Relevant bibliographies by topics / Eukaryotic cell

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Eukaryotic cell'

Author: Grafiati
Published: 4 June 2021
Last updated: 18 May 2024

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Journal articles on the topic "Eukaryotic cell"

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Martin, William F., Sriram Garg, and Verena Zimorski. "Endosymbiotic theories for eukaryote origin." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1678 (September 26, 2015): 20140330. http://dx.doi.org/10.1098/rstb.2014.0330.

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For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe.
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Martijn, Joran, and Thijs J. G. Ettema. "From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell." Biochemical Society Transactions 41, no. 1 (January 29, 2013): 451–57. http://dx.doi.org/10.1042/bst20120292.

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The evolutionary origin of the eukaryotic cell represents an enigmatic, yet largely incomplete, puzzle. Several mutually incompatible scenarios have been proposed to explain how the eukaryotic domain of life could have emerged. To date, convincing evidence for these scenarios in the form of intermediate stages of the proposed eukaryogenesis trajectories is lacking, presenting the emergence of the complex features of the eukaryotic cell as an evolutionary deus ex machina. However, recent advances in the field of phylogenomics have started to lend support for a model that places a cellular fusion event at the basis of the origin of eukaryotes (symbiogenesis), involving the merger of an as yet unknown archaeal lineage that most probably belongs to the recently proposed ‘TACK superphylum’ (comprising Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) with an alphaproteobacterium (the protomitochondrion). Interestingly, an increasing number of so-called ESPs (eukaryotic signature proteins) is being discovered in recently sequenced archaeal genomes, indicating that the archaeal ancestor of the eukaryotic cell might have been more eukaryotic in nature than presumed previously, and might, for example, have comprised primitive phagocytotic capabilities. In the present paper, we review the evolutionary transition from archaeon to eukaryote, and propose a new model for the emergence of the eukaryotic cell, the ‘PhAT (phagocytosing archaeon theory)’, which explains the emergence of the cellular and genomic features of eukaryotes in the light of a transiently complex phagocytosing archaeon.
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Ku, Chuan, and Arnau Sebé-Pedrós. "Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1786 (October 7, 2019): 20190098. http://dx.doi.org/10.1098/rstb.2019.0098.

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Understanding the diversity and evolution of eukaryotic microorganisms remains one of the major challenges of modern biology. In recent years, we have advanced in the discovery and phylogenetic placement of new eukaryotic species and lineages, which in turn completely transformed our view on the eukaryotic tree of life. But we remain ignorant of the life cycles, physiology and cellular states of most of these microbial eukaryotes, as well as of their interactions with other organisms. Here, we discuss how high-throughput genome-wide gene expression analysis of eukaryotic single cells can shed light on protist biology. First, we review different single-cell transcriptomics methodologies with particular focus on microbial eukaryote applications. Then, we discuss single-cell gene expression analysis of protists in culture and what can be learnt from these approaches. Finally, we envision the application of single-cell transcriptomics to protist communities to interrogate not only community components, but also the gene expression signatures of distinct cellular and physiological states, as well as the transcriptional dynamics of interspecific interactions. Overall, we argue that single-cell transcriptomics can significantly contribute to our understanding of the biology of microbial eukaryotes. This article is part of a discussion meeting issue ‘Single cell ecology’.
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Lane, Nick. "Origin of the Eukaryotic Cell." Molecular Frontiers Journal 01, no. 02 (December 2017): 108–20. http://dx.doi.org/10.1142/s2529732517400120.

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All complex life on Earth is composed of ‘eukaryotic’ cells. Eukaryotes arose just once in 4 billion years, via an endosymbiosis — bacteria entered a simple host cell, evolving into mitochondria, the ‘powerhouses’ of complex cells. Mitochondria lost most of their genes, retaining only those needed for respiration, giving eukaryotes ‘multi-bacterial’ power without the costs of maintaining thousands of complete bacterial genomes. These energy savings supported a substantial expansion in nuclear genome size, and far more protein synthesis from each gene.
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Chiyomaru, Katsumi, and Kazuhiro Takemoto. "Revisiting the hypothesis of an energetic barrier to genome complexity between eukaryotes and prokaryotes." Royal Society Open Science 7, no. 2 (February 2020): 191859. http://dx.doi.org/10.1098/rsos.191859.

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The absence of genome complexity in prokaryotes, being the evolutionary precursors to eukaryotic cells comprising all complex life (the prokaryote–eukaryote divide), is a long-standing question in evolutionary biology. A previous study hypothesized that the divide exists because prokaryotic genome size is constrained by bioenergetics (prokaryotic power per gene or genome being significantly lower than eukaryotic ones). However, this hypothesis was evaluated using a relatively small dataset due to lack of data availability at the time, and is therefore controversial. Accordingly, we constructed a larger dataset of genomes, metabolic rates, cell sizes and ploidy levels to investigate whether an energetic barrier to genome complexity exists between eukaryotes and prokaryotes while statistically controlling for the confounding effects of cell size and phylogenetic signals. Notably, we showed that the differences in bioenergetics between prokaryotes and eukaryotes were less significant than those previously reported. More importantly, we found a limited contribution of power per genome and power per gene to the prokaryote–eukaryote dichotomy. Our findings indicate that the prokaryote–eukaryote divide is hard to explain from the energetic perspective. However, our findings may not entirely discount the traditional hypothesis; in contrast, they indicate the need for more careful examination.
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Goodsell, David S. "Eukaryotic cell panorama." Biochemistry and Molecular Biology Education 39, no. 2 (March 2011): 91–101. http://dx.doi.org/10.1002/bmb.20494.

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Akiyoshi, Bungo, and Keith Gull. "Evolutionary cell biology of chromosome segregation: insights from trypanosomes." Open Biology 3, no. 5 (May 2013): 130023. http://dx.doi.org/10.1098/rsob.130023.

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Faithful transmission of genetic material is essential for the survival of all organisms. Eukaryotic chromosome segregation is driven by the kinetochore that assembles onto centromeric DNA to capture spindle microtubules and govern the movement of chromosomes. Its molecular mechanism has been actively studied in conventional model eukaryotes, such as yeasts, worms, flies and human. However, these organisms are closely related in the evolutionary time scale and it therefore remains unclear whether all eukaryotes use a similar mechanism. The evolutionary origins of the segregation apparatus also remain enigmatic. To gain insights into these questions, it is critical to perform comparative studies. Here, we review our current understanding of the mitotic mechanism in Trypanosoma brucei , an experimentally tractable kinetoplastid parasite that branched early in eukaryotic history. No canonical kinetochore component has been identified, and the design principle of kinetochores might be fundamentally different in kinetoplastids. Furthermore, these organisms do not appear to possess a functional spindle checkpoint that monitors kinetochore–microtubule attachments. With these unique features and the long evolutionary distance from other eukaryotes, understanding the mechanism of chromosome segregation in T. brucei should reveal fundamental requirements for the eukaryotic segregation machinery, and may also provide hints about the origin and evolution of the segregation apparatus.
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Cavalier-Smith, Thomas. "Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree." Biology Letters 6, no. 3 (December 23, 2009): 342–45. http://dx.doi.org/10.1098/rsbl.2009.0948.

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I discuss eukaryotic deep phylogeny and reclassify the basal eukaryotic kingdom Protozoa and derived kingdom Chromista in the light of multigene trees. I transfer the formerly protozoan Heliozoa and infrakingdoms Alveolata and Rhizaria into Chromista, which is sister to kingdom Plantae and arguably originated by synergistic double internal enslavement of green algal and red algal cells. I establish new subkingdoms (Harosa; Hacrobia) for the expanded Chromista. The protozoan phylum Euglenozoa differs immensely from other eukaryotes in its nuclear genome organization (trans-spliced multicistronic transcripts), mitochondrial DNA organization, cytochrome c -type biogenesis, cell structure and arguably primitive mitochondrial protein-import and nuclear DNA prereplication machineries. The bacteria-like absence of mitochondrial outer-membrane channel Tom40 and DNA replication origin-recognition complexes from trypanosomatid Euglenozoa roots the eukaryotic tree between Euglenozoa and all other eukaryotes (neokaryotes), or within Euglenozoa. Given their unique properties, I segregate Euglenozoa from infrakingdom Excavata (now comprising only phyla Percolozoa, Loukozoa, Metamonada), grouping infrakingdoms Euglenozoa and Excavata as the ancestral protozoan subkingdom Eozoa. I place phylum Apusozoa within the derived protozoan subkingdom Sarcomastigota. Clarifying early eukaryote evolution requires intensive study of properties distinguishing Euglenozoa from neokaryotes and Eozoa from neozoa (eukaryotes except Eozoa; ancestrally defined by haem lyase).
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Goley, Erin D. "Tiny cells meet big questions: a closer look at bacterial cell biology." Molecular Biology of the Cell 24, no. 8 (April 15, 2013): 1099–102. http://dx.doi.org/10.1091/mbc.e12-11-0788.

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While studying actin assembly as a graduate student with Matt Welch at the University of California at Berkeley, my interest was piqued by reports of surprising observations in bacteria: the identification of numerous cytoskeletal proteins, actin homologues fulfilling spindle-like functions, and even the presence of membrane-bound organelles. Curiosity about these phenomena drew me to Lucy Shapiro's lab at Stanford University for my postdoctoral research. In the Shapiro lab, and now in my lab at Johns Hopkins, I have focused on investigating the mechanisms of bacterial cytokinesis. Spending time as both a eukaryotic cell biologist and a bacterial cell biologist has convinced me that bacterial cells present the same questions as eukaryotic cells: How are chromosomes organized and accurately segregated? How is force generated for cytokinesis? How is polarity established? How are signals transduced within and between cells? These problems are conceptually similar between eukaryotes and bacteria, although their solutions can differ significantly in specifics. In this Perspective, I provide a broad view of cell biological phenomena in bacteria, the technical challenges facing those of us who peer into bacterial cells, and areas of common ground as research in eukaryotic and bacterial cell biology moves forward.
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Mills, Daniel B. "The origin of phagocytosis in Earth history." Interface Focus 10, no. 4 (June 12, 2020): 20200019. http://dx.doi.org/10.1098/rsfs.2020.0019.

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Phagocytosis, or ‘cell eating’, is a eukaryote-specific process where particulate matter is engulfed via invaginations of the plasma membrane. The origin of phagocytosis has been central to discussions on eukaryogenesis for decades­, where it is argued as being either a prerequisite for, or consequence of, the acquisition of the ancestral mitochondrion. Recently, genomic and cytological evidence has increasingly supported the view that the pre-mitochondrial host cell—a bona fide archaeon branching within the ‘Asgard’ archaea—was incapable of phagocytosis and used alternative mechanisms to incorporate the alphaproteobacterial ancestor of mitochondria. Indeed, the diversity and variability of proteins associated with phagosomes across the eukaryotic tree suggest that phagocytosis, as seen in a variety of extant eukaryotes, may have evolved independently several times within the eukaryotic crown-group. Since phagocytosis is critical to the functioning of modern marine food webs (without it, there would be no microbial loop or animal life), multiple late origins of phagocytosis could help explain why many of the ecological and evolutionary innovations of the Neoproterozoic Era (e.g. the advent of eukaryotic biomineralization, the ‘Rise of Algae’ and the origin of animals) happened when they did.
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Dissertations / Theses on the topic "Eukaryotic cell"

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Batenchuk, Cory. "Transcriptional Dynamics of the Eukaryotic Cell." Thesis, Université d'Ottawa / University of Ottawa, 2011. http://hdl.handle.net/10393/19722.

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Gene regulatory networks are dynamic and continuously remodelled in response to internal and external stimuli. To understand how these networks alter cellular phenotype in response towards specific challenges, my first project sought to develop a methodology to explore how the strength of genetic interactions changes according to environmental context. Defined as sensitivity-based epistasis, the results obtained using this methodology were compared to those generated under the conventional fitness-based approach. By integrating this information with gene expression profiles and physical interaction datasets, we demonstrate that sensitivity-based epistasis specifically highlights genetic interactions with a dynamic component. Having investigated how an external stimulus regulates network dynamics, we next sought to understand of how genome positioning impacts transcription kinetics. This feat was accomplished by cloning two gene-reporter constructs, representing contrasting promoter architectures, across 128 loci along chromosome III in S.Cerevisiae. By comparing expression and noise measurements for promoters with “covered” and “open” chromatin structures against a stochastic model for eukaryotic gene expression, we demonstrate that while promoter structure regulates burst frequency (the rate of promoter activation), positional effects in turn appear to primarily modulate burst size (the number of mRNA produced per gene activation event). By integrating these datasets with information describing global chromatin structure, we suggest that the acetylation state of chromatin regulates burst size across the genome. Interestingly, this hypothesis is further supported by nicotinamide-mediated inhibition of Sir2 which would appear to modulate burst size globally across the genome.
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Li, Zhaoqi Ph D. Massachusetts Institute of Technology. "Bioenergetics and metabolism of eukaryotic cell proliferation." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/130658.

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Thesis: Ph. D. in Biochemistry, Massachusetts Institute of Technology, Department of Biology, February, 2021
Cataloged from the official PDF of thesis. "February 2021." Vita. Page 179 blank.
Includes bibliographical references.
Cellular growth and proliferation necessitates the transformation of cell-external nutrients into biomass. Strategies of biomass accumulation across the kingdoms of life are diverse and range from carbon fixation by autotrophic organisms to direct biomass incorporation of consumed nutrients by heterotrophic organisms. The goal of this dissertation is to better understand the divergent and convergent modes of metabolism that support biomass accumulation and proliferation in eukaryotic cells. We first determined that the underlying mechanism behind why rapidly proliferating cells preferentially ferment the terminal glycolytic product pyruvate is due to an intrinsic deficiency of respiration to regenerate electron acceptors. We tested this model across an assorted array of proliferating cells and organisms ranging from human cancer cells to the baker's yeast Saccharomyces cerevesiae. We next determined that a major metabolic pathway of avid electron acceptor consumption in the context of biomass accumulation is the synthesis of lipids. Insights from this work has led to the realization that net-reductive pathways such as lipid synthesis may be rate-limited by oxidative reactions. Lastly, we established the green algae Chlorella vulgaris as a model system to study the comparative metabolism of photoautotrophic and heterotrophic growth. We determined that heterotrophic growth of plant cells is associated with aerobic glycolysis in a mechanism that may be suppressed by light. Collectively, these studies contribute to a more holistic understanding of the bioenergetics and metabolic pathways employed by eukaryotic cells to accumulate biomass and lay the foundation for future studies to understand proliferative metabolism.
by Zhaoqi Li.
Ph. D. in Biochemistry
Ph.D.inBiochemistry Massachusetts Institute of Technology, Department of Biology
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Vezzoli, A. "Analysis of bacterial proteins interfering with eukaryotic cell proliferation." Doctoral thesis, Università degli Studi di Milano, 2006. http://hdl.handle.net/2434/56617.

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Descriptions of a role of some bacterial pathogens in counteracting tumour progression in humans date back to the end of XIX century. Recently, it was reported that two members of the family of cupredoxins, azurin from P. aeruginosa and rusticyanin from A. ferrooxidans, are able to enter in and to induce apoptosis and/or cell cycle arrest in a number of different cancer cell-lines. The apoptotic effect mediated by azurin was confirmed also in vivo. One of the specific aims of this thesis was to assess whether the expression of cupredoxins in S. cerevisiae could recapitulate the effects observed in mammalian cancer cell-lines. The induction of cupredoxins expression in yeast caused a strong growth delay accompanied by high cytotoxicity and alterations in cellular morphologies and bud emergence. These findings validated S. cerevisiae as a system to screen the plethora of bacterial proteins with potential anti-tumoral activity. Since, at least in the case of azurin, the pro-apoptotic effects on cancer cells was traced to direct interaction with the tumor suppressor protein p53, we also investigated the possibility to find new bacterial-derived interactors of p53 through Yeast Two Hybrid System. During this screening we observed the strong interaction of a bacterial protein with murine and human p53. This interaction was extremely specific as P. aeruginosa and E. coli homologs did not exhibit a similar behaviour.
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Cosulich, Sabina Chiara. "Modulators of the cell cycle in fibroblasts." Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259439.

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Rindler, Paul Michael. "Eukaryotic replication, cis-acting elements, and instability of trinucleotide repeats." Oklahoma City : [s.n.], 2009.

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Beltramini, Amanda Michelle. "Eukaryotic-like serine/threonine kinase signaling in Staphylococcus aureus." Columbus, Ohio : Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1243368504.

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Schreiner, Patrick. "Structural investigation of two supramolecular complexes of the eukaryotic cell." Diss., lmu, 2008. http://nbn-resolving.de/urn:nbn:de:bvb:19-92522.

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Doostdar, Hamed. "Stable expression of eukaryotic p450 cDNA in mammalian cell lines." Thesis, University of Aberdeen, 1992. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602073.

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The P450 profile of HepG2 cells was studied using specific enzyme assays and well characterised monoclonal and polyclonal antibodies. These cells were shown to endogenously express cytochrome P450 1A1, P450 1A2 and P450 3A5 when the cells were treated with benz(a)anthracene or rifampicin respectively. HepG2 cells were adapted to grow in Williams' E medium supplemented with only 5% (v/v) fetal calf serum. These cells showed a significantly higher concentration of P450 1A2 protein when treated with benz(a)anthracene and could be detected by P450 1A2 specific antibodies on Western blots. Stable cell lines of HepG2 and Cos-7 cells capable of continuous expression of the Epstein-Barr virus nuclear antigen-1 (EBNA-1) were constructed. P450 2A6 cDNA was successfully expressed in the EBNA-1 transformed Cos-7 cell line for over 6 weeks. The rate of expression of this cDNA and the enzyme activity of the resulting protein was very low. No stable HepG2 EBNA-1 transformed cells capable of P450 2A6 expression was obtained.
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Wilson, Timothy Craig. "The role of mRNA stability and Fos protein in transient c-fos mRNA accumulation." Thesis, University of Cambridge, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.304567.

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Kipling, D. G. "Studies on replication origins in Saccharomyces cerevisiae." Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.253151.

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Books on the topic "Eukaryotic cell"

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A, Bryant J., and Francis D, eds. The eukaryotic cell cycle. New York: Taylor & Francis, 2008.

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Sadava, David. Cell biology: Organelle structure and function. Boston, Mass: Jones and Bartlett, 1993.

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Je kely, Ga spa r., ed. Eukaryotic membranes and cytoskeleton: Origins and evolution. New York, N.Y: Springer Science+Business Media, 2007.

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Sidney, Fleischer, and Fleischer Becca, eds. Biomembranes.: Eukaryotic (nonepithelial) cells. San Diego: Academic Press, 1989.

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The eukaryotic cell: Structure and function. Oxford: Blackwell, 1985.

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The eukaryotic cell: Structure and function. Oxford: Blackwell, 1985.

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P, Chapman G., Ainsworth C. C. 1954-, and Chatham C. J, eds. Eukaryote cell recognition: Concepts and model systems. Cambridge: Cambridge University Press, 1988.

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Sudhakaran, Perumana R., and Avadhesha Surolia, eds. Biochemical Roles of Eukaryotic Cell Surface Macromolecules. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-3381-1.

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Chakrabarti, Abhijit, and Avadhesha Surolia, eds. Biochemical Roles of Eukaryotic Cell Surface Macromolecules. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-11280-0.

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Caldecott, Keith W. Eukaryotic DNA damage surveillance and repair. Georgetown, Tex: Landes Bioscience/Eurekah.com, 2004.

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Book chapters on the topic "Eukaryotic cell"

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Gooch, Jan W. "Eukaryotic Cell." In Encyclopedic Dictionary of Polymers, 891. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6247-8_13707.

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Smith, C. A., and E. J. Wood. "Eukaryotic cell walls." In Cell Biology, 287–307. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4613-0441-8_9.

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Nasmyth, Kim. "A Eukaryotic Cell Cycle." In Genomic Instability and Immortality in Cancer, 159–69. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4615-5365-6_11.

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Igarashi, Kazuei, and Keiko Kashiwagi. "Bacterial and Eukaryotic Transport Systems." In Polyamine Cell Signaling, 433–48. Totowa, NJ: Humana Press, 2006. http://dx.doi.org/10.1007/978-1-59745-145-1_25.

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Janetopoulos, Chris, Yu Long, and Peter N. Devreotes. "Mechanisms of Eukaryotic Chemotaxis." In Cell Migration in Development and Disease, 33–45. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527604669.ch3.

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Livak, Kenneth J. "Eukaryotic Single-Cell mRNA Sequencing." In Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing, 343–65. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31350-4_14.

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Szulwach, Keith E., and Kenneth J. Livak. "Eukaryotic Single-Cell DNA Sequencing." In Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing, 367–84. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31350-4_15.

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Arrecubieta, Carlos, and Franklin D. Lowy. "Staphylococcus aureus-Eukaryotic Cell Interactions." In Gram-Positive Pathogens, 517–25. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555816513.ch42.

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DePamphilis, M. L., W. C. Burhans, L. T. Vassilev, and Z. S. Guo. "Eukaryotic Origins of DNA Replication." In DNA Replication and the Cell Cycle, 93–112. Berlin, Heidelberg: Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-642-77040-1_8.

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Cvrčková, Fatima. "A Brief History of Eukaryotic Cell Cycle Research." In Plant Cell Monographs, 67–93. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-69944-8_4.

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Conference papers on the topic "Eukaryotic cell"

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Wang, Jianye, Kaixuan Zhu, Gang Zhao, and Dayong Gao. "Effect of Temperature and Cryoprotectant Solutes on Water Permeability of SF21 Cell Membrane." In ASME 2013 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/sbc2013-14056.

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Insect cell as a host of viruses is extensively used for producing heterologous recombinant proteins. The eukaryotic proteins expressed by the insect cell is posttranslationally modified and harvested in a short period of time. The insect cell expression has been applied to both basic research and commercial applications. A large scale of proteins produced by the insect cell expression system are settled for researching the structure and function of the eukaryotic proteins, and the expression system integrated with routine biochemical techniques plays a significant role in diagnostic procedure and therapeutic approaches for the disease.
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Wu, Shinq-Jen, Cheng-Tao Wu, and Tsu-Tian Lee. "Computation Intelligent for Eukaryotic Cell-Cycle Gene Network." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.260339.

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Wu, Shinq-Jen, Cheng-Tao Wu, and Tsu-Tian Lee. "Computation Intelligent for Eukaryotic Cell-Cycle Gene Network." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.4397830.

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Hartman, H., and K. Matsuno. "The Origin and Evolution of the Cell." In Conference on the Origin and Evolution of Prokaryotic and Eukaryotic Cells. WORLD SCIENTIFIC, 1993. http://dx.doi.org/10.1142/9789814536219.

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Farahat, Waleed A., and H. Harry Asada. "Control of Eukaryotic Cell Migration Through Modulation of Extracellular Chemoattractant Gradients." In ASME 2010 Dynamic Systems and Control Conference. ASMEDC, 2010. http://dx.doi.org/10.1115/dscc2010-4190.

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Cell migration is fundamental to a wide range of biological and physiological functions including: wound healing, immune defense, cancer metastasis, as well as the formation and development of biological structures such as vascular and neural networks. In these diverse processes, cell migration is influenced by a broad set of external mechanical and biochemical cues, particularly the presence of (time dependent) spatial gradients of soluble chemoattractants in the extracellular domain. Many biological models have been proposed to explain the mechanisms leading to the migratory response of cells as a function of these external cues. Based on such models, here we propose approaches to controlling the chemotactic response of eukaryotic cells by modulating their micro-environments in vitro (for example, using a microfluidic chemotaxis chamber). By explicitly modeling i) chemoattractant-receptor binding kinetics, ii) diffusion dynamics in the extracellular domain, and iii) the chemotactic response of cells, models for the migration processes arise. Based on those models, optimal control formulations are derived. We present simulation results, and suggest experimental approaches to controlling cellular motility in vitro, which can be used as a basis for cellular manipulation and control.
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Pathak, Amit, and Sanjay Kumar. "A Multiscale Model of Cell Adhesion and Migration on Extracellular Matrices of Defined Stiffness and Adhesivity." In ASME 2011 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2011. http://dx.doi.org/10.1115/sbc2011-53757.

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Eukaryotic cells actively respond to variations in ligand density and stiffness of their extracellular matrix (ECM). This cell-ECM relationship plays an important role in regulating cell migration, wound healing, tumor invasion and metastasis. A better understanding of these mechanosenstive responses requires more rigorous models of the relationships between ECM biophysical properties, mechanotransductive signals, assembly of contractile and adhesive structures, and cell migration.
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Mollaeian, Keyvan, Yi Liu, and Juan Ren. "Investigation of Nanoscale Poroelasticity of Eukaryotic Cells Using Atomic Force Microscopy." In ASME 2017 Dynamic Systems and Control Conference. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/dscc2017-5254.

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Intracellular network deformation of the cell plays an important role in cellular shape formation. Recent studies suggest that cell reshaping and deformation due to external forces involves cellular volume, pore size, elasticity, and intracellular filaments polymerization rate changes. This behavior of live cells can be described by poroelastic models because of the porous structure of the cytoplasm. In this study, the poroelasticity of human mammary basel/claudin low carcinoma cell (MDA-MB-231) was investigated using indentation-based atomic force microscopy. The effects of cell deformation (i.e., indentation) rate on the poroelasticity of MDA-MB-231 cells were studied. Specifically, the cell poroelastic behavior (i.e., the diffusion coefficient) was quantified at different indenting velocities (0.2, 2, 10, 20, 100, 200 μm/s) by fitting the force-relaxation curves using a poroelastic model. It was found that the in general the MDA-MB-231 cells behaved poroelastic, and they were less poroelastic (i.e., with lower diffusion coefficient) at higher indenting velocities due to the local stiffening up caused by faster force loads. Poor poroelastic relaxation was observed when the indenting velocity was lower than 10 μm/s due to the intracelluar fluid redistribution during the slow indenting process to equilibrate the intracellular pressure. Moreover, the measurement results showed that the pore size reduction caused by local stiffening at faster indenting velocities is more dominant than the Young’s modulus in affecting the cell poroelasticity.
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Yuen, Douglas, and Christian Jacob. "Eukaryo: An Agent-based, Interactive Simulation of a Eukaryotic Cell." In Proceedings of the Artificial Life Conference 2016. Cambridge, MA: MIT Press, 2016. http://dx.doi.org/10.1162/978-0-262-33936-0-ch090.

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Yuen, Douglas, and Christian Jacob. "Eukaryo: An Agent-based, Interactive Simulation of a Eukaryotic Cell." In Proceedings of the Artificial Life Conference 2016. Cambridge, MA: MIT Press, 2016. http://dx.doi.org/10.7551/978-0-262-33936-0-ch090.

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Ranade, Esha, Fabio Fruggiero, and Carmen Del Vecchio. "Model of Eukaryotic Cell Protein Control Schemes via Manufacturing System Simulator." In 2023 9th International Conference on Control, Decision and Information Technologies (CoDIT). IEEE, 2023. http://dx.doi.org/10.1109/codit58514.2023.10284208.

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Reports on the topic "Eukaryotic cell"

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Cooper, Priscilla. Prokaryotic and eukaryotic cell-free systems for prototyping: CRADA Final Report. Office of Scientific and Technical Information (OSTI), October 2022. http://dx.doi.org/10.2172/1890450.

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Coplin, David, Isaac Barash, and Shulamit Manulis. Role of Proteins Secreted by the Hrp-Pathways of Erwinia stewartii and E. herbicola pv. gypsophilae in Eliciting Water-Soaking Symptoms and Initiating Galls. United States Department of Agriculture, June 2001. http://dx.doi.org/10.32747/2001.7580675.bard.

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Many bacterial pathogens of plants can inject pathogenicity proteins into host cells using a specialized type III secretion system encoded by hrpgenes. This system deliver effector proteins, into plant cells that function in both susceptible and resistant interactions. We have found that the virulence of Erwinia stewartii(Es; syn. Pantoea stewartii) and Erwinia herbicola pv. gypsophilae (Ehg, syn. Pantoea agglomerans), which cause Stewart's wilt of corn and galls on Gypsophila, respectively, depends on hrpgenes. The major objectives of this project were: To increase expression of hrpgenes in order to identify secreted proteins; to identify genes for proteins secreted by the type-III systems and determine if they are required for pathogenicity; and to determine if the secreted proteins can function within eukaryotic cells. We found that transcription of the hrp and effector genes in Es and Ehg is controlled by at least four genes that constitute a regulatory cascade. Environmental and/or physiological signaling appears to be mediated by the HrpX/HrpY two component system, with HrpX functioning as a sensor-kinase and HrpY as a response regulator. HrpYupregulateshrpS, which encodes a transcriptional enhancer. HrpS then activates hrpL, which encodes an alternate sigma factor that recognizes "hrp boxes". All of the regulatory genes are essential for pathogenicity, except HrpX, which appears only to be required for induction of the HR in tobacco by Es. In elucidating this regulatory pathway in both species, we made a number of significant new discoveries. HrpX is unusual for a sensor-kinase because it is cytoplasmic and contains PAS domains, which may sense the redox state of the bacterium. In Es, a novel methyl-accepting protein may function upstream of hrpY and repress hrp gene expression in planta. The esaIR quorum sensing system in Es represses hrp gene expression in Es in response to cell-density. We have discovered six new type III effector proteins in these species, one of which (DspE in Ehg and WtsE in Es) is common to both pathogens. In addition, Es wtsG, which is a homolog of an avrPpiB from P. syringae pv. pisi, and an Ehg ORF, which is a homolog of P. syringae pv. phaseolicola AvrPphD, were both demonstrated to encode virulence proteins. Two plasmidborne, Ehg Hop proteins, HsvG and PthG, are required for infection of gypsophilia, but interestingly, PthG also acts as an Avr elicitor in beets. Using a calmodulin-dependent adenylate cyclase (cyaA) reporter gene, we were successful in demonstrating that an HsvG-CyaA fusion protein can be transferred into human HeLa cells by the type-III system of enteropathogenic E. coli. This is a highly significant accomplishment because it is the first direct demonstration that an effector protein from a plant pathogenic bacterium is capable of being translocated into a eukaryotic cell by a type-III secretion system. Ehg is considered a limiting factor in Gypsophila production in Israel and Stewart’s Wilt is a serious disease in the Eastern and North Central USA, especially on sweet corn in epidemic years. We believe that our basic research on the characterization of type III virulence effectors should enable future identification of their receptors in plant cells. This may lead to novel approaches for genetically engineering resistant plants by modifying their receptors or inactivating effectors and thus blocking the induction of the susceptible response. Alternatively, hrp gene regulation might also provide a target for plant produced compounds that interfere with recognition of the host by the pathogen. Such strategies would be broadly applicable to a wide range of serious bacterial diseases on many crops throughout the USA and Israel.
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Chamovitz, Daniel, and Albrecht Von Arnim. Translational regulation and light signal transduction in plants: the link between eIF3 and the COP9 signalosome. United States Department of Agriculture, November 2006. http://dx.doi.org/10.32747/2006.7696515.bard.

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The COP9 signalosome (CSN) is an eight-subunit protein complex that is highly conserved among eukaryotes. Genetic analysis of the signalosome in the plant model species Arabidopsis thaliana has shown that the signalosome is a repressor of light dependent seedling development as mutant Arabidopsis seedlings that lack this complex develop in complete darkness as if exposed to light. These mutant plants die following the seedling stage, even when exposed to light, indicating that the COP9 signalosome also has a central role in the regulation of normal photomorphogenic development. The biochemical mode of action of the signalosome and its position in eukaryotic cell signaling pathways is a matter of controversy and ongoing investigation, and recent results place the CSN at the juncture of kinase signaling pathways and ubiquitin-mediated protein degradation. We have shown that one of the many CSN functions may relate to the regulation of translation through the interaction of the CSN with its related complex, eukaryotic initiation factor (eIF3). While we have established a physical connection between eIF3 subunits and CSN subunits, the physiological and developmental significance of this interaction is still unknown. In an effort to understand the biochemical activity of the signalosome, and its role in regulating translation, we originally proposed to dissect the contribution of "h" subunit of eIF3 (eIF3h) along the following specific aims: (i) Isolation and phenotypic characterization of an Arabidopsis loss-of-function allele for eIF3h from insertional mutagenesis libraries; (ii) Creation of designed gain and loss of function alleles for eIF3h on the basis of its nucleocytoplasmic distribution and its yeast-two-hybrid interactions with other eIF3 and signalosome partner proteins; (iii) Determining the contribution of eIF3h and its interaction with the signalosome by expressing specific mutants of eIF3h in the eIF3h- loss-of function background. During the course of the research, these goals were modified to include examining the genetic interaction between csn and eif3h mutations. More importantly, we extended our effort toward the genetic analysis of mutations in the eIF3e subunit, which also interacts with the CSN. Through the course of this research program we have made several critical scientific discoveries, all concerned with the apparent diametrically opposed roles of eIF3h and eIF3e. We showed that: 1) While eIF3e is essential for growth and development, eIF3h is not essential for growth or basal translation; 2) While eIF3e has a negative role in translational regulation, eIF3h is positively required for efficient translation of transcripts with complex 5' UTR sequences; 3) Over-accumulation of eIF3e and loss-of-function of eIF3h both lead to cop phenotypes in dark-grown seedlings. These results were published in one publication (Kim et al., Plant Cell 2004) and in a second manuscript currently in revision for Embo J. Are results have led to a paradigm shift in translation research – eIF3 is now viewed in all systems as a dynamic entity that contains regulatory subuits that affect translational efficiency. In the long-term agronomic outlook, the proposed research has implications that may be far reaching. Many important plant processes, including developmental and physiological responses to light, abiotic stress, photosynthate, and hormones operate in part by modulating protein translation [23, 24, 40, 75]. Translational regulation is slowly coming of age as a mechanism for regulating foreign gene expression in plants, beginning with translational enhancers [84, 85] and more recently, coordinating the expression of multiple transgenes using internal ribosome entry sites. Our contribution to understanding the molecular mode of action of a protein complex as fundamental as eIF3 is likely to lead to advances that will be applicable in the foreseeable future.
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Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7695881.bard.

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Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.
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Elbaum, Michael, and Peter J. Christie. Type IV Secretion System of Agrobacterium tumefaciens: Components and Structures. United States Department of Agriculture, March 2013. http://dx.doi.org/10.32747/2013.7699848.bard.

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Objectives: The overall goal of the project was to build an ultrastructural model of the Agrobacterium tumefaciens type IV secretion system (T4SS) based on electron microscopy, genetics, and immunolocalization of its components. There were four original aims: Aim 1: Define the contributions of contact-dependent and -independent plant signals to formation of novel morphological changes at the A. tumefaciens polar membrane. Aim 2: Genetic basis for morphological changes at the A. tumefaciens polar membrane. Aim 3: Immuno-localization of VirB proteins Aim 4: Structural definition of the substrate translocation route. There were no major revisions to the aims, and the work focused on the above questions. Background: Agrobacterium presents a unique example of inter-kingdom gene transfer. The process involves cell to cell transfer of both protein and DNA substrates via a contact-dependent mechanism akin to bacterial conjugation. Transfer is mediated by a T4SS. Intensive study of the Agrobacterium T4SS has made it an archetypal model for the genetics and biochemistry. The channel is assembled from eleven protein components encoded on the B operon in the virulence region of the tumor-inducing plasmid, plus an additional coupling protein, VirD4. During the course of our project two structural studies were published presenting X-ray crystallography and three-dimensional reconstruction from electron microscopy of a core complex of the channel assembled in vitro from homologous proteins of E. coli, representing VirB7, VirB9, and VirB10. Another study was published claiming that the secretion channels in Agrobacterium appear on helical arrays around the membrane perimeter and along the entire length of the bacterium. Helical arrangements in bacterial membranes have since fallen from favor however, and that finding was partially retracted in a second publication. Overall, the localization of the T4SS within the bacterial membranes remains enigmatic in the literature, and we believe that our results from this project make a significant advance. Summary of achievements : We found that polar inflations and other membrane disturbances relate to the activation conditions rather than to virulence protein expression. Activation requires low pH and nutrient-poor medium. These stress conditions are also reflected in DNA condensation to varying degrees. Nonetheless, they must be considered in modeling the T4SS as they represent the relevant conditions for its expression and activity. We identified the T4SS core component VirB7 at native expression levels using state of the art super-resolution light microscopy. This marker of the secretion system was found almost exclusively at the cell poles, and typically one pole. Immuno-electron microscopy identified the protein at the inner membrane, rather than at bridges across the inner and outer membranes. This suggests a rare or transient assembly of the secretion-competent channel, or alternatively a two-step secretion involving an intermediate step in the periplasmic space. We followed the expression of the major secreted effector, VirE2. This is a single-stranded DNA binding protein that forms a capsid around the transferred oligonucleotide, adapting the bacterial conjugation to the eukaryotic host. We found that over-expressed VirE2 forms filamentous complexes in the bacterial cytoplasm that could be observed both by conventional fluorescence microscopy and by correlative electron cryo-tomography. Using a non-retentive mutant we observed secretion of VirE2 from bacterial poles. We labeled the secreted substrates in vivo in order detect their secretion and appearance in the plant cells. However the low transfer efficiency and significant background signal have so far hampered this approach.
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Schuster, Gadi, and David Stern. Integration of phosphorus and chloroplast mRNA metabolism through regulated ribonucleases. United States Department of Agriculture, August 2008. http://dx.doi.org/10.32747/2008.7695859.bard.

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New potential for engineering chloroplasts to express novel traits has stimulated research into relevant techniques and genetic processes, including plastid transformation and gene regulation. This proposal continued our long time BARD-funded collaboration research into mechanisms that influence chloroplast RNA accumulation, and thus gene expression. Previous work on cpRNA catabolism has elucidated a pathway initiated by endonucleolytic cleavage, followed by polyadenylation and exonucleolytic degradation. A major player in this process is the nucleus-encoded exoribonuclease/polymerasepolynucleotidephoshorylase (PNPase). Biochemical characterization of PNPase has revealed a modular structure that controls its RNA synthesis and degradation activities, which in turn are responsive to the phosphate (P) concentration. However, the in vivo roles and regulation of these opposing activities are poorly understood. The objectives of this project were to define how PNPase is controlled by P and nucleotides, using in vitro assays; To make use of both null and site-directed mutations in the PNPgene to study why PNPase appears to be required for photosynthesis; and to analyze plants defective in P sensing for effects on chloroplast gene expression, to address one aspect of how adaptation is integrated throughout the organism. Our new data show that P deprivation reduces cpRNA decay rates in vivo in a PNPasedependent manner, suggesting that PNPase is part of an organismal P limitation response chain that includes the chloroplast. As an essential component of macromolecules, P availability often limits plant growth, and particularly impacts photosynthesis. Although plants have evolved sophisticated scavenging mechanisms these have yet to be exploited, hence P is the most important fertilizer input for crop plants. cpRNA metabolism was found to be regulated by P concentrations through a global sensing pathway in which PNPase is a central player. In addition several additional discoveries were revealed during the course of this research program. The human mitochondria PNPase was explored and a possible role in maintaining mitochondria homeostasis was outlined. As polyadenylation was found to be a common mechanism that is present in almost all organisms, the few examples of organisms that metabolize RNA with no polyadenylation were analyzed and described. Our experiment shaded new insights into how nutrient stress signals affect yield by influencing photosynthesis and other chloroplast processes, suggesting strategies for improving agriculturally-important plants or plants with novel introduced traits. Our studies illuminated the poorly understood linkage of chloroplast gene expression to environmental influences other than light quality and quantity. Finely, our finding significantly advanced the knowledge about polyadenylation of RNA, the evolution of this process and its function in different organisms including bacteria, archaea, chloroplasts, mitochondria and the eukaryotic cell. These new insights into chloroplast gene regulation will ultimately support plant improvement for agriculture
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Nelson, Nathan, and Randy Schekman. Functional Biogenesis of V-ATPase in the Vacuolar System of Plants and Fungi. United States Department of Agriculture, September 1996. http://dx.doi.org/10.32747/1996.7574342.bard.

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The vacuolar H+-ATPase (V-ATPase) is one of the most fundamental enzymes in nature. It pumps protons into the vacuolar system of eukaryotic cells and provides the energy for numerous transport systems. Through our BARD grant we discovered a novel family of membrane chaperones that modulate the amount of membrane proteins. We also elucidated the mechanism by which assembly factors guide the membrane sector of V-ATPase from the endoplasmic reticulum to the Golgi apparatus. The major goal of the research was to understand the mechanism of action and biogenesis of V-ATPase in higher plants and fungi. The fundamental question of the extent of acidification in organelles of the vacuolar system was addressed by studying the V-ATPase of lemon fruit, constructing lemon cDNAs libraries and study their expression in mutant yeast cells. The biogenesis of the enzyme and its function in the Golgi apparatus was studied in yeast utilizing a gallery of secretory mutants available in our laboratories. One of the goals of this project is to determine biochemically and genetically how V-ATPase is assembled into the different membranes of a wide variety of organelles and what is the mechanism of its action.The results of this project advanced out knowledge along these lines.
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