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Relevant bibliographies by topics / Cellular Gene Expression

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Academic literature on the topic 'Cellular Gene Expression'

Author: Grafiati

Published: 6 September 2023

Last updated: 7 September 2023

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Journal articles on the topic "Cellular Gene Expression"

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Raven, John A., Charles A. Knight, and John Beardall. "Cell size has gene expression and biophysical consequences for cellular function." Perspectives in Phycology 6, no. 1-2 (July 1, 2019): 81–94. http://dx.doi.org/10.1127/pip/2019/0086.

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TSUDA, Masaaki. "Gene Expression and Cellular Function." YAKUGAKU ZASSHI 113, no. 8 (1993): 537–55. http://dx.doi.org/10.1248/yakushi1947.113.8_537.

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Smith, James R., and Olivia M. Pereira-Smith. "Altered gene expression during cellular aging." Genome 31, no. 1 (January 1, 1989): 386–89. http://dx.doi.org/10.1139/g89-058.

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The limited division potential of normal human diploid fibroblasts in culture represents a model system for cellular aging. Observations indicate cellular senescence is an active process. Senescent cells, although unable to divide, are actively metabolizing. Hybrids from fusion of normal and immortal human cells exhibit limited division potential, suggesting that the phenotype of cellular senescence is dominant and supporting the hypothesis that senescence is genetically programmed. Fusion of immortal human cell lines with each other has identified four complementation groups for indefinite division. This indicates that a limited number of specific genes or processes are involved in senescence. Senescent cells express highly abundant DNA synthesis inhibitory messenger RNAs and produce a surface membrane associated protein inhibitor of DNA synthesis not expressed in young cells. Senescent cell membranes were used as immunogen to generate three monoclonal antibodies reacting specifically with senescent but not young cells in several normal human cell lines. We have also found that fibronectin messenger RNA accumulates to high levels in senescent cells. The role of these changes in gene expression in senescence is being explored.Key words: cellular senescence, human cells.

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Misteli, Tom, and David L. Spector. "The cellular organization of gene expression." Current Opinion in Cell Biology 10, no. 3 (June 1998): 323–31. http://dx.doi.org/10.1016/s0955-0674(98)80007-0.

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Samson, Frederick E. "OXYGEN, GENE EXPRESSION, AND CELLULAR FUNCTION." Shock 8, no. 5 (November 1997): 389. http://dx.doi.org/10.1097/00024382-199711000-00014.

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Samadani, Uzma, Alexander R. Judkins, Albert Akpalu, Eleonora Aronica, and Peter B. Crino. "Differential Cellular Gene Expression in Ganglioglioma." Epilepsia 48, no. 4 (April 2007): 646–53. http://dx.doi.org/10.1111/j.1528-1167.2007.00925.x.

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Frenk, Stephen, and Jonathan Houseley. "Gene expression hallmarks of cellular ageing." Biogerontology 19, no. 6 (February 28, 2018): 547–66. http://dx.doi.org/10.1007/s10522-018-9750-z.

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Canaan, Allon, Izhak Haviv, Alexander E. Urban, Vincent P. Schulz, Steve Hartman, Zhengdong Zhang, Dean Palejev, et al. "EBNA1 regulates cellular gene expression by binding cellular promoters." Proceedings of the National Academy of Sciences 106, no. 52 (December 22, 2009): 22421–26. http://dx.doi.org/10.1073/pnas.0911676106.

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Airoldi, Edoardo M., Curtis Huttenhower, David Gresham, Charles Lu, Amy A. Caudy, Maitreya J. Dunham, James R. Broach, David Botstein, and Olga G. Troyanskaya. "Predicting Cellular Growth from Gene Expression Signatures." PLoS Computational Biology 5, no. 1 (January 2, 2009): e1000257. http://dx.doi.org/10.1371/journal.pcbi.1000257.

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Hutton, Guo, Birchall, and Pearson. "Mucin gene expression in OME: cellular localization." Clinical Otolaryngology and Allied Sciences 23, no. 3 (June 1998): 281–82. http://dx.doi.org/10.1046/j.1365-2273.1998.0138f.x.

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Dissertations / Theses on the topic "Cellular Gene Expression"

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Ackrill, Andrew Michael. "Studies on expression of cellular genes in adenovirus-transformed cells." Thesis, University of Leeds, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328870.

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Janjua, Sadia. "Regulation of gene expression and survival in cellular stress." Thesis, University College London (University of London), 2005. http://discovery.ucl.ac.uk/1444756/.

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All organisms have developed regulated mechanisms to maintain homeostasis. At the cellular level, this normal functioning of cells is regulated by expression of regulatory genes that are required for normal cell function. Most cells in multicellular organisms are capable of altering gene expression in response to extracellular signals such as elevated temperature, ischaemia/reperfusion, inflammation, infection, cytokines, and amino acid analogues. In this thesis the effects of cellular stresses in the form of elevated temperature or simulated ischaemia have been investigated. Previous studies show that elevated temperature or simulated ischaemia can induce expression of heat shock proteins (Hsps) in order to prevent misfolding of cellular proteins. Moreover, it has been shown that the stress responsive transcription factor heat shock factor-1 (HSF-1) is phosphorylated and translocates to the nucleus to bind to heat shock elements within hsp gene promoters. In addition, HSF-1 can interact with other transcription factors such as the signal transducer and activator of transcription-1 (STAT-1), which is a latent cytoplasmic transcription factor activated in response to regulatory cytokines such as interferon gamma (IFNgamma). Preliminary data shows that elevated temperature can induce expression of Hsp90 in the STAT-1 deficient cell line (U3A) treated with IFNa (activates STAT-1 and STAT-2), but reduces the levels of Hsp90 expression in the U3A cell line treated with IFNa and IFNgammain combination. These findings suggest that there may be competition between STAT-1 homodimers and STAT-1/STAT-2 heterodimers and will require further investigation The STAT-1 transcription factor has previously been demonstrated to play a role in stress-induced apoptosis. In this study, STAT-1 is shown to be required for stress-induced apoptosis using the STAT-1 deficient U3A cell line. Cells lacking STAT-1 show reduced cell death/apoptosis in response to elevated temperature or simulated ischaemia. However, expression of STAT-1 in these cells restores sensitivity to stress-induced death. The C-terminal domain alone of STAT-1 is also able to enhance stress-induced cell death, and may be acting via a novel co-activator-type mechanism. Many protective agents have been identified that are able to reduce cell death due to ischaemic injury. Cardiotrophin-1 (CT-1), a member of the IL-6 family of cytokines, has been shown to protect rat neonatal cardiomyocytes subjected to simulated ischaemia via the p42/p44 MAPkinase and PI-3 Kinase pathways. In addition, the unrelated peptide urocortin (Ucn) also protects cardiomyocytes via the same pathway as CT-1 in response to simulated ischaemia and both CT-1 and Ucn induce Hsp expression. In this study, Ucn has been shown to be able to induce enhanced expression of CT-1 at mRNA and protein levels in response to simulated ischaemia. Moreover, the effect is mediated by activation of the CT-1 promoter and requires the transcription factor C/EBPp /NFIL-6. This finding indicates that a common pathway exists for these two protective agents with Ucn inducing CT-1 synthesis. Overall, the work performed indicates that multiple interacting pathways modulate the cellular stress response with either protective or damaging effects.

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Broderick, Peter. "The effect of EBV on host cellular gene expression." Thesis, University of Sussex, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.444349.

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Li, Zheng. "Integrating gene expression and metabolic profiles to optimize cellular functions." Diss., Connect to online resource - MSU authorized users, 2006.

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Thesis (Ph. D.)--Michigan State University. Dept. of Chemical Engineering and Materials Science, 2006.
Title from PDF t.p. (viewed on June 19, 2009) Includes bibliographical references (p. 166-180). Also issued in print.

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Romero, Claudia. "CELLULAR IMMUNE RESPONSE AND GENE EXPRESSION PROFILING IN CROHN'S DISE." Doctoral diss., University of Central Florida, 2004. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/2704.

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Despite the chronic debate in the etiology of crohn's disease (cd), a debilitating inflammatory bowel disease (ibd) closely related to ulcerative colitis (uc), an emerging interest in a possible mycobacterial role has been marked. Granuloma and pathologic manifestations in cd resemble aspects found in tuberculosis, leprosy and paratuberculosis. The latter, a chronic enteritis in cattle, goat, sheep and primates, which is similar to human enteritis, also known as cd, is caused by a fastidious, slow growing mycobacterium avium subspecies paratuberculosis (map). Due to the similarities between cd and paratuberculosis, a mycobacterial cause in cd has been proposed. Recent discovery of a possible association between nod2/card15 mutations and risk of cd added support to microorganism-host interactions. In this study, a possible mycobacterial role in cd etiology has been evaluated by investigating the presence of map dna, the state of the cellular immune response and microarray gene expression profiling in peripheral blood and surgical tissue from cd, uc and healthy control subjects. Nested pcr detected map dna in tissue from 10/12(83%) cd patients compared to 1/6(17%) non-ibd subjects. Fluorescence in situ hybridization (fish) with the aid of confocal scanning laser microscopy (cslm) detected map dna in 8/12(67%) cd subjects compared to 0/6(0%) in non-ibd subjects. The detection of map dna by either technique in tissue from cd subjects is significant compared to non-ibd subjects (p < 0.05). Map dna was also detected in both inflamed and non-inflamed tissue from patients with cd suggesting map infiltration in human tissue. Correlation of possible map presence and the function of polymorphonuclear leukocytes (pmn) and peripheral blood mononuclear cells (pbmc) in 19 cd patients and 12 controls have been evaluated. Pmn phagocytosis of viable fitc-map was suppressed in 13/19(68%) cd patients compared to 0/12(0%) in healthy controls (p<0.05). Pbmc phagocytosis of viable fitc-map was suppressed in 5/19(26%) of cd patients compared to 0/12(0%) of healthy controls (p<0.05). The proliferative response of pbmc with t-cell majority from cd and controls subjects was evaluated against pha, candida albicans, pwm and map ppd. Dysfunctional proliferative response against pha was found in 8/19(42%) cd patients compared to 1/12(8.3%) in controls suggesting possible t-cell anergy. Pbmc from 11 cd subjects reacted normally to pha, 7/11(64%) reacted strongly to map ppd suggesting previous exposure to mycobacteria, and 3/11(27%) did not react with map ppd suggesting lack of pre-exposure to mycobacteria. From the seven mycobacterial pre-exposed samples, 6/7(86%) showed a normal ability to recall antigens by activated macrophages when exposed to c. Albicans, and all 7 samples had a normal pwm response. Finally, microarray-chip technology was employed to identify the expression profile of genes that have a role in the immune response of cd patients. Rna was isolated from fresh buffy coats from 8 healthy controls, 2 cd, and 1 uc patients. Chips with an estimated of 30,000 human genes were hybridized to cdna from these samples. We found that 17% of the total number of genes was differentially expressed. Over 200 genes were involved in the immune response, 7 genes where common to both forms of ibd (uc and cd), and 8 genes were found to be either downregulated in cd and upregulated in uc or viceversa. The ifngr1 gene, which encodes the ligand-binding chain of the ifn-gamma receptor, was found to be downregulated in 2/2(100%) of cd patients, but not in uc patients. It is known that defects in ifngr1 are a cause of atypical mycobacterial infection and bcg infection. Patients suffering from this deficiency have an immunologic defect predisposing them to infection with mycobacteria. This correlates with the proposed theory as map being the causative agent of cd. Furthermore, the results indicate a host susceptibility requirement for the establishment of mycobacterial infection in cd patients. Further characterization of ifngr1 using real-time pcr is underway. Collectively, detection of map dna in the majority of cd tissue and the alteration in pmn and pbmc to respond efficiently to map may be related to the fact that mycobacterial pathogens infect phagocytic cells of susceptible hosts and consequently the immune response is dysregulated. Furthermore, the fact that a gene linked to mycobacterial susceptibility was found to be downregulated in cd patients only, strengthens the mycobacterial etiology of cd. In general, the data suggest a possible role for a bacterial pathogen in cd pathogenesis.
Ph.D.
Other
Burnett College of Biomedical Sciences
Biomolecular Sciences: Ph.D.

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Svensson, Valentine. "Probabilistic modelling of cellular development from single-cell gene expression." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/267937.

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The recent technology of single-cell RNA sequencing can be used to investigate molecular, transcriptional, changes in cells as they develop. I reviewed the literature on the technology, and made a large scale quantitative comparison of the different implementations of single cell RNA sequencing to identify their technical limitations. I investigate how to model transcriptional changes during cellular development. The general forms of expression changes with respect to development leads to nonparametric regression models, in the forms of Gaussian Processes. I used Gaussian process models to investigate expression patterns in early embryonic development, and compared the development of mice and humans. When using in vivo systems, ground truth time for each cell cannot be known. Only a snapshot of cells, all being in different stages of development can be obtained. In an experiment measuring the transcriptome of zebrafish blood precursor cells undergoing the development from hematopoietic stem cells to thrombocytes, I used a Gaussian Process Latent Variable model to align the cells according to the developmental trajectory. This way I could investigate which genes were driving the development, and characterise the different patterns of expression. With the latent variable strategy in mind, I designed an experiment to study a rare event of murine embryonic stem cells entering a state similar to very early embryos. The GPLVM can take advantage of the nonlinear expression patterns involved with this process. The results showed multiple activation events of genes as cells progress towards the rare state. An essential feature of cellular biology is that precursor cells can give rise to multiple types of progenitor cells through differentiation. In the immune system, naive T-helper cells differentiate to different sub-types depending on the infection. For an experiment where mice were infected by malaria, the T-helper cells develop into two cell types, Th1 and Tfh. I model this branching development using an Overlapping Mixture of Gaussian Processes, which let me identify both which cells belong to which branch, and learn which genes are involved with the different branches. Researchers have now started performing high-throughput experiments where spatial context of gene expression is recorded. Similar to how I identify temporal expression patterns, spatial expression patterns can be identified nonparametrically. To enable researchers to make use of this technique, I developed a very fast method to perform a statistical test for spatial dependence, and illustrate the result on multiple data sets.

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Simon, Kathryn D. "Effect of cellular zinc concentration on glucocorticoid induced gene expression." Diss., This resource online, 1996. http://scholar.lib.vt.edu/theses/available/etd-06062008-155344/.

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Zink, Amy Darlene. "Genetic analysis of the cellular control of [PSI] prion." Thesis, Georgia Institute of Technology, 1999. http://hdl.handle.net/1853/25295.

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Chemutai, Patricia. "Gene Expression in Long Term Myoblast /Myocete Cultures: m RNA expression (Acetylcholine Receptor and Galectin-3 gene)." Youngstown State University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1620382476783648.

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Pitstick, Amy L. "Nuclear Reorganization and Gene Expression During Muscle Cell Differentiation." Wright State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=wright1309997417.

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Books on the topic "Cellular Gene Expression"

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1932-, Massaro Donald, and Clerch Linda Biadasz 1948-, eds. Oxygen, gene expression, and cellular function. New York: M. Dekker, 1997.

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Luigi, Frati, and Aaronson Stuart A. 1942-, eds. Pathology of gene expression. New York: Raven Press, 1989.

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S, Dhindsa Dharam, Bahl Om P, National Institutes of Health (U.S.). Reproductive Biology Study Section., and National Institute of Child Health and Human Development (U.S.), eds. Molecular and cellular aspects of reproduction. New York: Plenum Press, 1986.

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NATO Advanced Study Institute on Free Radicals and Diseases: Gene Expression, Cellular Metabolism and Pathophysiology (2004 Spetsai, Greece). Free radicals and diseases: Gene expression, cellular metabolism and pathophysiology. Amsterdam: IOS Press, 2005.

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Schmitz, M. Lienhard, and Susanne Bacher. Mechanisms of signal transduction and inducible gene expression. Trivandrum, India: Research Signpost, 2004.

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Ovarian Workshop on Regulatory Processes and Gene Expression in the Ovary (1990 Maryville, Tenn.). Signaling mechanisms and gene expression in the ovary. Edited by Gibori Geula and Serono Symposia USA. New York: Springer-Verlag, 1991.

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European Workshop on Molecular and Cellular Endocrinology of the Testis. (4th 1986 Capri, Italy). Molecular and cellular endocrinology of the testis: Proceedings of the IV European Workshop on Molecular and Cellular Endocrinology of the Testis, Capri, Italy, 9-12 April 1986. Edited by Stefanini Mario 1916-. Amsterdam: Excerpta Medica, 1986.

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Nandan, Bhattacharyya, and Bhattacharyya Chandan, eds. Recent advances in life sciences. Kerala, India: Research Signpost, 2004.

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1918-, Stefanini Mario, ed. Molecular and cellular endocrinology of the testis: Proceedings of the IV European Workshop on Molecular and Cellular Endocrinology of the Testis, Capri, Italy, 9-12April 1986. Amsterdam: Excerpta Medica, 1986.

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Herlyn, Meenhard. Molecular and cellular biology of melanoma. Austin: R.G. Landes Co., 1993.

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Book chapters on the topic "Cellular Gene Expression"

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Montminy, Marc R. "Control of Transcription and Cellular Proliferation by cAMP." In Gene Expression, 76–92. Boston, MA: Birkhäuser Boston, 1993. http://dx.doi.org/10.1007/978-1-4684-6811-3_4.

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Kaufman, Lon S., Kathleen A. Marrs, Katherine M. F. Warpeha, Jie Gao, Keshab Bhattacharya, Judi Tilghman, and John F. Marsh. "Blue-Light Regulated Gene Expression." In Cellular Communication in Plants, 21–26. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4757-9607-0_4.

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Dougherty, Jonathan D., Nogi Park, Kurt E. Gustin, and Richard E. Lloyd. "Interference with Cellular Gene Expression." In The Picornaviruses, 163–80. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555816698.ch10.

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Truman, D. E. S. "The Evolution of Control Mechanisms in Cellular Differentiation." In Coordinated Regulation of Gene Expression, 299–310. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4613-2245-0_28.

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Byrd, Philip J., and Phillip H. Gallimore. "Transformation of Human Cells by Viral and Cellular Oncogenes." In Coordinated Regulation of Gene Expression, 131–42. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4613-2245-0_12.

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Rickenberg, H. V., K. L. Schaller, and B. H. Leichtling. "Differential Cellular Distribution of Cyclic AMP-Dependent Protein Kinase During Development of Dictyostelium Discoideum." In Gene Manipulation and Expression, 289–304. Dordrecht: Springer Netherlands, 1985. http://dx.doi.org/10.1007/978-94-011-6565-5_21.

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Jędrzejowicz, Joanna, and Piotr Jędrzejowicz. "Cellular Gene Expression Programming Classifier Learning." In Transactions on Computational Collective Intelligence V, 66–83. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-24016-4_4.

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Bartels, Dorothea, Don Nelson, Pekka Heino, Detlef Michel, Antonella Furini, Giovanni Bernacchia, Riccardo Velasco, et al. "Gene Expression during Water Stress." In Biochemical and Cellular Mechanisms of Stress Tolerance in Plants, 273–78. Berlin, Heidelberg: Springer Berlin Heidelberg, 1994. http://dx.doi.org/10.1007/978-3-642-79133-8_15.

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Grant, D. S., J. L. Kinsella, and H. K. Kleinman. "Gene Expression and Endothelial Cell Differentiation." In Molecular, Cellular, and Clinical Aspects of Angiogenesis, 19–29. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4613-0389-3_2.

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Fanning, Saranna, and Aaron P. Mitchell. "Infection-Associated Gene Expression—The Pathogen Perspective." In Candida albicans: Cellular and Molecular Biology, 253–69. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-50409-4_13.

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Conference papers on the topic "Cellular Gene Expression"

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SEGAL, E., A. BATTLE, and D. KOLLER. "DECOMPOSING GENE EXPRESSION INTO CELLULAR PROCESSES." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2002. http://dx.doi.org/10.1142/9789812776303_0009.

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"APOE Gene Expression in Patients with Alzheimer’s Disease." In International Conference on Cellular & Molecular Biology and Medical Sciences. Universal Researchers (UAE), 2016. http://dx.doi.org/10.17758/uruae.ae0916409.

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Subramanian, Vaishnavi, Benjamin Chidester, Jian Ma, and Minh N. Do. "Correlating cellular features with gene expression using CCA." In 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018). IEEE, 2018. http://dx.doi.org/10.1109/isbi.2018.8363694.

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Laug, Walter E. "HETEROGENOUS EXPRESSION OF PLASMINOGEN ACTIVATOR (PA) GENES IN THE HUMAN SARCOMA CELL LINE HT1080." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644395.

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Tumor cell derived PA activities are of crucial importance for tissue invasion and destruction by tumor cells. Therefore, we studied the expression of the PA genes in HT1080 cells using immunoenzymatic methods and specific PA gene probes.Immunenzymatic methods allowed only for the detection of urokinase like PA (u-PA) activities in HT1080 cells which was suppressed by treatment of the cells with dexamethasone (10-7 m). Despite the lack of u-PA activities, the cells still degraded extracellular tissue glycoproteins. Northern blot analysis with specific PA gene probe showed that HT1080 cells express both tissue type PA (t-PA) and u-PA. The enzymatic activities of t-PA were most likely masked by the simultaneous production of inhibitors of PA (PAI). Treatment of HT1080 cells with dexamethasone resulted in increased transcription of t-PA and decreased expression of the u-PA gene, explaining the unchanged tissue destruction by dexamethasone treated HT1080 cells.Cell clones secreting either large or small amounts of enzymatic PA activities were isolated from the parental HT1080 cell line using a fibrin agarose overlay technique.The expression of the u-PA gene was enhanced in high secreting PA clones compared to low secreting PA clones when analyzed on Northern blots. This heterogenous expression of the u-PA gene within the HT1080 cell line was confirmed by in situ hybridization with a specific u-PA gene probe.These findings demonstrate that PA gene expression can be missed with immunenzymatic methods due to simultaneous production of inhibitors of PA. In addition our results show that the expression of a given PA gene may be heterogenous on the cellular level within an established tumor cell line. These findings, therefore, suggest cellular variation of PA gene expression in tumor which may be of fundamental importance for tissue invasion and metastasis by cancer cells.

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Polstein, Lauren R., and Charles A. Gersbach. "Photoregulated Gene Expression in Human Cells With Light-Inducible Engineered Transcription Factors." In ASME 2012 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/sbc2012-80573.

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Systems for controlling gene expression in mammalian cells have a wide range of applications in medicine, biotechnology and basic science. An ideal gene regulatory system would allow for precise and specific control over the magnitude and kinetics of gene expression in space and time, while also exerting minimal influence on other genes and cellular components. Several gene regulatory systems have been developed in which orthogonal transcription machinery from prokaryotes or insects has been imported into mammalian cells and used to control the expression of a specific gene. Despite the transformative impact of these systems in biomedical and biological research, several limitations of these technologies restrict the scope of possible applications. For example, gene expression in these systems is controlled by a freely diffusible small molecule, such as an antibiotic or steroid. Consequently, it is not possible to achieve spatial control over gene expression within cell culture, tissues, or whole organisms. This is in contrast to natural mechanisms of biological regulation in which spatial control is critical, such as developmental patterning and tissue morphogenesis. Second, dynamic gene regulation requires the removal of these small molecules, which may be slow, laborious, and/or impractical for a particular application. To overcome these limitations, we have engineered an optogenetic system in which the magnitude of gene expression in human cells can be finely tuned by photoregulated synthetic transcription factors.

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Broni-Bediako, Cliford, Yuki Murata, Luiz H. B. Mormille, and Masayasu Atsumi. "Evolutionary NAS with Gene Expression Programming of Cellular Encoding." In 2020 IEEE Symposium Series on Computational Intelligence (SSCI). IEEE, 2020. http://dx.doi.org/10.1109/ssci47803.2020.9308346.

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"The Effect of Allicin on ZNF703 Gene Expression in GCC Lines." In International Conference on Cellular & Molecular Biology and Medical Sciences. Universal Researchers (UAE), 2016. http://dx.doi.org/10.17758/uruae.ae0916405.

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Henderson, Jonathan T., Garrett Shannon, Alexander I. Veress, and Corey P. Neu. "Newly Synthesized RNA and Intranuclear Strain Measurements in Living Cells Maintained Within Native Tissue." In ASME 2013 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/sbc2013-14202.

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The nucleus is a regulation center for cellular gene expression 1. Mechanical forces transfer to the nucleus directly and indirectly through cellular cytoskeletal structures and pathways 2, 3. The transmitted strains often cause nuclear deformation which is thought to trigger mechanosensitive gene expression within the nucleus 4. Protein dynamics inside the nucleus are additionally important for maintaining the nuclear structure and in facilitating gene expression at the transcription level 5. Probing spatiotemporal relationships between mechanical forces and localized gene expression (i.e. biophysical and biochemical factors) in the nuclei of cells is important in order to clarify variability observed in large and heterogeneous cell populations within complex tissues. This requires the development of innovative methods for intranuclear strain measurements of cells in situ, and the further capability to quantify associated biochemical responses. This abstract describes a method combining the simultaneous measurement of newly synthesized RNA with spatiotemporal intranuclear strain mapping in single cells embedded in native tissue.

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Ghusinga, Khem Raj, and Abhyudai Singh. "Effect of gene-expression bursts on stochastic timing of cellular events." In 2017 American Control Conference (ACC). IEEE, 2017. http://dx.doi.org/10.23919/acc.2017.7963265.

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LeDuc, Philip R., and Michael J. Betenbaugh. "Implementation of a Pharmocokinetic Approach to a Baculovirus System for Analytic Solutions to Virus and Cell Interactions." In ASME 1997 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 1997. http://dx.doi.org/10.1115/imece1997-0282.

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Abstract The baculovirus, Autographa californica multiple nuclear polyhedrosis virus (AcMNPV), expression system can be employed for a variety of different cellular applications. In recent years, this baculovirus system has been manipulated to serve as a recombinant system for the expression of heterologous proteins and as a possible retrovirus for gene therapy. A quantitative understanding of the cellular mechanics of virus trafficking would be useful in developing viral expression systems, understanding gene therapy and maximizing recombinant protein production. An analytic solution is presented which incorporates a pharmocokinetic system in order to analyze this problem of viral and cellular mechanics. The multiple stages of viral infection systems, specifically for the baculovirus system, include attachment, internalization, endosomal fusion, cytosol transportation, and nuclear accumulation. The effects of the rate parameters are investigated to determine the parameter sensitivity of the viral infection model in relation to accumulation of surface virus, internalized virus and nuclear virus. The concepts from this model can be used to design infection regimens for various cell lines and to analyze the inherent inefficiency of current baculovirus infecting systems. This approach can also be used to determine the effects of the rate-limiting behaviors exhibited by these types of cellular mechanics and can be further implemented to examine other types of infection applications including viral gene therapy [1].

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Reports on the topic "Cellular Gene Expression"

1

Chang-Liu, Chin-Mei, and G. E. Wolschak. Effect of passage number on cellular response DNA-damaging agents: cell survival and gene expression. Office of Scientific and Technical Information (OSTI), March 1996. http://dx.doi.org/10.2172/206623.

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Chang-Liu, C. M., and G. E. Woloschak. Effect of passage number on cellular response to DNA-damaging agents: Cell survival and gene expression. Office of Scientific and Technical Information (OSTI), August 1997. http://dx.doi.org/10.2172/515535.

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Fromm, A., Avihai Danon, and Jian-Kang Zhu. Genes Controlling Calcium-Enhanced Tolerance to Salinity in Plants. United States Department of Agriculture, March 2003. http://dx.doi.org/10.32747/2003.7585201.bard.

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The specific objectives of the proposed research were to identify, clone and characterize downstream cellular target(s) of SOS3 in Arabidopsis thaliana, to analyze the Ca2+-binding characteristics of SOS3 and the sos3-1 mutant and their interactions with SOS3 cellular targets to analyze the SOS3 cell-specific expression patterns, and its subcellular localization, and to assess the in vivo role of SOS3 target protein(s) in plant tolerance to salinity stress. In the course of the study, in view of recent opportunities in identifying Ca2+ - responsive genes using microarrays, the group at Weizmann has moved into identifying Ca2+-responsive stress genes by using a combination of aqeuorin-based measurements of cytosolic Ca and analysis by DNA microarrays of early Ca-responsive genes at the whole genome level. Analysis of SOS3 (University of Arizona) revealed its expression in both roots and shoots. However, the expression of this gene is not induced by stress. This is reminiscent of other stress proteins that are regulated by post-transcriptional mechanisms such as the activation by second messengers like Ca. Further analysis of the expression of the gene using promoter - GUS fusions revealed expression in lateral root primordial. Studies at the Weizmann Institute identified a large number of genes whose expression is up-regulated by a specific cytosolic Ca burst evoked by CaM antagonists. Fewer genes were found to be down-regulated by the Ca burst. Among the up-regulated genes many are associated with early stress responses. Moreover, this study revealed a large number of newly identified Ca-responsive genes. These genes could be useful to investigate yet unknown Ca-responsive gene networks involved in plant response to stress.

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Liu, Xuehui. Studies on the Role of Cellular Factor, YY1, in Herpes Simplex Virus Type 1 Late Gene Expression. Portland State University Library, January 2000. http://dx.doi.org/10.15760/etd.6732.

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Ghanim, Murad, Joe Cicero, Judith K. Brown, and Henryk Czosnek. Dissection of Whitefly-geminivirus Interactions at the Transcriptomic, Proteomic and Cellular Levels. United States Department of Agriculture, February 2010. http://dx.doi.org/10.32747/2010.7592654.bard.

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Our project focuses on gene expression and proteomics of the whitefly Bemisia tabaci (Gennadius) species complex in relation to the internal anatomy and localization of expressed genes and virions in the whitefly vector, which poses a major constraint to vegetable and fiber production in Israel and the USA. While many biological parameters are known for begomovirus transmission, nothing is known about vector proteins involved in the specific interactions between begomoviruses and their whitefly vectors. Identifying such proteins is expected to lead to the design of novel control methods that interfere with whitefly-mediated begomovirus transmission. The project objectives were to: 1) Perform gene expression analyses using microarrays to study the response of whiteflies (B, Q and A biotypes) to the acquisition of begomoviruses (Tomato yellow leaf curl (TYLCV) and Squash leaf curl (SLCV). 2) Construct a whitefly proteome from whole whiteflies and dissected organs after begomovirus acquisition. 3) Validate gene expression by q-RTPCR and sub-cellular localization of candidate ESTs identified in microarray and proteomic analyses. 4) Verify functionality of candidate ESTs using an RNAi approach, and to link these datasets to overall functional whitefly anatomical studies. During the first and second years biological experiments with TYLCV and SLCV acquisition and transmission were completed to verify the suitable parameters for sample collection for microarray experiments. The parameters were generally found to be similar to previously published results by our groups and others. Samples from whole whiteflies and midguts of the B, A and Q biotypes that acquired TYLCV and SLCV were collected in both the US and Israel and hybridized to B. tabaci microarray. The data we analyzed, candidate genes that respond to both viruses in the three tested biotypes were identified and their expression that included quantitative real-time PCR and co-localization was verified for HSP70 by the Israeli group. In addition, experiments were undertaken to employ in situ hybridization to localize several candidate genes (in progress) using an oligonucleotide probe to the primary endosymbiont as a positive control. A proteome and corresponding transcriptome to enable more effective protein identification of adult whiteflies was constructed by the US group. Further validation of the transmission route of begomoviruses, mainly SLCV and the involvement of the digestive and salivary systems was investigated (Cicero and Brown). Due to time and budget constraints the RNAi-mediated silencing objective to verify gene function was not accomplished as anticipated. HSP70, a strong candidate protein that showed over-expression after TYLCV and SLCV acquisition and retention by B. tabaci, and co-localization with TYLCV in the midgut, was further studies. Besides this protein, our joint research resulted in the identification of many intriguing candidate genes and proteins that will be followed up by additional experiments during our future research. To identify these proteins it was necessary to increase the number and breadth of whitefly ESTs substantially and so whitefly cDNAs from various libraries made during the project were sequenced (Sanger, 454). As a result, the proteome annotation (ID) was far more successful than in the initial attempt to identify proteins using Uniprot or translated insect ESTs from public databases. The extent of homology shared by insects in different orders was surprisingly low, underscoring the imperative need for genome and transcriptome sequencing of homopteran insects. Having increased the number of EST from the original usable 5500 generated several years ago to >600,000 (this project+NCBI data mining), we have identified about one fifth of the whitefly proteome using these new resources. Also we have created a database that links all identified whitefly proteins to the PAVEdb-ESTs in the database, resulting in a useful dataset to which additional ESTS will be added. We are optimistic about the prospect of linking the proteome ID results to the transcriptome database to enable our own and other labs the opportunity to functionally annotate not only genes and proteins involved in our area of interest (whitefly mediated transmission) but for the plethora of other functionalities that will emerge from mining and functionally annotating other key genes and gene families in whitefly metabolism, development, among others. This joint grant has resulted in the identification of numerous candidate proteins involved in begomovirus transmission by B. tabaci. A next major step will be to capitalize on validated genes/proteins to develop approaches to interfere with the virus transmission.

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Eshed-Williams, Leor, and Daniel Zilberman. Genetic and cellular networks regulating cell fate at the shoot apical meristem. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7699862.bard.

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The shoot apical meristem establishes plant architecture by continuously producing new lateral organs such as leaves, axillary meristems and flowers throughout the plant life cycle. This unique capacity is achieved by a group of self-renewing pluripotent stem cells that give rise to founder cells, which can differentiate into multiple cell and tissue types in response to environmental and developmental cues. Cell fate specification at the shoot apical meristem is programmed primarily by transcription factors acting in a complex gene regulatory network. In this project we proposed to provide significant understanding of meristem maintenance and cell fate specification by studying four transcription factors acting at the meristem. Our original aim was to identify the direct target genes of WUS, STM, KNAT6 and CNA transcription factor in a genome wide scale and the manner by which they regulate their targets. Our goal was to integrate this data into a regulatory model of cell fate specification in the SAM and to identify key genes within the model for further study. We have generated transgenic plants carrying the four TF with two different tags and preformed chromatin Immunoprecipitation (ChIP) assay to identify the TF direct target genes. Due to unforeseen obstacles we have been delayed in achieving this aim but hope to accomplish it soon. Using the GR inducible system, genetic approach and transcriptome analysis [mRNA-seq] we provided a new look at meristem activity and its regulation of morphogenesis and phyllotaxy and propose a coherent framework for the role of many factors acting in meristem development and maintenance. We provided evidence for 3 different mechanisms for the regulation of WUS expression, DNA methylation, a second receptor pathway - the ERECTA receptor and the CNA TF that negatively regulates WUS expression in its own domain, the Organizing Center. We found that once the WUS expression level surpasses a certain threshold it alters cell identity at the periphery of the inflorescence meristem from floral meristem to carpel fate [FM]. When WUS expression highly elevated in the FM, the meristem turn into indeterminate. We showed that WUS activate cytokinine, inhibit auxin response and represses the genes required for root identity fate and that gradual increase in WUCHEL activity leads to gradual meristem enlargement that affect phyllotaxis. We also propose a model in which the direction of WUS domain expansion laterally or upward affects meristem structure differently. We preformed mRNA-seq on meristems with different size and structure followed by k-means clustering and identified groups of genes that are expressed in specific domains at the meristem. We will integrate this data with the ChIP-seq of the 4 TF to add another layer to the genetic network regulating meristem activity.

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O'Neill, Sharman, Abraham Halevy, and Amihud Borochov. Molecular Genetic Analysis of Pollination-Induced Senescence in Phalaenopsis Orchids. United States Department of Agriculture, 1991. http://dx.doi.org/10.32747/1991.7612837.bard.

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The project investigated the molecular genetic and biochemical basis of pollination-induced senescence of Phalaenopsis flowers. This experimental system offered unique advantages in that senescence is strictly regulated by pollination, providing the basis to experimentally initiate and synchronize senescence in populations of flowers. The postpollination syndrome in the Phalaenopsis orchid system was dissected by investigating the temporal and spatial regulation of ACC synthase gene expression. In the stigma, pollen-borne auxin induces the expression of the auxin-regulated ACC synthase (PS-ACS2) gene, resulting in ACC synthesis within 1 h following pollination. Newly formed ACC is oxidized by basal constitutive ACC oxidase to ethylene, which then induces the expression of the ethylene-regulated ACC synthase(PS-ACS1) and oxidase (ACO1) genes for further autocatalytic production of ethylene. It is speculated that during the 6-h period following pollination, emasculation leads to the production or release of a sensitivity factor that sensitizes the cells of the stigma to ethylene. ACC and ethylene molecules are translocated from the stigma to the labellum and perianth where ethylene induces the expression of PS-ACS1 and ACO1 resulting in an increased production of ACC and ethylene. Organ-localized ethylene is responsible for inrolling and senescence of the labellum and perianth. The regulation of ethylene sensitivity and signal transduction events in pollinated flowers was also investigated. The increase in ethylene sensitivity appeared in both the flower column and the perianth, and was detected as early as 4 h after pollination. The increase in ethylene sensitivity following pollination was not dependent on endogenous ethylene production. Application of linoleic and linoleic acids to Phalaenopsis and Dendrobium flowers enhanced their senescence and promoted ethylene production. Several major lipoxygenase pathway products including JA-ME, traumatic acid, trans-2-hexenal and cis-3-hexenol, also enhanced flower senescence. However, lipoxygenase appears to not be directly involved in the endogenous regulation of pollination-induced Phalaenopsis and Dendrobium flower senescence. The data suggest that short-chain saturated fatty acids may be the ethylene "sensitivity factors" produced following pollination, and that their mode of action involves a decrease in the order of specific regions i the membrane lipid bilayer, consequently altering ethylene action. Examination of potential signal transduction intermediates indicate a direct involvement of GTP-binding proteins, calcium ions and protein phosphorylation in the cellular signal transduction response to ethylene following pollination. Modulations of cytosolic calcium levels allowed us to modify the flowers responsiveness to ethylene.

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Barg, Rivka, Erich Grotewold, and Yechiam Salts. Regulation of Tomato Fruit Development by Interacting MYB Proteins. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7592647.bard.

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Background to the topic: Early tomato fruit development is executed via extensive cell divisions followed by cell expansion concomitantly with endoreduplication. The signals involved in activating the different modes of growth during fruit development are still inadequately understood. Addressing this developmental process, we identified SlFSM1 as a gene expressed specifically during the cell-division dependent stages of fruit development. SlFSM1 is the founder of a class of small plant specific proteins containing a divergent SANT/MYB domain (Barg et al 2005). Before initiating this project, we found that low ectopic over-expression (OEX) of SlFSM1 leads to a significant decrease in the final size of the cells in mature leaves and fruits, and the outer pericarp is substantially narrower, suggesting a role in determining cell size and shape. We also found the interacting partners of the Arabidopsis homologs of FSM1 (two, belonging to the same family), and cloned their tomato single homolog, which we named SlFSB1 (Fruit SANT/MYB–Binding1). SlFSB1 is a novel plant specific single MYB-like protein, which function was unknown. The present project aimed at elucidating the function and mode of action of these two single MYB proteins in regulating tomato fruit development. The specific objectives were: 1. Functional analysis of SlFSM1 and its interacting protein SlFSB1 in relation to fruit development. 2. Identification of the SlFSM1 and/or SlFSB1 cellular targets. The plan of work included: 1) Detailed phenotypic, histological and cellular analyses of plants ectopically expressing FSM1, and plants either ectopically over-expressing or silenced for FSB1. 2) Extensive SELEX analysis, which did not reveal any specific DNA target of SlFSM1 binding, hence the originally offered ChIP analysis was omitted. 3) Genome-wide transcriptional impact of gain- and loss- of SlFSM1 and SlFSB1 function by Affymetrix microarray analyses. This part is still in progress and therefore results are not reported, 4) Search for additional candidate partners of SlFSB1 revealed SlMYBI to be an alternative partner of FSB1, and 5) Study of the physical basis of the interaction between SlFSM1 and SlFSB1 and between FSB1 and MYBI. Major conclusions, solutions, achievements: We established that FSM1 negatively affects cell expansion, particularly of those cells with the highest potential to expand, such as the ones residing inner to the vascular bundles in the fruit pericarp. On the other hand, FSB1 which is expressed throughout fruit development acts as a positive regulator of cell expansion. It was also established that besides interacting with FSM1, FSB1 interacts also with the transcription factor MYBI, and that the formation of the FSB1-MYBI complex is competed by FSM1, which recognizes in FSB1 the same region as MYBI does. Based on these findings a model was developed explaining the role of this novel network of the three different MYB containing proteins FSM1/FSB1/MYBI in the control of tomato cell expansion, particularly during fruit development. In short, during early stages of fruit development (Phase II), the formation of the FSM1-FSB1 complex serves to restrict the expansion of the cells with the greatest expansion potential, those non-dividing cells residing in the inner mesocarp layers of the pericarp. Alternatively, during growth phase III, after transcription of FSM1 sharply declines, FSB1, possibly through complexing with the transcription factor MYBI serves as a positive regulator of the differential cell expansion which drives fruit enlargement during this phase. Additionally, a novel mechanism was revealed by which competing MYB-MYB interactions could participate in the control of gene expression. Implications, both scientific and agricultural: The demonstrated role of the FSM1/FSB1/MYBI complex in controlling differential cell growth in the developing tomato fruit highlights potential exploitations of these genes for improving fruit quality characteristics. Modulation of expression of these genes or their paralogs in other organs could serve to modify leaf and canopy architecture in various crops.

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Sun, Lina, Yanan Han, Hua Wang, Huanyu Liu, Shan Liu, Hongbin Yang, Xiaoxia Ren, and Ying Fang. MicroRNAs as Potential Biomarkers for the Diagnosis of Inflammatory Bowel Disease: A Systematic Review and Meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, February 2022. http://dx.doi.org/10.37766/inplasy2022.2.0027.

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Review question / Objective: The purpose of this systematic review was to systematically review the clinical studies regarding miRNAs as diagnostic biomarkers for inflammatory bowel disease and assess the overall diagnostic accuracy of miRNAs. Condition being studied: The symptoms of inflammatory bowel disease (IBD) are highly variable. The diagnosis of IBD must be made through medical history, physical, laboratory, radiologic, endoscopic, and histological examinations. However, these diagnostic techniques are not specific and sometimes even equivocal. Therefore, reliable biomarkers are urgently needed in the diagnosis of IBD. Several clinical and preclinical researches have shown that dysregulated microRNAs (miRNAs) play a crucial role in IBD development. miRNAs, as single-stranded noncoding RNAs that contain 22-24 nucleotides, can post-transcriptionally regulate gene expression by blocking mRNA translation or degrading target mRNAs. miRNAs are widely involved in physiological and pathological cellular processes, such as differentiation, proliferation and apoptosis. Besides, they are stable, noninvasive, and resistant to degradation by ribonucleases, making them valuable targets in the diagnosis, monitoring, prognosis, and treatment of diseases. To date, inconsistent results have been found about miRNA expression profiling in the patients with IBD. Moreover, the diagnostic accuracy of miRNAs for IBD has not been reported in any meta-analysis.

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Funkenstein, Bruria, and Cunming Duan. GH-IGF Axis in Sparus aurata: Possible Applications to Genetic Selection. United States Department of Agriculture, November 2000. http://dx.doi.org/10.32747/2000.7580665.bard.

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Many factors affect growth rate in fish: environmental, nutritional, genetics and endogenous (physiological) factors. Endogenous control of growth is very complex and many hormone systems are involved. Nevertheless, it is well accepted that growth hormone (GH) plays a major role in stimulating somatic growth. Although it is now clear that most, if not all, components of the GH-IGF axis exist in fish, we are still far from understanding how fish grow. In our project we used as the experimental system a marine fish, the gilthead sea bream (Sparus aurata), which inhabits lagoons along the Mediterranean and Atlantic coasts of Europe, and represents one of the most important fish species used in the mariculture industry in the Mediterranean region, including Israel. Production of Sparus is rapidly growing, however, in order for this production to stay competitive, the farming of this fish species has to intensify and become more efficient. One drawback, still, in Sparus extensive culture is that it grows relatively slow. In addition, it is now clear that growth and reproduction are physiological interrelated processes that affect each other. In particular sexual maturation (puberty) is known to be closely related to growth rate in fish as it is in mammals, indicating interactions between the somatotropic and gonadotropic axes. The goal of our project was to try to identify the rate-limiting components(s) in Sparus aurata GH-IGF system which might explain its slow growth by studying the ontogeny of growth-related genes: GH, GH receptor, IGF-I, IGF-II, IGF receptor, IGF-binding proteins (IGFBPs) and Pit-1 during early stages of development of Sparus aurata larvae from slow and fast growing lines. Our project was a continuation of a previous BARD project and could be divided into five major parts: i) obtaining additional tools to those obtained in the previous project that are necessary to carry out the developmental study; ii) the developmental expression of growth-related genes and their cellular localization; iii) tissue-specific expression and effect of GH on expression of growth-related genes; iv) possible relationship between GH gene structure, growth rate and genetic selection; v) the possible role of the IGF system in gonadal development. The major findings of our research can be summarized as follows: 1) The cDNAs (complete or partial) coding for Sparus IGFBP-2, GH receptor and Pit-1 were cloned. Sequence comparison reveals that the primary structure of IGFBP-2 protein is 43-49% identical to that of zebrafish and other vertebrates. Intensive efforts resulted in cloning a fragment of 138 nucleotides, coding for 46 amino acids in the proximal end of the intracellular domain of GH receptor. This is the first fish GH receptor cDNA that had been cloned to date. The cloned fragment will enable us to complete the GH - receptor cloning. 2) IGF-I, IGF-II, IGFBP-2, and IGF receptor transcripts were detected by RT-PCR method throughout development in unfertilized eggs, embryos, and larvae suggesting that these mRNAs are products of both the maternal and the embryonic genomes. Preliminary RT-PCR analysis suggest that GH receptor transcript is present in post-hatching larvae already on day 1. 3) IGF-1R transcripts were detected in all tissues tested by RT-PCR with highest levels in gill cartilage, skin, kidney, heart, pyloric caeca, and brain. Northern blot analysis detected IGF receptor only in gonads, brain and gill cartilage but not in muscle; GH increased slightly brain and gill cartilage IGF-1R mRNA levels. 4) IGFBP-2 transcript were detected only in liver and gonads, when analyzed by Northern blots; RT-PCR analysis revealed expression in all tissues studied, with the highest levels found in liver, skin, gonad and pyloric caeca. 5) Expression of IGF-I, IGF-II, IGF-1R and IGFBP-2 was analyzed during gonadal development. High levels of IGF-I and IGFBP-2 expression were found in bisexual young gonads, which decreased during gonadal development. Regardless of maturational stage, IGF-II levels were higher than those of IGF-L 6) The GH gene was cloned and its structure was characterized. It contains minisatellites of tandem repeats in the first and third introns that result in high level of genetic polymorphism. 7) Analysis of the presence of IGF-I and two types of IGF receptor by immunohistochemistry revealed tissue- and stage-specific expression during larval development. Immunohistochemistry also showed that IGF-I and its receptors are present in both testicular and ovarian cells. Although at this stage we are not able to pinpoint which is the rate-limiting step causing the slow growth of Sparus aurata, our project (together with the previous BARD) yielded a great number of experimental tools both DNA probes and antibodies that will enable further studies on the factors regulating growth in Sparus aurata. Our expression studies and cellular localization shed new light on the tissue and developmental expression of growth-related genes in fish.

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