Journal articles: 'Reading frame'

1

George, James F., Yasushi Matsuura, Jacquelyn A. Byrne, Eugene L. Liu, Denise R. Shaw, and John F. Kearney. "A Developmental Bias in Reading Frame Usage by Human Fetal Thymic TCRBDJ Transcripts is not Present in Genomic TCRBDJ Rearrangements." Developmental Immunology 7, no. 1 (1999): 9–15. http://dx.doi.org/10.1155/1999/16178.

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We have previously reported that reading-frame usage and functional diversification is developmentally regulated, with virtually all TCRB DJ mRNA transcripts using a single reading frame at 8 weeks of gestational age, tapering to 50% by adult life. We used the polymerase chain reaction to create genomic libraries of DJ rearrangements in the TCRB locus from thymuses at 7.7, 10, and 16 weeks of gestational age, and from adult thymuses. Clones were randomly picked and sequenced to determine junctional sequences and reading-frame utilization. The resulting data address the hypothesis that cells bearing genomic joints in reading frame one are preferentially selected during fetal life. This hypothesis predicts that reading- frame bias would also be observed among genomic DJ joints. Instead, we observed random utilization of the three possible D-region reading frames among genomic D1s1 => J1s1 joints during fetal life. Similar results were obtained at 7.7 weeks of gestational age in a second thymus in which both RNA and DNA were simultaneously isolated and used to create libraries of TCRBDJ transcripts or rearrangements. We conclude that reading-frame utilization is random among genomic D1s1-JB1s1 rearrangements and that the preferential usage of a single reading frame among mRNA transcripts of TCRB DJ transcripts is the result of preferential transcription of genomic TCRB DJ joints in a single reading frame, or that TCRB DJ transcripts have a longer half-life than transcripts in reading frames two or three.

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Tarlinton, D., A. Strasser, M. McLean, and A. Basten. "DH element reading frame selection is influenced by an Ig heavy chain transgene, but not by bcl-2." Journal of Immunology 154, no. 7 (April 1, 1995): 3341–50. http://dx.doi.org/10.4049/jimmunol.154.7.3341.

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Abstract Mouse B cell precursors containing Ig DHJH junctions in one particular reading frame are selectively lost during B cell development. In this register, arbitrarily referred to as reading frame 2, DHJH junctions give rise to an open reading frame starting upstream of the DH element and including the DHJH-peptide fused to the constant region of IgM. Expression of this protein, called D mu, has been strongly implicated in the loss of B cell precursors containing reading frame 2 DHJH junctions. In an attempt to elucidate the means of D mu counterselection, we have examined the reading frame distribution of DHJH junctions in peripheral B cells from mice transgenic for either the human bcl-2 oncogene or for a functionally rearranged Ig mu heavy chain. In bcl-2 transgenic mice, reading frame 2 accounted for < 5% of the DHJH junctions in peripheral B cells, a value not significantly different from controls. Reading frames 1 and 3 were equally represented among the remaining junctions. By contrast, the reading frame distribution of endogenous DHJH junctions in splenic B cells from Ig mu heavy chain transgenic mice showed no evidence of bias against D mu encoding DHJH junctions. Reading frames 2 and 3 accounted for 27% and 30% of the sequenced DHJH junctions, respectively, and the remaining 43% were reading frame 1. Thus although the presence of BCL-2 cannot prevent the selective loss of reading frame 2 DHJH B cells, a functional mu heavy chain can. These results suggest that D mu-expressing B cell precursors may be selectively lost because of the premature and inappropriate cessation of heavy chain gene rearrangement rather than because of the induction of an apoptotic process which can be blocked by BCL-2.

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Strick, C. A., and T. D. Fox. "Saccharomyces cerevisiae positive regulatory gene PET111 encodes a mitochondrial protein that is translated from an mRNA with a long 5' leader." Molecular and Cellular Biology 7, no. 8 (August 1987): 2728–34. http://dx.doi.org/10.1128/mcb.7.8.2728-2734.1987.

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The yeast nuclear gene PET111 is required specifically for translation of the mitochondrion-coded mRNA for cytochrome c oxidase subunit II. We have determined the nucleotide sequence of a 3-kilobase segment of DNA that carries PET111. The sequence contains a single long open reading frame that predicts a basic protein of 718 amino acids. The PET111 gene product is a mitochondrial protein, since a hybrid protein which includes the amino-terminal 154 amino acids of PET111 fused to beta-galactosidase is specifically associated with mitochondria. PET111 is translated from a 2.9-kilobase mRNA which, interestingly, has an extended 5'-leader sequence containing four short open reading frames upstream of the long open reading frame. These open reading frames exhibit an interesting pattern of overlap with each other and with the PET111 reading frame.

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Strick, C. A., and T. D. Fox. "Saccharomyces cerevisiae positive regulatory gene PET111 encodes a mitochondrial protein that is translated from an mRNA with a long 5' leader." Molecular and Cellular Biology 7, no. 8 (August 1987): 2728–34. http://dx.doi.org/10.1128/mcb.7.8.2728.

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The yeast nuclear gene PET111 is required specifically for translation of the mitochondrion-coded mRNA for cytochrome c oxidase subunit II. We have determined the nucleotide sequence of a 3-kilobase segment of DNA that carries PET111. The sequence contains a single long open reading frame that predicts a basic protein of 718 amino acids. The PET111 gene product is a mitochondrial protein, since a hybrid protein which includes the amino-terminal 154 amino acids of PET111 fused to beta-galactosidase is specifically associated with mitochondria. PET111 is translated from a 2.9-kilobase mRNA which, interestingly, has an extended 5'-leader sequence containing four short open reading frames upstream of the long open reading frame. These open reading frames exhibit an interesting pattern of overlap with each other and with the PET111 reading frame.

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Fontein, Lucie. "Reading Structure through the Frame." Perspecta 31 (2000): 50. http://dx.doi.org/10.2307/1567250.

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6

Márquez, Viter, Daniel N. Wilson, Warren P. Tate, Francisco Triana-Alonso, and Knud H. Nierhaus. "Maintaining the Ribosomal Reading Frame." Cell 118, no. 1 (July 2004): 45–55. http://dx.doi.org/10.1016/j.cell.2004.06.012.

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Hughes, Austin L., Kristi Westover, Jack da Silva, David H. O'Connor, and David I. Watkins. "Simultaneous Positive and Purifying Selection on Overlapping Reading Frames of the tat andvpr Genes of Simian Immunodeficiency Virus." Journal of Virology 75, no. 17 (September 1, 2001): 7966–72. http://dx.doi.org/10.1128/jvi.75.17.7966-7972.2001.

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ABSTRACT Tat-specific cytotoxic T cells have previously been shown to exert positive Darwinian selection favoring amino acid replacements of an epitope of simian immunodeficiency virus (SIV). The region of thetat gene encoding this epitope falls within a region of overlap between the tat and vpr reading frames, and nonsynonymous nucleotide substitutions in thetat reading frame were found to occur disproportionately in such a way as to cause synonymous changes in the vprreading frame. Comparison of published complete SIV genomes showed Tat to be the least conserved at the amino acid level of nine proteins encoded by the virus, while Vpr was one of the most conserved. Numerous parallel amino acid changes occurred within the Tat epitope independently in different monkeys, and purifying selection on thevpr reading frame, by limiting acceptable nonsynonymous substitutions in the tat reading frame, evidently has enhanced the probability of parallel evolution.

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박선옥. "Checking Reading Assessment Frame through Analyzing TOPIK Reading Questions." Studies in Linguistics ll, no. 26 (January 2013): 71–93. http://dx.doi.org/10.17002/sil..26.201301.71.

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9

Wan, Ji, Xiangwei Gao, Yuanhui Mao, Xingqian Zhang, and Shu-Bing Qian. "A Coding Sequence-Embedded Principle Governs Translational Reading Frame Fidelity." Research 2018 (September 20, 2018): 1–15. http://dx.doi.org/10.1155/2018/7089174.

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Upon initiation at a start codon, the ribosome must maintain the correct reading frame for hundreds of codons in order to produce functional proteins. While some sequence elements are able to trigger programmed ribosomal frameshifting (PRF), very little is known about how the ribosome normally prevents spontaneous frameshift errors that can have dire consequences if uncorrected. Using high resolution ribosome profiling data sets, we discovered that the translating ribosome uses the 3′ end of 18S rRNA to scan the AUG-like codons after the decoding process. The postdecoding mRNA:rRNA interaction not only contributes to predominant translational pausing, but also provides a retrospective mechanism to safeguard the ribosome in the correct reading frame. Partially eliminating the AUG-like “sticky” codons in the reporter message leads to increased +1 frameshift errors. Remarkably, mutating the highly conserved CAU triplet of 18S rRNA globally changes the codon “stickiness”. Further supporting the role of “sticky” sequences in reading frame maintenance, the codon composition of open reading frames is highly optimized across eukaryotic genomes. These results suggest an important layer of information embedded within the protein-coding sequences that instructs the ribosome to ensure reading frame fidelity during translation.

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Nasyrova, Gulnara N. "Frame technology in textbooks for reading." Tambov University Review. Series: Humanities, no. 195 (2021): 75–86. http://dx.doi.org/10.20310/1810-0201-2021-26-195-75-86.

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We reveal means of knowledge representation (frame, script and plan) and M. Minskiy’s hierarchical structure of the frame. It highlights different means of applying the frame theory to the native pedagogics as a frame pedagogical technology which enables students to enlarge the volume of knowledge under study without enlarging the volume of time spent on it; as a way of arranging the vocabulary necessary for a text comprehension and as a way of compiling a student’s dictionary. We offer a hyperframe model “A Manual for Master’s Degree Students in International Relations”. We analyze stereotypical and structural lexical and semantic features of mass media texts included into this hyperframe. We focus on the stereotypical structure of exercises and tasks circulating in the hyperframe: pre-text, text and after-text. The article stresses the importance of stereotypical tasks in each module, like “Agree/Disagree” and “Discussion Points” in order to further develop the soft skills of the 21st century. We offer Quizlet as a way of electronic means of learning new vocabulary and prove the necessity of including tasks aimed at the development of academic writing. The study also points out the pedagogical technology “Flipped Classroom” as one of the methods of working with the textbooks for Reading.

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11

Choi, Jinah, Zhenming Xu, and Jing-hsiung Ou. "Triple Decoding of Hepatitis C Virus RNA by Programmed Translational Frameshifting." Molecular and Cellular Biology 23, no. 5 (March 1, 2003): 1489–97. http://dx.doi.org/10.1128/mcb.23.5.1489-1497.2003.

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ABSTRACT Ribosomes can be programmed to shift from one reading frame to another during translation. Hepatitis C virus (HCV) uses such a mechanism to produce F protein from the −2/+1 reading frame. We now report that the HCV frameshift signal can mediate the synthesis of the core protein of the zero frame, the F protein of the −2/+1 frame, and a 1.5-kDa protein of the −1/+2 frame. This triple decoding function does not require sequences flanking the frameshift signal and is apparently independent of membranes and the synthesis of the HCV polyprotein. Two consensus −1 frameshift sequences in the HCV type 1 frameshift signal facilitate ribosomal frameshifts into both overlapping reading frames. A sequence which is located immediately downstream of the frameshift signal and has the potential to form a double stem-loop structure can significantly enhance translational frameshifting in the presence of the peptidyl-transferase inhibitor puromycin. Based on these results, a model is proposed to explain the triple decoding activities of the HCV ribosomal frameshift signal.

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12

Hung, Che-Lun, and Chun-Yuan Lin. "Open Reading Frame Phylogenetic Analysis on the Cloud." International Journal of Genomics 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/614923.

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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 amongNorovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members ofNorovirus.

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Au, Hilda H., Gabriel Cornilescu, Kathryn D. Mouzakis, Qian Ren, Jordan E. Burke, Seonghoon Lee, Samuel E. Butcher, and Eric Jan. "Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection." Proceedings of the National Academy of Sciences 112, no. 47 (November 9, 2015): E6446—E6455. http://dx.doi.org/10.1073/pnas.1512088112.

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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 dicistrovirusIsraeli 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.

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14

Dixon, Kevin, Christopher D. Bayliss, Katherine Makepeace, E. Richard Moxon, and Derek W. Hood. "Identification of the Functional Initiation Codons of a Phase-Variable Gene of Haemophilus influenzae, lic2A, with the Potential for Differential Expression." Journal of Bacteriology 189, no. 2 (November 10, 2006): 511–21. http://dx.doi.org/10.1128/jb.00815-06.

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ABSTRACT Simple sequence repeats located within reading frames mediate phase-variable ON/OFF switches in gene expression by generating frameshifts. Multiple translation initiation codons in different reading frames are found upstream of most Haemophilus influenzae tetranucleotide repeat tracts, raising the possibility of multiple active reading frames and more than two levels of gene expression for these loci. Phase variation between three levels of gene expression (strong, weak, and none) was observed when lic2A was fused to a lacZ reporter gene. The lic2A 5′ CAAT repeat tract is preceded by four 5′ ATG codons (x, y, z1, and z2) in two reading frames. Each of these initiation codons was inactivated by site-directed mutagenesis. Strong expression from frame 1 was associated with x but not y. Weak expression from frame 2 was mainly dependent on the z2 codon, and there was no expression from frame 3. Using monoclonal antibodies specific for a digalactoside epitope of lipopolysaccharide whose synthesis requires Lic2A, two levels (strong and undetectable) of antibody reactivity were detected, suggesting that weak expression of lic2A is not discernible at the phenotypic level. Inactivation of the x initiation codon resulted in loss of strong expression of the digalactoside epitope and elevated killing by human serum. The failure to detect more than two phenotypes for lic2A, despite clear evidence of weak expression from the z1/z2 initiation codons, leaves open the question of whether or not multiple initiation codons are associated with more complex patterns of phenotypic variation rather than classical phase-variable switching between two phenotypes.

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15

Loeb, D. D., R. W. Padgett, S. C. Hardies, W. R. Shehee, M. B. Comer, M. H. Edgell, and C. A. Hutchison. "The sequence of a large L1Md element reveals a tandemly repeated 5' end and several features found in retrotransposons." Molecular and Cellular Biology 6, no. 1 (January 1986): 168–82. http://dx.doi.org/10.1128/mcb.6.1.168-182.1986.

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The complete nucleotide sequence of a 6,851-base pair (bp) member of the L1Md repetitive family from a selected random isolate of the BALB/c mouse genome is reported here. Five kilobases of the element contains two overlapping reading frames of 1,137 and 3,900 bp. The entire 3,900-bp frame and the 3' 600 bp of the 1,137-bp frame, when compared with a composite consensus primate L1 sequence, show a ratio of replacement to silent site differences characteristic of protein coding sequences. This more closely defines the protein coding capacity of this repetitive family, which was previously shown to possess a large open reading frame of undetermined extent. The relative organization of the 1,137- and 3,900-bp reading frames, which overlap by 14 bp, bears resemblance to protein-coding, mobile genetic elements. Homology can be found between the amino acid sequence of the 3,900-bp frame and selected domains of several reverse transcriptases. The 5' ends of the two L1Md elements described in this report have multiple copies, 4 2/3 copies and 1 2/3 copy, of a 208-bp direct tandem repeat. The sequence of this 208-bp element differs from the sequence of a previously defined 5' end for an L1Md element, indicating that there are at least two different 5' end motifs for L1Md.

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Loeb, D. D., R. W. Padgett, S. C. Hardies, W. R. Shehee, M. B. Comer, M. H. Edgell, and C. A. Hutchison. "The sequence of a large L1Md element reveals a tandemly repeated 5' end and several features found in retrotransposons." Molecular and Cellular Biology 6, no. 1 (January 1986): 168–82. http://dx.doi.org/10.1128/mcb.6.1.168.

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The complete nucleotide sequence of a 6,851-base pair (bp) member of the L1Md repetitive family from a selected random isolate of the BALB/c mouse genome is reported here. Five kilobases of the element contains two overlapping reading frames of 1,137 and 3,900 bp. The entire 3,900-bp frame and the 3' 600 bp of the 1,137-bp frame, when compared with a composite consensus primate L1 sequence, show a ratio of replacement to silent site differences characteristic of protein coding sequences. This more closely defines the protein coding capacity of this repetitive family, which was previously shown to possess a large open reading frame of undetermined extent. The relative organization of the 1,137- and 3,900-bp reading frames, which overlap by 14 bp, bears resemblance to protein-coding, mobile genetic elements. Homology can be found between the amino acid sequence of the 3,900-bp frame and selected domains of several reverse transcriptases. The 5' ends of the two L1Md elements described in this report have multiple copies, 4 2/3 copies and 1 2/3 copy, of a 208-bp direct tandem repeat. The sequence of this 208-bp element differs from the sequence of a previously defined 5' end for an L1Md element, indicating that there are at least two different 5' end motifs for L1Md.

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17

Chang, Yijan E., Laura Menotti, Felix Filatov, Gabriella Campadelli-Fiume, and Bernard Roizman. "UL27.5 Is a Novel γ2 Gene Antisense to the Herpes Simplex Virus 1 Gene Encoding Glycoprotein B." Journal of Virology 72, no. 7 (July 1, 1998): 6056–64. http://dx.doi.org/10.1128/jvi.72.7.6056-6064.1998.

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ABSTRACT An antibody made against the herpes simplex virus 1 US5 gene predicted to encode glycoprotein J was found to react strongly with two proteins, one with an apparent M r of 23,000 and mapping in the S component and one with a herpes simplex virus protein with an apparent M r of 43,000. The antibody also reacted with herpes simplex virus type 2 proteins forming several bands with apparent M rs ranging from 43,000 to 50,000. Mapping studies based on intertypic recombinants, analyses of deletion mutants, and ultimately, reaction of the antibody with a chimeric protein expressed by in-frame fusion of the glutathione S-transferase gene to an open reading frame antisense to the gene encoding glycoprotein B led to the definitive identification of the new open reading frame, designated UL27.5. Sequence analyses indicate the conservation of a short amino acid sequence common to US5 and UL27.5. The coding sequence of the herpes simplex virus UL27.5 open reading frame is strongly homologous to the sequence encoding the carboxyl terminus of the herpes simplex virus 2 UL27.5 sequence. However, both open reading frames could encode proteins predicted to be significantly larger than the mature UL27.5 proteins accumulating in the infected cells, indicating that these are either processed posttranslationally or synthesized from alternate, nonmethionine-initiating codons. The UL27.5 gene expression is blocked by phosphonoacetate, indicating that it is a γ2 gene. The product accumulated predominantly in the cytoplasm. UL27.5 is the third open reading frame found to map totally antisense to another gene and suggests that additional genes mapping antisense to known genes may exist.

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18

Michel, Christian J. "A genetic scale of reading frame coding." Journal of Theoretical Biology 355 (August 2014): 83–94. http://dx.doi.org/10.1016/j.jtbi.2014.03.029.

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Farabaugh, P. J. "How translational accuracy influences reading frame maintenance." EMBO Journal 18, no. 6 (March 15, 1999): 1427–34. http://dx.doi.org/10.1093/emboj/18.6.1427.

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Ebels, Fenny. "Reading the Frame: Signalling Politics in Nada." Neophilologus 93, no. 4 (July 9, 2009): 619–32. http://dx.doi.org/10.1007/s11061-009-9166-8.

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Sieber, Patricia, Matthias Platzer, and Stefan Schuster. "The Definition of Open Reading Frame Revisited." Trends in Genetics 34, no. 3 (March 2018): 167–70. http://dx.doi.org/10.1016/j.tig.2017.12.009.

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Schlüter, Gregor, Dagmara Boinska, and Susanne-Christine Nieman-Seyde. "Evidence for Translational Repression of the SOCS-1 Major Open Reading Frame by an Upstream Open Reading Frame." Biochemical and Biophysical Research Communications 268, no. 2 (February 2000): 255–61. http://dx.doi.org/10.1006/bbrc.2000.2109.

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23

Bullock, Timothy N. J., Anthony E. Patterson, Laura L. Franlin, Evangelia Notidis, and Laurence C. Eisenlohr. "Initiation Codon Scanthrough versus Termination Codon Readthrough Demonstrates Strong Potential for Major Histocompatibility Complex Class I–restricted Cryptic Epitope Expression." Journal of Experimental Medicine 186, no. 7 (October 6, 1997): 1051–58. http://dx.doi.org/10.1084/jem.186.7.1051.

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Accumulating evidence shows that the repertoire of major histocompatibility complex class I–restricted epitopes extends beyond conventional translation reading frames. Previously, we reported that scanthrough translation, where the initiating AUG of a primary open reading frame is bypassed, is most likely to account for the presentation of cryptic epitopes from alternative reading frames within the influenza A PR/8/34 nucleoprotein gene. Here, we confirm and extend these findings using an epitope cassette construct that features two well-defined CD8+ T cell (TCD8+) epitopes in alternative reading frames, each preceded by a single start codon. Expression of one epitope depends on scanning of the ribosome over the first AUG with translation initiation occurring at the second AUG. We find that scanthrough translation has great potency in our system, with its impact being modulated, as predicted, by the base composition surrounding the first initiation codon, the number of start codons preceding the point of alternate reading frame initiation, and the efficiency with which the epitope itself is generated. Additionally, we investigated the efficiency of eukaryotic translation termination codons, to assess codon readthrough as a mechanism for cryptic epitope expression from 3′ untranslated regions. In contrast with initiation codons, eukaryotic stop codons appear to be highly efficient at preventing expression of epitopes encoded in 3′ untranslated regions, suggesting that 3′ untranslated regions are not a common source of cryptic epitope substrate. We conclude that scanthrough is a powerful mechanism for the expression of epitopes encoded in upstream alternative open reading frames that may contribute significantly to TCD8+ responses and to tolerance induction.

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Wang, Rong-Fu, Samuel L. Johnston, Gang Zeng, Suzanne L. Topalian, Douglas J. Schwartzentruber, and Steven A. Rosenberg. "A Breast and Melanoma-Shared Tumor Antigen: T Cell Responses to Antigenic Peptides Translated from Different Open Reading Frames." Journal of Immunology 161, no. 7 (October 1, 1998): 3596–606. http://dx.doi.org/10.4049/jimmunol.161.7.3596.

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Abstract Infusion of TIL586 along with IL-2 into the autologous patient with metastatic melanoma resulted in the objective regression of tumor. Here, we report that screening a cDNA library from the 586mel cell line using CTL clones derived from TIL586 resulted in the isolation of a gene, CAG-3 (cancer Ag gene 3). Sequence analysis revealed that CAG-3 encodes an open reading frame identical to NY-ESO-1, which was recently reported to be recognized by autologous serum from a patient with esophageal cancer. Thus, NY-ESO-1 appears to be an immune target for both Ab- and T cell-mediated responses. Significantly, NY-ESO-1-specific CTL clones were capable of recognizing two HLA-A31-positive fresh and cultured breast tumors. To our knowledge, this represents the first direct demonstration that tumor-specific CTL clones can recognize both breast and melanoma tumor cells. A 10-mer antigenic peptide ESO10–53 (ASGPGGGAPR) was identified from the normal open reading frame of NY-ESO-1 based on its ability to sensitize HLA-A31-positive target cells for cytokine release and specific lysis. Interestingly, two additional CTL clones that were sensitized with NY-ESO-1 recognized two overlapping antigenic peptides derived from an alternative open reading frame of the same gene. These findings indicate that CTLs simultaneously responded to two different gene products translated from the normal and alternative reading frames of the same gene. Understanding of this mechanism by which the alternative reading frame is translated may have important implications in tumor immunology.

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Mayrand, Shawn-Marie, David A. Schwarz, and William R. Green. "An Alternative Translational Reading Frame Encodes an Immunodominant Retroviral CTL Determinant Expressed by an Immunodeficiency-Causing Retrovirus." Journal of Immunology 160, no. 1 (January 1, 1998): 39–50. http://dx.doi.org/10.4049/jimmunol.160.1.39.

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Abstract Recognition of virus-infected or transformed cells by CD8+ CTL requires a trimolecular complex composed of MHC class I, β2-microglobulin, and a specific foreign peptide composed of 8 to 10 linear amino acids. The generation of such CTL epitopes has traditionally been thought to be from the primary open reading frame encoding the viral or tumor-associated proteins. In this report it is demonstrated that a viral CTL epitope can also be generated from an alternative reading frame. Using a combination of synthetic peptides and Sindbis or vaccinia expression systems, MHC class I Kd-restricted BALB/cByJ CTL directed against defective gag gene constructs of the LP-BM5 virus complex that causes murine AIDS were shown to have specificity for the antigenic peptide SYNTGRFPPL. This epitope is generated in a novel fashion from the second open reading frame (ORF2) of both the defective and ecotropic helper virus components of LP-BM5. Importantly, lysis of target cells expressing BM5 ecotropic helper, and/or defective viral gag, demonstrated that the SYNTGRFPPL epitope is generated during the course of a normal retroviral infection. Furthermore, MAIDS-resistant BALB/cByJ mice also generated secondary restimulated CTL specific for SYNTGRFPPL following in vivo priming with the LP-BM5 retroviral complex. These data suggest that retroviruses, and potentially other viruses and foreign genes, are capable of expressing T cell epitopes from alternative open reading frames. If one considers the influence of self peptides on T cell development, these “alternative reading frame-derived” peptides could provide an important additional influence on the functional T cell repertoire.

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Pyataeva, Anna, and Anton Dzyuba. "Artificial neural network technology for lips reading." E3S Web of Conferences 333 (2021): 01009. http://dx.doi.org/10.1051/e3sconf/202133301009.

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The paper presents the use of neural networks for the task of automated speech reading by lips articulation. Speech recognition is performed in two stages. First, a face search is performed and the lips area is selected in a separate frame of the video sequence using Haar features. Then the sequence of frames goes to the input of deep learning convolutional and recurrent neural networks for speech viseme recognition. Experimental studies were carried out using independently obtained videos with Russian-speaking speakers.

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Yu, Dong, Gregory A. Smith, Lynn W. Enquist, and Thomas Shenk. "Construction of a Self-Excisable Bacterial Artificial Chromosome Containing the Human Cytomegalovirus Genome and Mutagenesis of the Diploid TRL/IRL13 Gene." Journal of Virology 76, no. 5 (March 1, 2002): 2316–28. http://dx.doi.org/10.1128/jvi.76.5.2316-2328.2002.

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ABSTRACT The full-length genome of human cytomegalovirus strain AD169 was cloned as an infectious bacterial artificial chromosome (BAC) plasmid, pAD/Cre. The BAC vector, flanked by LoxP sites, was inserted immediately after the Us28 open reading frame without deletion of any viral sequences. The BAC vector contained the Cre recombinase-encoding gene disrupted by an intron under control of the simian virus 40 early promoter. When pAD/Cre was transfected into primary human foreskin fibroblast cells, Cre was expressed and mediated site-specific recombination between the two LoxP sites, excising the BAC DNA backbone. This gave rise to progeny virus that was wild type with the exception of an inserted 34-bp LoxP site. We performed site-directed mutagenesis on pAD/Cre to generate a series of viruses in which the TRL/IRL13 diploid genes were disrupted and subsequently repaired. The mutants reach the same titer as the wild-type virus, indicating that the TRL/IRL13 open reading frames are not required for virus growth in cell culture. The sequence of the TRL13 open reading frame in the low-passage Toledo strain of human cytomegalovirus is quite different from the corresponding region in the AD169 strain. One of multiple changes is a frameshift mutation. As a consequence, strain Toledo encodes a putative TRL13 protein whose C-terminal domain is larger (extending through the TRL14 coding region) and encodes in a reading frame different from that of strain AD169. We speculate that the strain AD169 coding region has drifted during passage in the laboratory. We propose that TRL13 has been truncated in strain AD169 and that the partially overlapping TRL14 open reading frame is not functional. This view is consistent with the presence of both TRL13 and -14 on all mRNAs that we have mapped from this region, an organization that would include the much longer strain Toledo TRL13 open reading frame on the mRNAs.

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Purcell‐Gates, Victoria. "Epistemological Tensions in Reading Research and a Vision for the Future." Reading Research Quarterly 47, no. 4 (October 2012): 465–71. http://dx.doi.org/10.1002/rrq.031.

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AbstractThis essay book review examines the Handbook of Reading Research, Volume IV, edited by Michael. L. Kamil, P. David Pearson, Elizabeth Birr Moje, and Peter P. Afflerbach. Taking an overview perspective on the volume, the review addresses issues of epistemology and theoretical frames as they apply to the study and research of reading. The author concludes that the volume, as a whole, represents the still fractious nature of the theoretical underpinnings of reading research and suggests a move toward a more unitary sociocognitive frame for reading research that could inform future handbooks on reading research as well as future research designs, methods, and presentations.

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Peabody, D. S., and P. Berg. "Termination-reinitiation occurs in the translation of mammalian cell mRNAs." Molecular and Cellular Biology 6, no. 7 (July 1986): 2695–703. http://dx.doi.org/10.1128/mcb.6.7.2695-2703.1986.

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Many examples of internal translation initiation in eucaryotes have accumulated in recent years. In many cases terminators of upstream reading frames precede the internal initiation site, suggesting that translational reinitiation may be a mechanism for initiation at internal AUGs. To test this idea, a series of recombinants was constructed in the mammalian expression vector pSV2. Each contained a dicistronic transcription unit comprising the coding sequence for mouse dihydrofolate reductase (DHFR) followed by the gene for xanthine-guanine phosphoribosyl transferase (XGPRT) from Escherichia coli. Various versions of this pSV2dhfr-gpt recombinant plasmid altered the location at which the DHFR reading frame was terminated relative to the XGPRT initiation codon and demonstrated that this is a critical factor for the expression of XGPRT activity in transfected Cos-1 cells. Thus, when the DHFR frame terminated upstream or a very short distance downstream of the XGPRT initiator AUG, substantial levels of XGPRT activity were observed. When the DHFR frame terminated 50 nucleotides beyond the XGPRT initiator, activity was reduced about twofold. However, when the DHFR and XGPRT sequences were fused in-frame so that ribosomes which initiated at the DHFR AUG did not terminate until they encountered the XGPRT terminator, production of XGPRT activity was abolished. This dependence of internal translation initiation on the position of terminators of the upstream reading frame is consistent with the hypothesis that mammalian ribosomes are capable of translational reinitiation.

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30

Peabody, D. S., and P. Berg. "Termination-reinitiation occurs in the translation of mammalian cell mRNAs." Molecular and Cellular Biology 6, no. 7 (July 1986): 2695–703. http://dx.doi.org/10.1128/mcb.6.7.2695.

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Many examples of internal translation initiation in eucaryotes have accumulated in recent years. In many cases terminators of upstream reading frames precede the internal initiation site, suggesting that translational reinitiation may be a mechanism for initiation at internal AUGs. To test this idea, a series of recombinants was constructed in the mammalian expression vector pSV2. Each contained a dicistronic transcription unit comprising the coding sequence for mouse dihydrofolate reductase (DHFR) followed by the gene for xanthine-guanine phosphoribosyl transferase (XGPRT) from Escherichia coli. Various versions of this pSV2dhfr-gpt recombinant plasmid altered the location at which the DHFR reading frame was terminated relative to the XGPRT initiation codon and demonstrated that this is a critical factor for the expression of XGPRT activity in transfected Cos-1 cells. Thus, when the DHFR frame terminated upstream or a very short distance downstream of the XGPRT initiator AUG, substantial levels of XGPRT activity were observed. When the DHFR frame terminated 50 nucleotides beyond the XGPRT initiator, activity was reduced about twofold. However, when the DHFR and XGPRT sequences were fused in-frame so that ribosomes which initiated at the DHFR AUG did not terminate until they encountered the XGPRT terminator, production of XGPRT activity was abolished. This dependence of internal translation initiation on the position of terminators of the upstream reading frame is consistent with the hypothesis that mammalian ribosomes are capable of translational reinitiation.

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31

Matten, Sharlene R., Thomas D. Schneider, Steven Ringquist, and William S. A. Brusilow. "Identification of an Intragenic Ribosome Binding Site That Affects Expression of the uncB Gene of the Escherichia coli Proton-Translocating ATPase (unc) Operon." Journal of Bacteriology 180, no. 15 (August 1, 1998): 3940–45. http://dx.doi.org/10.1128/jb.180.15.3940-3945.1998.

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ABSTRACT The uncB gene codes for the a subunit of the Fo proton channel sector of the Escherichia coli F1 Fo ATPase. Control of expression of uncB appears to be exerted at some step after translational initiation. Sequence analysis by the perceptron matrices (G. D. Stormo, T. D. Schneider, L. Gold, and A. Ehrenfeucht, Nucleic Acids Res. 10:2997–3011, 1982) identified a potential ribosome binding site within the uncB reading frame preceding a five-codon reading frame which is shifted one base relative to theuncB reading frame. Elimination of this binding site by mutagenesis resulted in a four- to fivefold increase in expression of an uncB′-′lacZ fusion gene containing most ofuncB. Primer extension inhibition (toeprint) analysis to measure ribosome binding demonstrated that ribosomes could form an initiation complex at this alternative start site. Two fusions oflacZ to the alternative reading frame demonstrated that this site is recognized by ribosomes in vivo. The results suggest that expression of uncB is reduced by translational frameshifting and/or a translational false start at this site within the uncB reading frame.

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Walker, Michelle Portlance, Ingo Jordan, Thomas Briese, Nicole Fischer, and W. Ian Lipkin. "Expression and Characterization of the Borna Disease Virus Polymerase." Journal of Virology 74, no. 9 (May 1, 2000): 4425–28. http://dx.doi.org/10.1128/jvi.74.9.4425-4428.2000.

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ABSTRACT Borna disease virus is the prototype of a new family,Bornaviridae, within the order Mononegavirales, that is characterized by nuclear transcription, splicing, low level replication, and neurotropism. The products of five open reading frames predicted from the genomic sequence have been confirmed; however, expression of the sixth, corresponding to the putative viral polymerase (L), has not been demonstrated. Here, we describe expression and characterization of a 190-kDa protein proposed to represent L. Expression of this protein from the third transcription unit of the viral genome is dependent on a splicing event that fuses a small upstream open reading frame in frame with the larger downstream continuous open reading frame. The protein is detected by serum antibodies from infected rats and is present in the nucleus, where it colocalizes with the phosphoprotein. L is also shown to be phosphorylated by cellular kinases and to interact with the viral phosphoprotein in coimmunoprecipitation studies. These findings are consistent with the identity of the 190-kDa protein as the viral polymerase and provide insights and describe reagents that will be useful for Bornavirus molecular biology and pathobiology.

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Barnett, Tully. "Hyperparatextuality: Meaning-making in the digital reading frame." Book 2.0 10, no. 1 (May 1, 2020): 43–58. http://dx.doi.org/10.1386/btwo_00019_1.

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In this article, I propose the concept of hyperparatextuality as a way of looking beyond the digital paratext to consider the distributed state of immersive reading in digitized and read-in-browser environments. Beginning with a look at the history of the paratext and its relevance in the digital age, this article considers the hyperparatexts of the HathiTrust reading panes in particular to explore the relationship between digitized texts and the platforms that house them. The concept of paratext and its evolving meaning in the digital age has intrigued researchers for decades as literary production, circulation and consumption responds to digitization and digitalization. Digital paratexts might include fan communities, digital editions to material books in the form of official and unofficial content, Goodreads and other reading-related and review websites, and Kindle highlighting tools. However, digitization introduces new reading materialities, interfaces and frames with buttons, links and hypertextual content. These 'read-in-browser' environments, websites through which we access digitized literary works, introduce new paratexts into the reading experience and require different concepts to understand them. When digital paratexts are also hypertextual, they operate differently. This article proposes some ways of thinking about this.

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McKinlay, Judith. "NEGOTIATING THE FRAME FOR VIEWING THE DEATH OF JEZEBEL." Biblical Interpretation 10, no. 3 (2002): 305–23. http://dx.doi.org/10.1163/156851502760226284.

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AbstractThe details of the death of Jezebel as told in 2 Kgs 9: 30-37 stay in the mind long after the account has been read. In this reading I apply different interpretive frames in an attempt to understand the dynamics both within and behind the text, recognizing that Jezebel and the writer(s) can be seen in different lights depending on the viewing. A reading that highlights the "woman in the window" motif hints at a goddess dimension within the Jezebel frame, which resists the text's attempted erasure. An overlying psychoanalytical frame allows the text to be read as one of many textual grapplings with the M(Other) lingering within the body. The possibility of such an innate resistance provides an answer to the question whether such careful viewing of such a text matters.

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Pande, S., A. Vimaladithan, H. Zhao, and P. J. Farabaugh. "Pulling the ribosome out of frame by +1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA." Molecular and Cellular Biology 15, no. 1 (January 1995): 298–304. http://dx.doi.org/10.1128/mcb.15.1.298.

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Programmed translational frameshifts efficiently alter a translational reading frame by shifting the reading frame during translation. A +1 frameshift has two simultaneous requirements: a translational pause which occurs when either an inefficiently recognized sense or termination codon occupies the A site, and the presence of a special peptidyl-tRNA occupying the P site during the pause. The special nature of the peptidyl-tRNA reflects its ability to slip +1 on the mRNA or to facilitate binding of an incoming aminoacyl-tRNA out of frame in the A site. This second mechanism suggested that in some cases the first +1 frame tRNA could have an active role in frameshifting. We found that overproducing this tRNA can drive frameshifting, surprisingly regardless of whether frameshifting occurs by peptidyl-tRNA slippage or out-of-frame binding of aminoacyl-tRNA. This finding suggests that in both cases, the shift in reading frame occurs coincident with formation of a cognate codon-anticodon interaction in the shifted frame.

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Underwood, Mark R., Robert J. Harvey, Sylvia C. Stanat, Mary Lou Hemphill, Teresa Miller, John C. Drach, Leroy B. Townsend, and Karen K. Biron. "Inhibition of Human Cytomegalovirus DNA Maturation by a Benzimidazole Ribonucleoside Is Mediated through the UL89 Gene Product." Journal of Virology 72, no. 1 (January 1, 1998): 717–25. http://dx.doi.org/10.1128/jvi.72.1.717-725.1998.

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ABSTRACT 2-Bromo-5,6-dichloro-1-β-d-ribofuranosyl benzimidazole (BDCRB) is a member of a new class of benzimidazole ribonucleosides which inhibit human cytomegalovirus (HCMV) late in the replication cycle without inhibiting viral DNA synthesis. We show here that polygenomic concatemeric HCMV DNA does not mature to unit genome length in the presence of BDCRB. To discover the locus of action, virus resistant to BDCRB was selected by serial passage in the presence of the compound. Genetic mapping experiments with BDCRB-resistant virus demonstrated that the resistance phenotype mapped to one amino acid (Asp344Glu; low resistance) or two amino acids (Asp344Glu and Ala355Thr; high resistance) within the product of exon 2 of the HCMV UL89 open reading frame. The HCMV UL89 open reading frame and its homologs are among the most conserved open reading frames in the herpesviruses, and their products have sequence similarities to a known ATP-dependent endonuclease from the double-stranded DNA bacteriophage T4. These findings strongly suggest that BDCRB prevents viral DNA maturation by interacting with a UL89 gene product and that the UL89 open reading frame may encode an endonucleolytic subunit of the putative HCMV terminase. Further, since mammalian cell DNA replication does not involve a DNA maturation step, compounds which inhibit viral DNA maturation should be selective and safe.

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Nurlia, Putri, Sri Ramadhona, and Sinta Dwi Devita. "Using Story Frame Approach to Increase Students’ Reading Comprehension at Senior High School." JL3T ( Journal of Linguistics Literature and Language Teaching) 6, no. 2 (January 28, 2021): 139–44. http://dx.doi.org/10.32505/jl3t.v6i2.2259.

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Using the Story Structure Approach to Increase Students. Reading Comprehension at the tenth grade of SMAN 2 Kejuruan Muda. This research was conducted on the Story Frame technique to improve students' awareness of reading. It was done in the Senior High School. This research used a quantitative approach with an experimental class and a control class needed. As the sample, there were 28 students in each experimental and control classes. Test and observation were used in the data collection technique. Then the result of the test will score by using analytic score and the researchers used "t-test" formula to calculated the data by comparing students' pre-test and post-test. This study found that students reading post-test score in experimental class using story frame strategy had a higher score of 76,67 higher than the student control class and a score post-test of 67,62, based on the formula, the difference in control class learning without Story Frame strategy. In addition, the Story Frame technique has made their reading comprehension more important. Based on these results, it concluded that the Story Frame technique could increase students' reading comprehension. Thus the hyphothesis was approved by the research method.

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Heriyanto, Heriyanto, Tenia Wahyuningrum, and Gita Fadila Fitriana. "Classification of Javanese Script Hanacara Voice Using Mel Frequency Cepstral Coefficient MFCC and Selection of Dominant Weight Features." JURNAL INFOTEL 13, no. 2 (May 30, 2021): 84–93. http://dx.doi.org/10.20895/infotel.v13i2.657.

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This study investigates the sound of Hanacaraka in Javanese to select the best frame feature in checking the reading sound. Selection of the right frame feature is needed in speech recognition because certain frames have accuracy at their dominant weight, so it is necessary to match frames with the best accuracy. Common and widely used feature extraction models include the Mel Frequency Cepstral Coefficient (MFCC). The MFCC method has an accuracy of 50% to 60%. This research uses MFCC and the selection of Dominant Weight features for the Javanese language script sound Hanacaraka which produces a frame and cepstral coefficient as feature extraction. The use of the cepstral coefficient ranges from 0 to 23 or as many as 24 cepstral coefficients. In comparison, the captured frame consists of 0 to 10 frames or consists of eleven frames. A sound sampling of 300 recorded voice sampling was tested on 300 voice recordings of both male and female voice recordings. The frequency used is 44,100 kHz 16-bit stereo. The accuracy results show that the MFCC method with the ninth frame selection has a higher accuracy rate of 86% than other frames.

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Yin, Wan Yun, Shan Xia, Xiang Zhang, Ke Wei Ding, Ren Cai Jin, and Shou Chen Liu. "Precast Concrete Frame Structure." Applied Mechanics and Materials 256-259 (December 2012): 934–37. http://dx.doi.org/10.4028/www.scientific.net/amm.256-259.934.

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With the rapid development of building process of industrialization in China, obtained the rapid development of precast concrete frame structures. This article is reading about precast concrete frame structure system at home and abroad on the basis of article. For describes precast concrete frame structure project background and the testing of components, to research the behaviors of precast concrete frame structure system.

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40

Michel, Christian J. "Single-Frame, Multiple-Frame and Framing Motifs in Genes." Life 9, no. 1 (February 10, 2019): 18. http://dx.doi.org/10.3390/life9010018.

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We study the distribution of new classes of motifs in genes, a research field that has not been investigated to date. A single-frame motif SF has no trinucleotide in reading frame (frame 0) that occurs in a shifted frame (frame 1 or 2), e.g., the dicodon AAACAA is SF as the trinucleotides AAA and CAA do not occur in a shifted frame. A motif which is not single-frame SF is multiple-frame MF. Several classes of MF motifs are defined and analysed. The distributions of single-frame SF motifs (associated with an unambiguous trinucleotide decoding in the two 5'–3' and 3'–5' directions) and 5′ unambiguous motifs 5'U (associated with an unambiguous trinucleotide decoding in the 5'–3' direction only) are analysed without and with constraints. The constraints studied are: initiation and stop codons, periodic codons AAA,CCC,GGG,TTT, antiparallel complementarity and parallel complementarity. Taken together, these results suggest that the complementarity property involved in the antiparallel (DNA double helix, RNA stem) and parallel sequences could also be fundamental for coding genes with an unambiguous trinucleotide decoding in the two 5'–3' and 3'–5' directions or the 5'–3' direction only. Furthermore, the single-frame motifs SF with a property of trinucleotide decoding and the framing motifs F (also called circular code motifs; first introduced by Michel (2012)) with a property of reading frame decoding may have been involved in the early life genes to build the modern genetic code and the extant genes. They could have been involved in the stage without anticodon-amino acid interactions or in the Implicated Site Nucleotides (ISN) of RNA interacting with the amino acids. Finally, the SF and MF dipeptides associated with the SF and MF dicodons, respectively, are studied and their importance for biology and the origin of life discussed.

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Guo, Shaoru, Yong Guan, Hongye Tan, Ru Li, and Xiaoli Li. "Frame-based Neural Network for Machine Reading Comprehension." Knowledge-Based Systems 219 (May 2021): 106889. http://dx.doi.org/10.1016/j.knosys.2021.106889.

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Harries, Karsten. "In Response on Reading Structure through the Frame." Perspecta 31 (2000): 81. http://dx.doi.org/10.2307/1567253.

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Kim Do-Nam. "A Study of the Characteristic of Reading Frame." KOREAN EDUCATION ll, no. 96 (September 2013): 43–74. http://dx.doi.org/10.15734/koed..96.201309.43.

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Pohl, M., G. Theißen, and S. Schuster. "GC content dependency of open reading frame prediction." EMBnet.journal 18, A (April 29, 2012): 88. http://dx.doi.org/10.14806/ej.18.a.411.

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Alemany, Ignacio López. "Courting Don Quixote: An Aulic Frame of Reading." Cervantes: Bulletin of the Cervantes Society of America 33, no. 1 (2013): 49–70. http://dx.doi.org/10.1353/cer.2013.0013.

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Michel, Christian J. "An extended genetic scale of reading frame coding." Journal of Theoretical Biology 365 (January 2015): 164–74. http://dx.doi.org/10.1016/j.jtbi.2014.09.040.

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Vidovic, Damir. "Tumor immunotherapy with alternative reading frame peptide antigens." Immunobiology 209, no. 7 (November 2004): 535–44. http://dx.doi.org/10.1016/j.imbio.2004.06.002.

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Trifonov, E. N. "Recognition of correct reading frame by the ribosome." Biochimie 74, no. 4 (April 1992): 357–62. http://dx.doi.org/10.1016/0300-9084(92)90113-s.

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Yuan, J., B. Bush, A. Elbrecht, Y. Liu, T. Zhang, W. Zhao, and R. Blevins. "Enhanced homology searching through genome reading frame predetermination." Bioinformatics 20, no. 9 (February 19, 2004): 1416–27. http://dx.doi.org/10.1093/bioinformatics/bth115.

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Boyle, Alan P., and John A. Boyle. "Visualization of aligned genomic open reading frame data." Biochemistry and Molecular Biology Education 31, no. 1 (January 2003): 64–68. http://dx.doi.org/10.1002/bmb.2003.494031010144.

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Journal articles on the topic 'Reading frame'

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