A genetic scale of reading frame coding.

PubMed

Michel, Christian J

2014-08-21

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

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

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

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.

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.

Open Reading Frame Phylogenetic Analysis on the Cloud

PubMed Central

2013-01-01

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

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.

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

PubMed

Czeizler, Amalia; Garbarino, Ellen

2017-01-01

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

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

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

PubMed Central

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

2014-01-01

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

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

PubMed Central

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

1990-01-01

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

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

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.

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

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.

Encrypting Digital Camera with Automatic Encryption Key Deletion

NASA Technical Reports Server (NTRS)

Oakley, Ernest C. (Inventor)

2007-01-01

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

The 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

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

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.

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...

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.

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

PubMed

Büssow, Konrad; Hoffmann, Steve; Sievert, Volker

2002-12-19

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

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

PubMed Central

Firth, Andrew E

2008-01-01

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

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

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...

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

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.

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.

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.

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.

Electrooptic converter to control linear displacements of the large structures of the buildings and facilities

NASA Astrophysics Data System (ADS)

Vasilev, Aleksandr S.; Konyakhin, Igor A.; Timofeev, Alexander N.; Lashmanov, Oleg U.; Molev, Fedor V.

2015-05-01

The paper analyzes the construction matters and metrological parameters of the electrooptic converter to control linear displacements of the large structures of the buildings and facilities. The converter includes the base module, the processing module and a set of the reference marks. The base module is the main unit of the system, it includes the receiving optical system and the CMOS photodetector array that realizes the instrument coordinate system that controls the mark coordinates in the space. The methods of the frame-to-frame difference, adaptive threshold filtration, binarization and objects search by the tied areas to detect the marks against accidental contrast background is the basis of the algorithm. The entire algorithm is performed during one image reading stage and is based on the FPGA. The developed and manufactured converter experimental model was tested in laboratory conditions at the metrological bench at the distance between the base module and the mark 50±0.2 m. The static characteristic was read during the experiment of the reference mark displacement at the pitch of 5 mm in the horizontal and vertical directions for the displacement range 400 mm. The converter experimental model error not exceeding ±0.5 mm was obtained in the result of the experiment.

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.

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

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

Genome-wide sequencing and an open reading frame analysis of dichlorodiphenyltrichloroethane (DDT) susceptible (91-C) and resistant (91-R) Drosophila melanogaster laboratory populations

USDA-ARS?s Scientific Manuscript database

The Drosophila melanogaster 91-R and 91-C strains are of common origin, however, 91-R has been intensely selected for dichlorodiphenyltrichloroethane (DDT) resistance over six decades while 91-C has been maintained as the non-selected control strain. These fly strains represent a unique genetic res...

Region VI of cauliflower mosaic virus encodes a host range determinant.

PubMed Central

Schoelz, J; Shepherd, R J; Daubert, S

1986-01-01

A domain of cauliflower mosaic virus (CaMV) which controls systemic spread in two solanaceous hosts (Datura stramonium and Nicotiana bigelovii) was mapped to the first half of open reading frame 6. Whereas ordinary strains of CaMV are unable to infect solanaceous species except to replicate locally in inoculated leaves, a new CaMV strain (D4) induces chlorotic local lesions and systemically infects both D. stramonium and N. bigelovii. To determine which portion of the CaMV genome controls systemic spread of the virus in solanaceous hosts, nine recombinant genomes constructed between D4 and two ordinary strains of the virus were tested for their ability to infect solanaceous hosts. A 496-base-pair DNA segment comprising the first half of open reading frame 6 specified the type of local lesions and systemic spread of the virus in solanaceous hosts. Exchange of this segment of the genome between strains of CaMV converted a compatible host reaction to an incompatible (hypersensitive) one in response to infection. This suggests that the gene VI protein interacts with the plant to suppress hypersensitivity, the normal response of solanaceous hosts to CaMV infection. Images PMID:3785205

Gene expression regulation by upstream open reading frames and human disease.

PubMed

Barbosa, Cristina; Peixeiro, Isabel; Romão, Luísa

2013-01-01

Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism's response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders.

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.

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.

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

The effect of positive and negative message framing on short term continuous positive airway pressure compliance in patients with obstructive sleep apnea

PubMed Central

Czaban, Marcin; Berry, Marc P.; Nirmalan, Prajeshan; Brown, Richard; Birdseye, Adam; Woroszyl, Asia; Chapman, Julia; Kent, Brian D.; Hart, Nicholas; Rossi, Gian Paolo; Steier, Joerg

2018-01-01

Background Continuous positive airway pressure (CPAP), the best available treatment for obstructive sleep apnea (OSA), requires long-term compliance to be effective. Behavioral interventions may be used to improve adherence to CPAP. We aimed to investigate whether positive or negative message framing impacts on CPAP compliance in patients with OSA, when compared to standard care. Methods Consenting patients with confirmed OSA were randomly allocated to receive along with their CPAP either positively or negatively framed messages (Pos; Neg), or standard care (Con). Standardized motivational messages were read out to patients during an initial teaching session and through weekly telephone calls. Patients’ compliance data were reviewed 2 and 6 weeks following CPAP initiation. Results We randomized 112 patients to groups that were matched for age, BMI, and OSA severity. The positively framed group (Pos) showed greater CPAP usage after 2 weeks (total use 53.7±31.4 hours) as compared to the negatively framed and the control group (35.6±27.4 and 40.8±33.5 hours, P<0.05); however, no differences were seen at 6 weeks. There were more dropouts in the control group than in either framed groups (Pos n=5; Neg n=8; Con n=11; P<0.05). Conclusions Positively framed messages can improve CPAP adherence in patients with OSA in the short-term; however, strategies for implementing its long-term use need to be developed. PMID:29445540

The effect of positive and negative message framing on short term continuous positive airway pressure compliance in patients with obstructive sleep apnea.

PubMed

Pengo, Martino F; Czaban, Marcin; Berry, Marc P; Nirmalan, Prajeshan; Brown, Richard; Birdseye, Adam; Woroszyl, Asia; Chapman, Julia; Kent, Brian D; Hart, Nicholas; Rossi, Gian Paolo; Steier, Joerg

2018-01-01

Continuous positive airway pressure (CPAP), the best available treatment for obstructive sleep apnea (OSA), requires long-term compliance to be effective. Behavioral interventions may be used to improve adherence to CPAP. We aimed to investigate whether positive or negative message framing impacts on CPAP compliance in patients with OSA, when compared to standard care. Consenting patients with confirmed OSA were randomly allocated to receive along with their CPAP either positively or negatively framed messages (Pos; Neg), or standard care (Con). Standardized motivational messages were read out to patients during an initial teaching session and through weekly telephone calls. Patients' compliance data were reviewed 2 and 6 weeks following CPAP initiation. We randomized 112 patients to groups that were matched for age, BMI, and OSA severity. The positively framed group (Pos) showed greater CPAP usage after 2 weeks (total use 53.7±31.4 hours) as compared to the negatively framed and the control group (35.6±27.4 and 40.8±33.5 hours, P<0.05); however, no differences were seen at 6 weeks. There were more dropouts in the control group than in either framed groups (Pos n=5; Neg n=8; Con n=11; P<0.05). Positively framed messages can improve CPAP adherence in patients with OSA in the short-term; however, strategies for implementing its long-term use need to be developed.

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.

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

ERIC Educational Resources Information Center

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

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

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

PubMed Central

Sugita, Mamoru; Shinozaki, Kazuo; Sugiura, Masahiro

1985-01-01

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

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

PubMed

Sugita, M; Shinozaki, K; Sugiura, M

1985-06-01

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

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.

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.

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.

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.

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…

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.

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…

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…

Translational control of Nrf2 within the open reading frame

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

Perez-Leal, Oscar, E-mail: operez@temple.edu; Barrero, Carlos A.; Merali, Salim, E-mail: smerali@temple.edu

2013-07-19

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

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…

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

ERIC Educational Resources Information Center

Choo, Suzanne S.

2010-01-01

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

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

Melanin production by Rhizobium meliloti GR4 is linked to nonsymbiotic plasmid pRmeGR4b: cloning, sequencing, and expression of the tyrosinase gene mepA.

PubMed Central

Mercado-Blanco, J; García, F; Fernández-López, M; Olivares, J

1993-01-01

Melanin production by Rhizobium meliloti GR4 is linked to nonsymbiotic plasmid pRmeGR4b (140 MDa). Transfer of this plasmid to GR4-cured derivatives or to Agrobacterium tumefaciens enables these bacteria to produce melanin. Sequence analysis of a 3.5-kb PstI fragment of plasmid pRmeGR4b has revealed the presence of a open reading frame 1,481-bp that codes for a protein whose sequence shows strong homology to two conserved regions involved in copper binding in tyrosinases and hemocyanins. In vitro-coupled transcription-translation experiments showed that this open reading frame codes for a 55-kDa polypeptide. Melanin production in GR4 is not under the control of the RpoN-NifA regulatory system, unlike that in R. leguminosarum bv. phaseoli 8002. The GR4 tyrosinase gene could be expressed in Escherichia coli under the control of the lacZ promoter. For avoiding confusion with mel genes (for melibiose), a change of the name of the previously reported mel genes of R. leguminosarum bv. phaseoli and other organisms to mep genes (for melanin production) is proposed. Images PMID:8366027

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

PubMed Central

Vanderperre, Benoît; Lucier, Jean-François; Bissonnette, Cyntia; Motard, Julie; Tremblay, Guillaume; Vanderperre, Solène; Wisztorski, Maxence; Salzet, Michel; Boisvert, François-Michel; Roucou, Xavier

2013-01-01

A fully mature mRNA is usually associated to a reference open reading frame encoding a single protein. Yet, mature mRNAs contain unconventional alternative open reading frames (AltORFs) located in untranslated regions (UTRs) or overlapping the reference ORFs (RefORFs) in non-canonical +2 and +3 reading frames. Although recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals, direct evidence of large-scale alternative protein expression at the proteome level is still lacking. To determine the contribution of alternative proteins to the human proteome, we generated a database of predicted human AltORFs revealing a new proteome mainly composed of small proteins with a median length of 57 amino acids, compared to 344 amino acids for the reference proteome. We experimentally detected a total of 1,259 alternative proteins by mass spectrometry analyses of human cell lines, tissues and fluids. In plasma and serum, alternative proteins represent up to 55% of the proteome and may be a potential unsuspected new source for biomarkers. We observed constitutive co-expression of RefORFs and AltORFs from endogenous genes and from transfected cDNAs, including tumor suppressor p53, and provide evidence that out-of-frame clones representing AltORFs are mistakenly rejected as false positive in cDNAs screening assays. Functional importance of alternative proteins is strongly supported by significant evolutionary conservation in vertebrates, invertebrates, and yeast. Our results imply that coding of multiple proteins in a single gene by the use of AltORFs may be a common feature in eukaryotes, and confirm that translation of unconventional ORFs generates an as yet unexplored proteome. PMID:23950983

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.

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

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.

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

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.

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 World Factbook 2000

DTIC Science & Technology

2000-01-01

Loreto, election results: percent of vote by party - C90/NM coins, all framed by a green wreath Madre de Dios , Moquegua, Pasco, Piura, Puno, San 52.1...was brought under control. In Tumbes, Piura), Inca (from Cusco, Madre de Dios , FUJIMORI]; Civic Works Movement or OBRAS 1998, El Nino’s impact on...pollution from Literacy: industrial emissions; rivers polluted from raw sewage, definition: age 15 and over can read and write SOFIA N Bse c heavy metals

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.

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

Negative and Translation Termination-Dependent Positive Control of FLI-1 Protein Synthesis by Conserved Overlapping 5′ Upstream Open Reading Frames in Fli-1 mRNA

PubMed Central

Sarrazin, Sandrine; Starck, Joëlle; Gonnet, Colette; Doubeikovski, Alexandre; Melet, Fabrice; Morle, François

2000-01-01

The proto-oncogene Fli-1 encodes a transcription factor of the ets family whose overexpression is associated with multiple virally induced leukemias in mouse, inhibits murine and avian erythroid cell differentiation, and induces drastic perturbations of early development in Xenopus. This study demonstrates the surprisingly sophisticated regulation of Fli-1 mRNA translation. We establish that two FLI-1 protein isoforms (of 51 and 48 kDa) detected by Western blotting in vivo are synthesized by alternative translation initiation through the use of two highly conserved in-frame initiation codons, AUG +1 and AUG +100. Furthermore, we show that the synthesis of these two FLI-1 isoforms is regulated by two short overlapping 5′ upstream open reading frames (uORF) beginning at two highly conserved upstream initiation codons, AUG −41 and GUG −37, and terminating at two highly conserved stop codons, UGA +35 and UAA +15. The mutational analysis of these two 5′ uORF revealed that each of them negatively regulates FLI-1 protein synthesis by precluding cap-dependent scanning to the 48- and 51-kDa AUG codons. Simultaneously, the translation termination of the two 5′ uORF appears to enhance 48-kDa protein synthesis, by allowing downstream reinitiation at the 48-kDa AUG codon, and 51-kDa protein synthesis, by allowing scanning ribosomes to pile up and consequently allowing upstream initiation at the 51-kDa AUG codon. To our knowledge, this is the first example of a cellular mRNA displaying overlapping 5′ uORF whose translation termination appears to be involved in the positive control of translation initiation at both downstream and upstream initiation codons. PMID:10757781

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

PubMed

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

2014-11-01

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

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

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

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

1991-03-11

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

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

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.

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.

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

PubMed Central

Pelet, T; Curran, J; Kolakofsky, D

1991-01-01

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

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…

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.

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

PubMed Central

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

1987-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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

ERIC Educational Resources Information Center

Kunde, Meg

2017-01-01

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

Brucellosis vaccines based on the open reading frames from genomic island 3 of Brucella abortus.

PubMed

Gómez, Leonardo; Alvarez, Francisco; Betancur, Daniel; Oñate, Angel

2018-05-17

Brucella abortus is the etiological agent of brucellosis, a zoonotic disease affecting cattle and humans. This disease has been partially controlled in cattle by immunization with live attenuated B. abortus S19 and RB51 strains. However, use of these vaccine strains has been associated with safety issues in animals and humans. New vaccines have since emerged in the prevention of brucellosis, particularly DNA vaccines, which have shown effectiveness and a good safety profile. Their protection efficacy in mice is associated with the induction of Th1 type and cytotoxic T cell mediated immune response against structural antigens and virulence factors expressed during B. abortus infection. Some antigenic candidate for vaccine design against brucellosis (mainly DNA vaccines) have been obtained from genomic island 3 (GI-3) of B. abortus, which encodes several open reading frames (ORFs) involved in the intracellular survival and virulence of this pathogen. The immunogenicity and protection conferred by these DNA vaccines in a murine model is reviewed in this article, suggesting that some of them could be safe and effective vaccine candidates against to prevent B. abortus infection. Copyright © 2018 Elsevier Ltd. All rights reserved.

Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression

PubMed Central

Fahey, Ciara; Kenny, Elaine M; Terenin, Ilya M; Dmitriev, Sergey E; Cormican, Paul; Morris, Derek W; Shatsky, Ivan N; Baranov, Pavel V

2015-01-01

Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eukaryotic initiation factor 2 (eIF2). However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response. We carried out ribosome profiling of cultured human cells under conditions of severe stress induced with sodium arsenite. Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition. Nearly all resistant transcripts possess at least one efficiently translated upstream open reading frame (uORF) that represses translation of the main coding ORF under normal conditions. Site-specific mutagenesis of two identified stress resistant mRNAs (PPP1R15B and IFRD1) demonstrated that a single uORF is sufficient for eIF2-mediated translation control in both cases. Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products. DOI: http://dx.doi.org/10.7554/eLife.03971.001 PMID:25621764

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.

Framing messages about weight discrimination: impact on public support for legislation.

PubMed

Puhl, R M; Heuer, C; Sarda, V

2011-06-01

To assess the public support for potential legislation to prohibit weight-based discrimination against obese individuals in the United States, and to examine whether certain message frames about weight discrimination influence public support. Participants were randomly assigned to read one of the four paragraphs that framed the topic of weight discrimination in a distinct way (or a control condition with no paragraph). Participants were then asked to indicate their level of support for six antidiscrimination laws. A national sample of 1114 participants (48% women, 52% men), mean age 44.78 years (s.d. = 15.93). There was moderate support for several laws to prohibit weight-based discrimination, but gender differences were observed across experimental conditions indicating that some message frames may increase support for certain laws among women, but not men. However, message frames had no effect on support for laws with specific provisions to prohibit weight discrimination in the workplace, suggesting that public support for these particular legal measures is consistent and high (65% of men and 81% of women expressed support) regardless of how the issue of weight discrimination is framed to the public. The present findings provide evidence of current levels of public support for legislation to prohibit weight-based discrimination, and offer potential ways for policy makers and interest groups to communicate messages about weight discrimination in efforts to increase support.

Bijective transformation circular codes and nucleotide exchanging RNA transcription.

PubMed

Michel, Christian J; Seligmann, Hervé

2014-04-01

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

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

ERIC Educational Resources Information Center

Saarti, Jarmo; Raivio, Jouko

2011-01-01

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

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

PubMed Central

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

2011-01-01

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

Reading Videogames as (Authorless) Literature

ERIC Educational Resources Information Center

Berger, Richard; McDougall, Julian

2013-01-01

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

Analysis of genes involved in biosynthesis of the lantibiotic subtilin.

PubMed Central

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

1992-01-01

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

A Fast Event Preprocessor and Sequencer for the Simbol-X Low Energy Detector

NASA Astrophysics Data System (ADS)

Schanz, T.; Tenzer, C.; Maier, D.; Kendziorra, E.; Santangelo, A.

2009-05-01

The Simbol-X Low Energy Detector (LED), a 128×128 pixel DEPFET (Depleted Field Effect Transistor) array, will be read out at a very high rate (8000 frames/second) and, therefore, requires a very fast on board electronics. We present an FPGA-based LED camera electronics consisting of an Event Preprocessor (EPP) for on board data preprocessing and filtering of the Simbol-X low-energy detector and a related Sequencer (SEQ) to generate the necessary signals to control the readout.

The darkest EMCCD ever

NASA Astrophysics Data System (ADS)

Daigle, Olivier; Quirion, Pierre-Olivier; Lessard, Simon

2010-07-01

EMCCDs are devices capable of sub-electron read-out noise at high pixel rate, together with a high quantum efficiency (QE). However, they are plagued by an excess noise factor (ENF) which has the same effect on photometric measurement as if the QE would be halved. In order to get rid of the ENF, the photon counting (PC) operation is mandatory, with the drawback of counting only one photon per pixel per frame. The high frame rate capability of the EMCCDs comes to the rescue, at the price of increased clock induced charges (CIC), which dominates the noise budget of the EMCCD. The CIC can be greatly reduced with an appropriate clocking, which renders the PC operation of the EMCCD very efficient for faint flux photometry or spectroscopy, adaptive optics, ultrafast imaging and Lucky Imaging. This clocking is achievable with a new EMCCD controller: CCCP, the CCD Controller for Counting Photons. This new controller, which is now commercialized by Nüvü cameras inc., was integrated into an EMCCD camera and tested at the observatoire du mont-M'egantic. The results are presented in this paper.

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.

Walking the talk--speech activates the leg motor cortex.

PubMed

Liuzzi, Gianpiero; Ellger, Tanja; Flöel, Agnes; Breitenstein, Caterina; Jansen, Andreas; Knecht, Stefan

2008-09-01

Speech may have evolved from earlier modes of communication based on gestures. Consistent with such a motor theory of speech, cortical orofacial and hand motor areas are activated by both speech production and speech perception. However, the extent of speech-related activation of the motor cortex remains unclear. Therefore, we examined if reading and listening to continuous prose also activates non-brachiofacial motor representations like the leg motor cortex. We found corticospinal excitability of bilateral leg muscle representations to be enhanced by speech production and silent reading. Control experiments showed that speech production yielded stronger facilitation of the leg motor system than non-verbal tongue-mouth mobilization and silent reading more than a visuo-attentional task thus indicating speech-specificity of the effect. In the frame of the motor theory of speech this finding suggests that the system of gestural communication, from which speech may have evolved, is not confined to the hand but includes gestural movements of other body parts as well.

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.

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.

Mutations in Elongation Factor Ef-1α Affect the Frequency of Frameshifting and Amino Acid Misincorporation in Saccharomyces Cerevisiae

PubMed Central

Sandbaken, M. G.; Culbertson, M. R.

1988-01-01

A mutational analysis of the eukaryotic elongation factor EF-1α indicates that this protein functions to limit the frequency of errors during genetic code translation. We found that both amino acid misincorporation and reading frame errors are controlled by EF-1α. In order to examine the function of this protein, the TEF2 gene, which encodes EF-1α in Saccharomyces cerevisiae, was mutagenized in vitro with hydroxylamine. Sixteen independent TEF2 alleles were isolated by their ability to suppress frameshift mutations. DNA sequence analysis identified eight different sites in the EF-1α protein that elevate the frequency of mistranslation when mutated. These sites are located in two different regions of the protein. Amino acid substitutions located in or near the GTP-binding and hydrolysis domain of the protein cause suppression of frameshift and nonsense mutations. These mutations may effect mistranslation by altering the binding or hydrolysis of GTP. Amino acid substitutions located adjacent to a putative aminoacyl-tRNA binding region also suppress frameshift and nonsense mutations. These mutations may alter the binding of aminoacyl-tRNA by EF-1α. The identification of frameshift and nonsense suppressor mutations in EF-1α indicates a role for this protein in limiting amino acid misincorporation and reading frame errors. We suggest that these types of errors are controlled by a common mechanism or closely related mechanisms. PMID:3066688

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

PubMed Central

Hall, R L; Moyer, R W

1991-01-01

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

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

PubMed

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

2012-09-01

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

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

PubMed

Lee, Tae Kyoung; Kim, Hye Kyung

2017-12-01

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

When Do Natural Language Metaphors Influence Reasoning? A Follow-Up Study to Thibodeau and Boroditsky (2013)

PubMed Central

Steen, Gerard J.; Reijnierse, W. Gudrun; Burgers, Christian

2014-01-01

In this article, we offer a critical view of Thibodeau and Boroditsky who report an effect of metaphorical framing on readers' preference for political measures after exposure to a short text on the increase of crime in a fictitious town: when crime was metaphorically presented as a beast, readers became more enforcement-oriented than when crime was metaphorically framed as a virus. We argue that the design of the study has left room for alternative explanations. We report four experiments comprising a follow-up study, remedying several shortcomings in the original design while collecting more encompassing sets of data. Our experiments include three additions to the original studies: (1) a non-metaphorical control condition, which is contrasted to the two metaphorical framing conditions used by Thibodeau and Boroditsky, (2) text versions that do not have the other, potentially supporting metaphors of the original stimulus texts, (3) a pre-exposure measure of political preference (Experiments 1–2). We do not find a metaphorical framing effect but instead show that there is another process at play across the board which presumably has to do with simple exposure to textual information. Reading about crime increases people's preference for enforcement irrespective of metaphorical frame or metaphorical support of the frame. These findings suggest the existence of boundary conditions under which metaphors can have differential effects on reasoning. Thus, our four experiments provide converging evidence raising questions about when metaphors do and do not influence reasoning. PMID:25490704

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

ERIC Educational Resources Information Center

Harris, Pauline

2010-01-01

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

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

ERIC Educational Resources Information Center

Bell, Joyce

2007-01-01

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

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

ERIC Educational Resources Information Center

Simmons, Deborah

2015-01-01

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

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

DTIC Science & Technology

1984-12-01

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

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

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

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

1995-02-01

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

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

PubMed Central

1992-01-01

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

Novel Genes Encoding Hexadecanoic Acid Δ6-Desaturase Activity in a Rhodococcus sp.

PubMed

Araki, Hiroyuki; Hagihara, Hiroshi; Takigawa, Hirofumi; Tsujino, Yukiharu; Ozaki, Katsuya

2016-11-01

cis-6-Hexadecenoic acid, a major component of human sebaceous lipids, is involved in the defense mechanism against Staphylococcus aureus infection in healthy skin and closely related to atopic dermatitis. Previously, Koike et al. (Biosci Biotechnol Biochem 64:1064-1066, 2000) reported that a mutant strain of Rhodococcus sp. produced cis-6-hexadecenoate derivatives from palmitate alkyl esters. From the mutant Rhodococcus strain, we identified and sequenced two open reading frames present in an amplified 5.7-kb region; these open reading frames encoded tandemly repeated Δ6-desaturase-like genes, Rdes1 and Rdes2. A phylogenetic tree indicated that Rdes1 and Rdes2 were different from previously known Δ6-desaturase genes, and that they formed a new cluster. Rdes1 and Rdes2 were each introduced into vectors and then expressed separately in Escherichia coli, and the fatty acid composition of the transformed cells was analyzed by gas chromatography and mass spectrometry. The amount of cis-6-hexadecenoic acid was significantly higher in Rdes1- or Rdes2-transformed E. coli cells (twofold and threefold, respectively) than in vector-only control cells. These results showed that cis-6-hexadecenoic acid was produced in E. coli cells by the rhodococcal Δ6-desaturase-like proteins.

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

PubMed Central

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

2017-01-01

The ribosomal proteins play important roles in the growth and development of organisms. This study aimed to explore the function of NlRPL5 (GenBank KX379234), a ribosomal protein L5 gene, in the brown planthopper Nilaparvata lugens. The open reading frame of NlRPL5 was cloned from N. lugens based on a previous transcriptome analysis. The results revealed that the open reading frame of NlRPL5 is of 900 bp, encoding 299 amino acid residues. The reverse transcription quantitative PCR results suggested that the expression of NlRPL5 gene was stronger in gravid females, but was relatively low in nymphs, males, and newly emerged females. The expression level of NlRPL5 in the ovary was about twofolds of that in the head, thorax, or fat body. RNAi of dsNlRPL5 resulted in a significant reduction of mRNA levels, ∼50% decrease in comparison with the dsGFP control at day 6. Treatment of dsNlRPL5 significantly restricted the ovarian development, and decreased the number of eggs laid on the rice (Oryza sativa) plants. This study provided a new clue for further study on the function and regulation mechanism of NlRPL5 in N. lugens. PMID:28973571

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.

Non-coding functions of alternative pre-mRNA splicing in development

PubMed Central

Mockenhaupt, Stefan; Makeyev, Eugene V.

2015-01-01

A majority of messenger RNA precursors (pre-mRNAs) in the higher eukaryotes undergo alternative splicing to generate more than one mature product. By targeting the open reading frame region this process increases diversity of protein isoforms beyond the nominal coding capacity of the genome. However, alternative splicing also frequently controls output levels and spatiotemporal features of cellular and organismal gene expression programs. Here we discuss how these non-coding functions of alternative splicing contribute to development through regulation of mRNA stability, translational efficiency and cellular localization. PMID:26493705

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

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

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.

A Non-Canonical Initiation Site Is Required for Efficient Translation of the Dendritically Localized Shank1 mRNA

PubMed Central

Studtmann, Katrin; Ölschläger-Schütt, Janin; Buck, Friedrich; Richter, Dietmar; Sala, Carlo; Bockmann, Jürgen; Kindler, Stefan; Kreienkamp, Hans-Jürgen

2014-01-01

Local protein synthesis in dendrites enables neurons to selectively change the protein complement of individual postsynaptic sites. Though it is generally assumed that this mechanism requires tight translational control of dendritically transported mRNAs, it is unclear how translation of dendritic mRNAs is regulated. We have analyzed here translational control elements of the dendritically localized mRNA coding for the postsynaptic scaffold protein Shank1. In its 5′ region, the human Shank1 mRNA exhibits two alternative translation initiation sites (AUG+1 and AUG+214), three canonical upstream open reading frames (uORFs1-3) and a high GC content. In reporter assays, fragments of the 5′UTR with high GC content inhibit translation, suggesting a contribution of secondary structures. uORF3 is most relevant to translation control as it overlaps with the first in frame start codon (AUG+1), directing translation initiation to the second in frame start codon (AUG+214). Surprisingly, our analysis points to an additional uORF initiated at a non-canonical ACG start codon. Mutation of this start site leads to an almost complete loss of translation initiation at AUG+1, demonstrating that this unconventional uORF is required for Shank1 synthesis. Our data identify a novel mechanism whereby initiation at a non-canonical site allows for translation of the main Shank1 ORF despite a highly structured 5′UTR. PMID:24533096

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

Analysis of the L1 gene product of human papillomavirus type 16 by expression in a vaccinia virus recombinant.

PubMed

Browne, H M; Churcher, M J; Stanley, M A; Smith, G L; Minson, A C

1988-06-01

The L1 open reading frame of human papillomavirus type 16 (HPV16) has been expressed in vaccinia virus under the control of both the 7.5K early and late promoter, and the 4b major late promoter. Antibodies to a beta-galactosidase fusion protein containing a C-terminal portion of the HPV16 L1 gene product were used to compare the levels of L1 expression in the two recombinants, and showed that greater levels of expression were obtained when the gene was placed under the control of the 4b late promoter. Immunofluorescence studies revealed a nuclear location of the L1 gene product when expressed in vaccinia virus. Antibodies to the beta-galactosidase fusion protein detected a major polypeptide species of 57K and a minor species of 64K in Western blots of recombinant-infected cell lysates. The 64K species was not detected when cells were infected in the presence of tunicamycin, indicating that the primary translation product of the HPV16 L1 open reading frame is modified by N-linked glycosylation when expressed in vaccinia virus. Whereas antibodies to HPV16 L1 fusion proteins and to a peptide containing amino acids from the C terminus of HPV16 L1 reacted well in Western blots with the HPV16 L1 target expressed in vaccinia virus, no reactivity was observed with antibodies to bovine papillomavirus type 1 particles or to a HPV6b fusion protein.

Quality control in the diagnosis of Trichuris trichiura and Ascaris lumbricoides using the Kato-Katz technique: experience from three randomised controlled trials.

PubMed

Speich, Benjamin; Ali, Said M; Ame, Shaali M; Albonico, Marco; Utzinger, Jürg; Keiser, Jennifer

2015-02-05

An accurate diagnosis of soil-transmitted helminthiasis is important for individual patient management, for drug efficacy evaluation and for monitoring control programmes. The Kato-Katz technique is the most widely used method detecting soil-transmitted helminth eggs in faecal samples. However, detailed analyses of quality control, including false-positive and faecal egg count (FEC) estimates, have received little attention. Over a 3-year period, within the frame of a series of randomised controlled trials conducted in Pemba, United Republic of Tanzania, 10% of randomly selected Kato-Katz thick smears were re-read for Trichuris trichiura and Ascaris lumbricoides eggs. In case of discordant result (i.e. positive versus negative) the slides were re-examined a third time. A result was assumed to be false-positive or false-negative if the result from the initial reading did not agree with the quality control as well as the third reading. We also evaluated the general agreement in FECs between the first and second reading, according to internal and World Health Organization (WHO) guidelines. From the 1,445 Kato-Katz thick smears subjected to quality control, 1,181 (81.7%) were positive for T. trichiura and 290 (20.1%) were positive for A. lumbricoides. During quality control, very low rates of false-positive results were observed; 0.35% (n = 5) for T. trichiura and 0.28% (n = 4) for A. lumbricoides. False-negative readings of Kato-Katz thick smears were obtained in 28 (1.94%) and 6 (0.42%) instances for T. trichiura and A. lumbricoides, respectively. A high frequency of discordant results in FECs was observed (i.e. 10.0-23.9% for T. trichiura, and 9.0-11.4% for A. lumbricoides). Our analyses show that the rate of false-positive diagnoses of soil-transmitted helminths is low. As the probability of false-positive results increases after examination of multiple stool samples from a single individual, the potential influence of false-positive results on epidemiological studies and anthelminthic drug efficacy studies should be determined. Existing WHO guidelines for quality control might be overambitious and might have to be revised, specifically with regard to handling disagreements in FECs.

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

ERIC Educational Resources Information Center

Sutcliffe, Marcella P.

2016-01-01

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

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

ERIC Educational Resources Information Center

Kuldanek, Kelly

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

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

ERIC Educational Resources Information Center

Chapman, Lauren; Greenfield, Renee; Rinaldi, Claudia

2010-01-01

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

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

ERIC Educational Resources Information Center

Mason, Jessica; Giovanelli, Marcello

2017-01-01

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

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

ERIC Educational Resources Information Center

Donovan, Brian M.

2016-01-01

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

Framing obesity a disease: Indirect effects of affect and controllability beliefs on weight bias.

PubMed

Nutter, Sarah; Alberga, Angela S; MacInnis, Cara; Ellard, John H; Russell-Mayhew, Shelly

2018-05-24

Obesity has been declared a disease by the American and Canadian Medical Associations. Although these declarations sparked much debate as to the impact of framing obesity as a disease on weight bias, strong empirical research is needed to examine this impact. The current study examined the impact of framing obesity a disease on weight bias, focusing on moderating and mediating processes. A sample of 309 participants living in the United States or Canada was recruited from Crowdflower. Participants completed measures of demographics, ideology, general attitudes, and previous contact quality and quantity with people living with obesity. Participants then read one of three articles as part of an experimental manipulation framing obesity as a disease, obesity not as a disease, and a control article unrelated to obesity. Post-manipulation included measures of affect, disgust, empathy, blame, and weight bias. Orthogonal contrasts were used to compare the obesity-disease condition to the obesity-not-disease condition and control condition. The manipulation had a direct effect on affect (emotions), such that affect toward individuals with obesity was more positive in the obesity-disease condition than the obesity-not-disease and control condition combined. Exploration of moderating effects revealed that both the belief in a just world and weight satisfaction moderated the relationship between the obesity-disease manipulation and blame for obesity. Two models of indirect effects on weight bias were also examined, which demonstrated that the obesity-disease manipulation predicted less weight bias through more positive affect (model 1) as well as less weight bias through decreased blame among individuals high in belief in a just world (model 2). This study further highlights the complex effects of declaring obesity a disease, uncovering a new direction for future research into the role of affect as well as indirect effects of characterising obesity a disease on weight bias.

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.

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.

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.

Transcriptional analysis of the bglP gene from Streptococcus mutans.

PubMed

Cote, Christopher K; Honeyman, Allen L

2006-04-21

An open reading frame encoding a putative antiterminator protein, LicT, was identified in the genomic sequence of Streptococcus mutans. A potential ribonucleic antitermination (RAT) site to which the LicT protein would potentially bind has been identified immediately adjacent to this open reading frame. The licT gene and RAT site are both located 5' to a beta-glucoside PTS regulon previously described in S. mutans that is responsible for esculin utilization in the presence of glucose. It was hypothesized that antitermination is the regulatory mechanism that is responsible for the control of the bglP gene expression, which encodes an esculin-specific PTS enzyme II. To localize the promoter activity associated with the bglP locus, a series of transcriptional lacZ gene fusions was formed on a reporter shuttle vector using various DNA fragments from the bglP promoter region. Subsequent beta-galactosidase assays in S. mutans localized the bglP promoter region and identified putative -35 and -10 promoter elements. Primer extension analysis identified the bglP transcriptional start site. In addition, a terminated bglP transcript formed by transcriptional termination was identified via transcript mapping experiments. The physical location of these genetic elements, the RAT site and the promoter regions, and the identification of a short terminated mRNA support the hypothesis that antitermination regulates the bglP transcript.

Transcriptional analysis of the bglP gene from Streptococcus mutans

PubMed Central

Cote, Christopher K; Honeyman, Allen L

2006-01-01

Background An open reading frame encoding a putative antiterminator protein, LicT, was identified in the genomic sequence of Streptococcus mutans. A potential ribonucleic antitermination (RAT) site to which the LicT protein would potentially bind has been identified immediately adjacent to this open reading frame. The licT gene and RAT site are both located 5' to a beta-glucoside PTS regulon previously described in S. mutans that is responsible for esculin utilization in the presence of glucose. It was hypothesized that antitermination is the regulatory mechanism that is responsible for the control of the bglP gene expression, which encodes an esculin-specific PTS enzyme II. Results To localize the promoter activity associated with the bglP locus, a series of transcriptional lacZ gene fusions was formed on a reporter shuttle vector using various DNA fragments from the bglP promoter region. Subsequent beta-galactosidase assays in S. mutans localized the bglP promoter region and identified putative -35 and -10 promoter elements. Primer extension analysis identified the bglP transcriptional start site. In addition, a terminated bglP transcript formed by transcriptional termination was identified via transcript mapping experiments. Conclusion The physical location of these genetic elements, the RAT site and the promoter regions, and the identification of a short terminated mRNA support the hypothesis that antitermination regulates the bglP transcript. PMID:16630357

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

PubMed

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

2017-05-01

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

Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease

PubMed Central

Zhang, Peipei; Liu, Yan; Liu, Wenwen; Cao, Mengji; Massart, Sebastien; Wang, Xifeng

2017-01-01

To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat. PMID:28932215

Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease.

PubMed

Zhang, Peipei; Liu, Yan; Liu, Wenwen; Cao, Mengji; Massart, Sebastien; Wang, Xifeng

2017-01-01

To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae . Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae . Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.

The pro1(+) gene from Sordaria macrospora encodes a C6 zinc finger transcription factor required for fruiting body development.

PubMed Central

Masloff, S; Pöggeler, S; Kück, U

1999-01-01

During sexual morphogenesis, the filamentous ascomycete Sordaria macrospora differentiates into multicellular fruiting bodies called perithecia. Previously it has been shown that this developmental process is under polygenic control. To further understand the molecular mechanisms involved in fruiting body formation, we generated the protoperithecia forming mutant pro1, in which the normal development of protoperithecia into perithecia has been disrupted. We succeeded in isolating a cosmid clone from an indexed cosmid library, which was able to complement the pro1(-) mutation. Deletion analysis, followed by DNA sequencing, subsequently demonstrated that fertility was restored to the pro1 mutant by an open reading frame encoding a 689-amino-acid polypeptide, which we named PRO1. A region from this polypeptide shares significant homology with the DNA-binding domains found in fungal C6 zinc finger transcription factors, such as the GAL4 protein from yeast. However, other typical regions of C6 zinc finger proteins, such as dimerization elements, are absent in PRO1. The involvement of the pro1(+) gene in fruiting body development was further confirmed by trying to complement the mutant phenotype with in vitro mutagenized and truncated versions of the pro1 open reading frame. Southern hybridization experiments also indicated that pro1(+) homologues are present in other sexually propagating filamentous ascomycetes. PMID:10224253

The pro1(+) gene from Sordaria macrospora encodes a C6 zinc finger transcription factor required for fruiting body development.

PubMed

Masloff, S; Pöggeler, S; Kück, U

1999-05-01

During sexual morphogenesis, the filamentous ascomycete Sordaria macrospora differentiates into multicellular fruiting bodies called perithecia. Previously it has been shown that this developmental process is under polygenic control. To further understand the molecular mechanisms involved in fruiting body formation, we generated the protoperithecia forming mutant pro1, in which the normal development of protoperithecia into perithecia has been disrupted. We succeeded in isolating a cosmid clone from an indexed cosmid library, which was able to complement the pro1(-) mutation. Deletion analysis, followed by DNA sequencing, subsequently demonstrated that fertility was restored to the pro1 mutant by an open reading frame encoding a 689-amino-acid polypeptide, which we named PRO1. A region from this polypeptide shares significant homology with the DNA-binding domains found in fungal C6 zinc finger transcription factors, such as the GAL4 protein from yeast. However, other typical regions of C6 zinc finger proteins, such as dimerization elements, are absent in PRO1. The involvement of the pro1(+) gene in fruiting body development was further confirmed by trying to complement the mutant phenotype with in vitro mutagenized and truncated versions of the pro1 open reading frame. Southern hybridization experiments also indicated that pro1(+) homologues are present in other sexually propagating filamentous ascomycetes.

A multi-channel coronal spectrophotometer.

NASA Technical Reports Server (NTRS)

Landman, D. A.; Orrall, F. Q.; Zane, R.

1973-01-01

We describe a new multi-channel coronal spectrophotometer system, presently being installed at Mees Solar Observatory, Mount Haleakala, Maui. The apparatus is designed to record and interpret intensities from many sections of the visible and near-visible spectral regions simultaneously, with relatively high spatial and temporal resolution. The detector, a thermoelectrically cooled silicon vidicon camera tube, has its central target area divided into a rectangular array of about 100,000 pixels and is read out in a slow-scan (about 2 sec/frame) mode. Instrument functioning is entirely under PDP 11/45 computer control, and interfacing is via the CAMAC system.

Non-coding functions of alternative pre-mRNA splicing in development.

PubMed

Mockenhaupt, Stefan; Makeyev, Eugene V

2015-12-01

A majority of messenger RNA precursors (pre-mRNAs) in the higher eukaryotes undergo alternative splicing to generate more than one mature product. By targeting the open reading frame region this process increases diversity of protein isoforms beyond the nominal coding capacity of the genome. However, alternative splicing also frequently controls output levels and spatiotemporal features of cellular and organismal gene expression programs. Here we discuss how these non-coding functions of alternative splicing contribute to development through regulation of mRNA stability, translational efficiency and cellular localization. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

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…

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.

uAUG-mediated translational initiations are responsible for human mu opioid receptor gene expression

PubMed Central

Song, Kyu Young; Kim, Chun Sung; Hwang, Cheol Kyu; Choi, Hack Sun; Law, Ping-Yee; Wei, Li-Na; Loh, Horace H

2010-01-01

Abstract Mu opioid receptor (MOR) is the main site of interaction for major clinical analgesics, particularly morphine. MOR expression is regulated at the transcriptional and post-transcriptional levels. However, the protein expression of the MOR gene is relatively low and the translational control of MOR gene has not been well studied. The 5′-untranslated region (UTR) of the human MOR (OPRM1) mRNA contains four upstream AUG codons (uAUG) preceding the main translation initiation site. We mutated the four uAUGs individually and in combination. Mutations of the third uAUG, containing the same open reading frame, had the strongest inhibitory effect. The inhibitory effect caused by the third in-frame uAUG was confirmed by in vitro translation and receptor-binding assays. Toeprinting results showed that OPRM1 ribosomes initiated efficiently at the first uAUG, and subsequently re-initiated at the in-frame #3 uAUG and the physiological AUG site. This re-initiation resulted in negative expression of OPRM1 under normal conditions. These results indicate that re-initiation in MOR gene expression could play an important role in OPRM1 regulation. PMID:19438807

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.

Sub-electron read noise and millisecond full-frame readout with the near infrared eAPD array SAPHIRA

NASA Astrophysics Data System (ADS)

Finger, Gert; Baker, Ian; Alvarez, Domingo; Dupuy, Christophe; Ives, Derek; Meyer, Manfred; Mehrgan, Leander; Stegmeier, Jörg; Weller, Harald J.

2016-07-01

In 2007 ESO started a program at SELEX (now LEONARDO) to develop noiseless near infrared HgCdTe electron avalanche photodiode arrays (eAPD)[1][2][3]. This eAPD technology is only way to overcome the limiting CMOS noise barrier of near infrared sensors used for wavefront sensing and fringe tracking. After several development cycles of solid state engineering techniques which can be easily applied to the chosen growth technology of metal organic vapour phase epitaxy (MOVPE), the eAPD arrays have matured and resulted in the SAPHIRA arrays. They have a format of 320x256 pixels with a pitch of 24 μm. They now offer an unmatched combination of sub-electron read noise at millisecond frame readout rates. The first generation of SAPHIRA arrays were only sensitive in H and K-band. With the removal of a wide bandgap buffer layer the arrays are now sensitive from λ=0.8 μm to 2.5 μm with high quantum efficiency over the entire wavelength range. The high temperature anneal applied during the growth process produces material with superb cosmetic quality at an APD gain of over 600. The design of the SAPHIRA ROIC has also been revised and the new ME1000 ROIC has an optimized analogue chain and more flexible readout modes. The clock for the vertical shift register is now under external control. The advantage of this is that correlated-double-sampling and uncorrelated readout in the rolling shutter mode now have a duty cycle of 100% at the maximum frame rate. Furthermore, to reduce the readout noise rows can be read several times before and after row reset. Since the APD gain is sufficiently high that one photon produces many more electrons than the square root of kTC which is the charge uncertainty after reset, signals of one photon per exposure can be easily detected without the need for double correlated sampling. First results obtained with the fringe tracker in GRAVITY and the four SAPHIRA wavefront sensors installed in the CIAO adaptive optics systems of the four 8 meter telescopes of the VLTI have proven the unrivaled performance of the SAPHIRA eAPD technology. A future program is being assembled to develop eAPD arrays having a larger format of 1Kx1K capable of frame rates of 1.2 KHz. There are also good prospects to offer low dark current eAPD technology for large format science focal planes as well.

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

DOEpatents

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

2014-09-02

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

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

DOEpatents

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

2014-09-16

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

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.

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.

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.

Stringent control during carbon starvation of marine Vibrio sp. strain S14: molecular cloning, nucleotide sequence, and deletion of the relA gene.

PubMed Central

Flärdh, K; Axberg, T; Albertson, N H; Kjelleberg, S

1994-01-01

In order to evaluate the role of the stringent response in starvation adaptations of the marine Vibrio sp. strain S14, we have cloned the relA gene and generated relaxed mutants of this organism. The Vibrio relA gene was selected from a chromosomal DNA library by complementation of an Escherichia coli delta relA strain. The nucleotide sequence contains a 743-codon open reading frame that encodes a polypeptide that is identical in length and highly homologous to the E. coli RelA protein. The amino acid sequences are 64% identical, and they share some completely conserved regions. A delta relA::kan allele was generated by replacing 53% of the open reading frame with a kanamycin resistance gene. The Vibrio relA mutants displayed a relaxed control of RNA synthesis and failed to accumulate ppGpp during amino acid limitation. During carbon and energy starvation, a relA-dependent burst of ppGpp synthesis concomitant with carbon source depletion and growth arrest was observed. Also, in the absence of the relA gene, there was an accumulation of ppGpp during carbon starvation, but this was slower and smaller than that which occurred in the stringent strains, and it was preceded by a marked decrease in the [ATP]/[ADP] ratio. In both the wild-type and the relaxed strains, carbon source depletion caused an immediate decrease in the size of the GTP pool and a block of net RNA accumulation. The relA mutation did not affect long-term survival or the development of resistance against heat, ethanol, and oxidative stress during carbon starvation of Vibrio sp. strain S14. PMID:7928955

Basal exon skipping and nonsense-associated altered splicing allows bypassing complete CEP290 loss-of-function in individuals with unusually mild retinal disease.

PubMed

Barny, Iris; Perrault, Isabelle; Michel, Christel; Soussan, Mickael; Goudin, Nicolas; Rio, Marlène; Thomas, Sophie; Attié-Bitach, Tania; Hamel, Christian; Dollfus, Hélène; Kaplan, Josseline; Rozet, Jean-Michel; Gerard, Xavier

2018-05-16

CEP290 mutations cause a spectrum of ciliopathies from Leber congenital amaurosis type 10 (LCA10) to embryo-lethal Meckel syndrome (MKS). Using panel-based molecular diagnosis testing for inherited retinal diseases, we identified two individuals with some preserved vision despite biallelism for presumably truncating CEP290 mutations. The first one carried a homozygous 1 base-pair deletion in exon 17, introducing a premature termination codon (PTC) in exon 18 (c.1666del; p.Ile556Phefs*17). mRNA analysis revealed a basal exon skipping (BES) of exon 18, providing mutant cells with the ability to escape protein truncation, while disrupting the reading frame in controls. The second individual harbored compound heterozygous nonsense mutations in exon 8 (c.508A>T, p.Lys170*) and exon 32 (c.4090G>T, p.Glu1364*), respectively. Some CEP290 lacking exon 8 were detected in mutant fibroblasts but not in controls whereas some skipping of exon 32 occurred in both lines, but with higher amplitude in the mutant. Considering that the deletion of either exon maintains the reading frame in either line, skipping in mutant cells likely involves nonsense-associated altered splicing (NAS) alone (exon 8), or with BES (exon 32). Skipping of PTC-containing exons in mutant cells allowed production of CEP290 isoforms with preserved ability to assemble into a high molecular weight complex and to interact efficiently with proteins important for cilia formation and intraflagellar trafficking. In contrast, studying LCA10 and MKS fibroblasts we show moderate to severe cilia alterations, providing support for a correlation between disease severity and the ability of cells to express shortened, yet functional, CEP290 isoforms.

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.

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

PubMed

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

2011-12-01

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

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

PubMed Central

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

2011-01-01

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

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.

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.

An investigation of articulatory setting using real-time magnetic resonance imaging

PubMed Central

Ramanarayanan, Vikram; Goldstein, Louis; Byrd, Dani; Narayanan, Shrikanth S.

2013-01-01

This paper presents an automatic procedure to analyze articulatory setting in speech production using real-time magnetic resonance imaging of the moving human vocal tract. The procedure extracts frames corresponding to inter-speech pauses, speech-ready intervals and absolute rest intervals from magnetic resonance imaging sequences of read and spontaneous speech elicited from five healthy speakers of American English and uses automatically extracted image features to quantify vocal tract posture during these intervals. Statistical analyses show significant differences between vocal tract postures adopted during inter-speech pauses and those at absolute rest before speech; the latter also exhibits a greater variability in the adopted postures. In addition, the articulatory settings adopted during inter-speech pauses in read and spontaneous speech are distinct. The results suggest that adopted vocal tract postures differ on average during rest positions, ready positions and inter-speech pauses, and might, in that order, involve an increasing degree of active control by the cognitive speech planning mechanism. PMID:23862826

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.

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

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.

Local restoration of dystrophin expression with the morpholino oligomer AVI-4658 in Duchenne muscular dystrophy: a single-blind, placebo-controlled, dose-escalation, proof-of-concept study

PubMed Central

Kinali, Maria; Arechavala-Gomeza, Virginia; Feng, Lucy; Cirak, Sebahattin; Hunt, David; Adkin, Carl; Guglieri, Michela; Ashton, Emma; Abbs, Stephen; Nihoyannopoulos, Petros; Garralda, Maria Elena; Rutherford, Mary; Mcculley, Caroline; Popplewell, Linda; Graham, Ian R; Dickson, George; Wood, Matthew JA; Wells, Dominic J; Wilton, Steve D; Kole, Ryszard; Straub, Volker; Bushby, Kate; Sewry, Caroline; Morgan, Jennifer E; Muntoni, Francesco

2009-01-01

Summary Background Mutations that disrupt the open reading frame and prevent full translation of DMD, the gene that encodes dystrophin, underlie the fatal X-linked disease Duchenne muscular dystrophy. Oligonucleotides targeted to splicing elements (splice switching oligonucleotides) in DMD pre-mRNA can lead to exon skipping, restoration of the open reading frame, and the production of functional dystrophin in vitro and in vivo, which could benefit patients with this disorder. Methods We did a single-blind, placebo-controlled, dose-escalation study in patients with DMD recruited nationally, to assess the safety and biochemical efficacy of an intramuscular morpholino splice-switching oligonucleotide (AVI-4658) that skips exon 51 in dystrophin mRNA. Seven patients with Duchenne muscular dystrophy with deletions in the open reading frame of DMD that are responsive to exon 51 skipping were selected on the basis of the preservation of their extensor digitorum brevis (EDB) muscle seen on MRI and the response of cultured fibroblasts from a skin biopsy to AVI-4658. AVI-4658 was injected into the EDB muscle; the contralateral muscle received saline. Muscles were biopsied between 3 and 4 weeks after injection. The primary endpoint was the safety of AVI-4658 and the secondary endpoint was its biochemical efficacy. This trial is registered, number NCT00159250. Findings Two patients received 0·09 mg AVI-4658 in 900 μL (0·9%) saline and five patients received 0·9 mg AVI-4658 in 900 μL saline. No adverse events related to AVI-4658 administration were reported. Intramuscular injection of the higher-dose of AVI-4658 resulted in increased dystrophin expression in all treated EDB muscles, although the results of the immunostaining of EDB-treated muscle for dystrophin were not uniform. In the areas of the immunostained sections that were adjacent to the needle track through which AVI-4658 was given, 44–79% of myofibres had increased expression of dystrophin. In randomly chosen sections of treated EDB muscles, the mean intensity of dystrophin staining ranged from 22% to 32% of the mean intensity of dystrophin in healthy control muscles (mean 26·4%), and the mean intensity was 17% (range 11–21%) greater than the intensity in the contralateral saline-treated muscle (one-sample paired t test p=0·002). In the dystrophin-positive fibres, the intensity of dystrophin staining was up to 42% of that in healthy muscle. We showed expression of dystrophin at the expected molecular weight in the AVI-4658-treated muscle by immunoblot. Interpretation Intramuscular AVI-4658 was safe and induced the expression of dystrophin locally within treated muscles. This proof-of-concept study has led to an ongoing systemic clinical trial of AVI-4658 in patients with DMD. Funding UK Department of Health. PMID:19713152

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

Viral Evasion and Manipulation of Host RNA Quality Control Pathways

PubMed Central

2016-01-01

Viruses have evolved diverse strategies to maximize the functional and coding capacities of their genetic material. Individual viral RNAs are often used as substrates for both replication and translation and can contain multiple, sometimes overlapping open reading frames. Further, viral RNAs engage in a wide variety of interactions with both host and viral proteins to modify the activities of important cellular factors and direct their own trafficking, packaging, localization, stability, and translation. However, adaptations increasing the information density of small viral genomes can have unintended consequences. In particular, viral RNAs have developed features that mark them as potential targets of host RNA quality control pathways. This minireview focuses on ways in which viral RNAs run afoul of the cellular mRNA quality control and decay machinery, as well as on strategies developed by viruses to circumvent or exploit cellular mRNA surveillance. PMID:27226372

Viral Evasion and Manipulation of Host RNA Quality Control Pathways.

PubMed

Hogg, J Robert

2016-08-15

Viruses have evolved diverse strategies to maximize the functional and coding capacities of their genetic material. Individual viral RNAs are often used as substrates for both replication and translation and can contain multiple, sometimes overlapping open reading frames. Further, viral RNAs engage in a wide variety of interactions with both host and viral proteins to modify the activities of important cellular factors and direct their own trafficking, packaging, localization, stability, and translation. However, adaptations increasing the information density of small viral genomes can have unintended consequences. In particular, viral RNAs have developed features that mark them as potential targets of host RNA quality control pathways. This minireview focuses on ways in which viral RNAs run afoul of the cellular mRNA quality control and decay machinery, as well as on strategies developed by viruses to circumvent or exploit cellular mRNA surveillance. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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.

How silent is silent reading? Intracerebral evidence for top-down activation of temporal voice areas during reading.

PubMed

Perrone-Bertolotti, Marcela; Kujala, Jan; Vidal, Juan R; Hamame, Carlos M; Ossandon, Tomas; Bertrand, Olivier; Minotti, Lorella; Kahane, Philippe; Jerbi, Karim; Lachaux, Jean-Philippe

2012-12-05

As you might experience it while reading this sentence, silent reading often involves an imagery speech component: we can hear our own "inner voice" pronouncing words mentally. Recent functional magnetic resonance imaging studies have associated that component with increased metabolic activity in the auditory cortex, including voice-selective areas. It remains to be determined, however, whether this activation arises automatically from early bottom-up visual inputs or whether it depends on late top-down control processes modulated by task demands. To answer this question, we collaborated with four epileptic human patients recorded with intracranial electrodes in the auditory cortex for therapeutic purposes, and measured high-frequency (50-150 Hz) "gamma" activity as a proxy of population level spiking activity. Temporal voice-selective areas (TVAs) were identified with an auditory localizer task and monitored as participants viewed words flashed on screen. We compared neural responses depending on whether words were attended or ignored and found a significant increase of neural activity in response to words, strongly enhanced by attention. In one of the patients, we could record that response at 800 ms in TVAs, but also at 700 ms in the primary auditory cortex and at 300 ms in the ventral occipital temporal cortex. Furthermore, single-trial analysis revealed a considerable jitter between activation peaks in visual and auditory cortices. Altogether, our results demonstrate that the multimodal mental experience of reading is in fact a heterogeneous complex of asynchronous neural responses, and that auditory and visual modalities often process distinct temporal frames of our environment at the same time.

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.

The Complex World of Adolescent Literacy: Myths, Motivations, and Mysteries

PubMed Central

Moje, Elizabeth Birr; Overby, Melanie; Tysvaer, Nicole; Morris, Karen

2009-01-01

In this article, Elizabeth Birr Moje, Melanie Overby, Nicole Tysvaer, and Karen Morris challenge some of the prevailing myths about adolescents and their choices related to reading. The reading practices of youth from one urban community are examined using mixed methods in an effort to define what, how often, and why adolescents choose to read. By focusing on what features of texts youth find motivating, the authors find that reading and writing frequently occur in a range of literacy contexts outside school. However, only reading novels on a regular basis outside of school is shown to have a positive relationship to academic achievement as measured by school grades. This article describes how adolescents read texts that are embedded in social networks, allowing them to build social capital. Conclusions are framed in terms of the mysteries that remain — namely, how to build on what motivates adolescents' literacy practices in order to both promote the building of their social selves and improve their academic outcomes. PMID:19756223

Influencing health decision-making: A study of colour and message framing.

PubMed

Voss, Raymond P; Corser, Ryan; McCormick, Michael; Jasper, John D

2018-07-01

Previous research has provided evidence that colour associations and frame can influence behavioural intentions to engage in vaccination behaviours. In this study, the extension of these effects to sunscreen application behaviours was investigated. Additional colours and the manner in which colour primes were employed were also explored. Two hundred and eighty-six college students were primed with either short wavelength colours (blue/purple) or long wavelength colours (red/orange) as part of goal framed sunscreen information pamphlets. Self-reported behavioural intentions to apply sunscreen, immediate affective reaction to stimuli material, anticipated affect towards sunscreen use, and perceived efficacy of preventing skin cancer were measured. Individuals with no prior intention to use sunscreen expressed greater behavioural intentions to do so after reading a positively framed sunscreen pamphlet that was designed using short wavelength colours. The negatively framed messages and those presented in long wavelength colours did not enhance persuasion. In accordance with the Unification Theory of Framing, a match between the representations of the target behaviour, the colour prime, and the frame resulted in the greatest amount of persuasion. Creating communications with representations that match the target behaviour could be a powerful tool to increase compliance.

A series of vectors to construct lacZ fusions for the study of gene expression in Schizosaccharomyces pombe.

PubMed

Lafuente, M J; Petit, T; Gancedo, C

1997-12-22

We have constructed a series of plasmids to facilitate the fusion of promoters with or without coding regions of genes of Schizosaccharomyces pombe to the lacZ gene of Escherichia coli. These vectors carry a multiple cloning region in which fission yeast DNA may be inserted in three different reading frames with respect to the coding region of lacZ. The plasmids were constructed with the ura4+ or the his3+ marker of S. pombe. Functionality of the plasmids was tested measuring in parallel the expression of fructose 1,6-bisphosphatase and beta-galactosidase under the control of the fbp1+ promoter in different conditions.

Elective single-embryo transfer: persuasive communication strategies can affect choice in a young British population.

PubMed

van den Akker, O B A; Purewal, S

2011-12-01

This study tested the effectiveness of the framing effect and fear appeals to inform young people about the risks of multiple births and the option of selecting elective single-embryo transfer (eSET). A non-patient student sample (age (mean±SD) 23±5.5 years; n=321) were randomly allocated to one of seven groups: (1) framing effect: (1a) gain and (1b) loss frame; (2) fear appeal: (2a) high, (2b) medium and (2c) low fear; or (3) a control group: (3a) education and (3b) non-education. The primary outcome measure was the Attitudes towards Single Embryo Transfer questionnaire, before exposure to the messages (time 1) and immediately afterwards (time 2). Results revealed participants in the high fear, medium fear and gain condition demonstrated the most positive and significant differences (P<0.001 to P<0.05) in their knowledge, hypothetical intentions and modest changes in attitudes towards eSET than the low fear, loss frame and education and non-education messages. The results demonstrate that the use of complex persuasive communication techniques on a student population to promote immediate and hypothetical eSET preferences is more successful at promoting eSET than merely reporting educational content. Future research should investigate its application in a clinical population. A multiple pregnancy is a health risk to both infant and mother following IVF treatment. The aims of this study were to test the effectiveness of two persuasive communication techniques (the framing effect and fear appeals) to inform young people about the risks of multiple births and the hypothetical option of selecting elective single-embryo transfer (eSET) (i.e., only one embryo is transferred to the uterus using IVF treatment). A total of 321 non-patient student sample (mean age 23) were randomly allocated to read a message from one of seven groups: (1) framing effect: (1a) gain and (1b) loss frame; (2) fear appeal: (2a) high, (2b) medium and (2c) low fear; or (3) a control group: education (3a) and (3b) non-education. Participants completed the Attitudes towards Single Embryo Transfer questionnaire, before exposure to the messages (time 1) and immediately afterwards (time 2). Results revealed that participants in the high fear, medium fear and gain condition demonstrated the most positive and significant differences in their knowledge, hypothetical intentions and modest changes in attitudes towards eSET than the low fear, loss frame and education and non-education messages. This study recommends that health promotion based on the framing effect and fear appeals should be tested in clinical (patient) samples in the future. Copyright © 2011 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

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.

Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis.

PubMed

Legnini, Ivano; Di Timoteo, Gaia; Rossi, Francesca; Morlando, Mariangela; Briganti, Francesca; Sthandier, Olga; Fatica, Alessandro; Santini, Tiziana; Andronache, Adrian; Wade, Mark; Laneve, Pietro; Rajewsky, Nikolaus; Bozzoni, Irene

2017-04-06

Circular RNAs (circRNAs) constitute a family of transcripts with unique structures and still largely unknown functions. Their biogenesis, which proceeds via a back-splicing reaction, is fairly well characterized, whereas their role in the modulation of physiologically relevant processes is still unclear. Here we performed expression profiling of circRNAs during in vitro differentiation of murine and human myoblasts, and we identified conserved species regulated in myogenesis and altered in Duchenne muscular dystrophy. A high-content functional genomic screen allowed the study of their functional role in muscle differentiation. One of them, circ-ZNF609, resulted in specifically controlling myoblast proliferation. Circ-ZNF609 contains an open reading frame spanning from the start codon, in common with the linear transcript, and terminating at an in-frame STOP codon, created upon circularization. Circ-ZNF609 is associated with heavy polysomes, and it is translated into a protein in a splicing-dependent and cap-independent manner, providing an example of a protein-coding circRNA in eukaryotes. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

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…

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

PubMed Central

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

2013-01-01

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

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.

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.

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.

Ribosomal scanning past the primary initiation codon as a mechanism for expression of CTL epitopes encoded in alternative reading frames

PubMed Central

1996-01-01

An increasing amount of evidence has shown that epitopes restricted to MHC class I molecules and recognized by CTL need not be encoded in a primary open reading frame (ORF). Such epitopes have been demonstrated after stop codons, in alternative reading frames (RF) and within introns. We have used a series of frameshifts (FS) introduced into the Influenza A/PR/8 /34 nucleoprotein (NP) gene to confirm the previous in vitro observations of cryptic epitope expression, and show that they are sufficiently expressed to prime immune responses in vivo. This presentation is not due to sub-dominant epitopes, transcription from cryptic promoters beyond the point of the FS, or internal initiation of translation. By introducing additional mutations to the construct exhibiting the most potent presentation, we have identified initiation codon readthrough (termed scanthrough here, where the scanning ribosome bypasses the conventional initiation codon, initiating translation further downstream) as the likely mechanism of epitope production. Further mutational analysis demonstrated that, while it should operate during the expression of wild-type (WT) protein, scanthrough does not provide a major source of processing substrate in our system. These findings suggest (i) that the full array of self- and pathogen-derived epitopes available during thymic selection and infection has not been fully appreciated and (ii) that cryptic epitope expression should be considered when the specificity of a CTL response cannot be identified or in therapeutic situations when conventional CTL targets are limited, as may be the case with latent viral infections and transformed cells. Finally, initiation codon readthrough provides a plausible explanation for the presentation of exocytic proteins by MHC class I molecules. PMID:8879204

MLPA based detection of mutations in the dystrophin gene of 180 Polish families with Duchenne/Becker muscular dystrophy.

PubMed

Zimowski, Janusz G; Massalska, Diana; Holding, Mariola; Jadczak, Sylwia; Fidziańska, Elżbieta; Lusakowska, Anna; Kostera-Pruszczyk, Anna; Kamińska, Anna; Zaremba, Jacek

2014-01-01

Duchenne/Becker muscular dystrophy (DMD/BMD) is a recessive, X-linked disorder caused by a mutation in the dystrophin gene. Deletions account for approximately 60-65% of mutations, duplications for 5-10%. The remaining cases are mainly point mutations. According to Monaco theory clinical form of the disease depends on maintaining or disrupting the reading frame. The purpose of the study was to determine frequency and location of deletions and duplications in the dystrophin gene, to determine the compliance between maintaining/disrupting the reading frame and clinical form of the disease and to check the effectiveness of MLPA (multiplex ligation-dependent probe amplification) in the detection of these mutations in hemizygous patients and heterozygous female carriers. The material is composed of combined results of molecular diagnosis carried out in years 2009-2012 in 180 unrelated patients referred with the diagnosis of DMD/BMD tested by use of MLPA. We identified 110 deletions, 22 duplication (in one patient two different duplications were detected) and 2 point mutations. Deletions involved mainly exons 45-54 and 3-21, whereas most duplications involved exons 3-18. The compliance with Monaco theory was 95% for deletions and 76% for duplications. Most of mutations in the dystrophin gene were localized in the hot spots - different for deletions and duplications. MLPA enabled their quick identification, exact localization and determination whether or not they maintained or disrupted the reading frame. MLPA was also effective in detection of deletions and duplications in female carriers. Copyright © 2014 Polish Neurological Society. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

Duchenne Muscular Dystrophy and Becker Muscular Dystrophy Confirmed by Multiplex Ligation-Dependent Probe Amplification: Genotype-Phenotype Correlation in a Large Cohort.

PubMed

Vengalil, Seena; Preethish-Kumar, Veeramani; Polavarapu, Kiran; Mahadevappa, Manjunath; Sekar, Deepha; Purushottam, Meera; Thomas, Priya Treesa; Nashi, Saraswathi; Nalini, Atchayaram

2017-01-01

Studies of cases of Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) confirmed by multiplex ligation-dependent probe amplification (MLPA) have determined the clinical characteristics, genotype, and relations between the reading frame and phenotype for different countries. This is the first such study from India. A retrospective genotype-phenotype analysis of 317 MLPA-confirmed patients with DMD or BMD who visited the neuromuscular clinic of a quaternary referral center in southern India. The 317 patients comprised 279 cases of DMD (88%), 32 of BMD (10.1%), and 6 of intermediate phenotype (1.9%). Deletions accounted for 91.8% of cases, with duplications causing the remaining 8.2%. There were 254 cases of DMD (91%) with deletions and 25 (9%) due to duplications, and 31 cases (96.8%) of BMD with deletions and 1 (3.2%) due to duplication. All six cases of intermediate type were due to deletions. The most-common mutation was a single-exon deletion. Deletions of six or fewer exons constituted 68.8% of cases. The deletion of exon 50 was the most common. The reading-frame rule held in 90% of DMD and 94% of BMD cases. A tendency toward a lower IQ and earlier wheelchair dependence was observed with distal exon deletions, though a significant correlation was not found. The reading-frame rule held in 90% to 94% of children, which is consistent with reports from other parts of the world. However, testing by MLPA is a limitation, and advanced sequencing methods including analysis of the structure of mutant dystrophin is needed for more-accurate assessments of the genotype-phenotype correlation.

Self-complementary circular codes in coding theory.

PubMed

Fimmel, Elena; Michel, Christian J; Starman, Martin; Strüngmann, Lutz

2018-04-01

Self-complementary circular codes are involved in pairing genetic processes. A maximal [Formula: see text] self-complementary circular code X of trinucleotides was identified in genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel in Life 7(20):1-16 2017, J Theor Biol 380:156-177, 2015; Arquès and Michel in J Theor Biol 182:45-58 1996). In this paper, self-complementary circular codes are investigated using the graph theory approach recently formulated in Fimmel et al. (Philos Trans R Soc A 374:20150058, 2016). A directed graph [Formula: see text] associated with any code X mirrors the properties of the code. In the present paper, we demonstrate a necessary condition for the self-complementarity of an arbitrary code X in terms of the graph theory. The same condition has been proven to be sufficient for codes which are circular and of large size [Formula: see text] trinucleotides, in particular for maximal circular codes ([Formula: see text] trinucleotides). For codes of small-size [Formula: see text] trinucleotides, some very rare counterexamples have been constructed. Furthermore, the length and the structure of the longest paths in the graphs associated with the self-complementary circular codes are investigated. It has been proven that the longest paths in such graphs determine the reading frame for the self-complementary circular codes. By applying this result, the reading frame in any arbitrary sequence of trinucleotides is retrieved after at most 15 nucleotides, i.e., 5 consecutive trinucleotides, from the circular code X identified in genes. Thus, an X motif of a length of at least 15 nucleotides in an arbitrary sequence of trinucleotides (not necessarily all of them belonging to X) uniquely defines the reading (correct) frame, an important criterion for analyzing the X motifs in genes in the future.

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.

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.

Steerable Hopping Six-Legged Robot

NASA Technical Reports Server (NTRS)

Younse, Paulo; Aghazarian, Hrand

2010-01-01

The figure depicts selected aspects of a six-legged robot that moves by hopping and that can be steered in the sense that it can be launched into a hop in a controllable direction. This is a prototype of hopping robots being developed for use in scientific exploration of rough terrain on remote planets that have surface gravitation less than that of Earth. Hopping robots could also be used on Earth, albeit at diminished hopping distances associated with the greater Earth gravitation. The upper end of each leg is connected through two universal joints to an upper and a lower hexagonal frame, such that the tilt of the leg depends on the relative position of the two frames. Two non-back-driveable worm-gear motor drives are used to control the relative position of the two frames along two axes 120 apart, thereby controlling the common tilt of all six legs and thereby, further, controlling the direction of hopping. Each leg includes an upper and a lower aluminum frame segment with a joint between them. A fiberglass spring, connected via hinges to both segments, is used to store hopping energy prior to launch into a hop and to cushion the landing at the end of the hop. A cable for loading the spring is run into each leg through the center of the universal joints and then down along the center lines of the segments to the lower end of the leg. A central spool actuated by a motor with a harmonic drive and an electromagnetic clutch winds in all six cables to compress all six springs (thereby also flexing all six legs) simultaneously. To ensure that all the legs push off and land in the same direction, timing- belt pulley drives are attached to the leg segments, restricting the flexing and extension of all six legs to a common linear motion. In preparation for a hop, the spool can be driven to load the spring legs by an amount corresponding to a desired hop distance within range. The amount of compression can be computed from the reading of a shaft-angle encoder that indicates the amount by which the spool has been turned. When the robot is ready to hop, the electromagnetic clutch disengages the motor from the spool, thus releasing the cable restraints on the springs and allowing the springs to extend all six legs simultaneously.

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....

Isolation and characterization of a chitinase gene from entomopathogenic fungus Verticillium lecanii

PubMed Central

Zhu, Yanping; Pan, Jieru; Qiu, Junzhi; Guan, Xiong

2008-01-01

Entomopathogenic fungus Verticillium lecanii is a promising whitefly and aphid control agent. Chitinases secreted by this insect pathogen have considerable importance in the biological control of some insect pests. An endochitinase gene Vlchit1 from the fungus was cloned and overexpressed in Escherichia coli. The Vlchit1 gene not only contains an open reading frame (ORF) which encodes a protein of 423 amino acids (aa), but also is interrupted by three short introns. Vlchit1 protein showed that the chitinase Vlchit1 has a (a/b)8 TIM barrel structure. Overexpression test and Enzymatic activity assay indicated that the Vlchit1 is a functional enzyme that can hydrolyze the chitin substrate, so the Vlchit1 gene can service as a useful gene source for genetic manipulation leading to strain improvement of entomopathogenic fungi or constructing new transgenic plants with resistance to various fungal and insects pests. PMID:24031223

[Identification of a novel splicing mutation of PHEX gene in a pedigree affected with X-linked hypophosphatemia].

PubMed

Li, Jie; Xu, Peiwen; Huang, Sexin; Gao, Ming; Zou, Yang; Kang, Ranran; Gao, Yuan

2017-04-10

To identify potential mutation of PHEX gene in two patients from a family affected with X-linked hypophosphatemia (XLH). PCR and Sanger sequencing were performed on blood samples from the patients and 100 healthy controls. Reverse transcription-PCR (RT-PCR) was used to determine the mRNA expression in patient samples. A splicing site mutation, IVS21+2T>G, was found in the PHEX gene in both patients but not among the 100 healthy controls. RT-PCR confirmed that exon 21 of the PHEX gene was deleted. The novel splicing mutation IVS21+2T>G of the PHEX gene probably underlies the XLH in this pedigree. At the mRNA level, the mutation has led to removal of exon 21 and shift of the open reading frame (p.Val691fsx), resulting in premature termination of protein translation.

Role of eIF2α Kinases in Translational Control and Adaptation to Cellular Stress.

PubMed

Wek, Ronald C

2018-02-12

A central mechanism regulating translation initiation in response to environmental stress involves phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF2α). Phosphorylation of eIF2α causes inhibition of global translation, which conserves energy and facilitates reprogramming of gene expression and signaling pathways that help to restore protein homeostasis. Coincident with repression of protein synthesis, many gene transcripts involved in the stress response are not affected or are even preferentially translated in response to increased eIF2α phosphorylation by mechanisms involving upstream open reading frames (uORFs). This review highlights the mechanisms regulating eIF2α kinases, the role that uORFs play in translational control, and the impact that alteration of eIF2α phosphorylation by gene mutations or small molecule inhibitors can have on health and disease. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Teledyne H1RG, H2RG, and H4RG Noise Generator

NASA Technical Reports Server (NTRS)

Rauscher, Bernard J.

2015-01-01

This paper describes the near-infrared detector system noise generator (NG) that we wrote for the James Webb Space Telescope (JWST) Near Infrared Spectrograph (NIRSpec). NG simulates many important noise components including; (1) white "read noise", (2) residual bias drifts, (3) pink 1/f noise, (4) alternating column noise, and (5) picture frame noise. By adjusting the input parameters, NG can simulate noise for Teledyne's H1RG, H2RG, and H4RG detectors with and without Teledyne's SIDECAR ASIC IR array controller. NG can be used as a starting point for simulating astronomical scenes by adding dark current, scattered light, and astronomical sources into the results from NG. NG is written in Python-3.4.

Isolation and Genome Characterization of the Virulent Staphylococcus aureus Bacteriophage SA97

PubMed Central

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

2015-01-01

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

Characterization of Bombyx mori nucleopolyhedrovirus with a knockout of Bm17.

PubMed

Shen, Hongxing; Zhou, Yang; Zhang, Wen; Nin, Bin; Wang, Hua; Wang, Xiaochun; Shao, Shihe; Chen, Huiqing; Guo, Zhongjian; Liu, Xiaoyong; Yao, Qin; Chen, Keping

2012-12-01

Open reading frame 17 (Bm17) gene of Bombyx mori nucleopolyhedrovirus is a highly conserved gene in lepidopteran nucleopolyhedroviruses, but its function remains unknown. In this report, transient-expression and superinfection assays indicated that BM17 localized in the nucleus and cytoplasm of infected BmN cells. To determine the role of Bm17 in baculovirus life cycle, we constructed a Bm17 knockout virus and characterized its properties in cells. Analysis of the production and infection of budded virions, the level of viral DNA replication revealed showed that there was no significant difference among the mutant, the control, and the Bm17 repaired virus strains. These results suggest that BM17 is not essential for virus replication in cultured cells.

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.

Eukaryotic initiation factor 3 (eIF3) and 5’ mRNA leader sequences as agents of translational regulation in Arabidopsis. Final report

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

von Arnim, Albrecht G.

2015-02-04

Protein synthesis, or translation, consumes a sizable fraction of the cell’s energy budget, estimated at 5% and up to 50% in differentiated and growing cells, respectively. Plants also invest significant energy and biomass to construct and maintain the translation apparatus. Translation is regulated by a variety of external stimuli. Compared to transcriptional control, attributes of translational control include reduced sensitivity to stochastic fluctuation, a finer gauge of control, and more rapid responsiveness to environmental stimuli. Yet, our murky understanding of translational control allows few generalizations. Consequently, translational regulation is underutilized in the context of transgene regulation, although synthetic biologists aremore » now beginning to appropriate RNA-level gene regulation into their regulatory circuits. We also know little about how translational control contributes to the diversity of plant form and function. This project explored how an emerging regulatory mRNA sequence element, upstream open reading frames (uORFs), is integrated with the general translation initiation machinery to permit translational regulation on specific mRNAs.« less

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.

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.

Health warnings promote healthier dietary decision making: Effects of positive versus negative message framing and graphic versus text-based warnings.

PubMed

Rosenblatt, Daniel H; Bode, Stefan; Dixon, Helen; Murawski, Carsten; Summerell, Patrick; Ng, Alyssa; Wakefield, Melanie

2018-08-01

Food product health warnings have been proposed as a potential obesity prevention strategy. This study examined the effects of text-only and text-and-graphic, negatively and positively framed health warnings on dietary choice behavior. In a 2 × 5 mixed experimental design, 96 participants completed a dietary self-control task. After providing health and taste ratings of snack foods, participants completed a baseline measure of dietary self-control, operationalized as participants' frequency of choosing healthy but not tasty items and rejecting unhealthy yet tasty items to consume at the end of the experiment. Participants were then randomly assigned to one of five health warning groups and presented with 10 health warnings of a given form: text-based, negative framing; graphic, negative framing; text, positive framing; graphic, positive framing; or a no warning control. Participants then completed a second dietary decision making session to determine whether health warnings influenced dietary self-control. Linear mixed effects modeling revealed a significant interaction between health warning group and decision stage (pre- and post-health warning presentation) on dietary self-control. Negatively framed graphic health warnings promoted greater dietary self-control than other health warnings. Negatively framed text health warnings and positively framed graphic health warnings promoted greater dietary self-control than positively framed text health warnings and control images, which did not increase dietary self-control. Overall, HWs primed healthier dietary decision making behavior, with negatively framed graphic HWs being most effective. Health warnings have potential to become an important element of obesity prevention. Copyright © 2018 Elsevier Ltd. All rights reserved.

An Alternative Nested Reading Frame May Participate in the Stress-Dependent Expression of a Plant Gene

PubMed Central

Sheshukova, Ekaterina V.; Komarova, Tatiana V.; Ershova, Natalia M.; Shindyapina, Anastasia V.; Dorokhov, Yuri L.

2017-01-01

Although plants as sessile organisms are affected by a variety of stressors in the field, the stress factors for the above-ground and underground parts of the plant and their gene expression profiles are not the same. Here, we investigated NbKPILP, a gene encoding a new member of the ubiquitous, pathogenesis-related Kunitz peptidase inhibitor (KPI)-like protein family, that we discovered in the genome of Nicotiana benthamiana and other representatives of the Solanaceae family. The NbKPILP gene encodes a protein that has all the structural elements characteristic of KPI but in contrast to the proven A. thaliana KPI (AtKPI), it does not inhibit serine peptidases. Unlike roots, NbKPILP mRNA and its corresponding protein were not detected in intact leaves, but abiotic and biotic stressors drastically affected NbKPILP mRNA accumulation. In search of the causes of suppressed NbKPILP mRNA accumulation in leaves, we found that the NbKPILP gene is “matryoshka,” containing an alternative nested reading frame (ANRF) encoding a 53-amino acid (aa) polypeptide (53aa-ANRF) which has an amphipathic helix (AH). We confirmed ANRF expression experimentally. A vector containing a GFP-encoding sequence was inserted into the NbKPILP gene in frame with 53aa-ANRF, resulting in a 53aa-GFP fused protein that localized in the membrane fraction of cells. Using the 5′-RACE approach, we have shown that the expression of ANRF was not explained by the existence of a cryptic promoter within the NbKPILP gene but was controlled by the maternal NbKPILP mRNA. We found that insertion of mutations destroying the 53aa-ANRF AH resulted in more than a two-fold increase of the NbKPILP mRNA level. The NbKPILP gene represents the first example of ANRF functioning as a repressor of a maternal gene in an intact plant. We proposed a model where the stress influencing the translation initiation promotes the accumulation of NbKPILP and its mRNA in leaves. PMID:29312392

An Alternative Nested Reading Frame May Participate in the Stress-Dependent Expression of a Plant Gene.

PubMed

Sheshukova, Ekaterina V; Komarova, Tatiana V; Ershova, Natalia M; Shindyapina, Anastasia V; Dorokhov, Yuri L

2017-01-01

Although plants as sessile organisms are affected by a variety of stressors in the field, the stress factors for the above-ground and underground parts of the plant and their gene expression profiles are not the same. Here, we investigated NbKPILP , a gene encoding a new member of the ubiquitous, pathogenesis-related Kunitz peptidase inhibitor (KPI)-like protein family, that we discovered in the genome of Nicotiana benthamiana and other representatives of the Solanaceae family. The NbKPILP gene encodes a protein that has all the structural elements characteristic of KPI but in contrast to the proven A. thaliana KPI (AtKPI), it does not inhibit serine peptidases. Unlike roots, NbKPILP mRNA and its corresponding protein were not detected in intact leaves, but abiotic and biotic stressors drastically affected NbKPILP mRNA accumulation. In search of the causes of suppressed NbKPILP mRNA accumulation in leaves, we found that the NbKPILP gene is "matryoshka," containing an alternative nested reading frame (ANRF) encoding a 53-amino acid (aa) polypeptide (53aa-ANRF) which has an amphipathic helix (AH). We confirmed ANRF expression experimentally. A vector containing a GFP-encoding sequence was inserted into the NbKPILP gene in frame with 53aa-ANRF, resulting in a 53aa-GFP fused protein that localized in the membrane fraction of cells. Using the 5'-RACE approach, we have shown that the expression of ANRF was not explained by the existence of a cryptic promoter within the NbKPILP gene but was controlled by the maternal NbKPILP mRNA. We found that insertion of mutations destroying the 53aa-ANRF AH resulted in more than a two-fold increase of the NbKPILP mRNA level. The NbKPILP gene represents the first example of ANRF functioning as a repressor of a maternal gene in an intact plant. We proposed a model where the stress influencing the translation initiation promotes the accumulation of NbKPILP and its mRNA in leaves.

Tissue specific expression of the retinoic acid receptor-beta 2: regulation by short open reading frames in the 5'-noncoding region

PubMed Central

1994-01-01

The 40-S subunit of eukaryotic ribosomes binds to the capped 5'-end of mRNA and scans for the first AUG in a favorable sequence context to initiate translation. Most eukaryotic mRNAs therefore have a short 5'- untranslated region (5'-UTR) and no AUGs upstream of the translational start site; features that seem to assure efficient translation. However, approximately 5-10% of all eukaryotic mRNAs, particularly those encoding for regulatory proteins, have complex leader sequences that seem to compromise translational initiation. The retinoic-acid- receptor-beta 2 (RAR beta 2) mRNA is such a transcript with a long (461 nucleotides) 5'-UTR that contains five, partially overlapping, upstream open reading frames (uORFs) that precede the major ORF. We have begun to investigate the function of this complex 5'-UTR in transgenic mice, by introducing mutations in the start/stop codons of the uORFs in RAR beta 2-lacZ reporter constructs. When we compared the expression patterns of mutant and wild-type constructs we found that these mutations affected expression of the downstream RAR beta 2-ORF, resulting in an altered regulation of RAR beta 2-lacZ expression in heart and brain. Other tissues were unaffected. RNA analysis of adult tissues demonstrated that the uORFs act at the level of translation; adult brains and hearts of transgenic mice carrying a construct with either the wild-type or a mutant UTR, had the same levels of mRNA, but only the mutant produced protein. Our study outlines an unexpected role for uORFs: control of tissue-specific and developmentally regulated gene expression. PMID:7962071

Molecular cloning of hsf1 and hsbp1 cDNAs, and the expression of hsf1, hsbp1 and hsp70 under heat stress in the sea cucumber Apostichopus japonicus.

PubMed

Xu, Dongxue; Sun, Lina; Liu, Shilin; Zhang, Libin; Yang, Hongsheng

2016-08-01

The heat shock response (HSR) is known for the elevated synthesis of heat shock proteins (HSPs) under heat stress, which is mediated primarily by heat shock factor 1 (HSF1). Heat shock factor binding protein 1 (HSBP1) and feedback control of heat shock protein 70 (HSP70) are major regulators of the activity of HSF1. We obtained full-length cDNA of genes hsf1 and hsbp1 in the sea cucumber Apostichopus japonicus, which are the second available for echinoderm (after Strongylocentrotus purpuratus), and the first available for holothurian. The full-length cDNA of hsf1 was 2208bp, containing a 1326bp open reading frame encoding 441 amino acids. The full-length cDNA of hsbp1 was 2850bp, containing a 225bp open reading frame encoding 74 amino acids. The similarities of A. japonicus HSF1 with other species are low, and much higher similarity identities of A. japonicus HSBP1 were shared. Phylogenetic trees showed that A. japonicus HSF1 and HSBP1 were clustered with sequences from S. purpuratus, and fell into distinct clades with sequences from mollusca, arthropoda and vertebrata. Analysis by real-time PCR showed hsf1 and hsbp1 mRNA was expressed constitutively in all tissues examined. The expression of hsf1, hsbp1 and hsp70 in the intestine at 26°C was time-dependent. The results of this study might provide new insights into the regulation of heat shock response in this species. Copyright © 2016. Published by Elsevier Inc.

Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi.

PubMed

Deng, Youjin; Zhang, Qihui; Ming, Ray; Lin, Longji; Lin, Xiangzhi; Lin, Yiying; Li, Xiao; Xie, Baogui; Wen, Zhiqiang

2016-06-30

Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing. The roughly 72 kb genome shows all major features found in other Hypocreales: 14 common protein genes, large and small subunit rRNAs genes and 27 tRNAs genes. Gene arrangement comparison showed conserved gene orders in Hypocreales mitochondria are relatively conserved, with the exception of Acremonium chrysogenum and Acremonium implicatum. Mitochondrial genome comparison also revealed that intron length primarily contributes to mitogenome size variation. Seventeen introns were detected in six conserved genes: five in cox1, four in rnl, three in cob, two each in atp6 and cox3, and one in cox2. Four introns were found to contain two introns or open reading frames: cox3-i2 is a twintron containing two group IA type introns; cox2-i1 is a group IB intron encoding two homing endonucleases; and cox1-i4 and cox1-i3 both contain two open reading frame (ORFs). Analyses combining secondary intronic structures, insertion sites, and similarities of homing endonuclease genes reveal two group IA introns arranged side by side within cox3-i2. Mitochondrial data for H. aurantius provides the basis for further studies relating to population genetics and species identification.

Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi

PubMed Central

Deng, Youjin; Zhang, Qihui; Ming, Ray; Lin, Longji; Lin, Xiangzhi; Lin, Yiying; Li, Xiao; Xie, Baogui; Wen, Zhiqiang

2016-01-01

Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing. The roughly 72 kb genome shows all major features found in other Hypocreales: 14 common protein genes, large and small subunit rRNAs genes and 27 tRNAs genes. Gene arrangement comparison showed conserved gene orders in Hypocreales mitochondria are relatively conserved, with the exception of Acremonium chrysogenum and Acremonium implicatum. Mitochondrial genome comparison also revealed that intron length primarily contributes to mitogenome size variation. Seventeen introns were detected in six conserved genes: five in cox1, four in rnl, three in cob, two each in atp6 and cox3, and one in cox2. Four introns were found to contain two introns or open reading frames: cox3-i2 is a twintron containing two group IA type introns; cox2-i1 is a group IB intron encoding two homing endonucleases; and cox1-i4 and cox1-i3 both contain two open reading frame (ORFs). Analyses combining secondary intronic structures, insertion sites, and similarities of homing endonuclease genes reveal two group IA introns arranged side by side within cox3-i2. Mitochondrial data for H. aurantius provides the basis for further studies relating to population genetics and species identification. PMID:27376282

Purification, cDNA cloning, and regulation of lysophospholipase from rat liver.

PubMed

Sugimoto, H; Hayashi, H; Yamashita, S

1996-03-29

A lysophospholipase was purified 506-fold from rat liver supernatant. The preparation gave a single 24-kDa protein band on SDS-polyacrylamide gel electrophoresis. The enzyme hydrolyzed lysophosphatidylcholine, lysophosphatidylethanolamine, lysophosphatidylinositol, lysophosphatidylserine, and 1-oleoyl-2-acetyl-sn-glycero-3-phosphocholine at pH 6-8. The purified enzyme was used for the preparation of antibody and peptide sequencing. A cDNA clone was isolated by screening a rat liver lambda gt11 cDNA library with the antibody, followed by the selection of further extended clones from a lambda gt10 library. The isolated cDNA was 2,362 base pairs in length and contained an open reading frame encoding 230 amino acids with a Mr of 24,708. The peptide sequences determined were found in the reading frame. When the cDNA was expressed in Escherichia coli cells as the beta-galactosidase fusion, lysophosphatidylcholine-hydrolyzing activity was markedly increased. The deduced amino acid sequence showed significant similarity to Pseudomonas fluorescence esterase A and Spirulina platensis esterase. The three sequences contained the GXSXG consensus at similar positions. The transcript was found in various tissues with the following order of abundance: spleen, heart, kidney, brain, lung, stomach, and testis = liver. In contrast, the enzyme protein was abundant in the following order: testis, liver, kidney, heart, stomach, lung, brain, and spleen. Thus the mRNA abundance disagreed with the level of the enzyme protein in liver, testis, and spleen. When HL-60 cells were induced to differentiate into granulocytes with dimethyl sulfoxide, the 24-kDa lysophospholipase protein increased significantly, but the mRNA abundance remained essentially unchanged. Thus a posttranscriptional control mechanism is present for the regulation of 24-kDa lysophospholipase.

A stable RNA virus-based vector for citrus trees

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

Folimonov, Alexey S.; Folimonova, Svetlana Y.; Bar-Joseph, Moshe

Virus-based vectors are important tools in plant molecular biology and plant genomics. A number of vectors based on viruses that infect herbaceous plants are in use for expression or silencing of genes in plants as well as screening unknown sequences for function. Yet there is a need for useful virus-based vectors for woody plants, which demand much greater stability because of the longer time required for systemic infection and analysis. We examined several strategies to develop a Citrus tristeza virus (CTV)-based vector for transient expression of foreign genes in citrus trees using a green fluorescent protein (GFP) as a reporter.more » These strategies included substitution of the p13 open reading frame (ORF) by the ORF of GFP, construction of a self-processing fusion of GFP in-frame with the major coat protein (CP), or expression of the GFP ORF as an extra gene from a subgenomic (sg) mRNA controlled either by a duplicated CTV CP sgRNA controller element (CE) or an introduced heterologous CE of Beet yellows virus. Engineered vector constructs were examined for replication, encapsidation, GFP expression during multiple passages in protoplasts, and for their ability to infect, move, express GFP, and be maintained in citrus plants. The most successful vectors based on the 'add-a-gene' strategy have been unusually stable, continuing to produce GFP fluorescence after more than 4 years in citrus trees.« less

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.

Reframing Student Affairs Leadership: An Analysis of Organizational Frames of Reference and Locus of Control

ERIC Educational Resources Information Center

Tull, Ashley; Freeman, Jerrid P.

2011-01-01

Examined in this study were the identified frames of reference and locus of control used by 478 student affairs administrators. Administrator responses were examined to identify frames of reference most commonly used and their preference order. Locus of control most commonly used and the relationship between frames of reference and locus of…

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

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

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.

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

Using hidden Markov models and observed evolution to annotate viral genomes.

PubMed

McCauley, Stephen; Hein, Jotun

2006-06-01

ssRNA (single stranded) viral genomes are generally constrained in length and utilize overlapping reading frames to maximally exploit the coding potential within the genome length restrictions. This overlapping coding phenomenon leads to complex evolutionary constraints operating on the genome. In regions which code for more than one protein, silent mutations in one reading frame generally have a protein coding effect in another. To maximize coding flexibility in all reading frames, overlapping regions are often compositionally biased towards amino acids which are 6-fold degenerate with respect to the 64 codon alphabet. Previous methodologies have used this fact in an ad hoc manner to look for overlapping genes by motif matching. In this paper differentiated nucleotide compositional patterns in overlapping regions are incorporated into a probabilistic hidden Markov model (HMM) framework which is used to annotate ssRNA viral genomes. This work focuses on single sequence annotation and applies an HMM framework to ssRNA viral annotation. A description of how the HMM is parameterized, whilst annotating within a missing data framework is given. A Phylogenetic HMM (Phylo-HMM) extension, as applied to 14 aligned HIV2 sequences is also presented. This evolutionary extension serves as an illustration of the potential of the Phylo-HMM framework for ssRNA viral genomic annotation. The single sequence annotation procedure (SSA) is applied to 14 different strains of the HIV2 virus. Further results on alternative ssRNA viral genomes are presented to illustrate more generally the performance of the method. The results of the SSA method are encouraging however there is still room for improvement, and since there is overwhelming evidence to indicate that comparative methods can improve coding sequence (CDS) annotation, the SSA method is extended to a Phylo-HMM to incorporate evolutionary information. The Phylo-HMM extension is applied to the same set of 14 HIV2 sequences which are pre-aligned. The performance improvement that results from including the evolutionary information in the analysis is illustrated.

Pathogenic and multidrug-resistant Escherichia fergusonii from broiler chicken.

PubMed

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

2012-02-01

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

Chimeric bovine respiratory syncytial virus with attachment and fusion glycoproteins replaced by bovine parainfluenza virus type 3 hemagglutinin-neuraminidase and fusion proteins.

PubMed

Stope, M B; Karger, A; Schmidt, U; Buchholz, U J

2001-10-01

Chimeric bovine respiratory syncytial viruses (BRSV) expressing glycoproteins of bovine parainfluenza virus type 3 (BPIV-3) instead of BRSV glycoproteins were generated from cDNA. In the BRSV antigenome cDNA, the open reading frames of the major BRSV glycoproteins, attachment protein G and fusion protein F, were replaced individually or together by those of the BPIV-3 hemagglutinin-neuraminidase (HN) and/or fusion (F) glycoproteins. Recombinant virus could not be recovered from cDNA when the BRSV F open reading frame was replaced by the BPIV-3 F open reading frame. However, cDNA recovery of the chimeric virus rBRSV-HNF, with both glycoproteins replaced simultaneously, and of the chimeric virus rBRSV-HN, with the BRSV G protein replaced by BPIV-3 HN, was successful. The replication rates of both chimeras were similar to that of standard rBRSV. Moreover, rBRSV-HNF was neutralized by antibodies specific for BPIV-3, but not by antibodies specific to BRSV, demonstrating that the BRSV glycoproteins can be functionally replaced by BPIV-3 glycoproteins. In contrast, rBRSV-HN was neutralized by BRSV-specific antisera, but not by BPIV-3 specific sera, showing that infection of rBRSV-HN is mediated by BRSV F. Hemadsorption of cells infected with rBRSV-HNF and rBRSV-HN proved that BPIV-3 HN protein expressed by rBRSV is functional. Colocalization of the BPIV-3 glycoproteins with BRSV M protein was demonstrated by confocal laser scan microscopy. Moreover, protein analysis revealed that the BPIV-3 glycoproteins were present in chimeric virions. Taken together, these data indicate that the heterologous glycoproteins were not only expressed but were incorporated into the envelope of recombinant BRSV. Thus, the envelope glycoproteins derived from a member of the Respirovirus genus can together functionally replace their homologs in a Pneumovirus background.

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

PubMed Central

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

2010-01-01

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

Real-Time Detection and Reading of LED/LCD Displays for Visually Impaired Persons

PubMed Central

Tekin, Ender; Coughlan, James M.; Shen, Huiying

2011-01-01

Modern household appliances, such as microwave ovens and DVD players, increasingly require users to read an LED or LCD display to operate them, posing a severe obstacle for persons with blindness or visual impairment. While OCR-enabled devices are emerging to address the related problem of reading text in printed documents, they are not designed to tackle the challenge of finding and reading characters in appliance displays. Any system for reading these characters must address the challenge of first locating the characters among substantial amounts of background clutter; moreover, poor contrast and the abundance of specular highlights on the display surface – which degrade the image in an unpredictable way as the camera is moved – motivate the need for a system that processes images at a few frames per second, rather than forcing the user to take several photos, each of which can take seconds to acquire and process, until one is readable. We describe a novel system that acquires video, detects and reads LED/LCD characters in real time, reading them aloud to the user with synthesized speech. The system has been implemented on both a desktop and a cell phone. Experimental results are reported on videos of display images, demonstrating the feasibility of the system. PMID:21804957

Transcription of the cottontail rabbit papillomavirus early region and identification of two E6 polypeptides in COS-7 cells.

PubMed Central

Barbosa, M S; Wettstein, F O

1987-01-01

Cottontail rabbit papillomavirus (CRPV) early proteins are present at very low levels in virus-induced tumors and cannot be detected by immunological methods. Furthermore, cells in culture are not readily transformed by the virus. To overcome these difficulties in identifying and characterizing the putative transforming protein(s) coded by the E6 open reading frame, the early cottontail rabbit papillomavirus region was expressed under the control of the late simian virus 40 promoter. Mapping of the transcripts in transiently transfected COS-7 cells indicated that transcription was initiated in the late region of simian virus 40. Two E6-coded polypeptides were identified, representing translation products initiated at the first and second AUG codons. Images PMID:3039182

Genomic analysis of WCP30 Phage of Weissella cibaria for Dairy Fermented Foods.

PubMed

Lee, Young-Duck; Park, Jong-Hyun

2017-01-01

In this study, we report the morphogenetic analysis and genome sequence of a new WCP30 phage of Weissella cibaria , isolated from a fermented food. Based on its morphology, as observed by transmission electron microscopy, WCP30 phage belongs to the family Siphoviridae . Genomic analysis of WCP30 phage showed that it had a 33,697-bp double-stranded DNA genome with 41.2% G+C content. Bioinformatics analysis of the genome revealed 35 open reading frames. A BLASTN search showed that WCP30 phage had low sequence similarity compared to other phages infecting lactic acid bacteria. This is the first report of the morphological features and complete genome sequence of WCP30 phage, which may be useful for controlling the fermentation of dairy foods.

A tapeworm molecule manipulates vitellogenin expression in the beetle Tenebrio molitor

PubMed Central

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

2006-01-01

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

MicroRNA-mediated species-specific attenuation of influenza A virus.

PubMed

Perez, Jasmine T; Pham, Alissa M; Lorini, Maria H; Chua, Mark A; Steel, John; tenOever, Benjamin R

2009-06-01

Influenza A virus leads to yearly epidemics and sporadic pandemics. Present prophylactic strategies focus on egg-grown, live, attenuated influenza vaccines (LAIVs), in which attenuation is generated by conferring temperature sensitivity onto the virus. Here we describe an alternative approach to attenuating influenza A virus based on microRNA-mediated gene silencing. By incorporating nonavian microRNA response elements (MREs) into the open-reading frame of the viral nucleoprotein, we generate reassortant LAIVs for H1N1 and H5N1 that are attenuated in mice but not in eggs. MRE-based LAIVs show a greater than two-log reduction in mortality compared with control viruses lacking MREs and elicit a diverse antibody response. This approach might be combined with existing LAIVs to increase attenuation and improve vaccine safety.

Current control of PMSM based on maximum torque control reference frame

NASA Astrophysics Data System (ADS)

Ohnuma, Takumi

2017-07-01

This study presents a new method of current controls of PMSMs (Permanent Magnet Synchronous Motors) based on a maximum torque control reference frame, which is suitable for high-performance controls of the PMSMs. As the issues of environment and energy increase seriously, PMSMs, one of the AC motors, are becoming popular because of their high-efficiency and high-torque density in various applications, such as electric vehicles, trains, industrial machines, and home appliances. To use the PMSMs efficiently, a proper current control of the PMSMs is necessary. In general, a rotational coordinate system synchronizing with the rotor is used for the current control of PMSMs. In the rotating reference frame, the current control is easier because the currents on the rotating reference frame can be expressed as a direct current in the controller. On the other hand, the torque characteristics of PMSMs are non-linear and complex; the PMSMs are efficient and high-density though. Therefore, a complicated control system is required to involve the relation between the torque and the current, even though the rotating reference frame is adopted. The maximum torque control reference frame provides a simpler way to control efficiently the currents taking the torque characteristics of the PMSMs into consideration.

Assigning poetry reading as a way of introducing students to qualitative data analysis.

PubMed

Raingruber, Bonnie

2009-08-01

The aim of the paper is to explain how poetry reading can be used to teach interpretive analysis of qualitative data. A number of studies were located in the nursing literature that focused on using poetry to help students develop empathy for patients, to teach students to reflect on their own practice, and to assist them in developing self-understanding. No studies were found that described the use of poetry reading as a way of teaching the skill of interpretive analysis. There are, however, a number of parallels between the principles of poetry reading and qualitative analysis that suggest that this method of teaching would be successful. International papers published on PubMed, Medline, and CINAHL were reviewed to identify challenges facing educators and ways of teaching the process of qualitative data analysis using poetry reading. Using poetry reading to teach skills of qualitative data analysis helps motivate students, cultivates a reflective mindset, and develops the skill of working as a member of an interpretive group. Framing interpretive work as being like reading poetry helps students pick up more quickly on the art that is a major component of the work. This approach also helps students learn the importance of cultural and contextual particulars as they begin analyzing qualitative data. Using poetry reading to introduce students to the complex skill of qualitative data analysis is an effective pedagogical strategy.

Balancing Selection of a Frame-Shift Mutation in the MRC2 Gene Accounts for the Outbreak of the Crooked Tail Syndrome in Belgian Blue Cattle

PubMed Central

Li, Wanbo; Dive, Marc; Tamma, Nico; Michaux, Charles; Druet, Tom; Huijbers, Ivo J.; Isacke, Clare M.; Coppieters, Wouter; Georges, Michel; Charlier, Carole

2009-01-01

We herein describe the positional identification of a 2-bp deletion in the open reading frame of the MRC2 receptor causing the recessive Crooked Tail Syndrome in cattle. The resulting frame-shift reveals a premature stop codon that causes nonsense-mediated decay of the mutant messenger RNA, and the virtual absence of functional Endo180 protein in affected animals. Cases exhibit skeletal anomalies thought to result from impaired extracellular matrix remodeling during ossification, and as of yet unexplained muscular symptoms. We demonstrate that carrier status is very significantly associated with desired characteristics in the general population, including enhanced muscular development, and that the resulting heterozygote advantage caused a selective sweep which explains the unexpectedly high frequency (25%) of carriers in the Belgian Blue Cattle Breed. PMID:19779552

Can we make a carpet smart enough to detect falls?

PubMed

Muheidat, Fadi; Tyrer, Harry W

2016-08-01

In this paper, we have enhanced smart carpet, which is a floor based personnel detector system, to detect falls using a faster but low cost processor. Our hardware front end reads 128 sensors, with sensors output a voltage due to a person walking or falling on the carpet. The processor is Jetson TK1, which provides more computing power than before. We generated a dataset with volunteers who walked and fell to test our algorithms. Data obtained allowed examining data frames (a frame is a single scan of the carpet sensors) read from the data acquisition system. We used different algorithms and techniques, and varied the windows size of number of frames (WS ≥ 1) and threshold (TH) to build our data set, which later used machine learning to help decide a fall or no fall. We then used the dataset obtained from applying a set of fall detection algorithms and the video recorded for the fall pattern experiments to train a set of classifiers using multiple test options using the Weka framework. We measured the sensitivity and specificity of the system and other metrics for intelligent detection of falls. Results showed that Computational Intelligence techniques detect falls with 96.2% accuracy and 81% sensitivity and 97.8% specificity. In addition to fall detection, we developed a database system and web applications to retain these data for years. We can display this data in realtime and for all activities in the carpet for extensive data analysis any time in the future.

Origins of genes: "big bang" or continuous creation?

PubMed Central

Keese, P K; Gibbs, A

1992-01-01

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. PMID:1329098

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

PubMed Central

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

2015-01-01

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

A CGMMV genome-replicon vector with partial sequences of coat protein gene efficiently expresses GFP in Nicotiana benthamiana.

PubMed

Jailani, A Abdul Kader; Solanki, Vikas; Roy, Anirban; Sivasudha, T; Mandal, Bikash

2017-04-02

A highly infectious clone of Cucumber green mottle mosaic virus (CGMMV), a cucurbit-infecting tobamovirus was utilized for designing of gene expression vectors. Two versions of vector were examined for their efficacy in expressing the green fluorescent protein (GFP) in Nicotiana benthamiana. When the GFP gene was inserted at the stop codon of coat protein (CP) gene of the CGMMV genome without any read-through codon, systemic expression of GFP, as well as virion formation and systemic symptoms expression were obtained in N. benthamiana. The qRT-PCR analysis showed 23 fold increase of GFP over actin at 10days post inoculation (dpi), which increased to 45 fold at 14dpi and thereafter the GFP expression was significantly declined. Further, we show that when the most of the CP sequence is deleted retaining only the first 105 nucleotides, the shortened vector containing GFP in frame of original CP open reading frame (ORF) resulted in 234 fold increase of GFP expression over actin at 5dpi in N. benthamiana without the formation of virions and disease symptoms. Our study demonstrated that a simple manipulation of CP gene in the CGMMV genome while preserving the translational frame of CP resulted in developing a virus-free, rapid and efficient foreign protein expression system in the plant. The CGMMV based vectors developed in this study may be potentially useful for the production of edible vaccines in cucurbits. Copyright © 2017 Elsevier B.V. All rights reserved.

Reducing the Read Noise of HAWAII-2RG Detector Systems with Improved Reference Sampling and Subtraction (IRS2)

NASA Technical Reports Server (NTRS)

Rauscher, Bernard J.; Arendt, Richard G.; Fixsen, D. J.; Lander, Matthew; Lindler, Don; Loose, Markus; Moseley, S. H.; Wilson, Donna V.; Xenophontos, Christos

2012-01-01

IRS2 is a Wiener-optimal approach to using all of the reference information that Teledyne's HAWAII-2RG detector arrays provide. Using a new readout pattern, IRS2 regularly interleaves reference pixels with the normal pixels during readout. This differs from conventional clocking, in which the reference pixels are read out infrequently, and only in a few rows and columns around the outside edges of the detector array. During calibration, the data are processed in Fourier space, which is <;:lose to the noise's eigenspace. Using IRS2, we have reduced the read noise of the James Webb Space Telescope Near Infrared Spectrograph by 15% compared to conventional readout. We are attempting to achieve further gains by calibrating out recently recognized non-stationary noise that appears at the frame rate.

Surface developmental dyslexia is as prevalent as phonological dyslexia when appropriate control groups are employed.

PubMed

Wybrow, Dean P; Hanley, J Richard

2015-01-01

Previous investigations of the incidence of developmental surface and phonological dyslexia using reading-age-matched control groups have identified many more phonological dyslexics (poor nonword reading relative to irregular-word reading) than surface dyslexics (poor irregular-word reading relative to nonword reading). However, because the measures that have been used to estimate reading age include irregular-word reading ability, they appear inappropriate for assessing the incidence of surface dyslexia. The current study used a novel method for generating control groups whose reading ability was matched to that of the dyslexic sample. The incidence of surface dyslexia was assessed by comparing dyslexic performance with that of a control group who were matched with the dyslexics on a test of nonword reading. The incidence of phonological dyslexia was assessed with reference to a control group who were matched with the dyslexics at irregular-word reading. These control groups led to the identification of an approximately equal number of children with surface and phonological dyslexia. It appeared that selecting control participants who were matched with dyslexics for reading age led to the recruitment of individuals with relatively high nonword reading scores relative to their irregular-word reading scores compared with other types of control group. The theoretical implications of these findings are discussed.

Functional characterization of the triple gene block 1 (TGB1) gene of Pepino mosaic virus in tomato

USDA-ARS?s Scientific Manuscript database

Pepino mosaic virus (PepMV) has caused serious economic losses to many greenhouse tomato productions around the world. This potexvirus genome contains five major open reading frames (ORFs) encoding for a 164-kDa RNA-dependent RNA polymerase (RdRp), three triple gene block (TGB) proteins of 26, 14 an...

Complete genome sequence of Paris mosaic necrosis virus, a distinct member of the genus Potyvirus

USDA-ARS?s Scientific Manuscript database

The complete genomic sequence of a novel potyvirus was determined from Paris polyphylla var. yunnanensis. Its genomic RNA consists of 9,660 nucleotides (nt) excluding the 3’-terminal poly (A) tail, containing a single open reading frame (ORF) encoding a large polyprotein. The virus shares 52.1-69.7%...

Immunogenic Peptides (Vaccines) for the Treatment of Prostate and Breast Cancer | NCI Technology Transfer Center | TTC

Cancer.gov

Researchers at the NCI have developed a novel treatment for prostate and breast cancer using synthetic peptides derived from TARP, the T cell receptor gamma alternate reading frame protein. These immunogenic peptides from TARP elicit an immune response, triggering T cells to kill only the cancer cells within a patient.

Frames of Interaction in Dynamic Assessment: Developmental Diagnoses of Second Language Learning

ERIC Educational Resources Information Center

Poehner, Matthew E.; van Compernolle, Remi A.

2011-01-01

The Zone of Proximal Development (ZPD), first proposed by the Russian psychologist L.S. Vygotsky, is frequently cited as the theoretical basis behind Dynamic Assessment (DA). However, this concept has led to varied interpretations and practices in education. This paper outlines readings of the ZPD that motivate many current approaches to DA and…

Story Content as a Factor in Children's Moral Judgments.

ERIC Educational Resources Information Center

Moran, James D., III

This study investigates effects of perceived rule-breaking on the moral reasoning of young children. Thirty first-grade children (15 males and 15 females) were read 10 randomly ordered moral judgment stories by one of three experimenters. Each story was accompanied by a two-frame cartoon-like drawing depicting the action. Two stories of each of…

Whole-genome sequence of “Candidatus Liberibacter solanacearum” strain R1 from California

USDA-ARS?s Scientific Manuscript database

The draft whole-genome sequence of “Candidatus Liberibacter solanacearum” strain R1, isolated from a tomato plant in California, United States, is reported. The R1 strain genome is 1,204,257 bp in size (G+C content of 35.3%), encoding 1,101 open reading frames and 57 RNA genes....

NUCLEOTIDE SEQUENCING AND TRANSCRIPTIONAL MAPPING OF THE GENES ENCODING BIPHENYL DIOXYGENASE, A MULTICOM- PONENT 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. Six open reading frames were identified, four of which are homologous to the components of toluene dioxy...

Complete Genome Sequence of the Mesoplasma florum W37 Strain

PubMed Central

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

2013-01-01

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

Using Every Word and Image: Framing Graphic Novel Instruction in the Expanded Four Resources Model

ERIC Educational Resources Information Center

Meyer, Carla K.; Jiménez, Laura M.

2017-01-01

In many classrooms, teachers have started to incorporate graphic novels in classroom instruction. However, research has suggested that some readers may have limited understanding of how to read graphic novels, which can create challenges for teachers using the medium. Drawing from a larger study, this article highlights two cases, an expert…

Maintaining Developmentally Appropriate Literacy Practices in Standardized Classrooms: A Freirean Framed Review of the Literature

ERIC Educational Resources Information Center

Erickson, Joy Dangora

2018-01-01

Scholars [e.g., Carlsson-Paige, N., McLaughlin, G., & Almon, J. (2015). Reading instruction in kindergarten: Little to gain and much to lose. Retrieved December 11, 2015, from https://www.sarahlawrence.edu/cdi/media/pdf/ReadinginKindergartenreport.pdf] warn that outcome-oriented, kindergarten, literacy standards may encourage an overreliance…

A Journey Backwards: History through Style in Children's Fiction

ERIC Educational Resources Information Center

Ringrose, Christopher

2007-01-01

A & C Black's "Flashbacks" series invites its readers to "Read a "Flashback"..take a journey backwards in time". There are several ways in which children's fiction has encouraged its readers to engage with and care about history: through the presence of ghosts, through frame stories, time travel, or simply setting the narrative in the past.…

Draft genome sequence of “Candidatus Liberibacter asiaticus” from Diaphorina citri in Guangdong, China

USDA-ARS?s Scientific Manuscript database

The draft genome sequence of “Candidatus Liberibacter asiaticus” strain YCPsy from an Asian citrus psyllid (Diaphorina citri) in Guangdong of China is reported. The YCPsy strain has a genome size of 1,233,647 bp, 36.5% G+C content, 1,171 open reading frames (ORFs), and 53 RNAs....

PRIMARY STRUCTURE OF THE CYTOCHROME P450 LANOSTEROL 14A-DEMETHYLASE GENE FROM CANDIDA TROPICALIS

EPA Science Inventory

We report the nucleotide sequence of the gene and flanking DNA for the cytochrome P450 lanosterol 14 alpha-demethylase (14DM) from the yeast Candida tropicalis ATCC750. An open reading frame (ORF) of 528 codons encoding a 60.9-kD protein is identified. This ORF includes a charact...

Antibody recognition of porcine circovirus type 2 capsid protein epitopes after vaccination, infection, and disease

USDA-ARS?s Scientific Manuscript database

Open reading frame 2 (ORF2) of porcine circovirus type 2 (PCV2) codes for the 233-amino-acid capsid protein (CP). Baculovirus-based vaccines that express only ORF2 are protective against clinical disease following experimental challenge or natural infection. The goal of this study was to identify re...

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

USDA-ARS?s Scientific Manuscript database

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

Complete Genome Sequence of a Genomovirus Associated with Common Bean Plant Leaves in Brazil.

PubMed

Lamas, Natalia Silva; Fontenele, Rafaela Salgado; Melo, Fernando Lucas; Costa, Antonio Felix; Varsani, Arvind; Ribeiro, Simone Graça

2016-11-10

A new genomovirus has been identified in three common bean plants in Brazil. This virus has a circular genome of 2,220 nucleotides and 3 major open reading frames. It shares 80.7% genome-wide pairwise identity with a genomovirus recovered from Tongan fruit bat guano. Copyright © 2016 Lamas et al.

The Inner (and Unavoidable?) Violence of Reason: Re-Reading Heidegger via Education

ERIC Educational Resources Information Center

d'Agnese, Vasco

2015-01-01

Since Plato, Western thought has framed knowing as a method within "some realm of what is" and a predetermined "sphere of objects". The roots and the consequences of this stance towards reason and truth were noted by Heidegger, who equates the history of Western thought with the history of metaphysics. Since Plato, truth has…

Automated Yeast Transformation Protocol to Engineer S. cerevisiae Strains for Cellulosic Ethanol Production with Open Reading Frames that Express Proteins Binding to Xylose Isomerase Identified using Robotic Two-hybrid Screen

USDA-ARS?s Scientific Manuscript database

Commercialization of fuel ethanol production from lignocellulosic biomass has focused on engineering the glucose-fermenting industrial yeast Saccharomyces cerevisiae to utilize pentose sugars. Since S. cerevisiae naturally metabolizes xylulose, one approach involves introducing xylose isomerase (XI...

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

USDA-ARS?s Scientific Manuscript database

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. These techniques involve the production of full-length cDNA libraries as a source of plasmid-based clones to expres...

The RNA profile of porcine parvovirus 4, a Boca-like virus, is unique among the Parvoviruses

USDA-ARS?s Scientific Manuscript database

Phylogenetically, porcine parvovirus 4 (PPV4) is most related to bovine parvovirus 2 that has two open reading frames (ORFs), but its genome organization resembles that of members of the Bocavirus genus that has three ORFs. Although PPV4 transcribes its genome from a single promoter and the transcri...

Genome Sequence of JangDynasty, a Newly Isolated Mycobacteriophage

PubMed Central

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

2018-01-01

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

Complete Genome Sequence of Pseudomonas aeruginosa Phage AAT-1

PubMed Central

Andrade-Domínguez, Andrés

2016-01-01

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

Concepts and Directions for Literacy Coaching: Designing Critical Reform from the Ground Up

ERIC Educational Resources Information Center

Rodgers, Adrian

2014-01-01

A rapid proliferation of literacy coaching has occurred before adequate research could be undertaken to understand the interaction between coach and teacher. In this analysis of a study undertaken by a college campus-based coach working with teachers in a reading clinic setting, Rodgers applies 2 conceptual frames. The 1st conceptual frame…

Characterization of developmental and stress mediated expression of cinnamoyl-CoA reductase (CCR) in kenaf (Hibiscus cannabinus L.)

USDA-ARS?s Scientific Manuscript database

Cinnamoyl-CoA reductase (CCR) is an important enzyme for lignin biosynthesis as it catalyzes the first specific committed step in monolignol biosynthesis. We have cloned a full length coding sequence of CCR from kenaf (Hibiscus cannabinus L.), which contains a 1,020-bp open reading frame (ORF), enco...

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

USDA-ARS?s Scientific Manuscript database

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

Science from Kepler Collateral Data: 50 Kilosecond per Year from 13 Million Star?

NASA Technical Reports Server (NTRS)

Kolodziejczak, J. J.; Caldwell, D. A.

2011-01-01

As each Kepler frame is read out, light from each star in a CCD column accumulates in successive pixels as they wait for the next row to be read out. This accumulation is the same in the masked rows at the start of the readout and virtual rows at the end of the readout as it is in the science data. A range of these "smear" rows are added together for each long cadence and sent to the ground for calibration purposes. We will introduce and describe this smear collateral data, discuss and demonstrate its potential use for scientific studies exclusive of Kepler calibration,.

Framing preventive care messaging and cervical cancer screening in a health-insured population in South Africa: Implications for population-based communication?

PubMed

Adonis, Leegale; Paramanund, Jithen; Basu, Debashis; Luiz, John

2017-09-01

The impact of health message framing on cervical cancer screening uptake is poorly understood. In a prospective randomized control study with 748 females, aged 21-65 years with no Pap smear in the previous 3 years, they randomly received a loss-framed, gain-framed, or neutral health message (control) regarding cervical cancer screening by email. Screening rate in the control group was 9.58 percent (CI: 9.29%-9.87%), 5.71 percent (CI: 5.48%-6.98%) in the gain-framed group, and 8.53 percent (CI: 8.24%-8.81%) in the loss-framed group. Statistically there was no difference between the three screening rates. Framing of health messages may not be a significant consideration when communicating through emails.

Spontaneous mutations in the flhD operon generate motility heterogeneity in Escherichia coli biofilm.

PubMed

Horne, Shelley M; Sayler, Joseph; Scarberry, Nicholas; Schroeder, Meredith; Lynnes, Ty; Prüß, Birgit M

2016-11-08

Heterogeneity and niche adaptation in bacterial biofilm involve changes to the genetic makeup of the bacteria and gene expression control. We hypothesized that i) spontaneous mutations in the flhD operon can either increase or decrease motility and that ii) the resulting motility heterogeneity in the biofilm might lead to a long-term increase in biofilm biomass. We allowed the highly motile E. coli K-12 strain MC1000 to form seven- and fourteen-day old biofilm, from which we recovered reduced motility isolates at a substantially greater frequency (5.4 %) than from a similar experiment with planktonic bacteria (0.1 %). Biofilms formed exclusively by MC1000 degraded after 2 weeks. In contrast, biofilms initiated with a 1:1 ratio of MC1000 and its isogenic flhD::kn mutant remained intact at 4 weeks and the two strains remained in equilibrium for at least two weeks. These data imply that an 'optimal' biofilm may contain a mixture of motile and non-motile bacteria. Twenty-eight of the non-motile MC1000 isolates contained an IS1 element in proximity to the translational start of FlhD or within the open reading frames for FlhD or FlhC. Two isolates had an IS2 and one isolate had an IS5 in the open reading frame for FlhD. An additional three isolates contained deletions that included the RNA polymerase binding site, five isolates contained point mutations and small deletions in the open reading frame for FlhC. The locations of all these mutations are consistent with the lack of motility and further downstream within the flhD operon than previously published IS elements that increased motility. We believe that the location of the mutation within the flhD operon determines whether the effect on motility is positive or negative. To test the second part of our hypothesis where motility heterogeneity in a biofilm may lead to a long-term increase in biofilm biomass, we quantified biofilm biomass by MC1000, MC1000 flhD::kn, and mixtures of the two strains at ratios of 1:1, 10:1, and 1:10. After 3 weeks, biofilm of the mixed cultures contained up to five times more biomass than biofilm of each of the individual strains. Mutations in the flhD operon can exert positive or negative effects on motility, depending on the site of the mutation. We believe that this is a mechanism to generate motility heterogeneity within E. coli biofilm, which may help to maintain biofilm biomass over extended periods of time.

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

PubMed

Gallagher, Kristel M; Updegraff, John A

2011-07-01

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

Robust image alignment for cryogenic transmission electron microscopy.

PubMed

McLeod, Robert A; Kowal, Julia; Ringler, Philippe; Stahlberg, Henning

2017-03-01

Cryo-electron microscopy recently experienced great improvements in structure resolution due to direct electron detectors with improved contrast and fast read-out leading to single electron counting. High frames rates enabled dose fractionation, where a long exposure is broken into a movie, permitting specimen drift to be registered and corrected. The typical approach for image registration, with high shot noise and low contrast, is multi-reference (MR) cross-correlation. Here we present the software package Zorro, which provides robust drift correction for dose fractionation by use of an intensity-normalized cross-correlation and logistic noise model to weight each cross-correlation in the MR model and filter each cross-correlation optimally. Frames are reliably registered by Zorro with low dose and defocus. Methods to evaluate performance are presented, by use of independently-evaluated even- and odd-frame stacks by trajectory comparison and Fourier ring correlation. Alignment of tiled sub-frames is also introduced, and demonstrated on an example dataset. Zorro source code is available at github.com/CINA/zorro. Copyright © 2016 Elsevier Inc. All rights reserved.

Driving techniques for high frame rate CCD camera

NASA Astrophysics Data System (ADS)

Guo, Weiqiang; Jin, Longxu; Xiong, Jingwu

2008-03-01

This paper describes a high-frame rate CCD camera capable of operating at 100 frames/s. This camera utilizes Kodak KAI-0340, an interline transfer CCD with 640(vertical)×480(horizontal) pixels. Two output ports are used to read out CCD data and pixel rates approaching 30 MHz. Because of its reduced effective opacity of vertical charge transfer registers, interline transfer CCD can cause undesired image artifacts, such as random white spots and smear generated in the registers. To increase frame rate, a kind of speed-up structure has been incorporated inside KAI-0340, then it is vulnerable to a vertical stripe effect. The phenomena which mentioned above may severely impair the image quality. To solve these problems, some electronic methods of eliminating these artifacts are adopted. Special clocking mode can dump the unwanted charge quickly, then the fast readout of the images, cleared of smear, follows immediately. Amplifier is used to sense and correct delay mismatch between the dual phase vertical clock pulses, the transition edges become close to coincident, so vertical stripes disappear. Results obtained with the CCD camera are shown.

Detection of simulated microcalcifications in fixed mammary tissue: An ROC study of the effect of local versus global histogram equalization.

PubMed

Sund, T; Olsen, J B

2006-09-01

To investigate whether sliding window adaptive histogram equalization (SWAHE) of digital mammograms improves the detection of simulated calcifications, as compared to images normalized by global histogram equalization (GHE). Direct digital mammograms were obtained from mammary tissue phantoms superimposed with different frames. Each frame was divided into forty squares by a wire mesh, and contained granular calcifications randomly positioned in about 50% of the squares. Three radiologists read the mammograms on a display monitor. They classified their confidence in the presence of microcalcifications in each square on a scale of 1 to 5. Images processed with GHE were first read and used as a reference. In a later session, the same images processed with SWAHE were read. The results were compared using ROC methodology. When the total areas AZ were compared, the results were completely equivocal. When comparing the high-specificity partial ROC area AZ,0.2 below false-positive fraction (FPF) 0.20, two of the three observers performed best with the images processed with SWAHE. The difference was not statistically significant. When the reader's confidence threshold in malignancy is set at a high level, increasing the contrast of mammograms with SWAHE may enhance the visibility of microcalcifications without adversely affecting the false-positive rate. When the reader's confidence threshold is set at a low level, the effect of SWAHE is an increase of false positives. Further investigation is needed to confirm the validity of the conclusions.

UrQt: an efficient software for the Unsupervised Quality trimming of NGS data.

PubMed

Modolo, Laurent; Lerat, Emmanuelle

2015-04-29

Quality control is a necessary step of any Next Generation Sequencing analysis. Although customary, this step still requires manual interventions to empirically choose tuning parameters according to various quality statistics. Moreover, current quality control procedures that provide a "good quality" data set, are not optimal and discard many informative nucleotides. To address these drawbacks, we present a new quality control method, implemented in UrQt software, for Unsupervised Quality trimming of Next Generation Sequencing reads. Our trimming procedure relies on a well-defined probabilistic framework to detect the best segmentation between two segments of unreliable nucleotides, framing a segment of informative nucleotides. Our software only requires one user-friendly parameter to define the minimal quality threshold (phred score) to consider a nucleotide to be informative, which is independent of both the experiment and the quality of the data. This procedure is implemented in C++ in an efficient and parallelized software with a low memory footprint. We tested the performances of UrQt compared to the best-known trimming programs, on seven RNA and DNA sequencing experiments and demonstrated its optimality in the resulting tradeoff between the number of trimmed nucleotides and the quality objective. By finding the best segmentation to delimit a segment of good quality nucleotides, UrQt greatly increases the number of reads and of nucleotides that can be retained for a given quality objective. UrQt source files, binary executables for different operating systems and documentation are freely available (under the GPLv3) at the following address: https://lbbe.univ-lyon1.fr/-UrQt-.html .

Dynamics of ARF regulation that control senescence and cancer.

PubMed

Ko, Aram; Han, Su Yeon; Song, Jaewhan

2016-11-01

ARF is an alternative reading frame product of the INK4a/ARF locus, inactivated in numerous human cancers. ARF is a key regulator of cellular senescence, an irreversible cell growth arrest that suppresses tumor cell growth. It functions by sequestering MDM2 (a p53 E3 ligase) in the nucleolus, thus activating p53. Besides MDM2, ARF has numerous other interacting partners that induce either cellular senescence or apoptosis in a p53-independent manner. This further complicates the dynamics of the ARF network. Expression of ARF is frequently disrupted in human cancers, mainly due to epigenetic and transcriptional regulation. Vigorous studies on various transcription factors that either positively or negatively regulate ARF transcription have been carried out. However, recent focus on posttranslational modifications, particularly ubiquitination, indicates wider dynamic controls of ARF than previously known. In this review, we discuss the role and dynamic regulation of ARF in senescence and cancer. [BMB Reports 2016; 49(11): 598-606].

Power train and emission control: allocation procedure by OBD-II system for automotive technology

NASA Astrophysics Data System (ADS)

Kalita, Porag

2017-06-01

OBD-II, systems were designed to maintain low emissions of in use vehicles, including light and medium duty vehicles. In 1989, the California code of Regulations (CCR) known as OBD - II was adopted by the California Air Resource Board (CARB) and the objective to reduce hydrocarbon (HC) emission caused by malfunction of the vehicles emission control systems. OBD-II provides additional information to engineer for diagnosis and repair of emissions related problems. OBD-II, standardizes on the amount of memory (Freeze Frame) it uses to store the readings of the vehicle sensor when it logs on emission related Intermittent Trouble code (IT). The intent of OBD-II, systems is to detect most vehicle malfunctions when performance of a power train component or system deteriorates to the point that the vehicle’s HC emission exceed standard. The vehicle operator is notified at the time when the vehicle begins to marginally exceed emission standards, by illuminating the Malfunctions Indicator Light (MIL).

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

PubMed Central

Wright, Imogen A.; Travers, Simon A.

2014-01-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

Cellular Selenoprotein mRNA Tethering via Antisense Interactions with Ebola and HIV-1 mRNAs May Impact Host Selenium Biochemistry.

PubMed

Taylor, Ethan Will; Ruzicka, Jan A; Premadasa, Lakmini; Zhao, Lijun

2016-01-01

Regulation of protein expression by non-coding RNAs typically involves effects on mRNA degradation and/or ribosomal translation. The possibility of virus-host mRNA-mRNA antisense tethering interactions (ATI) as a gain-of-function strategy, via the capture of functional RNA motifs, has not been hitherto considered. We present evidence that ATIs may be exploited by certain RNA viruses in order to tether the mRNAs of host selenoproteins, potentially exploiting the proximity of a captured host selenocysteine insertion sequence (SECIS) element to enable the expression of virally-encoded selenoprotein modules, via translation of in-frame UGA stop codons as selenocysteine. Computational analysis predicts thermodynamically stable ATIs between several widely expressed mammalian selenoprotein mRNAs (e.g., isoforms of thioredoxin reductase) and specific Ebola virus mRNAs, and HIV-1 mRNA, which we demonstrate via DNA gel shift assays. The probable functional significance of these ATIs is further supported by the observation that, in both viruses, they are located in close proximity to highly conserved in-frame UGA stop codons at the 3' end of open reading frames that encode essential viral proteins (the HIV-1 nef protein and the Ebola nucleoprotein). Significantly, in HIV/AIDS patients, an inverse correlation between serum selenium and mortality has been repeatedly documented, and clinical benefits of selenium in the context of multi-micronutrient supplementation have been demonstrated in several well-controlled clinical trials. Hence, in the light of our findings, the possibility of a similar role for selenium in Ebola pathogenesis and treatment merits serious investigation.

Assessing Approaches to Teaching Systems Thinking: Reading Article vs. Game Play

NASA Astrophysics Data System (ADS)

Pfirman, S. L.; O'Garra, T.; Lee, J.; Bachrach, E.; Bachman, G.; Orlove, B. S.

2016-12-01

Problem-solving in the complex domain of climate change requires consideration of the dynamics of systems as wholes. The long time frame, coupled with multiple interacting elements is challenging to teach through traditionally linear approaches, such as lectures or reading. On the other hand some have claimed that games are potentially useful in teaching system skills, due to their iterative, interacting, and problem solving character. In this experiment, we evaluated the impact of the EcoChains: Arctic Crisis card game on participants' mental models using a `fuzzy cognitive mapping' approach. The study population included 41 participants randomly assigned to the treatment/game play n=21 and the control/reading illustrated article: n=20. To obtain cognitive maps from participants, the first step was explaining how to draw a map, using an unrelated map as an example. Following the explanation, participants were handed large sheets of paper and asked to write down all the concepts they could think of related to: Arctic marine & sea-ice ecosystems, including the species & inhabitants of these ecosystems, all the different factors that negatively affect the health of Arctic marine & sea-ice ecosystems, its species & inhabitants, all the different factors that positively affect the health of Arctic marine & sea-ice ecosystems, its species & inhabitants. Once participants had drafted their list of concepts, they were asked to construct maps with the concepts in the center followed by arrows drawn between them to represent the direction of relationships between concepts. After the intervention - either playing the EcoChains card game or reading the illustrated article - participants were handed back their maps, together with a different colored pencil from the one they used previously, and asked to adjust the maps based on what they had learned from playing Ecochains/reading the article. Results indicate that both playing EcoChains and reading an illustrated article with similar information, increased systems thinking. Assessment indicates that the text-based approach had greater quantitative gains as evaluated through the number of nodes and types of connections. Additional analysis is ongoing to examine potential differences in the quality of learning gains.

Designing Anti-Binge Drinking Prevention Messages: Message Framing vs. Evidence Type.

PubMed

Kang, Hannah; Lee, Moon J

2017-09-27

We investigated whether presenting anti-binge drinking health campaign messages in different message framing and evidence types influences college students' intention to avoid binge drinking, based on prospect theory (PT) and exemplification theory. A 2 (message framing: loss-framed message/gain-framed message) X 2 (evidence type: statistical/narrative) between-subjects factorial design with a control group was conducted with 156 college students. College students who were exposed to the loss-framed message condition exhibited a higher level of intention to avoid binge drinking in the near future than those who did not see any messages (the control group). This finding was mainly among non-binge drinkers. Regardless of evidence type, those who were exposed to the messages exhibited a higher level of intention to avoid binge drinking than those in the control group. This is also mainly among non-binge drinkers. We also found the main effects of message framing and evidence type on attitude toward the message and the main effect of message framing on attitude toward drinking.

Cloning, characterization, expression analysis and inhibition studies of a novel gene encoding Bowman-Birk type protease inhibitor from rice bean

USDA-ARS?s Scientific Manuscript database

This paper presents the first study describing the isolation, cloning and characterization of a full length gene encoding Bowman-Birk protease inhibitor (RbTI) from rice bean (Vigna umbellata). A full-length protease inhibitor gene with complete open reading frame of 327bp encoding 109 amino acids w...

Draft Genome Sequence of a Picorna-Like Virus Associated with Gill Tissue in Clinically Normal Brook Trout, Salvelinus fontinalis.

PubMed

Iwanowicz, Luke R; Iwanowicz, Deborah D; Adams, Cynthia R; Galbraith, Heather; Aunins, Aaron; Cornman, Robert S

2017-10-12

Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis , gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.

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

Treesearch

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

1999-01-01

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

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

USDA-ARS?s Scientific Manuscript database

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

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

USDA-ARS?s Scientific Manuscript database

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

The ferredoxin-thioredoxin reductase variable subunit gene from Anacystis nidulans.

PubMed

Szekeres, M; Droux, M; Buchanan, B B

1991-03-01

The ferredoxin-thioredoxin reductase variable subunit gene of Anacystis nidulans was cloned, and its nucleotide sequence was determined. A single-copy 219-bp open reading frame encoded a protein of 73 amino acid residues, with a calculated Mr of 8,400. The monocistronic transcripts were represented in a 400-base and a less abundant 300-base mRNA form.

Novel Readings: The History of a Writing Community by a Partial, Prejudiced, & Ignorant Historian

ERIC Educational Resources Information Center

King, Virginia

2013-01-01

In this article, I explore the history of a higher education writing community from its establishment in 2005 to the present day. In order to provide a model of community development which may be generalizable, this inherently "partial" and "prejudiced" Autoethnographic account is framed by themes taken from three of the novels of Jane Austen…

Deletion of Marek’s disease virus large subunit of ribonucleotide reductase (RR) impairs virus growth in vitro and in vivo

USDA-ARS?s Scientific Manuscript database

Marek’s disease virus (MDV), a highly cell-associated lymphotropic alphaherpesvirus, is the causative agent of a neoplastic disease in domestic chickens, called Marek’s disease (MD). In the unique long region of the MDV genome, open reading frames UL39 and UL40 encode the large and small subunits o...

Marek’s Disease Virus Encoded Ribonucleotide Reductase Large Subunit is not Essential for In Vitro Replication

USDA-ARS?s Scientific Manuscript database

Marek’s disease virus (MDV) infected cells express a viral ribonucleotide reductase (RR) that is distinguishable from that present in uninfected cells by monoclonal antibody T81. Open reading frames UL39 and UL40 of the MDV genome encode the large (RR1) and small (RR2) subunits of RR enzyme, respe...

Draft genome sequence of a picorna-like virus associated with gill tissue in clinically normal brook trout, Salvelinus fontinalis

USGS Publications Warehouse

Iwanowicz, Luke R.; Iwanowicz, Deborah; Adams, Cynthia; Galbraith, Heather S.; Aunins, Aaron W.; Cornman, Robert S.

2017-01-01

Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis, gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.

Common Ground between Form and Content: The Pragmatic Solution to the Bootstrapping Problem

ERIC Educational Resources Information Center

Oller, John W.

2005-01-01

The frame of reference for this article is second or foreign language (L2 or FL) acquisition, but the pragmatic bootstrapping hypothesis applies to language processing and acquisition in any context or modality. It is relevant to teaching children to read. It shows how connections between target language surface forms and their content can be made…

Erratum: ``Infrared Counterparts to Chandra X-Ray Sources in the Antennae'' (ApJ, 658, 319 [2007])

NASA Astrophysics Data System (ADS)

Clark, D. M.; Eikenberry, S. S.; Brandl, B. R.; Wilson, J. C.; Carson, J. C.; Henderson, C. P.; Hayward, T. L.; Barry, D. J.; Ptak, A. F.; Colbert, E. J. M.

2007-10-01

In equation (2), we incorrectly labeled one of the variables. Equations (1) and (2) should read:r1=ax1+by1+c,d1=dx1+ey1+f. (1) (2)These equations were used only to explain our image frame-tie method, and this change does not affect our results.

Genomic Sequences of Five Helicoverpa armigera Nucleopolyhedrovirus Genotypes from Spain That Differ in Their Insecticidal Properties

PubMed Central

Arrizubieta, Maite; Williams, Trevor; Caballero, Primitivo

2015-01-01

Helicoverpa armigera nucleopolyhedrovirus (HearNPV) has proved effective as the basis for various biological insecticides. Complete genome sequences of five Spanish HearNPV genotypes differed principally in the homologous regions (hrs) and the baculovirus repeat open reading frame (bro) genes, suggesting that they may be involved in the phenotypic differences observed among genotypes. PMID:26067949

Design and construction of a first-generation high-throughput integrated molecular biology platform for production of optimized synthetic genes and improved industrial strains

USDA-ARS?s Scientific Manuscript database

The molecular biological techniques for plasmid-based assembly and cloning of synthetic assembled gene open reading frames are essential for elucidating the function of the proteins encoded by the genes. These techniques involve the production of full-length cDNA libraries as a source of plasmid-bas...

Resurrecting Pragmatism as a Philosophical Frame for Understanding, Researching, and Developing Performance in the Small District Superintendency

ERIC Educational Resources Information Center

Ivory, Gary; McClellan, Rhonda; Hyle, Adrienne E.

2009-01-01

In this article, the authors propose that pragmatism is a perspective with great promise for understanding and researching the work of small district superintendents and developing the abilities of both pre-service students and in-service practitioners to do that work. They maintain, based on their reading of focus group interviews with small…

Child Readers and the Worlds of the Picture Book

ERIC Educational Resources Information Center

Baird, Adela; Laugharne, Janet; Maagerø, Eva; Tønnessen, Elise Seip

2016-01-01

Children as readers of picture books and the ways they respond to, and make meaning from, such texts are the focus of this article, which reports on a small-scale study undertaken in Norway and Wales, UK. The theoretical framing of the research draws on concepts of the multimodal ensemble in picture books and of the reading event as part of a…

Genome Sequence of JangDynasty, a Newly Isolated Mycobacteriophage.

PubMed

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

2018-05-24

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

Kittens! Inspired by Kittens! Undergraduate Theorists Inspired by YouTube

ERIC Educational Resources Information Center

Anderson, Diane Downer; Lewis, Mark; Peterson, Sarah; Griggs, Samantha; Grubb, Gina; Singer, Nicole; Fried, Simone; Krone, Elizabeth; Elko, Leigh; Narang, Jasmine

2010-01-01

A professor and students in an undergraduate honors research seminar were inspired to playfully link old and contemporary literacy theories to a 2.0 media artifact, the popular YouTube video Kittens! Inspired by Kittens! (KIbK) starring 6 year-old Maddie. In this article KIbK is theorized drawing on frames of school-based reading instruction,…

Mistaken identity of an open reading frame proposed for PCR-based identification of Mycoplasma bovis and the effect of polymorphisms and insertions on assay performance

USDA-ARS?s Scientific Manuscript database

Mycoplasma bovis is an important cause of disease in cattle and bison. Because the bacterium requires specialized growth conditions many diagnostic laboratories routinely use PCR to replace or complement conventional isolation and identification methods. A frequently used target of such assays is th...

Climbing robot. [caterpillar design

NASA Technical Reports Server (NTRS)

Kerley, James J. (Inventor); May, Edward L. (Inventor); Ecklund, Wayne D. (Inventor)

1993-01-01

A mobile robot for traversing any surface consisting of a number of interconnected segments, each interconnected segment having an upper 'U' frame member, a lower 'U' frame member, a compliant joint between the upper 'U' frame member and the lower 'U' frame member, a number of linear actuators between the two frame members acting to provide relative displacement between the frame members, a foot attached to the lower 'U' frame member for adherence of the segment to the surface, an inter-segment attachment attached to the upper 'U' frame member for interconnecting the segments, a power source connected to the linear actuator, and a computer/controller for independently controlling each linear actuator in each interconnected segment such that the mobile robot moves in a caterpillar like fashion.

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

PubMed Central

Breugelmans, Bert; Ansell, Brendan R. E.; Young, Neil D.; Amani, Parisa; Stroehlein, Andreas J.; Sternberg, Paul W.; Jex, Aaron R.; Boag, Peter R.; Hofmann, Andreas; Gasser, Robin B.

2015-01-01

All multicellular organisms studied to date have three right open reading frame kinase genes (designated riok-1, riok-2 and riok-3). Current evidence indicates that riok-1 and riok-2 have essential roles in ribosome biosynthesis, and that the riok-3 gene assists this process. In the present study, we conducted a detailed bioinformatic analysis of the riok gene family in 25 parasitic flatworms (platyhelminths) for which extensive genomic and transcriptomic data sets are available. We found that none of the flatworms studied have a riok-3 gene, which is unprecedented for multicellular organisms. We propose that, unlike in other eukaryotes, the loss of RIOK-3 from flatworms does not result in an evolutionary disadvantage due to the unique biology and physiology of this phylum. We show that the loss of RIOK-3 coincides with a loss of particular proteins associated with essential cellular pathways linked to cell growth and apoptosis. These findings indicate multiple, key regulatory functions of RIOK-3 in other metazoan species. Taking advantage of a known partial crystal structure of human RIOK-1, molecular modelling revealed variability in nucleotide binding sites between flatworm and human RIOK proteins. PMID:25976756

Single-cut genome editing restores dystrophin expression in a new mouse model of muscular dystrophy

PubMed Central

Amoasii, Leonela; Long, Chengzu; Li, Hui; Mireault, Alex A.; Shelton, John M.; Sanchez-Ortiz, Efrain; McAnally, John R.; Bhattacharyya, Samadrita; Schmidt, Florian; Grimm, Dirk; Hauschka, Stephen D.; Bassel-Duby, Rhonda; Olson, Eric N.

2017-01-01

Duchenne muscular dystrophy (DMD) is a severe, progressive muscle disease caused by mutations in the dystrophin gene. The majority of DMD mutations are deletions that prematurely terminate the dystrophin protein. Deletions of exon 50 of the dystrophin gene are among the most common single exon deletions causing DMD. Such mutations can be corrected by skipping exon 51, thereby restoring the dystrophin reading frame. Using clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9), we generated a DMD mouse model by deleting exon 50. These ΔEx50 mice displayed severe muscle dysfunction, which was corrected by systemic delivery of adeno-associated virus encoding CRISPR/Cas9 genome editing components. We optimized the method for dystrophin reading frame correction using a single guide RNA that created reframing mutations and allowed skipping of exon 51. In conjunction with muscle-specific expression of Cas9, this approach restored up to 90% of dystrophin protein expression throughout skeletal muscles and the heart of ΔEx50 mice. This method of permanently bypassing DMD mutations using a single cut in genomic DNA represents a step toward clinical correction of DMD mutations and potentially those of other neuromuscular disorders. PMID:29187645

Cloning and characterization of Bacillus subtilis iep, which has positive and negative effects on production of extracellular proteases.

PubMed

Tanaka, T; Kawata, M

1988-08-01

We have isolated a DNA fragment from Bacillus subtilis 168 which, when present in a high-copy plasmid, inhibited production of extracellular alkaline and neutral proteases. The gene responsible for this activity was referred to as iep. The open reading frame of iep was found to be incomplete in the cloned DNA fragment. When the intact iep gene was reconstructed after the missing part of the iep gene had been cloned, it showed an enhancing effect on the production of the extracellular proteases. The open reading frame encodes a polypeptide of 229 amino acids with a molecular weight of ca. 25,866. Deletion of two amino acids from the N-terminal half of the putative iep protein resulted in dual effects, i.e., a decrease in the inhibitory activity shown by the incomplete iep gene and a slight increase in the enhancing activity shown by the complete iep gene. These results show that the iep gene product is a bifunctional protein, containing inhibitory and enhancing activities for the exoprotease production in the N-terminal and C-terminal regions, respectively. It was found by genetic and functional analyses that iep lies very close to sacU.

Production of foot-and-mouth disease virus capsid proteins by the TEV protease.

PubMed

Puckette, Michael; Smith, Justin D; Gabbert, Lindsay; Schutta, Christopher; Barrera, José; Clark, Benjamin A; Neilan, John G; Rasmussen, Max

2018-06-10

Protective immunity to viral pathogens often includes production of neutralizing antibodies to virus capsid proteins. Many viruses produce capsid proteins by expressing a precursor polyprotein and related protease from a single open reading frame. The foot-and-mouth disease virus (FMDV) expresses a 3C protease (3Cpro) that cleaves a P1 polyprotein intermediate into individual capsid proteins, but the FMDV 3Cpro also degrades many host cell proteins and reduces the viability of host cells, including subunit vaccine production cells. To overcome the limitations of using the a wild-type 3Cpro in FMDV subunit vaccine expression systems, we altered the protease restriction sequences within a FMDV P1 polyprotein to enable production of FMDV capsid proteins by the Tobacco Etch Virus NIa protease (TEVpro). Separate TEVpro and modified FMDV P1 proteins were produced from a single open reading frame by an intervening FMDV 2A sequence. The modified FMDV P1 polyprotein was successfully processed by the TEVpro in both mammalian and bacterial cells. More broadly, this method of polyprotein production and processing may be adapted to other recombinant expression systems, especially plant-based expression. Published by Elsevier B.V.

In situ data analytics and indexing of protein trajectories.

PubMed

Johnston, Travis; Zhang, Boyu; Liwo, Adam; Crivelli, Silvia; Taufer, Michela

2017-06-15

The transition toward exascale computing will be accompanied by a performance dichotomy. Computational peak performance will rapidly increase; I/O performance will either grow slowly or be completely stagnant. Essentially, the rate at which data are generated will grow much faster than the rate at which data can be read from and written to the disk. MD simulations will soon face the I/O problem of efficiently writing to and reading from disk on the next generation of supercomputers. This article targets MD simulations at the exascale and proposes a novel technique for in situ data analysis and indexing of MD trajectories. Our technique maps individual trajectories' substructures (i.e., α-helices, β-strands) to metadata frame by frame. The metadata captures the conformational properties of the substructures. The ensemble of metadata can be used for automatic, strategic analysis within a trajectory or across trajectories, without manually identify those portions of trajectories in which critical changes take place. We demonstrate our technique's effectiveness by applying it to 26.3k helices and 31.2k strands from 9917 PDB proteins and by providing three empirical case studies. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

PubMed Central

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

1986-01-01

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

Nucleotide sequence of a resistance breaking mutant of southern bean mosaic virus.

PubMed

Lee, L; Anderson, E J

1998-01-01

SBMV-S is a resistance-breaking mutant of an Arkansas isolate of the bean strain of southern bean mosaic virus (SBMV-BARK) that is able to move systemically in Phaseolus vulgaris cvs. Pinto and Great Northern, whereas the wild-type SBMV-BARK causes local necrotic lesions and is restricted to the inoculated leaves of these hosts. Sequence analysis of the 4136 nucleotide genomes of SBMV-BARK and SBMV-S revealed seven nucleotide differences, but only four deduced amino acid changes. A single amino acid change occurred in the C-terminal region of the putative RNA-dependent RNA polymerase and three differences were identified in the N-terminal portion of the virus coat protein. SBMV-BARK and SBMV-S were compared with other sobemoviruses and were found to contain a high level of nucleotide sequence identity (91.3%) to SBMV-B. Unlike SBMV-B however, SBMV-BARK and SBMV-S contained four putative overlapping open reading frames, making them more similar in genome organization to the cowpea strain, SBMV-C. The possibility exists that mutations or even errors, that resulted in mis-identification of open reading frames, occurred in previously published information on nucleotide sequence and genomic organization for SBMV-B.

The virion glycoproteins of Ebola viruses are encoded in two reading frames and are expressed through transcriptional editing.

PubMed Central

Sanchez, A; Trappier, S G; Mahy, B W; Peters, C J; Nichol, S T

1996-01-01

In late 1994 and early 1995, Ebola (EBO) virus dramatically reemerged in Africa, causing human disease in the Ivory Coast and Zaire. Analysis of the entire glycoprotein genes of these viruses and those of other EBO virus subtypes has shown that the virion glycoprotein (130 kDa) is encoded in two reading frames, which are linked by transcriptional editing. This editing results in the addition of an extra nontemplated adenosine within a run of seven adenosines near the middle of the coding region. The primary gene product is a smaller (50-70 kDa), nonstructural, secreted glycoprotein, which is produced in large amounts and has an unknown function. Phylogenetic analysis indicates that EBO virus subtypes are genetically diverse and that the recent Ivory Coast isolate represents a new (fourth) subtype of EBO virus. In contrast, the EBO virus isolate from the 1995 outbreak in Kikwit, Zaire, is virtually identical to the virus that caused a similar epidemic in Yambuku, Zaire, almost 20 years earlier. This genetic stability may indicate that EBO viruses have coevolved with their natural reservoirs and do not change appreciably in the wild. Images Fig. 2 Fig. 3 PMID:8622982

Accumulation of RNA homologous to human papillomavirus type 16 open reading frames in genital precancers.

PubMed Central

Crum, C P; Nuovo, G; Friedman, D; Silverstein, S J

1988-01-01

The accumulation of human papillomavirus type 16 (HPV-16)-specific RNAs in tissue sections from biopsies of patients with genital precancers was studied by in situ hybridization with single-stranded 35S-labeled RNA. These analyses revealed that the most abundant early-region RNAs were derived from the E4 and E5 open reading frames (ORFs). RNAs homologous to the E6/E7 ORFs were also detected, whereas RNAs homologous to the intervening E1 ORF were not. This suggests that the E4 and E5 mRNAs are derived by splicing to the upstream E6/E7 ORFs, consistent with studies of HPV-11 in condylomata (L. T. Chow et al., Cancer Cells (Cold Spring Harbor) 5:55-72, 1987). Abundant RNAs homologous to the 5' portion of L1 were also detected. These RNAs were localized to the apical strata of the epithelium. HPV-16 RNAs accumulated in discrete regions of these lesions, and when present were most abundant in the upper cell layers of the precancerous epithelium. RNAs homologous to early ORFs were also detected in some germinal cells within the basal layer of the epithelium. Images PMID:2824859

Accumulation of RNA homologous to human papillomavirus type 16 open reading frames in genital precancers.

PubMed

Crum, C P; Nuovo, G; Friedman, D; Silverstein, S J

1988-01-01

The accumulation of human papillomavirus type 16 (HPV-16)-specific RNAs in tissue sections from biopsies of patients with genital precancers was studied by in situ hybridization with single-stranded 35S-labeled RNA. These analyses revealed that the most abundant early-region RNAs were derived from the E4 and E5 open reading frames (ORFs). RNAs homologous to the E6/E7 ORFs were also detected, whereas RNAs homologous to the intervening E1 ORF were not. This suggests that the E4 and E5 mRNAs are derived by splicing to the upstream E6/E7 ORFs, consistent with studies of HPV-11 in condylomata (L. T. Chow et al., Cancer Cells (Cold Spring Harbor) 5:55-72, 1987). Abundant RNAs homologous to the 5' portion of L1 were also detected. These RNAs were localized to the apical strata of the epithelium. HPV-16 RNAs accumulated in discrete regions of these lesions, and when present were most abundant in the upper cell layers of the precancerous epithelium. RNAs homologous to early ORFs were also detected in some germinal cells within the basal layer of the epithelium.

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

PubMed

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

2004-08-27

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

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

PubMed

Breugelmans, Bert; Ansell, Brendan R E; Young, Neil D; Amani, Parisa; Stroehlein, Andreas J; Sternberg, Paul W; Jex, Aaron R; Boag, Peter R; Hofmann, Andreas; Gasser, Robin B

2015-05-15

All multicellular organisms studied to date have three right open reading frame kinase genes (designated riok-1, riok-2 and riok-3). Current evidence indicates that riok-1 and riok-2 have essential roles in ribosome biosynthesis, and that the riok-3 gene assists this process. In the present study, we conducted a detailed bioinformatic analysis of the riok gene family in 25 parasitic flatworms (platyhelminths) for which extensive genomic and transcriptomic data sets are available. We found that none of the flatworms studied have a riok-3 gene, which is unprecedented for multicellular organisms. We propose that, unlike in other eukaryotes, the loss of RIOK-3 from flatworms does not result in an evolutionary disadvantage due to the unique biology and physiology of this phylum. We show that the loss of RIOK-3 coincides with a loss of particular proteins associated with essential cellular pathways linked to cell growth and apoptosis. These findings indicate multiple, key regulatory functions of RIOK-3 in other metazoan species. Taking advantage of a known partial crystal structure of human RIOK-1, molecular modelling revealed variability in nucleotide binding sites between flatworm and human RIOK proteins.

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

PubMed

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

2018-04-06

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

Accumulation of RNA homologous to human papillomavirus type 16 open reading frames in genital precancers

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

Crum, C.P.; Nuovo, G.; Friedman, D.

1988-01-01

The accumulation of human papillomavirus type 16 (HPV-16)-specific RNAs in tissue sections from biopsies of patients with genital precancers was studied by in situ hybridization with single-stranded /sup 35/S-labeled RNA. These analyses revealed that the most abundant early-region RNAs were derived from the E4 and E5 open reading frames (ORFs). RNAs homologous to the E6/E7 ORFs were also detected, whereas RNAs homologous to the intervening E1 ORF were not. This suggest that the E4 and E5 mRNAs are derived by splicing to the upstream E6/E7 ORFs, consistent with studies of HPV-11 in condylomata. Abundant RNAs homologous to the 5' portionmore » of L1 were also detected. These RNAs were localized to the apical strata of the epithelium. HPV-16 RNAs accumulated in discrete regions of these lesions, and when present were most abundant in the upper cell layers of the precancerous epithelium. RNAs homologous to early ORFs were also detected in some germinal cells within the basal layer of the epithelium.« less

Isolation of a novel human papillomavirus (type 51) from a cervical condyloma

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

Nuovo, G.J.; Crum, C.P.; Levine, R.U.

1988-04-01

The authors cloned the DNA from a novel human papillomavirus (HPV) present in a cervical condyloma. When DNA from this isolate was hybridized at high stringency with HPV types 1 through 50 (HPV-1 through HPV-50), it showed weak homology with HPV-6 and -16 and stronger homology with HPV-26. A detailed restriction endonuclease map was prepared which showed marked differences from the maps for other HPVs that have been isolated from the female genital tract. Reassociation kinetic analysis revealed that HPV-26 and this new isolate were less than 10% homologous; hence, the new isolate is a noel strain of HPV. Themore » approximate positions of the open reading frames of the new strain were surmised by hybridization with probes derived from individual open reading frames of HPV-16. In an analysis of 175 genital biopsies from patients with abnormal Papanicolaou smears, sequences hybridizing under highly stringent conditions to probes from this novel HPV type were found in 4.2, 6.1, and 2.4% of biopsies containing normal squamous epithelium, condylomata, and intraepithelial neoplasia, respectively. In addition, sequences homologous to probes from this novel isolate were detected in one of five cervical carcinomas examined.« less