Gotowe bibliografie tematyczne / Regulatory genes

Gotowa bibliografia na temat „Regulatory genes”

Autor: Grafiati
Data publikacji: 4 czerwca 2021
Data aktualizacji: 20 lutego 2023

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Artykuły w czasopismach na temat "Regulatory genes"

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Li, Ling, i Harald Vaessin. "Pan-neural Prospero terminates cell proliferation during Drosophila neurogenesis". Genes & Development 14, nr 2 (15.01.2000): 147–51. http://dx.doi.org/10.1101/gad.14.2.147.

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Organogenesis requires coordination between developmental specific regulators and genes governing cell proliferation. Here we show thatDrosophila prospero encodes a critical regulator of the transition from mitotically active cells to terminal differentiated neurons. Loss of pros results in aberrant expression of multiple cell-cycle regulatory genes and ectopic mitotic activity. In contrast, ectopic pros expression causes transcriptional suppression of multiple cell-cycle regulatory genes and premature termination of cell division. pros activity, hence, provides a critical regulatory link between neuronal lineage development and transcriptional regulation of cell cycle regulatory genes.
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Piro, Rosario Michael. "Are all genes regulatory genes?" Biology & Philosophy 26, nr 4 (29.03.2011): 595–602. http://dx.doi.org/10.1007/s10539-011-9251-9.

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Green, A. R., i J. A. Wyke. "NEGATIVE REGULATORY GENES". Lancet 326, nr 8469-8470 (grudzień 1985): 1434. http://dx.doi.org/10.1016/s0140-6736(85)92607-8.

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Chaturongakul, Soraya, Sarita Raengpradub, M. Elizabeth Palmer, Teresa M. Bergholz, Renato H. Orsi, Yuewei Hu, Juliane Ollinger, Martin Wiedmann i Kathryn J. Boor. "Transcriptomic and Phenotypic Analyses Identify Coregulated, Overlapping Regulons among PrfA, CtsR, HrcA, and the Alternative Sigma Factors σB, σC, σH, and σLinListeria monocytogenes". Applied and Environmental Microbiology 77, nr 1 (29.10.2010): 187–200. http://dx.doi.org/10.1128/aem.00952-10.

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ABSTRACTA set of sevenListeria monocytogenes10403S mutant strains, each bearing an in-frame null mutation in a gene encoding a key regulatory protein, was used to characterize transcriptional networks inL. monocytogenes; the seven regulatory proteins addressed include all fourL. monocytogenesalternative sigma factors (σB, σC, σH, and σL), the virulence gene regulator PrfA, and the heat shock-related negative regulators CtsR and HrcA. Whole-genome microarray analyses, used to identify regulons for each of these 7 transcriptional regulators, showed considerable overlap among regulons. Among 188 genes controlled by more than one regulator, 176 were coregulated by σB, including 92 genes regulated by both σBand σH(with 18 of these genes coregulated by σB, σH, and at least one additional regulator) and 31 genes regulated by both σBand σL(with 10 of these genes coregulated by σB, σL, and at least one additional regulator). Comparative phenotypic characterization measuring acid resistance, heat resistance, intracellular growth in J774 cells, invasion into Caco-2 epithelial cells, and virulence in the guinea pig model indicated contributions of (i) σBto acid resistance, (ii) CtsR to heat resistance, and (iii) PrfA, σB, and CtsR to virulence-associated characteristics. Loss of the remaining transcriptional regulators (i.e.,sigH,sigL, orsigC) resulted in limited phenotypic consequences associated with stress survival and virulence. Identification of overlaps among the regulons provides strong evidence supporting the existence of complex regulatory networks that appear to provide the cell with regulatory redundancies, along with the ability to fine-tune gene expression in response to rapidly changing environmental conditions.
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Mern, Demissew S., Seung-Wook Ha, Viola Khodaverdi, Nicole Gliese i Helmut Görisch. "A complex regulatory network controls aerobic ethanol oxidation in Pseudomonas aeruginosa: indication of four levels of sensor kinases and response regulators". Microbiology 156, nr 5 (1.05.2010): 1505–16. http://dx.doi.org/10.1099/mic.0.032847-0.

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In addition to the known response regulator ErbR (former AgmR) and the two-component regulatory system EraSR (former ExaDE), three additional regulatory proteins have been identified as being involved in controlling transcription of the aerobic ethanol oxidation system in Pseudomonas aeruginosa. Two putative sensor kinases, ErcS and ErcS′, and a response regulator, ErdR, were found, all of which show significant similarity to the two-component flhSR system that controls methanol and formaldehyde metabolism in Paracoccus denitrificans. All three identified response regulators, EraR (formerly ExaE), ErbR (formerly AgmR) and ErdR, are members of the luxR family. The three sensor kinases EraS (formerly ExaD), ErcS and ErcS′ do not contain a membrane domain. Apparently, they are localized in the cytoplasm and recognize cytoplasmic signals. Inactivation of gene ercS caused an extended lag phase on ethanol. Inactivation of both genes, ercS and ercS′, resulted in no growth at all on ethanol, as did inactivation of erdR. Of the three sensor kinases and three response regulators identified thus far, only the EraSR (formerly ExaDE) system forms a corresponding kinase/regulator pair. Using reporter gene constructs of all identified regulatory genes in different mutants allowed the hierarchy of a hypothetical complex regulatory network to be established. Probably, two additional sensor kinases and two additional response regulators, which are hidden among the numerous regulatory genes annotated in the genome of P. aeruginosa, remain to be identified.
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Koppenhöfer, Sonja, i Andrew S. Lang. "Interactions among Redox Regulators and the CtrA Phosphorelay in Dinoroseobacter shibae and Rhodobacter capsulatus". Microorganisms 8, nr 4 (14.04.2020): 562. http://dx.doi.org/10.3390/microorganisms8040562.

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Bacteria employ regulatory networks to detect environmental signals and respond appropriately, often by adjusting gene expression. Some regulatory networks influence many genes, and many genes are affected by multiple regulatory networks. Here, we investigate the extent to which regulatory systems controlling aerobic–anaerobic energetics overlap with the CtrA phosphorelay, an important system that controls a variety of behavioral processes, in two metabolically versatile alphaproteobacteria, Dinoroseobacter shibae and Rhodobacter capsulatus. We analyzed ten available transcriptomic datasets from relevant regulator deletion strains and environmental changes. We found that in D. shibae, the CtrA phosphorelay represses three of the four aerobic–anaerobic Crp/Fnr superfamily regulator-encoding genes (fnrL, dnrD, and especially dnrF). At the same time, all four Crp/Fnr regulators repress all three phosphorelay genes. Loss of dnrD or dnrF resulted in activation of the entire examined CtrA regulon, regardless of oxygen tension. In R. capsulatus FnrL, in silico and ChIP-seq data also suggested regulation of the CtrA regulon, but it was only with loss of the redox regulator RegA where an actual transcriptional effect on the CtrA regulon was observed. For the first time, we show that there are complex interactions between redox regulators and the CtrA phosphorelays in these bacteria and we present several models for how these interactions might occur.
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Thompson, Catriona M. A., James P. J. Hall, Govind Chandra, Carlo Martins, Gerhard Saalbach, Supakan Panturat, Susannah M. Bird i in. "Plasmids manipulate bacterial behaviour through translational regulatory crosstalk". PLOS Biology 21, nr 2 (14.02.2023): e3001988. http://dx.doi.org/10.1371/journal.pbio.3001988.

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Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator, controlling the host proteome through direct interaction with host mRNAs and interference with the host’s translational regulatory network. This mRNA interference leads to large-scale proteomic changes in metabolic genes, key regulators, and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ to be encoded on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle.
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Gluecksohn-Waelsch, Salome. "Regulatory genes in development". Trends in Genetics 3 (styczeń 1987): 123–27. http://dx.doi.org/10.1016/0168-9525(87)90201-0.

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Lu, Renfei, Hao Tang, Yue Qiu, Wenhui Yang, Huiying Yang, Dongsheng Zhou, Xinxiang Huang, Lingfei Hu i Yiquan Zhang. "Quorum sensing regulates the transcription of lateral flagellar genes in Vibrio parahaemolyticus". Future Microbiology 14, nr 12 (sierpień 2019): 1043–53. http://dx.doi.org/10.2217/fmb-2019-0048.

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Aim: Investigation of the lateral flagellar (Laf) genes transcription by the quorum sensing (QS) regulators AphA and OpaR in Vibrio parahaemolyticus. Materials & methods: Regulation mechanisms were assessed by combined utilization of swarming motility assay, qPCR, LacZ fusion, EMSA and DNase I footprinting. Results: AphA and OpaR oppositely regulate swarming motility and Laf genes. At high cell density, OpaR bound to the regulatory regions of motY-lafK-fliEFGHIJ, fliMNPQR-flhBA, fliDSTKLA-motAB and lafA to repress their transcription. At low cell density, AphA indirectly activated their transcription. Conclusion: OpaR repression of swarming motility was via its direct repression of Laf genes, while AphA exerted its regulatory effect on swarming motility through unknown regulator(s).
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Choi, Jeongjoon, i Eduardo A. Groisman. "Horizontally acquired regulatory gene activates ancestral regulatory system to promote Salmonella virulence". Nucleic Acids Research 48, nr 19 (12.10.2020): 10832–47. http://dx.doi.org/10.1093/nar/gkaa813.

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Abstract Horizontally acquired genes are typically regulated by ancestral regulators. This regulation enables expression of horizontally acquired genes to be coordinated with that of preexisting genes. Here, we report a singular example of the opposite regulation: a horizontally acquired gene that controls an ancestral regulator, thereby promoting bacterial virulence. We establish that the horizontally acquired regulatory gene ssrB is necessary to activate the ancestral regulatory system PhoP/PhoQ of Salmonella enterica serovar Typhimurium (S. Typhimurium) in mildly acidic pH, which S. Typhimurium experiences inside macrophages. SsrB promotes phoP transcription by binding upstream of the phoP promoter. SsrB also increases ugtL transcription by binding to the ugtL promoter region, where it overcomes gene silencing by the heat-stable nucleoid structuring protein H-NS, enhancing virulence. The largely non-pathogenic species S. bongori failed to activate PhoP/PhoQ in mildly acidic pH because it lacks both the ssrB gene and the SsrB binding site in the target promoter. Low Mg2+ activated PhoP/PhoQ in both S. bongori and ssrB-lacking S. Typhimurium, indicating that the SsrB requirement for PhoP/PhoQ activation is signal-dependent. By controlling the ancestral genome, horizontally acquired genes are responsible for more crucial abilities, including virulence, than currently thought.
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Rozprawy doktorskie na temat "Regulatory genes"

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Chen, Hairong [Verfasser]. "Functional analysis of candidate regulatory genes in regulatory T cells / Hairong Chen". Hannover : Bibliothek der Tierärztlichen Hochschule Hannover, 2013. http://d-nb.info/1032432594/34.

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Hodgkinson, Lisa Marie. "Matrix regulatory genes in the human lens". Thesis, University of East Anglia, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.490590.

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Purpose: The proteinases that cells employ to regulate the matrix include members of the zinc metalloproteinases; expression is likely to influence both the normal and injured human lens, which in tum can affect a number of biological functions e.g. migration. The current study therefore aimed to determine expression profiles in distinct regions ofthe human lens and following mechanical injury. Methods: For specific gene expression analyses the native human lens was dissected into three regions, using sham cataract surgical methods. Primary lens epithelial cell culture provided cells for analysis as a wounded lens system. Native lens capsular bags (CB) were cultured to assess short term wounding responses and ex vivo CBs (obtained with implanted intraocular lenses from cataract surgery sometime prior to death), were analysed to study the long term wounding responses. Total RNA extraction and reverse transcription technologies were developed for real time polymerase chain reaction amplification gene expression analysis. Protein expression was investigated using Western blotting techniques. Results: In the native lens, the overall MMP gene expression was low, while TIMP expression was high. Of the MMP family members, MTI-MMP was the most highly expressed in the epithelium, while MT2-MMP was the most abundant gene in the fibre cells. Moreover, the presence of unprocessed and activated MTI and MT2-MMP were confirmed by Western blotting. Selected adamalysin genes (ADAM-9, -10, -15 and -17) were highly expressed by all native lens regions. In the wounded lens and ex vivo samples transdifferentiation marker expression; alpha smooth muscle actin and fibronectin, was consistent with the different stages following cataract surgery. Significant elevation of specific gene expression was observed follo~ving injury, such as MMP-2, MMP-9, ADAM-9, ADAM-IS and ADAMTS-3. Conclusions: The present study demonstrates that regional distribution of MMPs, TIMPs, ADAMs and ADAMTSs occurs within the human lens. In the native lens expression of matrix degrading proteinases is generally low, while inhibitor expression is high. Following surgical injury, a significant increase in levels of specific genes, such as MMP-2 is observed; these particular genes are therefore likely to play key roles in the wound healing process after cataract surgery and are thus logical subjects for further investigation.
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Coll-Lladó, Clara. "Evolution of muscle regulatory genes in chordates". Thesis, University of St Andrews, 2016. http://hdl.handle.net/10023/16136.

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Uprety, Bhawana. "Transcriptional Regulatory Mechanisms of Ribosomal Protein Genes". OpenSIUC, 2015. https://opensiuc.lib.siu.edu/dissertations/1080.

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Ribosomal protein genes are crucial for ribosome biogenesis. The ribosome itself is responsible for protein synthesis and hence cellular growth and development. Intertwining network of proteins in conjugation with cellular environment such as nutrition and growth factors collectively regulate expression of the ribosomal protein genes. DNA microarray analysis has implicated the role of 26S proteasome in transcriptional regulation of the ribosomal protein genes tying protein degradation to protein synthesis pathway. To determine the mechanism as to how the 26S proteasome promotes transcription of the ribosomal protein genes a series of experiments were performed. The results reveal that the 19S subcomplex of the 26S proteasome is recruited to the promoters of the ribosomal protein genes in a TOR (Target of Rapamycin)-dependent manner. TOR signals environmental cues and controls the expression of the ribosomal protein genes. Thus recruited 19S proteasome subcomplex promotes transcriptional initiation via facilitation of the recruitment of co-activator NuA4 (Nucleasome acetyltransferase of histone H4) complex to activator Rap1. NuA4 enhances PIC (Pre-initiation complex) formation at the core promoter, but it is not clearly understood how does it do so. Researches have identified two different forms of TBP: TAF (TBP associated factor)-dependent form of TBP and TAF-independent form of TBP. This work shows that impaired association of NuA4 interferes with TFIID recruitment, but recruits TAF-independent form of TBP to the core promoter. This recruitment of TBP is dependent on SAGA (Spt-Ada-Gcn5-acetyltransferase). Like ribosomal protein genes, antisense transcription is also enhanced by TAFs. However, it remains unknown whether NuA4 also promotes TAF-regulated antisense transcription. The results illustrate that like ribosomal protein genes, transcription of GAL10 antisense is also promoted by NuA4 HAT (histone acetyl transferase). NuA4 HAT is recruited to the 3’-end of the GAL10 coding sequence, acetylates histone H4 and promotes GAL10 antisense transcription. This work also reveals the roles of other chromatin regulatory factors in controlling antisense transcription. Collectively, these results significantly advance our current understanding of the regulatory mechanisms of ribosomal protein genes’ expression and antisense transcription. The ribosome and antisense are involved in virtually all the biological processes. Aberrant expression of the ribosomal protein genes and antisense transcripts are associated with numerous human disorders including cancers and cardiovascular diseases. Therefore, analyses of their regulatory processes provide valuable information toward understanding the etiology of numerous human diseases with potential therapeutic interventions.
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Chan, Ping-kei. "The study of the regulatory elements of the human [beta]-globin gene". Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B31999062.

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Chan, Ping-kei, i 陳炳基. "The study of the regulatory elements of the human {221}-globin gene". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B31999062.

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Nora, Fabiana Roos. "Interactions between regulatory genes required for meristem development". Thesis, University of East Anglia, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.432435.

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Zhang, Yongquan. "Regulatory elements controlling the expression of OR37 genes". [S.l. : s.n.], 2007. http://nbn-resolving.de/urn:nbn:de:bsz:100-opus-2272.

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Aagaard, Jan Erik. "Evolution of floral regulatory genes in the Lamiales /". view abstract or download file of text, 2004. http://wwwlib.umi.com/cr/uoregon/fullcit?p3136400.

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Thesis (Ph. D.)--University of Oregon, 2004.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 96-104). Also available for download via the World Wide Web; free to University of Oregon users.
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Guo, Xiumei. "Regulatory and functional study of human cytoglobin". Click to view the E-thesis via HKUTO, 2007. http://sunzi.lib.hku.hk/hkuto/record/B3860145X.

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Książki na temat "Regulatory genes"

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Lindsay, Karen. Genetic characterisation of the regulatory genes of TOL plasmid pWWO. Birmingham: Universityof Birmingham, 1987.

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Sansom, Roger. Ingenious genes: How gene regulation networks evolve to control development. Cambridge, Mass: MIT Press, 2011.

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Cancer systems biology. Boca Raton: CRC Press, 2010.

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Bacterial Regulatory Networks. Norfolk, U.K: Caister Academic Press, 2012.

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Gene regulatory networks: Methods and protocols. New York: Humana Press, 2012.

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NATO/CEC, Advanced Research Workshop on "Post-Transcriptional Control of Gene Expression" (1990 Goslar Germany). Post-transcriptional control of gene expression. Berlin: Springer-Verlag, 1990.

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C, Baxter R., Gluckman Peter D i Rosenfeld Ron G, red. The insulin-like growth factors and their regulatory proteins: Proceedings of the Third International Symposium on Insulin-Like Growth Factors, Sydney, 6-10 February 1994. Amsterdam: Excerpta Medica, 1994.

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The regulatory genome: Gene regulatory networks in development and evolution. Oxford: Academic, 2005.

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Shmulevich, Ilya. Probabilistic boolean networks: The modeling and control of gene regulatory networks. Philadelphia: Society for Industrial and Applied Mathematics, 2010.

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R, Dougherty Edward, i Society for Industrial and Applied Mathematics., red. Probabilistic boolean networks: The modeling and control of gene regulatory networks. Philadelphia: Society for Industrial and Applied Mathematics, 2010.

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Części książek na temat "Regulatory genes"

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Rao, Neeraja, i Marilyn J. Telen. "Lutheran Antigens, Lutheran Regulatory Genes, and Lutheran Regulatory Gene Targets". W Molecular Basis of Human Blood Group Antigens, 281–97. Boston, MA: Springer US, 1995. http://dx.doi.org/10.1007/978-1-4757-9537-0_10.

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Murata, Mitsuyoshi, Hiromi Nishiyori-Sueki, Miki Kojima-Ishiyama, Piero Carninci, Yoshihide Hayashizaki i Masayoshi Itoh. "Detecting Expressed Genes Using CAGE". W Transcription Factor Regulatory Networks, 67–85. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0805-9_7.

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Safran, Marilyn, Naomi Rosen, Michal Twik, Ruth BarShir, Tsippi Iny Stein, Dvir Dahary, Simon Fishilevich i Doron Lancet. "The GeneCards Suite". W Practical Guide to Life Science Databases, 27–56. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-5812-9_2.

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AbstractThe GeneCards® database of human genes was launched in 1997 and has expanded since then to encompass gene-centric, disease-centric, and pathway-centric entities and relationships within the GeneCards Suite, effectively navigating the universe of human biological data—genes, proteins, cells, regulatory elements, biological pathways, and diseases—and the connections among them. The knowledgebase amalgamates information from >150 selected sources related to genes, proteins, ncRNAs, regulatory elements, chemical compounds, drugs, splice variants, SNPs, signaling molecules, differentiation protocols, biological pathways, stem cells, genetic tests, clinical trials, diseases, publications, and more and empowers the suite’s Next Generation Sequencing (NGS), gene set, shared descriptors, and batch query analysis tools.
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Cuozzo, Maria, Steve A. Kay i Nam-Hai Chua. "Regulatory Circuits of Light-Responsive Genes". W Plant Gene Research, 131–53. Vienna: Springer Vienna, 1988. http://dx.doi.org/10.1007/978-3-7091-6950-6_8.

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Kaur, Jaswinder, i Catherine Collins. "Regulatory genes in fungal secondary metabolism". W Fungal Biomolecules, 225–37. Chichester, UK: John Wiley & Sons, Ltd, 2015. http://dx.doi.org/10.1002/9781118958308.ch17.

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Hagen, Gretchen, i Tom Guilfoyle. "Auxin-responsive gene expression: genes, promoters and regulatory factors". W Auxin Molecular Biology, 373–85. Dordrecht: Springer Netherlands, 2002. http://dx.doi.org/10.1007/978-94-010-0377-3_9.

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Narberhaus, Franz. "Control of Bacterial Heat Shock and Virulence Genes by RNA Thermometers". W Regulatory RNAs in Prokaryotes, 183–93. Vienna: Springer Vienna, 2012. http://dx.doi.org/10.1007/978-3-7091-0218-3_10.

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Janostiak, Radoslav, i Narendra Wajapeyee. "RNA Modification Regulatory Genes in DNA Damage". W Epitranscriptomics, 249–62. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8808-2_19.

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Kaufmann, Kerstin, i Dijun Chen. "From Genes to Networks: Characterizing Gene-Regulatory Interactions in Plants". W Methods in Molecular Biology, 1–11. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7125-1_1.

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Zhang, Shilu, Sara Knaack i Sushmita Roy. "Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE". W Methods in Molecular Biology, 439–55. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2257-5_24.

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AbstractTranscriptional regulatory networks specify context-specific patterns of genes and play a central role in how species evolve and adapt. Inferring genome-scale regulatory networks in non-model species is the first step for examining patterns of conservation and divergence of regulatory networks. Transcriptomic data obtained under varying environmental stimuli in multiple species are becoming increasingly available, which can be used to infer regulatory networks. However, inference and analysis of multiple gene regulatory networks in a phylogenetic setting remains challenging. We developed an algorithm, Multi-species Regulatory neTwork LEarning (MRTLE), to facilitate such studies of regulatory network evolution. MRTLE is a probabilistic graphical model-based algorithm that uses phylogenetic structure, transcriptomic data for multiple species, and sequence-specific motifs in each species to simultaneously infer genome-scale regulatory networks across multiple species. We applied MRTLE to study regulatory network evolution across six ascomycete yeasts using transcriptomic measurements collected across different stress conditions. MRTLE networks recapitulated experimentally derived interactions in the model organism S. cerevisiae as well as non-model species, and it was more beneficial for network inference than methods that do not use phylogenetic information. We examined the regulatory networks across species and found that regulators associated with significant expression and network changes are involved in stress-related processes. MTRLE and its associated downstream analysis provide a scalable and principled framework to examine evolutionary dynamics of transcriptional regulatory networks across multiple species in a large phylogeny.
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Streszczenia konferencji na temat "Regulatory genes"

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Bonini, Rodrigo. "Speeding up Reinforcement Learning for Inference and Control of Gene Regulatory Networks". W LatinX in AI at Neural Information Processing Systems Conference 2019. Journal of LatinX in AI Research, 2019. http://dx.doi.org/10.52591/lxai2019120821.

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Motivated by the desire to understand genomic functions through interactions between genes and gene products, the research in the area of gene regulatory networks has become a very important object of study in recent years. Probabilistic Boolean Networks (PBN), which are rules-based dynamic systems, are some of the most studied mathematical models to represent networks and their regulations. However, frequently their representation, regulation, and interactions between genes are overly complex to learn and control, requiring a complex model. Reinforcement Learning (RL) is an interesting technique to deal with this problem because it can learn solutions without the need of a model. This approach is used to train autonomous agents who can find solutions to complex problems, including those of regulation and relationships between genes. But its classical approaches are slow when having to learn tasks with many states especially when these tasks have multiple goals and agents. Besides that, learning bad solutions can make the learning process even more difficult and slow. Therefore, some RL approaches and techniques need to be tested in order to verify the best way to flexibilize, adapt and improve them to intervene and control the gene networks.
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Teixeira, Lívia, Izabela Conceição, Paulo Caramelli, Marcelo Luizon i Karina Gomes. "ALZHEIMER’S DISEASE AND TYPE 2 DIABETES MELLITUS: COMMON MIRNAS, GENES AND REGULATORY BIOLOGICAL PATHWAYS". W XIII Meeting of Researchers on Alzheimer's Disease and Related Disorders. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1980-5764.rpda066.

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Background: The increased incidence of Type 2 Diabetes Mellitus (T2DM) in the 21st century, along with the higher risk of developing Alzheimer’s disease (AD) in diabetic patients have stimulated the search for pathways that link glycemic disorders to neurodegeneration. MicroRNAs (miRNAs) are non-coding RNAs that play key roles in regulating gene expression. Objective: To identify miRNAs, genes and their regulatory pathways in common in AD and T2DM. Methods: Literature search was carried out to find miRNAs commonly expressed in AD and T2DM. MiRTarBase database was used to provide experimentally validated information on the interactions between miRNAs and their target genes. The functional enrichment of molecular pathways differentially regulated by these miRNAs was performed using EnrichR with Reactome gene set annotation. Results: We found six circulating miRNAs commonly expressed in both diseases (hsa-mir-21; hsamir-103a-1; hsa-mir-103a-2; hsa-mir-107; hsa-mir-146a and hsa-mir-144), which regulate 129 target genes. The common pathways between AD and T2DM were related to inflammatory mediators, cell death and axon formation signalling with p-adjust <10-5. Conclusion: Our study provides evidence that AD and T2DM share common pathophysiological mechanisms and regulators miRNAs, and suggests miRNAs as potential markers related to both diseases.
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Kumar Das, Jayanta, Suvankar Ghosh, Ranjeet Kumar Rout i Pabitra Pal Choudhury. "A Study of P53 Gene and its Regulatory Genes Network". W 2018 8th International Conference on Cloud Computing, Data Science & Engineering (Confluence). IEEE, 2018. http://dx.doi.org/10.1109/confluence.2018.8442820.

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Yelbay, Belma, Alexander Gow i Hasan M. Jamil. "Ranking novel regulatory genes in gene expression profiles using NetExpress". W SAC 2017: Symposium on Applied Computing. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3019612.3021289.

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Liu, Zhongzhou, i Wenbin Hu. "FSM: A Fast Similarity Measurement for Gene Regulatory Networks via Genes' Influence Power". W Twenty-Eighth International Joint Conference on Artificial Intelligence {IJCAI-19}. California: International Joint Conferences on Artificial Intelligence Organization, 2019. http://dx.doi.org/10.24963/ijcai.2019/632.

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The problem of graph similarity measurement is fundamental in both complex networks and bioinformatics researches. Gene regulatory networks (GRNs) describe the interactions between the molecules in organisms, and are widely studied in the fields of medical AI. By measuring the similarity between GRNs, significant information can be obtained to assist the applications like gene functions prediction, drug development and medical diagnosis. Most of the existing similarity measurements have been focusing on the graph isomorphisms and are usually NP-hard problems. Thus, they are not suitable for applications in biology and clinical research due to the complexity and large-scale features of real-world GRNs. In this paper, a fast similarity measurement method called FSM for GRNs is proposed. Unlike the conventional measurements, it pays more attention to the differences between those influential genes. For the convenience and reliability, a new index defined as influence power is adopted to describe the influential genes which have greater position in a GRN. FSM was applied in nine datasets of various scales and is compared with state-of-art methods. The results demonstrated that it ran significantly faster than other methods without sacrificing measurement performance.
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Ashlock, Daniel, i Wendy Ashlock. "Impact of regulatory genes on optimization behavior". W 2012 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2012. http://dx.doi.org/10.1109/cec.2012.6252981.

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Qian Zhong, R. Boscolo, T. S. Gardner i V. P. Roychowdhury. "Inferring Regulatory Interactions between Transcriptional Factors and Genes by Propagating Known Regulatory Links". W 2007 4th Symposium on Computational Intelligence in Bioinformatics and Computational Biology. IEEE, 2007. http://dx.doi.org/10.1109/cibcb.2007.4221225.

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Chowdhury, Ahsan Raja, Madhu Chetty i Nguyen Xuan Vinh. "Adaptive regulatory genes cardinality for reconstructing genetic networks". W 2012 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2012. http://dx.doi.org/10.1109/cec.2012.6256462.

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Sanchez-Castillo, M., I. M. Tienda-Luna, D. Blanco-Navarro i M. C. Carrion-Perez. "Modified variational method for genes regulatory network learning". W 2010 10th International Conference on Signal Processing (ICSP 2010). IEEE, 2010. http://dx.doi.org/10.1109/icosp.2010.5656711.

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Wilson, Mary E., Lina M. González, Warren C. Ruder i Philip R. LeDuc. "Engineering Magnetic Nanomaterial Production in Magnetotactic Bacteria Through Gene Regulation". W ASME 2012 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/sbc2012-80446.

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Magnetotactic bacteria endogenously synthesize intracellular magnetic nanoparticles (magnetosomes); however, little is known regarding the genetic regulatory networks that control magnetosome production. In this paper, we explore the genetic response of Magnetospirillum magneticum strain AMB-1 to an applied electromagnetic field as a means to identify genes activated by magnetic stimulation. The expression of magnetosome island, flagellar and cytoskeletal genes was found to be differentially altered by magnetic stimulation at short and long times points. These results indicate previously uncharacterized endogenous gene network modules that could be exploited to engineer magnetic bacteria as magnetic nanomaterial producing-machines through gene regulation.
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Raporty organizacyjne na temat "Regulatory genes"

1

Gan, S. Molecular Regulatory Mechanisms of two Senscence-Specific Genes in Arabidopsis. Office of Scientific and Technical Information (OSTI), sierpień 2003. http://dx.doi.org/10.2172/833878.

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Lers, Amnon, i Gan Susheng. Study of the regulatory mechanism involved in dark-induced Postharvest leaf senescence. United States Department of Agriculture, styczeń 2009. http://dx.doi.org/10.32747/2009.7591734.bard.

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Postharvest leaf senescence contributes to quality losses in flowers and leafy vegetables. The general goal of this research project was to investigate the regulatory mechanisms involved in dark-induced leaf senescence. The regulatory system involved in senescence induction and control is highly complex and possibly involves a network of senescence promoting pathways responsible for activation of the senescence-associated genes. Pathways involving different internal signals and environmental factors may have distinctive importance in different leaf senescence systems. Darkness is known to have a role in enhancement of postharvest leaf senescence and for getting an insight into its regulatory mechanism/s we have applied molecular genetics and functional genomics approaches. The original objectives were: 1. Identification of dark-induced SAGs in Arabidopsis using enhancer/promoter trap lines and microarray approaches; 2. Molecular and functional characterization of the identified genes by analyzing their expression and examining the phenotypes in related knockout mutant plants; 3. Initial studies of promoter sequences for selected early dark-induced SAGs. Since genomic studies of senescence, with emphasis on dark-induced senescence, were early-on published which included information on potential regulatory genes we decided to use this new information. This is instead of using the uncharacterized enhancer/promoter trap lines as originally planned. We have also focused on specific relevant genes identified in the two laboratories. Based on the available genomic analyses of leaf senescence 10 candidate genes hypothesized to have a regulatory role in dark-induced senescence were subjected to both expression as well as functional analyses. For most of these genes senescence-specific regulation was confirmed, however, functional analyses using knock-out mutants indicated no consequence to senescence progression. The transcription factor WARK75 was found to be specifically expressed during natural and dark-induced leaf senescence. Functional analysis demonstrated that in detached leaves senescence under darkness was significantly delayed while no phenotypic consequences could be observed on growth and development, including no effect on natural leaf senescence,. Thus, WARKY75 is suggested to have a role in dark-induced senescence, but not in natural senescence. Another regulatory gene identified to have a role in senescence is MKK9 encoding for a Mitogen-Activated Protein Kinase Kinase 9 which is upregulated during senescence in harvested leaves as well as in naturally senescing leaves. MKK9 can specifically phosphorylate another kinase, MPK6. Both knockouts of MKK9 and MPK6 displayed a significantly senescence delay in harvested leaves and possibly function as a phosphorelay that regulates senescence. To our knowledge, this is the first report that clearly demonstrates the involvement of a MAP kinase pathway in senescence. This research not only revealed a new signal transduction pathway, but more important provided significant insights into the regulatory mechanisms underlying senescence in harvested leaves. In an additional line of research we have employed the promoter of the senescence-induced BFN1 gene as a handle for identifying components of the regulatory mechanism. This gene was shown to be activated during darkinduced senescence of detached leaves, as well as natural senescence. This was shown by following protein accumulation and promoter activity which demonstrated that this promoter is activated during dark-induced senescence. Analysis of the promoter established that, at least some of the regulatory sequences reside in an 80 bps long fragment of the promoter. Overall, progress was made in identification of components with a role in dark-induced senescence in this project. Further studies should be done in order to better understand the function of these components and develop approaches for modulating the progress of senescence in crop plants for the benefit of agriculture.
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Bartley, Laura, Y. Wu, L. Zhu, E. C. Brummer i M. Saha. Association Mapping of Cell Wall Synthesis Regulatory Genes and Cell Wall Quality in Switchgrass. Office of Scientific and Technical Information (OSTI), maj 2016. http://dx.doi.org/10.2172/1286475.

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Li, Li, Joseph Burger, Nurit Katzir, Yaakov Tadmor, Ari Schaffer i Zhangjun Fei. Characterization of the Or regulatory network in melon for carotenoid biofortification in food crops. United States Department of Agriculture, kwiecień 2015. http://dx.doi.org/10.32747/2015.7594408.bard.

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The general goals of the BARD research grant US-4423-11 are to understand how Or regulates carotenoid accumulation and to reveal novel strategies for breeding agricultural crops with enhanced β-carotene level. The original objectives are: 1) to identify the genes and proteins in the Or regulatory network in melon; 2) to genetically and molecularly characterize the candidate genes; and 3) to define genetic and functional allelic variation of these genes in a representative germplasm collection of the C. melo species. Or was found by the US group to causes provitamin A accumulation in chromoplasts in cauliflower. Preliminary genetic study from the Israeli group revealed that the melon Or gene (CmOr) completely co-segregated with fruit flesh color in a segregating mapping population and in a wide melon germplasm collection, which set the stage for the funded research. Major conclusions and achievements include: 1). CmOris proved to be the gene that controls melon fruit flesh color and represents the previously described gflocus in melon. 2). Genetic and molecular analyses of CmOridentify and confirm a single SNP that is responsible for the orange and non-orange phenotypes in melon fruit. 3). Alteration of the evolutionarily conserved arginine in an OR protein to both histidine or alanine greatly enhances its ability to promote carotenoid accumulation. 4). OR promotes massive carotenoid accumulation due to its dual functions in regulating both chromoplast biogenesis and carotenoid biosynthesis. 5). A bulk segregant transcriptome (BSRseq) analysis identifies a list of genes associated with the CmOrregulatory network. 6). BSRseq is proved to be an effective approach for gene discovery. 7). Screening of an EMS mutation library identifies a low β mutant, which contains low level of carotenoids due to a mutation in CmOrto produce a truncated form of OR protein. 8). low β exhibits lower germination rate and slow growth under salt stress condition. 9). Postharvest storage of fruit enhances carotenoid accumulation, which is associated with chromoplast development. Our research uncovers the molecular mechanisms underlying the Or-regulated high level of carotenoid accumulation via regulating carotenoidbiosynthetic capacity and storage sink strength. The findings provide mechanistic insights into how carotenoid accumulation is controlled in plants. Our research also provides general and reliable molecular markers for melon-breeding programs to select orange varieties, and offers effective genetic tools for pro-vitamin A enrichment in other important crops via the rapidly developed genome editing technology. The newly discovered low β mutant could lead to a better understanding of the Or gene function and its association with stress response, which may explain the high conservation of the Or gene among various plant species.
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Eshed, Yuval, i John Bowman. Harnessing Fine Scale Tuning of Endogenous Plant Regulatory Processes for Manipulation of Organ Growth. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696519.bard.

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Background and objectives: Manipulation of plant organ growth is one of the primary reasons for the success of mankind allowing increasing amounts of food for human and livestock consumption. In contrast with the successful selection for desirable growth characteristics using plant breeding, transgenic manipulations with single genes has met limited success. While breeding is based on accumulation of many small alterations of growth, usually arise from slight changes in expression patterns, transgenic manipulations are primarily based on drastic, non-specific up-regulation or knock down of genes that can exert different effects during different stages of development. To successfully harness transgenic manipulation to attain desirable plant growth traits we require the tools to subtly regulate the temporal and spatial activity of plant growth genes. Polar morphology along the adaxial/abaxial axis characterizes lateral organs of all plants. Juxtaposition of two cell types along this axis is a prerequisite of laminar growth induction. In the study summarized here, we addressed the following questions: Can we identify and harness components of the organ polarity establishment pathway for prolonged growth? Can we identify specific regulatory sequences allowing spatial and temporal manipulation in various stages of organ development? Can we identify genes associated with YABBY-induced growth alterations? Major conclusions and implications: We showed that regulated expression, both spatially and temporally of either organ polarity factors such as the YABBY genes, or the organ maturation program such as the CIN-TCPs can stimulate substantial growth of leaves and floral organs. Promoters for such fine manipulation could be identified by comparison of non-coding sequences of KAN1, where a highly conserved domain was found within the second intron, or by examination of multiple 5” regions of genes showing transient expression along leaf ontogeny. These promoters illustrate the context dependent action of any gene we examined thus far, and facilitate fine tuning of the complex growth process. Implications, both scientific and agricultural. The present study was carried out on the model organism Arabidopsis, and the broad application of its findings were tested in the tomato crop. We learned that all central regulators of organ polarity are functionally conserved, probably in all flowering plants. Thus, with minor modifications, the rules and mechanisms outlined in this work are likely to be general.
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Lifschitz, Eliezer, i Elliot Meyerowitz. The Relations between Cell Division and Cell Type Specification in Floral and Vegetative Meristems of Tomato and Arabidopsis. United States Department of Agriculture, luty 1996. http://dx.doi.org/10.32747/1996.7613032.bard.

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Meristems were the central issue of our project. Genes that are required for cell division, cell elongation, cell proliferation and cell fate were studied in the tomato system. The analysis of the dUTPase and threonine deaminase genes, along with the dissection of their regulatory regions is completed, while that of the RNR2 and PPO genes is at an advanced stage. All these genes were isolated in our laboratory. In addition, 8 different MADS box genes were studied in transgenic plants and their genetic relevances discovered. We have also shown that a given MADS box gene can modify the polarity of cell division without affecting the fate of the organ. In vivo interaction between two MADS box genes was demonstrated and the functional dependency of the tomato agamous gene on the TM5 gene product established. We have exploited the Knotted1 meristematic gene in conjunction with tomato leaf meristematic genes to show that simple and compound leaves and, for that matter, sepals and compound leaves, are formed by two different developmental programs. In this context we have also isolated and characterized the tomato Knotted1 gene (TKnl) and studied its expression pattern. A new program in which eight different meristematic genes in tomato will be studied emerged as a result of these studies. In essence, we have shown that it is possible to study and manipulate plant developmental systems using reverse genetic techniques and have provided a wealth of new molecular tools to interested colleagues working with tomato. Similarly, genes responsible for cell division, cell proliferation and cell fate were studied in Arabidopsis floral meristems. Among these genes are the TSO1, TSO2, HANABA TARANU and UNUSUAL FLORAL ORGANS genes, each affecting in its own way the number of pattern of cell divisions, and cell fate, in developing Arabodopsis flowers. In addition, new methods have been established for the assessment of the function of regulatory gene action in the different clonal layers of developing floral meristems.
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Peng, Zhaohua PEng, Palmela Ronald i Guo-Liang Wang. Identification of Cell Wall Synthesis Regulatory Genes Controlling Biomass Characteristics and Yield in Rice (Oryza Sativa). Office of Scientific and Technical Information (OSTI), kwiecień 2013. http://dx.doi.org/10.2172/1076786.

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Tucker, Mark L., Shimon Meir, Amnon Lers, Sonia Philosoph-Hadas i Cai-Zhong Jiang. Elucidation of signaling pathways that regulate ethylene-induced leaf and flower abscission of agriculturally important plants. United States Department of Agriculture, styczeń 2012. http://dx.doi.org/10.32747/2012.7597929.bard.

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The Problem: Abscission is a highly regulated process, occurring as a natural terminal stage of development, in which various organs are separated from the parent plant. In most plant species, the process is initiated by a decrease in active auxin in the abscission zone (AZ) and an increase in ethylene, and may be accelerated by postharvest or environmental stresses. Another potential key regulator in abscission is IDA (Inflorescence Deficient in Abscission), which was identified as an essential peptide signal for floral organ abscission in Arabidopsis. However, information is still lacking regarding the molecular mechanisms integrating all these regulators. In our previous BARD funded research we made substantial progress towards understanding these molecular events in tomato, and the study is still in progress. We established a powerful platform for analysis of genes for regulatory proteins expressed in AZ. We identified changes in gene expression for several transcription factors (TFs) directly linked to ethylene and auxin signaling and several additional regulatory proteins not so obviously linked to these hormones. Moreover, we demonstrated using a virus-induced gene silencing (VIGS) assay that several play a functional role in the onset of abscission. Based on these results we have selected 14 genes for further analysis in stably transformed tomato plants. All 14 genes were suppressed by RNA interference (RNAi) using a constitutive promoter, and 5 of them were also suppressed using an abscission-specific promoter. Transformations are currently at different stages of progress including some lines that already display an abscission phenotype. Objectives: We propose here to (1) complete the functional analysis of the stably transformed tomato plants with T2 lines and perform transcriptome analysis using custom abscission-specific microarrays; (2) conduct an indepth analysis of the role of IDA signaling in tomato leaf and flower abscission; (3) perform transcriptome and proteome analyses to extend the earlier gene expression studies to identify transcripts and proteins that are highly specific to the separation layer (i.e., target cells for cell separation) prior to the onset of abscission; (4) extend and compliment the work in tomato using a winnowed set of genes in soybean. Methodology: Next Generation Sequencing (NGS) of mRNA will be used to further increase the list of abscission-associated genes, and for preparation of a custom tomato abscission microarray to test altered gene expression in transgenic plants. Tandem mass spectrometry (LC-MS/MS) of protein extracts from leaf petiole, flower pedicel and their AZ tissues will be used to identify the proteome of the AZ before and during abscission. AZ-specific gene promoters will be used in stably transformed tomato plants to reduce non-target phenotypes. The bean pod mottle virus (BPMV) plasmid vectors will be used for VIGS analysis in soybean. Expected Contribution: Our study will provide new insights into the regulation of ethylene-induced abscission by further revealing the role of key regulators in the process. This will permit development of novel techniques for manipulating leaf and flower abscission, thereby improving the postharvest performance of agriculturally important crops.
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Prusky, Dov, Nancy P. Keller i Amir Sherman. global regulation of mycotoxin accumulation during pathogenicity of Penicillium expansum in postharvest fruits. United States Department of Agriculture, styczeń 2014. http://dx.doi.org/10.32747/2014.7600012.bard.

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Background to the topic- Penicilliumas a postharvest pathogen and producer of the mycotoxin PAT. Penicilliumspp. are destructive phytopathogens, capable of causing decay in many deciduous fruits, during postharvest handling and storage; and the resulting losses can amount to 10% of the stored produce and the accumulation of large amounts of the mycotoxinpatulin. The overall goal of this proposal is to identify critical host and pathogen factors that modulate P. expansummycotoxin genes and pathways which are required for PAT production and virulence. Our preliminary results indicated that gluconic acid are strongly affecting patulin accumulation during colonization. P. expansumacidifies apple fruit tissue during colonization in part through secretion of gluconic acid (GLA). Several publications suggested that GLA accumulation is an essential factor in P. expansumpathogenicity. Furthermore, down regulation of GOX2 significantly reduced PAT accumulation and pathogenicity. PAT is a polyketide and its biosynthesis pathway includes a 15-gene cluster. LaeA is a global regulator of mycotoxin synthesis. It is now known that patulin synthesis might be subjected to LaeA and sometimes by environmental sensing global regulatory factors including the carbon catabolite repressor CreA as well as the pH regulator factor PacC and nitrogen regulator AreA. The mechanisms by which LaeA regulates patulin synthesis was not fully known and was part of our work. Furthermore, the regulatory system that controls gene expression in accordance with ambient pH was also included in our work. PacC protein is in an inactive conformation and is unable to bind to the promoter sites of the target genes; however, under alkaline growth conditions activated PacC acts as both an activator of alkaline-expressed genes and a repressor of acid-expressed genes. The aims of the project- This project aims to provide new insights on the roles of LaeA and PacC and their signaling pathways that lead to GLA and PAT biosynthesis and pathogenicity on the host. Specifically, our specific aims were: i) To elucidate the mechanism of pH-controlled regulation of GLA and PAT, and their contribution to pathogenesis of P. expansum. We are interested to understanding how pH and/or GLA impact/s under PacC regulation affect PAT production and pathogenesis. ii) To characterize the role of LaeA, the global regulator of mycotoxin production, and its effect on PAT and PacC activity. iii) To identify the signaling pathways leading to GLA and PAT synthesis. Using state- of-the-art RNAseq technologies, we will interrogate the transcriptomes of laeAand pacCmutants, to identify the common signaling pathways regulating synthesis of both GLA and PAT. Major conclusions, solutions, achievements- In our first Aim our results demonstrated that ammonia secreted at the leading edge of the fungal colony induced transcript activation of the global pH modulator PacC and PAT accumulation in the presence of GLA. We assessed these parameters by: (i) direct exogenous treatment of P. expansumgrowing on solid medium; (ii) direct exogenous treatment on colonized apple tissue; (iii) growth under self-ammonia production conditions with limited carbon; and (iv) analysis of the transcriptional response to ammonia of the PAT biosynthesis cluster. Ammonia induced PAT accumulation concurrently with the transcript activation of pacCand PAT biosynthesis cluster genes, indicating the regulatory effect of ammonia on pacCtranscript expression under acidic conditions. Transcriptomic analysis of pH regulated processes showed that important genes and BARD Report - Project 4773 Page 2 of 10 functionalities of P. expansumwere controlled by environmental pH. The differential expression patterns of genes belonging to the same gene family suggest that genes were selectively activated according to their optimal environmental conditions to enable the fungus to cope with varying conditions and to make optimal use of available enzymes. Concerning the second and third Aims, we demonstrated that LaeA regulates several secondary metabolite genes, including the PAT gene cluster and concomitant PAT synthesis invitro. Virulence studies of ΔlaeAmutants of two geographically distant P. expansumisolates (Pe-21 from Israel and Pe-T01 from China) showed differential reduction in disease severity in freshly harvested fruit ranging from no reduction for Ch-Pe-T01 strains in immature fruit to 15–25% reduction for both strains in mature fruit, with the ΔlaeAstrains of Is-Pe-21 always showing a greater loss in virulence. Results suggest the importance of LaeA regulation of PAT and other secondary metabolites on pathogenicity. Our work also characterized for the first time the role of sucrose, a key nutritional factor present in apple fruit, as a negative regulator of laeAexpression and consequent PAT production in vitro. This is the first report of sugar regulation of laeAexpression, suggesting that its expression may be subject to catabolite repression by CreA. Some, but not all of the 54 secondary metabolite backbone genes in the P. expansumgenome, including the PAT polyketide backbone gene, were found to be regulated by LaeA. Together, these findings enable for the first time a straight analysis of a host factor that potentially activates laeAand subsequent PAT synthesis.
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Christopher, David A., i Avihai Danon. Plant Adaptation to Light Stress: Genetic Regulatory Mechanisms. United States Department of Agriculture, maj 2004. http://dx.doi.org/10.32747/2004.7586534.bard.

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Original Objectives: 1. Purify and biochemically characterize RB60 orthologs in higher plant chloroplasts; 2. Clone the gene(s) encoding plant RB60 orthologs and determine their structure and expression; 3. Manipulate the expression of RB60; 4. Assay the effects of altered RB60 expression on thylakoid biogenesis and photosynthetic function in plants exposed to different light conditions. In addition, we also examined the gene structure and expression of RB60 orthologs in the non-vascular plant, Physcomitrella patens and cloned the poly(A)-binding protein orthologue (43 kDa RB47-like protein). This protein is believed to a partner that interacts with RB60 to bind to the psbA5' UTR. Thus, to obtain a comprehensive view of RB60 function requires analysis of its biochemical partners such as RB43. Background & Achievements: High levels of sunlight reduce photosynthesis in plants by damaging the photo system II reaction center (PSII) subunits, such as D1 (encoded by the chloroplast tpsbAgene). When the rate of D1 synthesis is less than the rate of photo damage, photo inhibition occurs and plant growth is decreased. Plants use light-activated translation and enhanced psbAmRNA stability to maintain D1 synthesis and replace the photo damaged 01. Despite the importance to photosynthetic capacity, these mechanisms are poorly understood in plants. One intriguing model derived from the algal chloroplast system, Chlamydomonas, implicates the role of three proteins (RB60, RB47, RB38) that bind to the psbAmRNA 5' untranslated leader (5' UTR) in the light to activate translation or enhance mRNA stability. RB60 is the key enzyme, protein D1sulfide isomerase (Pill), that regulates the psbA-RN :Binding proteins (RB's) by way of light-mediated redox potentials generated by the photosystems. However, proteins with these functions have not been described from higher plants. We provided compelling evidence for the existence of RB60, RB47 and RB38 orthologs in the vascular plant, Arabidopsis. Using gel mobility shift, Rnase protection and UV-crosslinking assays, we have shown that a dithiol redox mechanism which resembles a Pill (RB60) activity regulates the interaction of 43- and 30-kDa proteins with a thermolabile stem-loop in the 5' UTR of the psbAmRNA from Arabidopsis. We discovered, in Arabidopsis, the PD1 gene family consists of II members that differ in polypeptide length from 361 to 566 amino acids, presence of signal peptides, KDEL motifs, and the number and positions of thioredoxin domains. PD1's catalyze the reversible formation an disomerization of disulfide bonds necessary for the proper folding, assembly, activity, and secretion of numerous enzymes and structural proteins. PD1's have also evolved novel cellular redox functions, as single enzymes and as subunits of protein complexes in organelles. We provide evidence that at least one Pill is localized to the chloroplast. We have used PDI-specific polyclonal and monoclonal antisera to characterize the PD1 (55 kDa) in the chloroplast that is unevenly distributed between the stroma and pellet (containing membranes, DNA, polysomes, starch), being three-fold more abundant in the pellet phase. PD1-55 levels increase with light intensity and it assembles into a high molecular weight complex of ~230 kDa as determined on native blue gels. In vitro translation of all 11 different Pill's followed by microsomal membrane processing reactions were used to differentiate among PD1's localized in the endoplasmic reticulum or other organelles. These results will provide.1e insights into redox regulatory mechanisms involved in adaptation of the photosynthetic apparatus to light stress. Elucidating the genetic mechanisms and factors regulating chloroplast photosynthetic genes is important for developing strategies to improve photosynthetic efficiency, crop productivity and adaptation to high light environments.
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