephanie; Crowe, Elizabeth C.; Thomas-Tate, Shurita; Johnson, Lakeisha Cooper; Lonigan, Christopher J.

2014-01-01

This paper describes the theoretical framework, as well as the development and testing of the intervention, "Comprehension Tools for Teachers" (CTT), which is composed of eight component interventions targeting malleable language and reading comprehension skills that emerging research indicates contribute to proficient reading for…

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.

Identification of a Linked Set of Genes in Serpulina hyodysenteriae (B204) Predicted To Encode Closely Related 39-Kilodalton Extracytoplasmic Proteins

PubMed Central

Gabe, Jeffrey D.; Dragon, Elizabeth; Chang, Ray-Jen; McCaman, Michael T.

1998-01-01

A tandem pair of nearly identical genes from Serpulina hyodysenteriae (B204) were cloned and sequenced. The full open reading frame of one gene and the partial open reading frame of the neighboring gene appear to encode secreted proteins which are homologous to, yet distinct from, the 39-kDa extracytoplasmic protein purified from the membrane fraction of S. hyodysenteriae. We have designated these newly identified genes vspA and vspB (for variable surface protein). PMID:9440540

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.

Envisioning Collaborative Composing in Music Education: Learning and Negotiation of Meaning in "operabyyou.com"

ERIC Educational Resources Information Center

Partti, Heidi; Westerlund, Heidi

2013-01-01

This qualitative instrumental case study examines collaborative composing in the "operabyyou.com" online music community from the perspective of learning by utilising the concept of a "community of practice" as a heuristic frame. The article suggests that although informal music practices offer important opportunities for…

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

Processing Time and Cognitive Effort of Longhand Note Taking When Reading and Summarizing a Structured or Linear Text

ERIC Educational Resources Information Center

Olive, Thierry; Barbier, Marie-Laure

2017-01-01

We examined longhand note taking strategies when reading and summarizing a source text that was formatted with bullets or that was presented in a single paragraph. We analyzed cognitive effort when reading the source text, when jotting notes, when reading the notes, and when composing the summary, as well as time spent in these activities and the…

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.

Introducing and Sustaining Close Reading and Writing through Poetry

ERIC Educational Resources Information Center

Timmermans, Karren M.; Johnson, Angie

2017-01-01

Close reading of poetry scaffolds readers and writers as they come to understand the form and function of poetry and transfer those skills to writing. In this teaching tip, the authors explain a way in which primary teachers can introduce close reading and move young students toward composing and presenting poetry.

Morphological Processing in Reading Disabled and Skilled Spanish Children

ERIC Educational Resources Information Center

Lazaro, Miguel; Camacho, Lourdes; Burani, Cristina

2013-01-01

This article presents the results of a lexical decision experiment in which the base frequency (BF) effect is explored in reading disabled children and skilled readers. Three groups of participants were created. The first group was composed of children with reading disorders, the second group of skilled readers matched with the first group for…

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

77 FR 34411 - Branch Technical Position on Concentration Averaging and Encapsulation

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-11

... of cartridge filters as a homogeneous waste: Cartridge filters are used to remove radioactive solids from various systems in a nuclear power plant. Filters are typically composed of thin metal or plastic frames with a corrugated or wound paper or synthetic filter media enclosed within the frame. Although the...

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

Rolling Circle Translation of Circular RNA in Living Human Cells.

PubMed

Abe, Naoko; Matsumoto, Ken; Nishihara, Mizuki; Nakano, Yukiko; Shibata, Aya; Maruyama, Hideto; Shuto, Satoshi; Matsuda, Akira; Yoshida, Minoru; Ito, Yoshihiro; Abe, Hiroshi

2015-11-10

We recently reported that circular RNA is efficiently translated by a rolling circle amplification (RCA) mechanism in a cell-free Escherichia coli translation system. Recent studies have shown that circular RNAs composed of exonic sequences are abundant in human cells. However, whether these circular RNAs can be translated into proteins within cells remains unclear. In this study, we prepared circular RNAs with an infinite open reading frame and tested their translation in eukaryotic systems. Circular RNAs were translated into long proteins in rabbit reticulocyte lysate in the absence of any particular element for internal ribosome entry, a poly-A tail, or a cap structure. The translation systems in eukaryote can accept much simpler RNA as a template for protein synthesis by cyclisation. Here, we demonstrated that the circular RNA is efficiently translated in living human cells to produce abundant protein product by RCA mechanism. These findings suggest that translation of exonic circular RNAs present in human cells is more probable than previously thought.

Rolling Circle Translation of Circular RNA in Living Human Cells

PubMed Central

Abe, Naoko; Matsumoto, Ken; Nishihara, Mizuki; Nakano, Yukiko; Shibata, Aya; Maruyama, Hideto; Shuto, Satoshi; Matsuda, Akira; Yoshida, Minoru; Ito, Yoshihiro; Abe, Hiroshi

2015-01-01

We recently reported that circular RNA is efficiently translated by a rolling circle amplification (RCA) mechanism in a cell-free Escherichia coli translation system. Recent studies have shown that circular RNAs composed of exonic sequences are abundant in human cells. However, whether these circular RNAs can be translated into proteins within cells remains unclear. In this study, we prepared circular RNAs with an infinite open reading frame and tested their translation in eukaryotic systems. Circular RNAs were translated into long proteins in rabbit reticulocyte lysate in the absence of any particular element for internal ribosome entry, a poly-A tail, or a cap structure. The translation systems in eukaryote can accept much simpler RNA as a template for protein synthesis by cyclisation. Here, we demonstrated that the circular RNA is efficiently translated in living human cells to produce abundant protein product by RCA mechanism. These findings suggest that translation of exonic circular RNAs present in human cells is more probable than previously thought. PMID:26553571

BRICHOS domain-containing leukocyte cell-derived chemotaxin 1-like cDNA from disk abalone Haliotis discus discus.

PubMed

Kim, Yucheol; De Zoysa, Mahanama; Lee, Youngdeuk; Whang, Ilson; Lee, Jehee

2010-11-01

A BRICHOS domain-containing leukocyte cell-derived chemotaxin 1-like cDNA was cloned from the disk abalone (Haliotis discus discus) and designated as AbLECT-1. A full-length (705 bp) of AbLECT-1 cDNA was composed of a 576 bp open reading frame that translates into a putative peptide of 192 amino acids. Deduced amino acid sequence of AbLECT-1 had 15.5- and 27.8% identity and similarity to human LECT-1, respectively. Quantitative real-time PCR analysis results showed that the mRNA of AbLECT-1 was constitutively expressed in abalone hemocytes, gills, mantle, muscle, digestive tract and hepatopancreas in a tissue-specific manner. Moreover, the AbLECT-1 transcription level was induced in hemocytes after challenge with Vibrio alginolyticus, Vibrio parahemolyticus, and Listeria monocytogenes suggesting that it may be involved in immune response reactions in abalone. Copyright 2010 Elsevier Ltd. All rights reserved.

Purification, cDNA cloning, and characterization of LysM-containing plant chitinase from horsetail (Equisetum arvense).

PubMed

Inamine, Saki; Onaga, Shoko; Ohnuma, Takayuki; Fukamizo, Tamo; Taira, Toki

2015-01-01

Chitinase-A (EaChiA), molecular mass 36 kDa, was purified from the vegetative stems of a horsetail (Equisetum arvense) using a series of column chromatography. The N-terminal amino acid sequence of EaChiA was similar to the lysin motif (LysM). A cDNA encoding EaChiA was cloned by rapid amplification of cDNA ends and polymerase chain reaction. It consisted of 1320 nucleotides and encoded an open reading frame of 361 amino acid residues. The deduced amino acid sequence indicated that EaChiA is composed of a N-terminal LysM domain and a C-terminal plant class IIIb chitinase catalytic domain, belonging to the glycoside hydrolase family 18, linked by proline-rich regions. EaChiA has strong chitin-binding activity, however, no antifungal activity. This is the first report of a chitinase from Equisetopsida, a class of fern plants, and the second report of a LysM-containing chitinase from a plant.

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.

Structural studies of ROK fructokinase YdhR from Bacillus subtilis : insights into substrate binding and fructose specificity.

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

Nocek, B.; Stein, A.; Jedrzejczak, R.

2011-02-18

The main pathway of bacterial sugar phosphorylation utilizes specific phosphoenolpyruvate phosphotransferase system (PTS) enzymes. In addition to the classic PTS system, a PTS-independent secondary system has been described in which nucleotide-dependent sugar kinases are used for monosaccharide phosphorylation. Fructokinase (FK), which phosphorylates d-fructose with ATP as a cofactor, has been shown to be a member of this secondary system. Bioinformatic analysis has shown that FK is a member of the 'ROK' (bacterial Repressors, uncharacterized Open reading frames, and sugar Kinases) sequence family. In this study, we report the crystal structures of ROK FK from Bacillus subtilis (YdhR) (a) apo andmore » in the presence of (b) ADP and (c) ADP/d-fructose. All structures show that YdhR is a homodimer with a monomer composed of two similar {alpha}/{beta} domains forming a large cleft between domains that bind ADP and d-fructose. Enzymatic activity assays support YdhR function as an ATP-dependent fructose kinase.« less

Molecular Mechanisms of Innate Immune Inhibition by Non-Segmented Negative-Sense RNA Viruses

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

Chatterjee, Srirupa; Basler, Christopher F.; Amarasinghe, Gaya K.

The host innate immune system serves as the first line of defense against viral infections. Germline-encoded pattern recognition receptors detect molecular patterns associated with pathogens and activate innate immune responses. Of particular relevance to viral infections are those pattern recognition receptors that activate type I interferon responses, which establish an antiviral state. The order Mononegavirales is composed of viruses that possess single-stranded, non-segmented negative-sense (NNS) RNA genomes and are important human pathogens that consistently antagonize signaling related to type I interferon responses. NNS viruses have limited encoding capacity compared to many DNA viruses, and as a likely consequence, most openmore » reading frames encode multifunctional viral proteins that interact with host factors in order to evade host cell defenses while promoting viral replication. In this review, we will discuss the molecular mechanisms of innate immune evasion by select NNS viruses. A greater understanding of these interactions will be critical in facilitating the development of effective therapeutics and viral countermeasures.« less

Slip of grip of a molecular motor on a crowded track: Modeling shift of reading frame of ribosome on RNA template

NASA Astrophysics Data System (ADS)

Mishra, Bhavya; Schütz, Gunter M.; Chowdhury, Debashish

2016-06-01

We develop a stochastic model for the programmed frameshift of ribosomes synthesizing a protein while moving along a mRNA template. Normally the reading frame of a ribosome decodes successive triplets of nucleotides on the mRNA in a step-by-step manner. We focus on the programmed shift of the ribosomal reading frame, forward or backward, by only one nucleotide which results in a fusion protein; it occurs when a ribosome temporarily loses its grip to its mRNA track. Special “slippery” sequences of nucleotides and also downstream secondary structures of the mRNA strand are believed to play key roles in programmed frameshift. Here we explore the role of an hitherto neglected parameter in regulating -1 programmed frameshift. Specifically, we demonstrate that the frameshift frequency can be strongly regulated also by the density of the ribosomes, all of which are engaged in simultaneous translation of the same mRNA, at and around the slippery sequence. Monte Carlo simulations support the analytical predictions obtained from a mean-field analysis of the stochastic dynamics.

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.

An open reading frame in intron seven of the sea urchin DNA-methyltransferase gene codes for a functional AP1 endonuclease.

PubMed

Cioffi, Anna Valentina; Ferrara, Diana; Cubellis, Maria Vittoria; Aniello, Francesco; Corrado, Marcella; Liguori, Francesca; Amoroso, Alessandro; Fucci, Laura; Branno, Margherita

2002-08-01

Analysis of the genome structure of the Paracentrotus lividus (sea urchin) DNA methyltransferase (DNA MTase) gene showed the presence of an open reading frame, named METEX, in intron 7 of the gene. METEX expression is developmentally regulated, showing no correlation with DNA MTase expression. In fact, DNA MTase transcripts are present at high concentrations in the early developmental stages, while METEX is expressed at late stages of development. Two METEX cDNA clones (Met1 and Met2) that are different in the 3' end have been isolated in a cDNA library screening. The putative translated protein from Met2 cDNA clone showed similarity with Escherichia coli endonuclease III on the basis of sequence and predictive three-dimensional structure. The protein, overexpressed in E. coli and purified, had functional properties similar to the endonuclease specific for apurinic/apyrimidinic (AP) sites on the basis of the lyase activity. Therefore the open reading frame, present in intron 7 of the P. lividus DNA MTase gene, codes for a functional AP endonuclease designated SuAP1.

Computer-Based Multimodal Composing Activities, Self-Revision, and L2 Acquisition through Writing

ERIC Educational Resources Information Center

Dzekoe, Richmond

2017-01-01

This study investigated how 22 advanced-low proficiency ESL students used computer-based multimodal composing activities (CBMCAs) to facilitate self-revision and learn English through academic writing in the USA. The CBMCAs involved a combination of writing, listening, visual analysis, and speaking activities. The research was framed within an…

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…

Binary CMOS image sensor with a gate/body-tied MOSFET-type photodetector for high-speed operation

NASA Astrophysics Data System (ADS)

Choi, Byoung-Soo; Jo, Sung-Hyun; Bae, Myunghan; Kim, Sang-Hwan; Shin, Jang-Kyoo

2016-05-01

In this paper, a binary complementary metal oxide semiconductor (CMOS) image sensor with a gate/body-tied (GBT) metal oxide semiconductor field effect transistor (MOSFET)-type photodetector is presented. The sensitivity of the GBT MOSFET-type photodetector, which was fabricated using the standard CMOS 0.35-μm process, is higher than the sensitivity of the p-n junction photodiode, because the output signal of the photodetector is amplified by the MOSFET. A binary image sensor becomes more efficient when using this photodetector. Lower power consumptions and higher speeds of operation are possible, compared to the conventional image sensors using multi-bit analog to digital converters (ADCs). The frame rate of the proposed image sensor is over 2000 frames per second, which is higher than those of the conventional CMOS image sensors. The output signal of an active pixel sensor is applied to a comparator and compared with a reference level. The 1-bit output data of the binary process is determined by this level. To obtain a video signal, the 1-bit output data is stored in the memory and is read out by horizontal scanning. The proposed chip is composed of a GBT pixel array (144 × 100), binary-process circuit, vertical scanner, horizontal scanner, and readout circuit. The operation mode can be selected from between binary mode and multi-bit mode.

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

Functional Grammar and Teaching of Reading--A Pedagogy Based on Graded Teaching of College English in China

ERIC Educational Resources Information Center

Xu, Tuo; Zhang, Beili

2015-01-01

This article discusses the importance of functional grammar and demonstrates its application to the teaching of reading among graded college students. Functional grammar holds that a discourse is composed of two levels: the interior level and the exterior level. Therefore, reading activities involve both linguistic elements and contexts.…

Toroidal surface complexes of bacteriophage {phi}12 are responsible for host-cell attachment

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

Leo-Macias, Alejandra; Katz, Garrett; Wei Hui

2011-06-05

Cryo-electron tomography and subtomogram averaging are utilized to determine that the bacteriophage {phi}12, a member of the Cystoviridae family, contains surface complexes that are toroidal in shape, are composed of six globular domains with six-fold symmetry, and have a discrete density connecting them to the virus membrane-envelope surface. The lack of this kind of spike in a reassortant of {phi}12 demonstrates that the gene for the hexameric spike is located in {phi}12's medium length genome segment, likely to the P3 open reading frames which are the proteins involved in viral-host cell attachment. Based on this and on protein mass estimatesmore » derived from the obtained averaged structure, it is suggested that each of the globular domains is most likely composed of a total of four copies of P3a and/or P3c proteins. Our findings may have implications in the study of the evolution of the cystovirus species in regard to their host specificity. - Research Highlights: > Subtomogram averaging reveals enhanced detail of a {phi}12 cystovirus surface protein complex. > The surface protein complex has a toroidal shape and six-fold symmetry. > It is encoded by the medium-size genome segment. > The proteins of the surface complex most likely are one copy of P3a and three copies of P3c.« less

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.

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.

Computerized Instruction in Translation Strategies for Students in Upper Elementary and Middle School Grades With Persisting Learning Disabilities in Written Language

PubMed Central

Niedo, Jasmin; Tanimoto, Steve; Thompson, Robert H.; Abbott, Robert D.; Berninger, Virginia W.

2016-01-01

Students in grades 5 to 9 (ages 10 to 14; 6 girls, 27 boys) who had persisting specific learning disabilities in transcription (handwriting and spelling) completed three kinds of composition tasks requiring translation (thought to written language) on iPads using alternating transcription modes (stylus or keyboard) across every three lessons: personal narratives (6 lessons) and written summaries about read source material (integrated reading-writing) and heard source material (integrated listening-writing) (12 lessons). Before composing summaries, students clicked sequentially one at a time onto translation strategies, which they read and heard through earphones, and could click on again as needed during summary writing: (a) Level I composing of the very next sentence, and (b) Level II composing of a higher-level discourse structure. ANOVAs showed that Level I strategies were used significantly more often than Level II strategies; but the main effect for transcription mode was not significant. Written summaries of read source material had more errors in main ideas and factual details than heard source materials, but not more irrelevant statements. Applications of results are discussed for using computers for writing instruction, not just accommodations, for students with persisting transcription disabilities. PMID:28670103

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…

Draft Genome Sequencing and Comparative Analysis of Aspergillus sojae NBRC4239

PubMed Central

Sato, Atsushi; Oshima, Kenshiro; Noguchi, Hideki; Ogawa, Masahiro; Takahashi, Tadashi; Oguma, Tetsuya; Koyama, Yasuji; Itoh, Takehiko; Hattori, Masahira; Hanya, Yoshiki

2011-01-01

We conducted genome sequencing of the filamentous fungus Aspergillus sojae NBRC4239 isolated from the koji used to prepare Japanese soy sauce. We used the 454 pyrosequencing technology and investigated the genome with respect to enzymes and secondary metabolites in comparison with other Aspergilli sequenced. Assembly of 454 reads generated a non-redundant sequence of 39.5-Mb possessing 13 033 putative genes and 65 scaffolds composed of 557 contigs. Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae. Comparative analysis identified serine carboxypeptidase and aspartic protease genes unique to A. sojae NBRC4239. While A. oryzae possessed three copies of α-amyalse gene, A. sojae NBRC4239 possessed only a single copy. Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae. The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries. PMID:21659486

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

Cloning and Sequence Analysis of Vibrio halioticoli Genes Encoding Three Types of Polyguluronate Lyase.

PubMed

Sugimura; Sawabe; Ezura

2000-01-01

The alginate lyase-coding genes of Vibrio halioticoli IAM 14596(T), which was isolated from the gut of the abalone Haliotis discus hannai, were cloned using plasmid vector pUC 18, and expressed in Escherichia coli. Three alginate lyase-positive clones, pVHB, pVHC, and pVHE, were obtained, and all clones expressed the enzyme activity specific for polyguluronate. Three genes, alyVG1, alyVG2, and alyVG3, encoding polyguluronate lyase were sequenced: alyVG1 from pVHB was composed of a 1056-bp open reading frame (ORF) encoding 352 amino acid residues; alyVG2 gene from pVHC was composed of a 993-bp ORF encoding 331 amino acid residues; and alyVG3 gene from pVHE was composed of a 705-bp ORF encoding 235 amino acid residues. Comparison of nucleotide and deduced amino acid sequences among AlyVG1, AlyVG2, and AlyVG3 revealed low homologies. The identity value between AlyVG1 and AlyVG2 was 18.7%, and that between AlyVG2 and AlyVG3 was 17.0%. A higher identity value (26.0%) was observed between AlyVG1 and AlyVG3. Sequence comparison among known polyguluronate lyases including AlyVG1, AlyVG2, and AlyVG3 also did not reveal an identical region in these sequences. However, AlyVG1 showed the highest identity value (36.2%) and the highest similarity (73.3%) to AlyA from Klebsiella pneumoniae. A consensus region comprising nine amino acid (YFKAGXYXQ) in the carboxy-terminal region previously reported by Mallisard and colleagues was observed only in AlyVG1 and AlyVG2.

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

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…

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.

The Controllable Ball Joint Mechanism

NASA Astrophysics Data System (ADS)

Tung, Yung Cheng; Chieng, Wei-Hua; Ho, Shrwai

A controllable ball joint mechanism with three rotational degrees of freedom is proposed in this paper. The mechanism is composed of three bevel gears, one of which rotates with respect to a fixed frame and the others rotate with respect to individual floating frames. The output is the resultant motion of the differential motions by the motors that rotates the bevel gears at the fixed frame and the floating frames. The mechanism is capable of a large rotation, and the structure is potentially compact. The necessary inverse and forward kinematic analyses as well as the derivation of kinematic singularity are provided according to the kinematical equivalent structure described in this paper.

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.

Aristotle's "Rhetoric": Reinterpreting Invention.

ERIC Educational Resources Information Center

Quandahl, Ellen

1986-01-01

Shows that Aristotle's common topics are part of a theory of interpretation rather than a collection of devices for invention. Argues that it is more Aristotelian and more useful to understand composing as interpretation and not invention. Uses scholarship to inform pedagogy and to reorient composing toward acts of reading. (EL)

Pre-Service Teachers' Perceptions on Game Based Learning Scenarios in Primary Reading and Writing Instruction Courses

ERIC Educational Resources Information Center

Karadag, Ruhan

2015-01-01

The aim of this study was to explore pre-service teachers' perceptions on the use of game-based learning in a Primary Reading and Writing Instruction Course. A mixed method research was used in the study. Participants were composed of a total of 189 pre-service teachers taking the Primary Reading and Writing Instruction course during the fall term…

The role of message framing in promoting MMR vaccination: evidence of a loss-frame advantage.

PubMed

Abhyankar, Purva; O'Connor, Daryl B; Lawton, Rebecca

2008-01-01

This study examined the effects of message framing on intentions to obtain the measles, mumps and rubella (MMR) vaccine for one's child and investigated whether Theory of Planned Behaviour (TPB) and perceived outcome efficacy variables mediate and/or moderate message framing effects. One hundred and forty women read either a loss-framed or gain-framed message and then completed measures assessing their intentions to obtain the MMR vaccine for their child, and TPB and outcome efficacy variables. Exposure to the loss frame increased intentions to obtain the MMR vaccine and influenced perceptions of outcome efficacy. This suggests that outcome efficacy, but not other TPB variables may mediate framing effects within the context of MMR vaccination. Message frame, in addition to TPB variables, significantly predicted unique variance in behavioural intentions. These findings are discussed within the context of Prospect Theory, perceived risk and prevention/detection behaviours.

Beyond the Enthymeme: Sorites, Critical Thinking, and the Composing Process.

ERIC Educational Resources Information Center

Hill, Carolyn

A teacher presents a writing exercise designed to facilitate audience-directed, critical thinking during the process of composing, that starts students thinking in terms of sorites and enthymemes. Students first read a CIA manual, "Psychological Operations in Guerrilla Warfare," that instructs the Contra guerrillas in illegal acts and…

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.

Drawing on Text Features for Reading Comprehension and Composing

ERIC Educational Resources Information Center

Risko, Victoria J.; Walker-Dalhouse, Doris

2011-01-01

Students read multiple-genre texts such as graphic novels, poetry, brochures, digitized texts with videos, and informational and narrative texts. Features such as overlapping illustrations and implied cause-and-effect relationships can affect students' comprehension. Teaching with these texts and drawing attention to organizational features hold…

Planning actions in robot automated operations

NASA Technical Reports Server (NTRS)

Das, A.

1988-01-01

Action planning in robot automated operations requires intelligent task level programming. Invoking intelligence necessiates a typical blackboard based architecture, where, a plan is a vector between the start frame and the goal frame. This vector is composed of partially ordered bases. A partial ordering of bases presents good and bad sides in action planning. Partial ordering demands the use of a temporal data base management system.

"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

Proteomic Characterization of Bovine Herpesvirus 4 Extracellular Virions

PubMed Central

Lété, Céline; Palmeira, Leonor; Leroy, Baptiste; Mast, Jan; Machiels, Bénédicte; Wattiez, Ruddy; Vanderplasschen, Alain

2012-01-01

Gammaherpesviruses are important pathogens in human and animal populations. During early events of infection, these viruses manipulate preexisting host cell signaling pathways to allow successful infection. The different proteins that compose viral particles are therefore likely to have critical functions not only in viral structures and in entry into target cell but also in evasion of the host's antiviral response. In this study, we analyzed the protein composition of bovine herpesvirus 4 (BoHV-4), a close relative of the human Kaposi's sarcoma-associated herpesvirus. Using mass spectrometry-based approaches, we identified 37 viral proteins associated with extracellular virions, among which 24 were resistant to proteinase K treatment of intact virions. Analysis of proteins associated with purified capsid-tegument preparations allowed us to define protein localization. In parallel, in order to identify some previously undefined open reading frames, we mapped peptides detected in whole virion lysates onto the six frames of the BoHV-4 genome to generate a proteogenomic map of BoHV-4 virions. Furthermore, we detected important glycosylation of three envelope proteins: gB, gH, and gp180. Finally, we identified 38 host proteins associated with BoHV-4 virions; 15 of these proteins were resistant to proteinase K treatment of intact virions. Many of these have important functions in different cellular pathways involved in virus infection. This study extends our knowledge of gammaherpesvirus virions composition and provides new insights for understanding the life cycle of these viruses. PMID:22896609

Ameliorating pathogenesis by removing an exon containing a missense mutation: a potential exon-skipping therapy for laminopathies.

PubMed

Scharner, J; Figeac, N; Ellis, J A; Zammit, P S

2015-06-01

Exon skipping, as a therapy to restore a reading frame or switch protein isoforms, is under clinical trial. We hypothesised that removing an in-frame exon containing a mutation could also improve pathogenic phenotypes. Our model is laminopathies: incurable tissue-specific degenerative diseases associated with LMNA mutations. LMNA encodes A-type lamins, that together with B-type lamins, form the nuclear lamina. Lamins contain an alpha-helical central rod domain composed of multiple heptad repeats. Eliminating LMNA exon 3 or 5 removes six heptad repeats, so shortens, but should not otherwise significantly alter, the alpha-helix. Human Lamin A or Lamin C with a deletion corresponding to amino acids encoded by exon 5 (Lamin A/C-Δ5) localised normally in murine lmna-null cells, rescuing both nuclear shape and endogenous Lamin B1/emerin distribution. However, Lamin A carrying pathogenic mutations in exon 3 or 5, or Lamin A/C-Δ3, did not. Furthermore, Lamin A/C-Δ5 was not deleterious to wild-type cells, unlike the other Lamin A mutants including Lamin A/C-Δ3. Thus Lamin A/C-Δ5 function as effectively as wild-type Lamin A/C and better than mutant versions. Antisense oligonucleotides skipped LMNA exon 5 in human cells, demonstrating the possibility of treating certain laminopathies with this approach. This proof-of-concept is the first to report the therapeutic potential of exon skipping for diseases arising from missense mutations.

Nucleotide sequences of Dictyostelium discoideum developmentally regulated cDNAs rich in (AAC) imply proteins that contain clusters of asparagine, glutamine, or threonine.

PubMed

Shaw, D R; Richter, H; Giorda, R; Ohmachi, T; Ennis, H L

1989-09-01

A Dictyostelium discoideum repetitive element composed of long repeats of the codon (AAC) is found in developmentally regulated transcripts. The concentration of (AAC) sequences is low in mRNA from dormant spores and growing cells and increases markedly during spore germination and multicellular development. The sequence hybridizes to many different sized Dictyostelium DNA restriction fragments indicating that it is scattered throughout the genome. Four cDNA clones isolated contain (AAC) sequences in the deduced coding region. Interestingly, the (AAC)-rich sequences are present in all three reading frames in the deduced proteins, i.e., AAC (asparagine), ACA (threonine) and CAA (glutamine). Three of the clones contain only one of these in-frame so that the individual proteins carry either asparagine, threonine, or glutamine clusters, not mixtures. However, one clone is both glutamine- and asparagine-rich. The (AAC) portion of the transcripts are reiterated 300 times in the haploid genome while the other portions of the cDNAs represent single copy genes, whose sequences show no similarity other than the (AAC) repeats. The repeated sequence is similar to the opa or M sequence found in Drosophila melanogaster notch and homeo box genes and in fly developmentally regulated transcripts. The transcripts are present on polysomes suggesting that they are translated. Although the function of these repeats is unknown, long amino acid repeats are a characteristic feature of extracellular proteins of lower eukaryotes.

Effects of message framing on self-report and accelerometer-assessed physical activity across age and gender groups.

PubMed

Li, Kin-Kit; Cheng, Sheung-Tak; Fung, Helene H

2014-02-01

This study compared message-framing effects on physical activity (PA) across age and gender groups. Participants included 111 younger and 100 older adults (68% were women), randomly assigned to read gain-framed or loss-framed PA messages in promotion pamphlets, and who wore accelerometers for the following 14 days. Using regression analyses controlling for demographic and health factors, we found significant age-by-gender-by-framing interactions predicting self-report (B = -4.39, p = .01) and accelerometer-assessed PA (B = -2.44, p = .02) during the follow-up period. Gain-framed messages were more effective than loss-framed messages in promoting PA behaviors only among older men. We speculated that the age-related positivity effect, as well as the age and gender differences in issue involvement, explained the group differences in framing. In addition, more time availability and higher self-efficacy among older men might have contributed to the results.

A Theory of Secondary Teachers' Adaptations When Implementing a Reading Intervention Program

ERIC Educational Resources Information Center

Leko, Melinda M.; Roberts, Carly A.; Pek, Yvonne

2015-01-01

This study examined the causes and consequences of secondary teachers' adaptations when implementing a research-based reading intervention program. Interview, observation, and artifact data were collected on five middle school intervention teachers, leading to a grounded theory composed of the core component, reconciliation through adaptation, and…

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.

Numerical analysis and comparison of three types of herringbone frame structure for highway subgrade slopes protection

NASA Astrophysics Data System (ADS)

Nie, Yihua; Tang, Saiqian; Xu, Yang; Mao, Kunli

2018-04-01

In order to obtain mechanical response distribution of herringbone frame structure for highway subgrade slopes protection and select the best structure type, 3D numerical models of three types herringbone frame structure were established and analyzed in finite element software ANSYS. Indoor physical model of soil slope protected by herringbone frame structure was built and mechanical response of the frame structure was measured by loading tests. Numerical results indicate slope foot is the stress most disadvantageous location. Comparative analysis shows that structure composed of mortar rubble base layer and precast concrete blocks paving layer is the best one for resisting deformation and structure with cement mortar base layer and precast concrete blocks paving layer is the best one for being of low stress.

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

Effectiveness of Using Graphic Illustrations with Social Studies Textual Materials. Final Report.

ERIC Educational Resources Information Center

Davis, O. L., Jr.

This study explores the effectiveness of using graphic illustrations with written text in promoting learning in social studies by junior high students. Two groups of experimental reading materials, one group composed of three narratives with related graphic illustrations and the other composed of three narratives alone, were prepared and…

Molecular cloning in Arabidopsis thaliana of a new protein phosphatase 2C (PP2C) with homology to ABI1 and ABI2.

PubMed

Rodriguez, P L; Leube, M P; Grill, E

1998-11-01

We report the cloning of both the cDNA and the corresponding genomic sequence of a new PP2C from Arabidopsis thaliana, named AtP2C-HA (for homology to ABI1/ABI2). The AtP2C-HA cDNA contains an open reading frame of 1536 bp and encodes a putative protein of 511 amino acids with a predicted molecular mass of 55.7 kDa. The AtP2C-HA protein is composed of two domains, a C-terminal PP2C catalytic domain and a N-terminal extension of ca. 180 amino acid residues. The deduced amino acid sequence is 55% and 54% identical to ABI1 and ABI2, respectively. Comparison of the genomic structure of the ABI1, ABI2 and AtP2C-HA genes suggests that they belong to a multigene family. The expression of the AtP2C-HA gene is up-regulated by abscisic acid (ABA) treatment.

Woot, an Active Gypsy-Class Retrotransposon in the Flour Beetle, Tribolium Castaneum, Is Associated with a Recent Mutation

PubMed Central

Beeman, R. W.; Thomson, M. S.; Clark, J. M.; DeCamillis, M. A.; Brown, S. J.; Denell, R. E.

1996-01-01

A recently isolated, lethal mutation of the homeotic Abdominal gene of the red flour beetle Tribolium castaneum is associated with an insertion of a novel retrotransposon into an intron. Sequence analysis indicates that this retrotransposon, named Woot, is a member of the gypsy family of mobile elements. Most strains of T. castaneum appear to harbor ~25-35 copies of Woot per genome. Woot is composed of long terminal repeats of unprecedented length (3.6 kb each), flanking an internal coding region 5.0 kb in length. For most copies of Woot, the internal region includes two open reading frames (ORFs) that correspond to the gag and pol genes of previously described retrotransposons and retroviruses. The copy of Woot inserted into Abdominal bears an apparent single frameshift mutation that separates the normal second ORF into two. Woot does not appear to generate infectious virions by the criterion that no envelop gene is discernible. The association of Woot with a recent mutation suggests that this retroelement is currently transpositionally active in at least some strains. PMID:8722793

Performances of multiprocessor multidisk architectures for continuous media storage

NASA Astrophysics Data System (ADS)

Gennart, Benoit A.; Messerli, Vincent; Hersch, Roger D.

1996-03-01

Multimedia interfaces increase the need for large image databases, capable of storing and reading streams of data with strict synchronicity and isochronicity requirements. In order to fulfill these requirements, we consider a parallel image server architecture which relies on arrays of intelligent disk nodes, each disk node being composed of one processor and one or more disks. This contribution analyzes through bottleneck performance evaluation and simulation the behavior of two multi-processor multi-disk architectures: a point-to-point architecture and a shared-bus architecture similar to current multiprocessor workstation architectures. We compare the two architectures on the basis of two multimedia algorithms: the compute-bound frame resizing by resampling and the data-bound disk-to-client stream transfer. The results suggest that the shared bus is a potential bottleneck despite its very high hardware throughput (400Mbytes/s) and that an architecture with addressable local memories located closely to their respective processors could partially remove this bottleneck. The point- to-point architecture is scalable and able to sustain high throughputs for simultaneous compute- bound and data-bound operations.

Characterization of a cDNA encoding a protein involved in formation of the skeleton during development of the sea urchin Lytechinus pictus.

PubMed

Livingston, B T; Shaw, R; Bailey, A; Wilt, F

1991-12-01

In order to investigate the role of proteins in the formation of mineralized tissues during development, we have isolated a cDNA that encodes a protein that is a component of the organic matrix of the skeletal spicule of the sea urchin, Lytechinus pictus. The expression of the RNA encoding this protein is regulated over development and is localized to the descendents of the micromere lineage. Comparison of the sequence of this cDNA to homologous cDNAs from other species of urchin reveal that the protein is basic and contains three conserved structural motifs: a signal peptide, a proline-rich region, and an unusual region composed of a series of direct repeats. Studies on the protein encoded by this cDNA confirm the predicted reading frame deduced from the nucleotide sequence and show that the protein is secreted and not glycosylated. Comparison of the amino acid sequence to databases reveal that the repeat domain is similar to proteins that form a unique beta-spiral supersecondary structure.

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.

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.

CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription

PubMed Central

Carlson, Jonathan; Yan, Jiyu; Akinsiku, Olusimidele T.; Schaefer, Malinda; Sabbaj, Steffanie; Bet, Anne; Levy, David N.; Heath, Sonya; Tang, Jianming; Kaslow, Richard A.; Walker, Bruce D.; Ndung’u, Thumbi; Goulder, Philip J.; Heckerman, David; Hunter, Eric; Goepfert, Paul A.

2010-01-01

Retroviruses pack multiple genes into relatively small genomes by encoding several genes in the same genomic region with overlapping reading frames. Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs). At least some ARFs have the potential to encode proteins of unknown function, and their antigenic properties can be considered as cryptic epitopes (CEs). To examine the extent of active immune response to virally encoded CEs, we analyzed human leukocyte antigen class I–associated polymorphisms in HIV-1 gag, pol, and nef genes from a large cohort of South Africans with chronic infection. In all, 391 CEs and 168 conventional epitopes were predicted, with the majority (307; 79%) of CEs derived from antisense transcripts. In further evaluation of CD8 T cell responses to a subset of the predicted CEs in patients with primary or chronic infection, both sense- and antisense-encoded CEs were immunogenic at both stages of infection. In addition, CEs often mutated during the first year of infection, which was consistent with immune selection for escape variants. These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity. PMID:20065064

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

Enhancing Health Message Framing With Metaphor and Cultural Values: Impact on Latinas' Cervical Cancer Screening.

PubMed

Spina, Melissa; Arndt, Jamie; Landau, Mark J; Cameron, Linda D

2018-02-05

An integration of message framing and sociocultural literature suggests that ethnic health disparities may be reduced by incorporating minority groups' cultural values into persuasive health messages. Framing messages with metaphors represents one promising strategy for harnessing cultural values to change health outcomes. Still, the effectiveness of metaphoric health messages in minority populations has received virtually no empirical attention. To fill this gap, the present study tested whether a health message using a cancer-screening metaphor targeting collectivism and familism values would engage individual differences in these values to predict Papanicolaou (Pap) smear intentions among Latinas. Latina women (N = 168) completed an online survey including measures of collectivism and familism. They were randomized to read a message about Pap smears featuring the metaphor the body is a family or no metaphor before reporting their Pap smear intentions. Regression analyses revealed a pattern of interactions suggesting metaphoric messages engage targeted cultural values: For Latinas reading the family metaphor message, collectivism and familism positively predicted Pap smear intentions, whereas for Latinas reading the no-metaphor message, these values did not predict intentions. This study offers a foundation for further examination of the potential for metaphoric health messages that connect to cultural values to reduce ethnic health disparities. Implications and directions for future research are discussed.

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.

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

Building Schema through Writing: The Effects of Writing as a Pre-Reading Activity on Delayed Recall of Narrative Text.

ERIC Educational Resources Information Center

Marino, Jacqueline L.; And Others

Drawing upon research on the composing process and schema theory, a study explored the effects of a generative writing task presented prior to reading on the delayed recall of fourth grade students. The purpose of the study was to determine if a writing task that required the learner to identify with events in a text to be read later would assist…

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

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.

Teaching Students to Compose Informational Poetic Riddles to Further Scientific Understanding

ERIC Educational Resources Information Center

Frye, Elizabeth M.; Bradbury, Leslie; Gross, Lisa A.

2016-01-01

In most elementary schools, students spend more time reading and writing narrative texts and less time with informational texts. Yet, the Common Core State Standards advocate that informational texts comprise nearly half of K-8 students' entire academic reading, including content areas like science and social studies. The authors propose remixing…

Comprehending, Composing, and Celebrating Graphic Poetry

ERIC Educational Resources Information Center

Calo, Kristine M.

2011-01-01

The use of graphic poetry in classrooms is encouraged as a way to engage students and motivate them to read and write poetry. This article discusses how graphic poetry can help students with their comprehension of poetry while tapping into popular culture. It is organized around three main sections--reading graphic poetry, writing graphic poetry,…

Integrating Reading, Writing, and Thinking Skills into the Music Class.

ERIC Educational Resources Information Center

Duke, Charles R.

Music education is uniquely suited to reinforce several basic skills that are part of the overall reading and writing processes of students. These skills include freedom of expression and the fluency of ideas, identifying a composer's purpose and message, and reasoning and comprehension. Musicians should develop the habit of using journals for…

Comprehension Tools for Teachers: Reading for Understanding from Prekindergarten through Fourth Grade

PubMed Central

Connor, Carol McDonald; Phillips, Beth M.; Kaschak, Michael; Apel, Kenn; Kim, Young-Suk; Al Otaiba, Stephanie; Crowe, Elizabeth C.; Thomas-Tate, Shurita; Johnson, Lakeisha Cooper; Lonigan, Christopher J.

2015-01-01

This paper describes the theoretical framework, as well as the development and testing of the intervention, Comprehension Tools for Teachers (CTT), which is composed of eight component interventions targeting malleable language and reading comprehension skills that emerging research indicates contribute to proficient reading for understanding for prekindergarteners through fourth graders. Component interventions target processes considered largely automatic as well as more reflective processes, with interacting and reciprocal effects. Specifically, we present component interventions targeting cognitive, linguistic, and text-specific processes, including morphological awareness, syntax, mental-state verbs, comprehension monitoring, narrative and expository text structure, enacted comprehension, academic knowledge, and reading to learn from informational text. Our aim was to develop a tool set composed of intensive meaningful individualized small group interventions. We improved feasibility in regular classrooms through the use of design-based iterative research methods including careful lesson planning, targeted scripting, pre- and postintervention proximal assessments, and technology. In addition to the overall framework, we discuss seven of the component interventions and general results of design and efficacy studies. PMID:26500420

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.

Group Differences between English and Spanish Speakers' Reading Fluency Growth in Bilingual Immersion Education

ERIC Educational Resources Information Center

Taub, Gordon E.; Sivo, Stephen A.; Puyana, Olivia E.

2017-01-01

This study investigates second language acquisition of learners enrolled in a dual language/two-way bilingual immersion program. Two groups of third-grade students participated in this study. The first group was composed of Spanish-dominant participants learning English, and the second group was composed of English-dominant students learning…

Reading as Mediated and Mediating Action: Composing Meaning for Literature through Multimedia Interpretive Texts.

ERIC Educational Resources Information Center

Smagorinsky, Peter; O'Donnell-Allen, Cindy

1998-01-01

Analyzes the effort of a small group of high school seniors to interpret the character of Laertes in Shakespeare's "Hamlet" through a "body biography," a life-sized human outline they filled with images and words representing their understanding of the character. Examines their discussion as they composed their text. (PA)

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

The Relationship between Retail Merchandising in the Content Area and Its Effect on Comprehension and Reading Rate as Measured by Retail Merchandising Reading Tests Given to Selected Secondary School Students in Metropolitan Toronto.

ERIC Educational Resources Information Center

Best, Jane

A total of 99 students from a Toronto secondary vocational school participated in a study to determine whether students who studied retail merchandising differed significantly in comprehension and reading rate from students who did not study retail merchandising. An experimental group composed of 50 merchandising students and a control group of 49…

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…

1. General view, outbuildings. The seed house composed of the ...

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

1. General view, outbuildings. The seed house composed of the greenhouse, a storeroom (shed), a classroom (over a former ice pit), and a kitchen (over a cellar)-stands on the right. The barn roof is visible at center and the gift shop (former stable) stands on the left (Note the carved stone posts framing the gateway). - John Bartram House & Garden, Greenhouse, 54th Street & LIndbergh Boulevard, Philadelphia, Philadelphia County, PA

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…

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.

The Effects of Cuento Therapy on Reading Achievement and Psychological Outcomes of Mexican-American Students

ERIC Educational Resources Information Center

Ramirez, Sylvia Z.; Jain, Sachin; Flores-Torres, Leila L.; Perez, Roxanna; Carlson, Ralph

2009-01-01

This investigation evaluated the effects of cuento therapy (an intervention using Spanish-language tales) on children's self-esteem, affect, and reading test performance. The sample was composed of 58 third-grade Mexican-American students who were randomly assigned to the treatment and control groups. The results showed a mean self-esteem gain…

RIF's Guide to Developing a Program.

ERIC Educational Resources Information Center

Smithsonian Institution, Washington, DC.

The Reading is FUNdamental program is funded by the Ford Foundation and sponsored by the Smithsonian Institution. Its advisory board is composed of people from diverse fields. It is designed to motivate children to read through experiencing the joy and pride of owning books of their own choice, and its purpose is to help develop and give technical…

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.

Topography of Vesta Surface

NASA Image and Video Library

2011-08-26

This view of the topography of asteroid Vesta surface is composed of several images obtained with the framing camera on NASA Dawn spacecraft on August 6, 2011. The image mosaic is shown superimposed on a digital terrain model.

Development of a CFRP Engine Thrust Frame for the Next Generation Launchers

NASA Astrophysics Data System (ADS)

Fatemi, Javad; van der Bas, Finn; Cruijssen, Henk

2012-07-01

This paper addresses the activities related to the development of technologies for a composite Engine Thrust Frame (ETF) for the next generation launchers. In particular, the design and analyses of a full Carbon Fibre Reinforced Plastic (CFRP) engine thrust frame are presented in more detail. The ETF concept is composed of three main parts, i.e. an aluminium top-ring which connects the ETF to the upper-stage tank, a CFRP cone, and a CFRP cone-cap which connects the Vinci engine to the ETF. The main challenging requirements for development of a CFRP ETF are recalled. The ETF concept and its mechanical performances are assessed.

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.

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

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.

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.

Effective Instruction for Persisting Dyslexia in Upper Grades: Adding Hope Stories and Computer Coding to Explicit Literacy Instruction.

PubMed

Thompson, Robert; Tanimoto, Steve; Lyman, Ruby Dawn; Geselowitz, Kira; Begay, Kristin Kawena; Nielsen, Kathleen; Nagy, William; Abbott, Robert; Raskind, Marshall; Berninger, Virginia

2018-05-01

Children in grades 4 to 6 ( N =14) who despite early intervention had persisting dyslexia (impaired word reading and spelling) were assessed before and after computerized reading and writing instruction aimed at subword, word, and syntax skills shown in four prior studies to be effective for treating dyslexia. During the 12 two-hour sessions once a week after school they first completed HAWK Letters in Motion© for manuscript and cursive handwriting, HAWK Words in Motion© for phonological, orthographic, and morphological coding for word reading and spelling, and HAWK Minds in Motion© for sentence reading comprehension and written sentence composing. A reading comprehension activity in which sentences were presented one word at a time or one added word at a time was introduced. Next, to instill hope they could overcome their struggles with reading and spelling, they read and discussed stories about struggles of Buckminister Fuller who overcame early disabilities to make important contributions to society. Finally, they engaged in the new Kokopelli's World (KW)©, blocks-based online lessons, to learn computer coding in introductory programming by creating stories in sentence blocks (Tanimoto and Thompson 2016). Participants improved significantly in hallmark word decoding and spelling deficits of dyslexia, three syntax skills (oral construction, listening comprehension, and written composing), reading comprehension (with decoding as covariate), handwriting, orthographic and morphological coding, orthographic loop, and inhibition (focused attention). They answered more reading comprehension questions correctly when they had read sentences presented one word at a time (eliminating both regressions out and regressions in during saccades) than when presented one added word at a time (eliminating only regressions out during saccades). Indicators of improved self-efficacy that they could learn to read and write were observed. Reminders to pay attention and stay on task needed before adding computer coding were not needed after computer coding was added.

Chinese Readers Can Perceive a Word Even When It's Composed of Noncontiguous Characters

ERIC Educational Resources Information Center

Ma, Guojie; Pollatsek, Alexander; Li, Yugang; Li, Xingshan

2017-01-01

This study explored whether readers could recognize a word composed of noncontiguous characters (a "cross-character word") in Chinese reading. All 3 experiments employed Chinese 4-character strings ABCD, where both AB and CD were 2-character words. In the cross-character word condition, AC was a word but in the control condition, AC was…

What Must Be Taught about Writing: Five Kinds of Knowledge and Five Kinds of Composing

ERIC Educational Resources Information Center

Wilhelm, Jeff, Ed.

2012-01-01

Students need to develop five kinds of knowledge to be successful in any kind of specific reading or writing task. These kinds of knowledge can be developed through five different kinds of composing that lead to deep understanding of how texts are constructed with specific content to create particular effects and meaning. Following this process…

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.

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…

Coincidence ion imaging with a fast frame camera

NASA Astrophysics Data System (ADS)

Lee, Suk Kyoung; Cudry, Fadia; Lin, Yun Fei; Lingenfelter, Steven; Winney, Alexander H.; Fan, Lin; Li, Wen

2014-12-01

A new time- and position-sensitive particle detection system based on a fast frame CMOS (complementary metal-oxide semiconductors) camera is developed for coincidence ion imaging. The system is composed of four major components: a conventional microchannel plate/phosphor screen ion imager, a fast frame CMOS camera, a single anode photomultiplier tube (PMT), and a high-speed digitizer. The system collects the positional information of ions from a fast frame camera through real-time centroiding while the arrival times are obtained from the timing signal of a PMT processed by a high-speed digitizer. Multi-hit capability is achieved by correlating the intensity of ion spots on each camera frame with the peak heights on the corresponding time-of-flight spectrum of a PMT. Efficient computer algorithms are developed to process camera frames and digitizer traces in real-time at 1 kHz laser repetition rate. We demonstrate the capability of this system by detecting a momentum-matched co-fragments pair (methyl and iodine cations) produced from strong field dissociative double ionization of methyl iodide.

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.

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.

Excitement, Adventure, Indifference: Romance Readers' Perceptions of How Romance Reading Impacts Their Sex Lives

ERIC Educational Resources Information Center

Anderton, Gretchen E.

2009-01-01

This mixed-methods study examined romance readers' perceptions of how reading romance novels has impacted their sex lives, feelings about their sex partners, knowledge of sexuality and their sexual behavior. Fifty-three women romance readers over the age of 18 completed an online survey composed of multiple choice and open-ended essay questions. …

The Influence of Reading and Writing Habits Associated with Education on the Neuropsychological Performance of Brazilian Adults

ERIC Educational Resources Information Center

Pawlowski, Josiane; Remor, Eduardo; de Mattos Pimenta Parente, Maria Alice; de Salles, Jerusa Fumagalli; Fonseca, Rochele Paz; Bandeira, Denise Ruschel

2012-01-01

This study evaluated the influence of the frequency of reading and writing habits (RWH) associated with education on the performance of adults in brief neuropsychological tasks. A sample of 489 Brazilian subjects, composed of 71% women, aged 21-80 years, with 2-23 years of formal education, was evaluated by the Brazilian Brief Neuropsychological…

Supporting Orthographic Learning at the Beginning Stage of Learning to Read Chinese as a Second Language

ERIC Educational Resources Information Center

Chang, Li-Yun; Xu, Yi; Perfetti, Charles A.; Zhang, Juan; Chen, Hsueh-Chih

2014-01-01

Learning to read a second language (L2) is especially challenging when a target L2 requires learning new graphic forms. Learning Chinese, which consists of thousands of characters composed of hundreds of basic writing units, presents such a challenge of orthographic learning for adult English speakers at the beginning stages of learning. In this…

Molecular cloning, sequence and structural analysis of dehairing Mn(2+) dependent alkaline serine protease (MASPT) of Bacillus pumilus TMS55.

PubMed

Ibrahim, Kalibulla Syed; Muniyandi, Jeyaraj; Pandian, Shunmugiah Karutha

2011-10-01

Leather industries release a large amount of pollution-causing chemicals which creates one of the major industrial pollutions. The development of enzyme based processes as a potent alternative to pollution-causing chemicals is useful to overcome this issue. Proteases are enzymes which have extensive applications in leather processing and in several bioremediation processes due to their high alkaline protease activity and dehairing efficacy. In the present study, we report cloning, characterization of a Mn2+ dependent alkaline serine protease gene (MASPT) of Bacillus pumilus TMS55. The gene encoding the protease from B. pumilus TMS55 was cloned and its nucleotide sequence was determined. This gene has an open reading frame (ORF) of 1,149 bp that encodes a polypeptide of 383 amino acid residues. Our analysis showed that this polypeptide is composed of 29 residues N-terminal signal peptide, a propeptide of 79 residues and a mature protein of 275 amino acids. We performed bioinformatics analysis to compare MASPT enzyme with other proteases. Homology modeling was employed to model three dimensional structure for MASPT. Structural analysis showed that MASPT structure is composed of nine α-helices and nine β-strands. It has 3 catalytic residues and 14 metal binding residues. Docking analysis showed that residues S223, A260, N263, T328 and S329 interact with Mn2+. This study allows initial inferences about the structure of the protease and will allow the rational design of its derivatives for structure-function studies and also for further improvement of the enzyme.

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.

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

OpenMP Parallelization and Optimization of Graph-based Machine Learning Algorithms

DTIC Science & Technology

2016-05-01

composed of hyper - spectral video sequences recording the release of chemical plumes at the Dugway Proving Ground. We use the 329 frames of the...video. Each frame is a hyper - spectral image with dimension 128 × 320 × 129, where 129 is the dimension of the channel of each pixel. The total number of...j=1 . Then we use the nested for- loop to calculate the values of WXY by the formula (1). We then put the corresponding value in an array which

Effective Beginning Handwriting Instruction: Multi-Modal, Consistent Format for 2 Years, and Linked to Spelling and Composing

ERIC Educational Resources Information Center

Wolf, Beverly; Abbott, Robert D.; Berninger, Virginia W.

2017-01-01

In Study 1, the treatment group (N = 33 first graders, M = 6 years 10 months, 16 girls) received Slingerland multi-modal (auditory, visual, tactile, motor through hand, and motor through mouth) manuscript (unjoined) handwriting instruction embedded in systematic spelling, reading, and composing lessons; and the control group (N = 16 first graders,…

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.

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

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.

Faces of Pluto Animation

NASA Image and Video Library

2015-06-11

This frame from a movie, composed of images taken by NASA New Horizons, shows Pluto as it rotates about its axis. The images were taken May 28-June 3, 2015, from distances ranging from approximately 56 million kilometers to 48.5 million kilometers.

Topography of Troughs on Vesta

NASA Image and Video Library

2011-08-23

This view of the topography of asteroid Vesta surface is composed of several images obtained with the clear filter in the framing camera on NASA Dawn spacecraft on August 6, 2011. The image has a resolution of about 260 meters per pixel.

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.

The Effect of Stories for Thinking on Reading and Listening Comprehension: A Case Study in Turkey

ERIC Educational Resources Information Center

Tok, Sükran; Mazl, Aysegül

2015-01-01

This study has been conducted in order to examine the effects of the stories for thinking on 5th graders' reading comprehension and listening comprehension. A pretest-post test control group quasi-experimental design was used in the study. The sample of the etstudy was composed of 74 5th graders attending public elementary schools. The data have…

Into the Curriculum. Art: The Z Was Zapped [and] Art: Friendly Plastic [and] Music: American Composers [and] Reading/Language Arts: Chocolate Day [and] Science: Moose [and] Social Studies: Women's History Project.

ERIC Educational Resources Information Center

Rossi, Marie; And Others

1995-01-01

A group of six articles describes activities for art, music, reading/language arts, science, and social studies. Each article includes library media skills objectives, curriculum objectives, grade levels, resources, instructional roles, activity and procedures for completion, evaluation, and follow-up. (AEF)

Updated optical read/write memory system components

NASA Technical Reports Server (NTRS)

1974-01-01

A survey of the building blocks of the electro-optic read/write system was made. Critical areas and alternate paths are discussed. The latest PLZT block data composer is analyzed. Stricter controls in the production and fabrication of PLZT are implied by the performance of the BDC. A reverse charge before erase has eliminated several problems observed in the parallel plane charging process for photoconductor-thermoplastic hologram storage.

The Difficulties Experienced by Teacher Candidates in Their Own Process of Elementary Reading and Writing Education, and Their Current Solution

ERIC Educational Resources Information Center

Gündogmus, Hatice Degirmenci

2018-01-01

The purpose of the current research is to identify the difficulties which teacher candidates studying elementary school teaching experienced in their past elementary reading and writing education and which cannot be forgotten, and to find out their solution for eliminating these difficulties. The study group of the research is composed of 118…

Seeing is believing: video classification for computed tomographic colonography using multiple-instance learning.

PubMed

Wang, Shijun; McKenna, Matthew T; Nguyen, Tan B; Burns, Joseph E; Petrick, Nicholas; Sahiner, Berkman; Summers, Ronald M

2012-05-01

In this paper, we present development and testing results for a novel colonic polyp classification method for use as part of a computed tomographic colonography (CTC) computer-aided detection (CAD) system. Inspired by the interpretative methodology of radiologists using 3-D fly-through mode in CTC reading, we have developed an algorithm which utilizes sequences of images (referred to here as videos) for classification of CAD marks. For each CAD mark, we created a video composed of a series of intraluminal, volume-rendered images visualizing the detection from multiple viewpoints. We then framed the video classification question as a multiple-instance learning (MIL) problem. Since a positive (negative) bag may contain negative (positive) instances, which in our case depends on the viewing angles and camera distance to the target, we developed a novel MIL paradigm to accommodate this class of problems. We solved the new MIL problem by maximizing a L2-norm soft margin using semidefinite programming, which can optimize relevant parameters automatically. We tested our method by analyzing a CTC data set obtained from 50 patients from three medical centers. Our proposed method showed significantly better performance compared with several traditional MIL methods.

Seeing is Believing: Video Classification for Computed Tomographic Colonography Using Multiple-Instance Learning

PubMed Central

Wang, Shijun; McKenna, Matthew T.; Nguyen, Tan B.; Burns, Joseph E.; Petrick, Nicholas; Sahiner, Berkman

2012-01-01

In this paper we present development and testing results for a novel colonic polyp classification method for use as part of a computed tomographic colonography (CTC) computer-aided detection (CAD) system. Inspired by the interpretative methodology of radiologists using 3D fly-through mode in CTC reading, we have developed an algorithm which utilizes sequences of images (referred to here as videos) for classification of CAD marks. For each CAD mark, we created a video composed of a series of intraluminal, volume-rendered images visualizing the detection from multiple viewpoints. We then framed the video classification question as a multiple-instance learning (MIL) problem. Since a positive (negative) bag may contain negative (positive) instances, which in our case depends on the viewing angles and camera distance to the target, we developed a novel MIL paradigm to accommodate this class of problems. We solved the new MIL problem by maximizing a L2-norm soft margin using semidefinite programming, which can optimize relevant parameters automatically. We tested our method by analyzing a CTC data set obtained from 50 patients from three medical centers. Our proposed method showed significantly better performance compared with several traditional MIL methods. PMID:22552333

Molecular cloning, overexpression, purification, and sequence analysis of the giant panda (Ailuropoda melanoleuca) ferritin light polypeptide.

PubMed

Fu, L; Hou, Y L; Ding, X; Du, Y J; Zhu, H Q; Zhang, N; Hou, W R

2016-08-30

The complementary DNA (cDNA) of the giant panda (Ailuropoda melanoleuca) ferritin light polypeptide (FTL) gene was successfully cloned using reverse transcription-polymerase chain reaction technology. We constructed a recombinant expression vector containing FTL cDNA and overexpressed it in Escherichia coli using pET28a plasmids. The expressed protein was then purified by nickel chelate affinity chromatography. The cloned cDNA fragment was 580 bp long and contained an open reading frame of 525 bp. The deduced protein sequence was composed of 175 amino acids and had an estimated molecular weight of 19.90 kDa, with an isoelectric point of 5.53. Topology prediction revealed one N-glycosylation site, two casein kinase II phosphorylation sites, one N-myristoylation site, two protein kinase C phosphorylation sites, and one cell attachment sequence. Alignment indicated that the nucleotide and deduced amino acid sequences are highly conserved across several mammals, including Homo sapiens, Cavia porcellus, Equus caballus, and Felis catus, among others. The FTL gene was readily expressed in E. coli, which gave rise to the accumulation of a polypeptide of the expected size (25.50 kDa, including an N-terminal polyhistidine tag).

Genome sequence of an enhancin gene-rich nucleopolyhedrovirus (NPV) from Agrotis segetum: collinearity with Spodoptera exigua multiple NPV.

PubMed

Jakubowska, Agata K; Peters, Sander A; Ziemnicka, Jadwiga; Vlak, Just M; van Oers, Monique M

2006-03-01

The genome sequence of a Polish isolate of Agrotis segetum nucleopolyhedrovirus (AgseNPV-A) was determined and analysed. The circular genome is composed of 147,544 bp and has a G+C content of 45.7 mol%. It contains 153 putative, non-overlapping open reading frames (ORFs) encoding predicted proteins of more than 50 aa, together making up 89.8 % of the genome. The remaining 10.2 % of the DNA constitutes non-coding regions and homologous-repeat regions. One hundred and forty-three AgseNPV-A ORFs are homologues of previously reported baculovirus gene sequences. There are ten unique ORFs and they account for 3 % of the genome in total. All 62 lepidopteran baculovirus genes, including the 29 core baculovirus genes, were found in the AgseNPV-A genome. The gene content and gene order of AgseNPV-A are most similar to those of Spodoptera exigua (Se) multiple NPV and their shared homologous genes are 100 % collinear. Three putative enhancin genes were identified in the AgseNPV-A genome. In phylogenetic analysis, the AgseNPV-A enhancins form a cluster separated from enhancins of the Mamestra species NPVs.

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.

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.

The Moderating Role of Mood and Personal Relevance on Persuasive Effects of Gain- and Loss-Framed Health Messages.

PubMed

Wirtz, John G; Sar, Sela; Ghuge, Shreyas

2015-01-01

We predicted that mood would moderate the relation between message framing and two outcome variables, message evaluation and behavioral intention, when the message was personally relevant to the target audience. Participants (N = 242) were randomly assigned to an experimental condition in which a positive or negative mood was induced. Participants then read and evaluated a health message that emphasized potential benefits or risks associated with a vaccine. As predicted, participants who received a loss-framed message reported higher message evaluation and intention scores but only when the message was personally relevant and they were in a positive mood.

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.

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.

Rapid naming, reading and comprehension in students with learning difficulties.

PubMed

Silva, Cláudia da; Cunha, Vera Lúcia Orlandi; Pinheiro, Fábio Henrique; Capellini, Simone Aparecida

2012-01-01

To compare and correlate the performance of students with learning difficulties in rapid naming, reading and comprehension. Participants were 32 students from 4th grade of elementary school of both genders, with ages between 11 years and 4 months and 12 years and 7 months. The first and second oral reading of a text selected based on the indication of 4th grade teachers were conducted, as well as the first and second reading comprehension task composed by four questions presented right after the reading, to which students should answered orally, and the rapid naming task from the Test of Cognitive-Linguistic Performance, individual version. Differences were found between the first and the second comprehension scores, and between rapid naming, first and second reading. There was a strong correlation between comprehension and reading, suggesting that the performance in the first reading significantly influenced the performance in the second reading, which also occurred for comprehension. The delay in the activities of naming, reading and comprehension in the first evaluation provoked failures in the phoneme-grapheme conversion that may be enough to cause learning difficulties in reading.

Coincidence ion imaging with a fast frame camera

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

Lee, Suk Kyoung; Cudry, Fadia; Lin, Yun Fei

2014-12-15

A new time- and position-sensitive particle detection system based on a fast frame CMOS (complementary metal-oxide semiconductors) camera is developed for coincidence ion imaging. The system is composed of four major components: a conventional microchannel plate/phosphor screen ion imager, a fast frame CMOS camera, a single anode photomultiplier tube (PMT), and a high-speed digitizer. The system collects the positional information of ions from a fast frame camera through real-time centroiding while the arrival times are obtained from the timing signal of a PMT processed by a high-speed digitizer. Multi-hit capability is achieved by correlating the intensity of ion spots onmore » each camera frame with the peak heights on the corresponding time-of-flight spectrum of a PMT. Efficient computer algorithms are developed to process camera frames and digitizer traces in real-time at 1 kHz laser repetition rate. We demonstrate the capability of this system by detecting a momentum-matched co-fragments pair (methyl and iodine cations) produced from strong field dissociative double ionization of methyl iodide.« less

Quantum reference frames and their applications to thermodynamics.

PubMed

Popescu, Sandu; Sainz, Ana Belén; Short, Anthony J; Winter, Andreas

2018-07-13

We construct a quantum reference frame, which can be used to approximately implement arbitrary unitary transformations on a system in the presence of any number of extensive conserved quantities, by absorbing any back action provided by the conservation laws. Thus, the reference frame at the same time acts as a battery for the conserved quantities. Our construction features a physically intuitive, clear and implementation-friendly realization. Indeed, the reference system is composed of the same types of subsystems as the original system and is finite for any desired accuracy. In addition, the interaction with the reference frame can be broken down into two-body terms coupling the system to one of the reference frame subsystems at a time. We apply this construction to quantum thermodynamic set-ups with multiple, possibly non-commuting conserved quantities, which allows for the definition of explicit batteries in such cases.This article is part of a discussion meeting issue 'Foundations of quantum mechanics and their impact on contemporary society'. © 2018 The Author(s).

A Study of Base Frequency in Spanish Skilled and Reading-Disabled Children: All Children Benefit from Morphological Processing in Defining Complex Pseudowords

ERIC Educational Resources Information Center

Lazaro, Miguel

2012-01-01

In this study, the base frequency (BF) effect is explored in reading-disabled and skilled readers of Spanish. A pseudoword definition task was completed by two groups of children. The pseudowords were composed from existing stems and affixes. The results show a facilitatory BF effect, suggesting that all children benefited from this aspect of…

Those Who Can Coach Can Teach: Collaborating With Athletic Coaches to Raise the Level of Students' Close Reading, Argumentation Skills, and Academic Agency

ERIC Educational Resources Information Center

Ehrenworth, Mary; Minor, Cornelius; Federman, Mark; Jennings, James; Messer, Katherine; McCloud, Christopher

2015-01-01

Building on the work of John Hattie, Richard Kent, and Tom Newkirk, a think tank collaborative in New York City's high schools works to raise the level of students' close reading, argumentation, and agency across the curriculum by teaching students to analyze athletic competitions, to compose sports arguments, and to transfer and apply these…

The Difficulties Experienced by Teachers in the Process of Primary Reading and Writing Instruction and Their Solution Offers for Eliminating These Difficulties

ERIC Educational Resources Information Center

Gündogmus, Hatice Degirmenci

2018-01-01

The purpose of the current research is to identify the difficulties that primary school teachers experience in the primary reading and writing instruction, and to find out their solution offers for eliminating these difficulties. The study group of the research is composed of 51 primary school teachers selected by criterion sampling as a type of…

Rail inspection system based on iGPS

NASA Astrophysics Data System (ADS)

Fu, Xiaoyan; Wang, Mulan; Wen, Xiuping

2018-05-01

Track parameters include gauge, super elevation, cross level and so on, which could be calculated through the three-dimensional coordinates of the track. The rail inspection system based on iGPS (indoor/infrared GPS) was composed of base station, receiver, rail inspection frame, wireless communication unit, display and control unit and data processing unit. With the continuous movement of the inspection frame, the system could accurately inspect the coordinates of rail; realize the intelligent detection and precision measurement. According to principle of angle intersection measurement, the inspection model was structured, and detection process was given.

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.

Probabilistic choice between symmetric disparities in motion stereo matching for a lateral navigation system

NASA Astrophysics Data System (ADS)

Ershov, Egor; Karnaukhov, Victor; Mozerov, Mikhail

2016-02-01

Two consecutive frames of a lateral navigation camera video sequence can be considered as an appropriate approximation to epipolar stereo. To overcome edge-aware inaccuracy caused by occlusion, we propose a model that matches the current frame to the next and to the previous ones. The positive disparity of matching to the previous frame has its symmetric negative disparity to the next frame. The proposed algorithm performs probabilistic choice for each matched pixel between the positive disparity and its symmetric disparity cost. A disparity map obtained by optimization over the cost volume composed of the proposed probabilistic choice is more accurate than the traditional left-to-right and right-to-left disparity maps cross-check. Also, our algorithm needs two times less computational operations per pixel than the cross-check technique. The effectiveness of our approach is demonstrated on synthetic data and real video sequences, with ground-truth value.

Dysfunctional growth hormone receptor in a strain of sex-linked dwarf chicken: evidence for a mutation in the intracellular domain.

PubMed

Agarwal, S K; Cogburn, L A; Burnside, J

1994-09-01

The sex-linked dwarf (dwdw) chicken represents a valuable animal model for studying GH insensitivity and the consequence of mutations in the GH receptor (GHR) gene. We have recently reported undetectable hepatic GH-binding activity and an aberrantly sized transcript in a strain of dwdw chickens obtained from Arbor Acre Farms, Inc. (Glastonbury, CT, USA). Southern blot analysis of the chicken GHR (cGHR) gene revealed a restriction-fragment length polymorphism in HindIII and EcoRI digests of genomic DNA in this strain of dwdw chicken. In order to localize the molecular mutation, we analysed the gene structure and determined the complete sequence of the 3' untranslated region (3' UTR) of the normal cGHR. With the use of this information, we located a large deletion in the 3' end of the cGHR gene of the Connecticut (CT) strain of dwdw chicken. This deletion (1773 bp) contained 27 highly conserved amino acids of the 3' end of the coding region, the in-frame stop codon, a less frequently used poly(A) signal that is normally found 445 bp downstream of the stop codon, and a large portion of the 3' UTR. Because of this deletion, 27 novel amino acids were substituted and the open reading frame was extended for an additional 26 amino acids before reaching the transcriptional termination site. The predicted amino acid sequence of the novel carboxyl-terminus of the dwdw cGHR is largely hydrophobic with a polylysine tail, whereas the carboxyl-terminus of the wild-type (DwDw) cGHR is composed of hydrophilic amino acids.(ABSTRACT TRUNCATED AT 250 WORDS)

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.

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.

ARC-1981-AC81-7065

NASA Image and Video Library

1981-08-23

Range : 2.3 million km. ( 1.4 million miles ) P-24067C This Voyager 2 photograph of Titan, a satellite of Saturn, shows some detail in the cloud systems. The southern hemisphere appears lighter in contrast, a well defined band is seen near the equator, and a dark collar is evident at the north pole. All these bands are associated with the cloud circulation in titan's atmosphere. The extended haze, composed of of sub-micron size particles, is seen clearly around the satellite's limb. This image was composed from blue, green, and violet frames.

Compare Gene Calls

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

Ecale Zhou, Carol L.

2016-07-05

Compare Gene Calls (CGC) is a Python code used for combining and comparing gene calls from any number of gene callers. A gene caller is a computer program that predicts the extends of open reading frames within genomes of biological organisms.

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 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.

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.

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.

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.

Meet David, Our Teacher's Helper.

ERIC Educational Resources Information Center

Newell, William; And Others

1984-01-01

DAVID, Dynamic Audio Video Instructional Device, is composed of a conventional videotape recorder, a microcomputer, and a video controller, and has been successfully used for speech reading and sign language instruction with deaf students. (CL)

Wave mode identification of electrostatic noise observed with ISEE 3 in the deep tail boundary layer

NASA Technical Reports Server (NTRS)

Tsutsui, M.; Matsumoto, H.; Strangeway, R. J.; Tsurutani, B. T.; Phillips, J. L.

1991-01-01

The characteristics of the VLF electrostatic noise observed with ISEE 3 in the low-latitude boundary layer of distant geomagnetic tail are examined using a display format for the wave dynamic spectra different from that used by Scarf et al. (1984). It is shown that the observed noise is composed of impulsive bursts. The results of the detailed analysis of the noise parameters are used to develop a model of plasma wave behavior in the plasma rest frame. A hypothesis is proposed that the wide frequency extent of the noise spectra is composed of Doppler effects of waves propagating nearly omnidirectionally within the plasma rest frame, which is moving with the electron bulk speed. On the basis of this hypothesis, the wavelength of the observed waves were determined from the width of the frequency extent and the measured electron bulk speed. It is shown that the wavelength ranges from 2 to 8 times the plasma Debye length.

Fine tangled pili expressed by Haemophilus ducreyi are a novel class of pili.

PubMed Central

Brentjens, R J; Ketterer, M; Apicella, M A; Spinola, S M

1996-01-01

Haemophilus ducreyi synthesizes fine, tangled pili composed predominantly of a protein whose apparent molecular weight is 24,000 (24K). A hybridoma, 2D8, produced a monoclonal antibody (MAb) that bound to a 24K protein in H. ducreyi strains isolated from diverse geographic locations. A lambda gt11 H. ducreyi library was screened with MAb 2D8. A 3.5-kb chromosomal insert from one reactive plaque was amplified and ligated into the pCRII vector. The recombinant plasmid, designated pHD24, expressed a 24K protein in Escherichia coli INV alpha F that bound MAb 2D8. The coding sequence of the 24K gene was localized by exonuclease III digestion. The insert contained a 570-bp open reading frame, designated ftpA (fine, tangled pili). Translation of ftpA predicted a polypeptide with a molecular weight of 21.1K. The predicted N-terminal amino acid sequence of the polypeptide encoded by ftpA was identical to the N-terminal amino acid sequence of purified pilin and lacked a cleavable signal sequence. Primer extension analysis of ftpA confirmed the lack of a leader peptide. The predicted amino acid sequence lacked homology to known pilin sequences but shared homology with the sequences of E. coli Dps and Treponema pallidum antigen TpF1 or 4D, proteins which associate to form ordered rings. An isogenic pilin mutant, H. ducreyi 35000ftpA::mTn3(Cm), was constructed by shuttle mutagenesis and did not contain pili when examined by electron microscopy. We conclude that H. ducreyi synthesizes fine, tangled pili that are composed of a unique major subunit, which may be exported by a signal sequence independent mechanism. PMID:8550517

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

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

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.

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.

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.

47 CFR 36.125 - Local switching equipment-Category 3.

Code of Federal Regulations, 2010 CFR

2010-10-01

... electronic analog or digital remote line locations. Equipment used for the identification, recording and... which has a common intermediate distributing frame, market group or other separately identifiable... composed of an electronic analog or digital host office and all of its remote locations. A host/remote...

Ceres RC3 Animation

NASA Image and Video Library

2015-05-11

In this closest-yet view of Ceres, the brightest spots within a crater in the northern hemisphere are revealed to be composed of many smaller spots. This frame is from an animation of sequences taken by NASA Dawn spacecraft on May 4, 2015. http://photojournal.jpl.nasa.gov/catalog/PIA19547

Lack of visual field asymmetries for spatial cueing in reading parafoveal Chinese characters.

PubMed

Luo, Chunming; Dell'Acqua, Roberto; Proctor, Robert W; Li, Xingshan

2015-12-01

In two experiments, we investigated whether visual field (VF) asymmetries of spatial cueing are involved in reading parafoveal Chinese characters. These characters are different from linearly arranged alphabetic words in that they are logograms that are confined to a constant, square-shaped area and are composed of only a few radicals. We observed a cueing effect, but it did not vary with the VF in which the Chinese character was presented, regardless of whether the cue validity (the ratio of validly to invalidly cued targets) was 1:1 or 7:3. These results suggest that VF asymmetries of spatial cueing do not affect the reading of parafoveal Chinese characters, contrary to the reading of alphabetic words. The mechanisms of spatial attention in reading parafoveal English-like words and Chinese characters are discussed.

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

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".

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.

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

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.

Rolled-out collectors

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

Shurcliff, W.A.

1979-04-01

SolaRoll is a solar collector material composed of extruded strips of black ethylene propylene diene monomer (EPDM) that is suitable for water or air type collectors. SolaRoll is provided in rolls and consists of an absorber mat with tubes and fins and a framing strip comprising all the parts of the collector frame. The rolls are bent in a counterflow pattern to cover the entire collector area and the mat is fastened with a thermosetting mastic adhesive. The heat transfer fluid is plain water as freezing does not injure the EPDM. Installation of the glazing in the framing strip ismore » described. EPDM has the disadvantage of low thermal conductivity but its use does not require antifreeze or a heat exchanger. Design options and suitable applications of SolaRoll systems are discussed.« less

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

Coincidence electron/ion imaging with a fast frame camera

NASA Astrophysics Data System (ADS)

Li, Wen; Lee, Suk Kyoung; Lin, Yun Fei; Lingenfelter, Steven; Winney, Alexander; Fan, Lin

2015-05-01

A new time- and position- sensitive particle detection system based on a fast frame CMOS camera is developed for coincidence electron/ion imaging. The system is composed of three major components: a conventional microchannel plate (MCP)/phosphor screen electron/ion imager, a fast frame CMOS camera and a high-speed digitizer. The system collects the positional information of ions/electrons from a fast frame camera through real-time centroiding while the arrival times are obtained from the timing signal of MCPs processed by a high-speed digitizer. Multi-hit capability is achieved by correlating the intensity of electron/ion spots on each camera frame with the peak heights on the corresponding time-of-flight spectrum. Efficient computer algorithms are developed to process camera frames and digitizer traces in real-time at 1 kHz laser repetition rate. We demonstrate the capability of this system by detecting a momentum-matched co-fragments pair (methyl and iodine cations) produced from strong field dissociative double ionization of methyl iodide. We further show that a time resolution of 30 ps can be achieved when measuring electron TOF spectrum and this enables the new system to achieve a good energy resolution along the TOF axis.

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.

A Comparison of the Development of Self-Concept and Achievement in Reading of Students in the First, Third, and Fifth Year of Attendance in Graded and Nongraded Elementary Schools.

ERIC Educational Resources Information Center

Lawson, Robert Ewell

The purpose of this study was to compare the development of self-concept and achievement in reading of students in the first, third, and fifth year of attendance in graded and nongraded schools. The population of this study was composed of 338 selected students from six elementary schools in Kokomo, Indiana, and the experimental group was composed…

Parents as "Help Labor": Inner-City Teachers' Narratives of Parent Involvement

ERIC Educational Resources Information Center

Christianakis, Mary

2011-01-01

This article examines teachers' perceptions of parent involvement through the narratives of 15 racially and linguistically diverse teachers who worked together at Jefferson Elementary, an inner-city school in Northern California composed mostly of African-American, Latino, and Asian students. One overarching research question framed the…

Enhancing reading performance through action video games: the role of visual attention span.

PubMed

Antzaka, A; Lallier, M; Meyer, S; Diard, J; Carreiras, M; Valdois, S

2017-11-06

Recent studies reported that Action Video Game-AVG training improves not only certain attentional components, but also reading fluency in children with dyslexia. We aimed to investigate the shared attentional components of AVG playing and reading, by studying whether the Visual Attention (VA) span, a component of visual attention that has previously been linked to both reading development and dyslexia, is improved in frequent players of AVGs. Thirty-six French fluent adult readers, matched on chronological age and text reading proficiency, composed two groups: frequent AVG players and non-players. Participants performed behavioural tasks measuring the VA span, and a challenging reading task (reading of briefly presented pseudo-words). AVG players performed better on both tasks and performance on these tasks was correlated. These results further support the transfer of the attentional benefits of playing AVGs to reading, and indicate that the VA span could be a core component mediating this transfer. The correlation between VA span and pseudo-word reading also supports the involvement of VA span even in adult reading. Future studies could combine VA span training with defining features of AVGs, in order to build a new generation of remediation software.

Eye movements when reading sentences with handwritten words.

PubMed

Perea, Manuel; Marcet, Ana; Uixera, Beatriz; Vergara-Martínez, Marta

2016-10-17

The examination of how we read handwritten words (i.e., the original form of writing) has typically been disregarded in the literature on reading. Previous research using word recognition tasks has shown that lexical effects (e.g., the word-frequency effect) are magnified when reading difficult handwritten words. To examine this issue in a more ecological scenario, we registered the participants' eye movements when reading handwritten sentences that varied in the degree of legibility (i.e., sentences composed of words in easy vs. difficult handwritten style). For comparison purposes, we included a condition with printed sentences. Results showed a larger reading cost for sentences with difficult handwritten words than for sentences with easy handwritten words, which in turn showed a reading cost relative to the sentences with printed words. Critically, the effect of word frequency was greater for difficult handwritten words than for easy handwritten words or printed words in the total times on a target word, but not on first-fixation durations or gaze durations. We examine the implications of these findings for models of eye movement control in reading.

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…

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

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.

Rearrangement of a large novel Pseudomonas aeruginosa gene island in strains isolated from a patient developing ventilator-associated pneumonia.

PubMed

Singh, G; Srinivasan, R; Cheng, J; Peng, Z; Fujimura, K; Baek, M S; Panzer, A R; Tringe, S G; Chen, F; Sorek, R; Weng, L; Bristow, J; Wiener-Kronish, J P; Lynch, S V

2014-07-01

Bacterial gene islands add to the genetic repertoire of opportunistic pathogens. Here, we perform comparative analyses of three Pseudomonas aeruginosa strains isolated sequentially over a 3-week period from a patient with ventilator-associated pneumonia (VAP) who received clindamycin and piperacillin-tazobactam as part of their treatment regime. While all three strains appeared to be clonal by standard pulsed-field gel electrophoresis, whole-genome sequencing revealed subtle alterations in the chromosomal organization of the last two strains; specifically, an inversion event within a novel 124-kb gene island (PAGI 12) composed of 137 open reading frames [ORFs]. Predicted ORFs in the island included metabolism and virulence genes. Overexpression of a gene island-borne putative β-lactamase gene was observed following piperacillin-tazobactam exposure and only in those strains that had undergone the inversion event, indicating altered gene regulation following genomic remodeling. Examination of a separate cohort of 76 patients with VAP for integration at this tRNA(lys) recombination site demonstrated that patients exhibiting evidence of integration at this site had significantly higher 28-day mortality. These findings provide evidence that P. aeruginosa can integrate, rapidly remodel, and express exogenous genes, which likely contributes to its fitness in a clinical setting. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Rearrangement of a Large Novel Pseudomonas aeruginosa Gene Island in Strains Isolated from a Patient Developing Ventilator-Associated Pneumonia

PubMed Central

Singh, G.; Srinivasan, R.; Cheng, J.; Peng, Z.; Fujimura, K.; Baek, M. S.; Panzer, A. R.; Tringe, S. G.; Chen, F.; Sorek, R.; Weng, L.; Bristow, J.; Wiener-Kronish, J. P.

2014-01-01

Bacterial gene islands add to the genetic repertoire of opportunistic pathogens. Here, we perform comparative analyses of three Pseudomonas aeruginosa strains isolated sequentially over a 3-week period from a patient with ventilator-associated pneumonia (VAP) who received clindamycin and piperacillin-tazobactam as part of their treatment regime. While all three strains appeared to be clonal by standard pulsed-field gel electrophoresis, whole-genome sequencing revealed subtle alterations in the chromosomal organization of the last two strains; specifically, an inversion event within a novel 124-kb gene island (PAGI 12) composed of 137 open reading frames [ORFs]. Predicted ORFs in the island included metabolism and virulence genes. Overexpression of a gene island-borne putative β-lactamase gene was observed following piperacillin-tazobactam exposure and only in those strains that had undergone the inversion event, indicating altered gene regulation following genomic remodeling. Examination of a separate cohort of 76 patients with VAP for integration at this tRNAlys recombination site demonstrated that patients exhibiting evidence of integration at this site had significantly higher 28-day mortality. These findings provide evidence that P. aeruginosa can integrate, rapidly remodel, and express exogenous genes, which likely contributes to its fitness in a clinical setting. PMID:24789195

Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1.

PubMed

Mongodin, Emmanuel F; Shapir, Nir; Daugherty, Sean C; DeBoy, Robert T; Emerson, Joanne B; Shvartzbeyn, Alla; Radune, Diana; Vamathevan, Jessica; Riggs, Florenta; Grinberg, Viktoria; Khouri, Hoda; Wackett, Lawrence P; Nelson, Karen E; Sadowsky, Michael J

2006-12-01

Arthrobacter sp. strains are among the most frequently isolated, indigenous, aerobic bacterial genera found in soils. Member of the genus are metabolically and ecologically diverse and have the ability to survive in environmentally harsh conditions for extended periods of time. The genome of Arthrobacter aurescens strain TC1, which was originally isolated from soil at an atrazine spill site, is composed of a single 4,597,686 basepair (bp) circular chromosome and two circular plasmids, pTC1 and pTC2, which are 408,237 bp and 300,725 bp, respectively. Over 66% of the 4,702 open reading frames (ORFs) present in the TC1 genome could be assigned a putative function, and 13.2% (623 genes) appear to be unique to this bacterium, suggesting niche specialization. The genome of TC1 is most similar to that of Tropheryma, Leifsonia, Streptomyces, and Corynebacterium glutamicum, and analyses suggest that A. aurescens TC1 has expanded its metabolic abilities by relying on the duplication of catabolic genes and by funneling metabolic intermediates generated by plasmid-borne genes to chromosomally encoded pathways. The data presented here suggest that Arthrobacter's environmental prevalence may be due to its ability to survive under stressful conditions induced by starvation, ionizing radiation, oxygen radicals, and toxic chemicals.

Molecular identification and characterization of clustered regularly interspaced short palindromic repeat (CRISPR) gene cluster in Taylorella equigenitalis.

PubMed

Hara, Yasushi; Hayashi, Kyohei; Nakajima, Takuya; Kagawa, Shizuko; Tazumi, Akihiro; Moore, John E; Matsuda, Motoo

2013-09-01

Clustered regularly interspaced short palindromic repeats (CRISPRs), of approximately 10,000 base pairs (bp) in length, were shown to occur in the Japanese Taylorella equigenitalis strain, EQ59. The locus was composed of the putative CRISPRs-associated with 5 (cas5), RAMP csd1, csd2, recB, cas1, a leader region, 13 CRISPR consensus sequence repeats (each 32 bp; 5'-TCAGCCACGTTCGCGTGGCTGTGTGTTTAAAG-3'). These were in turn separated by 12 non repetitive unique spacer regions of similar length. In addition, a leader region, a transposase/IS protein, a leader region, and cas3 were also seen. All seven putative open reading frames carry their ribosome binding sites. Promoter consensus sequences at the -35 and -10 regions and putative intrinsic ρ-independent transcription terminator regions also occurred. A possible long overlap of 170 bp in length occurred between the recB and cas1 loci. Positive reverse transcription PCR signals of cas5, RAMP csd1, csd2-recB/cas1, and cas3 were generated. A putative secondary structure of the CRISPR consensus repeats was constructed. Following this, CRISPR results of the T. equigenitalis EQ59 isolate were subsequently compared with those from the Taylorella asinigenitalis MCE3 isolate.

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

Kim, Kyoung Mi; Cho, Hana; Kim, Yoon Ki, E-mail: yk-kim@korea.ac.kr

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

Cotesia vestalis parasitization suppresses expression of a Plutella xylostella thioredoxin.

PubMed

Shi, M; Zhao, S; Wang, Z-H; Stanley, D; Chen, X-X

2016-12-01

Thioredoxins (Trxs) are a family of small, highly conserved and ubiquitous proteins involved in protecting organisms against toxic reactive oxygen species. In this study, a typical thioredoxin gene, PxTrx, was isolated from Plutella xylostella. The full-length cDNA sequence is composed of 959 bp containing a 321 bp open reading frame that encodes a predicted protein of 106 amino acids, a predicted molecular weight of 11.7 kDa and an isoelectric point of 5.03. PxTrx was mainly expressed in larval Malpighian tubules and the fat body. An enriched recombinant PxTrx had insulin disulphide reductase activity and stimulated Human Embryonic Kidney 293 (HEK293) cell proliferation. It also protected supercoiled DNA and living HEK293 cells from H 2 O 2 -induced damage. Parasitization by Cotesia vestalis and injections of 0.05 and 0.01 equivalents of C. vestalis Bracovirus (CvBv), the symbiotic virus carried by the parasitoid, led to down-regulation of PxTrx expression in host fat body. Taken together, our results indicate that PxTrx contributes to the maintenance of P. xylostella cellular haemostasis. Host fat body expression of PxTrx is strongly attenuated by parasitization and by injections of CvBv. © 2016 The Royal Entomological Society.

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

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.

Differentially Fed Metal Frame Antenna With Common Mode Suppression for Biomedical Smartband Applications

NASA Astrophysics Data System (ADS)

Xu, Li-Jie; Duan, Zhu

2018-04-01

This paper proposes a differentially fed metal frame antenna for biomedical smartband applications. It occupies a planar area of 40 × 20 mm, operating at 2.45-GHz industrial, scientific, and medical band. The proposed antenna is composed of an external metal frame and an internal metal box acting as ground for electronics. Through a differential feeding to two copper strips located between the metal frame and the metal box, a rectangular ring slot is excited with common mode suppression capability. The antenna prototype is designed in free space, and then adapted to on-body scenario for both repeater and transmitter cases. Additionally, the proposed differential feeding is modified to the traditional single port, demonstrating the half-size miniaturization technique. Finally, the simulated results are verified by measurement. The proposed antenna's simple structure and satisfactory performance makes it a perfect candidate for future medical smartband applications, monitoring the physiological parameters of humans for health-care purposes.

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

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

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....

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

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

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

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

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

2000-03-05

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

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.

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.

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

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.

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.)

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....

Optimal read/write memory system components

NASA Technical Reports Server (NTRS)

Kozma, A.; Vander Lugt, A.; Klinger, D.

1972-01-01

Two holographic data storage and display systems, voltage gradient ionization system, and linear strain manipulation system are discussed in terms of creating fast, high bit density, storage device. Components described include: novel mounting fixture for photoplastic arrays; corona discharge device; and block data composer.

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.

Persuading People to Drink Less Alcohol: The Role of Message Framing, Temporal Focus and Autonomy.

PubMed

Churchill, Susan; Pavey, Louisa; Jessop, Donna; Sparks, Paul

2016-11-01

Health information can be used to try to persuade people to follow safe drinking recommendations. However, both the framing of information and the dispositional characteristics of message recipients need to be considered. An online study was conducted to examine how level of autonomy moderated the effect on drinking behaviour of gain- and loss-framed messages about the short- vs. long-term consequences of alcohol use. At Time 1, participants (N = 335) provided demographic information and completed a measure of autonomy. At Time 2, participants reported baseline alcohol use and read a gain-framed or loss-framed health message that highlighted either short- or long-term outcomes of alcohol consumption. Alcohol consumption was reported 7 days later. The results showed a significant three-way interaction between message framing (loss vs. gain), temporal focus (short-term vs. long-term) and autonomy. For low-autonomy (but not high-autonomy) individuals, the loss-framed health message was associated with lower levels of alcohol consumption than was the gain-framed message but only if the short-term outcomes were conveyed. This research provides evidence that the interaction between message framing and temporal focus may depend on a person's level of autonomy, which has implications for health promotion and the construction of effective health communication messages. We examined how autonomy moderated the effect on drinking behaviour of gain- and loss-framed messages about the short- vs. long-term consequences of alcohol use. For low-autonomy individuals, the loss-framed health message was associated with lower alcohol consumption than was the gain-framed message but only if the short-term outcomes were conveyed. © The Author 2016. Medical Council on Alcohol and Oxford University Press. All rights reserved.

Selfish DNA in protein-coding genes of Rickettsia.

PubMed

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

2000-10-13

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

Fluency and reading comprehension in students with reading difficulties.

PubMed

Nascimento, Tânia Augusto; Carvalho, Carolina Alves Ferreira de; Kida, Adriana de Souza Batista; Avila, Clara Regina Brandão de

2011-12-01

To characterize the performance of students with reading difficulties in decoding and reading comprehension tasks as well as to investigate the possible correlations between them. Sixty students (29 girls) from 3rd to 5th grades of public Elementary Schools were evaluated. Thirty students (Research Group - RG), ten from each grade, were nominated by their teachers as presenting evidences of learning disabilities. The other thirty students were indicated as good readers, and were matched by gender, age and grade to the RG, composing the Comparison Group (CG). All subjects were assessed regarding the parameters of reading fluency (rate and accuracy in words, pseudowords and text reading) and reading comprehension (reading level, number and type of ideas identified, and correct responses on multiple choice questions). The RG presented significantly lower scores than the CG in fluency and reading comprehension. Different patterns of positive and negative correlations, from weak to excellent, among the decoding and comprehension parameters were found in both groups. In the RG, low values of reading rate and accuracy were observed, which were correlated to low scores in comprehension and improvement in decoding, but not in comprehension, with grade increase. In CG, correlation was found between different fluency parameters, but none of them was correlated to the reading comprehension variables. Students with reading and writing difficulties show lower values of reading fluency and comprehension than good readers. Fluency and comprehension are correlated in the group with difficulties, showing that deficits in decoding influence reading comprehension, which does not improve with age increase.

Elementary Accounting. A Programed Text. Revised. Edition Code-3.

ERIC Educational Resources Information Center

Army Finance School, Fort Benjamin Harrison, IN.

This programed text is designed to teach the basic elements of the double entry system of accounting, including basic terms, procedures, definitions, and principles used. The text consists of frames, which are sequenced instructional steps and, in most cases, are composed of two parts. The first part states a fact or relates information and asks a…

Sexualities in Education: A Reader. Counterpoints: Studies in the Postmodern Theory of Education. Volume 367

ERIC Educational Resources Information Center

Meiners, Erica R., Ed.; Quinn, Therese, Ed.

2012-01-01

With germinal texts, new writings, and related art, "Sexualities in Education: A Reader" illuminates a broad scope of analysis and organization. Composed of a framing essay and nine sections edited by established and emerging scholars and addressing critical topics for researchers and students of sexualities and education, the text…

The Apis mellifera filamentous virus genome

USDA-ARS?s Scientific Manuscript database

A complete reference genome of the Apis mellifera Filamentous virus (AmFV) was determined using Illumina Hiseq sequencing. The AmFV genome is a double strand DNA molecule of approximately 498’500 nucleotides with a GC content of 50.8%. It encompasses 251 non overlapping open reading frames (ORFs), e...

Fender Bender Physics.

ERIC Educational Resources Information Center

Bevin, Roy Q.; Raudebaugh, Robert A.

This book is based on an integrated approach to science and technology and targets middle schools students. Each unit includes a teacher's guide and eight science activities. Units include: (1) "The Mousetrap Car"; (2) "The CO2 Car"; and (3) "The Space Frame Vehicle". Supplemental materials consist of seven readings including: (1) "Brainstorming";…

Direct enzyme assay evidence confirms aldehyde reductase function of Ydr541cp and Ygl039wp from Saccharomyces cerevisiae

USDA-ARS?s Scientific Manuscript database

Aldehyde reductase gene ARI1 is a recently characterized member of intermediate subfamily under SDR (short-chain dehydrogenase/reductase) superfamily that revealed mechanisms of in situ detoxification of furfural and HMF for tolerance of Saccharomyces cerevisiae. Uncharacterized open reading frames ...

Visual Servoing via Navigation Functions

DTIC Science & Technology

2002-02-06

kernel was adequate). The PC is equipped with a Data Translations12 DT3155 frame grabber connected to a standard 30Hz NTSC video camera. Using MATLAB’s C...Richard M. Murray, Zexiang Li, and S. Shankar Sastry. A Mathematical Introduction to Robotic Manipulation. CRC Press, Reading, Mass., 1994. [26] Dan Pedoe

93. DETAIL OF GENERAL ELECTRIC 250HP SYNCHRONOUS MOTOR FROM DRIVE ...

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

93. DETAIL OF GENERAL ELECTRIC 250-HP SYNCHRONOUS MOTOR FROM DRIVE END. MOTOR BADGE PLATE READS 263 AMP, 400 VOLT, FRAME 6274-D #4940649, 250 HORSEPOWER, TYPE TSR, 3 PHASE, 60 CYCLE, SPEED 300 RPM. - Shenandoah-Dives Mill, 135 County Road 2, Silverton, San Juan County, CO

Effects of the HN gene c-terminal extensions on the Newcastle disease virus virulence

USDA-ARS?s Scientific Manuscript database

The hemagglutinin-neuraminidase (HN) of Newcastle disease virus (NDV) is a multifunctional protein that has receptor recognition, neuraminidase and fusion promotion activities. Sequence analysis revealed that the HN gene of many extremely low virulence NDV strains encodes a larger open reading frame...

PRIMARY STRUCTURE OF THE P450 LANOSTEROL DEMETHYLASE GENE FROM SACCHAROMYCES CEREVISIAE

EPA Science Inventory

We have sequenced the structural gene and flanking regions for lanosterol 14 alpha-demethylase (14DM) from Saccharomyces cerevisiae. An open reading frame of 530 codons encodes a 60.7-kDa protein. When this gene is disrupted by integrative transformation, the resulting strain req...

Perceptual Specificity Effects in Rereading: Evidence from Eye Movements

ERIC Educational Resources Information Center

Sheridan, Heather; Reingold, Eyal M.

2012-01-01

The present experiments examined perceptual specificity effects using a rereading paradigm. Eye movements were monitored while participants read the same target word twice, in two different low-constraint sentence frames. The congruency of perceptual processing was manipulated by either presenting the target word in the same distortion typography…

Using Metaphors to Teach Organization Theory

ERIC Educational Resources Information Center

Taber, Tom D.

2007-01-01

Metaphors were used to teach systems thinking and to clarify concepts of organizational theory in an introductory MBA management course. Gareth Morgan's metaphors of organization were read by students and applied as frames to analyze a business case. In addition, personal metaphors were written by individual students in order to describe the…

Three sorghum serpin recombinant proteins inhibit midgut trypsin activity and growth of corn earworm

USDA-ARS?s Scientific Manuscript database

The sorghum (Sorghum bicolor) genome contains at least 17 putative serpin (serine protease inhibitor) open reading frames, some of which are induced by pathogens. Recent transcriptome studies found that most of the putative serpins are expressed but their roles are unknown. Four sorghum serpins were...

From Mosquitos to Humans: Genetic Evolution of Zika Virus

PubMed Central

Wang, Lulan; Valderramos, Stephanie G.; Wu, Aiping; Ouyang, Songying; Li, Chunfeng; Brasil, Patricia; Bonaldo, Myrna; Coates, Thomas; Nielsen-Saines, Karin; Jiang, Taijiao; Aliyari, Roghiyh; Cheng, Genhong

2017-01-01

Initially isolated in 1947, Zika virus (ZIKV) has recently emerged as significant public health concern. Sequence analysis of all 41 known ZIKV RNA open reading frames to date indicates that ZIKV has undergone significant changes in both protein and nucleotide sequences during the past half century. PMID:27091703

Reactions to framing of cessation messages: insights from dual-smoker couples.

PubMed

Lipkus, Isaac M; Ranby, Krista W; Lewis, Megan A; Toll, Benjamin

2013-12-01

Couples in which both members smoke (dual-smoker couples) have not been the explicit target of cessation interventions. Quit rates are lower and relapse rates are higher among individuals in dual-smoker couples. A potentially effective strategy to motivate dual-smoker couples to quit is to convey messages that highlight how the positive outcomes of quitting (gain frame) or the negative outcomes of continued smoking (loss frame) affect the couple rather than the individual smoker. We explored whether dual-smoker couples' smoking behaviors (e.g., amount smoked) and desire to quit would differ as a function of message frame (gain vs. loss) or outcome focus (individual vs. couple). Dual-smoker couples (N = 40) completed a baseline survey and were then randomized to review gain- or loss-framed messages that varied whether the outcomes influenced the individual or the couple. Main outcomes were desire to quit after reading messages and smoking behaviors at a 1-month follow-up. Couple-focused messages produced the strongest desire to quit and decreased amount of cigarettes smoked at follow-up. The latter effect was mediated by desire to quit. Loss-framed messages produced inconsistent effects on desire to quit. There were no significant interactions between outcome focus and message framing. Findings suggest that messages emphasizing how smoking affects both partners can motivate cessation among dual-smoker couples. Contrary to findings showing that gain-framed messages motivate cessation targeting individual smokers, results suggest that loss-framed messages may be more persuasive than gain-framed messages when the target of the outcome involves significant others.

Study to investigate design, fabrication and test of low cost concepts for large hybrid composite helicopter fuselage, phase 2

NASA Technical Reports Server (NTRS)

Adams, K. M.; Lucas, J. J.

1977-01-01

The development of a frame/stringer/skin fabrication technique for composite airframe construction was studied as a low cost approach to the manufacturer of larger helicopter airframe components. A center cabin aluminum airframe section of the Sikorsky CH-53D, was selected for evaluation as a composite structure. The design, as developed, is composed of a woven KEVLAR R-49/epoxy skin and graphite/epoxy frames and stringers. The single cure concept is made possible by the utilization of pre-molded foam cores, over which the graphite/epoxy pre-impregnated frame and stringer reinforcements are positioned. Bolted composite channel sections were selected as the optimum joint construction. The applicability of the single cure concept to larger realistic curved airframe sections, and the durability of the composite structure in a realistic spectrum fatigue environment, was described.

Origins of Genes: "Big Bang" or Continuous Creation?

NASA Astrophysics Data System (ADS)

Kesse, Paul K.; Gibbs, Adrian

1992-10-01

Many protein families are common to all cellular organisms, indicating that many genes have ancient origins. Genetic variation is mostly attributed to processes such as mutation, duplication, and rearrangement of ancient modules. Thus it is widely assumed that much of present-day genetic diversity can be traced by common ancestry to a molecular "big bang." A rarely considered alternative is that proteins may arise continuously de novo. One mechanism of generating different coding sequences is by "overprinting," in which an existing nucleotide sequence is translated de novo in a different reading frame or from noncoding open reading frames. The clearest evidence for overprinting is provided when the original gene function is retained, as in overlapping genes. Analysis of their phylogenies indicates which are the original genes and which are their informationally novel partners. We report here the phylogenetic relationships of overlapping coding sequences from steroid-related receptor genes and from tymovirus, luteovirus, and lentivirus genomes. For each pair of overlapping coding sequences, one is confined to a single lineage, whereas the other is more widespread. This suggests that the phylogenetically restricted coding sequence arose only in the progenitor of that lineage by translating an out-of-frame sequence to yield the new polypeptide. The production of novel exons by alternative splicing in thyroid receptor and lentivirus genes suggests that introns can be a valuable evolutionary source for overprinting. New genes and their products may drive major evolutionary changes.

High-Efficiency "-1" and "-2" Ribosomal Frameshiftings Revealed by Force Spectroscopy.

PubMed

Tsai, Te-Wei; Yang, Haopeng; Yin, Heng; Xu, Shoujun; Wang, Yuhong

2017-06-16

Ribosomal frameshifting is a rare but ubiquitous process that is being studied extensively. Meanwhile, frameshifting motifs without any secondary mRNA structures were identified but rarely studied experimentally. We report unambiguous observation of highly efficient "-1" and "-2" frameshiftings on a GA 7 G slippery mRNA without the downstream secondary structure, using force-induced remnant magnetization spectroscopy combined with unique probing schemes. The result represents the first experimental evidence of multiple frameshifting steps. It is also one of the rare reports of the "-2" frameshifting. Our assay removed the ambiguity of transcriptional slippage involvement in other frameshifting assays. Two significant insights for the frameshifting mechanism were revealed. First, EF-G·GTP is indispensable to frameshifting. Although EFG·GDPCP has been shown to prompt translocation before, we found that it could not induce frameshifting. This implies that the GTP hydrolysis is responsible for the codon-anticodon re-pairing in frameshifting, which corroborates our previous mechanical force measurement of EF-G·GTP. Second, translation in all three reading frames of the slippery sequence can be induced by the corresponding in-frame aminoacyl tRNAs. Although A-site tRNA is known to affect the partition between "0" and "-1" frameshifting, it has not been reported that all three reading frames can be translated by their corresponding tRNAs. The in vitro results were confirmed by toe-printing assay and protein sequencing.

Detection of novel NF1 mutations and rapid mutation prescreening with Pyrosequencing.

PubMed

Brinckmann, Anja; Mischung, Claudia; Bässmann, Ingelore; Kühnisch, Jirko; Schuelke, Markus; Tinschert, Sigrid; Nürnberg, Peter

2007-12-01

Neurofibromatosis type 1 (NF1) is caused by mutations in the neurofibromin (NF1) gene. Mutation analysis of NF1 is complicated by its large size, the lack of mutation hotspots, pseudogenes and frequent de novo mutations. Additionally, the search for NF1 mutations on the mRNA level is often hampered by nonsense-mediated mRNA decay (NMD) of the mutant allele. In this study we searched for mutations in a cohort of 38 patients and investigated the relationship between mutation type and allele-specific transcription from the wild-type versus mutant alleles. Quantification of relative mRNA transcript numbers was done by Pyrosequencing, a novel real-time sequencing method whose signals can be quantified very accurately. We identified 21 novel mutations comprising various mutation types. Pyrosequencing detected a definite relationship between allelic NF1 transcript imbalance due to NMD and mutation type in 24 of 29 patients who all carried frame-shift or nonsense mutations. NMD was absent in 5 patients with missense and silent mutations, as well as in 4 patients with splice-site mutations that did not disrupt the reading frame. Pyrosequencing was capable of detecting NMD even when the effects were only moderate. Diagnostic laboratories could thus exploit this effect for rapid prescreening for NF1 mutations as more than 60% of the mutations in this gene disrupt the reading frame and are prone to NMD.

Large-scale automated analysis of news media: a novel computational method for obesity policy research.

PubMed

Hamad, Rita; Pomeranz, Jennifer L; Siddiqi, Arjumand; Basu, Sanjay

2015-02-01

Analyzing news media allows obesity policy researchers to understand popular conceptions about obesity, which is important for targeting health education and policies. A persistent dilemma is that investigators have to read and manually classify thousands of individual news articles to identify how obesity and obesity-related policy proposals may be described to the public in the media. A machine learning method called "automated content analysis" that permits researchers to train computers to "read" and classify massive volumes of documents was demonstrated. 14,302 newspaper articles that mentioned the word "obesity" during 2011-2012 were identified. Four states that vary in obesity prevalence and policy (Alabama, California, New Jersey, and North Carolina) were examined. The reliability of an automated program to categorize the media's framing of obesity as an individual-level problem (e.g., diet) and/or an environmental-level problem (e.g., obesogenic environment) was tested. The automated program performed similarly to human coders. The proportion of articles with individual-level framing (27.7-31.0%) was higher than the proportion with neutral (18.0-22.1%) or environmental-level framing (16.0-16.4%) across all states and over the entire study period (P<0.05). A novel approach to the study of how obesity concepts are communicated and propagated in news media was demonstrated. © 2014 The Obesity Society.

A propaganda index for reviewing problem framing in articles and manuscripts: an exploratory study.

PubMed

Gambrill, Eileen; Reiman, Amanda

2011-01-01

To determine the effectiveness of an index in increasing recognition of misleading problem framing in articles and manuscripts. A propaganda index consisting of 32 items was developed drawing on related literature. Seventeen subjects who review manuscripts for possible publication were requested to read five recent published reports of randomized controlled trials concerning social anxiety and to identify indicators of propaganda (defined as encouraging beliefs and actions with the least thought possible). They then re-read the same five articles using a propaganda index to note instances of propaganda. Convenience sample of individuals who review manuscripts for possible publication and sample of recent published reports of randomized controlled trials regarding social anxiety in five different journals by different authors, blinded by author and journal. Data showed that there was a high rate of propagandistic problem framing in reports of RCTs regarding social anxiety such as hiding well argued alternative views and vagueness. This occurred in 117 out of 160 opportunities over five research reports. A convenience sample of 17 academics spotted only 4.5 percent of propaganda indicators. This increased to 64 percent with use of the 32 item propaganda index. Use of a propaganda index increased recognition of related indicators. However many instances remained undetected. This propaganda index warrants further exploration as a complement to reporting guidelines such as CONSORT and PRISMA.

A Propaganda Index for Reviewing Problem Framing in Articles and Manuscripts: An Exploratory Study

PubMed Central

Gambrill, Eileen; Reiman, Amanda

2011-01-01

Objective To determine the effectiveness of an index in increasing recognition of misleading problem framing in articles and manuscripts. Design A propaganda index consisting of 32 items was developed drawing on related literature. Seventeen subjects who review manuscripts for possible publication were requested to read five recent published reports of randomized controlled trials concerning social anxiety and to identify indicators of propaganda (defined as encouraging beliefs and actions with the least thought possible). They then re-read the same five articles using a propaganda index to note instances of propaganda. Data source Convenience sample of individuals who review manuscripts for possible publication and sample of recent published reports of randomized controlled trials regarding social anxiety in five different journals by different authors, blinded by author and journal. Results Data showed that there was a high rate of propagandistic problem framing in reports of RCTs regarding social anxiety such as hiding well argued alternative views and vagueness. This occurred in 117 out of 160 opportunities over five research reports. A convenience sample of 17 academics spotted only 4.5 percent of propaganda indicators. This increased to 64 percent with use of the 32 item propaganda index. Use of a propaganda index increased recognition of related indicators. However many instances remained undetected. Conclusion This propaganda index warrants further exploration as a complement to reporting guidelines such as CONSORT and PRISMA. PMID:21647426

Determining the locations of the various CIRC recording format information blocks (user data blocks, C2 and C1 words and EFM frames) on a recorded compact disc

NASA Technical Reports Server (NTRS)

Howe, Dennis G.

1993-01-01

Just prior to its being EFM modulated (i.e., converted to eight-to-fourteen channel data by the EFM encoder) and written to a Compact Disc (CD), information that passes through the CIRC Block Encoder is grouped into 33-byte blocks referred to as EFM frames. Twenty four of the bytes that make up a given EFM frame are user data that was input into the CIRC encoder at various (different) times, 4 of the bytes of this same EFM frame were created by the C2 ECC encoder (each at a different time), and another 4 were created by the C1 ECC encoder (again, each at a different time). The one remaining byte of the given EFM frame, which is known as the EFM frame C&D (for Control & Display) byte, carries information that identifies which portion of the current disc program track the given EFM frame belongs to and also specifies the location of the given EFM frame on the disc (in terms of a time stamp that has a resolution of l/75th second, or 98 EFM frames). (Note: since the program track and time information is stored as a 98-byte word, a logical group consisting of 98 consecutive EFM frames must be read, and their respective C&D bytes must be catenated and decoded, before the program track identification and time position information that pertains to the entire block of 98 EFM frames can be obtained.) The C&D byte is put at the start (0th byte) of an EFM frame in real time; its placement completes the construction of the EFM frame - it is assigned just before the EFM frame enters the EFM encoder. Four distinct blocks of data are referred to: 24-byte User Input Data Blocks; 28-byte C2 words; 32-byte C1 words; and 33-byte EFM frames.

Cheetah: A high frame rate, high resolution SWIR image camera

NASA Astrophysics Data System (ADS)

Neys, Joel; Bentell, Jonas; O'Grady, Matt; Vermeiren, Jan; Colin, Thierry; Hooylaerts, Peter; Grietens, Bob

2008-10-01

A high resolution, high frame rate InGaAs based image sensor and associated camera has been developed. The sensor and the camera are capable of recording and delivering more than 1700 full 640x512pixel frames per second. The FPA utilizes a low lag CTIA current integrator in each pixel, enabling integration times shorter than one microsecond. On-chip logics allows for four different sub windows to be read out simultaneously at even higher rates. The spectral sensitivity of the FPA is situated in the SWIR range [0.9-1.7 μm] and can be further extended into the Visible and NIR range. The Cheetah camera has max 16 GB of on-board memory to store the acquired images and transfer the data over a Gigabit Ethernet connection to the PC. The camera is also equipped with a full CameralinkTM interface to directly stream the data to a frame grabber or dedicated image processing unit. The Cheetah camera is completely under software control.

Study to investigate design, fabrication and test of low cost concepts for large hybrid composite helicopter fuselage, phase 1

NASA Technical Reports Server (NTRS)

Adams, K. M.; Lucas, J. J.

1975-01-01

The development of a frame/stringer/skin fabrication technique for composite airframe construction was studied as a low cost approach to the manufacture of large helicopter airframe components. A center cabin aluminum airframe section of the Sikorsky CH-53D helicopter was selected for evaluation as a composite structure. The design, as developed, is composed of a woven KEVLAR-49/epoxy skin and graphite/epoxy frames and stringers. To support the selection of this specific design concept a materials study was conducted to develop and select a cure compatible graphite and KEVLAR-49/epoxy resin system, and a foam system capable of maintaining shape and integrity under the processing conditions established. The materials selected were, Narmco 5209/Thornel T-300 graphite, Narmco 5209/KEVLAR-49 woven fabric, and Stathane 8747 polyurethane foam. Eight specimens were fabricated, representative of the frame, stringer, and splice joint attachments. Evaluation of the results of analysis and test indicate that design predictions are good to excellent except for some conservatism of the complex frame splice.

Illustrating Praxis: Comic Composition, Narrative Rhetoric, and Critical Multiliteracies

ERIC Educational Resources Information Center

Comer, Kathryn

2015-01-01

Thus far, pedagogical discussions about comics in the college classroom have focused primarily on "reading," with less attention paid to the complementary potential of "composing" comics. This essay advocates using narrative theory alongside comic studies to provide students and teachers with a flexible, transferable vocabulary…

Pairing Linguistic and Music Intelligences

ERIC Educational Resources Information Center

DiEdwardo, MaryAnn Pasda

2005-01-01

This article describes how music in the language classroom setting can be a catalyst for developing reading, writing, and understanding skills. Studies suggest that pairing music and linguistic intelligences in the college classroom improves students' grades and abilities to compose theses statements for research papers in courses that emphasize…

The effect of character contextual diversity on eye movements in Chinese sentence reading.

PubMed

Chen, Qingrong; Zhao, Guoxia; Huang, Xin; Yang, Yiming; Tanenhaus, Michael K

2017-12-01

Chen, Huang, et al. (Psychonomic Bulletin & Review, 2017) found that when reading two-character Chinese words embedded in sentence contexts, contextual diversity (CD), a measure of the proportion of texts in which a word appears, affected fixation times to words. When CD is controlled, however, frequency did not affect reading times. Two experiments used the same experimental designs to examine whether there are frequency effects of the first character of two-character words when CD is controlled. In Experiment 1, yoked triples of characters from a control group, a group matched for character CD that is lower in frequency, and a group matched in frequency with the control group, but higher in character CD, were rotated through the same sentence frame. In Experiment 2 each character from a larger set was embedded in a separate sentence frame, allowing for a larger difference in log frequency compared to Experiment 1 (0.8 and 0.4, respectively). In both experiments, early and later eye movement measures were significantly shorter for characters with higher CD than for characters with lower CD, with no effects of character frequency. These results place constraints on models of visual word recognition and suggest ways in which Chinese can be used to tease apart the nature of context effects in word recognition and language processing in general.

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.

Representation of Knowledge

DTIC Science & Technology

1980-03-01

structure composed of nodes representing semantic primitives. From this structure, a French translation of the input is generated. The translation serves as a...Style: range: (Burgers, Chinese, American, Seafood, French ) default: American if-added: (Update Alternatives of Restaurant) Times-of-Operation: range: a...Restaurant Frame is used to modify the list of alternative restaurants once a particular cuisine is chosen. In some systems, trigger procedures

LAMBDA 2M GaAs—A multi-megapixel hard X-ray detector for synchrotrons

NASA Astrophysics Data System (ADS)

Pennicard, D.; Smoljanin, S.; Pithan, F.; Sarajlic, M.; Rothkirch, A.; Yu, Y.; Liermann, H. P.; Morgenroth, W.; Winkler, B.; Jenei, Z.; Stawitz, H.; Becker, J.; Graafsma, H.

2018-01-01

Synchrotrons can provide very intense and focused X-ray beams, which can be used to study the structure of matter down to the atomic scale. In many experiments, the quality of the results depends strongly on detector performance; in particular, experiments studying dynamics of samples require fast, sensitive X-ray detectors. "LAMBDA" is a photon-counting hybrid pixel detector system for experiments at synchrotrons, based on the Medipix3 readout chip. Its main features are a combination of comparatively small pixel size (55 μm), high readout speed at up to 2000 frames per second with no time gap between images, a large tileable module design, and compatibility with high-Z sensors for efficient detection of higher X-ray energies. A large LAMBDA system for hard X-ray detection has been built using Cr-compensated GaAs as a sensor material. The system is composed of 6 GaAs tiles, each of 768 by 512 pixels, giving a system with approximately 2 megapixels and an area of 8.5 by 8.5 cm2. While the sensor uniformity of GaAs is not as high as that of silicon, its behaviour is stable over time, and it is possible to correct nonuniformities effectively by postprocessing of images. By using multiple 10 Gigabit Ethernet data links, the system can be read out at the full speed of 2000 frames per second. The system has been used in hard X-ray diffraction experiments studying the structure of samples under extreme pressure in diamond anvil cells. These experiments can provide insight into geological processes. Thanks to the combination of high speed readout, large area and high sensitivity to hard X-rays, it is possible to obtain previously unattainable information in these experiments about atomic-scale structure on a millisecond timescale during rapid changes of pressure or temperature.

New Options for Usability Testing Projects in Business Communication Courses

ERIC Educational Resources Information Center

Jameson, Daphne A.

2013-01-01

The increasing availability of recording technologies makes it easier to include usability testing projects in business communication courses. Usability testing is a method of discovering whether people can navigate, read, and understand a print or electronic communication well enough to achieve a particular purpose in a reasonable time frame.…

Complete genome sequence of yam chlorotic necrosis virus, a novel macluravirus infecting yam

USDA-ARS?s Scientific Manuscript database

Complete genomic sequence of a novel member of the genus Macluravirus was determined from yam plants with chlorotic and necrotic symptoms in China. The genomic RNA consists of 8,261 nucleotides (nt) excluding the 3’-terminal poly (A) tail, containing one long open reading frame (ORF) encoding a larg...

Reading the Newspaper as a Social Text

ERIC Educational Resources Information Center

Segall, Avner; Schmidt, Sander

2006-01-01

In today's culture, some of the most commonly shared experiences involve the mass media. The media--film, television, radio, newspapers, magazines, music, advertising, and software industries--have become primary avenues through which most come to know about the world, both near and far. They help frame the world, elevating certain issues, and the…

Reading Queer Television: Some Notes on Method

ERIC Educational Resources Information Center

Marshall, Daniel

2016-01-01

In this article the author presents his reflection on the framing of mass queer television as a technology within the cultural politics of gender and sexuality; and, next, discusses the mass production of these representations in terms of the mass production of modes of intelligibility of LGBT subjects. To narrow the argument, he focuses his…

Textual Encounters and Pedagogic Interventions

ERIC Educational Resources Information Center

Vicars, Mark

2009-01-01

School, typically, is no place to be caught being queer and knowledge about homosexuality for the majority of young lesbian, gay and bisexual people is routinely constructed within communities of practice. In this paper, I draw upon my own and others' literacy practices to show how our identities and readings of texts were framed by being…

Diagnostic Assay for Rickettsia japonica

PubMed Central

Hanaoka, Nozomu; Matsutani, Minenosuke; Kawabata, Hiroki; Yamamoto, Seigo; Fujita, Hiromi; Sakata, Akiko; Azuma, Yoshinao; Ogawa, Motohiko; Takano, Ai; Watanabe, Haruo; Kishimoto, Toshio; Shirai, Mutsunori; Kurane, Ichiro

2009-01-01

We developed a specific and rapid detection system for Rickettsia japonica and R. heilongjiangensis, the causative agents of spotted fever, using a TaqMan minor groove binder probe for a particular open reading frame (ORF) identified by the R. japonica genome project. The target ORF was present only in R. japonica–related strains. PMID:19961684

Framing the Text: Using Storyboards to Engage Students with Reading

ERIC Educational Resources Information Center

Bruce, David L.

2011-01-01

Storyboards deliver a narrative through discrete visual representations. The purpose of the storyboards was always to "scaffold" the final product and students were free to add, delete, or adapt those images that were most helpful to their project. The storyboards served as a brainstorming activity, much like a prewriting exercise for a written…

Frames of Reference in Spatial Memories Acquired From Language

ERIC Educational Resources Information Center

Mou, Weimin; Zhang, Kan; McNamara, Timothy P.

2004-01-01

Four experiments examined reference systems in spatial memories acquired from language. Participants read narratives that located 4 objects in canonical (front, back, left, right) or noncanonical (left front, right front, left back, right back) positions around them. Participants' focus of attention was first set on each of the 4 objects, and then…

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

USDA-ARS?s Scientific Manuscript database

Clematis chlorotic mottle virus (ClCMV) is a previously undescribed virus associated with yellow mottling and veining, chlorotic ring spots, line pattern mosaics, and flower distortion and discoloration on ornamental Clematis. The ClCMV genome is 3,880nt in length with 5 putative open reading frames...

Reaching New Horizons: Gifted and Talented Education for Culturally and Linguistically Diverse Students.

ERIC Educational Resources Information Center

Castellano, Jaime A., Ed.; Diaz, Eva I., Ed.

This book provides 14 readings on issues in the education of gifted and talented students from culturally or linguistically diverse populations. Its overall theme is the insoluble and reciprocal dependence of excellence and equity in education. Chapters include: (1) "Framing an Historical Context for the Education of Culturally and Linguistically…

"Now I Look at All the Kids Differently": Cracking Teacher Candidates' Assumptions about School Achievement in Urban Communities

ERIC Educational Resources Information Center

Lazar, Althier; Sharma, Suniti

2016-01-01

This mixed-methods study explores the impact of teacher preparation coursework on 141 teacher candidates' understandings about educational equality, school achievement, and meritocracy. Framed by pedagogies of discomfort, the program included readings, discussions, simulations, films, and direct work with emergent bilingual students. Findings from…

Time and Outcome Framing in Intertemporal Tradeoffs

ERIC Educational Resources Information Center

Scholten, Marc; Read, Daniel

2013-01-01

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…

cDNA encoding a polypeptide including a hevein sequence

DOEpatents

Raikhel, N.V.; Broekaert, W.F.; Namhai Chua; Kush, A.

1993-02-16

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids.

Students' Framing of a Reading Annotation Tool in the Context of Research-Based Teaching

ERIC Educational Resources Information Center

Dahl, Jan Erik

2016-01-01

In the studied master's course, students participated both as research objects in a digital annotation experiment and as critical investigators of this technology in their semester projects. The students' role paralleled the researcher's role, opening an opportunity for researcher-student co-learning within what is often referred to as…

NUCLEOTIDE SEQUENCING AND TRANSCRIPTIONAL MAPPING OF THE GENES ENCODING BIPHENYL DIOXYGENASE, A MULTICOMPONENT POLYCHLORINATED-BIPHENYL-DEGRADING ENZYME IN PSEUDOMONAS STRAIN LB400

EPA Science Inventory

The DNA region encoding biphenyl dioxygenase, the first enzyme in the biphenyl-polychlorinated biphenyl degradation pathway of Pseudomonas species strain LB400, was sequenced. ix open reading frames were identified, four of which are, homologous to the components of toluene dioxy...

Playing with the Multiple Intelligences: How Play Helps Them Grow

ERIC Educational Resources Information Center

Eberle, Scott G.

2011-01-01

Howard Gardner first posited a list of "multiple intelligences" as a liberating alternative to the assumptions underlying traditional IQ testing in his widely read study "Frames of Mind" (1983). Play has appeared only in passing in Gardner's thinking about intelligence, however, even though play instructs and trains the verbal, interpersonal,…

Toward a Positive Explanation of Student Differences in Reading Growth

ERIC Educational Resources Information Center

Adams, Curt M.; Palmer, Anna H.

2017-01-01

Background: Education has much in common with professions that are using positive psychology and positive organizational scholarship to transform practice, yet the science behind peak human and group functioning has been slow to displace deficit-based framing of reform policies and improvement strategies in education. Purpose of the Study: This…

Milestone reached for ORFeome Collaboration | Office of Cancer Genomics

Cancer.gov

The ORFeome Collaboration (OC) is a team of academic and commercial entities which have generated the largest collection of clones containing verified open-reading frames (ORFs) of known human genes. The clones are made available to researchers worldwide through multiple distributors. This valuable resource allows researchers to easily express and study human genes.

Edwardsiella ictaluri Encodes an Acid Activated Urease that is Required for Intracellular Replication in Channel Catfish Ictalurus punctatus Macrophages

USDA-ARS?s Scientific Manuscript database

Genomic analysis indicated that Edwardsiella ictaluri encodes a putative ureasepathogenicity island containing 9 open reading frames, including urea and ammonium transporters. In vitro studies with the wild-type E. ictaluri and a ureG::kan urease mutant strain indicated that E. ictaluri is significa...

Southern Tomato Virus: The Link between the Families Totiviridae and Partitiviridae

USDA-ARS?s Scientific Manuscript database

A dsRNA virus with a genome of 3.5 kb was isolated from field and greenhouse-grown tomato plants of different cultivars and geographic locations in North America. Cloning and sequencing of the viral genome showed the presence of two partially overlapping open reading frames (ORFs) and a genomic orga...

Teachers' Perceptions and Pedagogical Content Knowledge of Phonological Awareness, Phonics, and Dyslexia

ERIC Educational Resources Information Center

Williams, Jennifer S.

2012-01-01

In 2011, a small Midwestern school district referred an increasing number of 2nd-4th grade students, with reading problems due to phonetic and phonological awareness deficits, to the district's intervention team. Framed in Shulman's pedagogical content knowledge model and the International Dyslexia Association's phonological deficit theory of…

Purification and Analysis of Colorful Hypothetical Open Reading Frames: An Inexpensive Gateway Laboratory

ERIC Educational Resources Information Center

DeSantis, Kara A.; Reinking, Jeffrey L.

2011-01-01

This laboratory exercise is an inquiry-based investigation developed around the core experiment where students, working alone or in groups, each purify and analyze their own prescreened colored proteins using immobilized metal affinity chromatography (IMAC). Here, we present reagents and protocols that allow 12 different proteins to be purified in…

Reconsidering the Hypothetical Adolescent in Evaluating and Teaching Young Adult Literature

ERIC Educational Resources Information Center

Sulzer, Mark A.; Thein, Amanda Haertling

2016-01-01

Courses on teaching young adult literature (YAL) often encourage preservice English language arts teachers to consider their future students as they evaluate texts for classroom use. In this study, Sulzer and Thein analyzed preservice teachers' responses to familiar questions used to frame discussions of YAL--questions that ask them to read on…

Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses

USDA-ARS?s Scientific Manuscript database

Solenopsis invicta virus 2 is a single-stranded positive-sense picorna-like RNA virus with an unusual genome structure. The monopartite genome of approximately 11 kb contains four short open reading frames in its 5' one third, three of which encode proteins with homology to picornavirus-like jelly-r...

Words on the Screen: Broadening Analyses of Interactions among Fanfiction Writers and Reviewers

ERIC Educational Resources Information Center

Magnifico, Alecia Marie; Curwood, Jen Scott; Lammers, Jayne C.

2015-01-01

Young fanfiction writers use the Internet to build networks of reading, writing and editing--literacy practices that are highly valued in schools, universities and workplaces. While prior research shows that online spaces frame multiple kinds of participation as legitimate, much of this work focuses on the extensive contributions of exceptional…

A NOVEL CADHERIN-LIKE GENE FROM WESTERN CORN ROOTWORM, DIABROTICA VIRGIFERA VIRGIFERA (COLEOPTERA: CHRYSOMELIDAE), LARVAL MIDGUT TISSUE

EPA Science Inventory

A cadherin-like gene and its mRNA were cloned from western corn rootworm (Diabrotica virgifera virgifera: Coleoptera), an economically important agricultural pest in North America and Europe. The full length cDNA (5371 bp in length) encodes an open reading frame for a 1688 amino ...

Assembling, Disassembling and Reassembling "Youth Services" in Austerity Britain

ERIC Educational Resources Information Center

Youdell, Deborah; McGimpsey, Ian

2015-01-01

This paper moves from a reading of processes that are transforming public services in ways that amount to a dismantling of the welfare state in the UK. In order to interrogate these processes, the paper focuses on "youth" and "youth services". Framed by an analysis of the aggressive disinvestment of "austerity", we…

Ancient India: The Asiatic Ethiopians.

ERIC Educational Resources Information Center

Scott, Carolyn McPherson

This curriculum unit was developed by a participant in the 1993 Fulbright-Hays Program "India: Continuity and Change." The unit attempts to place India in the "picture frame" of the ancient world as a part of a whole, not as a separate entity. Reading materials enable students to draw broader general conclusions based on the…

Renal transplantation from hepatitis B surface antigen (HBsAg)-positive donors to HBsAg-negative recipients: a case of post-transplant fulminant hepatitis associated with an extensively mutated hepatitis B virus strain and review of the current literature.

PubMed

Magiorkinis, E; Paraskevis, D; Pavlopoulou, I D; Kantzanou, M; Haida, C; Hatzakis, A; Boletis, I N

2013-08-01

The purpose of this study was to present a fatal case of fulminant hepatitis B (FHB) that developed in a renal transplant recipient, immunized against hepatitis B, 1 year post transplantation. Polymerase chain reaction amplification and full genome sequencing were performed to investigate whether specific mutations were associated with hepatitis B virus (HBV) transmission and FHB. Molecular analysis revealed multiple mutations in various open reading frames of HBV, the most important being the G145R escape mutation and a frameshift mutation-insertion (1838insA) within the pre-C/C reading frame. Our results highlight the possibility of developing FHB, despite previous immunization against HBV or administration of hyperimmune gammaglobulin, because of the selection of escape virus mutants. The current literature and guidelines regarding renal transplantation from hepatitis B surface antigen (HBsAg)-positive to HBsAg-negative patients were also reviewed. © 2013 John Wiley & Sons A/S.

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

PubMed

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

2014-05-01

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

Large diversity of the piggyBac-like elements in the genome of Tribolium castaneum

PubMed Central

Wang, Jianjun; Du, Yuzhou; Wang, Suzhi; Brown, Sue; Park, Yoonseong

2011-01-01

The piggyBac transposable element, originally discovered in the cabbage looper, Trichoplusia ni, has been widely used in insect transgenesis including the red flour beetle Tribolium castaneum. We surveyed piggyBac-like (PLE) sequences in the genome of Tribolium castaneum by homology searches using as queries the diverse PLE sequences that have been described previously. The search yielded a total of 32 piggyBac-like elements (TcPLEs) which were classified into 14 distinct groups. Most of the TcPLEs contain defective functional motifs in that they are lacking inverted terminal repeats or have disrupted open reading frames. Only one single copy of TcPLE1 appears to be intact with imperfect 16 bp inverted terminal repeats flanking an open reading frame encoding a transposase of 571 amino acid residues. Many copies of TcPLEs were found to be inserted into or close to other transposon-like sequences. This large diversity of TcPLEs with generally low copy numbers suggests multiple invasions of the TcPLEs over a long evolutionary time without extensive multiplications or occurrence of rapid loss of TcPLEs copies. PMID:18342253

The flaA locus of Bacillus subtilis is part of a large operon coding for flagellar structures, motility functions, and an ATPase-like polypeptide.

PubMed Central

Albertini, A M; Caramori, T; Crabb, W D; Scoffone, F; Galizzi, A

1991-01-01

We cloned and sequenced 8.3 kb of Bacillus subtilis DNA corresponding to the flaA locus involved in flagellar biosynthesis, motility, and chemotaxis. The DNA sequence revealed the presence of 10 complete and 2 incomplete open reading frames. Comparison of the deduced amino acid sequences to data banks showed similarities of nine of the deduced products to a number of proteins of Escherichia coli and Salmonella typhimurium for which a role in flagellar functioning has been directly demonstrated. In particular, the sequence data suggest that the flaA operon codes for the M-ring protein, components of the motor switch, and the distal part of the basal-body rod. The gene order is remarkably similar to that described for region III of the enterobacterial flagellar regulon. One of the open reading frames was translated into a protein with 48% amino acid identity to S. typhimurium FliI and 29% identity to the beta subunit of E. coli ATP synthase. PMID:1828465

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

PubMed

Pooma, W; Petty, I T

1996-08-01

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

Archaebacterial rhodopsin sequences: Implications for evolution

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1991-01-01

It was proposed over 10 years ago that the archaebacteria represent a separate kingdom which diverged very early from the eubacteria and eukaryotes. It follows that investigations of archaebacterial characteristics might reveal features of early evolution. So far, two genes, one for bacteriorhodopsin and another for halorhodopsin, both from Halobacterium halobium, have been sequenced. We cloned and sequenced the gene coding for the polypeptide of another one of these rhodopsins, a halorhodopsin in Natronobacterium pharaonis. Peptide sequencing of cyanogen bromide fragments, and immuno-reactions of the protein and synthetic peptides derived from the C-terminal gene sequence, confirmed that the open reading frame was the structural gene for the pharaonis halorhodopsin polypeptide. The flanking DNA sequences of this gene, as well as those of other bacterial rhodopsins, were compared to previously proposed archaebacterial consensus sequences. In pairwise comparisons of the open reading frame with DNA sequences for bacterio-opsin and halo-opsin from Halobacterium halobium, silent divergences were calculated. These indicate very considerable evolutionary distance between each pair of genes, even in the dame organism. In spite of this, three protein sequences show extensive similarities, indicating strong selective pressures.

Demonstration of retrotransposition of the Tf1 element in fission yeast.

PubMed

Levin, H L; Boeke, J D

1992-03-01

Tf1, a retrotransposon from fission yeast, has LTRs and coding sequences resembling the protease, reverse transcriptase and integrase domains of retroviral pol genes. A unique aspect of Tf1 is that it contains a single open reading frame whereas other retroviruses and retrotransposons usually possess two or more open reading frames. To determine whether Tf1 can transpose, we overproduced Tf1 transcripts encoded by a plasmid copy of the element marked with a neo gene. Approximately 0.1-4.0% of the cell population acquired chromosomally inherited resistance to G418. DNA blot analysis demonstrated that such strains had acquired both Tf1 and neo specific sequences within a restriction fragment of the same size; the size of this restriction fragment varied between different isolates. Structural analysis of the cloned DNA flanking the Tf1-neo element of two transposition candidates with the same regions in the parent strain showed that the ability to grow on G418 was due to transposition of Tf1-neo and not other types of recombination events.

Human molybdopterin synthase gene: identification of a bicistronic transcript with overlapping reading frames.

PubMed Central

Stallmeyer, B; Drugeon, G; Reiss, J; Haenni, A L; Mendel, R R

1999-01-01

A universal molybdenum-containing cofactor (MoCo) is essential for the activity of all human molybdoenzymes, including sulphite oxidase. The free cofactor is highly unstable, and all organisms share a similar biosynthetic pathway. The involved enzymes exhibit homologies, even between bacteria and humans. We have exploited these homologies to isolate a cDNA for the heterodimeric molybdopterin (MPT)-synthase. This enzyme is necessary for the conversion of an unstable precursor into molybdopterin, the organic moiety of MoCo. The corresponding transcript shows a bicistronic structure, encoding the small and large subunits of the MPT-synthase in two different open reading frames (ORFs) that overlap by 77 nucleotides. In various human tissues, only one size of mRNA coinciding with the bicistronic transcript was detected. In vitro translation and mutagenesis experiments demonstrated that each ORF is translated independently, leading to the synthesis of a 10-kDa protein and a 21-kDa protein for the small and large subunits, respectively, and indicated that the 3'-proximal ORF of the bicistronic transcript is translated by leaky scanning. PMID:10053003

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

PubMed Central

Panning, B; Smiley, J R

1993-01-01

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

Functional analysis of human foamy virus accessory reading frames.

PubMed Central

Baunach, G; Maurer, B; Hahn, H; Kranz, M; Rethwilm, A

1993-01-01

Foamy viruses belong to the retroviruses which possess a complex genome structure. The human foamy virus (HFV) isolate bears three open reading frames (the so-called bel genes) in the 3' region of the genome which have been reported to give rise to possibly six different proteins via alternative splicing (W. Muranyi and R. M. Flügel, J. Virol. 65:727-735, 1991). In order to analyze the requirements of these proteins for HFV replication in vitro, we constructed a set of single and combinatory bel gene mutants of an infectious molecular clone of HFV. The mutant which lacked the transacting activator, bel-1, was found to be replication incompetent. All other mutants replicated equally well and gave rise to comparable titers of infectious cell-free virus. When HFV proviruses were put under the control of a heterologous promoter (simian virus 40), none of the accessory gene products was found to be required for expression of structural (gag) proteins. There was no evidence for a posttranscriptional regulatory protein that is present in other complex retroviruses. Images PMID:8394455

Genomic variation of the fibropapilloma-associated marine turtle herpes virus across seven geographic areas and three host species

USGS Publications Warehouse

Greenblatt, R.J.; Quackenbush, S.L.; Casey, R.N.; Rovnak, J.; Balazs, G.H.; Work, Thierry M.; Casey, J.W.; Sutton, C.A.

2005-01-01

Fibropapillomatosis (FP) of marine turtles is an emerging neoplastic disease associated with infection by a novel turtle herpesvirus, fibropapilloma-associated turtle herpesvirus (FPTHV). This report presents 23 kb of the genome of an FPTHV infecting a Hawaiian green turtle (Chelonia mydas). By sequence homology, the open reading frames in this contig correspond to herpes simplex virus genes UL23 through UL36. The order, orientation, and homology of these putative genes indicate that FPTHV is a member of the Alphaherpesvirinae. The UL27-, UL30-, and UL34-homologous open reading frames from FPTHVs infecting nine FP-affected marine turtles from seven geographic areas and three turtle species (C. mydas, Caretta caretta, and Lepidochelys olivacea) were compared. A high degree of nucleotide sequence conservation was found among these virus variants. However, geographic variations were also found: the FPTHVs examined here form four groups, corresponding to the Atlantic Ocean, West pacific, mid-Pacific, and east Pacific. Our results indicate that FPTHV was established in marine turtle populations prior to the emergence of FP as it is currently known.

Differential regulation of hepatitis B virus core protein expression and genome replication by a small upstream open reading frame and naturally occurring mutations in the precore region.

PubMed

Zong, Li; Qin, Yanli; Jia, Haodi; Ye, Lei; Wang, Yongxiang; Zhang, Jiming; Wands, Jack R; Tong, Shuping; Li, Jisu

2017-05-01

Hepatitis B virus (HBV) transcribes two subsets of 3.5-kb RNAs: precore RNA for hepatitis B e antigen (HBeAg) expression, and pregenomic RNA for core and P protein translation as well as genome replication. HBeAg expression could be prevented by mutations in the precore region, while an upstream open reading frame (uORF) has been proposed as a negative regulator of core protein translation. We employed replication competent HBV DNA constructs and transient transfection experiments in Huh7 cells to verify the uORF effect and to explore the alternative function of precore RNA. Optimized Kozak sequence for the uORF or extra ATG codons as present in some HBV genotypes reduced core protein expression. G1896A nonsense mutation promoted more efficient core protein expression than mutated precore ATG, while a +1 frameshift mutation was ineffective. In conclusion, various HBeAg-negative precore mutations and mutations affecting uORF differentially regulate core protein expression and genome replication. Copyright © 2017 Elsevier Inc. All rights reserved.

ORF157 from the Archaeal Virus Acidianus Filamentous Virus 1 Defines a New Class of Nuclease▿

PubMed Central

Goulet, Adeline; Pina, Mery; Redder, Peter; Prangishvili, David; Vera, Laura; Lichière, Julie; Leulliot, Nicolas; van Tilbeurgh, Herman; Ortiz-Lombardia, Miguel; Campanacci, Valérie; Cambillau, Christian

2010-01-01

Acidianus filamentous virus 1 (AFV1) (Lipothrixviridae) is an enveloped filamentous virus that was characterized from a crenarchaeal host. It infects Acidianus species that thrive in the acidic hot springs (>85°C and pH <3) of Yellowstone National Park, WY. The AFV1 20.8-kb, linear, double-stranded DNA genome encodes 40 putative open reading frames whose sequences generally show little similarity to other genes in the sequence databases. Because three-dimensional structures are more conserved than sequences and hence are more effective at revealing function, we set out to determine protein structures from putative AFV1 open reading frames (ORF). The crystal structure of ORF157 reveals an α+β protein with a novel fold that remotely resembles the nucleotidyltransferase topology. In vitro, AFV1-157 displays a nuclease activity on linear double-stranded DNA. Alanine substitution mutations demonstrated that E86 is essential to catalysis. AFV1-157 represents a novel class of nuclease, but its exact role in vivo remains to be determined. PMID:20200253

Immortalized Muscle Cell Model to Test the Exon Skipping Efficacy for Duchenne Muscular Dystrophy

PubMed Central

Nguyen, Quynh

2017-01-01

Duchenne muscular dystrophy (DMD) is a lethal genetic disorder that most commonly results from mutations disrupting the reading frame of the dystrophin (DMD) gene. Among the therapeutic approaches employed, exon skipping using antisense oligonucleotides (AOs) is one of the most promising strategies. This strategy aims to restore the reading frame, thus producing a truncated, yet functioning dystrophin protein. In 2016, the Food and Drug Administration (FDA) conditionally approved the first AO-based drug, eteplirsen (Exondys 51), developed for DMD exon 51 skipping. An accurate and reproducible method to quantify exon skipping efficacy is essential for evaluating the therapeutic potential of different AOs sequences. However, previous in vitro screening studies have been hampered by the limited proliferative capacity and insufficient amounts of dystrophin expressed by primary muscle cell lines that have been the main system used to evaluate AOs sequences. In this paper, we illustrate the challenges associated with primary muscle cell lines and describe a novel approach that utilizes immortalized cell lines to quantitatively evaluate the exon skipping efficacy in in vitro studies. PMID:29035327

Translation from a DMD exon 5 IRES results in a functional dystrophin isoform that attenuates dystrophinopathy in humans and mice.

PubMed

Wein, Nicolas; Vulin, Adeline; Falzarano, Maria S; Szigyarto, Christina Al-Khalili; Maiti, Baijayanta; Findlay, Andrew; Heller, Kristin N; Uhlén, Mathias; Bakthavachalu, Baskar; Messina, Sonia; Vita, Giuseppe; Passarelli, Chiara; Brioschi, Simona; Bovolenta, Matteo; Neri, Marcella; Gualandi, Francesca; Wilton, Steve D; Rodino-Klapac, Louise R; Yang, Lin; Dunn, Diane M; Schoenberg, Daniel R; Weiss, Robert B; Howard, Michael T; Ferlini, Alessandra; Flanigan, Kevin M

2014-09-01

Most mutations that truncate the reading frame of the DMD gene cause loss of dystrophin expression and lead to Duchenne muscular dystrophy. However, amelioration of disease severity has been shown to result from alternative translation initiation beginning in DMD exon 6 that leads to expression of a highly functional N-truncated dystrophin. Here we demonstrate that this isoform results from usage of an internal ribosome entry site (IRES) within exon 5 that is glucocorticoid inducible. We confirmed IRES activity by both peptide sequencing and ribosome profiling in muscle from individuals with minimal symptoms despite the presence of truncating mutations. We generated a truncated reading frame upstream of the IRES by exon skipping, which led to synthesis of a functional N-truncated isoform in both human subject-derived cell lines and in a new DMD mouse model, where expression of the truncated isoform protected muscle from contraction-induced injury and corrected muscle force to the same level as that observed in control mice. These results support a potential therapeutic approach for patients with mutations within the 5' exons of DMD.

Large Terrain Continuous Level of Detail 3D Visualization Tool

NASA Technical Reports Server (NTRS)

Myint, Steven; Jain, Abhinandan

2012-01-01

This software solved the problem of displaying terrains that are usually too large to be displayed on standard workstations in real time. The software can visualize terrain data sets composed of billions of vertices, and can display these data sets at greater than 30 frames per second. The Large Terrain Continuous Level of Detail 3D Visualization Tool allows large terrains, which can be composed of billions of vertices, to be visualized in real time. It utilizes a continuous level of detail technique called clipmapping to support this. It offloads much of the work involved in breaking up the terrain into levels of details onto the GPU (graphics processing unit) for faster processing.

Constructing Instruction for Struggling Writers: What and How

ERIC Educational Resources Information Center

Fitzgerald, Jill

2013-01-01

To respond to the articles in the current issue, I begin with an amalgamated conception of a transactional universe of reciprocal reading and composing processes that includes cognitive and social processes. Next, I situate the four studies in the current issue according to their epistemological emphases in the transactional conception. Three…

Music: Instrumental Techniques, Strings.

ERIC Educational Resources Information Center

Ryan, Philip

A course in music which emphasizes harmony is presented. The approach used is a laboratory one in which pupils will develop skill in playing orchestral string instruments, sing, listen to, read and compose music with emphasis on elementary concepts of harmony. Course objectives include: (1) The student will select the title of a familiar melody…

Music: Instrumental Techniques, Woodwinds.

ERIC Educational Resources Information Center

Baker, Melvin

A course in introduction to music emphasizing modes and forms is presented. The approach used is a laboratory approach in which pupils will develop skill in playing wood-wind instruments, sing, listen to, read and compose music with emphasis on identification of elementary concepts of mode and form. Course objectives include: (1) pupil will select…

Woodworking: Grades 7-12.

ERIC Educational Resources Information Center

Instructional Objectives Exchange, Los Angeles, CA.

The woodworking collection is composed of 55 objectives and related evaluation items for use in grades 7 through 12. Each sample contains the objective, test items, and criteria for judging the adequacy of the response. Woodworking categories being measured include sharpening, adjusting, using and caring for tools; reading a working drawing; stock…

Composing Change: The Role of Graduate Education in Sustaining a Digital Scholarly Future

ERIC Educational Resources Information Center

Blair, Kristine L.

2014-01-01

In "Reading the Archives: Ten Years on Nonlinear ("Kairos") History," James Kalmbach acknowledges the significant role graduate students have played as digital innovators in the field, particularly in the formation of "Kairos: A Journal of Rhetoric, Technology, Pedagogy" in 1996. Graduate students in the Rhetoric and…

Foods and Nutrition. Student Modules and Instructor's Guide.

ERIC Educational Resources Information Center

South Carolina State Dept. of Education, Columbia. Office of Vocational Education.

These 64 performance-based instructional modules are for the home economics content area of food and nutrition. Each module is composed of an introduction for the student, a performance objective, a variety of learning activities (reading assignments, tasks, written assignments), content information, a student self-check, recommended references,…

Using ZWDOS to Communicate in Chinese on PC.

ERIC Educational Resources Information Center

Xie, Tianwei

1995-01-01

Describes the availability, installation, and use of the ZhonWen Disk Operating System (ZWDOS) to display, print, and transmit Chinese characters on conventional International Business Machines (IBM) personal computers and IBM-compatible machines. Also discussed is the use of ZWDOS to compose electronic mail messages, read newsgroups, and access…

Instrumental Techniques--Band, Course Numbers: Music: 5642.45, 5643.45.

ERIC Educational Resources Information Center

Sutton, Mack

An introduction to music emphasizing harmony, this course provides a laboratory approach in which pupils will develop skill in playing brass and woodwind instruments, sing, listen to, read and compose music with emphasis on elementary concepts of harmony. This handbook provides, in outline format, the following: Course Description; Course…

Instructional Note: The Interpretive-Paraphrase Workshop

ERIC Educational Resources Information Center

Houp, G. Wesley

2004-01-01

This article describes the interpretive paraphrase class workshop method, which emphasizes dialogue as a centerpiece of the composing process and provides students with opportunities to re-envision their compositions based on the alternative readings of their peers. A major goal of this writing workshop is to create and sustain student-talk about…

Basic Composition and Enriched Integration in Idiom Processing: An EEG Study

ERIC Educational Resources Information Center

Canal, Paolo; Pesciarelli, Francesca; Vespignani, Francesco; Molinaro, Nicola; Cacciari, Cristina

2017-01-01

We investigated the extent to which the literal meanings of the words forming literally plausible idioms (e.g., "break the ice") are semantically composed and how the idiomatic meaning is integrated in the unfolding sentence representation. Participants read ambiguous idiom strings embedded in highly predictable, literal, and idiomatic…

Listening as an Act of Composing.

ERIC Educational Resources Information Center

Ronald, Katharine; Roskelly, Hephzibah

The fact that students have not learned to listen may be the reason some of them cannot write. Listening is an active process requiring the same skills of prediction, hypothesizing, checking, revising, and generalization that reading and writing demand. The following three exercises were designed to make students conscious of themselves as active…

Launching Family Message Journals.

ERIC Educational Resources Information Center

Wollman-Bonilla, Julie

This lesson introduces Family Message Journals, a tool for encouraging family involvement and supporting writing to reflect and learn. First and second graders are led into composing through demonstration, guided writing, and finally independent writing of messages that they will bring home for family to read and write a reply. During the three…

Literary Scholars Processing Poetry and Constructing Arguments

ERIC Educational Resources Information Center

Warren, James E.

2006-01-01

Previous studies of the professional discourse of literary studies have focused solely on published scholarly articles and have produced contradictory evidence regarding the knowledge-building function of literary argument. In this study, 9 English department faculty members use a "think-aloud" procedure to read four lyric poems and compose a…

Relationship between Sociometric Type and Self-Attributions for Academic Failure in a Spanish Sample from Secondary Education

ERIC Educational Resources Information Center

Inglés, Cándido J.; Aparisi, D.; Delgado, B.; Granados, L.; García-Fernández, José M.

2017-01-01

Introduction: The aim of this study was to analyze the relationship between sociometric types, behavioral categories and self-attributions for academic failure ("Ability", "Effort" or "External Causes") in "Reading", "Mathematics" and "General". Method: The total sample was composed of…

Preparing Teachers for Urban Schools: An Annotated Bibliography for Teacher Education.

ERIC Educational Resources Information Center

Clothier, Grant; And Others

This annotated bibliography developed by Cooperative Urban Teacher Education (CUTE) staff members presents a selective reading list for undergraduate teacher education candidates preparing to work in inner-city schools. An interdisciplinary team composed of a psychiatrist, a sociologist, and teacher educators categorized the 187 entries under the…

Teen magazines as educational texts on dating violence: the $2.99 approach.

PubMed

Kettrey, Heather Hensman; Emery, Beth C

2010-11-01

This study analyzed the portrayal of dating violence in teen magazines published in the United States. Such an investigation is important because previous research indicates that dating violence is a serious problem facing adolescents, teen magazines overemphasize the importance of romantic relationships, and teens who read this genre frequently or for education/advice are especially susceptible to its messages. Results indicated that although teen magazines do frame dating violence as a cultural problem, they are much more likely to utilize an individual frame that emphasizes the victim. Results were discussed as they apply to the responsibilities of professionals working with adolescents.

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.

Functional relevance of three proopiomelanocortin (POMC) genes in darkening camouflage, blind-side hypermelanosis, and appetite of Paralichthys olivaceus.

PubMed

Kang, Duk-Young; Kim, Hyo-Chan

2015-01-01

To determine whether proopiomelanocortin (POMC) genes are involved in darkening color camouflage, blind-side hypermelanosis, and appetite in flatfish, we isolated and cloned three POMC genes from the pituitary of the olive flounder (Paralichthys olivaceus) and compared their amino acid (aa) structures to those of POMC genes from other animals. Next, we examined the relationship of these pituitary POMC genes to camouflage color change, blind-side hypermelanosis, and appetite by quantifying mRNA expression. Olive flounder (of)-POMC1, 2, and 3 cDNAs consisted of 648-bp, 582-bp, and 693-bp open reading frames (ORF) encoding 216 aa, 194 aa, and 231 aa residues, respectively. Structurally, the three of-POMC cDNAs consisted of seven peptides (signal peptide, N-POMC, α-MSH, CLIP, N-β-LPH, β-MSH and β-END [or END-like peptide]) that are similar to those of other fish POMC cDNAs. α-MSH encoded a protein composed of 13 aa and β-MSH encoded a protein composed of 17 aa. The three POMC genes were predominantly expressed in the pituitary gland, but they were also expressed in a variety of tissues, including brain, eye, kidney, heart, testis, and skin. of-POMC2 exhibited the highest expression, while of-POMC3 displayed the lowest expression. The relative levels of of-POMC1 and 3 mRNAs were not influenced by background color and feeding (or fasting), but the relative level of of-POMC2 mRNA significantly increased in response to a dark background and fasting. The relative levels of of-POMC1 and 2 mRNAs were significantly higher in hypermelanic fish; however, we did not determine a direct anorexigenic or orexigenic relationship for the three POMC genes. These results indicate that pituitary POMC genes are related to darkening color change and the differentiation of pigment cells, but they are not directly related to appetite. Copyright © 2014 Elsevier Inc. All rights reserved.

RAPSearch: a fast protein similarity search tool for short reads

PubMed Central

2011-01-01

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

Single Cell Genome Amplification Accelerates Identification of the Apratoxin Biosynthetic Pathway from a Complex Microbial Assemblage

PubMed Central

Grindberg, Rashel V.; Ishoey, Thomas; Brinza, Dumitru; Esquenazi, Eduardo; Coates, R. Cameron; Liu, Wei-ting; Gerwick, Lena; Dorrestein, Pieter C.; Pevzner, Pavel; Lasken, Roger; Gerwick, William H.

2011-01-01

Filamentous marine cyanobacteria are extraordinarily rich sources of structurally novel, biomedically relevant natural products. To understand their biosynthetic origins as well as produce increased supplies and analog molecules, access to the clustered biosynthetic genes that encode for the assembly enzymes is necessary. Complicating these efforts is the universal presence of heterotrophic bacteria in the cell wall and sheath material of cyanobacteria obtained from the environment and those grown in uni-cyanobacterial culture. Moreover, the high similarity in genetic elements across disparate secondary metabolite biosynthetic pathways renders imprecise current gene cluster targeting strategies and contributes sequence complexity resulting in partial genome coverage. Thus, it was necessary to use a dual-method approach of single-cell genomic sequencing based on multiple displacement amplification (MDA) and metagenomic library screening. Here, we report the identification of the putative apratoxin. A biosynthetic gene cluster, a potent cancer cell cytotoxin with promise for medicinal applications. The roughly 58 kb biosynthetic gene cluster is composed of 12 open reading frames and has a type I modular mixed polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS) organization and features loading and off-loading domain architecture never previously described. Moreover, this work represents the first successful isolation of a complete biosynthetic gene cluster from Lyngbya bouillonii, a tropical marine cyanobacterium renowned for its production of diverse bioactive secondary metabolites. PMID:21533272

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

PubMed

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

2013-08-01

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

Molecular cloning, sequence analysis and phylogeny of first caudata g-type lysozyme in axolotl (Ambystoma mexicanum).

PubMed

Yu, Haining; Gao, Jiuxiang; Lu, Yiling; Guang, Huijuan; Cai, Shasha; Zhang, Songyan; Wang, Yipeng

2013-11-01

Lysozymes are key proteins that play important roles in innate immune defense in many animal phyla by breaking down the bacterial cell-walls. In this study, we report the molecular cloning, sequence analysis and phylogeny of the first caudate amphibian g-lysozyme: a full-length spleen cDNA library from axolotl (Ambystoma mexicanum). A goose-type (g-lysozyme) EST was identified and the full-length cDNA was obtained using RACE-PCR. The axolotl g-lysozyme sequence represents an open reading frame for a putative signal peptide and the mature protein composed of 184 amino acids. The calculated molecular mass and the theoretical isoelectric point (pl) of this mature protein are 21523.0 Da and 4.37, respectively. Expression of g-lysozyme mRNA is predominantly found in skin, with lower levels in spleen, liver, muscle, and lung. Phylogenetic analysis revealed that caudate amphibian g-lysozyme had distinct evolution pattern for being juxtaposed with not only anura amphibian, but also with the fish, bird and mammal. Although the first complete cDNA sequence for caudate amphibian g-lysozyme is reported in the present study, clones encoding axolotl's other functional immune molecules in the full-length cDNA library will have to be further sequenced to gain insight into the fundamental aspects of antibacterial mechanisms in caudate.

Molecular characterization, tissue distribution and expression analysis of TRIM25 in Gallus gallus domesticus.

PubMed

Feng, Ze-Qing; Cheng, Yang; Yang, Hui-Ling; Zhu, Qing; Yu, Dandan; Liu, Yi-Ping

2015-04-25

TRIM25, a member of the tripartite motif-containing (TRIM) family of proteins, plays an important role in cell proliferation, protein modification, and the RIG-I-mediated antiviral signaling pathway. However, relatively few studies have investigated the molecular characterization, tissue distribution, and potential function of TRIM25 in chickens. In this study, we cloned the full-length cDNA of chicken TRIM25 that is composed of 2706 bp. Sequence analyses revealed that TRIM25 contains a 1902-bp open-reading frame that probably encodes a 633-amino acid protein. Multiple comparisons with deduced amino acid sequences revealed that the RING finger and B30.2 domains of chicken TRIM25 share a high sequence similarity with human and murine TRIM25, indicating that these domains are critical for the function of chicken TRIM25. qPCR assays revealed that TRIM25 is highly expressed in the spleen, thymus and lungs in chickens. Furthermore, we observed that TRIM25 expression was significantly upregulated both in vitro and in vivo following infection with Newcastle disease virus. TRIM25 expression was also significantly upregulated in chicken embryo fibroblasts upon stimulation with poly(I:C) or poly(dA:dT). Taken together, these findings suggest that TRIM25 plays an important role in antiviral signaling pathways in chickens. Copyright © 2015 Elsevier B.V. All rights reserved.

Duck hepatitis A virus structural proteins expressed in insect cells self-assemble into virus-like particles with strong immunogenicity in ducklings.

PubMed

Wang, Anping; Gu, Lingling; Wu, Shuang; Zhu, Shanyuan

2018-02-01

Duck hepatitis A virus (DHAV), a non-enveloped ssRNA virus, can cause a highly contagious disease in young ducklings. The three capsid proteins of VP0, VP1 and VP3 are translated within a single large open reading frame (ORF) and hydrolyzed by protease 3CD. However, little is known on whether the recombinant viral structural proteins (VPs) expressed in insect cells could spontaneously assemble into virus-like particles (VLPs) and whether these VLPs could induce protective immunity in young ducklings. To address these issues, the structural polyprotein precursor gene P1 and the protease gene 3CD were amplified by PCR, and the recombinant proteins were expressed in insect cells using a baculovirus expression system for the characterization of their structures and immunogenicity. The recombinant proteins expressed in Sf9 cells were detected by indirect immunofluorescence assay and Western blot analysis. Electron microscopy showed that the recombinant proteins spontaneously assembled into VLPs in insect cells. Western blot analysis of the purified VLPs revealed that the VLPs were composed with the three structural proteins. In addition, vaccination with the VLPs induced high humoral immune response and provided strong protection. Therefore, our findings may provide a framework for development of new vaccines for the prevention of duck viral hepatitis. Copyright © 2018 Elsevier B.V. All rights reserved.