Relevant bibliographies by topics / Genetic transcription – Regulation

Contents

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

Academic literature on the topic 'Genetic transcription – Regulation'

Author: Grafiati
Published: 4 June 2021
Last updated: 29 January 2023

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Journal articles on the topic "Genetic transcription – Regulation"

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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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Wierda, Rutger, and Peter van den Elsen. "Genetic and Epigenetic Regulation of CCR5 Transcription." Biology 1, no. 3 (December 13, 2012): 869–79. http://dx.doi.org/10.3390/biology1030869.

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Kim, Kwoneel, Hyoeun Bang, Kibaick Lee, and Jung Kyoon Choi. "Genetic Architecture of Transcription and Chromatin Regulation." Genomics & Informatics 13, no. 2 (2015): 40. http://dx.doi.org/10.5808/gi.2015.13.2.40.

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Basu, Urmimala, Alicia M. Bostwick, Kalyan Das, Kristin E. Dittenhafer-Reed, and Smita S. Patel. "Structure, mechanism, and regulation of mitochondrial DNA transcription initiation." Journal of Biological Chemistry 295, no. 52 (October 30, 2020): 18406–25. http://dx.doi.org/10.1074/jbc.rev120.011202.

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Mitochondria are specialized compartments that produce requisite ATP to fuel cellular functions and serve as centers of metabolite processing, cellular signaling, and apoptosis. To accomplish these roles, mitochondria rely on the genetic information in their small genome (mitochondrial DNA) and the nucleus. A growing appreciation for mitochondria's role in a myriad of human diseases, including inherited genetic disorders, degenerative diseases, inflammation, and cancer, has fueled the study of biochemical mechanisms that control mitochondrial function. The mitochondrial transcriptional machinery is different from nuclear machinery. The in vitro re-constituted transcriptional complexes of Saccharomyces cerevisiae (yeast) and humans, aided with high-resolution structures and biochemical characterizations, have provided a deeper understanding of the mechanism and regulation of mitochondrial DNA transcription. In this review, we will discuss recent advances in the structure and mechanism of mitochondrial transcription initiation. We will follow up with recent discoveries and formative findings regarding the regulatory events that control mitochondrial DNA transcription, focusing on those involved in cross-talk between the mitochondria and nucleus.
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Braun, Christian J., Peter M. Bruno, Max A. Horlbeck, Luke A. Gilbert, Jonathan S. Weissman, and Michael T. Hemann. "Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation." Proceedings of the National Academy of Sciences 113, no. 27 (June 20, 2016): E3892—E3900. http://dx.doi.org/10.1073/pnas.1600582113.

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Targeted transcriptional regulation is a powerful tool to study genetic mediators of cellular behavior. Here, we show that catalytically dead Cas9 (dCas9) targeted to genomic regions upstream or downstream of the transcription start site allows for specific and sustainable gene-expression level alterations in tumor cells in vitro and in syngeneic immune-competent mouse models. We used this approach for a high-coverage pooled gene-activation screen in vivo and discovered previously unidentified modulators of tumor growth and therapeutic response. Moreover, by using dCas9 linked to an activation domain, we can either enhance or suppress target gene expression simply by changing the genetic location of dCas9 binding relative to the transcription start site. We demonstrate that these directed changes in gene-transcription levels occur with minimal off-target effects. Our findings highlight the use of dCas9-mediated transcriptional regulation as a versatile tool to reproducibly interrogate tumor phenotypes in vivo.
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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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Fish, Richard J., and Marguerite Neerman-Arbez. "Fibrinogen gene regulation." Thrombosis and Haemostasis 108, no. 09 (2012): 419–26. http://dx.doi.org/10.1160/th12-04-0273.

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SummaryThe Aα, Bβ and γ polypeptide chains of fibrinogen are encoded by a three gene cluster on human chromosome four. The fibrinogen genes (FGB-FGA-FGG) are expressed almost exclusively in hepatocytes where their output is coordinated to ensure a sufficient mRNA pool for each chain and maintain an abundant plasma fibrinogen protein level. Fibrinogen gene expression is controlled by the activity of proximal promoters which contain binding sites for hepatocyte transcription factors, including proteins which influence fibrinogen transcription in response to acute-phase inflammatory stimuli. The fibrinogen gene cluster also contains cis regulatory elements; enhancer sequences with liver activities identified by sequence conservation and functional genomics. While the transcriptional control of this gene cluster is fascinating biology, the medical impetus to understand fibrinogen gene regulation stems from the association of cardiovascular disease risk with high level circulating fibrinogen. In the general population this level varies from about 1.5 to 3.5 g/l. This variation between individuals is influenced by genotype, suggesting there are genetic variants contributing to fibrinogen levels which reside in fibrinogen regulatory loci. A complete picture of how fibrinogen genes are regulated will therefore point towards novel sources of regulatory variants. In this review we discuss regulation of the fibrinogen genes from proximal promoters and enhancers, the influence of acute-phase stimulation, post-transcriptional regulation by miRNAs and functional regulatory variants identified in genetic studies. Finally, we discuss the fibrinogen locus in light of recent advances in understanding chromosomal architecture and suggest future directions for researching the mechanisms that control fibrinogen expression.
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Fung, Jenny N., Jane E. Girling, Samuel W. Lukowski, Yadav Sapkota, Leanne Wallace, Sarah J. Holdsworth-Carson, Anjali K. Henders, et al. "The genetic regulation of transcription in human endometrial tissue." Human Reproduction 32, no. 4 (February 8, 2017): 893–904. http://dx.doi.org/10.1093/humrep/dex006.

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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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Bilecki, Wiktor, and Marzena Maćkowiak. "Gene Expression and Epigenetic Regulation in the Prefrontal Cortex of Schizophrenia." Genes 14, no. 2 (January 18, 2023): 243. http://dx.doi.org/10.3390/genes14020243.

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Schizophrenia pathogenesis remains challenging to define; however, there is strong evidence that the interaction of genetic and environmental factors causes the disorder. This paper focuses on transcriptional abnormalities in the prefrontal cortex (PFC), a key anatomical structure that determines functional outcomes in schizophrenia. This review summarises genetic and epigenetic data from human studies to understand the etiological and clinical heterogeneity of schizophrenia. Gene expression studies using microarray and sequencing technologies reported the aberrant transcription of numerous genes in the PFC in patients with schizophrenia. Altered gene expression in schizophrenia is related to several biological pathways and networks (synaptic function, neurotransmission, signalling, myelination, immune/inflammatory mechanisms, energy production and response to oxidative stress). Studies investigating mechanisms driving these transcriptional abnormalities focused on alternations in transcription factors, gene promoter elements, DNA methylation, posttranslational histone modifications or posttranscriptional regulation of gene expression mediated by non-coding RNAs.
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Dissertations / Theses on the topic "Genetic transcription – Regulation"

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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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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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Lee, Yiu-fai Angus. "Tissue-specific transcriptional regulation of Sox2." Click to view the E-thesis via HKUTO, 2007. http://sunzi.lib.hku.hk/HKUTO/record/B3955739X.

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Lee, Yiu-fai Angus, and 李耀輝. "Tissue-specific transcriptional regulation of Sox2." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B3955739X.

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Ching, Chi-yun Johannes, and 程子忻. "Transcriptional regulation of p16INK4a expression by the forkhead box transcription factor FOXM1." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B29466192.

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Pang, Ting-kai Ronald. "Transcriptional regulation of the human secretin receptor gene /." Hong Kong : University of Hong Kong, 2002. http://sunzi.lib.hku.hk/hkuto/record.jsp?B25059324.

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Jahangiri, Leila. "Combinatorial gene regulation by T-domain transcription factors." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610328.

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Cleavinger, Peter Jay. "Role of the long terminal repeat in transcriptional regulation of rous sarcoma virus gene expression." free to MU campus, to others for purchase, 1996. http://wwwlib.umi.com/cr/mo/fullcit?p9841207.

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Ye, Chaoyang. "Transcription regulation of adeno-associated viruses." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/4709.

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Thesis (Ph. D.)--University of Missouri-Columbia, 2007.
"May 2007" The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Vita. Includes bibliographical references.
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Books on the topic "Genetic transcription – Regulation"

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

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Transcriptional regulation: Methods and protocols. New York: Humana Press, 2012.

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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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Courey, Albert J. Mechanisms in transcriptional regulation. Malden, MA: Blackwell Pub., 2008.

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Gene transcription: Mechanisms and control. London: Blackwell Science, 2001.

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D, Licht Jonathan, and Ravid Katya, eds. Transcription factors: Normal and malignant development of blood cells. New York: Wiley-Liss, 2001.

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

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Gene control. New York: Garland Science, 2010.

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Plant transcription factors: Methods and protocols. New York: Humana, 2011.

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L, Peterson Craig, and Smale Stephen T, eds. Transcriptional regulation in eukaryotes: Concepts, strategies, and techniques. 2nd ed. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory Press, 2009.

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Book chapters on the topic "Genetic transcription – Regulation"

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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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Quarrie, S. A., A. Steed, V. Lazić-jančić, and D. Kovačević. "Genetic variation in ABA production in maize determines the extent of drought-induced gene transcription." In Progress in Plant Growth Regulation, 770–77. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2458-4_95.

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Boycheva, Irina, Ralitsa Georgieva, Lubomir Stoilov, and Vasilissa Manova. "Effects of light and UV-C radiation on the transcriptional activity of COP1 and HY5 gene homologues in barley." In Mutation breeding, genetic diversity and crop adaptation to climate change, 478–86. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0049.

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Abstract Photomorphogenic regulators COP1 (Constitutive Photomorphogenic 1) and HY5 (Elongated Hypocotyl 5) play a key role in plant development by guiding the transition from dark to light growth. In Arabidopsis they are also implicated in the transcriptional control of photolyase genes. Here we characterize the transcript abundance of COP1 and HY5 gene homologues in barley in relation to light-grown conditions and UV-damage response. Etiolated and green 6-day-old seedlings were UV-C irradiated and exposed to light or kept in darkness. The abundance of barley COP1 and HY5 transcripts was assessed by real-time RT-PCR. In etiolated leaves we found several-fold lower levels of COP1 transcripts which reached the levels of the green ones after 1 h of light exposure. Barley HY5 transcripts were very low in the dark-grown seedlings and after 1 h of illumination they increased drastically to levels significantly exceeding those measured in the green leaves. Both genes were upregulated by light in the irradiated plants as well, but to a lesser extent compared with their controls, probably due to the presence of non-repaired DNA damage in the etiolated leaves soon after irradiation. The enhanced transcription of barley COP1 under light is unexpected in view of the well-known function of COP1 as a negative regulator of plant photomorphogenesis but conforms to the positive role reported for AtCOP1 in UV-B signalling. HY5 is recognized as a stimulator of light-inducible genes and our data support such a role for the barley HY5 homologue as well. Our study shows that, in barley seedlings, the regulation of COP1 and HY5 gene expression is achieved through light-positive transcriptional modulation, suggesting that both genes contribute to the de-etiolation phase in barley. According to our knowledge, this is the first quantitation of the COP1 and HY5 mRNAs in barley that also regards the UV-damage response of this crop.
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Jubete, Yolanda, Juan Carlos Zabala, Antonio Juárez, and Fernando De La Cruz. "Transcriptional Regulation of α-Hemolysin Genetic Expression: hly M, a sequence contained in hly C, modulates hemolysin transcription." In Developments in Plant Pathology, 379–97. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0746-4_26.

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Weihe, Andreas, Karsten Liere, and Thomas Börner. "Transcription and Transcription Regulation in Chloroplasts and Mitochondria of Higher Plants." In Organelle Genetics, 297–325. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-22380-8_12.

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Petracek, Marie E., and W. F. Thompson. "Post-Transcriptional Light Regulation of Nuclear-Encoded Genes." In Genetic Engineering, 1–10. Boston, MA: Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4199-8_1.

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Birge, Edward A. "Transcription and Translation: Processes and Basic Regulation." In Bacterial and Bacteriophage Genetics, 85–114. New York, NY: Springer New York, 1994. http://dx.doi.org/10.1007/978-1-4757-2328-1_4.

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Birge, Edward A. "Transcription and Translation: Processes and Basic Regulation." In Bacterial and Bacteriophage Genetics, 103–41. New York, NY: Springer New York, 2000. http://dx.doi.org/10.1007/978-1-4757-3258-0_4.

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Polosa, Paola Loguercio, Marina Roberti, and Palmiro Cantatore. "Mechanism and Regulation of Mitochondrial Transcription in Animal Cells." In Organelle Genetics, 271–95. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-22380-8_11.

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Cairney, J., D. K. Villalon, S. Chang, M. A. D. L. Dias, and R. J. Newton. "Stress-Related Genes in Woody Plants: Transcriptional and Post-Transcriptional Regulation." In Somatic Cell Genetics and Molecular Genetics of Trees, 277–83. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-011-3983-0_38.

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Conference papers on the topic "Genetic transcription – Regulation"

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"Expression analysis and regulation of general transcription repressor, TaDr1, in bread wheat under drought." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-217.

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Frasca, Fabrizio, Matteo Matteucci, Marco Masseroli, and Marco Morelli. "Modeling Gene Transcriptional Regulation by Means of Hyperplanes Genetic Clustering." In 2018 International Joint Conference on Neural Networks (IJCNN). IEEE, 2018. http://dx.doi.org/10.1109/ijcnn.2018.8489054.

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"Role of GATA-family transcription factors in the regulation of chlorophyll biosynthesis in green unicellular algae Chlamydomonas reinhardtii." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-033.

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Wang, JiuYun, GuoLong Ruan, and ZhongMing Li. "Effects of the Transcriptional Rate on the Genetic Positive - Negative Feedback Regulation System." In 2009 First International Conference on Information Science and Engineering. IEEE, 2009. http://dx.doi.org/10.1109/icise.2009.535.

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Ishihama, Akira, Hiroshi Ogasawara, Tomohiro Shimada, Jun Teramoto, Akiko Hasegawa, Yoshimasa Umezawa, Koshiro Yabuki, et al. "Multi-Scale Genetics towards Understanding the Hierarchy of Transcription Factor Network in Genome Regulation." In 2006 IEEE International Symposium on MicroNanoMechanical and Human Science. IEEE, 2006. http://dx.doi.org/10.1109/mhs.2006.320221.

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"Involvement of the red light receptors phytochrome A and phytochrome B in the regulation of gene expression of the plastid transcription apparatus by cytokinin during de-etiolation of A. thaliana." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-039.

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Al-Souhibani, Norah A., Maha Al-Ghamidi, Wijdan Al-Ahmadi, and Khalid SA Khabar. "Abstract A077: Post-transcriptional regulation of CXCR4 by the tristetraprolin/HuR axis in breast cancer." In Abstracts: AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications - October 3-6, 2013; San Diego, CA. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1557-3125.advbc-a077.

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Alalem, Mohamed, Alpana Ray, and Bimal Ray. "Abstract A042: Role of mTOR as a transcriptional regulator in breast cancer." In Abstracts: AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications - October 3-6, 2013; San Diego, CA. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1557-3125.advbc-a042.

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Reports on the topic "Genetic transcription – Regulation"

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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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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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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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4

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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5

Ohad, Nir, and Robert Fischer. Regulation of Fertilization-Independent Endosperm Development by Polycomb Proteins. United States Department of Agriculture, January 2004. http://dx.doi.org/10.32747/2004.7695869.bard.

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Arabidopsis mutants that we have isolated, encode for fertilization-independent endosperm (fie), fertilization-independent seed2 (fis2) and medea (mea) genes, act in the female gametophyte and allow endosperm to develop without fertilization when mutated. We cloned the FIE and MEA genes and showed that they encode WD and SET domain polycomb (Pc G) proteins, respectively. Homologous proteins of FIE and MEA in other organisms are known to regulate gene transcription by modulating chromatin structure. Based on our results, we proposed a model whereby both FIE and MEA interact to suppress transcription of regulatory genes. These genes are transcribed only at proper developmental stages, as in the central cell of the female gametophyte after fertilization, thus activating endosperm development. To test our model, the following questions were addressed: What is the Composition and Function of the Polycomb Complex? Molecular, biochemical, genetic and genomic approaches were offered to identify members of the complex, analyze their interactions, and understand their function. What is the Temporal and Spatial Pattern of Polycomb Proteins Accumulation? The use of transgenic plants expressing tagged FIE and MEA polypeptides as well as specific antibodies were proposed to localize the endogenous polycomb complex. How is Polycomb Protein Activity Controlled? To understand the molecular mechanism controlling the accumulation of FIE protein, transgenic plants as well as molecular approaches were proposed to determine whether FIE is regulated at the translational or posttranslational levels. The objectives of our research program have been accomplished and the results obtained exceeded our expectation. Our results reveal that fie and mea mutations cause parent-of-origin effects on seed development by distinct mechanisms (Publication 1). Moreover our data show that FIE has additional functions besides controlling the development of the female gametophyte. Using transgenic lines in which FIE was not expressed or the protein level was reduced during different developmental stages enabled us for the first time to explore FIE function during sporophyte development (Publication 2 and 3). Our results are consistent with the hypothesis that FIE, a single copy gene in the Arabidopsis genome, represses multiple developmental pathways (i.e., endosperm, embryogenesis, shot formation and flowering). Furthermore, we identified FIE target genes, including key transcription factors known to promote flowering (AG and LFY) as well as shoot and leaf formation (KNAT1) (Publication 2 and 3), thus demonstrating that in plants, as in mammals and insects, PcG proteins control expression of homeobox genes. Using the Yeast two hybrid system and pull-down assays we demonstrated that FIE protein interact with MEA via the N-terminal region (Publication 1). Moreover, CURLY LEAF protein, an additional member of the SET domain family interacts with FIE as well. The overlapping expression patterns of FIE, with ether MEA or CLF and their common mutant phenotypes, demonstrate the versatility of FIE function. FIE association with different SET domain polycomb proteins, results in differential regulation of gene expression throughout the plant life cycle (Publication 3). In vitro interaction assays we have recently performed demonstrated that FIE interacts with the cell cycle regulatory component Retinobalsoma protein (pRb) (Publication 4). These results illuminate the potential mechanism by which FIE may restrain embryo sac central cell division, at least partly, through interaction with, and suppression of pRb-regulated genes. The results of this program generated new information about the initiation of reproductive development and expanded our understanding of how PcG proteins regulate developmental programs along the plant life cycle. The tools and information obtained in this program will lead to novel strategies which will allow to mange crop plants and to increase crop production.
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6

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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7

Dubcovsky, Jorge, Tzion Fahima, Ann Blechl, and Phillip San Miguel. Validation of a candidate gene for increased grain protein content in wheat. United States Department of Agriculture, January 2007. http://dx.doi.org/10.32747/2007.7695857.bard.

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High Grain Protein Content (GPC) of wheat is important for improved nutritional value and industrial quality. However, selection for this trait is limited by our poor understanding of the genes involved in the accumulation of protein in the grain. A gene with a large effect on GPC was detected on the short arm of chromosome 6B in a Triticum turgidum ssp. dicoccoides accession from Israel (DIC, hereafter). During the previous BARD project we constructed a half-million clones Bacterial Artificial Chromosome (BAC) library of tetraploid wheat including the high GPC allele from DIC and mapped the GPC-B1 locus within a 0.3-cM interval. Our long-term goal is to provide a better understanding of the genes controlling grain protein content in wheat. The specific objectives of the current project were to: (1) complete the positional cloning of the GPC-B1 candidate gene; (2) characterize the allelic variation and (3) expression profile of the candidate gene; and (4) validate this gene by using a transgenic RNAi approach to reduce the GPC transcript levels. To achieve these goals we constructed a 245-kb physical map of the GPC-B1 region. Tetraploid and hexaploid wheat lines carrying this 245-kb DIC segment showed delayed senescence and increased GPC and grain micronutrients. The complete sequencing of this region revealed five genes. A high-resolution genetic map, based on approximately 9,000 gametes and new molecular markers enabled us to delimit the GPC-B1 locus to a 7.4-kb region. Complete linkage of the 7.4-kb region with earlier senescence and increase in GPC, Zn, and Fe concentrations in the grain suggested that GPC-B1 is a single gene with multiple pleiotropic effects. The annotation of this 7.4-kb region identified a single gene, encoding a NAC transcription factor, designated as NAM-B1. Allelic variation studies demonstrated that the ancestral wild wheat allele encodes a functional NAC transcription factor whereas modern wheat varieties carry a non-functional NAM-B1 allele. Quantitative PCR showed that transcript levels for the multiple NAMhomologues were low in flag leaves prior to anthesis, after which their levels increased significantly towards grain maturity. Reduction in RNA levels of the multiple NAMhomologues by RNA interference delayed senescence by over three weeks and reduced wheat grain protein, Zn, and Fe content by over 30%. In the transgenic RNAi plants, residual N, Zn and Fe in the dry leaves was significantly higher than in the control plants, confirming a more efficient nutrient remobilization in the presence of higher levels of GPC. The multiple pleiotropic effects of NAM genes suggest a central role for these genes as transcriptional regulators of multiple processes during leaf senescence, including nutrient remobilization to the developing grain. The cloning of GPC-B1 provides a direct link between the regulation of senescence and nutrient remobilization and an entry point to characterize the genes regulating these two processes. This may contribute to their more efficient manipulation in crops and translate into food with enhanced nutritional value. The characterization of the GPC-B1 gene will have a significant impact on wheat production in many regions of the world and will open the door for the identification of additional genes involved in the accumulation of protein in the grain.
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8

Applebaum, Shalom W., Lawrence I. Gilbert, and Daniel Segal. Biochemical and Molecular Analysis of Juvenile Hormone Synthesis and its Regulation in the Mediterranean Fruit Fly (Ceratitis capitata). United States Department of Agriculture, 1995. http://dx.doi.org/10.32747/1995.7570564.bard.

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Original Objectives and revisions: (1) "To determine the biosynthetic pathway of JHB3 in the adult C. capitata CA in order to establish parameters for the future choice and synthesis of suitable inhibitors". Modified: to determine the pattern of FR-7 biosynthesis during normal reproductive maturation, and identify enzymes potentially involved in its synthesis. (2) "To correlate allatal epoxidase activity to the biosynthesis of JHB3 at different stages of reproductive maturation/vitellogenesis and evaluate the hypothesis that a specific JH-epoxidase may be rate limiting". Modified: to study the effects of epoxidase inhibitors on the pattern of allatal JH biosynthesis in vitro and on female reproduction in vive. (3) "To probe and clone the gene homologous to ap from C. capitata, determine its exon-intron organization, sequence it and demonstrate its spatial and temporal expression in larvae, pupae and adults." The "Medfly" (Ceratitis capitata) is a serious polyphagous fruit pest, widely distributed in subtropical regions. Damage is caused by oviposition and subsequent development of larvae. JH's are dominant gonadotropic factors in insects. In the higher Diptera, to which the Medfly belongs, JHB3 is a major homolog. It comprises 95% of the total JH produced in vitro in D. melanogaster, with JH-III found as a minor component. The biosynthesis of both JH-III and JHB3 is dependent on epoxidation of double bonds in the JH molecule. The specificity of such epoxidases is unknown. The male accessory gland D. melanogaster produces a Sex Peptide, transferred to the female during copulation. SP reduces female receptivity while activating specific JH biosynthesis in vitro and inducing oviposition in vive. It also reduces pheromone production and activates CA of the moth Helicoverpa armigera. In a previous study, mutants of the apterous (ap) gene of D. melanogaster were analyzed. This gene induces previteilogenic arrest which can be rescued by external application of JH. Considerable progress has been made in recombinant DNA technology of the Medfly. When fully operative, it might be possible to effectively transfer D. melanogaster endocrine gene-lesions into the Medfly as a strategy for their genetic control. A marked heterogeneity in the pattern of JH homologs produced by Medfly CA was observed. Contrary to the anticipated biosynthesis of JHB;, significant amounts of an unknown JH-like compound, of unknown structure and provisionally termed FR-7, were produced, in addition to significant amounts of JH-III and JHB3. Inhibitors of monooxygenases, devised for their effects on ecdysteroid biosynthesis, affect Medfly JH biosynthesis but do not reduce egg deposition. FR-7 was isolated from incubation media of Medfly CA and examined by various MS procedures, but its structure is not yet resolved. MS analysis is being done in collaboration with Professor R.R.W. Rickards of the Australian National University in Canberra, Australia. A homologue of the ap gene of D. melanogaster exists in the Medfly. LIM domains and the homeo-domain, important for the function of the D. melanogaster ap gene, are conserved here too. Attempts to clone the complete gene were unsuccessful. Due to the complexity of JH homologs, presence of related FR-7 in the biosynthetic products of Medfly CA and lack of reduction in eggs deposited in the presence of monooxygenase inhibitors, inhibition of epoxidases is not a feasible alternative to control Medfly reproduction, and raises questions which cannot be resolved within the current dogma of hormonal control of reproduction in Diptera. The Medfly ap gene has similar domains to the D. melanogaster ap gene. Although mutant ap genes are involved in JH deficiency, ap is a questionable candidate for an endocrine lesion, especially since the D. melanogoster gene functions is a transcription factor.
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9

Fridman, Eyal, and Eran Pichersky. Tomato Natural Insecticides: Elucidation of the Complex Pathway of Methylketone Biosynthesis. United States Department of Agriculture, December 2009. http://dx.doi.org/10.32747/2009.7696543.bard.

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Plant species synthesize a multitude of specialized compounds 10 help ward off pests. and these in turn may well serve as an alternative to synthetic pesticides to reduce environmental damage and health risks to humans. The general goal of this research was to perform a genetic and biochemical dissection of the natural-insecticides methylketone pathway that is specific to the glandular trichomes of the wild species of tomato, Solanumhabrochaites f. glabratum (accession PI126449). Previous study conducted by us have demonstrated that these compounds are synthesized de novo as a derivate pathway of the fatty acid biosynthesis, and that a key enzyme. designated MethylketoneSynthase 1 (MKS 1). catalyzes conversion of the intermediate B-ketoacyl- ACPs to the corresponding Cn-1 methylketones. The approach taken in this proposed project was to use an interspecific F2 population. derived from the cross between the cultivated lV182 and the wild species PIl26449. for three objectives: (i) Analyze the association between allelic status of candidate genes from the fatty acid biosynthesis pathway with the methylketone content in the leaves (ii) Perform bulk segregant analysis of genetic markers along the tomato genome for identifying genomic regions that harbor QTLs for 2TD content (iii) Apply differential gene expression analysis using the isolated glands of bulk segregant for identifying new genes that are involved in the pathway. The genetic mapping in the interspecific F2 population included app. 60 genetic markers, including the candidate genes from the FAS pathway and SSR markers spread evenly across the genome. This initial; screening identified 5 loci associated with MK content including the candidate genes MKS1, ACC and MaCoA:ACP trans. Interesting observation in this genetic analysis was the connection between shape and content of the glands, i.e. the globularity of the four cells, typical to the wild species. was associated with increased MK in the segregating population. In the next step of the research transcriptomic analysis of trichomes from high- and 10w-MK plants was conducted. This analysis identified a new gene, Methy1ketone synthase 2 (MKS2), whose protein product share sequence similarity to the thioesterase super family of hot-dog enzymes. Genetic analysis in the segregating population confirmed its association with MK content, as well as its overexpression in E. coli that led to formation of MK in the media. There are several conclusions drawn from this research project: (i) the genetic control of MK accumulation in the trichomes is composed of biochemical components in the FAS pathway and its vicinity (MKS 1 and MKS2). as well as genetic factors that mediate the morphology of these specialized cells. (ii) the biochemical pathway is now realized different from what was hypothesized before with MKS2 working upstream to I\1KS 1 and serves as the interface between primary (fatty acids) and secondary (MK) metabolism. We are currently testing the possible physical interactions between these two proteins in vitro after the genetic analysis showed clear epistatic interactions. (iii) the regulation of the pathway that lead to specialized metabolism in the wild species is largely mediated by transcription and one of the achievements of this project is that we were able to isolate and verify the specificity of the MKS1 promoter to the trichomes which allows manipulation of the pathways in these cells (currently in progress). The scientific implications of this research project is the advancement in our knowledge of hitherto unknown biochemical pathway in plants and new leads for studying a new family in plants (hot dog thioesterase). The agricultural and biotechnological implication are : (i) generation of new genetic markers that could assist in importing this pathway to cultivated tomato hence enhancing its natural resistance to insecticides, (ii) the discovery of MKS2 adds a new gene for genetic engineering of plants for making new fatty acid derived compounds. This could be assisted with the use of the isolated and verified MKS1 promoter. The results of this research were summarized to a manuscript that was published in Plant Physiology (cover paper). to a chapter in a proceeding book. and one patent was submitted in the US.
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10

Ori, Naomi, and Mark Estelle. Role of GOBLET and Auxin in Controlling Organ Development and Patterning. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7697122.bard.

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The size and shape of plant leaves are extremely diverse within and among species, and are also sensitive to growth conditions. Compound leaves, such as those of tomato, maintain morphogenetic activity during early stages of their development, enabling them to elaborate lateral appendages such as leaflets. The aim of the research project was to understand the interaction between the plant hormone auxin, the putative auxin response inhibitor ENTIRE (E, SlIAA9) and the NAM/CUC transcription factor GOBLET (GOB) in compound-leaf development in tomato (Solanum lycopersicum). The specific aims of the project were: 1. Investigation of the role of GOB in compound-leaf development. 2. Characterization of E function in auxin signaling. 3. Characterization of the role of auxin in compound-leaf development. 4. Investigation of the genetic and molecular interaction between E and GOB. 5. Investigate the role of these factors in fruit development. There were no major changes in these objectives. GOB was shown to mark and promote the boundaries between the leaf and initiating leaflets. Its accurate distribution was found to be required for proper leaflet initiation and separation. E was found to interact with the TIR1 and AFB6 proteins in an auxin-dependant manner, indicating that these are functional auxin receptors that mediate E degradation in the presence of auxin. This was further supported by the stabilization of E by a mutation in domain II of the protein, which is thought to mediate its auxin-dependant degradation. Over expression of this stabilized form in tomato leaves and characterization of the e mutant phenotype and the E expression domain indicated that E acts between initiating leaflets to inhibit auxin response and lamina growth. Generation and analysis of tomato plants expressing the auxin response reporter DR5::VENUS, and analysis of the effect of auxin microapplication or overexpression of an auxin biosynthesis gene, indicated that auxin marks the sites of leaflet initiation and promotes lamina growth. Investigation of the molecular and genetic interaction between auxin, GOB and E revealed a complex network of mutual regulation that is utilized to precisely pattern the leaf margin in a manner that enables the combination of tight control and flexibility. E, auxin and GOB were shown to affect fruit development and fruit set, and in an extension of the project are currently utilized to identify new players that affect these processes. The research project yielded enhanced understanding of the mechanisms of compound leaf patterning and provided tools that will enable the manipulation of leaf shape and fruit set.
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