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Relevant bibliographies by topics / Eukaryotic cells

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Academic literature on the topic 'Eukaryotic cells'

Author: Grafiati

Published: 4 June 2021

Last updated: 30 July 2024

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Journal articles on the topic "Eukaryotic cells"

1

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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Brueckner, Julia, and William F. Martin. "Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes." Genome Biology and Evolution 12, no. 4 (March 6, 2020): 282–92. http://dx.doi.org/10.1093/gbe/evaa047.

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Abstract Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.

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Sokol, Kerry A., and Neil E. Olszewski. "The Putative Eukaryote-LikeO-GlcNAc Transferase of the Cyanobacterium Synechococcus elongatus PCC 7942 Hydrolyzes UDP-GlcNAc and Is Involved in Multiple Cellular Processes." Journal of Bacteriology 197, no. 2 (November 10, 2014): 354–61. http://dx.doi.org/10.1128/jb.01948-14.

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The posttranslational addition of a single O-linked β-N-acetylglucosamine (O-GlcNAc) to serine or threonine residues regulates numerous metazoan cellular processes. The enzyme responsible for this modification,O-GlcNAc transferase (OGT), is conserved among a wide variety of organisms and is critical for the viability of many eukaryotes. Although OGTs with domain structures similar to those of eukaryotic OGTs are predicted for many bacterial species, the cellular roles of these OGTs are unknown. We have identified a putative OGT in the cyanobacteriumSynechococcus elongatusPCC 7942 that shows active-site homology and similar domain structure to eukaryotic OGTs. An OGT deletion mutant was created and found to exhibit several phenotypes. Without agitation, mutant cells aggregate and settle out of the medium. The mutant cells have higher free inorganic phosphate levels, wider thylakoid lumen, and differential accumulation of electron-dense inclusion bodies. These phenotypes are rescued by reintroduction of the wild-type OGT but are not fully rescued by OGTs with single amino acid substitutions corresponding to mutations that reduce eukaryotic OGT activity.S. elongatusOGT purified fromEscherichia colihydrolyzed the sugar donor, UDP-GlcNAc, while the mutant OGTs that did not fully rescue the deletion mutant phenotypes had reduced or no activity. These results suggest that bacterial eukaryote-like OGTs, like their eukaryotic counterparts, influence multiple processes.

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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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Field, Mark C., and Michael P. Rout. "Pore timing: the evolutionary origins of the nucleus and nuclear pore complex." F1000Research 8 (April 3, 2019): 369. http://dx.doi.org/10.12688/f1000research.16402.1.

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The name “eukaryote” is derived from Greek, meaning “true kernel”, and describes the domain of organisms whose cells have a nucleus. The nucleus is thus the defining feature of eukaryotes and distinguishes them from prokaryotes (Archaea and Bacteria), whose cells lack nuclei. Despite this, we discuss the intriguing possibility that organisms on the path from the first eukaryotic common ancestor to the last common ancestor of all eukaryotes did not possess a nucleus at all—at least not in a form we would recognize today—and that the nucleus in fact arrived relatively late in the evolution of eukaryotes. The clues to this alternative evolutionary path lie, most of all, in recent discoveries concerning the structure of the nuclear pore complex. We discuss the evidence for such a possibility and how this impacts our views of eukaryote origins and how eukaryotes have diversified subsequent to their last common ancestor.

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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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Brunet, Thibaut, and Detlev Arendt. "From damage response to action potentials: early evolution of neural and contractile modules in stem eukaryotes." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1685 (January 5, 2016): 20150043. http://dx.doi.org/10.1098/rstb.2015.0043.

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Eukaryotic cells convert external stimuli into membrane depolarization, which in turn triggers effector responses such as secretion and contraction. Here, we put forward an evolutionary hypothesis for the origin of the depolarization–contraction–secretion (DCS) coupling, the functional core of animal neuromuscular circuits. We propose that DCS coupling evolved in unicellular stem eukaryotes as part of an ‘emergency response’ to calcium influx upon membrane rupture. We detail how this initial response was subsequently modified into an ancient mechanosensory–effector arc, present in the last eukaryotic common ancestor, which enabled contractile amoeboid movement that is widespread in extant eukaryotes. Elaborating on calcium-triggered membrane depolarization, we reason that the first action potentials evolved alongside the membrane of sensory-motile cilia, with the first voltage-sensitive sodium/calcium channels (Na v /Ca v ) enabling a fast and coordinated response of the entire cilium to mechanosensory stimuli. From the cilium, action potentials then spread across the entire cell, enabling global cellular responses such as concerted contraction in several independent eukaryote lineages. In animals, this process led to the invention of mechanosensory contractile cells. These gave rise to mechanosensory receptor cells, neurons and muscle cells by division of labour and can be regarded as the founder cell type of the nervous system.

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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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Koukal, M., I. Trebichavský, J. Horáček, and V. Štěpánová. "Phages in eukaryotic cells." Folia Microbiologica 30, no. 3 (June 1985): 327–28. http://dx.doi.org/10.1007/bf02923527.

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Snider, Martin D. "Glycoproteins in Eukaryotic cells." Cell 40, no. 4 (April 1985): 733. http://dx.doi.org/10.1016/0092-8674(85)90331-9.

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Dissertations / Theses on the topic "Eukaryotic cells"

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Wadaan, Mohammad A. M. "Genetic and cellular studies of apogamic plasmodium development in Physarum polycephalum." Thesis, University of Sheffield, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.391038.

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Dickinson, P. "Fibronectin gene expression in higher eukaryotic cells." Thesis, University of Manchester, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.378322.

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Huang, George T. J. "Molecular cloning and characterization of multiple transcripts of the hamster ALG7 gene." Thesis, Boston University, 1992. https://hdl.handle.net/2144/31297.

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Thesis (D.Sc.D.)--Boston University, Henry M. Goldman School of Graduate Dentistry, 1992 (Oral Biology).
Includes bibliographical references (leaves 70-84).
The ALG7 gene encodes the tunicamycin-sensitive, dolichol-P-dependent Nacetylglucosamine- 1-phosphate transferase, GPT, that catalyzes the synthesis of the first dolichollinked sugar, Dol-PP-GlcNAc, in the N-glycosylation pathway. ALG7 has been evQlutionarily conserved and is essential for growth in all eukaryotes. The ALG7 gene expression in yeast is known to be regulated in part by the 3' untranslated regions (UTR) of the ALG7 multiple transcripts at the posttranscriptional level. To examine the regulatory features of the mammalian ALG7 gene, cloning and characterization of the hamster ALG7 mRNAs were undertaken. Polymerase chain reaction (PCR) using a single ALG7 gene-specific primer was performed to clone the cDNAs corresponding to the 3' and 5' ends of the ALG7 mRNAs from the Chinese hamster ovary (CHO) cells. The initial Northern blot analysis using a hamster ALG7 genomic DNA as a probe has shown that in the CHO cells the ALG7 gene is transcribed into three major messages, approximately 1.5, 1.9, and 2.2 kb in size. The 1.9 kb transcripts were cloned and sequenced. There is one consensus polyadenylation signal AAUAAA located 12 nucleotides (nt) upstream to the major poly(A) site. Three additional minor poly(A) sites are located at 18, 21 and 29 nt downstream from the AAUAAA sequence in this 1.9 kb class of mRNAs. [TRUNCATED]

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Tsolou, Avgi. "Cellular responses to uncapped telomeres in eukaryotic cells." Thesis, University of Newcastle Upon Tyne, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.442349.

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Johnston, Kelly L. "The interaction of Wolbachia bacteria with eukaryotic cells." Thesis, University of Liverpool, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420296.

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Boudarène, Lydia. "Transcription factor target search in live eukaryotic cells." Paris 7, 2013. http://www.theses.fr/2013PA077004.

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La régulation de l'expression des gènes est un mécanisme étroitement régulé. Au coeur de ce système, les facteurs de transcription jouent un rôle majeur dans l'initiation de la transcription, en induisant le recrutement de la machinerie transcriptionelle sur les séquences régulatrices des gènes. Pour ce faire, les facteurs de transcription doivent trouver et se fixer sur leur séquence cible de -10 paires de bases, au sein d'un génome composé de plusieurs milliards de paires de bases, et ce, dans un laps de temps compatible avec celui des processus biologique. Le mécanisme de recherche de cible a été largement étudié au cours des quarante dernières années, de manière théorique, in vitro et in vivo chez les bactéries et les levures. Au cours de l'étude présentée dans cette thèse, l'introduction au sein du génome de cellules eucaryotes du système modèle bactérien Répresseur Tétracycline-Opérateur Tétracycline, représentant respectivement le chercheur et la cible, a permis de révéler que le chercheur explore le noyau en combinant un processus de diffusion libre en trois dimensions, des fixations non-spécifiques ainsi qu'une diffusion en une dimension le long de l’ADN. L'efficacité de fixation sur la séquence cible de notre système modèle s'est avérée être plus faible que prévue, impliquant la prise en compte d'autres paramètres, tels que la concentration locale de facteurs de transcription ou l'organisation spatiale de la chromatine afin d'avoir une compréhension globale du mécanisme de régulation de l'expression génique
Gene regulation is a tightly controlled mechanism throughout evolution. At the core of this process, transcription factors play a major role in transcription initiation by binding and inducing transcriptional machinery recruitment at gene regulatory sequences. To execute their function, transcription factors have to find and bind on their -10 base pair target sequence within a genome of billions of base pairs in timing consistent with biological processes. In the last 40 years, target search process has been widely studied theoretically as well as in vitro and in vivo in bacteria and yeast, but not in high eukaryotes. In the work presented in this thesis, we show the eukaryotic live cell observations of an exogenously introduced bacterial Tetracycline Repressor System binding on an artificial gene array of Tetracycline Operator target sites. The target search mechanism of the Tetracycline Repressor exhibits diffusion in the nucleus by combining a free three-dimensional local and global diffusion, non-specific binding and one-dimensional sliding on the DNA. The binding efficiency on the target was found to be orders of magnitude lower than expected, suggesting that parameters such as local protein concentration or chromatin organization have to be considered for a global understanding of gene expression regulation

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Ren, Pei-Hsien. "Infection of eukaryotic cells by fibrillar polyglutamine aggregates /." May be available electronically:, 2007. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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Lucas, Paul. "Cationic polypeptides for gene delivery to eukaryotic cells." Thesis, University of Bath, 1995. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.307110.

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Clark, Francis. "A computational study of gene structure and splicing in model eukaryote organisms /." St. Lucia, Qld, 2003. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe17395.pdf.

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Jones, Emma. "Localizing RNA polymerase subunits in human cells." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299096.

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Books on the topic "Eukaryotic cells"

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Schaechter, Moselio. Eukaryotic microbes. Amsterdam: Elsevier/Academic Press, 2012.

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

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Tager, Joseph M., Angelo Azzi, Sergio Papa, and Ferruccio Guerrieri, eds. Organelles in Eukaryotic Cells. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4613-0545-3.

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

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

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Dexter, Dyer Betsey, and Obar Robert, eds. The Origin of eukaryotic cells. New York: Van Nostrand Reinhold, 1985.

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Kulakovskaya, Tatiana, Evgeny Pavlov, and Elena N. Dedkova, eds. Inorganic Polyphosphates in Eukaryotic Cells. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-41073-9.

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Oelschlaeger, Tobias A., and Jörg Hacker, eds. Bacterial Invasion into Eukaryotic Cells. Boston, MA: Springer US, 2000. http://dx.doi.org/10.1007/978-1-4757-4580-1.

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Compans, Richard W., ed. Protein Traffic in Eukaryotic Cells. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76389-2.

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L, DePamphilis Melvin, ed. DNA replication in eukaryotic cells. [Plainview, New York]: Cold Spring Harbor Laboratory Press, 1996.

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Book chapters on the topic "Eukaryotic cells"

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Pismen, Len. "Eukaryotic Cells." In Active Matter Within and Around Us, 91–112. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-68421-1_5.

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Zhegunov, Gennadiy, and Denys Pogozhykh. "Eukaryotic Cells." In The Frontiers Collection, 85–104. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-27552-4_3.

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Mierke, Claudia Tanja. "Focus on Eukaryotic Cells." In Cellular Mechanics and Biophysics, 35–56. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-58532-7_2.

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Hall, Andrew C., David M. Pickles, and Alister G. Macdonald. "Aspects of Eukaryotic Cells." In Advances in Comparative and Environmental Physiology, 29–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-642-77115-6_2.

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Azzi, Angelo, Michele Müller, and Néstor Labonia. "The Mitochondrial Respiratory Chain." In Organelles in Eukaryotic Cells, 1–8. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4613-0545-3_1.

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Kadenbach, Bernhard, Andrea Schlerf, Thomas Mengel, Ludger Hengst, Xinan Cao, Guntram Suske, C. Eckerskorn, and F. Lottspeich. "Tissue-Specific Expression of Nuclear Genes for Mitochondrial Enzymes." In Organelles in Eukaryotic Cells, 143–56. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4613-0545-3_10.

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Douce, Roland, Claude Alban, Maryse A. Block, and Jacques Joyard. "The Plastid Envelope Membranes: Purification, Composition and Role in Plastid Biogenesis." In Organelles in Eukaryotic Cells, 157–76. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4613-0545-3_11.

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Tabak, H. F., and B. Distel. "Biogenesis of Peroxisomes." In Organelles in Eukaryotic Cells, 177–85. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4613-0545-3_12.

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Opperdoes, Fred R., and Paul A. M. Michels. "Biogenesis and Evolutionary Origin of Peroxisomes." In Organelles in Eukaryotic Cells, 187–95. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4613-0545-3_13.

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Guerrieri, Ferruccio, Jan Kopecky, and Franco Zanotti. "Functional and Immunological Characterization of Mitochondrial F0F1 ATP-Synthase." In Organelles in Eukaryotic Cells, 197–208. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4613-0545-3_14.

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Conference papers on the topic "Eukaryotic cells"

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HanZhongwei, Wang Wenyong, Fang Yan, and Ma Fahui. "The three-dimensional modeling eukaryotic cells." In 2010 International Conference on Computer Application and System Modeling (ICCASM 2010). IEEE, 2010. http://dx.doi.org/10.1109/iccasm.2010.5622307.

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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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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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Robinson, Tom. "Creating synthetic eukaryotic cells with giant lipid vesicles and microfluidics." In Emerging Investigators in Microfluidics Conference. València: Fundació Scito, 2021. http://dx.doi.org/10.29363/nanoge.eimc.2021.035.

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Bar, Nadav S., and Rahmi Lale. "Modeling and control of the protein synthesis process in eukaryotic cells." In 2008 47th IEEE Conference on Decision and Control. IEEE, 2008. http://dx.doi.org/10.1109/cdc.2008.4739378.

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Shahimin, M. Mohamad, N. M. B. Perney, S. Brooks, N. Hanley, K. L. Wright, J. S. Wilkinson, and T. Melvin. "Optical propulsion of mammalian eukaryotic cells on an integrated channel waveguide." In SPIE MOEMS-MEMS, edited by Holger Becker and Bonnie L. Gray. SPIE, 2011. http://dx.doi.org/10.1117/12.874019.

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Rajabi, N., J. Bahnemann, T. N. Tzeng, A. P. Zeng, and J. Muller. "Microfluidic device for the continuous preparation of eukaryotic cells for metabolic analysis." In 2013 IEEE 26th International Conference on Micro Electro Mechanical Systems (MEMS). IEEE, 2013. http://dx.doi.org/10.1109/memsys.2013.6474227.

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Akinsola, Rasaq. "Quantification of E. coli invasion into eukaryotic cells by Imaging flow cytometry." In European Microscopy Congress 2020. Royal Microscopical Society, 2021. http://dx.doi.org/10.22443/rms.emc2020.1242.

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Reports on the topic "Eukaryotic cells"

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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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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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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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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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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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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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