Relevant bibliographies by topics / Genetic transcription

Contents

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

Academic literature on the topic 'Genetic transcription'

Author: Grafiati
Published: 4 June 2021
Last updated: 29 July 2024

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Journal articles on the topic "Genetic transcription"

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NOMURA, Teruaki, and Akira ISHIHAMA. "Transcription regulation of genetic information. Properties of transcriptional signals." Kagaku To Seibutsu 23, no. 10 (1985): 632–39. http://dx.doi.org/10.1271/kagakutoseibutsu1962.23.632.

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Guo, Shaobin, Zeqi Xu, Lujie Lin, Yan Guo, Jingying Li, Chunhua Lu, Xianai Shi, and Huanghao Yang. "Using CIVT-SELEX to Select Aptamers as Genetic Parts to Regulate Gene Circuits in a Cell-Free System." International Journal of Molecular Sciences 24, no. 3 (February 1, 2023): 2833. http://dx.doi.org/10.3390/ijms24032833.

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The complexity of genetic circuits has not seen a significant increase over the last decades, even with the rapid development of synthetic biology tools. One of the bottlenecks is the limited number of orthogonal transcription factor–operator pairs. Researchers have tried to use aptamer–ligand pairs as genetic parts to regulate transcription. However, most aptamers selected using traditional methods cannot be directly applied in gene circuits for transcriptional regulation. To that end, we report a new method called CIVT-SELEX to select DNA aptamers that can not only bind to macromolecule ligands but also undergo significant conformational changes, thus affecting transcription. The single-stranded DNA library with affinity to our example ligand human thrombin protein is first selected and enriched. Then, these ssDNAs are inserted into a genetic circuit and tested in the in vitro transcription screening to obtain the ones with significant inhibitory effects on downstream gene transcription when thrombins are present. These aptamer–thrombin pairs can inhibit the transcription of downstream genes, demonstrating the feasibility and robustness of their use as genetic parts in both linear DNAs and plasmids. We believe that this method can be applied to select aptamers of any target ligands and vastly expand the genetic part library for transcriptional regulation.
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Wang, R., E. Halper-Stromberg, M. Szymanski-Pierce, S. S. Bassett, and D. Avramopoulos. "Genetic determinants of neuroglobin transcription." neurogenetics 15, no. 1 (December 24, 2013): 65–75. http://dx.doi.org/10.1007/s10048-013-0388-3.

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Chua, Gordon. "Systematic genetic analysis of transcription factors to map the fission yeast transcription-regulatory network." Biochemical Society Transactions 41, no. 6 (November 20, 2013): 1696–700. http://dx.doi.org/10.1042/bst20130224.

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Mapping transcriptional-regulatory networks requires the identification of target genes, binding specificities and signalling pathways of transcription factors. However, the characterization of each transcription factor sufficiently for deciphering such networks remains laborious. The recent availability of overexpression and deletion strains for almost all of the transcription factor genes in the fission yeast Schizosaccharomyces pombe provides a valuable resource to better investigate transcription factors using systematic genetics. In the present paper, I review and discuss the utility of these strain collections combined with transcriptome profiling and genome-wide chromatin immunoprecipitation to identify the target genes of transcription factors.
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Sansó, Miriam, and Robert P. Fisher. "Modelling the CDK-dependent transcription cycle in fission yeast." Biochemical Society Transactions 41, no. 6 (November 20, 2013): 1660–65. http://dx.doi.org/10.1042/bst20130238.

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CDKs (cyclin-dependent kinases) ensure directionality and fidelity of the eukaryotic cell division cycle. In a similar fashion, the transcription cycle is governed by a conserved subfamily of CDKs that phosphorylate Pol II (RNA polymerase II) and other substrates. A genetic model organism, the fission yeast Schizosaccharomyces pombe, has yielded robust models of cell-cycle control, applicable to higher eukaryotes. From a similar approach combining classical and chemical genetics, fundamental principles of transcriptional regulation by CDKs are now emerging. In the present paper, we review the current knowledge of each transcriptional CDK with respect to its substrate specificity, function in transcription and effects on chromatin modifications, highlighting the important roles of CDKs in ensuring quantity and quality control over gene expression in eukaryotes.
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Newton, A., N. Ohta, G. Ramakrishnan, D. Mullin, and G. Raymond. "Genetic switching in the flagellar gene hierarchy of Caulobacter requires negative as well as positive regulation of transcription." Proceedings of the National Academy of Sciences 86, no. 17 (September 1989): 6651–55. http://dx.doi.org/10.1073/pnas.86.17.6651.

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Caulobacter crescentus flagellar (fla, flb, or flg) genes are periodically expressed in the cell cycle and they are organized in a regulatory hierarchy. We have analyzed the genetic interactions required for fla gene expression by determining the effect of mutations in 30 known fla genes on transcription from four operons in the hook gene cluster. These results show that the flaO (transcription unit III) and flbF (transcription unit IV) operons are located at or near the top of the hierarchy. They also reveal an extensive network of negative transcriptional controls that are superimposed on the positive regulatory cascade described previously. The strong negative autoregulation observed for the flaN (transcription unit I), flbG (transcription unit II), and flaO (transcription unit III) promoters provides one possible mechanism for turning off fla gene expression at the end of the respective synthetic periods. We suggest that these positive and negative transcriptional interactions are components of genetic switches that determine the sequence in which fla genes are turned on and off in the C. crescentus cell cycle.
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Fazlollahi, Mina, Ivor Muroff, Eunjee Lee, Helen C. Causton, and Harmen J. Bussemaker. "Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets." Proceedings of the National Academy of Sciences 113, no. 13 (March 10, 2016): E1835—E1843. http://dx.doi.org/10.1073/pnas.1517140113.

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Regulation of gene expression by transcription factors (TFs) is highly dependent on genetic background and interactions with cofactors. Identifying specific context factors is a major challenge that requires new approaches. Here we show that exploiting natural variation is a potent strategy for probing functional interactions within gene regulatory networks. We developed an algorithm to identify genetic polymorphisms that modulate the regulatory connectivity between specific transcription factors and their target genes in vivo. As a proof of principle, we mapped connectivity quantitative trait loci (cQTLs) using parallel genotype and gene expression data for segregants from a cross between two strains of the yeast Saccharomyces cerevisiae. We identified a nonsynonymous mutation in the DIG2 gene as a cQTL for the transcription factor Ste12p and confirmed this prediction empirically. We also identified three polymorphisms in TAF13 as putative modulators of regulation by Gcn4p. Our method has potential for revealing how genetic differences among individuals influence gene regulatory networks in any organism for which gene expression and genotype data are available along with information on binding preferences for transcription factors.
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Frank, Steven A. "Optimization of Transcription Factor Genetic Circuits." Biology 11, no. 9 (August 31, 2022): 1294. http://dx.doi.org/10.3390/biology11091294.

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Transcription factors (TFs) affect the production of mRNAs. In essence, the TFs form a large computational network that controls many aspects of cellular function. This article introduces a computational method to optimize TF networks. The method extends recent advances in artificial neural network optimization. In a simple example, computational optimization discovers a four-dimensional TF network that maintains a circadian rhythm over many days, successfully buffering strong stochastic perturbations in molecular dynamics and entraining to an external day–night signal that randomly turns on and off at intervals of several days. This work highlights the similar challenges in understanding how computational TF and neural networks gain information and improve performance.
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Drazen, Jeffrey M., and Eric S. Silverman. "Genetic Determinants of 5–Lipoxygenase Transcription." International Archives of Allergy and Immunology 118, no. 2-4 (1999): 275–78. http://dx.doi.org/10.1159/000024098.

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Seo, Young Jun, Shigeo Matsuda, and Floyd E. Romesberg. "Transcription of an Expanded Genetic Alphabet." Journal of the American Chemical Society 131, no. 14 (April 15, 2009): 5046–47. http://dx.doi.org/10.1021/ja9006996.

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Dissertations / Theses on the topic "Genetic transcription"

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Xie, Yunwei. "Nucleosomes, transcription and transcription regulation in Archaea." Connect to resource, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1127830717.

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Thesis (Ph. D.)--Ohio State University, 2005.
Title from first page of PDF file. Document formatted into pages; contains xiv, 200 p.; also includes graphics (some col.). Includes bibliographical references (p. 167-197). Available online via OhioLINK's ETD Center
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Sigvardsson, Mikael. "Regulation of immunoglobulin transcription during B-cell differentiation." Lund : Lund University, 1995. http://books.google.com/books?id=TJNqAAAAMAAJ.

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Greenberg, Norman Michael. "Cellulase gene transcription in Cellulomonas fimi and an Agrobacterium." Thesis, University of British Columbia, 1988. http://hdl.handle.net/2429/28836.

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Transcriptional analysis was used to investigate the molecular mechanisms which effect cellulase gene expression in the gram-positive bacterium Cellulomonas fimi strain ATCC 484 and the gram-negative bacterium Agrobacterium sp. strain ATCC 21400. The cenA, cex and cenB genes of C. fimi encoding the extracellular β-1,4-endoglucanase, EngA (EC 3.2.1.4; Mr 48,700), the extracellular β-1, 4-exoglucanase, Exg (EC 3.2.1.91; Mr 47,300) and the extracellular β-1,4-endoglucanase EngB (EC 3.2.1.4; Mr 110,000) respectively, were characterised. By northern blot analysis, cenA mRNA was detected in C. fimi RNA prepared from glycerol- and carboxymethylcellulose (CMC)-grown cells but not in RNA from glucose-grown cells. The cex mRNA was found only in RNA from CMC-grown cells. The cenB mRNA was found in all three preparations of RNA. Therefore, the expression of these genes is subject to regulation by the carbon source provided to C. fimi. High resolution nuclease SI protection studies with unique 5'-labeled DNA probes and C. fimi RNA isolated in vivo, were used to map the 5' termini of cenA and cex mRNAs. Two cenA mRNA 5' ends, 11 bases apart, mapped 51 and 62 bases upstream of the cenA start codon, suggesting that in vivo, cenA transcription was directed from two promoters in tandem. The cex mRNA 5' end was found to map 28 bases upstream of the cex start codon. Using SI mapping with unlabeled DNA probes and C. fimi RNA which had been isolatedin vivo but which had been 5'-labeled in vitro with vaccinia virus capping enzyme confirmed that true transcription initiation sites for cenA and cex mRNA had been identified. The SI mapping revealed mRNA 3' termini 1,438, 1,449, and 1, 464 bases from the major cenA start site, and one 3' terminus 1,564 bases from the major cex mRNA start site, in good agreement with the northern blot data. High resolution SI studies were also used to show that abundant mRNA 5' ends mapped upstream of the cenB start codon in RNA prepared from CMC-grown cells, while less-abundant species mapped 52 bases closer to the ATG codon in RNA prepared from C. fimi grown on any one of the three substrates. These results seem to indicate a tandem promoter arrangement with an ATG-proximal promoter directing low-level constitutive cenB transcription and a more distal promoter directing higher levels of cenB transcription as a result of C. fimi growth on cellulosic substrate. Steady- state levels were determined for cenA, cex and cenB mRNAs with RNA prepared from glycerol-, glucose-, and CMC-grown cultures of C. fimi in slot-blot hybridisations with radiolabeled oligodeoxyribonucleotide probes. A cex-linked gene (clg) was identified by sequence inspection and SI mapping. Transcripts of the abg gene encoding the β-glucosidase (Abg, EC 3.2.2.21/ Mr 50,000) of Agrobacterium sp. strain ATCC 21400 were also characterised. Northern blot analysis of Agrobacterium RNA revealed the size of the in vivo abgmRNA was approximately 1,500 bases in length. High resolution SI mapping determined abg mRNA 5' ends 22 bases upstream of the abg ATG codon and 3' ends 71 bases downstream of the abg stop codon.
Science, Faculty of
Microbiology and Immunology, Department of
Graduate
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Dibbens, Justin Andrew. "Studies on the control of late gene transcription in coliphage 186 /." Title page, contents and summary only, 1990. http://web4.library.adelaide.edu.au/theses/09PH/09phd543.pdf.

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Zak, Daniel Edward. "Structured modeling of mammalian transcription networks." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 374 p, 2005. http://proquest.umi.com/pqdweb?did=954050761&sid=7&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Greberg, Maria Hellqvist. "Cloning and characterization of FREACs, human forkhead transcription factors." Göteborg : Dept. of Cell and Molecular Biology, Göteborg University, 1997. http://catalog.hathitrust.org/api/volumes/oclc/39751934.html.

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Elzi, David John. "Transcriptional properties of the Kaiso class of transcription factors /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/5027.

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Sajjadi, Fereydoun G. "Modualtion [sic] of transcription by sequences contained in the 5’-flanking region of a Drosophila melanogaster tRNAVal4 gene." Thesis, University of British Columbia, 1985. http://hdl.handle.net/2429/24910.

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Transfer RNA genes require "positive" 5'-flanking sequences to direct efficient transcription. In order to delimit the modulatory sequences present in the 5'-flank of a Drosophila tRNA Val₄ gene, an extensive series of deletion mutants was constructed and end-points determined by dideoxy sequencing. The mutants were transcribed in vitro in a Drosophila Schneider II cell-free extract. Twenty nucleotides of the 5'-flank immediately adjacent to the mature tRNA coding sequence were required for transcription. Negative modulatory sequences were contained between positions -20 to -30 and -45 to -70 relative to the mature coding sequence. The -45 to -70 sequence shares homology with inhibitory sequences previously described in the 5'-flank of tRNA genes, except that this sequence was significantly larger in length. Sequences contained between positions -38 and -45 act as positive modulatory sequences which enhance the level of transcription. In addition, a Transcription Modulation Element (TME) was identified between nucleotides -33 and -38. The TME was also found in the 5'-flanking sequences of various other tRNA genes and preliminary data suggests that it enhances transcription efficiency through its position relative to the D and T control regions
Medicine, Faculty of
Medical Genetics, Department of
Graduate
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Schoenborn, Jamie R. "Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing Ifng transcription /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/5098.

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Sajjadi, Fereydoun G. "The sequence TNNCT modulates transcription of a Drosophila Melanogaster tRNA ₄ gene." Thesis, University of British Columbia, 1987. http://hdl.handle.net/2429/27522.

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The transcription efficiency of transfer RNA genes is modulated by sequences contained in their 5'-flanking region. For a tRNA val₄ gene a pentanucleotide with the sequence TCGCT was identified between positions -33 and -38. I have previously proposed that this sequence may be involved in specifically determining the rate of transcription of this gene. A general form of this sequence, TNNCT was found associated with other Drosophila tRNA genes which showed high ill vitro transcription efficiency. To further elucidate the role of TCGCT in tRNA transcription, single and double base-pair changes were created in the sequence TCGCT using site-specific mutagenesis. Mutations in the nucleotides -38T, -35C and -34T showed decreased levels of transcription whereas nucleotide changes at the nucleotides -37C and -36G did not reduce template activity. Therefore the sequence which modulates transcription of the tRNAVal₄ gene does have the general form TNNCT. Competition experiments between the Val₄ mutant -38G.-35A and a tRNASer₇ gene showed the TNNCT mutant to be a better competitor for transcription than the wild type template. Experiments analyzing the time-course of transcription, the effects of temperature and the effects of ionic strength indicated that TNNCT was not involved in determining the efficiency of stable complex formation. It is proposed that the pentanucleotide is probably responsible for influencing the rate of initiation of transcription. A sequence TGCCT contained in the anticodon stem/loop region of the Val₄ gene was also mutagenized and shown to be involved in complex stability or the elongation of Val₄ tRNAs. Using deletion analysis of the 5'-flanking sequences of a tRNASer₇ gene, a second positive transcription regulatory element was delimited. This sequence was also found in the 5'-flanks of the tRNAVal₄ and a tRNAArg gene.
Medicine, Faculty of
Medical Genetics, Department of
Graduate
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Books on the topic "Genetic transcription"

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Julian, Burke, ed. Gene structure and transcription. Oxford, England: IRL Press, 1988.

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Julian, Burke, ed. Gene structure and transcription. 2nd ed. Oxford: IRL Press at Oxford University Press, 1992.

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Klaus, Grasser, ed. Regulation of transcription in plants. Oxford: Blackwell Pub., 2006.

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D, Hames B., and Glover David M, eds. Transcription and splicing. Oxford, England: IRL Press, 1988.

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1932-, Eckstein Fritz, and Lilley, David M. J. 1948-, eds. Mechanisms of transcription. Berlin: Springer, 1997.

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C, Conaway Ronald, and Conaway Joan Weliky, eds. Transcription: Mechanisms and regulation. New York: Raven Press, 1994.

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Yuan, Ling, and Sharyn E. Perry. Plant transcription factors: Methods and protocols. New York: Humana, 2011.

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Inc, ebrary, ed. Genetics. 2nd ed. New Delhi: New Age International (P) Ltd., Publishers, 2009.

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Lutz, Nover, ed. Plant promoters and transcription factors. Berlin: Springer-Verlag, 1994.

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L, McKnight Steven, and Yamamoto Keith R, eds. Transcriptional regulation. Plainview, N.Y: Cold Spring Harbor Laboratory Press, 1992.

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Book chapters on the topic "Genetic transcription"

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Schaal, Thomas D., Michael C. Holmes, Edward J. Rebar, and Casey C. Case. "Novel Approaches to Controlling Transcription." In Genetic Engineering, 137–78. Boston, MA: Springer US, 2002. http://dx.doi.org/10.1007/978-1-4615-0721-5_7.

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Hemenway, Cynthia L., and Steven A. Lommel. "Manipulating Plant Viral RNA Transcription Signals." In Genetic Engineering, 171–95. Boston, MA: Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4199-8_10.

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Smith, C. A., and E. J. Wood. "Transcription and the genetic code." In Molecular Biology and Biotechnology, 38–62. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4615-3866-0_3.

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Oh, Hwanhee, and Jihye Paik. "Genetic Ablation of FOXO in Mice to Investigate Its Physiological Role." In FOXO Transcription Factors, 239–48. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8900-3_20.

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Sollner-Webb, B., J. Tower, V. Culotta, and J. Windle. "Transcription of Cloned Eukaryotic Ribosomal RNA Genes." In Genetic Engineering: Principles and Methods, 309–32. Boston, MA: Springer US, 1985. http://dx.doi.org/10.1007/978-1-4684-4973-0_14.

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Salafranca, Julia, Zhichao Ai, Lihui Wang, Irina A. Udalova, and Erinke van Grinsven. "Analysis of Neutrophil Morphology and Function Under Genetic Perturbation of Transcription Factors In Vitro." In Transcription Factor Regulatory Networks, 69–86. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2815-7_6.

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Singh, Harinder. "Molecular Cloning of Genes Encoding Transcription Factors with the Use of Recognition Site Probes." In Genetic Engineering, 317–30. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4613-0641-2_16.

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Tobin, E. M., J. A. Brusslan, J. S. Buzby, G. A. Karlin-Neumann, D. M. Kehoe, P. A. Okubara, S. A. Rolfe, L. Sun, and T. Yamada. "Phytochrome Regulation of Transcription: Biochemical and Genetic Approaches." In Phytochrome Properties and Biological Action, 167–79. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-75130-1_11.

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Sawasaki, Tatsuya, Ryo Morishita, Mudeppa D. Gouda, and Yaeta Endo. "Methods for High-Throughput Materialization of Genetic Information Based on Wheat Germ Cell-Free Expression System." In In Vitro Transcription and Translation Protocols, 95–106. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-388-2_5.

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Golub, T. R., G. F. Barker, K. Stegmaier, and D. G. Gilliland. "The TEL Gene Contributes to the Pathogenesis of Myeloid and Lymphoid Leukemias by Diverse Molecular Genetic Mechanisms." In Chromosomal Translocations and Oncogenic Transcription Factors, 67–79. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60479-9_5.

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Conference papers on the topic "Genetic transcription"

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Reis, Gustavo, Nuno Fonseca, and Francisco Ferndandez. "Genetic Algorithm Approach to Polyphonic Music Transcription." In 2007 IEEE International Symposium on Intelligent Signal Processing. IEEE, 2007. http://dx.doi.org/10.1109/wisp.2007.4447608.

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Mukhopadhyay, Anirban, Darrell Whitley, and Renato Tinós. "An efficient implementation of iterative partial transcription for the traveling salesman problem." In GECCO '21: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3449639.3459368.

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Chang, Xiaoyu, Wengang Zhou, Chunguang Zhou, and Yanchun Liang. "Prediction of Transcription Factor Binding Sites Using Genetic Algorithm." In 2006 1ST IEEE Conference on Industrial Electronics and Applications. IEEE, 2006. http://dx.doi.org/10.1109/iciea.2006.257271.

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Reis, Gustavo, and Francisco Fernandez Vega. "Electronic synthesis using genetic algorithms for automatic music transcription." In the 9th annual conference. New York, New York, USA: ACM Press, 2007. http://dx.doi.org/10.1145/1276958.1277348.

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"Neutrality through Transcription & Translation in Genetic Algorithm Representation." In International Conference on Evolutionary Computation Theory and Applications. SciTePress - Science and and Technology Publications, 2012. http://dx.doi.org/10.5220/0004156702200225.

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Tishin, A. E., O. I. Yarovaya, S. S. Efstifeeva, A. R. Imatdinov, and I. R. Imatdinov. "MINIGENOMIC AND PSEUDOTYPED SYSTEMS FOR SCREENING COMPOUNDS WITH ANTIVIRAL ACTIVITY." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-262.

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This research describes approaches and genetic constructs used for high-performance screening studies of organic compounds exhibiting inhibitory activity against the replication-transcription machinery of the Puumala virus.
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Millstein, Joshua, Carrie Breton, Talat Islam, and Benjamin A. Raby. "Methylation Mediated Genetic Effects On Transcription May Affect Susceptibility To Asthma." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a3493.

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Reis, Gustavo, Nuno Fonseca, Francisco Fernandez, and Anibal Ferreira. "A Genetic Algorithm Approach with Harmonic Structure Evolution for Polyphonic Music Transcription." In 2008 IEEE International Symposium on Signal Processing and Information Technology (ISSPIT). IEEE, 2008. http://dx.doi.org/10.1109/isspit.2008.4775722.

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Wang, Wanyu, Xiaoyu Chang, and Chunguang Zhou. "Combining Greedy Method and Genetic Algorithm to Identify Transcription Factor Binding Sites." In 2006 Sixth International Conference on Hybrid Intelligent Systems (HIS'06). IEEE, 2006. http://dx.doi.org/10.1109/his.2006.264898.

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Reis, Gustavo, and Francisco Vega. "A novel approach to automatic music transcription using electronic synthesis and genetic algorithms." In the 2007 GECCO conference companion. New York, New York, USA: ACM Press, 2007. http://dx.doi.org/10.1145/1274000.1274054.

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Reports on the topic "Genetic transcription"

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Pichersky, Eran, Alexander Vainstein, and Natalia Dudareva. Scent biosynthesis in petunia flowers under normal and adverse environmental conditions. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7699859.bard.

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The ability of flowering plants to prosper throughout evolution, and for many crop plants to set fruit, is strongly dependent on their ability to attract pollinators. To that end many plants synthesize a spectrum of volatile compounds in their flowers. Scent is a highly dynamic trait that is strongly influenced by the environment. However, with high temperature conditions becoming more common, the molecular interplay between this type of stress and scent biosynthesis need to be investigated. Using petunia as a model system, our project had three objectives: (1) Determine the expression patterns of genes encoding biosynthetic scent genes (BSGs) and of several genes previously identified as encoding transcription factors involved in scent regulation under normal and elevated temperature conditions. (2) Examine the function of petunia transcription factors and a heterologous transcription factor, PAPl, in regulating genes of the phenylpropanoid/benzenoid scent pathway. (3) Study the mechanism of transcriptional regulation by several petunia transcription factors and PAPl of scent genes under normal and elevated temperature conditions by examining the interactions between these transcription factors and the promoters of target genes. Our work accomplished the first two goals but was unable to complete the third goal because of lack of time and resources. Our general finding was that when plants grew at higher temperatures (28C day/22C night, vs. 22C/16C), their scent emission decreased in general, with the exception of a few volatiles such as vanillin. To understand why, we looked at gene transcription levels, and saw that generally there was a good correlation between levels of transcriptions of gene specifying enzymes for specific scent compounds and levels of emission of the corresponding scent compounds. Enzyme activity levels, however, showed little difference between plants growing at different temperature regimes. Plants expressing the heterologous gene PAPl showed general increase in scent emission in control temperature conditions but emission decreased at the higher temperature conditions, as seen for control plants. Finally, expression of several transcription factor genes decreased at high temperature, but expression of new transcription factor, EOB-V, increased, implicating it in the decrease of transcription of BSGs. The major conclusion of this work is that high temperature conditions negatively affect scent emission from plants, but that some genetic engineering approaches could ameliorate this problem.
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Neff, Michael. Molecular genetic analysis of activation-tagged transcription factors thought to be involved in photomorphogenesis. Office of Scientific and Technical Information (OSTI), June 2011. http://dx.doi.org/10.2172/1116581.

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Stern, David B., and Gadi Schuster. Manipulation of Gene Expression in the Chloroplast: Control of mRNA Stability and Transcription Termination. United States Department of Agriculture, December 1993. http://dx.doi.org/10.32747/1993.7568750.bard.

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Chloroplasts are the site of photosynthesis and of other essential biosynthetic activities in plant cells. Chloroplasts are semi-autonomous organelles, since they contain their own genomes and protein biosynthetic machinery, but depend on the coordinate expression of nuclear genes to assemble macromolecular complexes. The bioeingineering of plants requires manipulation of chloroplast gene expression, and thus a knowledge of the molecular mechanisms that modulate mRNA and protein production. In this proposal the heterotrophic green alga Chlamydomonas reinhardtii has been used as a model system to understand the control and interrelationships between transcription termination, mRNA 3' end processing and mRNA stability in chloroplasts. Chlamydomonas is a unique and ideal system in which to address these issues, because the chloroplast can be easily manipulated by genetic transformation techniques. This research uncovered new and important information on chloroplast mRNA 3' end formation and mRNA stability. In particular, the 3' untranslated regions of chloroplast mRNAs were shown not to be efficient transcription terminators. The endonucleolytic site in the 3' untranslated region was characterized by site directed mutagensis and the role of several 3' untranslated regions in modulating RNA stability and translation has been studied. This information will allow us to experimentally manipulate the expression of chloroplast genes in vivo by post-transcriptional mechanisms, and should be widely applicable to other higher plant systems.
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Eshed-Williams, Leor, and Daniel Zilberman. Genetic and cellular networks regulating cell fate at the shoot apical meristem. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7699862.bard.

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The shoot apical meristem establishes plant architecture by continuously producing new lateral organs such as leaves, axillary meristems and flowers throughout the plant life cycle. This unique capacity is achieved by a group of self-renewing pluripotent stem cells that give rise to founder cells, which can differentiate into multiple cell and tissue types in response to environmental and developmental cues. Cell fate specification at the shoot apical meristem is programmed primarily by transcription factors acting in a complex gene regulatory network. In this project we proposed to provide significant understanding of meristem maintenance and cell fate specification by studying four transcription factors acting at the meristem. Our original aim was to identify the direct target genes of WUS, STM, KNAT6 and CNA transcription factor in a genome wide scale and the manner by which they regulate their targets. Our goal was to integrate this data into a regulatory model of cell fate specification in the SAM and to identify key genes within the model for further study. We have generated transgenic plants carrying the four TF with two different tags and preformed chromatin Immunoprecipitation (ChIP) assay to identify the TF direct target genes. Due to unforeseen obstacles we have been delayed in achieving this aim but hope to accomplish it soon. Using the GR inducible system, genetic approach and transcriptome analysis [mRNA-seq] we provided a new look at meristem activity and its regulation of morphogenesis and phyllotaxy and propose a coherent framework for the role of many factors acting in meristem development and maintenance. We provided evidence for 3 different mechanisms for the regulation of WUS expression, DNA methylation, a second receptor pathway - the ERECTA receptor and the CNA TF that negatively regulates WUS expression in its own domain, the Organizing Center. We found that once the WUS expression level surpasses a certain threshold it alters cell identity at the periphery of the inflorescence meristem from floral meristem to carpel fate [FM]. When WUS expression highly elevated in the FM, the meristem turn into indeterminate. We showed that WUS activate cytokinine, inhibit auxin response and represses the genes required for root identity fate and that gradual increase in WUCHEL activity leads to gradual meristem enlargement that affect phyllotaxis. We also propose a model in which the direction of WUS domain expansion laterally or upward affects meristem structure differently. We preformed mRNA-seq on meristems with different size and structure followed by k-means clustering and identified groups of genes that are expressed in specific domains at the meristem. We will integrate this data with the ChIP-seq of the 4 TF to add another layer to the genetic network regulating meristem activity.
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Arazi, Tzahi, Vivian Irish, and Asaph Aharoni. Micro RNA Targeted Transcription Factors for Fruit Quality Improvement. United States Department of Agriculture, July 2008. http://dx.doi.org/10.32747/2008.7592651.bard.

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Fruits are unique to flowering plants and represent an important component of human and animal diets. Development and maturation of tomato fruit is a well-programmed process, and yet, only a limited number of factors involved in its regulation have been characterized. Micro-RNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in animals and plants. Plant miRNAs have a vital role in the generation of plant forms through post-transcriptional regulation of the accumulation of developmental regulators, especially transcription factors. Recently, we and others have demonstrated that miRNAs and other type of small RNAs are expressed in tomato fruit, and target putative transcription factors during its development and maturation. The original objectives of the approved proposal were: 1. To identify fruit miRNA transcription factor target genes through a bioinformatic approach. 2. To identify fruit miRNA transcription factor target genes up-regulated in tomato Dicer-like 1 silenced fruit. 3. To establish the biological functions of selected transcription factors and examine their utility for improving fleshy fruit quality trait. This project was approved by BARD as a feasibility study to allow initial experiments to peruse objective 2 as described above in order to provide initial evidence that miRNAs do play a role in fruit development. The approach planned to achieve objective 2, namely to identify miRNA transcription factor targets was to clone and silence the expression of a tomato DCL1 homolog in different stages of fruit development and examine alterations to gene expression in such a fruit in order to identify pathways and target genes that are regulated by miRNA via DCL1. In parallel, we characterized two transcription factors that are regulated by miRNAs in the fruit. We report here on the cloning of tomato DCL1 homolog, characterization of its expression in fruit flesh and peel of wild type and ripening mutants and generation of transgenic plants that silence SlDCL1 specifically in the fruit. Our results suggest that the tomato homolog of DCL1, which is the major plant enzyme involved in miRNA biogenesis, is present in fruit flesh and peel and differentially expressed during various stages of fruit development. In addition, its expression is altered in ripening mutants. We also report on the cloning and expression analysis of Sl_SBP and Sl_ARF transcription factors, which serve as targets of miR157 and miR160, respectively. Our data suggest that Sl_SBP levels are highest during fruit ripening supporting a role for this gene in that process. On the other hand Sl_ARF is strongly expressed in green fruit up to breaker indicating a role for that gene at preripening stage which is consistent with preliminary in_situ analyses that suggest expression in ovules of immature green fruit. The results of this feasibility study together with our previous results that miRNAs are expressed in the fruit indeed provide initial evidence that these regulators and their targets play roles in fruit development and ripening. These genes are expected to provide novel means for genetic improvement of tomato fleshy fruit.
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Sessa, Guido, and Gregory Martin. Role of GRAS Transcription Factors in Tomato Disease Resistance and Basal Defense. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696520.bard.

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The research problem: Bacterial spot and bacterial speck diseases of tomato are causedby strains of Xanthomonas campestris pv. vesicatoria (Xcv) and Pseudomonas syringae pv.tomato (Pst), respectively. These bacteria colonize aerial parts of the plant and causesignificant losses in tomato production worldwide. Protection against Xcv and Pst bycultural practices or chemical control has been unsuccessful and there are only limitedsources of genetic resistance to these pathogens. In previous research supported in part byBARD IS-3237-01, we extensively characterized changes in tomato gene expression uponthe onset of spot and speck disease resistance. A remarkable finding of these studies wasthe inducibility in tomato leaves by both Xcv and Pst strains of genes encodingtranscriptional activator of the GRAS family, which has not been previously linked todisease resistance. Goals: Central goals of this research were to investigate the role of GRAS genes in tomatoinnate immunity and to assess their potential use for disease control.Specific objectives were to: 1. Identify GRAS genes that are induced in tomato during thedefense response and analyze their role in disease resistance by loss-of-function experiments.2. Overexpress GRAS genes in tomato and characterize plants for possible broad-spectrumresistance. 3. Identify genes whose transcription is regulated by GRAS family. Our main achievements during this research program are in three major areas:1. Identification of tomato GRAS family members induced in defense responses andanalysis of their role in disease resistance. Genes encoding tomato GRAS family memberswere retrieved from databases and analyzed for their inducibility by Pst avirulent bacteria.Real-time RT-PCR analysis revealed that six SlGRAS transcripts are induced during theonset of disease resistance to Pst. Further expression analysis of two selected GRAS genesshowed that they accumulate in tomato plants in response to different avirulent bacteria orto the fungal elicitor EIX. In addition, eight SlGRAS genes, including the Pst-induciblefamily members, were induced by mechanical stress in part in a jasmonic acid-dependentmanner. Remarkably, SlGRAS6 gene was found to be required for tomato resistance to Pstin virus-induced gene silencing (VIGS) experiments.2. Molecular analysis of pathogen-induced GRAS transcriptional activators. In aheterologous yeast system, Pst-inducible GRAS genes were shown to have the ability toactivate transcription in agreement with their putative function of transcription factors. Inaddition, deletion analysis demonstrated that short sequences at the amino-terminus ofSlGRAS2, SlGRAS4 and SlGRAS6 are sufficient for transcriptional activation. Finally,defense-related SlGRAS proteins were found to localize to the cell nucleus. 3. Disease resistance and expression profiles of transgenic plants overexpressing SlGRASgenes. Transgenic plants overexpressing SlGRAS3 or SlGRAS6 were generated. Diseasesusceptibility tests revealed that these plants are not more resistant to Pst than wild-typeplants. Gene expression profiles of the overexpressing plants identified putative direct orindirect target genes regulated by SlGRAS3 and SlGRAS6. Scientific and agricultural significance: Our research activities established a novel linkbetween the GRAS family of transcription factors, plant disease resistance and mechanicalstress response. SlGRAS6 was found to be required for disease resistance to Pstsuggesting that this and possibly other GRAS family members are involved in thetranscriptional reprogramming that takes place during the onset of disease resistance.Their nuclear localization and transcriptional activation ability support their proposed roleas transcription factors or co-activators. However, the potential of utilizing GRAS familymembers for the improvement of plant disease resistance in agriculture has yet to bedemonstrated.
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Shani, Moshe, and C. P. Emerson. Genetic Manipulation of the Adipose Tissue via Transgenesis. United States Department of Agriculture, April 1995. http://dx.doi.org/10.32747/1995.7604929.bard.

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The long term goal of this study was to reduce caloric and fat content of beef and other red meats by means of genetic modification of the animal such that fat would not be accumulated. This was attempted by introducing into the germ line myogenic regulatory genes that would convert fat tissue to skeletal muscle. We first determined the consequences of ectopic expression of the myogenic regulatory gene MyoD1. It was found that deregulation of MyoD1 did not result in ectopic skeletal muscle formation but rather led to embryonic lethalities, probably due to its role in the control of the cell cycle. This indicated that MyoD1 should be placed under stringent control to allow survival. Embryonic lethalities were also observed when the regulatory elements of the adipose-specific gene adipsin directed the expression of MyoD1 or myogenin cDNAs, suggesting that these sequences are probably not strong enough to confer tissue specificity. To determine the specificity of the control elements of another fat specific gene (adipocyte protein 2-aP2), we fused them to the bacterial b-galactosidase reporter gene and established stable transgenic strains. The expression of the reporter gene in none of the strains was adipose specific. Each strain displayed a unique pattern of expression in various cell lineages. Most exciting results were obtained in a transgenic strain in which cells migrating from the ventro-lateral edge of the dermomyotome of developing somites to populate the limb buds with myoblasts were specifically stained for lacZ. Since the control sequences of the adipsin or aP2 genes did not confer fat specificity in transgenic mice we have taken both molecular and genetic approaches as an initial effort to identify genes important in the conversion of a multipotential cell such as C3H10T1/2 cell to adipoblast. Several novel adipocyte cell lines have been established that differ in the expression of transcription factors of the C/EBP family known to be markers for adipocyte differentiation. These studies revealed that one of the genetic programming changes which occur during 10T1/2 conversion from multipotential cell to a committed adipoblast is the ability to linduce C/EBPa gene expression. It is expected that further analysis of this gene would identify elements which regulate this lineage-specific expression. Such elements might be good candidates in future attempts to convert adipoblasts to skeletal muscle cells in vivo.
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Wagner, D. Ry, Eliezer Lifschitz, and Steve A. Kay. Molecular Genetic Analysis of Flowering in Arabidopsis and Tomato. United States Department of Agriculture, May 2002. http://dx.doi.org/10.32747/2002.7585198.bard.

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The primary objectives for the US lab included: the characterization of ELF3 transcription and translation; the creation and characterization of various transgenic lines that misexpress ELF3; defining genetic pathways related to ELF3 function regulating floral initiation in Arabidopsis; and the identification of genes that either interact with or are regulated by ELF3. Light quality, photoperiod, and temperature often act as important and, for some species, essential environmental cues for the initiation of flowering. However, there is relatively little information on the molecular mechanisms that directly regulate the developmental pathway from the reception of the inductive light signals to the onset of flowering and the initiation of floral meristems. The ELF3 gene was identified as possibly having a role in light-mediated floral regulation since elj3 mutants not only flower early, but exhibit light-dependent circadian defects. We began investigating ELF3's role in light signalling and flowering by cloning the ELF3 gene. ELF3 is a novel gene only present in plant species; however, there is an ELF3 homolog within Arabidopsis. The Arabidopsis elj3 mutation causes arrhythmic circadian output in continuous light; however, we show conclusively normal circadian function with no alteration of period length in elj3 mutants in dark conditions and that the light-dependent arrhythmia observed in elj3 mutants is pleiotropic on multiple outputs regardless of phase. Plants overexpressing ELF3 have an increased period length in constant light and flower late in long-days; furthermore, etiolated ELF3-overexpressing seedlings exhibit a decreased acute CAB2 response after a red light pulse, whereas the null mutant is hypersensitive to acute induction. This finding suggests that ELF3 negatively regulates light input to both the clock and its outputs. To determine whether ELF3's action is phase dependent, we examined clock resetting by light pulses and constructed phase response curves. Absence of ELF3 activity causes a significant alteration of the phase response curve during the subjective night, and overexpression of ELF3 results in decreased sensitivity to the resetting stimulus, suggesting that ELF3 antagonizes light input to the clock during the night. Indeed, the ELF3 protein interacts with the photoreceptor PHYB in the yeast two-hybrid assay and in vitro. The phase ofELF3 function correlates with its peak expression levels of transcript and protein in the subjective night. ELF3 action, therefore, represents a mechanism by which the oscillator modulates light resetting. Furthermore, flowering time is dependent upon proper expression ofELF3. Scientifically, we've made a big leap in the understanding of the circadian system and how it is coupled so tightly with light reception in terms of period length and clock resetting. Agriculturally, understanding more about the way in which the clock perceives and relays temporal information to pathways such as those involved in the floral transition can lead to increased crop yields by enabling plants to be grown in suboptimal conditions.
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Paran, Ilan, and Allen Van Deynze. Regulation of pepper fruit color, chloroplasts development and their importance in fruit quality. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598173.bard.

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Pepper exhibits large natural variation in chlorophyll content in the immature fruit. To dissect the genetic and molecular basis of this variation, we conducted QTL mapping for chlorophyll content in a cross between light and dark green-fruited parents, PI 152225 and 1154. Two major QTLs, pc1 and pc10, that control chlorophyll content by modulation of chloroplast compartment size in a fruit-specific manner were detected in chromosomes 1 and 10, respectively. The pepper homolog of GOLDEN2- LIKE transcription factor (CaGLK2) was found as underlying pc10, similar to its effect on tomato fruit chloroplast development. A candidate gene for pc1was found as controlling chlorophyll content in pepper by the modulation of chloroplast size and number. Fine mapping of pc1 aided by bulked DNA and RNA-seq analyses enabled the identification of a zinc finger transcription factor LOL1 (LSD-One-Like 1) as a candidate gene underlying pc1. LOL1 is a positive regulator of oxidative stress- induced cell death in Arabidopsis. However, over expression of the rice ortholog resulted in an increase of chlorophyll content. Interestingly, CaAPRR2 that is linked to the QTL and was found to affect immature pepper fruit color in a previous study, did not have a significant effect on chlorophyll content in the present study. Verification of the candidate's function was done by generating CRISPR/Cas9 knockout mutants of the orthologues tomato gene, while its knockout experiment in pepper by genome editing is under progress. Phenotypic similarity as a consequence of disrupting the transcription factor in both pepper and tomato indicated its functional conservation in controlling chlorophyll content in the Solanaceae. A limited sequence diversity study indicated that null mutations in CaLOL1 and its putative interactorCaMIP1 are present in C. chinensebut not in C. annuum. Combinations of mutations in CaLOL1, CaMIP1, CaGLK2 and CaAPRR2 are required for the creation of the extreme variation in chlorophyll content in Capsicum.
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Ginzberg, Idit, and Walter De Jong. Molecular genetic and anatomical characterization of potato tuber skin appearance. United States Department of Agriculture, September 2008. http://dx.doi.org/10.32747/2008.7587733.bard.

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Potato (Solanum tuberosum L.) skin is composed of suberized phellem cells, the outer component of the tuber periderm. The focus of the proposed research was to apply genomic approaches to identify genes that control tuber skin appearance - smooth and shiny skin is highly preferred by the customers while russeted/netted skin potatoes are rejected. The breeding program (at Cornell University) seeks to develop smooth-skin varieties but has encountered frequent difficulties as inheritance of russeting involves complementary action by independently segregating genes, where a dominant allele at each locus is required for any degree of skin russeting. On the other hand, smooth-skin varieties frequently develop unsightly russeting in response to stress conditions, mainly high soil temperatures. Breeding programs in Israel aimed towards the improvement of heat tolerant varieties include skin quality as one of the desired characteristics. At the initiation of the present project it was unclear whether heat induced russeting and genetically inherited russeting share the same genes and biosynthesis pathways. Nevertheless, it has been suggested that russeting might result from increased periderm thickness, from strong cohesion between peridermal cells that prevents the outer layers from sloughing off, or from altered suberization processes in the skin. Hence, the original objectives were to conduct anatomical study of russet skin development, to isolate skin and russeting specific genes, to map the loci that determine the russet trait, and to compare with map locations the candidate russet specific genes, as well as to identify marker alleles that associated with russet loci. Anatomical studies suggested that russet may evolve from cracking at the outer layers of the skin, probably when skin development doesn’t meet the tuber expansion rate. Twodimensional gel electrophoresis and transcript profiling (cDNA chip, potato functional genomic project) indicated that in comparison to the parenchyma tissue, the skin is enriched with proteins/genes that are involved in the plant's responses to biotic and abiotic stresses and further expand the concept of the skin as a protective tissue containing an array of plantdefense components. The proteomes of skin from heat stressed tubers and native skin didn’t differ significantly, while transcript profiling indicated heat-related increase in three major functional groups: transcription factors, stress response and protein degradation. Exceptional was ACC synthase isogene with 4.6 fold increased level in the heat stressed skin. Russeting was mapped to two loci: rusB on chromosome 4 and rusC on chromosome 11; both required for russeting. No evidence was found for a third locus rusA that was previously proposed to be required for russeting. In an effort to find a link between the russeting character and the heat-induced russeting an attempt was made to map five genes that were found in the microarray experiment to be highly induced in the skin under heat stress in the segregating russet population. Only one gene was polymorphic; however it was localized to chromosome 2, so cannot correspond to rusB or rusC. Evaluation of AFLP markers tightly linked to rusB and rusC showed that these specific alleles are not associated with russeting in unrelated germplasm, and thus are not useful for MAS per se. To develop markers useful in applied breeding, it will be necessary to screen alleles of additional tightly linked loci, as well as to identify additional russet (heat-induced and/or native) related genes.
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