Relevant bibliographies by topics / Genetic transcription factors

Academic literature on the topic 'Genetic transcription factors'

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Published: 4 June 2021
Last updated: 20 February 2023

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Journal articles on the topic "Genetic transcription factors"

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Keller, Andrew D. "Model genetic circuits encoding autoregulatory transcription factors." Journal of Theoretical Biology 172, no. 2 (January 1995): 169–85. http://dx.doi.org/10.1006/jtbi.1995.0014.

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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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Becskei, Attila. "Tuning up Transcription Factors for Therapy." Molecules 25, no. 8 (April 20, 2020): 1902. http://dx.doi.org/10.3390/molecules25081902.

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The recent developments in the delivery and design of transcription factors put their therapeutic applications within reach, exemplified by cell replacement, cancer differentiation and T-cell based cancer therapies. The success of such applications depends on the efficacy and precision in the action of transcription factors. The biophysical and genetic characterization of the paradigmatic prokaryotic repressors, LacI and TetR and the designer transcription factors, transcription activator-like effector (TALE) and CRISPR-dCas9 revealed common principles behind their efficacy, which can aid the optimization of transcriptional activators and repressors. Further studies will be required to analyze the linkage between dissociation constants and enzymatic activity, the role of phase separation and squelching in activation and repression and the long-range interaction of transcription factors with epigenetic regulators in the context of the chromosomes. Understanding these mechanisms will help to tailor natural and synthetic transcription factors to the needs of specific applications.
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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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Ibrahim, Lara, Jaleh Mesgarzadeh, Ian Xu, Evan T. Powers, R. Luke Wiseman, and Michael J. Bollong. "Defining the Functional Targets of Cap‘n’collar Transcription Factors NRF1, NRF2, and NRF3." Antioxidants 9, no. 10 (October 21, 2020): 1025. http://dx.doi.org/10.3390/antiox9101025.

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The NRF transcription factors NRF1, NRF2, and NRF3, are a subset of Cap‘n’collar transcriptional regulators which modulate the expression of genes harboring antioxidant-response element (ARE) sequences within their genomic loci. Despite the emerging physiological importance of NRF family members, the repertoire of their genetic targets remains incompletely defined. Here we use RNA-sequencing-based transcriptional profiling and quantitative proteomics to delineate the overlapping and differential genetic programs effected by the three NRF transcription factors. We then create consensus target gene sets regulated by NRF1, NRF2, and NRF3 and define the integrity of these gene sets for probing NRF activity in mammalian cell culture and human tissues. Together, our data provide a quantitative assessment of how NRF family members sculpt proteomes and transcriptomes, providing a framework to understand the critical physiological importance of NRF transcription factors and to establish pharmacologic approaches for therapeutically activating these transcriptional programs in disease.
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Sapelnikov, O. V., A. A. Kulikov, O. O. Favorova, N. A. Matveeva, D. I. Cherkashin, O. A. Nikolaeva, and R. S. Akchurin. "Genetic, Epigenetic and Transcription Factors in Atrial Fibrillation." Rational Pharmacotherapy in Cardiology 15, no. 3 (July 6, 2019): 407–15. http://dx.doi.org/10.20996/1819-6446-2019-15-3-407-415.

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Atrial fibrillation (AF) is one of the most common arrhythmia that occurs in patients with cardiovascular diseases. Congenital forms of AF are quite rare. Many studies have shown that genetic, epigenetic and transcription factors may play an important role in the development and the progression of AF. In our review, studies have been conducted on the identification of mutations in ionic and non-ionic channels, possibly associated with AF. These mutations were found only in isolated groups of patients with AF, and in general, monogenic forms of AF are a rare subtype of the disease. Genomic association studies have helped to identify potential links between single nucleotide polymorphisms and AF. The risk of AF in the general population is likely to be determined by the interaction between environmental factors and many alleles. In recent years, the emergence of a genome-wide associative studies has significantly expanded the understanding of the genetic basis for the inheritance of AF and has led to the emergence of new evidence of the important role of genetic factors in the development of AF, in the risk stratification of AF and the recurrence of AF. Epigenetic factors are also important in AF. Epigenetic therapy aimed at treating a disease through exposure to epigenome is currently under development. A newly emerged area of ablatogenomics includes the use of genetic profiles that allow assessing the likelihood of recurrence of AF after catheter ablation. The results of genetic studies in AF show that, in addition to their role in the appearance of congenital heart pathologies, transcription factors play an important role in the pathogenesis of AF.
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Poulat, Francis. "Non-Coding Genome, Transcription Factors, and Sex Determination." Sexual Development 15, no. 5-6 (2021): 295–307. http://dx.doi.org/10.1159/000519725.

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In vertebrates, gonadal sex determination is the process by which transcription factors drive the choice between the testicular and ovarian identity of undifferentiated somatic progenitors through activation of 2 different transcriptional programs. Studies in animal models suggest that sex determination always involves sex-specific transcription factors that activate or repress sex-specific genes. These transcription factors control their target genes by recognizing their regulatory elements in the non-coding genome and their binding motifs within their DNA sequence. In the last 20 years, the development of genomic approaches that allow identifying all the genomic targets of a transcription factor in eukaryotic cells gave the opportunity to globally understand the function of the nuclear proteins that control complex genetic programs. Here, the major transcription factors involved in male and female vertebrate sex determination and the genomic profiling data of mouse gonads that contributed to deciphering their transcriptional regulation role will be reviewed.
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Schödel, Johannes, David Robert Mole, and Peter John Ratcliffe. "Pan-genomic binding of hypoxia-inducible transcription factors." Biological Chemistry 394, no. 4 (April 1, 2013): 507–17. http://dx.doi.org/10.1515/hsz-2012-0351.

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Abstract Hypoxia-inducible transcription factors (HIFs) mediate the cellular response to hypoxia. HIF-DNA binding triggers a transcriptional program that acts to both restore oxygen homeostasis and adapt cells to low oxygen availability. In this context, HIF is centrally involved in many physiologic and pathophysiological processes such as development, high altitude adaptation, ischemic disease, inflammation, and cancer. The recent development of chromatin immunoprecipitation coupled to genome-wide DNA sequence analysis allows the position and extent of HIF binding to DNA to be characterized across the entire genome and correlated with genetic, epigenetic, and transcriptional analyses. This review summarizes recent pan-genomic analyses of HIF binding and HIF-dependent transcriptional regulation.
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Kamikubo, Yasuhiko. "Genetic compensation of RUNX family transcription factors in leukemia." Cancer Science 109, no. 8 (August 2018): 2358–63. http://dx.doi.org/10.1111/cas.13664.

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Ozanne, Bradford W., Heather J. Spence, Lynn C. McGarry, and Robert F. Hennigan. "Invasion is a genetic program regulated by transcription factors." Current Opinion in Genetics & Development 16, no. 1 (February 2006): 65–70. http://dx.doi.org/10.1016/j.gde.2005.12.012.

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Dissertations / Theses on the topic "Genetic transcription factors"

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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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Woo, Andrew Jonghan. "Characterization and identification of transcription factors that bind to the tumor necrosis factor -308 polymorphism." University of Western Australia. School of Biomedical and Chemical Sciences, 2003. http://theses.library.uwa.edu.au/adt-WU2004.0044.

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[Formulae and special characters can only be approximated. Please see the pdf version of this abstract for an accurate reproduction.] Tumor necrosis factor (TNF) is a pleiotropic cytokine that mediates a long list of immunological and pathophysiological processes. TNF is produced by a wide variety of cells including immune and non-immune cells, however in most cell types TNF is not expressed prior to stimulation. The function of TNF is mediated via its trimeric domain by binding to TNF receptors that are found on most types of cells, especially of the haematopoietic systems, hence transpiring its effects on a wide variety of cells and organ systems. The cytotoxic (apoptosis) and pro-inflammatory (differentiation, proliferation and activation) functions of TNF are protective but can also result in pathological or deleterious consequences. A biallelic G to A transition polymorphism in the promoter region of TNF at nucleotide position 308 from the transcription start site is suggested to be involved in differential transcriptional regulation of TNF expression. The high TNF producing 308A allele is associated with susceptibility to or worse outcome of many infectious diseases in addition to autoimmune and other pathophysiological conditions. A previous study in our laboratory observed a selective affinity towards the polymorphic 308A allele by an EMSA protein(s) complex, named E. Several other protein complexes were found along with complex E and one of them was identified as Sp1. The identification of complex E was unsuccessful but it was hypothesized to play a major role as transcriptional activator in 308A allele individuals hence transpiring its effect in various pathophysiological states. In this study, the EMSA complexes observed in the TNF promoter region between nucleotides 322 to 283, encompassing the 308 polymorphism, is characterized. EMSA using mutated oligonucleotides mapped the binding sites of complexes B, C, D and E. TRANSFAC database search in addition to previous work revealed the identity of complex C as Sp1 but the rest of complexes remained unknown. Moreover, in contrast to our previous study, the protein(s) in the complex E was found to preferentially bind 308G nucleotide hence posing as a transcriptional repressor, resulting in decreased production state of TNF in 308G allele individuals than 308A allele individuals. In order to characterize putative transcription factors binding to the promoter region, first the biochemical characteristics such as the effects of temperature, salts and cations on DNA binding ability of EMSA complexes were studied. EMSA complexes B, C, DI and E required cations, probably Zn+2, to bind DNA. By optimizing a technique that couples EMSA with SDS-PAGE, the molecular weight of C, DI and E was determined. A novel technique that couples EMSA with IEF determined the pI of complexes B, C, D, DI and E. Although a commonly used technique of identifying unknown DNA-binding protein of interest, Yeast One-Hybrid assay, did not identify complex E, the novel identification method involving chromatography, two-dimensional electrophoresis, EMSA, mass spectrometry and database interrogation successfully identified TNF EMSA complex E as transcription factor Ying Yang 1 (YY1). Supershift EMSA confirmed complex E as YY1. In addition, the supershift assay showed presence of Sp1 and Sp3 in complex C. Similarly, complex DI is identified as Sp3. The novel method in identifying DNA-binding proteins is particularly useful as this technique allows identification of protein seen in EMSA without the need of extensive identification process. YY1 binds to a 6 base pair sequence, 5? TTGAGG 3?, from nt 295 to 290 of TNF promoter. The loss of affinity in 308A allele is caused by transition of underlined G nucleotide to A. The determined and described molecular weight of YY1 in literature is 60 kDa while the theoretical weight is 45 kDa. Both the determined and theoretical pI of YY1 is 5.8. YY1 is a multifunctional transcription factor implicated in both positive and negative regulation of gene expression as well as in initiation of transcription. It is ubiquitously expressed in growing, differentiated, and growth-arrested cells. Although future experiment is yet to establish in vivo presence of YY1 in TNF promoter, our study so far provides convincing evidence that the putative transcription factor that has selective affinity towards 308G allele is indeed YY1.
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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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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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Tai, C. P. Andrew. "An in vivo analysis of specificity of gene transactivation by SOX proteins." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B36906438.

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Tai, C. P. Andrew, and 戴賜鵬. "An in vivo analysis of specificity of gene transactivation by SOX proteins." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B36906438.

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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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Mekala, Vijaya Krishna Wysocka-Diller Joanna. "Isolation and characterization of Scarecrow suppressor mutants in Arabidopsis thaliana." Auburn, Ala, 2008. http://repo.lib.auburn.edu/EtdRoot/2008/FALL/Biological_Sciences/Thesis/Mekala_Vijaya_18.pdf.

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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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Eustis, Robyn Lynn. "The Role of Pyrococcus furiosus Transcription Factor E in Transcription Iniitiation." PDXScholar, 2015. https://pdxscholar.library.pdx.edu/open_access_etds/2522.

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All sequenced archaeal genomes encode a general transcription factor, TFE, which is highly conserved and homologous to the alpha subunit of the eukaryotic transcription factor TFIIE. TFE functions to increase promoter opening efficiency during transcription initiation, although the mechanism for this is unclear. The N-terminus of TFE contains a common DNA binding motif, a winged helix. At the tip of this winged helix is a highly conserved region of aromatic amino acids that is close to DNA during initiation. TFE activation can compensate for mutations in another transcription factor, TFB2, which is homologous to TFIIB. P. furiosus encodes two paralogs of the eukaryotic RNA polymerase II transcription factor TFIIB: TFB1 and TFB2. TFB2 lacks a portion of the highly conserved N-terminus, and functions in transcription complexes at a lower efficiency than TFB1. It has been demonstrated that the presence of TFE is able to assist in transcription with TFB2 in vitro bringing its efficiency to almost TFB1 levels. Thus, TFB2 provides a unique opportunity to evaluate the function of the TFE winged helix in transcription. In this study the aromatic patch of the TFE winged helix was mutated to test its role in activation of TFB1 and TFB2-containing transcription complexes, because this aromatic patch is required for full TFE activity especially when NTP concentrations are low.
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Books on the topic "Genetic transcription factors"

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Transcription factors and human disease. New York: Oxford University Press, 1998.

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

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

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Latchman, David S. Eukaryotic transcription factors. 5th ed. Great Britain: Academic Press, 2008.

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Eukaryotic transcription factors. 4th ed. Oxford: Academic, 2004.

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Latchman, David S. Eukaryotic transcription factors. 5th ed. Amsterdam: Elsevier/Academic Press, 2008.

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Furlong, Eileen E. M. Tissue-specific regulation of gene expression by the transcription factors Ying-Yang 1 and nuclear factor 1. Dublin: University College Dublin, 1996.

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

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

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Book chapters on the topic "Genetic transcription factors"

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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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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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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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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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Han, Yuanhong, Dong-Man Khu, Ivone Torres-Jerez, Michael Udvardi, and Maria J. Monteros. "Plant Transcription Factors as Novel Molecular Markers for Legumes." In Sustainable use of Genetic Diversity in Forage and Turf Breeding, 421–25. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-8706-5_61.

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Cominelli, Eleonora, Giuliana Gusmaroli, Lucio Conti, Domenico Allegra, Katia Petroni, and Chiara Tonelli. "Role of Arabidopsis MYB transcription factors in osmotic stress." In Plant Tolerance to Abiotic Stresses in Agriculture: Role of Genetic Engineering, 181–94. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4323-3_13.

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Labelle, Yves, and Olivier Delattre. "Chromosome Translocations Generating Chimeric Transcription Factors, Unique Genetic Events with Pleiotropic Cellular Consequences." In Oncogenes as Transcriptional Regulators, 77–105. Basel: Birkhäuser Basel, 1997. http://dx.doi.org/10.1007/978-3-0348-8934-6_3.

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Hrmova, Maria, and Sergiy Lopato. "Enhancing Abiotic Stress Tolerance in Plants by Modulating Properties of Stress Responsive Transcription Factors." In Genomics of Plant Genetic Resources, 291–316. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-7575-6_12.

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Nieva, Claudia, Dimosthenis Kizis, Adela Goday, Victoria Lumbreras, and Montserrat Pagès. "PLANT AP2/EREBP AND bZIP TRANSCRIPTION FACTORS: STRUCTURE AND FUNCTION." In Plant Tolerance to Abiotic Stresses in Agriculture: Role of Genetic Engineering, 157–80. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4323-3_12.

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Paro, Renato, Ueli Grossniklaus, Raffaella Santoro, and Anton Wutz. "Chromatin Dynamics." In Introduction to Epigenetics, 29–47. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-68670-3_2.

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AbstractThe nucleus of a eukaryotic cell is a very busy place. Not only during replication of the DNA, but at any time in the cell cycle specific enzymes need access to genetic information to process reactions such as transcription and DNA repair. Yet, the nucleosomal structure of chromatin is primarily inhibitory to these processes and needs to be resolved in a highly orchestrated manner to allow developmental, organismal, and cell type-specific nuclear activities. This chapter explains how nucleosomes organize and structure the genome by interacting with specific DNA sequences. Variants of canonical histones can change the stability of the nucleosomal structure and also provide additional epigenetic layers of information. Chromatin remodeling complexes work locally to alter the regular beads-on-a-string organization and provide access to transcription and other DNA processing factors. Conversely, factors like histone chaperones and highly precise templating and copying mechanisms are required for the reassembly of nucleosomes and reestablishment of the epigenetic landscape after passage of activities processing DNA sequence information. A very intricate molecular machinery ensures a highly dynamic yet heritable chromatin template.
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Conference papers on the topic "Genetic transcription factors"

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Katyshev, A. I., N. B. Katysheva, I. V. Fedoseeva, and G. B. Borovskii. "INVESTIGATION OF INDIVIDUAL MITOCHONDRIAL TRANSCRIPTION TERMINATION FACTORS (mTERFs) ROLE IN REALIZATION OF GENETIC PROCESSES IN ARABIDOPSIS MITOCHONDRIA." In The All-Russian Scientific Conference with International Participation and Schools of Young Scientists "Mechanisms of resistance of plants and microorganisms to unfavorable environmental". SIPPB SB RAS, 2018. http://dx.doi.org/10.31255/978-5-94797-319-8-917-920.

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Shabaldin, A. V., L. N. Igisheva, and A. A. Rumyanceva. "CONTRIBUTION OF GENETIC PREDICTORS TO FORMATION OF HEALTH DEFICIENCY IN THE SEPARATE PERIOD AFTER CARDIAC SURGERY TREATMENT OF CONGENITAL HEART DEFECTS." In I International Congress “The Latest Achievements of Medicine, Healthcare, and Health-Saving Technologies”. Kemerovo State University, 2023. http://dx.doi.org/10.21603/-i-ic-151.

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Objective: To study the contribution of xenobiotic biotransformation enzyme genes, transcription factors, inflammatory and immune response receptors in determining health deficiency in the separated period after cardiac surgery for congenital heart disease. Materials and methods. 116 children who underwent radical correction of CHD were examined. An assessment of the catamnesis of these children and genetic typing of genes encoding enzymes for the biotransformation of xeno- and endobiotics (GSTP, CYP1A2, CYP1A1), involved in the determination of cardiogenesis and processes in cardiomyocytes (CRELD-1, GATA-6, NOTCH-1), innate ( TREM-1) and adaptive (HLA-DR) immunity. The search for predictors of functioning deficit by physical, psycho-emotional, social, mental types was carried out using multiple logistic regression. Results. The level of functioning of various components of health one year after surgical treatment was associated with the same factors. These factors negatively affecting the health of children one year after heart surgery were: unfavorable living conditions, as well as genetic predictor markers HLA-DRB1*07 and Creld1 T/C (rs9878047)*T.
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Moiseenko, T., E. Frantsiyants, M. Vovkochina, M. Adamyan, N. Chernikova, D. Vodolazhsky, and V. Bandovkina. "EP582 Association between changes in relative expression of genetic loci encoding transcription factors and age and endometrial cancer grade." In ESGO Annual Meeting Abstracts. BMJ Publishing Group Ltd, 2019. http://dx.doi.org/10.1136/ijgc-2019-esgo.639.

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Andrechek, ER. "Abstract P1-03-04: Genomic Prediction and Genetic Validation of a Role for the E2F Transcription Factors in Breast Cancer." In Abstracts: Thirty-Third Annual CTRC‐AACR San Antonio Breast Cancer Symposium‐‐ Dec 8‐12, 2010; San Antonio, TX. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/0008-5472.sabcs10-p1-03-04.

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El-Esawi, Mohamed A. "Functional Role of NAC Transcription Factors in Stress Responses and Genetic Diversity of Rice Plants Grown under Salt Stress Conditions." In 1st International Electronic Conference on Biological Diversity, Ecology and Evolution. Basel, Switzerland: MDPI, 2021. http://dx.doi.org/10.3390/bdee2021-09532.

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Roberts, Michael, Nicole Briceno, Jamie Bugel, Catherine Campbell, Mary Dickinson, Trevor McCarthy, Phoebe Oldach, Natalie Stanley, and Jeffrey Forrester. "Abstract 4202: Genetic re-programming of the AML cell line HL-60 during differentiation: Roles of the EGR/NAB and NR4A transcription factors." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-4202.

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Malcata, F. Xavier. "Engineering of microalgae toward biodiesel: Facts and prospects." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/jeul5047.

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Excessive release to the atmosphere of greenhouse-effect gases—arising from combustion of fossil fuels, has urged a worldwide search for alternative sources of environment-friendly fuels; microalgae constitute an interesting possibility, owing to their widespread presence in most habitats and unique ability to synthesize oil. Microalgae require indeed only sunlight and water to grow—both freely available; together with CO2 as source of carbon—which concomitantly conveys a path for its direct sequestering from the atmosphere; and low-cost inorganic sources of phosphorus and nitrogen. However, the efficiency of the associated metabolic processes is still poor—and this has so far hampered economic feasibility of such microbial factories for eventual manufacture of biodiesel. Recent advances in genetic engineering tools, systems and synthetic biology, and bioinformatics and omics have widened the portfolio of possibilities for tailor-made genome engineering of microalgae. A holistic approach is needed to metabolic engineering, in which various aspects of cellular metabolism—including transcription factors, transporters, competing pathways, and balance between growth and proliferation are to be taken into account. In attempts to harness the potential of genetic engineering upon microalga-mediated oil production, a realistic assessment of risks and opportunities is a must. The current state-of-the-art of metabolic engineering approaches will accordingly be presented, aimed at enhancing lipid productivity by microalgal strains; technical issues will be critically discussed as well. An overview of the challenges and prospects for technical applicability of such techniques will be tackled, focused on oil for esterification downstream as biodiesel—along with ethical concerns associated to large-scale utilization of such tools.
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"WOX and KNOX transcription factors in symbiotic nodule development." 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/plantgen2019-098.

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"Clusters of transcription factor binding sites in plant genomes." 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/plantgen2019-042.

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Vieira, Daniella Serafin Couto, Laura Otto Walter, Ana Carolina Rabello de Moraes, João Péricles da Silva Jr, and Maria Cláudia Santos Silva. "CROSS-SECTIONAL ANALYSIS OF CLINICAL AND MORPHOLOGICAL FACTORS OF BREAST CANCER IMMUNOPHENOTYPES: A COMPARATIVE STUDY OF TWO DIFFERENT METHODOLOGIES OVER A 24‑YEAR HISTORICAL SERIES." In Scientifc papers of XXIII Brazilian Breast Congress - 2021. Mastology, 2021. http://dx.doi.org/10.29289/259453942021v31s1043.

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Introduction: Breast cancer (BC) is the most incident form of cancer in women worldwide. The widespread use of breast screening programs, as well advances in molecular biology, and new drugs in chemotherapy have contributed to the recent survival rate improvement in high income countries. Furthermore, the study of cancer genome led to the elucidation of the intrinsic subtypes of invasive breast cancer (IBC), consequently, the success rate of targeted therapies improved the outcome in patients. However, considering that immunohistochemistry (IHC) is one of the main methods to determine the profile of protein expression in surgical pathology, most antibodies used have a presumed or already established role and represent proteins whose transcription has been previously described in genetic profile studies. Objectives: Describe the prevalence of IBC in women admitted to a public hospital in Brazil from 1994 to 2018, to establish a correlation between two models of immunohistochemical analysis, the 13th St. Gallen Conference classification and the biomarkerdefined subtypes based on HER2 and estrogen receptor (ER) status, and to investigate the profile of these cases. Methods: Retrospective database analysis was performed. 1,335 women with histologic diagnosis of IBC were included in the study from a public hospital in Brazil between 1994 and 2018. Frequencies and univariate associations were estimated by using chi-square tests. Agreement between the immunohistochemical groups were tested by using Cohen’s kappa coefficients. Results: The mean age was 56.1 years. The most prevalent subtype was luminal B/HER2 and the frequency of tumors with worse prognosis was 62.7%. An association was found between histological grade 3 (G3) and the worst prognostic subtypes: non-luminal A (OR=31.18; 95%CI 13.76–70.64), TNBC (OR=8.77; 95%CI 6.20–12.41), non-ER+/HER2- (OR=5.37; 95%CI 4.11–7.04) and ER-/HER2- (OR=8.50; 95%CI 6.10–11.85). A similar association was found for nuclear G3: non-luminal A (OR=6.3; 95%CI 4.29–9.47), TNBC (OR=5.14; 95%CI 3.64–7.31), non-ER+/HER2- (OR=4.83; 95%CI 3.80–6.15) and ER-/HER2- (OR=5.41; 95%CI 3.92–7.50). When the two models of immunohistochemical analysis were compared, the results showed an agreement rate of 99.48% to 100%. Conclusions: Our results show that most cases had worse outcomes, and there was absolute agreement between the two models of immunohistochemical analysis. These results can contribute to institutions that do not have molecular investigation, enabling accessible tools in routine practice.
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Reports on the topic "Genetic transcription factors"

1

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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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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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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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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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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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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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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Sela, Shlomo, and Michael McClelland. Desiccation Tolerance in Salmonella and its Implications. United States Department of Agriculture, May 2013. http://dx.doi.org/10.32747/2013.7594389.bard.

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Salmonella enterica is a worldwide food-borne pathogen, which regularly causes large outbreaks of food poisoning. Recent outbreaks linked to consumption of contaminated foods with low water-activity, have raised interest in understanding the factors that control fitness of this pathogen to dry environment. Consequently, the general objective of this study was to extend our knowledge on desiccation tolerance and long-term persistence of Salmonella. We discovered that dehydrated STm entered into a viable-but-nonculturable state, and that addition of chloramphenicol reduced bacterial survival. This finding implied that adaptation to desiccation stress requires de-novo protein synthesis. We also discovered that dried STm cells develop cross-tolerance to multiple stresses that the pathogen might encounter in the agriculture/food environment, such as high or low temperatures, salt, and various disinfectants. These findings have important implications for food safety because they demonstrate the limitations of chemical and physical treatments currently utilized by the food industry to completely inactivate Salmonella. In order to identify genes involved in desiccation stress tolerance, we employed transcriptomic analysis of dehydrated and wet cells and direct screening of knock-out mutant and transposon libraries. Transcriptomic analysis revealed that dehydration induced expression of ninety genes and down-regulated seven. Ribosomal structural genes represented the most abundant functional group with a relatively higher transcription during dehydration. Other large classes of induced functional groups included genes involved in amino acid metabolism, energy production, ion transport, transcription, and stress response. Initial genetic analysis of a number of up-regulated genes was carried out). It was found that mutations in rpoS, yahO, aceA, nifU, rpoE, ddg,fnr and kdpE significantly compromised desiccation tolerance, supporting their role in desiccation stress response.
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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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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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