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Academic literature on the topic 'Promoter analysi'

Author: Grafiati

Published: 11 March 2023

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Journal articles on the topic "Promoter analysi"

1

Nore, Beston F., Tayfoor Jalil Mahmoud, and Ban Mousa Rashid. "Sequence Verifications and Promoter Analysis of The Prolactin Gene." Journal of Zankoy Sulaimani - Part A 15, no. 1 (December 17, 2012): 71–77. http://dx.doi.org/10.17656/jzs.10234.

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Chiang, Jeffrey, Wai Lim Ku, Kairong Cui, Keji Zhao, and Richard J. Hodes. "The use of alternative promoters in T cell development." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 165.20. http://dx.doi.org/10.4049/jimmunol.200.supp.165.20.

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Abstract Many mammalian genes, including a number involved in immune development and function, use multiple promoters encoding expression of the same protein product. To understand the function of alternative promotors during T cell development, we carried out genome-wide RNA-Seq analysis of DN, DP, CD4 and CD8 thymocytes. 26% (2469/9595) of genes expressed by thymocytes used two or more alternative promotors at some point in T cell development. However, only 3.2% (80/2469) of the genes which utilized two or more promoters showed the difference of promotor activity among different T cell developmental stages which were validated by selected representative genes with qPCR assay. To analyze mechanisms of alternative promoter regulation, DNase hypersensitivity sites were mapped, and ChIP-Seq with anti-H3K4me3 antibodies was performed in the same thymic subpopulations. To determine the in vivo functional role of alternative promotors for T cell development, several genes were selected for study by deletion of individual promoters by CRISPR technology. We have initially generated mice with deletion of distal or proximal promotor of the lck gene and demonstrated distinct functional roles of the two promoters: the proximal lck promoter is critical for early stages of thymic T cell development while the distal promoter was necessary for normal T cell activation. Ongoing studies will characterize more broadly the functional role of alternative promoter expression in thymocyte development, and the mechanisms mediating selective promoter activity.

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He, Yang, Tao Zhao, Fang Chen, Changchun Song, Chongchao Zhong, and Zhi Luo. "Functional Analysis of the Promoter Regions of Two Apoptosis-Related Genes (Bcl-2 and Cycs) and Their Regulation by Zn in Yellow Catfish." International Journal of Molecular Sciences 22, no. 12 (June 11, 2021): 6291. http://dx.doi.org/10.3390/ijms22126291.

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B-cell lymphoma 2 (Bcl-2) and cytochrome c (Cycs) are two important proteins relevant to cellular apoptosis. In this study, we characterized the functions of the promoter regions of two apoptosis-related genes, Bcl-2 and Cycs, in yellow catfish Pelteobagrus fulvidraco. We obtained a 1989 bp Bcl-2 promoter and an 1830 bp Cycs promoter and predicted several key transcription factor binding sites (TFBSs) on the promoters, such as Kruppel-like factor 4 (KLF4), signal transducer and activator of transcription factor 3 (STAT3), forkhead box O (FOXO), metal-responsive element (MRE) and hepatocyte nuclear factor 1α (HNF-1α). Zinc (Zn) increased the activities of the Bcl-2 promoter but decreased the activities of the Cycs promoter. Metal-responsive transcription factor 1 (MTF-1) and HNF-1α directly bound with Bcl-2 and Cycs promoters, and they positively regulated the activity of the Bcl-2 promoter but negatively regulated the activity of the Cycs promoter. Zn promoted the binding ability of HNF-1α to the Bcl-2 promoter but decreased its binding ability to the Cycs promoter. However, Zn had no significant effect on the binding capability of MTF-1 to the regions of Bcl-2 and Cycs promoters. Zn upregulated the mRNA and total protein expression of Bcl-2 but downregulated the mRNA and total protein expression of Cycs. At the same time, Annexin V–FITC/PI staining showed that Zn significantly reduced the apoptosis of primary hepatocytes. For the first time, our study provides evidence for the MRE and HNF-1α response elements on the Bcl-2 and Cycs promoters, offering new insight into the mechanism by which Zn affects apoptosis in vertebrates.

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Zhu, Guangwei, Qiang Huang, Wei Zheng, Yongjian Huang, Jin Hua, Shugang Yang, Jinfu Zhuang, et al. "LPS Upregulated VEGFR-3 Expression Promote Migration and Invasion in Colorectal Cancer via a Mechanism of Increased NF-κB Binding to the Promoter of VEGFR-3." Cellular Physiology and Biochemistry 39, no. 5 (2016): 1665–78. http://dx.doi.org/10.1159/000447868.

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Background and Aim: Lipopolysaccharide(LPS) could promote the progression of colorectal cancer, but the specific regulatory mechanisms are largely unknown. So, this study aim to clarify the mechanisms that LPS upregulated VEGFR-3, which promotes colorectal cancer cells migration and invasion with a mechanism of increased NF-κB bind to the promoter of VEGFR-3. Methods: The present study examined the VEGFR-3 expression in colorectal cancer tissues and analyzed the relationship between the VEGFR-3 expression with clinical parameters. PCR, Western blot, CCK-8, colone formation assay, and Transwell assay detected that LPS promoted the migration and invasion and the role of VEGFR-3 in the process of colorectal carcinoma in vitro. Used the methods of promoter analysis, EMSA assay and ChIP assay to explore the mechanisms LPS increased the expression of VEGFR-3. Results: VEGFR-3 was significantly high expression in the colorectal cancer tissues. And the high expression was associated with the TNM stage and lymph node metastasis of colorectal cancer. LPS could promote the migration and invasion, which could be blocked by the neutralizing antibody IgG of VEGFR-3. And found that -159 nt to +65 nt was the crucial region of VEGFR-3 promoter. And detected that the NF-κB was important transcription factor for the VEGFR-3 promoter. And LPS could increase NF-κB binding to VEGFR-3 promoter and upregulated the expression of VEGFR-3 to exert biological functions. Conclusion: We have elucidated the relationship between LPS and the VEGFR-3 expression and revealed that VEGFR-3 play very important role in the process of LPS promoting the migration and invasion of colorectal cancer cells. Further illuminated the mechanism that LPS upregulated VEGFR-3 expression via increased NF-κB bind to the promoter of VEGFR-3.

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Arsenijevic, Slavica, and Ljubisa Topisirovic. "Molecular analysis of mutatedLactobacillus acidophiluspromoter-like sequence P15." Canadian Journal of Microbiology 46, no. 10 (October 1, 2000): 938–45. http://dx.doi.org/10.1139/w00-077.

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The promoter-like sequence P15 that was previously cloned from the chromosome of Lactobacillus acidophilus ATCC 4356 is active in Lactobacillus reuteri, Lactobacillus plantarum, Lactobacillus acidophilus, and Escherichia coli, but not in Lactococcus lactis. N-methyl-N-nitroso-N-guanidine (MNNG) mutagenesis of P15 was used to select for a promoter active in L. lactis MG1363. Molecular analysis of the mutated promoter (designated P16) revealed a 90 bp deletion and a T[Formula: see text]A transversion. This deletion, in combination with the addition to the transversion, created a promoter with putative -35 and -10 hexamers identical to the consensus promoter sequence found in E. coli and Bacillus subtilis vegetative promoters. The activity of P16 was measured by its ability to promote chloramphenicol resistance in different bacteria when inserted in the promoter-probe plasmid pBV5030 (designated pLA16). The MIC of chloramphenicol in L. lactis, L. reuteri, L. plantarum, E. coli, and L. acidophilus harbouring pLA16 were 30, 170, 180, >500, and 3 µg/mL, respectively. This represents an increase in promoter activity compared to P15 in L. reuteri of 3-fold, in L. plantarum of 9-fold, and in E. coli of at least 2.5-fold, but a decrease in L. acidophilus of 7-fold.Key words: Lactobacillus acidophilus, promoter-like sequence, mutagenesis.

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Schneider, Klaus, and Christoph F. Beck. "Promoter-probe vectors for the analysis of divergently arranged promoters." Gene 42, no. 1 (January 1986): 37–48. http://dx.doi.org/10.1016/0378-1119(86)90148-4.

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Wang, Y. "Green tissue-specific analysis of a cloned rbcS promoter from Lemna gibba." Czech Journal of Genetics and Plant Breeding 50, No. 3 (September 12, 2014): 235–40. http://dx.doi.org/10.17221/200/2013-cjgpb.

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Many plant genetic engineering taskss require the spatial expression of genes which in turn depends upon the availability of specific promoters. The present paper analyses the green-tissue characteristics of a new L. gibba rbcS promoter driving the expression of the gus gene in transgenic tobacco. A 1491 bp rbcS (small subunit of ribulose bisphosphate carboxylase) promoter was isolated from Lemna gibba. The sequence analysis revealed that this promoter is different from the previously reported rbcS promoter and is named SSU5C. A 1438 bp fragment of the SSU5C promoter was fused with the gus gene and transgenic tobacco plants were generated. The analysis of T<sub>1</sub> tobacco p1438-gus revealed that GUS expression driven by the SSU5C promoter was detected in the green part of vegetative organs. The promoter deletion analysis confirmed a region from position –152 to –49 relative to the start of transcription containing boxes X, Y and Z, while a positive regulatory region conferred green tissue-specific expression. Further functional analysis of constructs of box-X, Y, Z, which was fused with the basal SSU5C promoter, confirmed that the boxes X, Y and Z represent the new minimized functional promoter, respectively, and are able to direct green tissue-specific expression. This promoter may be used for gene expression in a tissue-specific manner in plant molecular breeding.

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Kininis, Miltiadis, and W. Lee Kraus. "A Global View of Transcriptional Regulation by Nuclear Receptors: Gene Expression, Factor Localization, and DNA Sequence Analysis." Nuclear Receptor Signaling 6, no. 1 (January 2008): nrs.06005. http://dx.doi.org/10.1621/nrs.06005.

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Recent genomic analyses of transcription factor binding, histone modification, and gene expression have provided a global view of transcriptional regulation by nuclear receptors (NRs) that complements an existing large body of literature on gene-specific studies. The picture emerging from these genomic studies indicates that NRs bind at promoter-proximal and promoter-distal enhancers in conjunction with other transcription factors (e.g., activator protein-1, Sp1 and FOXA1). This binding promotes the recruitment of coregulators that mediate the posttranslational modification of histones at promoters and enhancers. Ultimately, signaling through liganded NRs stimulates changes in the occupancy of RNA polymerase II (Pol II) or the activation of preloaded Pol II at target promoters. Chromosomal looping and/or Pol II tracking may underlie promoter-enhancer communication. Interestingly, the direct target genes of NR signaling represent a limited subset of all the genes regulated by NR ligands, with the rest being regulated through secondary effects. As suggested by previous gene-specific analyses, NR-mediated outcomes are highly cell type- and promoter-specific, highlighting the complexity of transcriptional regulation by NRs and the value of genomic analyses for identifying commonly shared patterns. Overall, NRs share common themes in their patterns of localization and transcriptional regulation across mammalian genomes. In this review, we provide an overview of recent advances in the understanding of NR-mediated transcription garnered from genomic analyses of gene expression, factor localization, and target DNA sequences.

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Chen, Shu-Wei, Kun Wu, Wu-Hong Lv, Fang Chen, Chang-Chun Song, and Zhi Luo. "Functional Analysis of Two Zinc (Zn) Transporters (ZIP3 and ZIP8) Promoters and Their Distinct Response to MTF1 and RREB1 in the Regulation of Zn Metabolism." International Journal of Molecular Sciences 21, no. 17 (August 26, 2020): 6135. http://dx.doi.org/10.3390/ijms21176135.

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ZIP (zinc-regulated transporters, iron-regulated transporter-like protein) family plays an important role in organism Zn balance. This research identified the promoter regions of ZIP3 and ZIP8, two members of ZIP family, from a freshwater teleost yellow catfish Pelteobagrus fulvidraco, characterized the binding sequences of the metal-responsive transcription factor-1 (MTF-1) and Ras responsive element binding protein 1 (RREB1) on their promoter regions. The present study cloned and obtained the 2027 bp of ZIP3 promoter and 1664 bp of ZIP8 promoter, and predicted several key elements on their promoters, such as the binding sites of CREB (cAMP-response element binding protein), KLF4 (Kruppel like factor 4), MTF-1 and RREB1. The sequence deletion from −361 bp to −895 bp down-regulated the luciferase activity of ZIP3 promoter, and the deletion from −897 bp to −1664 bp down-regulated the luciferase activity of ZIP8 promoter. Within different deletion plasmids, the relative luciferase activities of ZIP3 and ZIP8 promoters changes to Zn incubation in a Zn concentration-dependent manner. The site mutagenesis and EMSA (electrophoretic mobility shift assay) found that the −1327 bp/−1343 bp MTF-1 binding site and the −248 bp/−267 bp RREB1 binding site on the ZIP3 promoter, and the −1543 bp/−1557 bp MTF-1 binding site on the ZIP8 promoter are functional sites. Low Zn increased the binding capability between MTF-1 and its responsive site on the ZIP3 promoter, and high Zn increased the transcriptional activation ZIP3 by RREB1; Zn also promoted the binding ability between MTF-1 and its responsive element on the ZIP8 promoter. This study provides the first direct evidence for the response elements of MTF-1 and RREB1 on ZIP3 and MTF-1 on ZIP8 to Zn, which are very important for the evaluation of Zn nutrition and toxicity in vertebrates.

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Choi, Jae Young, Soo-Jin Kwon, Jong Yul Roh, Tae-Jin Yang, Ming Shun Li, Beom-Seok Park, Yonggyun Kim, Soo-Dong Woo, Byung Rae Jin, and Yeon Ho Je. "Analysis of promoter activity of selected Cotesia plutellae bracovirus genes." Journal of General Virology 90, no. 5 (May 1, 2009): 1262–69. http://dx.doi.org/10.1099/vir.0.009472-0.

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In a previous study, we cloned 27 discrete genome segments of Cotesia plutellae bracovirus (CpBV) and provided the complete nucleotide sequences and annotation. Seven putative coding regions were predicted from one of the largest segments, CpBV-S30. The activity of promoters associated with six predicted ORFs from this segment were investigated using both transient and baculovirus expression assays with enhanced green fluorescent protein as a reporter gene. CpBV promoters showed activity earlier than the polyhedrin promoter and the activity of some of these promoters was superior to that of the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) ie-1 promoter in the baculovirus expression assays. The promoter of ORF3004 showed the highest level of activity in insect cells, exhibiting 24 % of the activity obtained with the AcMNPV polyhedrin promoter in Sf9 cells. In Spodoptera exigua larvae, the ORF3006 promoter showed the highest activity, with about 35 % of the activity measured with the polyhedrin promoter. In addition, analysis of the ORF3006 promoter revealed that the region between −382 and −422 from the translation start point was critical for activity of this promoter. These results suggest that the CpBV-S30 promoters characterized here could be useful tools in a variety of biotechnological applications, such as gene expression analyses and insecticide development.

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Dissertations / Theses on the topic "Promoter analysi"

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Kokulapalan, Wimalanathan. "Genome-wide Computational Analysis of Chlamydomonas reinhardtii Promoters." Miami University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=miami1320638327.

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Qi, Zhan [Verfasser], and Veit [Akademischer Betreuer] Hornung. "Large-scale analysis of Drosophila core promoter function using synthetic promoters / Zhan Qi ; Betreuer: Veit Hornung." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2019. http://d-nb.info/1188200240/34.

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Phillips, Julian Peter. "Promoter analysis in transgenic sugar beet." Thesis, De Montfort University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.391084.

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Oliveira, Junior Silvio De. "Revalorisation des effluents thermiques industriels : analyse exergétique, entropique et économique." Vandoeuvre-les-Nancy, INPL, 1991. http://docnum.univ-lorraine.fr/public/INPL_T_1991_OLIVEIRA_JUNIOR_S_D.pdf.

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ADans la partie 1, nous développons l'analyse entropique et exergétique des processus de transfert de chaleur et de matière de la séparation et du mélangeage d'un mélange binaire, pour définir les conditions optimales de tels systèmes, qui sont les principaux éléments des machines à absorption. Nous présentons une méthode graphique d'élaboration des bilans d'exergie et de calcul des pertes exergétiques lors d'une séparation/mélangeage d'un mélange binaire. Sont présentes les diagrammes exergie-concentration et exergie-enthalpie pour les couples H2O-LiBr et NH3-H2O. Dans la partie 2, nous présentons de nouvelles configurations de structures de promoteurs de turbulence pour des films ruisselants qui provoquent un mélangeage transversal du film en assurant les conditions de mouillabilité film-paroi et ayant des bonnes performances thermiques et des faibles couts de fabrication. L’évaluation du comportement de ces structures est faite à partir de la comparaison de leurs coefficients de transfert de chaleur et de la production spécifique globale d'entropie avec un tube lisse ayant la même géométrie et sous les mêmes conditions d'opération. Dans la partie 3, nous présentons de nouvelles structures et des nouveaux types de thermotransformateurs et frigo-pompes pour la revalorisation des effluents thermiques industriels. Ce sont deux systèmes à absorption pure et deux systèmes hybrides à absorption-compression mécanique et absorption-ejecto-compression. Nous développons une méthode d'analyse exergo-économique de ces systèmes basés sur une fonction de valeur technico-économique qui caractérise la performance combinée thermique et économique des systèmes. Les performances de ces systèmes sont comparées dans des conditions d'opération industrielles à travers l'emploi des logiciels PACA-design. Pour chaque condition d'opération nous identifions les systèmes les plus performants en utilisant la fonction de valeur technico-économique

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Bohne, Alexandra-Viola. "Analyse von Komponenten der organellären Transkriptionsmaschinerien aus Arabidopsis thaliana und Nicotiana tabacum." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2009. http://dx.doi.org/10.18452/15965.

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Die Gesamtheit mitochondrialer Gene sowie ein Teil der plastidären Gene photosynthetischer Eukaryoten wird durch kernkodierte Phagentyp-RNA-Polymerasen transkribiert. In der vorliegenden Arbeit wurden unter Verwendung eines homologen in vitro-Transkriptionssystems, die spezifischen Funktionen der Phagentyp-RNA-Polymerasen RpoTm, RpoTp und RpoTmp aus Arabidopsis untersucht. Während RpoTmp keine Präferenz für die angebotenen Promotoren zeigte, transkribierten RpoTm und RpoTp eine überlappende Gruppe mitochondrialer und plastidärer Promotoren vielfältiger Architektur. RpoTm und RpoTp präsentierten eine Kofaktor-unabhängige Fähigkeit zur Promotorerkennung bei Angebot superhelikaler DNA-Matrizen. Eine selektive Promotornutzung sowie die Unfähigkeit zur spezifischen Transkription linearer Promotormatrizen in vitro implizieren die Assoziation zusätzlicher, in die Promotorerkennung und/oder DNA-Aufschmelzung involvierter Kofaktoren in vivo. Die in vitro-Erkennung mitochondrialer Promotoren durch eine plastidäre Phagentyp-RNA-Polymerase (und umgekehrt) sowie weitere Ähnlichkeiten der Transkriptionsapparate der Mitochondrien und Plastiden, wie die strukturelle Organisation ihrer Promotoren und die phylogenetische Herkunft ihrer kernkodierten Transkriptasen inspirierte in planta Studien zur spezifischen Transkription eines mitochondrialen Promotors in den Plastiden. Hierzu wurde die Expression des nptII-Reportergens unter Kontrolle des mitochondrialen PatpA-Promotors aus Oenothera in transplastomischen Tabakpflanzen analysiert. Die durchgeführten Studien belegen eine korrekte Transkription des mitochondrialen PatpA-Promotors durch eine plastidäre Phagentyp-RNA-Polymerase in in vitro-Transkriptionsassays sowie in transplastomischen Tabakpflanzen. Diese Resultate enthüllen weitere unerwartete Ähnlichkeiten der organellären Genexpression, die aufschlussreiche evolutionäre Einblicke erlauben und verbesserte Anwendungen zur Manipulation plastidärer Genome ermöglichen könnten.
All mitochondrial and a subset of plastidial genes of photosynthetically active eukaryotes are transcribed by nuclear-encoded, phage-type RNA polymerases. In this study, a homologous in vitro transcription system was used to define the specific functions of Arabidopsis phage-type RNA polymerases RpoTm, RpoTp and RpoTmp in organellar transcription. RpoTmp displayed no significant promoter specificity, whereas RpoTm and RpoTp were able to accurately initiate transcription from overlapping subsets of mitochondrial and plastidial promoters of diverse architecture. RpoTm and RpoTp thereby demonstrated an intrinsic capability to recognize promoters on supercoiled DNA templates without the aid of protein cofactors. A selective promoter recognition by the phage-type RNAPs in vitro and the inability to recognize promoters on linear templates imply that auxiliary factors are required for efficient initiation of transcription and/or DNA melting in vivo. Crosswise recognition of organellar promoters by the phage-type RNA polymerases in vitro as well as other similarities of the mitochondrial and plastidial transcription machineries such as promoter structures and the phylogenetic origin inspired in planta studies to investigate specific transcription of a mitochondrial promoter in plastids. Therefore, the expression of an nptII reporter gene under control of the mitochondrial PatpA promoter from Oenothera was analyzed in transplastomic tobacco plants. The data presented here demonstrate the faithful recognition of the mitochondrial PatpA promoter by a plastid RNA polymerase both in in vitro transcription assays and in transplastomic tobacco plants. These findings disclose further unexpected similarities of the organellar gene expression systems which deliver interesting evolutionary insights and might facilitate improved applications for chloroplast genome engineering.

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Featherstone, Mark S. "Structural analysis of the polyomavirus late promoter." Thesis, McGill University, 1986. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=72778.

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He, Bing. "Systematic analysis of enhancer and promoter interactions." Diss., University of Iowa, 2015. https://ir.uiowa.edu/etd/1972.

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Transcriptional enhancers represent the primary basis for differential gene expression. These elements regulate cell type specificity, development, and evolution, with many human diseases resulting from altered enhancer activity. To date, a key gap in our knowledge is how enhancers select specific promoters for activation. To fill this gap, in this thesis, I first developed an Integrated Method for Predicting Enhancer Targets (IM-PET). Leveraging abundant “omics” data, I devised and characterized multiple genomic features for distinguishing true enhancer-promoter (EP) pairs from non-interacting pairs. I integrated these features into a probabilistic predictor for EP interactions. Multiple validation experiments demonstrated a significant improvement over extent state-of-the-art approaches. Systematic analyses of EP interactions across twelve human cell types reveals global features of EP interactions. Second, we used a well-established viral infection model to map the dynamic changes of enhancers and super-enhancers during the CD8+ T cell responses. Our analysis illustrated the complexity and dynamics of the underlying EP interactome during cell differentiation. Taking advantage of the predicted EP interactions, we constructed stage-specific transcriptional regulatory networks, which is critical for understanding the regulatory mechanism during CD8+ T cell differentiation. Third, recent progress in mapping technologies for chromatin interactions has led to a rapid increase in this type of interaction data. However, there is a lack of a comprehensive depository for chromatin interactions identified by all major technologies. To address this problem, we have developed the 4DGenome database through comprehensive literature curation of experimentally derived interactions. We envision a wide range of investigations will benefit from this carefully curated database.

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Collins, Malcolm Robert. "Characterisation of the human α2(I) procollagen promoter-binding proteins." Doctoral thesis, University of Cape Town, 1993. http://hdl.handle.net/11427/27139.

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In an attempt to elucidate the transcriptional mechanisms that regulate the expression of the human α2(I) procollagen gene, cis-acting DNA-elements within the proximal promoter were identified and their corresponding trans-acting factors characterised. The fibroblast cell lines used in this study had previously been transformed with either simian virus 40 (SVWI-38) or by γ-radiation (CT-1). The SVWI-38 fibroblasts do not produce any α2(I) collagen chains, whereas the CT-1 cell line produces normal type I collagen. Previous studies suggested that trans-acting factor(s) may be responsible for the inactivation of the α2(I) procollagen gene in SVWI-38 fibroblasts (Parker et. al. (1989) J. Biol. Chem 264, 7147-7152; Parker et. al. (1992) Nucleic Acids Res. 20, 5825-5830). In this study, the SVWI-38 proximal promoter (-350 to +54) was sequenced and shown to be normal, thereby ruling out any possibility that mutations within this region was responsible for inactivation of the gene.

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Danevad, Margrete. "Functional analysis of the murine LI-Cadherin promoter." [S.l.] : [s.n.], 2004. http://www.diss.fu-berlin.de/2004/165/index.html.

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Chaidir, Nadia. "Whole-genome comparative promoter sequence analysis in plants." Thesis, McGill University, 2014. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=123303.

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Large-scale genome-wide comparative analyses are now made possible by the increasing number of publicly available high-quality genome sequence data for numerous plant species. To understand the mechanisms of transcriptional regulation, computational analysis tools were used to find overrepresented and conserved DNA sequences, i.e. cis-regulatory elements. Datasets used as positive input for computational identification of regulatory regions commonly include promoters of co-regulated genes or promoters of orthologous genes (Wang and Stormo, 2003).We discovered de novo motif using two approaches, seperately; 1) discovery based on orthology relationship of the genes in 18 plant species and 2) discovery based on co-regulated genes in specific tissues from soybean gene expression RNA-Seq data. In the first approach, a combination of several bioinformatics tools were used to predict motifs in promoter region based on clusters of orthologous genes in whole-genome datasets of Arabidopsis lyrata, Arabidopsis thaliana, Brachypodium distachyon, Carica papaya, Chlamydomonas reinhardtii, Glycine max, Linus usitatissimum, Malus domestica, Manihot esculenta, Medicago truncatula, Oryza sativa, Physcomitrella patens, Populus trichocarpa, Selaginella moellendorfii, Sorghum bicolor, Vitis vinivera, Volvox carteri and Zea mays. The results have shown that many promoters of orthologous plant genes contain similar cis-regulatory motifs. In addition, inclusion of more evolutionary distant organism led to detection of very conserved motifs, i.e. motifs that have similar function in wider variety of organisms. In the second approach, bioinformatics tools were used to find motifs in promoter region of co-regulated genes in shoot apical meristem and shoot epidermis of three soybean cultivars. The results have shows that promoters of co-regulated genes in specific tissues contain similar cis-regulatory motifs.Since generating genome-scale datasets requires extensive computational resources that are not always readily available, we created a relational database that houses pre-computed and post-processed whole-genome comparative analysis of promoter regions. The database contains motif sequences, annotations, clusters of orthologous genes and other useful information associated with them, for 18 plant genomes.
L'étude d'association pangénomique est maintenant rendue possible par le nombre de séquences génétiques de hautes qualités qui sont disponibles pour plusieurs espèces végétales. Pour comprendre les mécanismes de régulation de la transcription, un nombre d'outils d'analyses informatiques ont été développé pour identifier les éléments cis-régulatoires. Les bases de données utilisées comme saisie positive pour l'identification informatique des régions de régulation incluent communément les promoteurs des gènes co-régulés ainsi que des gènes orthologues (Wang et Stormo, 2003).Pour découvrir les motifs de novo, nous avons utilisé deux techniques; 1) une découverte basée sur la relation orthologue des gènes de 18 espèces végétales et, 2) une découverte basée sur les gènes co-régulés dans certains tissus végétales spécifiques provenant de données de séquençage d'ARN de soja. Dans la première approche nous avons utilisé une combinaison de plusieurs outils bioinformatiques pour prédire les motifs des promoteurs basés sur des groupes de gènes orthologues trouvés dans les bases de données des génomes entiers d'Arabidopsis lyrata, Arabidopsis thaliana, Brachypodium distachyon, Carica papaya, Chlamydomonas reinhardtii, Glycine max, Linus usitissimum, Malus domestica, Manihot esculenta, Medicago truncutula, Oryza sativa, Physcomitrella patens, Populus trichocarpa, Selaginella moellendorfii, Sorghum bicolor, Vitis vinivera, Volvox carteri et Zea mays. Les résultats ont démontré que, dans les plantes, plusieurs promoteurs de gènes orthologues contiennent des motifs cis-régulatoires similaires. En plus, en incluant des espèces évolutivement éloignées dans les analyses, nous avons été capable de démontrer que ces motifs sont conservés. Dans la deuxième partie, nous avons fait une analyse comparant les séquences des promoteurs co-régulés dans les méristèmes apicaux ainsi que dans l'épiderme de trois cultivars de soja; Clark sauvage, mutant a 5-feuilles et mutant glabre. Les résultats ont démontré que les promoteurs des gènes co-régulés en différents tissus contiennent des motifs cis-régulatoires similaires. Générer des données à l'échelle génomique demande une puissance informatique énorme qui n'est pas toujours disponible. En conséquence, nous avons créé une base de données pour 18 génomes de plantes composée de séquences de promoteurs, de motifs, d'annotations et des groupes de gènes orthologues ainsi que d'autres informations associées avec ceux-ci.

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Books on the topic "Promoter analysi"

1

Phillips, Julian Peter. Promoter analysis in transgenic sugar beet. Leicester: De Montfort University, 1995.

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Petrisor, Bradley Allan. Analysis of the insulin receptor-related gene promoter. Ottawa: National Library of Canada, 1994.

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Yesilyurt, Serhat. Surrogates for numerical simulations; optimization of eddy-promoter heat exchangers. Hampton, Va: Institute for Computer Applications in Science and Engineering, 1993.

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T, Patera Anthony, and Langley Research Center, eds. Surrogates for numerical simulations, optimization of eddy-promoter heat exchanges. Hampton, Va: National Aeronautics and Space Administration, Langley Research Center, 1993.

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Antoniou, Hariclia. Functional promoter analysis of the endothelial constitutive nitric oxide synthase gene. Ottawa: National Library of Canada, 1995.

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Webber, P. M. Analysis of the promoter region of the Xenopus borealis N-Cadherin gene. [s.l.]: typescript, 1993.

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Yang, Chunzhong. Cloning, regulation, and promoter analysis of the cadA gene in Dictyostelium discoideum. Ottawa: National Library of Canada, 1998.

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Doherty, Anne-Marie. A critical analysis of the role of the school nurse as health promoter. [s.l: The Author], 1997.

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Ebisuzaki, Lawrence Kentaro. Promoter analysis of the sporulation-specific gene SPS4 of the yeast Saccharomyces cerevisiae. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1993.

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Roessing, Lesley. No more "us" and "them": Classroom lessons and activities to promote peer respect. Lanham, Maryland: Rowman & Littlefield Education, 2012.

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Book chapters on the topic "Promoter analysi"

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Werner, T. "Promoter Analysis." In Bioinformatics and Genome Analysis, 65–82. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-662-04747-7_4.

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Megraw, Molly, and Artemis G. Hatzigeorgiou. "MicroRNA Promoter Analysis." In Methods in Molecular Biology, 149–61. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-005-2_11.

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Santos, Efrén, Ricardo Pacheco, Liliana Villao, Luis Galarza, Daniel Ochoa, Carlos Jordán, and José Flores. "Promoter Analysis in Banana." In Banana: Genomics and Transgenic Approaches for Genetic Improvement, 157–79. Singapore: Springer Singapore, 2016. http://dx.doi.org/10.1007/978-981-10-1585-4_11.

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Quail, Peter H., Wesley B. Bruce, Katayoon Dehesh, and Jacqueline Dulson. "phyA Gene Promoter Analysis." In Plant Molecular Biology 2, 499–508. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4615-3304-7_48.

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Eguchi, Takanori, Satoshi Kubota, and Masaharu Takigawa. "Promoter Analyses of CCN Genes." In Methods in Molecular Biology, 177–85. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6430-7_18.

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Morshed, Mahboob, Junko Yamamoto, Shusuke Sano, Ken-Ichi Nishijima, Masamichi Kamihira, and Shinji Iijima. "Biochemical analysis of chicken ovalbumin promoter." In Animal Cell Technology: Basic & Applied Aspects, 301–7. Dordrecht: Springer Netherlands, 2006. http://dx.doi.org/10.1007/1-4020-4457-7_41.

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Napoli, Sara. "Detailed Analysis of Promoter-Associated RNA." In Methods in Molecular Biology, 199–213. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-547-7_15.

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Rani, T. Sobha, S. Durga Bhavani, and S. Bapi Raju. "Promoter Recognition Using Neural Network Approaches." In Computational Intelligence and Pattern Analysis in Biological Informatics, 71–97. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2010. http://dx.doi.org/10.1002/9780470872352.ch4.

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Mahringer, Christian A. "Analyzing Digital Trace Data to Promote Discovery – The Case of Heatmapping." In Business Process Management Workshops, 209–20. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-94343-1_16.

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AbstractBusiness Process Management and Routine Dynamics are two streams of research that both explore process. To this end, Business Process Management has developed a rich array of methods that can be used to analyze digital trace data. Routine Dynamics has put less emphasis on the analysis of digital trace data, but it has advanced a methodological approach that promotes discovery, i.e., the process that actors perform and experience as they develop novel insights. This paper argues that the analysis of digital trace data can promote the process of discovery. It uses heatmapping as a specific example to show how analyzing digital trace data can promote discovery. The paper thus emphasizes a specific way how Business Process Management and Routine Dynamics can fertilize each other.

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Gonye, Gregory E., Praveen Chakravarthula, James S. Schwaber, and Rajanikanth Vadigepalli. "From Promoter Analysis to Transcriptional Regulatory Network Prediction Using PAINT." In Gene Function Analysis, 49–68. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-547-3_4.

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Conference papers on the topic "Promoter analysi"

1

Jürgenson, Evelin, Armands Auzinš, and Marija Burinskienė. "Land Value Capture to Promote Local Development in Baltics: a Comparative study of Estonia, Latvia and Lithuania." In Environmental Engineering. VGTU Technika, 2017. http://dx.doi.org/10.3846/enviro.2017.106.

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By capturing value increase, it should be used for specific purposes in the way that would support implementation of infrastructure projects and promote local development. Accordingly, the stakeholders’ interests have to be balanced and fair decision-making promoted. The research emphasises on comparative analysis of Estonian, Latvian and Lithuanian experiences in covering development costs and absorbing value increase. The purpose of the study is to give an overview of the land value capture as well as to discuss how it promotes local development and what is an institutional environment supporting it in three Baltic countries with similar historical evolution during last two decades. The functions of local authorities and spatial planning systems have been analysed in the study. The comparative analysis and synthesis, the logical-constructive and graphical methods mainly are used for the research. Direct and indirect models, which are used for the absorption of the surplus value of developed land, have been observed in the study. The outcome of the research shows an interim conclusion for Estonia, Latvia and Lithuania, and it may contribute to comparative analysis in larger – European context – in order to get an overview of land value capture across Europe.

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ESKIN, ELEAZAR, URI KEICH, MIKHAIL S. GELFAND, and PAVEL A. PEVZNER. "GENOME-WIDE ANALYSIS OF BACTERIAL PROMOTER REGIONS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2002. http://dx.doi.org/10.1142/9789812776303_0004.

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BOŻEK, KATARZYNA, SZYMON M. KIEŁBASA, ACHIM KRAMER, and HANSPETER HERZEL. "PROMOTER ANALYSIS OF MAMMALIAN CLOCK CONTROLLED GENES." In Proceedings of the 7th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2007). IMPERIAL COLLEGE PRESS, 2007. http://dx.doi.org/10.1142/9781860949920_0007.

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Futagami, T., H. Sakai, K. Kakugawa, A. Fujimoto, T. Fukuhara, Y. Fujiwara, and S. Sakurai. "Debris flows promoted by mechanical deterioration of the ground due to eutrophication of hillside ecosystems." In RISK ANALYSIS 2010. Southampton, UK: WIT Press, 2010. http://dx.doi.org/10.2495/risk100591.

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"Promoter motif inference and annotation of promoter sequences in bacterial genomes based on the analysis of structures of alternative sigma factor-promoter complexes." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-034.

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"Promoter motif inference and annotation of promoter sequences in bacterial genomes based on the analysis of structures of alternative sigma factor-promoter complexes." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/bgrs/sb-2022-034.

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Weaver, Jessica, Carolyn Lee-Parsons, and Erin Cram. "In planta promoter analysis using the FAST method." In 2014 40th Annual Northeast Bioengineering Conference (NEBEC). IEEE, 2014. http://dx.doi.org/10.1109/nebec.2014.6972975.

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Singh, Abhyudai, Cesar A. Vargas, and Rajesh Karmakar. "Stochastic analysis of genetic promoter architectures with memory." In 2013 IEEE 52nd Annual Conference on Decision and Control (CDC). IEEE, 2013. http://dx.doi.org/10.1109/cdc.2013.6761034.

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Sahingil, Mehmet Cihan, and Yakup Ozkazanc. "Complexity analysis of gene promoter regions in human chromosomes." In 2014 22nd Signal Processing and Communications Applications Conference (SIU). IEEE, 2014. http://dx.doi.org/10.1109/siu.2014.6830316.

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ZHU, J., and M. Q. ZHANG. "CLUSTER, FUNCTION AND PROMOTER: ANALYSIS OF YEAST EXPRESSION ARRAY." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 1999. http://dx.doi.org/10.1142/9789814447331_0045.

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Reports on the topic "Promoter analysi"

1

Hammond, Sha S. Analysis of Hypothetical Promoter Domains of DKFZp564A1164, NPHS1 and HSPOX1 Genes. Office of Scientific and Technical Information (OSTI), March 2004. http://dx.doi.org/10.2172/15013619.

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Shapira, Roni, Judith Grizzle, Nachman Paster, Mark Pines, and Chamindrani Mendis-Handagama. Novel Approach to Mycotoxin Detoxification in Farm Animals Using Probiotics Added to Feed Stuffs. United States Department of Agriculture, May 2010. http://dx.doi.org/10.32747/2010.7592115.bard.

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T-2 toxin, a toxic product belongs to the trichothecene mycotoxins, attracts major interest because of its severe detrimental effects on the health of human and farm animals. The occurrence of trichothecenes contamination is global and they are very resistant to physical or chemical detoxification techniques. Trichothecenes are absorbed in the small intestine into the blood stream. The hypothesis of this project was to develop a protecting system using probiotic bacteria that will express trichothecene 3-O-acetyltransferase (Tri101) that convert T-2 to a less toxic intermediate to reduce ingested levels in-situ. The major obstacle that we had faced during the project is the absence of stable and efficient expression vectors in probiotics. Most of the project period was invested to screen and isolate strong promoter to express high amounts of the detoxify enzyme on one hand and to stabilize the expression vector on the other hand. In order to estimate the detoxification capacity of the isolated promoters we had developed two very sensitive bioassays.The first system was based on Saccharomyces cerevisiae cells expressing the green fluorescent protein (GFP). Human liver cells proliferation was used as the second bioassay system.Using both systems we were able to prove actual detoxification on living cells by probiotic bacteria expressing Tri101. The first step was the isolation of already discovered strong promoters from lactic acid bacteria, cloning them downstream the Tri101 gene and transformed vectors to E. coli, a lactic acid bacteria strain Lactococcuslactis MG1363, and a probiotic strain of Lactobacillus casei. All plasmid constructs transformed to L. casei were unstable. The promoter designated lacA found to be the most efficient in reducing T-2 from the growth media of E. coli and L. lactis. A prompter library was generated from L. casei in order to isolate authentic probiotic promoters. Seven promoters were isolated, cloned downstream Tri101, transformed to bacteria and their detoxification capability was compared. One of those prompters, designated P201 showed a relatively high efficiency in detoxification. Sequence analysis of the promoter region of P201 and another promoter, P41, revealed the consensus region recognized by the sigma factor. We further attempted to isolate an inducible, strong promoter by comparing the protein profiles of L. casei grown in the presence of 0.3% bile salt (mimicking intestine conditions). Six spots that were consistently overexpressed in the presence of bile salts were isolated and identified. Their promoter reigns are now under investigation and characterization.

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Zhou, Ting, Roni Shapira, Peter Pauls, Nachman Paster, and Mark Pines. Biological Detoxification of the Mycotoxin Deoxynivalenol (DON) to Improve Safety of Animal Feed and Food. United States Department of Agriculture, July 2010. http://dx.doi.org/10.32747/2010.7613885.bard.

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The trichothecene deoxynivalenol (DON, vomitoxin), one of the most common mycotoxin contaminants of grains, is produced by members of the Fusarium genus. DON poses a health risk to consumers and impairs livestock performance because it causes feed refusal, nausea, vomiting, diarrhea, hemolytic effects and cellular injury. The occurrence of trichothecenes contamination is global and they are very resistant to physical or chemical detoxification techniques. Trichothecenes are absorbed in the small intestine into the blood stream. The overall objective of this project was to develop a protecting system using probiotic bacteria that will express trichothecene 3-O-acetyltransferase (Tri101) that convert T-2 to a less toxic intermediate to reduce ingested levels in-situ. The major obstacle that we had faced during the project is the absence of stable and efficient expression vectors in probiotics. Most of the project period was invested to screen and isolate strong promoter to express high amounts of the detoxify enzyme on one hand and to stabilize the expression vector on the other hand. In order to estimate the detoxification capacity of the isolated promoters we had developed two very sensitive bioassays.The first system was based on Saccharomyces cerevisiae cells expressing the green fluorescent protein (GFP). Human liver cells proliferation was used as the second bioassay system.Using both systems we were able to prove actual detoxification on living cells by probiotic bacteria expressing Tri101. The first step was the isolation of already discovered strong promoters from lactic acid bacteria, cloning them downstream the Tri101 gene and transformed vectors to E. coli, a lactic acid bacteria strain Lactococcuslactis MG1363, and a probiotic strain of Lactobacillus casei. All plasmid constructs transformed to L. casei were unstable. The promoter designated lacA found to be the most efficient in reducing T-2 from the growth media of E. coli and L. lactis. A prompter library was generated from L. casei in order to isolate authentic probiotic promoters. Seven promoters were isolated, cloned downstream Tri101, transformed to bacteria and their detoxification capability was compared. One of those prompters, designated P201 showed a relatively high efficiency in detoxification. Sequence analysis of the promoter region of P201 and another promoter, P41, revealed the consensus region recognized by the sigma factor. We further attempted to isolate an inducible, strong promoter by comparing the protein profiles of L. casei grown in the presence of 0.3% bile salt (mimicking intestine conditions). Six spots that were consistently overexpressed in the presence of bile salts were isolated and identified. Their promoter reigns are now under investigation and characterization.

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Brinckerhoff, Constance E. Genetic Analysis of a Single Nucleotide Polymorphism in the Matrix Metalloproteinase 1 Promoter in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, July 2002. http://dx.doi.org/10.21236/ada407580.

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Brinckerhoff, Constqance B. Genetic Analysis of a Single Nucleotide Polymorphism in the Matrix Metalloproteinase 1 Promoter in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, July 2003. http://dx.doi.org/10.21236/ada419338.

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Porat, Ron, Doron Holland, and Linda Walling. Identification of Citrus Fruit-Specific and Pathogen-Induced Promoters and Their Use in Molecular Engineering. United States Department of Agriculture, January 2001. http://dx.doi.org/10.32747/2001.7585202.bard.

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This one year BARD project was funded to develop methods to monitor promoter activity a gene expression patterns in citrus fruit. To fulfill this goal, we divided the research tasks between both labs so that the Israeli side evaluated the use of microprojectile bombardment ; a tool to evaluate transient gene expression in various citrus fruit tissues, and the US side optimized technical parameters required for Agrobacterium-mediated transformation of various citrus cultivars. Microprojectile bombardment appeared to be a very efficient method for transient gene expression analysis in citrus leaf tissues but was somewhat less applicable in fruit tissues. Nevertheless, we did succeeded to achieve significant levels of 35S-GUS gene expression in young green flavedo tissue. However, only single random spots of 35S-GUS gene expression were detected mature flavedo and in juice sacs and albedo tissue. Overall, we assume that following some more technical improvements particle bombardment could provide a useful technique to rapidly analyze promoter activity at least in the flavedo tissue. For Agrobacterium-mediated transformation, we found that shoot cultures of 'Washington' navel oranges,'Fairchild' mandarins,'Eureca' lemons,'Troyer' citrange and various grapefruits provided a more reliable and consistent source of tissue for transformation than germinated seedlings. Moreover, various growth media's (McCown, Quoirin & Lepoivre, DCR) further improved shoot and root growth relative to MS mineral media, which is commonly used. Also pure white light (using bulbs which do not emit UV or blue light) improved shoot growth in various citrus varieties, and paromomycin appeared to be a more efficient antibiotic for the selection of transgenic plants than Kanamycin. Overall, these optimizations improve transformation efficacy and shoot growth and rooting capacity. In addition to the development of transformation methods, both Israeli and US labs achieved progress in the identification of citrus fruit-specific promoters. In Israel, we isolated a 3.6 kb promoter fragment of the thiamine biosynthesis c-thi gene, which is highly expressed in fruit peel tissue, whereas in the US we isolated a 1.5 kb promoter fragment of the citrus seed-specific cDNA CssH. The identification of more fruit-specific cDNAs and their corresponding promoter regions is currently in progress.

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Aziz, Md Abdul, Sarah Jafrin, Md Abdul Barek, Shamima Nasrin Anonna, and Mohammad Safiqul Islam. The Association between Matrix Metalloproteinase-3 -1171 (5A/6A) Promoter Polymorphism and Cancer Susceptibility: An Updated Meta-Analysis and Trial Sequential Analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, August 2022. http://dx.doi.org/10.37766/inplasy2022.8.0049.

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Review question / Objective: The polymorphism of the 5A/6A promoter region of matrix metalloproteinases-3-1171 has been comprehensively studied to evaluate its risk associated with various cancers. We performed this updated meta-analysis to clarify the inconclusive outcomes of previous studies and to verify the link of this specific variant with the cancer risk. Eligibility criteria: For the literature covered in this meta-analysis, the authors followed some standards as inclusion criteria: (a) comparative case-control or cohort (different case groups) studies stating the correlation of MMP-3 -1171 (5A/6A) variant with cancer risk; (b) Available genotype and allele data in cases and controls; (c) Sufficient data to determine ORs (odds ratios) with 95% Cis (confidence intervals). The substandard studies were: (a) Review articles, commentaries and duplicate studies; (b) Study graph apart from case-control comparative approaches; (c) Studies having inadequate genotypic information to compute ORs with 95% CIs.

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Hane, G. J. Government-promoted collective research and development in Japan: Analyses of the organization through case studies. Office of Scientific and Technical Information (OSTI), June 1990. http://dx.doi.org/10.2172/6831428.

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Cappers, Peter, Charles Goldman, Michele Chait, George Edgar, Jeff Schlegel, and Wayne Shirley. Financial Analysis of Incentive Mechanisms to Promote Energy Efficiency: Case Study of a Prototypical Southwest Utility. Office of Scientific and Technical Information (OSTI), March 2009. http://dx.doi.org/10.2172/949969.

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Lers, Amnon, and Gan Susheng. Study of the regulatory mechanism involved in dark-induced Postharvest leaf senescence. United States Department of Agriculture, January 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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