Academic literature on the topic 'Biochemical compartmentalization'
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Journal articles on the topic "Biochemical compartmentalization"
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Diekmann, Yoan, and José B. Pereira-Leal. "Evolution of intracellular compartmentalization." Biochemical Journal 449, no. 2 (December 14, 2012): 319–31. http://dx.doi.org/10.1042/bj20120957.
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Cells compartmentalize their biochemical functions in a variety of ways, notably by creating physical barriers that separate a compartment via membranes or proteins. Eukaryotes have a wide diversity of membrane-based compartments, many that are lineage- or tissue-specific. In recent years, it has become increasingly evident that membrane-based compartmentalization of the cytosolic space is observed in multiple prokaryotic lineages, giving rise to several types of distinct prokaryotic organelles. Endosymbionts, previously believed to be a hallmark of eukaryotes, have been described in several bacteria. Protein-based compartments, frequent in bacteria, are also found in eukaryotes. In the present review, we focus on selected intracellular compartments from each of these three categories, membrane-based, endosymbiotic and protein-based, in both prokaryotes and eukaryotes. We review their diversity and the current theories and controversies regarding the evolutionary origins. Furthermore, we discuss the evolutionary processes acting on the genetic basis of intracellular compartments and how those differ across the domains of life. We conclude that the distinction between eukaryotes and prokaryotes no longer lies in the existence of a compartmentalized cell plan, but rather in its complexity.
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Wassef, Marion, Jean Pierre Zanetta, Arlette Brehier, and Constantino Sotelo. "Transient biochemical compartmentalization of Purkinje cells during early cerebellar development." Developmental Biology 111, no. 1 (September 1985): 129–37. http://dx.doi.org/10.1016/0012-1606(85)90441-5.
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Duso, Lorenzo, and Christoph Zechner. "Stochastic reaction networks in dynamic compartment populations." Proceedings of the National Academy of Sciences 117, no. 37 (August 31, 2020): 22674–83. http://dx.doi.org/10.1073/pnas.2003734117.
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Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and typically very challenging to analyze computationally. Recent studies have made progress toward addressing this problem in the context of specific biological systems, but a general and sufficiently effective approach remains lacking. In this work, we propose a mathematical framework based on counting processes that allows us to study dynamic compartment populations with arbitrary interactions and internal biochemistry. We derive an efficient description of the dynamics in terms of differential equations which capture the statistics of the population. We demonstrate the relevance of our approach by analyzing models inspired by different biological processes, including subcellular compartmentalization and tissue homeostasis.
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Gartshteyn, Yevgeniya, Anca D. Askanase, Ruijiang Song, Shoiab Bukhari, Matthew Dragovich, Kieran Adam, and Adam Mor. "SLAMF6 compartmentalization enhances T cell functions." Life Science Alliance 6, no. 2 (December 8, 2022): e202201533. http://dx.doi.org/10.26508/lsa.202201533.
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Signaling lymphocyte activation molecule family member 6 (SLAMF6) is a T cell co-receptor. Previously, we showed that SLAMF6 clustering was required for T cell activation. To better understand the relationship between SLAMF6 location and function and to evaluate the role of SLAMF6 as a therapeutic target, we investigated how its compartmentalization on the cell surface affects T cell functions. We used biochemical and co-culture assays to show that T cell activity is enhanced when SLAMF6 colocalizes with the CD3 complex. Mechanistically, co-immunoprecipitation analysis revealed the SLAMF6-interacting proteins to be those essential for signaling downstream of T cell receptor, suggesting the two receptors share downstream signaling pathways. Bispecific anti-CD3/SLAMF6 antibodies, designed to promote SLAMF6 clustering with CD3, enhanced T cell activation. Meanwhile, anti-CD45/SLAMF6 antibodies inhibited SLAMF6 clustering with T cell receptor, likely because of the steric hindrance, but nevertheless enhanced T cell activation. We conclude that SLAMF6 bispecific antibodies have a role in modulating T cell responses, and future work will evaluate the therapeutic potential in tumor models.
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Scott, JD, and DW Carr. "Subcellular Localization of the Type II cAMP-Dependent Protein Kinase." Physiology 7, no. 4 (August 1, 1992): 143–48. http://dx.doi.org/10.1152/physiologyonline.1992.7.4.143.
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Diverse biochemical effects of different neurotransmitters or hormones that stimulate cAMP production may occur through activation of compartmentalized pools of cAMP-dependent protein kinase (PKA). Evidence suggests that compartmentalization of type II PKA is maintained through protein-protein interactions between the regulatory subunit and specific anchoring proteins.
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Koch, C., and A. Zador. "The function of dendritic spines: devices subserving biochemical rather than electrical compartmentalization." Journal of Neuroscience 13, no. 2 (February 1, 1993): 413–22. http://dx.doi.org/10.1523/jneurosci.13-02-00413.1993.
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Martin, William. "Evolutionary origins of metabolic compartmentalization in eukaryotes." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1541 (March 12, 2010): 847–55. http://dx.doi.org/10.1098/rstb.2009.0252.
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Many genes in eukaryotes are acquisitions from the free-living antecedents of chloroplasts and mitochondria. But there is no evolutionary ‘homing device’ that automatically directs the protein product of a transferred gene back to the organelle of its provenance. Instead, the products of genes acquired from endosymbionts can explore all targeting possibilities within the cell. They often replace pre-existing host genes, or even whole pathways. But the transfer of an enzymatic pathway from one compartment to another poses severe problems: over evolutionary time, the enzymes of the pathway acquire their targeting signals for the new compartment individually, not in unison. Until the whole pathway is established in the new compartment, newly routed individual enzymes are useless, and their genes will be lost through mutation. Here it is suggested that pathways attain novel compartmentation variants via a ‘minor mistargeting’ mechanism. If protein targeting in eukaryotic cells possesses enough imperfection such that small amounts of entire pathways continuously enter novel compartments, selectable units of biochemical function would exist in new compartments, and the genes could become selected. Dual-targeting of proteins is indeed very common within eukaryotic cells, suggesting that targeting variation required for this minor mistargeting mechanism to operate exists in nature.
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Lee, Kevin F. H., Cary Soares, and Jean-Claude Béïque. "Examining Form and Function of Dendritic Spines." Neural Plasticity 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/704103.
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The majority of fast excitatory synaptic transmission in the central nervous system takes place at protrusions along dendrites called spines. Dendritic spines are highly heterogeneous, both morphologically and functionally. Not surprisingly, there has been much speculation and debate on the relationship between spine structure and function. The advent of multi-photon laser-scanning microscopy has greatly improved our ability to investigate the dynamic interplay between spine form and function. Regulated structural changes occur at spines undergoing plasticity, offering a mechanism to account for the well-described correlation between spine size and synapse strength. In turn, spine structure can influence the degree of biochemical and perhaps electrical compartmentalization at individual synapses. Here, we review the relationship between dendritic spine morphology, features of spine compartmentalization and synaptic plasticity. We highlight emerging molecular mechanisms that link structural and functional changes in spines during plasticity, and also consider circumstances that underscore some divergence from a tight structure-function coupling. Because of the intricate influence of spine structure on biochemical and electrical signalling, activity-dependent changes in spine morphology alone may thus contribute to the metaplastic potential of synapses. This possibility asserts a role for structural dynamics in neuronal information storage and aligns well with current computational models.
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Adamkov, Marian, Sandra Hurta Csizmar, Veronika Mestanova, Desanka Vybohova, and Bibiana Krajnakova. "IS SURVIVIN LEVEL IDENTICAL BETWEEN ADENOMAS OF PROXIMAL AND DISTAL COLON?" Revista Argentina de Anatomía Clínica 14, no. 2 (July 29, 2022): 58–64. http://dx.doi.org/10.31051/1852.8023.v14.n2.37625.
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Objectives: Considerable differences are known between proximal and distal colon, these include embryological, anatomical, histological, biochemical, and physiological characteristics. Above mentioned distinctions may influence development of variable clinico-morphological entities. Multifunctional antiapoptotic protein survivin participates in regulation of cell cycle, apoptotic cascades, and stimulates angiogenesis. Material and methods: We assessed immunohistochemically expression pattern of antiapoptotic protein survivin in a panel of 243 colon adenomas to determine its association with colon localization. In each section, subcellular compartmentalization of survivin and intensity of immunoreaction were evaluated. Results: Survivin was expressed in 190 cases (78.2%). Statistical analysis confirmed a significant correlation of subcellular survivin compartmentalization and intensity of immunoreaction with colon localization of adenomas. Conclusions: Taking into account unique features of survivin, its expression pattern in proximally sided adenomas, and distinctions between left and right colon, we suppose that survivin level may contribute to higher proliferative phenotype of proximal adenomas.
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Vallés, Ana Sofía, and Francisco J. Barrantes. "Nanoscale Sub-Compartmentalization of the Dendritic Spine Compartment." Biomolecules 11, no. 11 (November 15, 2021): 1697. http://dx.doi.org/10.3390/biom11111697.
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Compartmentalization of the membrane is essential for cells to perform highly specific tasks and spatially constrained biochemical functions in topographically defined areas. These membrane lateral heterogeneities range from nanoscopic dimensions, often involving only a few molecular constituents, to micron-sized mesoscopic domains resulting from the coalescence of nanodomains. Short-lived domains lasting for a few milliseconds coexist with more stable platforms lasting from minutes to days. This panoply of lateral domains subserves the great variety of demands of cell physiology, particularly high for those implicated in signaling. The dendritic spine, a subcellular structure of neurons at the receiving (postsynaptic) end of central nervous system excitatory synapses, exploits this compartmentalization principle. In its most frequent adult morphology, the mushroom-shaped spine harbors neurotransmitter receptors, enzymes, and scaffolding proteins tightly packed in a volume of a few femtoliters. In addition to constituting a mesoscopic lateral heterogeneity of the dendritic arborization, the dendritic spine postsynaptic membrane is further compartmentalized into spatially delimited nanodomains that execute separate functions in the synapse. This review discusses the functional relevance of compartmentalization and nanodomain organization in synaptic transmission and plasticity and exemplifies the importance of this parcelization in various neurotransmitter signaling systems operating at dendritic spines, using two fast ligand-gated ionotropic receptors, the nicotinic acetylcholine receptor and the glutamatergic receptor, and a second-messenger G-protein coupled receptor, the cannabinoid receptor, as paradigmatic examples.
Dissertations / Theses on the topic "Biochemical compartmentalization"
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Weitz, Maximilian [Verfasser], Friedrich C. [Akademischer Betreuer] Simmel, and Tim [Akademischer Betreuer] Liedl. "Compartmentalization of synthetic biochemical systems / Maximilian Weitz. Gutachter: Tim Liedl ; Friedrich C. Simmel. Betreuer: Friedrich C. Simmel." München : Universitätsbibliothek der TU München, 2014. http://d-nb.info/1052995535/34.
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Matusiewicz, Malgorzata. "Using biochemical indicators to determine the recommended dietary allowance (RDA) and body ascorbate compartmentalization for juvenile rainbow trout /." The Ohio State University, 1994. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487857546387809.
Full textBook chapters on the topic "Biochemical compartmentalization"
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Helmchen, Fritjof. "Biochemical compartmentalization in dendrites." In Dendrites, 251–86. Oxford University Press, 2007. http://dx.doi.org/10.1093/acprof:oso/9780198566564.003.0010.
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Helmchen, Fritjof, and U. Valentin Nägerl. "Biochemical compartmentalization in dendrites." In Dendrites, 285–324. Oxford University Press, 2016. http://dx.doi.org/10.1093/acprof:oso/9780198745273.003.0010.
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Verma, D. P. S. "Developing Crops with Tolerance to Salinity and Drought Stress." In Feeding a World Population of More Than Eight Billion People. Oxford University Press, 1998. http://dx.doi.org/10.1093/oso/9780195113129.003.0019.
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Availability of water is the most important factor for crop productivity. A vast area (more than 50 million hectares) of agricultural land throughout the world suffers from recurring droughts, resulting in poor crop productivity (Carter, 1975). An equally large area of land is affected by high salinity. Even though irrigated agriculture has increased significantly during the past twenty years, the high capital cost of this process and the resulting increase in salinity is making this approach difficult to adopt. Furthermore, excessive irrigation is lowering the water tables, reducing water availability even more. Drought and salinity are formidable obstacles to the development of new varieties that can give sufficient yield under water stress conditions (Boyer, 1982). Some plants have evolved adaptations to water deficit and high salinity. These adaptations encompass a wide variety of plant characteristics (McCue and Hanson, 1990), including developmental and structural traits, time of flowering, rooting patterns, leaf waxiness, and physiological mechanisms such as the ability to exclude salt or the compartmentalization of ions within the cell (Binzel et al., 1988). Obviously, these are Multigenic traits, and most of them are determined by gene products that have not yet been characterized. The Multigenic nature of the phenotypes has thwarted attempts to characterize these mechanisms at the genetic level and has hindered efforts to produce osmotolerant plants by traditional breeding and somaclonal variations (Vasil, 1990). Among the biochemical traits in the adaptation of plants to water stresses, synthesis and accumulation of compatible osmolytes and changes in patterns of carbon and nitrogen metabolism are most important. Plants accumulate energy-rich metabolites under water stress; the most prevalent of these are proline and betaines (Yancey et al., 1982). Concentration of K+ and organic solutes (primarily polyols) has been shown to increase in direct proportion to changes in osmotic stress in many bacteria, algae, and higher plants. With the recent advances in genetic transformation of crop plants, genes encoding entire biosynthetic pathways or that augment the rate-limiting step in an adaptive process can now be transferred to any crop plant.
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West-Eberhard, Mary Jane. "Modularity." In Developmental Plasticity and Evolution. Oxford University Press, 2003. http://dx.doi.org/10.1093/oso/9780195122343.003.0009.
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Modularity, like the responsiveness that gives rise to it during development and evolution, is a universal property of living things and a fundamental determinant of how they evolve. Modularity refers to the properties of discreteness and dissociability among parts and integration within parts. There are many other words for the same thing, such as atomization (Wagner, 1995), individualization (Larson and Losos, 1996), autonomy (Nijhout, 1991b), dislocation (Schwanwitsch, 1924), decomposability (Wimsatt, 1981), discontinuity (Alberch, 1982), gene nets (Bonner, 1988), subunit organization (West-Eberhard, 1992a, 1996), compartments or compartmentation (Garcia-Bellido et al., 1979; Zuckerkandl, 1994; Maynard-Smith and Szathmary, 1995; Kirschner and Gerhart, 1998), and compartmentalization (Gerhart and Kirschner, 1997). One purpose of this chapter is to give consistent operational meaning to the concept of modularity in organisms. Seger and Stubblefield (1996, p. 118) note that organisms show “natural planes of cleavage” among organ systems, biochemical pathways, life stages, and behaviors that allow independent selection of different ones. They ask, “What determines where these planes of cleavage are located” and suggest that a “theory of organic articulations” may give insight into the laws of correlation, without specifying what the laws of articulation may be. Wagner (1995, p. 282) recognizes the importance of modularity and proposes a “building block” concept of homology where structural units often correspond to units of function, but concludes (after Rosenberg, 1985) that “there exists no way to distinguish an adequate from an inadequate atomization of the organisms.” Here I propose that modularity has a specific developmental basis (see also West-Eberhard, 1989, 1992a, 1996; see also Larson and Losos, 1996). Modular traits are subunits of the phenotype that are determined by the switches or decision points that organize development, whether of morphology, physiology, or behavior. Development can be seen as a branching series of decision points, including those caused by physical borders such as membranes or contact zones of growing or diffusing parts (e.g., see Meinhardt, 1982; see also chapter 5, on development). Each decision point demarcates the expression or use of a trait—a modular set—and subordinate branches demarcate lower level modular subunits, producing modular sets within modular sets.
Conference papers on the topic "Biochemical compartmentalization"
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Tourlomousis, Filippos, and Robert C. Chang. "2D and 3D Multiscale Computational Modeling of Dynamic Microorgan Devices as Drug Screening Platforms." In ASME 2015 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/imece2015-52734.
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The ability to incorporate three-dimensional (3D) hepatocyte-laden hydrogel constructs using layered fabrication approaches into devices that can be perfused with drugs enables the creation of dynamic microorgan devices (DMDs) that offer an optimal analog of the in vivo liver metabolism scenario. The dynamic nature of such in vitro metabolism models demands reliable numerical tools to determine the optimum process, material, and geometric parameters for the most effective metabolic conversion of the perfused drug into the liver microenvironment. However, there is a current lack of literature that integrates computational approaches to guide the optimum design of such devices. The groundwork of the present numerical study has been laid by our previous study [1], where the authors modeled in 2D an in vitro DMD of arbitrary dimensions and identified the modeling challenges towards meaningful results. These constructs are hosted in the chamber of the microfluidic device serving as walls of the microfluidic array of channels through which a fluorescent drug substrate is perfused into the microfluidic printed channel walls at a specified volumetric flow rate assuring Stokes flow conditions (Re<<1). Due to the porous nature of the hydrogel walls, a metabolized drug product is collected at the outlet port. A rigorous FEM based modeling approach is presented for a single channel parallel model geometry (1 free flow channel with 2 porous walls), where the hydrodynamics, mass transfer and pharmacokinetics equations are solved numerically in order to yield the drug metabolite concentration profile at the DMD outlet. The fluid induces shear stresses are assessed both in 3D, with only 27 cells modeled as single compartment voids, where all of the enzymatic reactions are assumed to take place. In this way, the mechanotransduction effect that alters the hepatocyte metabolic activity is assessed for a small scale model. This approach overcomes the numerical limitations imposed by the cell density (∼1012 cells/m3) of the large scale DMD device. In addition, a compartmentalization technique is proposed in order to assess the metabolism process at the subcellular level. The numerical results are validated with experiments to reveal the robustness of the proposed modeling approach and the necessity of scaling the numerical results by preserving dynamic and biochemical similarity between the small and large scale model.
Reports on the topic "Biochemical compartmentalization"
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Ehrlich, Marcelo, John S. Parker, and Terence S. Dermody. Development of a Plasmid-Based Reverse Genetics System for the Bluetongue and Epizootic Hemorrhagic Disease Viruses to Allow a Comparative Characterization of the Function of the NS3 Viroporin in Viral Egress. United States Department of Agriculture, September 2013. http://dx.doi.org/10.32747/2013.7699840.bard.
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Project Title: "Development of a plasmid-based reverse genetics system for the Bluetongue and Epizootic Hemorrhagic Disease viruses to allow comparative characterization of the function of the NS3 viroporin in viral egress". Project details: No - IS-4192-09; Participants – Ehrlich M. (Tel Aviv University), Parker J.S. (Cornell University), DermodyT.S. (Vanderbilt University); Period - 2009-2013. Orbiviruses are insect-borne infectious agents of ruminants that cause diseases with considerable economical impact in Israel and the United States. The recent outbreaks of BTV in Europe and of Epizootic Hemorrhagic Disease Virus (EHDV) in Israel, underscore the need for: (i) a better comprehension of the infection process of orbiviruses, (ii) the identification of unique vs. common traits among different orbiviruses, (iii) the development of novel diagnosis and treatment techniques and approaches; all aimed at the achievement of more effective control and treatment measures. It is the context of these broad goals that the present project was carried out. To fulfill our long-term goal of identifying specific viral determinants of virulence, growth, and transmission of the orbiviruses, we proposed to: (i) develop reverse genetics systems for BTV and EHDV2-Ibaraki; and (ii) identify the molecular determinants of the NS3 nonstructural protein related to viroporin/viral egress activities. The first objective was pursued with a two-pronged approach: (i) development of a plasmid-based reverse genetics system for BTV-17, and (ii) development of an "in-vitro" transcription-based reverse genetics system for EHDV2-Ibaraki. Both approaches encountered technical problems that hampered their achievement. However, dissection of the possible causes of the failure to achieve viral spread of EHDV2-Ibaraki, following the transfection of in-vitro transcribed genomic segments of the virus, revealed a novel characteristic of EHDV2-Ibaraki infection: an uncharacteristically low fold increase in titer upon infection of different cell models. To address the function and regulation of NS3 we employed the following approaches: (i) development (together with Anima Cell Metrology) of a novel technique (based on the transfection of fluorescently-labeledtRNAs) that allows for the detection of the levels of synthesis of individual viral proteins (i.e. NS3) in single cells; (ii) development of a siRNA-mediated knockdown approach for the reduction in levels of expression of NS3 in EHDV2-Ibaraki infected cells; (iii) biochemical and microscopy-based analysis of the localization, levels and post-translational modifications of NS3 in infected cells. In addition, we identified the altered regulation and spatial compartmentalization of protein synthesis in cells infected with EHDV2-Ibaraki or the mammalian reovirus. In EHDV2-Ibaraki-infected cells such altered regulation in protein synthesis occurs in the context of a cell stress reponse that includes the induction of apoptosis, autophagy and activation of the stressrelated kinase c-Jun N-terminal Kinase (JNK). Interestingly, inhibition of such stress-related cellular processes diminishes the production of infectious virions, suggesting that EHDV usurps these responses for the benefit of efficient infection. Taken together, while the present project fell short of the generation of novel reverse genetics systems for orbiviruses, the development of novel experimental approaches and techniques, and their employment in the analysis of EHDV-infected cells, yielded novel insights in the interactions of orbiviruses with mammalian cells.