Relevant bibliographies by topics / Reading frame

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Reading frame'

Author: Grafiati
Published: 25 May 2024

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Journal articles on the topic "Reading frame"

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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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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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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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Dissertations / Theses on the topic "Reading frame"

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Ward, Karen. "Margins and the frame of reading." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq24940.pdf.

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SPITALI, Pietro. "ANTISENSE MEDIATED DYSTROPHIN READING FRAME RESTORATION." Doctoral thesis, Università degli studi di Ferrara, 2010. http://hdl.handle.net/11392/2389323.

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Exon skipping using antisense oligonucleotides (AONs) has successfully been used to reframe the mRNA in various DMD (Duchenne muscular dystrophy) patients carrying deletions and in the mdx mouse model. This study can be devided in two parts: in the first part we have tested the feasibility of the exon skipping approach for patients with small mutations in in-frame exons, while in the second part a quantitative comparison of exon skipping revealing techniques is addressed. We first identified 55 novel disease-causing point mutations. We selected 5 patients with nonsense or frameshifting mutations in exons 10, 16, 26, 33 and 34. Wild type and mutation specific 2‟OMePS AONs were tested in cell-free splicing assays and in cultured cells derived from the selected patients. The results obtained confirm cell-free splicing assay as an alternative system to test exon skipping propensity when patients‟ cells are unavailable. In myogenic cells, similar levels of exon skipping were observed for wild type and mutation specific AONs for exons 16, 26 and 33, while for exon 10 and exon 34 the efficiency of the AONs was significantly different. Interestingly, in some cases skipping efficiencies for mutated exons were quite dissimilar compared to what previously reported for the respective wild type exons. This behaviour may be related to effect of the mutations on exon skipping propensity and highlights the complexity of identifying optimal AONs for skipping exons with small mutations. In the second part we compared different techniques to reveal the exon skipping levels in the muscles of 7 different mdx mice. An absolute quantification of the dystrophin transcript amount was possible using a digital array. Results underline the low expression of the dytrophin gene and the amount needed to correctly quantify the exon skipping percentage.
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Lindström, Mikael. "Functional characterization of the alternative reading frame protein p14ARF /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-917-x.

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Amin, Unum. "Cellular characterisation of small Open Reading Frame function in Drosophila melanogaster." Thesis, University of Sussex, 2016. http://sro.sussex.ac.uk/id/eprint/65080/.

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As our knowledge of the genome expands, so does our understanding of the characteristics of what we define as genes. Small Open Reading Frame (smORF) genes have eluded gene annotation until very recently, and evidence is mounting that these very short nucleotide sequences encode functional peptides that are ≤100 amino acids in size. From work conducted in the fruit fly, our lab has successfully characterised three Drosophila smORFs, of which two have been shown to have a function in higher vertebrates, including humans. The functional characterisation of one of these conserved smORF encoded peptides (SEPs), Hemotin, is presented in this thesis. Though the overall number is still low compared to the abundance of potential smORF-encoding genes in Drosophila, the information gathered here allows us to speculate on the wider role of smORF peptides through cell-based imaging studies conducted on Drosophila cells. Here, I will discuss the various techniques that can and should be employed in order to study the functions of SEPs. Chapter III describes the various phenotypic studies conducted on the Hemotin smORF which is expressed in Drosophila haemocytes, and are integral to the fruit fly immune system. This study showed that connecting subcellular localisation of an SEP to a direct functional assay in cells can reveal functional characteristics of the peptide for further study. Chapter IV details the results from a tagging-transfection assay, which began initially as a way to independently corroborate the translation of smORF mRNAs that were assessed as such by Ribosome Profiling. This experiment resulted in the discovery of several mitochondrial-localised SEPs in Drosophila S2 cells, opening the door for the direct functional assay described in Chapter V. The results from a small-scale RNAi screen conducted on the mitochondria of S2 cells provided a reliable read-out for functionality of a large proportion of the smORFs that were screened. This assay can potentially be used as a phenotypic read-out of mitochondrial-SEP function in any cell or tissue type. Elucidation of smORFs and the functions of the peptides that they encode will help us to expand the Drosophila proteome, along with providing evidence of their functionality across every organism in which they are found. Considering that characterised SEPs play very important roles in physiology and health, it is time for smORFs to be acknowledged as the important genomic elements that they are.
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Forrest, Megan E. "Regulation of Mammalian Messenger RNA Stability via the Open Reading Frame." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1579862741902687.

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Nerlick, Stephen Tyler. "Inhibition of Xnos1 Translation by Structural Elements in the Open Reading Frame." Scholarly Repository, 2008. http://scholarlyrepository.miami.edu/oa_theses/141.

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The spatio-temporal regulation of translation is critical to the proper development of all organisms. The presence of Translational Control Elements (TCEs) in Un-Translated Regions (UTRs) is one feature common to all regulated eukaryotic mRNAs examined to date. These TCEs serve as binding sites for sequence specific proteins or small regulatory RNAs that recruit other accessory proteins that inhibit translation. Xnos1, a localized RNA in the germ plasm of Xenopus, is negatively regulated by an unknown mechanism. We used in vivo and in vitro translation assays, competition assays, and ribosome binding assays in order to determine the location of the Xnos1 TCE and its mechanism of repression. The Xnos1 TCE is located in the open reading frame, a departure from the canonical translational regulation mechanisms. This TCE is predicted to form conserved secondary structures in the first 75 nucleotides of the open reading frame (ORF). In vitro translation assays demonstrated that the repression can be partially relieved by either denaturing the transcripts or by introducing point mutations that weaken the secondary structure. This TCE cannot be relieved by competition and therefore is likely not to require the presence of a repressor protein. The structural regulation of translation by a TCE in the open reading frame is a novel mechanism of repression for a eukaryotic mRNA.
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Mumtaz, Muhammad Ali Shahzad. "High-throughput assessment of small open reading frame translation in Drosophila melanogaster." Thesis, University of Sussex, 2016. http://sro.sussex.ac.uk/id/eprint/65096/.

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Hundreds of thousands of putative small ORFs (smORFs) sequences are present in eukaryotic genomes, potentially coding for peptides less than 100 amino acids. smORFs have been deemed non-coding on the basis of their high numbers and their small size that makes it extremely challenging to assess their functionality both bioinformatically and biochemically. The recently developed Ribo-Seq technique, which is the deep sequencing of ribosome footprints, has generated significant controversy by showing extensive translation of smORFs outside of annotated protein coding regions, including putative non-coding RNAs.. Our lab adapted the Ribo-Seq technique by combining it with the polysome fractionation in order to assess smORF translation in Drosophila S2 cells. This thesis provides a high-throughput assessment of smORF translation in Drosophila melanogaster by firstly implementing complementary techniques such as transfection-tagging and Mass spectrometry methods in order to provide an independent corroboration of the S2 cell data (Chapter 3). Secondly, the in order to expand the catalogue of smORFs that are translated, I significantly improve upon the yield and sequencing efficiency of the Poly-Ribo-Seq protocol while adapting it to Drosophila embryos and then implementing it across embryogenesis divided in to Early, Mid and Late stages (Chapter 4). Currently, there is still a lot of debate in the field with regards to Ribo-Seq data analysis, and various computational metrics have been developed aimed at discerning 'real' translation events to background noise. Chapter 5 explores some of the metrics developed and establishes a translation cut-off suitable for designating small ORFs as translated. Altogether, the improvements introduced to the protocol and my data analysis shows the translation of 500 annotated smORFs, 500 smORFs in long non-coding RNAs and 5,000 uORFs, of which only one-third of each type of smORF has previous evidence of translation. These findings strengthen the establishment of smORFs as a distinct class of genes that significantly expand the protein coding complement of the genome.
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Chavez, Elisabeth [Verfasser]. "Reading Beyond the Diaspora : A Responsible Reading of Recent North American Fiction Outside the Ethnicity Frame / Elisabeth Chavez." Berlin : Freie Universität Berlin, 2021. http://d-nb.info/1229917292/34.

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Ren, Qian. "Characterization of alternative reading frame selection by a viral internal ribosome entry site." Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/48576.

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Dicistroviruses possess a positive-sense, monopartite single-strand RNA genome that encodes two open reading frames containing the nonstructural and structural polyproteins (ORF1 and ORF2) separated by the intergenic region (IGR) internal ribosome entry site (IRES). Translation of each ORF is directed by distinct IRESs, a 5’ untranslated region (UTR) and an IGR IRES. Previous bioinformatic studies have shown that a subset of dicistroviruses contain an overlapping gene in the +1 translational reading frame within the structural polyprotein gene near the IGR IRES region. We hypothesize that the IGR IRES directs translation of two overlapping ORFs, a novel +1 frame ORFx and the 0 frame ORF which encodes the viral structural polyprotein. In this thesis, using Israeli acute paralysis virus (IAPV) as a model, the existence and start site of ORFx were identified using mutagenesis and Mass Spectrometry analyses. In addition, the structural elements within the IAPV IGR IRES that determine alternative reading frame translation initiation were explored. Lastly, the localization of overexpressed tagged-ORFx in Drosophila S2 cells was examined to gain insights of its function. Summarizing, we have discovered a novel mechanism that increases the coding capacity of a virus through an IGR IRES. These studies of IAPV IGR-IRES will further our understanding of IRESs mediated translation initiation and reading frame decoding.
Medicine, Faculty of
Biochemistry and Molecular Biology, Department of
Graduate
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Yates, Paula Rachel. "A functional characterisation of the African swine fever virus open reading frame k9L." Thesis, University of Liverpool, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.283497.

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Books on the topic "Reading frame"

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Demaria, Cristina, and Patrizia Violi. Reading Memory Sites through Signs. Nieuwe Prinsengracht 89 1018 VR Amsterdam Nederland: Amsterdam University Press, 2023. http://dx.doi.org/10.5117/9789463722810.

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What can space tell us about our past? Which stories do memory sites narrate? Which memories do they transmit? And, more importantly, how can we read their meanings? Semiotics can provide us with a homogeneous, shareable and theoretically sound methodology to analyse space within a comparable and common frame of reference for scholars of memory studies and traumatic heritage, as well as for historians, architects and museum curators. The book describes in clear and understandable language the main semiotic concepts that can be used to analyse space, illustrating them with carefully chosen case studies of memory spaces – monuments, museums, post-war urban restoration, filmed and virtual space – in order to show the applicability and efficacy of a semiotic methodology.
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Reading frames in modern fiction. Princeton, N.J: Princeton University Press, 1985.

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1963-, Smith Christopher, ed. Readings on Ethan Frome. San Diego, CA: Greenhaven Press, 2000.

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1723-1780, Blackstone William Sir, and William Blackstone Collection (Library of Congress), eds. An analysis of Blackstone's commentaries on the laws of England: In a series of questions, to which the student is to frame his own answers, by reading that work. Clark, NJ: Lawbook Exchange, Ltd., 2008.

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Wharton, Edith. Ethan Frome: And Related Readings. Evanston, IL, USA: McDougal Littell, 1997.

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Dietz, Mary E. Framework for comprehension: A cognitive approach to children's literature through mediating frames. East Aurora, N.Y: D.O.K. Publishers, 1988.

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Per una lettura espressiva della frase francese: Riflessioni teoriche ed approccio metodologico. Verona: QuiEdit, 2011.

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Nehru Memorial Museum and Library, ed. Beyond the frames of environmental history: Reading an adivasi movement in colonial India. New Delhi: Nehru Memorial Museum and Library, 2015.

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Wharton, Edith. Ethan Frome: Unabridged and unadapted from the original text : and with ten related readings. Lodi, N.J: Everbind Books, 2003.

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Doorbar, John. Identification of proteins encoded by the major open reading frames of human papillomavirus type 1 (HPV-1): Productionof specific antisera. Birmingham: University of Birmingham, 1985.

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Book chapters on the topic "Reading frame"

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Gooch, Jan W. "Open Reading Frame." In Encyclopedic Dictionary of Polymers, 912. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6247-8_14387.

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Arnemann, J. "Open-reading frame (ORF)." In Springer Reference Medizin, 1784–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-48986-4_3551.

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Arnemann, J. "Open-reading frame (ORF)." In Lexikon der Medizinischen Laboratoriumsdiagnostik, 1. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-662-49054-9_3551-1.

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Lefranc, Marie-Paule. "Open Reading Frame (ORF)." In Encyclopedia of Systems Biology, 1566–67. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_672.

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Kang, Dong-chul, and Paul B. Fisher. "Complete Open Reading Frame (C-ORF) Technique." In Cancer Genomics and Proteomics, 123–33. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-335-6_8.

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Ebels, Fenny. "Reading the Frame: Signalling Politics in Nada." In Tracing Paradigms: One Hundred Years of Neophilologus, 147–61. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-33585-8_14.

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Frost, Simon R. "Commodity Readers: An Introduction to a Frame for Reading." In The History of Reading, Volume 3, 27–45. London: Palgrave Macmillan UK, 2011. http://dx.doi.org/10.1057/9780230316737_3.

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Gamerschlag, Thomas, and Wiebke Petersen. "On the Fictive Reading of German Steigen ‘Climb, Rise’: A Frame Account." In Language, Cognition, and Mind, 239–61. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-50200-3_12.

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AbstractFictive motion, i.e., the figurative stative use of verbs of motion, has attracted much attention in cognitive linguistics as a paradigm case for how basic dynamic concepts are exploited figuratively in concept formation (Langacker 1986; Matsumoto 1996; Talmy 2000; Matlock 2004a, b inter alia). In this paper, we present a case study of the fictive motion reading of the German movement verb steigen ‘climb, rise’ and explore how it can be related to the various dynamic readings of the verb. In our account of steigen, which builds on Gamerschlag, Geuder & Petersen’s (2014) analysis of the dynamic readings of the verb, we contrast the different readings in terms of frames, i.e., recursive attribute-value structures in the sense of Barsalou (1992) and Petersen (2007/2015).
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Buchow, H. D., E. Tschachler, R. C. Gallo, and M. Reitz. "HIV-I Replication Requires an Intact Integrase Reading Frame." In Haematology and Blood Transfusion / Hämatologie und Bluttransfusion, 402–5. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-642-74621-5_68.

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Guo, Shaoru, Yong Guan, and Ru Li. "Multi-Perspective Frame Element Representation for Machine Reading Comprehension." In Communications in Computer and Information Science, 123–34. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-7224-1_10.

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Conference papers on the topic "Reading frame"

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Regan, D., and X. H. Hong. "Motion-Defined Letter Reading Test." In Noninvasive Assessment of the Visual System. Washington, D.C.: Optica Publishing Group, 1991. http://dx.doi.org/10.1364/navs.1991.we2.

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We have compared detection and spatial discrimination for motion-defined (MD) and contrast-defined (CD) form in normally-sighted subjects using a hardware stimulus generator of our own design and fabrication.1 The device displays approximately 1000 dots on a Tektronix 608 display with 100 frames/sec. The dot display is superimposed on a uniform patch of light so that dot contrast can be controlled. A new dot pattern can be generated every frame from a very large menu of patterns. The dot pattern contains a rectangular area whose aspect ratio, orientation, size and location can be controlled on a frame-by-frame basis. The speed and direction of motion of dots inside and outside the rectangle can be controlled independently. When all dots are stationary, the rectangle is perfectly camouflaged. When the velocity of dots inside the rectangle is sufficiently different from the velocity of dots outside the rectangle, the camouflaged rectangle is clearly visible to normally-sighted subjects. In this situation, the rectangle is rendered visible by relative motion. If we switch off all dots outside the rectangle, the rectangle is rendered visible by luminance contrast.
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Ponnala, L., D. L. Bitzer, A. Stomp, and M. A. Vouk. "A computational model for reading frame maintenance." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.259717.

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Ponnala, L., D. L. Bitzer, A. Stomp, and M. A. Vouk. "A computational model for reading frame maintenance." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.4398462.

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Aleksandrov, A. Yu, K. A. Antipov, A. V. Platonov, and A. A. Tikhonov. "On a satellite stabilization in the Konig frame." In 2015 International Conference on Mechanics-Seventh Polyakhov's Reading. IEEE, 2015. http://dx.doi.org/10.1109/polyakhov.2015.7106711.

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Guo, Shaoru, Ru Li, Hongye Tan, Xiaoli Li, Yong Guan, Hongyan Zhao, and Yueping Zhang. "A Frame-based Sentence Representation for Machine Reading Comprehension." In Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics. Stroudsburg, PA, USA: Association for Computational Linguistics, 2020. http://dx.doi.org/10.18653/v1/2020.acl-main.83.

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Ashlock, Wendy, and Suprakash Datta. "Detecting retroviruses using reading frame information and side effect machines." In 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2010. http://dx.doi.org/10.1109/cibcb.2010.5510699.

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Moore, N., and J. W. Jaromczyk. "Finding a longest open reading frame of an alternatively spliced gene." In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). IEEE, 2011. http://dx.doi.org/10.1109/bibmw.2011.6112377.

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Kim, Dongjae, Aria S. Hahn, Shang-Ju Wu, Niels W. Hanson, Kishori M. Konwar, and Steven J. Hallam. "FragGeneScan-plus for scalable high-throughput short-read open reading frame prediction." In 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2015. http://dx.doi.org/10.1109/cibcb.2015.7300341.

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Guo, Shaoru, Yong Guan, Ru Li, Xiaoli Li, and Hongye Tan. "Incorporating Syntax and Frame Semantics in Neural Network for Machine Reading Comprehension." In Proceedings of the 28th International Conference on Computational Linguistics. Stroudsburg, PA, USA: International Committee on Computational Linguistics, 2020. http://dx.doi.org/10.18653/v1/2020.coling-main.237.

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Abe, Yamaguchi, Takemura, Takeuchi, and Yamada. "400K Pixel Full Frame Reading Out Fit-CCD Color Pick Up System." In IEEE International Conference on Consumer Electronics. IEEE, 1990. http://dx.doi.org/10.1109/icce.1990.665958.

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Reports on the topic "Reading frame"

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Ward, Kimiora. Sierra Nevada Network high elevation white pine monitoring: 2021 annual report. National Park Service, 2024. http://dx.doi.org/10.36967/2302327.

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Five-needle white pines (Family Pinaceae, Genus Pinus, Subgenus Strobus), and in particular whitebark pine (Pinus albicaulis), limber pine (P. flexilis), and foxtail pine (P. balfouriana) are foundation species in upper subalpine and treeline forests of several National Park Service Pacific West Region parks, including Sequoia and Kings Canyon National Parks (SEKI) and Yosemite National Park (YOSE). The Sierra Nevada Network Inventory & Monitoring Program, in collaboration with the Klamath Network, Upper Columbia Basin Network, and Mojave Desert Network have implemented a joint long-term monitoring protocol to assess the current status and future trends in high elevation white pine communities. Key demographic parameters within white pine forest communities will be estimated by monitoring individual trees within permanent plots through time. This report documents the results of the 2021 field season, which was the eighth year of monitoring in Sequoia and Kings Canyon National Parks (SEKI) and Yosemite National Park (YOSE). The 2021 goal was to complete the third full re-measure of the second of three rotating panels (Panel 2) for each species-park population: YOSE-whitebark pine, SEKI-whitebark pine, and SEKI-foxtail pine. Each panel consists of 12 permanent 50 x 50 m (2,500 m2) plots that were randomly selected for each of the three populations. The full sampling array thus includes a total of 36 whitebark pine plots in YOSE, 36 whitebark pine plots in SEKI, and 36 foxtail pine plots in SEKI. Data from plot surveys will be used to characterize white pine forest community dynamics in SEKI and YOSE, including changes in tree species composition, forest structure, forest health, and demographics. The first full measure of all Panel 2 plots was completed over two years in 2013-2014, then a full remeasure of both parks? whitebark pine Panel 2 was conducted in 2016, with 10 of 12 SEKI-foxtail plots sampled that year. A third remeasure of all Panel 2 plots was not possible in 2021 because a smaller crew size was necessary during the COVID-19 pandemic. In total, the crew visited 37 sites, and sampled 31, during the 2021 field season. One plot in the YOSE whitebark pine frame was uninstalled before reading and one plot in the SEKI whitebark pine frame was uninstalled after reading, both for safety concerns. Four plots were not visited due to lack of capacity with the reduced crew size: one in each of the YOSE and SEKI whitebark frames, and three in the SEKI foxtail frame. A plot from Panel 3 in each of the parks? whitebark frames was measured, for a total of 11 plots measured in each whitebark pine frame. Nine plots were measured in the SEKI foxtail pine frame. Within the 31 plots completed, a total of 5,728 trees was measured. Species composition, forest structure, and factors affecting tree health and reproduction, including incidence and severity of white pine blister rust (Cronartium ribicola) infection, mountain pine beetle (Dendroctonus ponderosae) infestation, dwarf mistletoe (Arceuthobium spp.) infection, canopy kill, female cone production and regeneration were recorded. During the 2021 field season, crews continued to count the total number of mature cones per tree for whitebark and foxtail pine, use crown condition codes to assess crown health, and tag individual seedlings to be tracked through time. All three of these procedures started in 2017 and are to be evaluated by each of the three participating networks over several years, to determine whether they should become permanent changes to the monitoring protocol. In YOSE, 11 whitebark pine plots were re-measured, from Panels 2 and 3. A total of 2,810 trees were sampled, which included 586 live whitebark pine trees and 2,097 other live conifers. An additional 127 trees (including 17 whitebark pine) were recorded as dead. The forest crew noted little sign of white pine blister rust (WPBR) in Yosemite in 2021, and just a single inactive canker was observed on one whitebark pine in Panel 3, Plot 42, near Dana Meadows. This infection was new to plot 42, and it expands the total number of plots where white pine blister rust has been documented in Yosemite to six. The crew also noted little mountain pine beetle activity, documenting beetle galleries on 15 lodgepole pines in three Panel 2 plots. Dwarf mistletoe was not observed. The average number of live whitebark pine trees per plot was 53 (SD = 56). This was a low cone crop year for whitebark pine, with two percent of live whitebark pine trees producing female cones. Cone bearing trees averaged 2 (SD = 1) cones per tree. Whitebark pine seedling density averaged 90 (SD = 157) seedlings per hectare. The largest number of whitebark pine seedlings found in a plot was four, and three of the eleven plots contained whitebark seedlings. In SEKI, 10 of 12 Panel 2, and one Panel 3, whitebark pine plots were re-measured. Within these plots, 1,246 live whitebark pine, 30 live foxtail pine, and 861 other live conifers were sampled. WPBR was infrequently documented in the SEKI whitebark frame as well, with indicators of infection in Plot 31 near Window Creek and Plot 44 near Upper State Lake. These were the first infections documented in these plots, bringing the number of plots where WPBR has been documented in the SEKI whitebark panel to nine. Although WPBR was documented in Plot 27 near Charlotte Dome in 2016, it was not documented this year because putative cankers showing three signs of infection in 2016 showed only two or fewer signs in 2021. Mountain pine beetle activity was observed in one live lodgepole pine and two recently dead whitebark pine, within three plots in the SEKI whitebark sample frame. An exception to the low levels of mountain pine beetle activity was outside Plot 31 in the Window Creek area, where the forest crew noted many recently dead whitebark pine with signs of beetle activity. Dwarf mistletoe was not encountered. The average number of live whitebark pine trees per plot was 113 (SD = 86). Less than one percent of live whitebark pine trees produced female cones, each producing on average 2 (SD = 1) cones. Whitebark seedling regeneration averaged 303 (SD = 319) seedlings per hectare. The largest number of whitebark seedlings found in a plot was eight, and eight of the 11 plots contained whitebark seedlings. Nine of the 12 SEKI foxtail Panel 3 plots were remeasured. Within these plots, 413 live foxtail pine, 67 live whitebark pine, and 402 other live conifers were sampled. Ninety-two dead or recently dead trees were also documented, 65 of which were foxtail pine. No signs of blister rust infection, mistletoe, or mountain pine beetle were observed in the foxtail plots sampled. The average number of foxtail pine trees per plot was 46 (SD = 33). Fifty-four percent of the foxtail pine trees produced female cones, averaging 14 (SD =15) cones/tree. Only one foxtail pine seedling was recorded within the 9 foxtail pine plots, resulting in an estimated 14 (SD = 41) seedlings per hectare. Eight whitebark pine seedlings were also found within two plots.
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Kuznetsov, Victor, Vladislav Litvinenko, Egor Bykov, and Vadim Lukin. A program for determining the area of the object entering the IR sensor grid, as well as determining the dynamic characteristics. Science and Innovation Center Publishing House, April 2021. http://dx.doi.org/10.12731/bykov.0415.15042021.

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Currently, to evaluate the dynamic characteristics of objects, quite a large number of devices are used in the form of chronographs, which consist of various optical, thermal and laser sensors. Among the problems of these devices, the following can be distinguished: the lack of recording of the received data; the inaccessibility of taking into account the trajectory of the object flying in the sensor area, as well as taking into consideration the trajectory of the object during the approach to the device frame. The signal received from the infrared sensors is recorded in a separate document in txt format, in the form of a table. When you turn to the document, data is read from the current position of the input data stream in the specified list by an argument in accordance with the given condition. As a result of reading the data, it forms an array that includes N number of columns. The array is constructed in a such way that the first column includes time values, and columns 2...N- the value of voltage . The algorithm uses cycles that perform the function of deleting array rows where there is a fact of exceeding the threshold value in more than two columns, as well as rows where the threshold level was not exceeded. The modified array is converted into two new arrays, each of which includes data from different sensor frames. An array with the coordinates of the centers of the sensor operation zones was created to apply the Pythagorean theorem in three-dimensional space, which is necessary for calculating the exact distance between the zones. The time is determined by the difference in the response of the first and second sensor frames. Knowing the path and time, we are able to calculate the exact speed of the object. For visualization, the oscillograms of each sensor channel were displayed, and a chronograph model was created. The chronograph model highlights in purple the area where the threshold has been exceeded.
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3

Loebenstein, Gad, William Dawson, and Abed Gera. Association of the IVR Gene with Virus Localization and Resistance. United States Department of Agriculture, August 1995. http://dx.doi.org/10.32747/1995.7604922.bard.

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We have reported that localization of TMV in tobacco cultivars with the N gene, is associated with a 23 K protein (IVR) that inhibited replication of several plant viruses. This protein was also found in induced resistant tissue of Nicotiana glutinosa x Nicotiana debneyi. During the present grant we found that TMV production is enhanced in protoplasts and plants of local lesion responding tobacco cultivars exposed to 35oC, parallel to an almost complete suppression of the production of IVR. We also found that IVR is associated with resistance mechanisms in pepper cultivars. We succeeded to clone the IVR gene. In the first attempt we isolated a clone - "101" which had a specific insert of 372 bp (the full length gene for the IVR protein of 23 kD should be around 700 bp). However, attempts to isolate the full length gene did not give clear cut results, and we decided not to continue with this clone. The amino acid sequence of the N-terminus of IVR was determined and an antiserum was prepared against a synthetic peptide representing amino acids residues 1-20 of IVR. Using this antiserum as well as our polyclonal antiserum to IVR a new clone NC-330 was isolated using lamba-ZAP library. This NC-330 clone has an insert of about 1 kB with an open reading frame of 596 bp. This clone had 86.6% homology with the first 15 amino acids of the N-terminal part of IVR and 61.6% homology with the first 23 amino acids of IVR. In the QIA expression system and western blotting of the expressed protein, a clear band of about 21 kD was obtained with IVR antiserum. This clone was used for transformation of Samsun tobacco plants and we have presently plantlets which were rooted on medium containing kanamycin. Hybridization with this clone was also obtained with RNA from induced resistant tissue of Samsun NN but not with RNA from healthy control tissue of Samsun NN, or infected or healthy tissue of Samsun. This further strengthens the previous data that the NC 330 clone codes for IVR. In the U.S. it was shown that IVR is induced in plants containing the N' gene when infected with mutants of TMV that elicit the HR. This is a defined system in which the elicitor is known to be due to permutations of the coat protein which can vary in elicitor strength. The objective was to understand how IVR synthesis is induced after recognition of elicitor coat protein in the signal transduction pathway that leads to HR. We developed systems to manipulate induction of IVR by modifying the elicitor and are using these elicitor molecules to isolate the corresponding plant receptor molecules. A "far-western" procedure was developed that found a protein from N' plants that specifically bind to elicitor coat proteins. This protein is being purified and sequenced. This objective has not been completed and is still in progress. We have reported that localization of TMV in tobacco cultivars with the N gene, is associated with a 23 K protein (IVR) that inhibited replication of several plant viruses. This protein was also found in induced resistant tissue of Nicotiana glutinosa x Nicotiana debneyi.
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Dawson, William O., Moshe Bar-Joseph, Charles L. Niblett, Ron Gafny, Richard F. Lee, and Munir Mawassi. Citrus Tristeza Virus: Molecular Approaches to Cross Protection. United States Department of Agriculture, January 1994. http://dx.doi.org/10.32747/1994.7570551.bard.

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Citrus tristeza virus (CTV) has the largest genomes among RNA viruses of plants. The 19,296-nt CTV genome codes for eleven open reading frames (ORFs) and can produce at least 19 protein products ranging in size from 6 to 401 kDa. The complex biology of CTV results in an unusual composition of CTV-specific RNAs in infected plants which includes multiple defective RNAs and mixed infections. The complex structure of CTV populations poses special problems for diagnosis, strain differentiation, and studies of pathogenesis. A manipulatable genetic system with the full-length cDNA copy of the CTV genome has been created which allows direct studies of various aspects of the CTV biology and pathology. This genetic system is being used to identify determinants of the decline and stem-pitting disease syndromes, as well as determinants responsible for aphid transmission.
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McElwain, Terry F., Eugene Pipano, Guy H. Palmer, Varda Shkap, Stephn A. Hines, and Wendy C. Brown. Protection of Cattle against Babesiosis: Immunization against Babesia bovis with an Optimized RAP-1/Apical Complex Construct. United States Department of Agriculture, September 1999. http://dx.doi.org/10.32747/1999.7573063.bard.

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Previous research and current efforts at control of babesiosis fall short of meeting the needs of countries where the disease is endemic, such as Israel, as well as the needs of exporting countries and countries bordering on endemic areas, such as the U.S. Our long-term goal is to develop improved methods of immunization against bovine babesiosis based on an understanding of the molecular mechanisms of immune protection and parasite targets of a protective immune response. In our previous BARD project, we established the basis for focusing on rhoptry antigens as components of a subunit vaccine against bovine babesiosis, and for additional research to better characterize rhoptry associated protein-1 (RAP-1) as a target of protective immunity. In this continuation BARD project, our objectives were to [1] optimize the immune response against RAP-1, and [2] identify additional rhoptry candidate vaccine antigens. The entire locus encoding B. bovis RAP-1 was sequenced, and the rap-1 open reading frame compared among several strains. Unlike B. bigemina, in which multiple gene copies with variant domains encode RAP-1, the B. bovis RAP-1 locus contains only two identical genes which are conserved among strains. Through testing of multiple truncated constructs of rRAP-1, one or more immunodominant T cell epitopes were mapped to the amino terminal half of RAP-1. At least one linear and one conformational B cell epitope have been demonstrated in the same amino terminal construct, which in B. bigemina RAP-1 also contains an epitope recognized by neutralizing antibody. The amine terminal half of the molecule represents the most highly conserved part of the gene family and contains motifs conserved broadly among the apicomplexa. In contrast, the carboxy terminal half of B. bovis RAP-1 is less well conserved and contains multiple repeats encoding a linear B cell epitope potentially capable of inducing an ineffective, T cell independent, type 2 immune response. Therefore, we are testing an amino terminal fragment of RAP-1 (RAP-1N) in an immunization trial in cattle. Cattle have beer immunized with RAP-1N or control antigen, and IL-12 with Ribi adjuvant. Evaluation of the immune response is ongoing, and challenge with virulent B. bovis will occur in the near future. While no new rhoptry antigens were identified, our studies did identify and characterize a new spherical body antigen (SBP3), and several heat shock proteins (HSP's). The SBP3 and HSP21 antigens stimulate T cells from immune cattle and are considered new vaccine candidates worthy of further testing. Overall, we conclude that a single RAP-1 vaccine construct representing the conserved amino terminal region of the molecule should be sufficient for immunization against all strains of B. bovis. While results of the ongoing immunization trial will direct our next research steps, results at this time are consistent with our long term goal of designing a subunit vaccine which contains only the epitopes relevant to induction of protective immunity. Parallel studies are defining the mechanisms of protective immunity. Apicomplexan protozoa, including babesiosis and malaria, cause persistent diseases for which control is inadequate. The apical organelles are defining features of these complex protozoa, and have been conserved through the evolutionary process, Past and current BARD projects on babesiosis have established the validity and potential of exploiting these conserved organelles in developing improved control methods applicable to all apicomplexan diseases.
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Barefoot, Susan F., Bonita A. Glatz, Nathan Gollop, and Thomas A. Hughes. Bacteriocin Markers for Propionibacteria Gene Transfer Systems. United States Department of Agriculture, June 2000. http://dx.doi.org/10.32747/2000.7573993.bard.

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The antibotulinal baceriocins, propionicin PLG-1 and jenseniin G., were the first to be identified, purified and characterized for the dairy propionibaceria and are produced by Propionibacterium thoenii P127 and P. thoenii/jensenii P126, respectively. Objectives of this project were to (a) produce polyclonal antibodies for detection, comparison and monitoring of propionicin PLG-1; (b) identify, clone and characterize the propionicin PLG-1 (plg-1) and jenseniin G (jnG) genes; and (3) develop gene transfer systems for dairy propionibacteria using them as models. Polyclonal antibodies for detection, comparison and monitoring of propionicin PLG-1 were produced in rabbits. Anti-PLG-1 antiserum had high titers (256,000 to 512,000), neutralized PLG-1 activity, and detected purified PLG-1 at 0.10 mg/ml (indirect ELISA) and 0.033 mg/ml (competitive indirect ELISA). Thirty-nine of 158 strains (most P. thoenii or P. jensenii) yielded cross-reacting material; four strains of P. thoenii, including two previously unidentified bacteriocin producers, showed biological activity. Eight propionicin-negative P127 mutants produced neither ELISA response nor biological activity. Western blot analyses of supernates detected a PLG-1 band at 9.1 kDa and two additional protein bands with apparent molecular weights of 16.2 and 27.5 kDa. PLG-1 polyclonal antibodies were used for detection of jenseniin G. PLG-1 antibodies neutralized jenseniin G activity and detected a jenseniin G-sized, 3.5 kDa peptide. Preliminary immunoprecipitation of crude preparations with PLG-1 antibodies yielded three proteins including an active 3-4 kDa band. Propionicin PLG-1 antibodies were used to screen a P. jensenii/thoenii P126 genomic expression library. Complete sequencing of a cloned insert identified by PLG-1 antibodies revealed a putative response regulator, transport protein, transmembrane protein and an open reading frame (ORF) potentially encoding jenseniin G. PCR cloning of the putative plg-1 gene yielded a 1,100 bp fragment with a 355 bp ORF encoding 118 amino acids; the deduced N-terminus was similar to the known PLG-1 N-terminus. The 118 amino acid sequence deduced from the putative plg-1 gene was larger than PLG-1 possibly due to post-translational processing. The product of the putative plg-1 gene had a calculated molecular weight of 12.8 kDa, a pI of 11.7, 14 negatively charged residues (Asp+Glu) and 24 positively charged residues (Arg+Lys). The putative plg-1 gene was expressed as an inducible fusion protein with a six-histidine residue tag. Metal affinity chromatography of the fused protein yielded a homogeneous product. The fused purified protein sequence matched the deduced putative plg-1 gene sequence. The data preliminarily suggest that both the plg-1 and jnG genes have been identified and cloned. Demonstrating that antibodies can be produced for propionicin PLG-1 and that those antibodies can be used to detect, monitor and compare activity throughout growth and purification was an important step towards monitoring PLG-1 concentrations in food systems. The unexpected but fortunate cross-reactivity of PLG-1 antibodies with jenseniin G led to selective recovery of jenseniin G by immunoprecipitation. Further refinement of this separation technique could lead to powerful affinity methods for rapid, specific separation of the two bacteriocins and thus facilitate their availability for industrial or pharmaceutical uses. Preliminary identification of genes encoding the two dairy propionibacteria bacteriocins must be confirmed; further analysis will provide means for understanding how they work, for increasing their production and for manipulating the peptides to increase their target species. Further development of these systems would contribute to basic knowledge about dairy propionibacteria and has potential for improving other industrially significant characteristics.
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Tayeb, Shahab. Protecting Our Community from the Hidden Vulnerabilities of Today’s Intelligent Transportation Systems. Mineta Transportation Institute, May 2022. http://dx.doi.org/10.31979/mti.2022.2132.

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The ever-evolving technology interwoven into the transportation industry leaves it frequently at risk for cyber-attacks. This study analyzes the security of a common in-vehicle network, the Controller Area Network (CAN), standard in most vehicles being manufactured today. Like many other networks, CAN comes with inherent vulnerabilities that leave CAN implementations at risk of being targeted by cybercriminals. Such vulnerabilities range from eavesdropping, where the attacker can read the raw data traversing the vehicle, to spoofing, where the attacker can place fabricated traffic on the network. The research team initially performed a simulation of CAN traffic generation followed by hardware implementation of the same on a test vehicle. Due to the concealed and untransparent nature of CAN, the team reverse-engineered the missing parameters through a series of passive "sniffing attacks" (attacks using data reading utilities called packet sniffers) on the network and then demonstrated the feasibility of the attack by placing fabricated frames on the CAN.
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Leis, Brian. PR-214-163713-R01 Review of Response Requirements and Criteria for Plain Dents. Chantilly, Virginia: Pipeline Research Council International, Inc. (PRCI), January 2020. http://dx.doi.org/10.55274/r0011648.

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Beginning in 2007 the I and I committee has developed an expansive set of modeling and full-scale testing projects dealing with mechanical damage, considering the severity of damage response to pressure and pressure cycling and its assessment, its detection and sizing, and its management. While much data and insight has been developed, the practicable outcomes are limited to tools to predict the burst pressure specific to collapse-controlled failure and fatigue response specific to plain dents. Simple practical acceptance guidelines have however not emerged. The subcontract sought completion of Task 1 of Project MD-4-13. Thus, information was gathered and reviewed concerning the body of knowledge developed by PRCI and others with a view to best define a plain dent such that: 1) simple management guidelines can be established; 2) such dents can be readily distinguished relative to other damage features; and 3) gaps in existing technology can be identified and bridged to enable developing management guidelines for other more complex dents. In complement to that, the subcontract's scope sought comments concerning definitions of dent-related damage to pipelines, which is addressed in large part by this report. Subsequent Tasks in this Project will benefit from these outcomes as they establish the technical foundation to define the response time frame when managing such features.
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Appleyard, Bruce, Jonathan Stanton, and Chris Allen. Toward a Guide for Smart Mobility Corridors: Frameworks and Tools for Measuring, Understanding, and Realizing Transportation Land Use Coordination. Mineta Transportation Institue, December 2020. http://dx.doi.org/10.31979/mti.2020.1805.

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The coordination of transportation and land use (also known as “smart growth”) has been a long-standing goal for planning and engineering professionals, but to this day it remains an elusive concept to realize. Leaving us with this central question -- how can we best achieve transportation and land use coordination at the corridor level? In response, this report provides a review of literature and practice related to sustainability, livability, and equity (SLE) with a focus on corridor-level planning. Using Caltrans’ Corridor Planning Process Guide and Smart Mobility Framework as guideposts, this report also reviews various principles, performance measures, and place typology frameworks, along with current mapping and planning support tools (PSTs). The aim being to serve as a guidebook that agency staff can use for reference, synergizing planning insights from various data sources that had not previously been brought together in a practical frame. With this knowledge and understanding, a key section provides a discussion of tools and metrics and how they can be used in corridor planning. For illustration purposes, this report uses the Smart Mobility Calculator (https://smartmobilitycalculator. netlify.app/), a novel online tool designed to make key data easily available for all stakeholders to make better decisions. For more information on this tool, see https://transweb.sjsu.edu/research/1899-Smart-Growth-Equity-Framework-Tool. The Smart Mobility Calculator is unique in that it incorporates statewide datasets on urban quality and livability which are then communicated through a straightforward visualization planners can readily use. Core sections of this report cover the framework and concepts upon which the Smart Mobility Calculator is built and provides examples of its functionality and implementation capabilities. The Calculator is designed to complement policies to help a variety of agencies (MPOs, DOTs, and local land use authorities) achieve coordination and balance between transportation and land use at the corridor level.
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Antignus, Yehezkiel, Ernest Hiebert, Shlomo Cohen, and Susan Webb. Approaches for Studying the Interaction of Geminiviruses with Their Whitefly Vector Bemisia tabaci. United States Department of Agriculture, July 1995. http://dx.doi.org/10.32747/1995.7604928.bard.

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The DNA of tomato yellow leaf curl virus (TYLCB) was detected in its whitefly vector, Bemisia tabaci, by dot spot hybridization as early as 1 h after acquisition access. The retention of the virus nucleic acid in the vector was at least 23 days after a 48 h acquisition access. However, the retention of TYLCV coat protein did not exceed 10 days. No replicative forms of TYLCV could be detected in B. tabaci, indicating a non-propagative relationship with the vector. Whiteflies were not able to accumulate naked virion ssDNA, virus cloned dsDNA, or virions with impaired coat protein. Deletion, frameshift, and single amino acid mutations were inserted into open reading frames (ORFs) V1 and V2 (Coat protein) of TYLCV. The ability of these mutants to replicate, to spread and to induce symptoms was tested both in leaf disks and in intact plants. No replication was found in tissues that were infected with a deletion mutant that lacked the carboxy half of the coat protein gene. Residual amounts of ssDNA and dsDNA were detected i tissues infected with a frameshift mutant in which an early termination at the extreme part of the protein. Two other mutants in which a single amino acid was changed in the overlapping part of V1 and V2 were able to spread systemically but infections remained symptomless and the production of ssDNA and dsDNA were significantly lower. These mutants were acquired and transmitted by Bemisia tabaci. Procedures for the the dissection, fixation and embedding of whiteflies were developed. The anatomy and ultrastructure of the salivary gland and the midgut of Bemisia tabaci and Trialeurodes vaporariorum (a vector and non-vector of geminiviruses respectively) was studied and described. Monoclonal antibodies against bean golden mosaic virus (BGMV) with narrow and broad spectrum were prepared. Transmission studies of tomato mottle geminivirus (TMoV) by B. tabaci were carried out. These studies were essential for a further work aimed to understand the interaction of geminiviruses with the insect and their localization in its tissues. To enable the production of transgenic plants procedures were developed for tomato transformation with both Agrobacterium and microparticle bombardment.
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