Relevant bibliographies by topics / SLF gene

Academic literature on the topic 'SLF gene'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "SLF gene"

1

Li, Wentao, and Roger T. Chetelat. "Unilateral incompatibility gene ui1.1 encodes an S-locus F-box protein expressed in pollen of Solanum species." Proceedings of the National Academy of Sciences 112, no. 14 (March 23, 2015): 4417–22. http://dx.doi.org/10.1073/pnas.1423301112.

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Unilateral interspecific incompatibility (UI) is a postpollination, prezygotic reproductive barrier that prevents hybridization between related species when the female parent is self-incompatible (SI) and the male parent is self-compatible (SC). In tomato and related Solanum species, two genes, ui1.1 and ui6.1, are required for pollen compatibility on pistils of SI species or hybrids. We previously showed that ui6.1 encodes a Cullin1 (CUL1) protein. Here we report that ui1.1 encodes an S-locus F-box (SLF) protein. The ui1.1 gene was mapped to a 0.43-cM, 43.2-Mbp interval at the S-locus on chromosome 1, but positional cloning was hampered by low recombination frequency. We hypothesized that ui1.1 encodes an SLF protein(s) that interacts with CUL1 and Skp1 proteins to form an SCF-type (Skp1, Cullin1, F-box) ubiquitin E3 ligase complex. We identified 23 SLF genes in the S. pennellii genome, of which 19 were also represented in cultivated tomato (S. lycopersicum). Data from recombination events, expression analysis, and sequence annotation highlighted 11 S. pennellii genes as candidates. Genetic transformations demonstrated that one of these, SpSLF-23, is sufficient for ui1.1 function. A survey of cultivated and wild tomato species identified SLF-23 orthologs in each of the SI species, but not in the SC species S. lycopersicum, S. cheesmaniae, and S. galapagense, pollen of which lacks ui1.1 function. These results demonstrate that pollen compatibility in UI is mediated by protein degradation through the ubiquitin–proteasome pathway, a mechanism related to that which controls pollen recognition in SI.
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Schwarzenberger, P., SE Spence, JM Gooya, D. Michiel, DT Curiel, FW Ruscetti, and JR Keller. "Targeted gene transfer to human hematopoietic progenitor cell lines through the c-kit receptor." Blood 87, no. 2 (January 15, 1996): 472–78. http://dx.doi.org/10.1182/blood.v87.2.472.bloodjournal872472.

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In this report, we describe a novel gene therapy approach for hematopoietic stem/progenitor cells using a specific receptor-mediated gene transfection procedure to target c-kit+ cell lines. The vector consists of plasmid DNA containing a luciferase reporter gene that is condensed by electrostatic forces with polylysine (PL) covalently linked to streptavidin (binds biotinylated ligand) and PL covalently linked to adenovirus (AD; to achieve endosomal lysis) with the final addition of biotinylated steel factor (SLF-biotin). Targeted transfection of growth factor-dependent hematopoietic progenitor cell lines that express c-kit showed specific luciferase gene expression over cell lines that did not express c-kit. This effect was dependent on the dose of SLF-biotin and was competed by excess SLF or with monoclonal antibodies that recognize c-kit and block the binding of SLF to its receptor. Maximum transfection efficiency (> 90%) requires a 2- hour incubation period of the vector with the cells, and maximum gene expression occurred 30 hours later. Removal of the endosomalytic agent, AD, from the vector resulted in the loss of gene expression. Vector targeting was versatile and could be changed by the addition of other biotinylated ligands. In principle, this vector should be broadly applicable to deliver genes to hematopoietic stem/progenitor cells in vitro and in vivo.
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Miyazawa, K., K. Toyama, A. Gotoh, PC Hendrie, C. Mantel, and HE Broxmeyer. "Ligand-dependent polyubiquitination of c-kit gene product: a possible mechanism of receptor down modulation in M07e cells." Blood 83, no. 1 (January 1, 1994): 137–45. http://dx.doi.org/10.1182/blood.v83.1.137.137.

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Abstract Quantities of proteins in cells are balanced by protein synthesis and degradation. Protein ubiquitination is an important adenosine- triphosphate dependent proteolytic pathway for “short-lived” proteins. We show that soluble steel-factor (SLF) stimulation at 37 degrees C rapidly induced polyubiquitination of c-kit protein in growth-factor- dependent human-myeloid cell line M07e, resulting in smeared, retarded migration of c-kit protein in sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the molecular weight region of 145 kD. Receptor ubiquitination was almost completely absent when cells were treated with SLF at 4 degrees C or at 37 degrees C in the presence of 0.2% sodium azide, or when the cells were pretreated with anti-c-kit monoclonal antibody or genistein, a tyrosine-kinase inhibitor. This suggested that c-kit ubiquitination was ligand dependent and appeared to require intrinsic tyrosine-kinase activation of the c-kit protein. Flow-cytometric analysis of c-kit expression on the cell surface of M07e cells showed down modulation of c-kit within 5 minutes after soluble-SLF treatment at 37 degrees C. However, rapid receptor down modulation was almost completely suppressed when cells were treated with SLF at 4 degrees C or at 37 degrees C in the presence of 0.2% sodium azide, conditions that concomitantly suppressed polyubiquitination of c-kit protein. In addition, these conditions almost completely suppressed radiolabeled SLF (125I-SLF) internalization after ligand-receptor interaction. Pulse-chase studies of 35S-methionine-labeled c-kit protein showed that SLF stimulation at 37 degrees C strikingly enhanced c-kit degradation (T1/2; approximately 20 minutes) compared with that in cells stimulated with SLF at 4 degrees C or at 37 degrees C with 0.2% sodium azide. However, in the presence of chloroquine, which blocks lysosomal degradation, this ligand-induced c-kit degradation at 37 degrees C was only suppressed in part. These data suggest that SLF-induced polyubiquitination of the c- kit receptor protein may play a role in regulation of c-kit-encoded protein-receptor expression in M07e cells.
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Miyazawa, K., K. Toyama, A. Gotoh, PC Hendrie, C. Mantel, and HE Broxmeyer. "Ligand-dependent polyubiquitination of c-kit gene product: a possible mechanism of receptor down modulation in M07e cells." Blood 83, no. 1 (January 1, 1994): 137–45. http://dx.doi.org/10.1182/blood.v83.1.137.bloodjournal831137.

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Quantities of proteins in cells are balanced by protein synthesis and degradation. Protein ubiquitination is an important adenosine- triphosphate dependent proteolytic pathway for “short-lived” proteins. We show that soluble steel-factor (SLF) stimulation at 37 degrees C rapidly induced polyubiquitination of c-kit protein in growth-factor- dependent human-myeloid cell line M07e, resulting in smeared, retarded migration of c-kit protein in sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the molecular weight region of 145 kD. Receptor ubiquitination was almost completely absent when cells were treated with SLF at 4 degrees C or at 37 degrees C in the presence of 0.2% sodium azide, or when the cells were pretreated with anti-c-kit monoclonal antibody or genistein, a tyrosine-kinase inhibitor. This suggested that c-kit ubiquitination was ligand dependent and appeared to require intrinsic tyrosine-kinase activation of the c-kit protein. Flow-cytometric analysis of c-kit expression on the cell surface of M07e cells showed down modulation of c-kit within 5 minutes after soluble-SLF treatment at 37 degrees C. However, rapid receptor down modulation was almost completely suppressed when cells were treated with SLF at 4 degrees C or at 37 degrees C in the presence of 0.2% sodium azide, conditions that concomitantly suppressed polyubiquitination of c-kit protein. In addition, these conditions almost completely suppressed radiolabeled SLF (125I-SLF) internalization after ligand-receptor interaction. Pulse-chase studies of 35S-methionine-labeled c-kit protein showed that SLF stimulation at 37 degrees C strikingly enhanced c-kit degradation (T1/2; approximately 20 minutes) compared with that in cells stimulated with SLF at 4 degrees C or at 37 degrees C with 0.2% sodium azide. However, in the presence of chloroquine, which blocks lysosomal degradation, this ligand-induced c-kit degradation at 37 degrees C was only suppressed in part. These data suggest that SLF-induced polyubiquitination of the c- kit receptor protein may play a role in regulation of c-kit-encoded protein-receptor expression in M07e cells.
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5

Yip-Schneider, MT, M. Horie, and HE Broxmeyer. "Transcriptional induction of pim-1 protein kinase gene expression by interferon gamma and posttranscriptional effects on costimulation with steel factor." Blood 85, no. 12 (June 15, 1995): 3494–502. http://dx.doi.org/10.1182/blood.v85.12.3494.bloodjournal85123494.

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Steel factor (SLF) synergizes with interferon gamma (IFN gamma) to stimulate proliferation of the human factor-dependent cell line MO7e. We examined the effects of IFN gamma and SLF treatment, alone or in combination, on the expression of a 33-kD cytoplasmic protein serine/threonine kinase designated pim-1 whose expression has been closely associated with proliferation induced by related myeloid cytokines. IFN gamma alone, but not SLF, stimulated expression of pim-1 RNA and protein in MO7e cells; compared with IFN gamma alone, costimulation with IFN gamma and SLF resulted in a twofold to threefold increase in pim-1 message and protein expression, correlating with synergistic effects on cell proliferation. Both IFN gamma and IFN gamma/SLF induced pim-1 mRNA in the absence of de novo protein synthesis. Nuclear run-on assays showed that, although IFN gamma alone increased the rate of pim-1 gene transcription, costimulation with IFN gamma and SLF did not further potentiate this effect; however, the stability of pim-1 message was significantly enhanced in the presence of both cytokines. An IFN gamma-responsive element within the 5′ flanking region of the pim-1 gene that could confer IFN gamma responsiveness on a heterologous promoter was identified. This sequence, designated PMGAS, formed a specific complex with Stat (signal transducers and activators of transcription) 1 alpha (the p91 subunit of the transcription factor ISGF3 [interferon-stimulated gene factor 3]) in IFN gamma-treated cell extracts, suggesting that the transcriptional effects of IFN gamma on pim-1 expression may be mediated by Stat 1 alpha.
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Ren, Yi, Qingzhu Hua, Jiayan Pan, Zhike Zhang, Jietang Zhao, Xinhua He, Yonghua Qin, and Guibing Hu. "SKP1-like protein, CrSKP1-e, interacts with pollen-specific F-box proteins and assembles into SCF-type E3 complex in ‘Wuzishatangju’ (Citrus reticulata Blanco) pollen." PeerJ 8 (December 22, 2020): e10578. http://dx.doi.org/10.7717/peerj.10578.

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S-ribonuclease (S-RNase)-based self-incompatibility (SI) mechanisms have been extensively studied in Solanaceae, Rosaceae and Plantaginaceae. S-RNase-based SI is controlled by two closely related genes, S-RNase and S-locus F-box (SLF), located at a polymorphic S-locus. In the SI system, the SCF-type (SKP1-CUL1-F-box-RBX1) complex functions as an E3 ubiquitin ligase complex for ubiquitination of non-self S-RNase. Pummelo (Citrus grandis) and several mandarin cultivars are suggested to utilize an S-RNase-based SI system. However, the molecular mechanism of the non-S-factors involved in the SI reaction is not straightforward in Citrus. To investigate the SCF-type E3 complex responsible for the SI reaction in mandarin, SLF, SKP1-like and CUL1 candidates potentially involved in the SI reaction of ‘Wuzishatangju’ (Citrus reticulata Blanco) were identified based on the genome-wide identification and expression analyses. Sixteen pollen-specific F-box genes (CrFBX1-CrFBX16), one pollen-specific SKP1-like gene (CrSKP1-e) and two CUL1 genes (CrCUL1A and CrCUL1B) were identified and cloned from ‘Wuzishatangju’. Yeast two-hybrid (Y2H) and in vitro binding assays showed that five CrFBX proteins could bind to CrSKP1-e, which is an ortholog of SSK1 (SLF-interacting-SKP1-like), a non-S-factor responsible for the SI reaction. Luciferase complementation imaging (LCI) and in vitro binding assays also showed that CrSKP1-e interacts with the N-terminal region of both CrCUL1A and CrCUL1B. These results indicate that CrSKP1-e may serve as a functional member of the SCF-type E3 ubiquitin ligase complex in ‘Wuzishatangju’.
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Faust, E. A., D. C. Saffran, D. Toksoz, D. A. Williams, and O. N. Witte. "Distinctive growth requirements and gene expression patterns distinguish progenitor B cells from pre-B cells." Journal of Experimental Medicine 177, no. 4 (April 1, 1993): 915–23. http://dx.doi.org/10.1084/jem.177.4.915.

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Long-term bone marrow cultures have been useful in determining gene expression patterns in pre-B cells and in the identification of cytokines such as interleukin 7 (IL-7). We have developed a culture system to selectively grow populations of B lineage restricted progenitors (pro-B cells) from murine bone marrow. Pro-B cells do not grow in response to IL-7, Steel locus factor (SLF), or a combination of the two. c-kit, the SLF receptor, and the IL-7 receptor are both expressed by pro-B cells, indicating that the lack of response is not simply due to the absence of receptors. Furthermore, SLF is not necessary for the growth of pro-B cells since they could be expanded on a stromal line derived from Steel mice that produces no SLF. IL-7 responsiveness in pre-B cells is associated with an increase in n-myc expression and is correlated with immunoglobulin (Ig) gene rearrangements. Although members of the ets family of transcription factors and the Pim-1 kinase are expressed by pro-B cells, n-myc is not expressed. Pro-B cells maintain Ig genes in the germline configuration, which is correlated with a low level of recombination activating genes 1 and 2 (Rag-1 and 2) mRNA expression, but high expression of sterile mu and terminal deoxynucleotidyl transferase. Pro-B cells are unable to grow separated from the stromal layer by a porous membrane, indicating that stromal contact is required for growth. These results suggest that pro-B cells are dependent on alternative growth signals derived from bone marrow stroma and can be distinguished from pre-B cells by specific patterns of gene expression.
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Lu, Li, Michael C. Heinrich, Li-Sheng Wang, Mu-Shui Dai, Amy J. Zigler, Lin Chai, and Hal E. Broxmeyer. "Retroviral-Mediated Gene Transduction of c-kit Into Single Hematopoietic Progenitor Cells From Cord Blood Enhances Erythroid Colony Formation and Decreases Sensitivity to Inhibition by Tumor Necrosis Factor- and Transforming Growth Factor-β1." Blood 94, no. 7 (October 1, 1999): 2319–32. http://dx.doi.org/10.1182/blood.v94.7.2319.419k14_2319_2332.

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The c-kit receptor and its ligand, steel factor (SLF), are critical for optimal hematopoiesis. We evaluated effects of transducing cord blood (CB) progenitor cells with a retrovirus encoding humanc-kit cDNA. CD34+ cells were sorted as a population or as 1 cell/well for cells expressing high levels of CD34+++ and different levels of c-kit (++, +, Lo/−), transduced and then cultured in the presence of granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-3 (IL-3), IL-6, erythropoietin (Epo) +/− SLF in the absence of serum. At a single-cell level, transduction with c-kit, but not with control (neo only), virus significantly increased colony formation, especially by erythroid and multipotential progenitors. The enhancing effect of c-kit transduction was inversely correlated with expression of c-kit protein before transduction. The greatest enhancing effects were noted in CD34+++kitLo/− cells transduced with c-kit. The stimulating effect was apparent even in the absence of exogenously added SLF, but in the presence of GM-CSF, IL-3, IL-6, and Epo. Enzyme-linked immunosorbent assay (ELISA) of SLF protein, reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of SLF mRNA expression in CD34+ cells, and use of neutralizing antibodies to SLF and/or c-kit suggested the presence of endogenous, although probably very low level, expression of SLF by these progenitor cells. Transduction of c-kit significantly decreased sensitivity of progenitor cells to the inhibitory effects of transforming growth factor-β1 and tumor necrosis factor-.c-kit–transduced cells had increased expression ofc-kit protein and decreased spontaneous or cytokine-induced apoptosis. Our results suggest that transduced c-kit into selected progenitor cells can enhance proliferation and decrease apoptosis and that endogenous SLF may mediate this effect.
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Shubber, E. K., and Z. MT Jaffer. "Establishment of HPRT and DHFR Gene Mutation Assays as biomarkers In Sheep lung fibroblasts (SLF)." Journal of Biotechnology Research Center 4, no. 2 (June 1, 2010): 11–17. http://dx.doi.org/10.24126/jobrc.2010.4.2.111.

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The aim of this research is to establish a gene mutation assay for examining the integrity of animal cell genome for nuclear transfer technique. Lung fibroblasts which were expanded from 4 months old female lamb were selected as target cells. These cells were coded (SLF) as Sheep lung cells. Growth characterization, doubling time, chromosomal number and structural integrity were checked after their growth in RPMI-1640 medium. For HPRT-gene mutation assay, the cells were plated at density of 1×103cells/plate and grown in medium containing toxic concentrations of 6-thioguanine; while for DHFR -gene mutation assay, toxic concentration of methotrexate was used as a selective agent. Those cells were grown for 15 days; mutant colonies either 6TGr or MTXr were reinoculated in a selective medium for further 8 weeks for checking the stability of phenotypic expression of mutant cells. The results revealed that SLF cells has spontaneous frequencies of HPRT, and DHFR gene mutations equal to 16 and 22×10-3 event/ generation/ cell, respectivel.These levels are normal comparing with other animal cell types, and these assays could be applied on other somatic cells.
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Lu, L., M. Xiao, D. W. Clapp, Z. H. Li, and H. E. Broxmeyer. "High efficiency retroviral mediated gene transduction into single isolated immature and replatable CD34(3+) hematopoietic stem/progenitor cells from human umbilical cord blood." Journal of Experimental Medicine 178, no. 6 (December 1, 1993): 2089–96. http://dx.doi.org/10.1084/jem.178.6.2089.

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Umbilical cord blood is rich in hematopoietic stem and progenitor cells and has recently been used successfully in the clinic as an alternative source of engrafting and marrow repopulating cells. With the likelihood that cord blood stem/progenitor cells will be used for gene therapy to correct genetic disorders, we evaluated if a TK-neo gene could be directly transduced in a stable manner into single isolated subsets of purified immature hematopoietic cells that demonstrate self-renewed ability as estimated by colony replating capacity. Sorted CD34(3+) cells from cord blood were prestimulated with erythropoietin (Epo), steel factor (SLF), interleukin (IL)-3, and granulocyte-macrophage colony stimulating factor (GM-CSF) and transduced with the gene in two ways. CD34(3+) cells were incubated with retroviral-containing supernatant from TK-neo vector-producing cells, washed, and plated directly or resorted as CD34(3+) cells into single wells containing a single cell or 10 cells. Alternatively, CD34(3+) cells were sorted as a single cell/well and then incubated with viral supernatant. These cells were cultured with Epo, SLF, IL-3, and GM-CSF +/- G418. The TK-neo gene was introduced at very high efficiency into low numbers of or isolated single purified CD34(3+) immature hematopoietic cells without stromal cells as a source of virus or accessory cells. Proviral integration was detected in primary G418-resistant(R) colonies derived from single immature hematopoietic cells, and in cells from replated colonies derived from G418R-colony forming unit-granulocyte erythroid macrophage megakaryocyte (CFU-GEMM) and -high proliferative potential colony forming cells (HPP-CFC). This demonstrates stable expression of the transduced gene into single purified stem/progenitor cells with replating capacity, results that should be applicable for future clinical studies that may utilize selected subsets of stem/progenitor cells for gene therapy.
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Dissertations / Theses on the topic "SLF gene"

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Czyzyk, Rafal Sebastian. "Role of the SLF gene in self-compatability in Petunia hybrida." Thesis, University of Nottingham, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.546518.

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Guo, Ling. "Identification of novel SLE susceptibility genes by microarray analysis and candidate gene association study." Oklahoma City : [s.n.], 2008.

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Guerra, Sandra. "Gene polymorphisms in SLE." Thesis, King's College London (University of London), 2013. https://kclpure.kcl.ac.uk/portal/en/theses/gene-polymorphisms-in-sle(96ff1bac-bcca-40f1-bfd7-24bc87dc7a25).html.

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Systemic lupus erythematosus (SLE) is an autoimmune disease, with a strong genetic component. It is characterised by hyperactive T and B cells, chronic inflammation and the production of antinuclear autoantibodies. SLE affects mostly women of child baring age, with a 9:1 ratio, women to men and has been reported to be more prevalent in people of non-European ancestry. In the era of genome-wide association studies (GWAS), elucidating the genetic factors present in SLE has been very successful, with over 28 confirmed disease susceptibility loci mapped and a number of candidate genes identified. During this thesis I fine mapped IL18 as it had previously been reported to be associated with SLE, SNP rs360719. After fine mapping and subphenotype analysis in UK and African American cohorts, I was unable to replicate the published association. Although genetic data did not confirm IL18 to be associated with SLE, I demonstrated increased IL-18 serum levels in SLE renal patients compared to SLE patients. I further analysed IL10, another previously associated SLE candidate loci in our current SLE GWAS cohort (4000 cases and 9000 controls) of European ancestry. I again was unable to replicate the previous association, however using other SLE GWAS data showed SNP rs3024505 to be associated in Northern European samples. Further analysing our SLE GWAS, I located IKZF3 as a candidate loci. I identified an associated block of 56 SNPS and located the association to a single SNP rs2941509, p=1.46xlQ-8. Furthermore, I demonstrated an allelic imbalance in this SNP, with the protective G allele being expressed 1.5 times greater than the risk A allele, in controls. These data here demonstrated in this thesis indicates the importance of fine mapping candidate loci and verification of previously associated loci. This thesis contributes to the current knowledge of SLE by demonstrating discrepancies in published association data and showing the importance of larger studies.
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Wang, Dali. "Adaptive Double Self-Organizing Map for Clustering Gene Expression Data." Fogler Library, University of Maine, 2003. http://www.library.umaine.edu/theses/pdf/WangD2003.pdf.

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Anderson, George. "Existentially self deceptive storytelling : a new genre." Thesis, University of Westminster, 2009. https://westminsterresearch.westminster.ac.uk/item/90vq0/existentially-self-deceptive-storytelling-a-new-genre.

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This thesis is an exploration into the function and form of storytelling. Its initial assumption is that consciousness is a genetically transmitted mechanism which generates a concept of self by creating a story. In this formulation, the consciousness is called narrative-consciousness. Since the concept of self necessarily suggests its opposite and this in turn involves awareness of existential futility, the purpose of the story, generated by the narrative-consciousness, is seen to be, in the first instance, the hiding of this unavoidable and potentially damaging awareness. This thesis suggests that to achieve this goal the story must be based on the process of self-deception. The thesis shows that, in general, self-deception involves three significant components in its bid to separate any two paradoxical ideas: unease, process and hiding and that each of these maps onto a particular component in the final narrative of the self. The narrative created by a consciousness hiding, in particular, the awareness of existential angst is given the specific name existentially-selfdeceptive- story, with an acronym ESDeS. The thesis goes on to suggest that such a narrative-consciousness could produce written stories that follow the same pattern, in which case the stories are called existentially-self-deceptive-novels, with an acronym ESDeN. Such a story or genre is then shown to be part of a continuum consisting of up to three distinct ways of dealing with existential futility. The thesis labels these Story-1, Story-2 and Story-3 respectively but reserves the name ESDeN for a subset of Story-2. Analyses of three of these stories, Heart of Darkness, Chance and Thinks concludes that the genre necessarily includes genre-markers, bracketing deaths and repetition, can also include other optional components such as the self-deceptive process or the parent-child mechanism but that its defining characteristic is its division between an overt plot and a covert plot which contains a collusive death of a character identified with existential angst. A covert plot is necessarily available but it is, by definition, not easily discovered. Its successful hiding is made possible, primarily, by foregrounding the overt content of the novel at the expense of the covert. In this sense, the only necessary requirement of the overt content is it should distract and it does this best when the reader cooperates by investing time in interpretation: that is, in order to disguise the ultimate the reader concentrates on the proximal. Finally, the thesis mirrors the endings of each ESDeN by drawing attention to the fact that this collusion will not work for long: just as self-deception cannot withstand too much contrary evidence, the covert plot will not stand too many rereadings. Inevitably, for the true ESDeS, another point of recognition will occur and this will necessitate the renewal or replacement of the ESDeS.
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Sun, Wei [Verfasser]. "RNA isoform analyses of Drosophila Dscam gene and Xenopus tropicalis clustered Protocadherin genes provide insights for neuronal self-avoidance / Wei Sun." Berlin : Freie Universität Berlin, 2016. http://d-nb.info/1098185358/34.

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Zhang, Yan, and 张彦. "Association studies of systemic lupus erythematosus (SLE) : from novel susceptibility loci to gene-gene interaction." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hdl.handle.net/10722/211557.

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Systemic lupus erythematosus (SLE) is characterized as an autoimmune disorder with unclear etiology. To identify the genetic effect of SLE, a genome wide association study (GWAS) and its further replication were conducted on SLE patients in Asian populations and ethnically matched controls. Before this study, most of the confirmed association loci were identified by GWAS studies in European populations. Apart from the established associations, we identified a SLE susceptible single nucleotide polymorphisms (SNP) located in ETS1 (rs1128334, P=2.3E-11, OR=1.29) in four different cohorts. This locus is probably an Asian-specific susceptibility locus since no Caucasian study has reported further validation in the last years. A new susceptibility variant in UHRF1BP1 (rs13205210, P=4.4E-09, OR=1.49) independent from the previously confirmed SNPs in Caucasian study was also confirmed to be associated with SLE in the Hong Kong Chinese population. Meta-analysis was performed by introducing another Chinese Han GWAS data set from Anhui province, China. Three loci, TET3-DGUOK, CD80, DRAM1, were confirmed to be associated with SLE. Two loci with suggestive signals in Hong Kong GWAS and further replication were also confirmed by the meta-analysis: PTTG1-MiRNA146a, YDJC. In order to identify the genetic effect for females who have predominant chance to suffer from SLE, X chromosome specific meta-analysis based on the Hong Kong and Anhui GWAS data and further replication study were performed by considering the difference between females and males. A signal in PRPS2, and three independent signals in the Xq28 were confirmed with the replication in three different cohorts by considering both females and males. Gene-gene interactions were also investigated genome-widely in a hypothesis free manner based on the meta-analysis results. The further validation processes were preceeded based on each independent GWAS data set. Four pairswise interacting loci were found and cross validated by three methods including logistic regression and Multifactor Dimensionality Reduction (MDR) and information gain theory based on the Anhui GWAS data set. Further studies are still needed to better explain the real features of genetic epistasis and the potential biological roles. By incorporating two GWAS from the same population, the population difference is efficiently avoided. Together with the putative gene-gene interactions, this study presents a comprehensive analysis based on the GWAS data conducted on SLE. It may shed new light on the disease mechanisms of SLE.
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8

Raciti, Daniela. "A large-scale gene discovery screen identifies over hundred solute carrier (SLC) genes with organ specific expression patterns in the Xenopus embryo /." Zürich : ETH, 2007. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=17204.

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9

Morimoto, Takuya. "Insights into the evolution and establishment of the Prunus-specific self-incompatibility recognition mechanism." 京都大学 (Kyoto University), 2017. http://hdl.handle.net/2433/225645.

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10

Jonsson, Per. "Improving Clustering of Gene Expression Patterns." Thesis, University of Skövde, Department of Computer Science, 2000. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-482.

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The central question investigated in this project was whether clustering of gene expression patterns could be done more biologically accurate by providing the clustering technique with additional information about the genes as input besides the expression levels. With the term biologically accurate we mean that the genes should not only be clustered together according to their similarities in expression profiles, but also according to their functional similarity in terms of functional annotation and metabolic pathway. The data was collected at AstraZeneca R&D Mölndal Sweden and the applied computational technique was self-organising maps. In our experiments we used the combination of expression profiles together with enzyme classification annotation as input for the self-organising maps instead of just the expression profiles. The results were evaluated both statistically and biologically. The statistical evaluation showed that our method resulted in a small decrease in terms of compactness and isolation. The biological evaluation showed that our method resulted in clusters with greater functional homogeneity with respect to enzyme classification, functional hierarchy and metabolic pathway annotation.

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Books on the topic "SLF gene"

1

OUR GENEROUS GENE. [Place of publication not identified]: THE GENEROUS Press, 2015.

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LeBell, Gene. Gene LeBell's handbook of self-defense. Los Angeles, CA: Pro-Action Pub., 1996.

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R, Schroeder Stephen, Oster-Granite Mary Lou, and Thompson Travis, eds. Self-injurious behavior: Gene-brain-behavior relationships. Washington, DC: American Psychological Association, 2002.

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Schroeder, Stephen R., Mary Lou Oster-Granite, and Travis Thompson, eds. Self-injurious behavior: Gene-brain-behavior relationships. Washington: American Psychological Association, 2002. http://dx.doi.org/10.1037/10457-000.

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LeBell, Gene. Gene LeBell's grappling and self-defense for the young adult. Los Angeles, CA: Pro-Action Pub., 1996.

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Wolfert, Margaretha Adriana. Self-assembling systems based on synthetic polymers for gene delivery. Birmingham: University of Birmingham, 1998.

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The selfish gene pool: An evolutionarily stable system. Lanham, Md: University Press of America, 1996.

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V, Kabanov Alexander, Felgner Philip L. 1950-, and Seymour L. W, eds. Self-assembling complexes for gene delivery: From laboratory to clinical trial. Chichester: Wiley, 1998.

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Kurup, Smita. The molecular characterisation of the self-incompatibility gene from Papaver rhoeas L. Birmingham: University of Birmingham, 1995.

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Cadwallader, Graham P. Transcriptional regulation of a member of the Brassica oleracea self-incompatibility gene family. Birmingham: University of Birmingham, 1995.

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Book chapters on the topic "SLF gene"

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Cornish, E. C., J. M. Pettitt, and A. E. Clarke. "Self-Incompatibility Genes in Flowering Plants." In Plant Gene Research, 117–30. Vienna: Springer Vienna, 1988. http://dx.doi.org/10.1007/978-3-7091-6950-6_7.

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Hodgson, Clague P. "Gene Self-Assembly (GENSA)." In Manufacturing of Gene Therapeutics, 33–43. Boston, MA: Springer US, 2002. http://dx.doi.org/10.1007/978-1-4615-1353-7_3.

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Jankowski, Richard. "A Gene for Altruism?" In Altruism and Self-Interest in Democracies, 95–108. New York: Palgrave Macmillan US, 2015. http://dx.doi.org/10.1057/9781137391537_6.

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Sullivan, Millicent O. "Self-Unpacking Gene Delivery Scaffolds." In Organelle-Specific Pharmaceutical Nanotechnology, 207–30. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2010. http://dx.doi.org/10.1002/9780470875780.ch12.

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Busch, R. H., and D. D. Stuthman. "Self-Pollinated Crop Breeding: Concepts and Successes." In Gene Manipulation in Plant Improvement II, 21–37. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4684-7047-5_2.

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Sorum, Eve C. "The Self-Elegy." In A Companion to Poetic Genre, 93–103. Chichester, UK: John Wiley & Sons, Ltd, 2011. http://dx.doi.org/10.1002/9781444344318.ch7.

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Nanni, Luca. "Computational Inference of DNA Folding Principles: From Data Management to Machine Learning." In Special Topics in Information Technology, 79–88. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-85918-3_7.

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AbstractDNA is the molecular basis of life and would total about three meters if linearly untangled. To fit in the cell nucleus at the micrometer scale, DNA has, therefore, to fold itself into several layers of hierarchical structures, which are thought to be associated with functional compartmentalization of genomic features like genes and their regulatory elements. For this reason, understanding the mechanisms of genome folding is a major biological research problem. Studying chromatin conformation requires high computational resources and complex data analyses pipelines. In this chapter, we first present the PyGMQL software for interactive and scalable data exploration for genomic data. PyGMQL allows the user to inspect genomic datasets and design complex analysis pipelines. The software presents itself as a easy-to-use Python library and interacts seamlessly with other data analysis packages. We then use the software for the study of chromatin conformation data. We focus on the epigenetic determinants of Topologically Associating Domains (TADs), which are region of high self chromatin interaction. The results of this study highlight the existence of a “grammar of genome folding” which dictates the formation of TADs and boundaries, which is based on the CTCF insulator protein. Finally we focus on the relationship between chromatin conformation and gene expression, designing a graph representation learning model for the prediction of gene co-expression from gene topological features obtained from chromatin conformation data. We demonstrate a correlation between chromatin topology and co-expression, shedding a new light on this debated topic and providing a novel computational framework for the study of co-expression networks.
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Kaski, Samuel. "SOM-Based Exploratory Analysis of Gene Expression Data." In Advances in Self-Organising Maps, 124–31. London: Springer London, 2001. http://dx.doi.org/10.1007/978-1-4471-0715-6_18.

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Wedell, Nina. "The Effect of Non-Self Genes on the Behaviour of Hosts." In Genes and Behaviour, 157–80. Chichester, UK: John Wiley & Sons, Ltd, 2019. http://dx.doi.org/10.1002/9781119313663.ch8.

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Vedder, Ulrike. "Poetological Lists: Writing-Scenes in Contemporary Literature." In Forms of List-Making: Epistemic, Literary, and Visual Enumeration, 209–24. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-76970-3_10.

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AbstractThe article focuses on literary lists the items of which demonstrate the practice of writing, that is, those which evoke a “writing-scene” (R. Campe). These poetological lists consolidate the self-reflexive potential of literary texts, gather elements of narration in list form, stage the conditions for a non-linear narrative in the list or even thematize the “genea-logic” of narrative and writing. Under consideration are four lists (all in the second half of the twentieth century) from the most disparate of genres: lyric poetry (Inger Christensen), the manifesto (Jack Kerouac), the novel (Italo Calvino), and the autobiography (Roland Barthes). Each of these lists reflects not only the process of writing and poetics but also genre specificity.
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Conference papers on the topic "SLF gene"

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Wu, Yizhong, Renbin Xiao, Yifang Zhong, and Hanmin Shi. "A Study on Computer Aided Bionic Design System Based on Self-Organization of Modelons." In ASME 2000 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2000. http://dx.doi.org/10.1115/detc2000/dac-14521.

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Abstract All the design activities of new products are top-down processes, in turn, conceptual design, functional design, structural design and detailed design. Unfortunately, design activity under the most traditional CAD systems belongs to a bottom-up process that has many disadvantages such as low efficiency, difficulty of modification and limitation of original thoughts of designers. This paper will describe a new approach for product design, i.e., computer aided bionic design (CABD), integrating both top-down and bottom-up process, which imitates partible attribute of functional structure and self-organization mechanism of cells of organism. Bionic design includes constructing of modelons that constitute a product through computer aided conceptual design (CACD) and structural design, building of product’s local structural gene and global structural gene through self-organization planning of constraints, generating of modelons and automatic assembling of modelons based on the self-organization mechanism under the control of product structural gene. A prototype system based on this approach has been implemented and an example will be presented in this paper.
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Hoffman, RW, ER Dow, NB Perumal, GV Rocha, E. Nantz, N. Shaikh, B. Steere, B. Kechavarzi, RJ Benschop, and RE Higgs. "42 Gene expression profile from 1,760 sle patients reveals novel complex interferon responsive gene networks." In LUPUS 2017 & ACA 2017, (12th International Congress on SLE &, 7th Asian Congress on Autoimmunity). Lupus Foundation of America, 2017. http://dx.doi.org/10.1136/lupus-2017-000215.42.

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Fewings, Nicole L., Sanjay Swaminathan, David Booth, and Ming Wei Lin. "258 NK gene signature in SLE." In 13th International Congress on Systemic Lupus Erythematosus (LUPUS 2019), San Francisco, California, USA, April 5–8, 2019, Abstract Presentations. Lupus Foundation of America, 2019. http://dx.doi.org/10.1136/lupus-2019-lsm.258.

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Kornev, A. A., V. V. Vysochinskaya, N. A. Knyazev, A. K. Emel'yanov, and A. A. Bogdanov. "Transfection of human peripheral blood T-lymphocytes with synthetic small interfering RNAs: selection of an effective technique." In Global science. Development and novelty. L-Journal, 2020. http://dx.doi.org/10.18411/gsdn-25-12-2020-04.

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It has been shown that the state of the human immune system and its activity determines the development, course and prognosis of many oncological diseases. To date, various immunotherapeutic approaches have been developed, of which the most promising is adoptive cell therapy (ACT). An increase in the effectiveness of this type of therapy could be achieved by using synthetic small interfering RNAs (siRNAs) to suppress the expression of key immune checkpoint (ICI) genes (PD1, CTL4) in T-lymphocytes, which are involved in cellular immunosuppression. However, there is a problem of selecting an effective method for delivering such siRNAs to T-lymphocytes. In the present study, we developed a synthetic siRNA specific to the mRNA sequence of the PD1 gene and evaluated the efficiency of its delivery to activated human T-lymphocytes using chemically modified siRNA, histone H1, – 18 – Global science. Development and novelty and the liposomal agent HiperFect. Ex vivo activated T-lymphocytes from healthy donors were used. The efficiency of siRNA transfection into cells and its confirmation was assessed using flow cytofluorometry and confocal microscopy. As a result of the study, a high (51%) efficiency of transfection into these cells using chemically modified "self-delivering" siRNA was shown. For other methods of delivery of miRNA to T-lymphocytes, low efficiency is shown. Thus, our data suggest that of the three approaches used in this work for miRNAs delivery to activated T-lymphocytes, the most effective is the use of “self-delivering” chemically modified cholesterol miRNA.
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Frenkel, Zakhar M., and Alexander I. Melker. "Self-activating gene as a nonlinear oscillator." In Third International Workshop on Nondestructive Testing and Computer Simulations in Science and Engineering, edited by Alexander I. Melker. SPIE, 2000. http://dx.doi.org/10.1117/12.375422.

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Oyarzun, D. A. "Gene circuits for self-tuning metabolic pathways." In IET/SynbiCITE Engineering Biology Conference. Institution of Engineering and Technology, 2016. http://dx.doi.org/10.1049/cp.2016.1220.

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Markby, Greg, Vicky Macrae, Kim Summers, and Brendan Corcoran. "OP1 Severity-dependent gene expression in canine myxomatous mitral valve disease." In Scottish Cardiovascular Forum – 23rd annual meeting, University of Strathclyde, Saturday 1st February 2020. BMJ Publishing Group Ltd and British Cardiovascular Society, 2020. http://dx.doi.org/10.1136/heartjnl-2020-scf.1.

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Saz, Oscar, Mortaza Doulaty, and Thomas Hain. "Background-tracking acoustic features for genre identification of broadcast shows." In 2014 IEEE Spoken Language Technology Workshop (SLT). IEEE, 2014. http://dx.doi.org/10.1109/slt.2014.7078560.

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Lavoie, Erick, Laurie Hendren, Frederic Desprez, and Miguel Correia. "Genet: A Quickly Scalable Fat-Tree Overlay for Personal Volunteer Computing using WebRTC." In 2019 IEEE 13th International Conference on Self-Adaptive and Self-Organizing Systems (SASO). IEEE, 2019. http://dx.doi.org/10.1109/saso.2019.00023.

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Bell, P. J., M. J. F. Gales, P. Lanchantin, X. Liu, Y. Long, S. Renals, P. Swietojanski, and P. C. Woodland. "Transcription of multi-genre media archives using out-of-domain data." In 2012 IEEE Spoken Language Technology Workshop (SLT 2012). IEEE, 2012. http://dx.doi.org/10.1109/slt.2012.6424244.

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Reports on the topic "SLF gene"

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Westwood, James H., Yaakov Tadmor, and Hanan Eizenberg. Identifying the genes involved in host root perception by root parasitic weeds: Genetic and transcriptomic analysis of Orobanche hybrids differing in signal response specificity. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598145.bard.

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Seeds of the root parasitic plants of the genus Orobanchegerminate specifically in response to host-derived germination signals, which enables parasites to detect and attack preferred hosts. The best characterized class of germination stimulants is the strigolactones (SL), although some species respond to sesquiterpene lactones such as dehydrocostuslactone (DCL). Despite great progress in characterizing the SL signaling system in plants, the mechanism(s) by which parasite species detect specific compounds remains poorly understood. The goal of our project was to identify and characterize the genes responsible for stimulant specificity in O. cernuaand O. cumana. These two species are closely related, but differ in host range, with O. cernuaparasitizingSolanaceous crops such as tomato (and responding to SLs), and O. cumanaspecifically parasitizing sunflower (and responding to DCL). We used a genetic approach based on O. cernuax O. cumanahybrids to associate germination response with genes. We found that these parasite species each have multiple copies of KAI2d genes, which function in SL perception. In O. cernua, the OrceKAI2d2 responds to SL stimulants and is most consistently associated with hybrid lines that respond to SLs. For O. cumana, an apparently linked block of KAI2d genes was associated with response to DCL in hybrid lines, but we found no strong evidence that any of the OrcuKAI2d genes specifically recognize the DCL stimulant. Remarkably, one O. cumanagene, OrcuKAI2d5, responds to certain SLs in a genetic complementation assay, even though hybrid lines containing this gene show fidelity to DCL. In summary, we have identified the SL receptor in O. cernua, but the DCL receptor in O. cumanaremains unknown. Our data point to involvement of additional genes and yet greater levels of complexity regulating germination specificity in Orobanche. BARD Report - Project 4616 Page 2 of 8
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Zamir, Dani, Steven Tanksley, and Robert Fluhr. Cloning a Fusarium Resistance Gene in Tomato Based on Knowledge of its Map Position. United States Department of Agriculture, July 1995. http://dx.doi.org/10.32747/1995.7604934.bard.

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The objectives of this project were to develop the tools and methodologies for positional cloning of genes in tomato and apply them for the cloning a Fusarium resistance gene - I2.. The feasibility of positional cloning of disease resistance genes was demonstrated for Pto which confers resistance to pseudomonas (Martin et al. 1993). The Fusarium resistance gene was mapped genetically and physically and was found to be in close proximity to TG 105 (Segal et al. 1992). To obtain fine mapping of gene I2, and additional target genes in future projects, a high density linkage map was developed (Tanksley et al. 1992; Broun and Tanksley 1993). In addition two permanent mapping populations were constructed: a recombinant inbred (Paran et al. 1995; Zamir et al. 1993) and an introgression line population (Eshed et al. 1992; Eshed and Zamir 1994). Using these resources we determined that the I2 locus shows complete co-segregation, down to a resolution of a few Kb, with SL8 which shows architectural similarity with other plant resistance genes. Transformation and complementation analysis is in progress (Ori et al. in preparation).
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Zhang, Bingqi. Self-assembled pentablock copolymers for selective and sustained gene delivery. Office of Scientific and Technical Information (OSTI), May 2011. http://dx.doi.org/10.2172/1029551.

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Skormin, Victor, and Douglas Summerville. Recognition of Computer Viruses by Detecting Their Gene of Self Replication. Fort Belvoir, VA: Defense Technical Information Center, March 2006. http://dx.doi.org/10.21236/ada448622.

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Ohad, Nir, and Robert Fischer. Regulation of plant development by polycomb group proteins. United States Department of Agriculture, January 2008. http://dx.doi.org/10.32747/2008.7695858.bard.

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Our genetic and molecular studies have indicated that FIE a WD-repeat Polycomb group (PcG) protein takes part in multi-component protein complexes. We have shown that FIE PcG protein represses inappropriate programs of development during the reproductive and vegetative phases of the Arabidopsis life cycle. Moreover, we have shown that FIE represses the expression of key regulatory genes that promote flowering (AG and LFY), embryogenesis (LEC1), and shoot formation (KNAT1). These results suggest that the FIE PcG protein participates in the formation of distinct PcG complexes that repress inappropriate gene expression at different stages of plant development. PcG complexes modulate chromatin compactness by modifying histones and thereby regulate gene expression and imprinting. The main goals of our original project were to elucidate the biological functions of PcG proteins, and to understand the molecular mechanisms used by FIE PcG complexes to repress the expression of its gene targets. Our results show that the PcG complex acts within the central cell of the female gametophyte to maintain silencing of MEA paternal allele. Further more we uncovered a novel example of self-imprinting mechanism by the PgG complex. Based on results obtained in the cures of our research program we extended our proposed goals and elucidated the role of DME in regulating plant gene imprinting. We discovered that in addition to MEA,DME also imprints two other genes, FWA and FIS2. Activation of FWA and FIS2 coincides with a reduction in 5-methylcytosine in their respective promoters. Since endosperm is a terminally differentiated tissue, the methylation status in the FWA and FIS2 promoters does not need to be reestablished in the following generation. We proposed a “One-Way Control” model to highlight differences between plant and animal genomic imprinting. Thus we conclude that DEMETER is a master regulator of plant gene imprinting. Future studies of DME function will elucidate its role in processes and disease where DNA methylation has a key regulatory role both in plants and animals. Such information will provide valuable insight into developing novel strategies to control and improve agricultural traits and overcome particular human diseases.
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Aly, Radi, James H. Westwood, and Carole L. Cramer. Novel Approach to Parasitic Weed Control Based on Inducible Expression of Cecropin in Transgenic Plants. United States Department of Agriculture, May 2003. http://dx.doi.org/10.32747/2003.7586467.bard.

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Our overall goal was to engineer crop plants with enhanced resistance to Orobanche (broomrape) based on the inducible expression of sarcotoxin-like peptide (SLP). A secondary objective was to localize small proteins such as SLP in the host-parasite union in order to begin characterizing the mechanism of SLP toxicity to Orobanche. We have successfully accomplished both of these objectives and have demonstrated that transgenic tobacco plants expressing SLP under control of the HMG2 promoter show enhanced resistance to O. aegyptiaca and O. ramosa . Furthermore, we have shown that proteins much larger than the SLP move into Orobanche tubercles from the host root via either symplastic or apoplastic routes. This project was initiated with the finding that enhanced resistance to Orobanche could be conferred on tobacco, potato, and tomato by expression of SLP (Sarcotoxin IA is a 40-residue peptide produced as an antibiotic by the flesh fly, Sarcophaga peregrina ) under the control of a low-level, root-specific promoter. To improve the level of resistance, we linked the SLP gene to the promoter from HMG2, which is strongly inducible by Orobanche as it parasitizes the host. The resulting transgenic plants express SLP and show increased resistance to Orobanche. Resistance in this case is manifested by increased growth and yield of the host in the presence of the parasite as compared to non-transgenic plants, and decreased parasite growth. The mechanism of resistance appears to operate post-attachment as the parasite tubercles attached to the transgenic root plants turned necrotic and failed to develop normally. Studies examining the movement of GFP (approximately 6X the size of SLP) produced in tobacco roots showed accumulation of green fluorescence in tubercles growing on transformed plants but not in those growing on wild-type plants. This accumulation occurs regardless of whether the GFP is targeted to the cytoplasm (translocated symplastically) or the apoplastic space (translocated in xylem). Plants expressing SLP appear normal as compared to non-transgenic plants in the absence of Orobanche, so there is no obvious unintended impact on the host plant from SLP expression. This project required the creation of several gene constructs and generation of many transformed plant lines in order to address the research questions. The specific objectives of the project were to: 1. Make gene constructs fusing Orobanche-inducible promoter sequences to either the sarcotoxin-like peptide (SLP) gene or the GFP reporter gene. 2. Create transgenic plants containing gene constructs. 3. Characterize patterns of transgene expression and host-to-parasite movement of gene products in tobacco ( Nicotiana tabacum L.) and Arabidopsis thaliana (L.). 4. Characterize response of transgenic potato ( Solanum tuberosum L.) and tomato ( Lycopersicon esculentum Mill .) to Orobanche in lab, greenhouse, and field. Objectives 1 and 2 were largely accomplished during the first year during Dr. Aly's sabbatical visit to Virginia Tech. Transforming and analyzing plants with all the constructs has taken longer than expected, so efforts have concentrated on the most important constructs. Work on objective 4 has been delayed pending the final results of analysis on tobacco and Arabidopsis transgenic plants. The implications of this work are profound, because the Orobanche spp. is an extremely destructive weed that is not controlled effectively by traditional cultural or herbicidal weed control strategies. This is the first example of engineering resistance to parasitic weeds and represents a unique mode of action for selective control of these weeds. This research highlights the possibility of using this technique for resistance to other parasitic species and demonstrates the feasibility of developing other novel strategies for engineering resistance to parasitic weeds.
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Prusky, Dov, Nancy P. Keller, and Amir Sherman. global regulation of mycotoxin accumulation during pathogenicity of Penicillium expansum in postharvest fruits. United States Department of Agriculture, January 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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Chejanovsky, Nor, and Bruce A. Webb. Potentiation of pest control by insect immunosuppression. United States Department of Agriculture, July 2004. http://dx.doi.org/10.32747/2004.7587236.bard.

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Our original aims were to elucidate the mechanisms through which the immunosuppressive insect virus, the Campoletis sonorensis polydnavirus (CsV) promotes replication of a well-characterized pathogenic virus, the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) in hosts that are mildly or non-permissive to virus replication. According to the BARD panels criticism we modified our short-term goals (see below). Thus, in this feasibility study (one-year funding) we aimed to show that: 1. S. littoralis larvae mount an immune response against a baculovirus infection. 2. Immunosuppression of an insect pest improves the ability of a viral pathogen (a baculovirus) to infect the pest. 3. S. littoralis cells constitute an efficient tool to study some aspects of the anti- viral immune response. We achieved the above objectives by: 1. Finding melanized viral foci upon following the baculoviral infection in S . littoralis larvae infected with a polyhedra - positive AcMNPV recombinant that expressed the GFP gene under the control of the Drosophila heat shock promoter. 2. Studying the effect of AcMNPV-infection in S . littoralis immunosuppressed by parasitation with the Braconidae wasp Chelonus inanitus that bears the CiV polydna virus, that resulted in higher susceptibility of S. littoralis to AcMNPV- infection. 3. Proving that S. littoralis hemocytes resist AcMNPV -infection. 4. Defining SL2 as a granulocyte-like cell line and demonstrating that as littoralis hemocytic cell line undergoes apoptosis upon AcMNPV -infection. 5. Showing that some of the recombinant AcMNPV expressing the immuno-suppressive polydna virus CsV- vankyrin genes inhibit baculoviral-induced lysis of SL2 cells. This information paves the way to elucidate the mechanisms through which the immuno- suppressive polydna insect viruses promote replication of pathogenic baculoviruses in lepidopteran hosts that are mildly or non-permissive to virus- replication by: - Assessing the extent to which and the mechanisms whereby the immunosuppressive viruses, CiV and CsV or their genes enhance AcMNPV replication in polydnavirus- immunosuppressed H. zea and S. littoralis insects and S. littoralis cells. - Identifying CiV and CsV genes involved in the above immunosuppression (e.g. inhibiting cellular encapsulation and disrupting humoral immunity). This study will provide insight to the molecular mechanisms of viral pathogenesis and improve our understanding of insect immunity. This knowledge is of fundamental importance to controlling insect vectored diseases of humans, animals and plants and essential to developing novel means for pest control (including baculoviruses) that strategically weaken insect defenses to improve pathogen (i.e. biocontrol agent) infection and virulence.
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Or, Etti, Tai-Ping Sun, Amnon Lichter, and Avichai Perl. Characterization and Manipulation of the Primary Components in Gibberellin Signaling in the Grape Berry. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592649.bard.

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Seedless cultivars dominate the table grape industry. In these cultivars it is mandatory to apply gibberellin (GA) to stimulate berry development to a commercially acceptable size. These cultivars differ in their sensitivity to GA application, and it frequently results in adverse effects such as decreased bud fertility and increased fruit drop. Our long term goals are to (1) understand the molecular basis for the differential sensitivity and identify markers for selection of sensitive cultivars (2) to develop new strategies for targeted manipulation of the grape berry response to GA that will eliminate the need in GA application and the undesirable effects of GA on the vine, while maintaining its desirable effects on the berry. Both strategies are expected to reduce production cost and meet growing consumer demand for reduced use of chemicals. This approach relies on a comprehensive characterization of the central components in the GA signaling cascade in the berry. Several key components in the GA signaling pathway were identified in Arabidopsis and rice, including the GA receptors, GID1s, and a family of DELLA proteins that are the major negative regulators of the GA response. GA activates its response pathway by binding to GID1s, which then target DELLAs for degradation via interaction with SLY, a DELLA specific F-box protein. In grape, only one DELLA gene was characterized prior to this study, which plays a major role in inhibiting GA-promoted stem growth and GA-repressed floral induction but it does not regulate fruit growth. Therefore, we speculated that other DELLA family member(s) may control GA responses in berry, and their identification and manipulation may result in GA-independent berry growth. In the current study we isolated two additional VvDELLA family members, two VvGID1 genes and two VvSLY genes. Arabidopsis anti-AtRGA polyclonal antibodies recognized all three purified VvDELLA proteins, but its interaction with VvDELLA3 was weaker. Overexpression of the VvDELLAs, the VvGID1s, and the VvSLYs in the Arabidopsis mutants ga1-3/rga-24, gid1a-2/1c-2 and sly1-10, respectively, rescued the various mutant phenotypes. In vitro GAdependent physical interaction was shown between the VvDELLAs and the VvGID1s, and GAindependent interaction was shown between the VvDELLAs and VvSLYs. Interestingly, VvDELLA3 did not interact with VvGID1b. Together, the results indicate that the identified grape homologs serve as functional DELLA repressors, receptors and DELLA-interacting F-box proteins. Expression analyses revealed that (1) VvDELLA2 was expressed in all the analyzed tissues and was the most abundant (2) VvDELLA1 was low expressed in berries, confirming former study (3) Except in carpels and very young berries, VvDELLA3 levels were the lowest in most tissues. (4) Expression of both VvGID1s was detected in all the grape tissues, but VvGID1b transcript levels were significantly higher than VvGID1a. (5) In general, both VvDELLAs and VvGID1s transcripts levels increased as tissues aged. Unfertilized and recently fertilized carpels did not follow this trend, suggesting different regulatory mechanism of GA signaling in these stages. Characterization of the response to GA of various organs in three seedless cultivars revealed differential response of the berries and rachis. Interestingly, VvDELLA3 transcript levels in the GA-unresponsive berries of cv. Spring blush were significantly higher compared to their levels in the highly responsive berries of cv. Black finger. Assuming that VvDELLA2 and VvDELLA3 are regulating berry size, constructs carrying potential dominant mutations in each gene were created. Furthermore, constitutive silencing of these genes by mIR is underway, to reveal the effect of each gene on the berry phenotype.
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10

Chejanovsky, Nor, and Suzanne M. Thiem. Isolation of Baculoviruses with Expanded Spectrum of Action against Lepidopteran Pests. United States Department of Agriculture, December 2002. http://dx.doi.org/10.32747/2002.7586457.bard.

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Our long-term goal is to learn to control (expand and restrict) the host range of baculoviruses. In this project our aim was to expand the host range of the prototype baculovirus Autographa cali/arnica nuclear polyhedrosis virus (AcMNPV) towards American and Israeli pests. To achieve this objective we studied AcMNPV infection in the non-permissive hosts L. dispar and s. littoralis (Ld652Y and SL2 cells, respectively) as a model system and the major barriers to viral replication. We isolated recombinant baculoviruses with expanded infectivity towards L. dispar and S. littoralis and tested their infectivity towards other Lepidopteran pests. The restricted host range displayed by baculoviruses constitutes an obstacle to their further implementation in the control of diverse Lepidopteran pests, increasing the development costs. Our work points out that cellular defenses are major role blocks to AcMNPV replication in non- and semi-permissive hosts. Therefore a major determinant ofbaculovirus host range is the ability of the virus to effectively counter cellular defenses of host cells. This is exemplified by our findings showing tliat expressing the viral gene Ldhrf-l overcomes global translation arrest in AcMNPV -infected Ld652Y cells. Our data suggests that Ld652Y cells have two anti-viral defense pathways, because they are subject to global translation arrest when infected with AcMNPV carrying a baculovirus apoptotic suppressor (e.g., wild type AcMNPV carryingp35, or recombinant AcMNPV carrying Opiap, Cpiap. or p49 genes) but apoptose when infected with AcMNPV-Iacking a functional apoptotic suppressor. We have yet to elucidate how hrf-l precludes the translation arrest mechanism(s) in AcMNPV-infected Ld652Y cells. Ribosomal profiles of AcMNPV infected Ld652Y cells suggested that translation initiation is a major control point, but we were unable to rule-out a contribution from a block in translation elongation. Phosphorylation of eIF-2a did not appear to playa role in AcMNPV -induced translation arrest. Mutagenesis studies ofhrf-l suggest that a highly acidic domain plays a role in precluding translation arrest. Our findings indicate that translation arrest may be linked to apoptosis either through common sensors of virus infection or as a consequence of late events in the virus life-cycle that occur only if apoptosis is suppressed. ~ AcMNPV replicates poorly in SL2 cells and induces apoptosis. Our studies in AcMNPV - infected SL2ceils led us to conclude that the steady-state levels of lEI (product of the iel gene, major AcMNPV -transactivator and multifunctional protein) relative to those of the immediate early viral protein lEO, playa critical role in regulating the viral infection. By increasing the IEl\IEO ratio we achieved AcMNPV replication in S. littoralis and we were able to isolate recombinant AcMNPV s that replicated efficiently in S. lifforalis cells and larvae. Our data that indicated that AcMNPV - infection may be regulated by an interaction between IE 1 and lED (of previously unknown function). Indeed, we showed that IE 1 associates with lED by using protein "pull down" and immunoprecipitation approaches High steady state levels of "functional" IE 1 resulted in increased expression of the apoptosis suppressor p35 facilitating AcMNPV -replication in SL2 cells. Finally, we determined that lED accelerates the viral infection in AcMNPV -permissive cells. Our results show that expressing viral genes that are able to overcome the insect-pest defense system enable to expand baculovirus host range. Scientifically, this project highlights the need to further study the anti-viral defenses of invertebrates not only to maximi~e the possibilities for manipulating baculovirus genomes, but to better understand the evolutionary underpinnings of the immune systems of vertebrates towards virus infection.
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