Academic literature on the topic 'Oligomeric size'
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Journal articles on the topic "Oligomeric size"
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Larson, Megan E., Susan J. Greimel, Fatou Amar та ін. "Selective lowering of synapsins induced by oligomeric α-synuclein exacerbates memory deficits". Proceedings of the National Academy of Sciences 114, № 23 (2017): E4648—E4657. http://dx.doi.org/10.1073/pnas.1704698114.
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Mounting evidence indicates that soluble oligomeric forms of amyloid proteins linked to neurodegenerative disorders, such as amyloid-β (Aβ), tau, or α-synuclein (αSyn) might be the major deleterious species for neuronal function in these diseases. Here, we found an abnormal accumulation of oligomeric αSyn species in AD brains by custom ELISA, size-exclusion chromatography, and nondenaturing/denaturing immunoblotting techniques. Importantly, the abundance of αSyn oligomers in human brain tissue correlated with cognitive impairment and reductions in synapsin expression. By overexpressing WT human αSyn in an AD mouse model, we artificially enhanced αSyn oligomerization. These bigenic mice displayed exacerbated Aβ-induced cognitive deficits and a selective decrease in synapsins. Following isolation of various soluble αSyn assemblies from transgenic mice, we found that in vitro delivery of exogenous oligomeric αSyn but not monomeric αSyn was causing a lowering in synapsin-I/II protein abundance. For a particular αSyn oligomer, these changes were either dependent or independent on endogenous αSyn expression. Finally, at a molecular level, the expression of synapsin genes SYN1 and SYN2 was down-regulated in vivo and in vitro by αSyn oligomers, which decreased two transcription factors, cAMP response element binding and Nurr1, controlling synapsin gene promoter activity. Overall, our results demonstrate that endogenous αSyn oligomers can impair memory by selectively lowering synapsin expression.
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Dalgėdienė, Indrė, Asta Lučiūnaitė, and Aurelija Žvirblienė. "Activation of Macrophages by Oligomeric Proteins of Different Size and Origin." Mediators of Inflammation 2018 (November 18, 2018): 1–13. http://dx.doi.org/10.1155/2018/7501985.
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Activation of macrophages is one of the key processes in generating the immune response against pathogens or misfolded/aggregated otherwise unharmful host’s proteins. Antigens and their immune complexes (IC) may shape macrophage phenotype in various directions. Data on the impact of protein structure during inflammation are evident; however, some separate steps of this process involving changes in macrophage phenotype are not fully understood. Our aim was to investigate the phenotype of macrophages after activation with different oligomeric proteins and their IC. We have used amyloid beta (Aβ1–42) that plays a role in neurodegenerative inflammation as a model of host-associated protein and three oligomeric viral antigens as pathogen-associated proteins. Murine cell lines J774, BV-2, and macrophage primary cell culture were treated with oligomeric proteins and their IC. After 48 h, expression of surface markers F4/80, CD68, CD86, and CD206 and secreted cytokines IL-10, IL-12, IL-23, and TNF-αwas analysed. Aβ1–42oligomers stimulated expression of both inflammatory and anti-inflammatory molecules; however, fibrils induced less intense expression of markers investigated as compared to small and large oligomers. Two out of three viral oligomeric proteins induced the inflammatory response of macrophages. Data suggest that macrophage activation pattern depends on the origin, size, and structure of oligomeric proteins.
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Sudipa, Saha. "Oligomeric structure and molecular chaperone function of eye lens protein α-crystallin – A Review". Journal of Indian Chemical Society Vol. 93, Nov 2016 (2016): 1233–42. https://doi.org/10.5281/zenodo.5639119.
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Department of Biotechnology, St. Xavier’s College, Kolkata-700 016, India <em>E-mail </em>: sahasudipa74@yahoo.co.in <em>Manuscript received 03 August 2016, accepted 26 August 2016</em> α-Crystallin, the major eye lens protein, exists as a large oligomer of two subunits, αA- and αB-crystallin. α-Crystallin exists in solution as a polydisperse high molecular mass aggregate with a molecular weight distribution ranging from 300,000 to over 1 million. Crystallization attempts of both the natural and recombinant α-crystallin of vertebrate were not fruitful so far because of the polydispersed nature of the protein oligomer. It is seen that despite the enormous number of studies on the structure of α-crystallin, the oligomeric sructure of α-crystallin is still the subject of much debate and speculation. It is generally believed that large oligomeric structure of α-crystallin or other sHSPs is prerequisite for their chaperone-like function. Although most chaperones are oligomers, whether oligomerization is absolutely required for protein stability or for chaperone function is not yet established.
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Pokrajac, Lisa, Clara Baik, J. Robin Harris, Naghmeh S. Sarraf, and Michael Palmer. "Partial oligomerization of pyolysin induced by a disulfide-tethered mutant." Biochemistry and Cell Biology 90, no. 6 (2012): 709–17. http://dx.doi.org/10.1139/o2012-029.
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The bacterial toxin pyolysin (PLO) belongs to the family of cholesterol-dependent cytolysins (CDCs), which form large, ring-shaped oligomeric pores in cholesterol-containing membranes. Monomeric CDC molecules have a structure of four domains, with domains 2 and 3 packed against each other. After binding to target membranes containing cholesterol, toxin monomers oligomerize into pre-pore complexes. Trans-membrane pores form when the pre-pores insert into the lipid bilayer. Membrane insertion requires each subunit in the pre-pore to undergo a significant change in conformation, including the separation of domains 2 and 3. We here characterize a pyolysin mutant with an engineered disulfide bond between domains 2 and 3. The disulfide-tethered mutant binds to membranes but does not form oligomers. When mixed with wild type PLO, the two proteins form hybrid oligomers, which are reduced in size and arc-shaped rather than ring-shaped. With equimolar mixtures or the disulfide mutant in slight excess, the hybrid oligomers retain pore-forming activity, while a larger excess of the mutant suppresses pore formation. These results support a “partially cooperative” mode of protein activity, in which a limited number of functional subunits within an oligomer have to cooperate to initiate membrane insertion and pore formation.
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Gurevich, Vsevolod V. "Do arrestin oligomers have specific functions?" Cell Signaling 1, no. 1 (2023): 42–46. http://dx.doi.org/10.46439/signaling.1.009.
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Arrestins are a small family of versatile regulators of cell signaling. Arrestins regulate signaling and trafficking of G protein-coupled receptors, regulate and direct to particular subcellular compartments numerous protein kinases, ubiquitin ligases, etc. Three out of four arrestin subtypes expressed in vertebrates self-associate, each forming oligomers of a distinct size and shape. While the structures of the solution oligomers of arrestin-1, -2, and -3 have been elucidated, no function specific for the oligomeric form of either of these three subtypes has been identified thus far. Considering how multi-functional average-sized (~45 kDa) arrestin proteins were found to be, it appears likely that certain functions are predominantly or exclusively fulfilled by monomeric and oligomeric forms of each subtype.
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Sanganna Gari, Raghavendar Reddy, Patrick Seelheim, Brendan Marsh, Volker Kiessling, Carl E. Creutz, and Lukas K. Tamm. "Quaternary structure of the small amino acid transporter OprG from Pseudomonas aeruginosa." Journal of Biological Chemistry 293, no. 44 (2018): 17267–77. http://dx.doi.org/10.1074/jbc.ra118.004461.
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Pseudomonas aeruginosa is an opportunistic human pathogen that causes nosocomial infections. The P. aeruginosa outer membrane contains specific porins that enable substrate uptake, with the outer membrane protein OprG facilitating transport of small, uncharged amino acids. However, the pore size of an eight-stranded β-barrel monomer of OprG is too narrow to accommodate even the smallest transported amino acid, glycine, raising the question of how OprG facilitates amino acid uptake. Pro-92 of OprG is critically important for amino acid transport, with a P92A substitution inhibiting transport and the NMR structure of this variant revealing that this substitution produces structural changes in the barrel rim and restricts loop motions. OprG may assemble into oligomers in the outer membrane (OM) whose subunit interfaces could form a transport channel. Here, we explored the contributions of the oligomeric state and the extracellular loops to OprG's function. Using chemical cross-linking to determine the oligomeric structures of both WT and P92A OprG in native outer membranes and atomic force microscopy, and single-molecule fluorescence of the purified proteins reconstituted into lipid bilayers, we found that both protein variants form oligomers, supporting the notion that subunit interfaces in the oligomer could provide a pathway for amino acid transport. Furthermore, performing transport assays with loop-deleted OprG variants, we found that these variants also can transport small amino acids, indicating that the loops are not solely responsible for substrate transport. We propose that OprG functions as an oligomer and that conformational changes in the barrel–loop region might be crucial for its activity.
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Melotto, Eunice, L. Carl Greve, and John M. Labavitch. "PECTIN OLIGOMERS - POTENTIAL ENDOGENOUS REGULATORS OF RIPENING?" HortScience 27, no. 6 (1992): 653g—653. http://dx.doi.org/10.21273/hortsci.27.6.653g.
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Acid hydrolysis-generated pectic oligomers have been shown to affect ripening of tomato fruit by inducing both acceleration of reddening and increased ethylene biosynthesis (Campbell & Labavitch, 1991 Plant Physiol 97:706-713). In the present work, homogeneous size classes of these oligomers were demonstrated to have different impacts on ethylene production of tomato fruit pericarp discs. Endogenous oligomeric material of the same size classes was isolated from ripening tomato tissues and also tested for biological activity. They promoted some aspects of ripening as shown by increased ACC and ethylene production, which suggests that pectic oligomers are potential regulators of the ripening process in tomatoes. A metabolic origin for these oligomers is suggested by the fact that they are produced by in vitro polygalacturonase I treatment of polygalacturonic acid or tomato pectin.
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Wojciechowska, Daria, Michał Taube, Karolina Rucińska, Joanna Maksim, and Maciej Kozak. "Oligomerization of Human Cystatin C—An Amyloidogenic Protein: An Analysis of Small Oligomeric Subspecies." International Journal of Molecular Sciences 23, no. 21 (2022): 13441. http://dx.doi.org/10.3390/ijms232113441.
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Human cystatin C (HCC), an amyloidogenic protein, forms dimers and higher oligomers (trimers, tetramers and donut like large oligomers) via a domain-swapping mechanism. The aim of this study was the characterization of the HCC oligomeric states observed within the pH range from 2.2 to 10.0 and also in conditions promoting oligomerization. The HCC oligomeric forms obtained in different conditions were characterized using size exclusion chromatography, dynamic light scattering and small-angle X-ray scattering. The marked ability of HCC to form tetramers at low pH (2.3 or 3.0) and dimers at pH 4.0–5.0 was observed. HCC remains monomeric at pH levels above 6.0. Based on the SAXS data, the structure of the HCC tetramer was proposed. Changes in the environment (from acid to neutral) induced a breakdown of the HCC tetramers to dimers. The tetrameric forms of human cystatin C are formed by the association of the dimers without a domain-swapping mechanism. These observations were confirmed by their dissociation to dimers at pH 7.4.
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Stoneman, Michael R., Naomi Raicu, Gabriel Biener, and Valerică Raicu. "Fluorescence-based Methods for the Study of Protein-Protein Interactions Modulated by Ligand Binding." Current Pharmaceutical Design 26, no. 44 (2020): 5668–83. http://dx.doi.org/10.2174/1381612826666201116120934.
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Background: The growing evidence that G protein-coupled receptors (GPCRs) not only form oligomers but that the oligomers also may modulate the receptor function provides a promising avenue in the area of drug design. Highly selective drugs targeting distinct oligomeric sub-states offer the potential to increase efficacy while reducing side effects. In this regard, determining the various oligomeric configurations and geometric sub-states of a membrane receptor is of utmost importance. Methods: In this report, we have reviewed two techniques that have proven to be valuable in monitoring the quaternary structure of proteins in vivo: Fӧrster resonance energy transfer (FRET) spectrometry and fluorescence intensity fluctuation (FIF) spectrometry. In FRET spectrometry, distributions of pixel-level FRET efficiency are analyzed using theoretical models of various quaternary structures to determine the geometry and stoichiometry of protein oligomers. In FIF spectrometry, spatial fluctuations of fluorescent molecule intensities are analyzed to reveal quantitative information on the size and stability of protein oligomers. Results: We demonstrate the application of these techniques to a number of different fluorescence-based studies of cells expressing fluorescently labeled membrane receptors, both in the presence and absence of various ligands. The results show the effectiveness of using FRET spectrometry to determine detailed information regarding the quaternary structure receptors form, as well as FIF and FRET for determining the relative abundance of different-sized oligomers when an equilibrium forms between such structures. Conclusion: FRET and FIF spectrometry are valuable techniques for characterizing membrane receptor oligomers, which are of great benefit to structure‐based drug design.
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BÖDE, Csaba, Ferenc G. TÖLGYESI, László SMELLER, Karel HEREMANS, Sergiy V. AVILOV, and Judit FIDY. "Chaperone-like activity of alpha-crystallin is enhanced by high-pressure treatment." Biochemical Journal 370, no. 3 (2003): 859–66. http://dx.doi.org/10.1042/bj20021097.
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α-Crystallin, an oligomeric protein in vertebrate eye lens, is a member of the small heat-shock protein family. Several papers pointed out that its chaperone-like activity could be enhanced by increasing the temperature. We demonstrate in the present study that structural perturbations by high hydrostatic pressures up to 300MPa also enhance this activity. In contrast with temperature-induced changes, the pressure-induced enhancement is reversible. After pressure release, the extra activity is lost with a relaxation time of 2.0±0.5h. Structural alterations contributing to the higher activity were studied with IR and fluorescence spectroscopy, and light-scattering measurements. The results suggest that while the secondary structure barely changes under pressure, the interactions between the subunits weaken, the oligomers dissociate, the area of accessible hydrophobic surfaces significantly increases and the environment of tryptophan residues becomes slightly more polar. It seems that structural flexibility and the total surface area of the oligomers are the key factors in the chaperone capacity, and that the increase in the chaperone activity does not require the increase in the oligomer size as was assumed previously [Burgio, Kim, Dow and Koretz (2000) Biochem. Biophys. Res. Commun. 268, 426—432]. After pressure release, the structure of subunits are reorganized relatively quickly, whereas the oligomer size reaches its original value slowly with a relaxation time of 33±4 h. In our interpretation, both the fast and slow structural rearrangements have an impact on the functional relaxation.
Dissertations / Theses on the topic "Oligomeric size"
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Yardley, Paul. "Preparation and evaluation of low migration oligomeric photoinitiators with a repeating photoactive site." Thesis, University of Hull, 2009. http://hydra.hull.ac.uk/resources/hull:13654.
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UV-curing is an efficient, environmentally friendly technology used extensively for a variety of applications including food packaging. Its limitation is that small photoinitiator molecules may migrate into the foodstuff which, although not necessarily harmful, is undesirable and is subject to legislative requirements. In order to meet these requirements a variety of oligomeric photoinitiators based on benzophenone have ,been prepared. To maximise their photoinitiating capability these have been prepared with a repeat photoinitiating unit and it has been attempted to minimise the non-photoinitiating portion of the molecule. To evaluate migration a simple UV method of detecting and measuring migration has been developed and successfully validated. Twenty four oligomers with a repeat photoinitiating unit have been prepared with six of these shown to be low-migrating with a seventh capable of being used as a low migrating oligomeric photo initiator due to exhibiting a rapid speed of cure at low photoinitiator concentrations.
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Narikiyo, Hayato. "Development of Functional Materials Based on Polyhedral Oligomeric Silsesquioxane with Flexible Side-Chains." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263688.
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付記する学位プログラム名: 充実した健康長寿社会を築く総合医療開発リーダー育成プログラム<br>京都大学<br>新制・課程博士<br>博士(工学)<br>甲第23227号<br>工博第4871号<br>京都大学大学院工学研究科高分子化学専攻<br>(主査)教授 田中 一生, 教授 秋吉 一成, 教授 古賀 毅<br>学位規則第4条第1項該当<br>Doctor of Philosophy (Engineering)<br>Kyoto University<br>DGAM
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Huang, Jiahao. "Design, Synthesis, and Self-Assembly of Nano-Sized Shape Amphiphiles Based on Polyhedral Oligomeric Silsesquioxane and Perylene Bisimides." University of Akron / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=akron1603670714151325.
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Eberley, William Arthur. "Hydrogen-bonding residues at the asymmetric dimer site of tRNAHis guanylyltransferase and their contributions to oligomeric state and activity." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1306943230.
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SIMON, STEPHANIE. "Structure fonctionnelle de l'acetylcholinesterase : mise en evidence d'un nouveau site regulateur. organisation des oligomeres." Paris 6, 1999. http://www.theses.fr/1999PA066473.
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Nous nous sommes interesses aux aspects moleculaires, structuraux et catalytiques de l'acetylcholinesterase (ache). L'ache de gymnote est la plus rapide parmi les differentes cholinesterases. La premiere partie de la these est consacree au clonage et a l'analyse de la structure du gene codant l'ache de gymnote. Cette enzyme possede un peptide c-terminal de type t (code par son dernier exon), necessaire pour l'oligomerisation de l'ache. Le domaine catalytique comporte un peptide additionnel de 29 residus, situe a la surface de la molecule a l'oppose de l'entree de la gorge catalytique. L'analyse du gene codant l'ache de gymnote montre que le domaine catalytique est code par trois exons. L'expression de constructions partiellement genomiques dans des cellules de mammiferes conduit a des epissages anormaux, qui n'existent pas in vivo. Dans une deuxieme partie, nous avons utilise des aches chimeres rat/gymnote pour determiner les sites de liaison de trois anticorps monoclonaux inhibiteurs de l'ache de gymnote. Deux de ces anticorps inhibent l'enzyme en se liant avec le site peripherique situe a la surface de l'ache, a l'entree de la gorge catalytique. Le troisieme anticorps se lie dans la region de la porte arriere theorique. C'est la premiere indication experimentale que du role de l'hypothetique porte arriere dans le mecanisme catalytique. Dans la troisieme partie, nous avons cherche a definir un domaine de la sous-unite catalytique d'ache de type t qui assure son association avec le sous-unite collagenique (colq). On sait qu'un motif peptidique (prad) de la partie n-terminale de colq est suffisant pour assembler ces molecules heteromeriques. Nous savions aussi que le peptide t est necessaire pour cette interaction. Nous avons pu montrer qu'il est suffisant pour associer quatre sous-unites d'ache ou d'autres proteines avec le prad. Il constitue donc un domaine independant, que nous avons appele le domaine wat (tryptophan amphiphilic tetramerization).
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Zhuang, Rong-Chuan. "Synthesis of polymers and oligomers containing fluorinated side groups for the construction of hydrophobic surfaces." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2005. http://nbn-resolving.de/urn:nbn:de:swb:14-1120215670616-23184.
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Oligomers and polymers based on functionalized Rf-amides were successfully synthesized for the fabrication of hydrophobic surfaces with either linear or network structure. Firstly, new functionalized Rf-amides (RfCONH-, Rf is a perfluoroalkyl segment) were developed in most cases by a one step reaction and a simple work-up procedure. The reaction behaviors of synthesized Rf-amides in polyreactions were well understood. New fluorinated oligoester polyols, blocked IPDI's, and end-hydroxyl terminated oligo(urea urethane)s have been synthesized, the detail structures and properties are well understood. These materials could be suitable components of powder coatings. On the other hand, the end-hydroxyl terminated oligo(urea urethane)s could be used as reactive additives in high solid content and water-borne coatings. Hydrophobic smooth surfaces based on linear polymers, poly(urea urethane)s and alternating MI copolymers, containing fluorinated side groups were successfully constructed. The attachment of fluorinated side groups into polymers can dramatically alter the surfaces of corresponding polymers from more hydrophilic to hydrophobic due to the enrichment of fluorinated side groups on the top of the surface. The backbone configuration, the polarity of backbones, and the thermal treatment on surfaces can influence the surface properties of corresponding materials. Finally, hydrophobic surfaces of cross-linked polyurethanes as model top coatings were constructed under melt condition at high temperature (180 and 190 oC) using the combination of fluorinated oligouretdiones and non-fluorinated oligoester polyols. It was found that the hydrophobicity of resulting cured films is a matter of the competition between the formation of cross-linking network and the segregation of fluoromoieties on the top of the surface.
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Kelly, Jennifer Yvonne DeSimone Joseph M. "Novel fluoroelastomers composed of tetrafluoroethylene and vinylidene fluoride oligomers synthesized in carbon dioxide for use in soft lithography to enable a platform for the fabrication of shape- and size-specific, monodisperse biomaterials." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2008. http://dc.lib.unc.edu/u?/etd,1934.
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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2008.<br>Title from electronic title page (viewed Dec. 11, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.
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Ren, Yan-Guo. "Poly(A)-Specific Ribonuclease (PARN)." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2001. http://publications.uu.se/theses/91-554-5194-2/.
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Pisterzi, Luca Francis. "Pairing Form with Function: The Oligomeric Size and Configuration of G Protein-coupled Receptors." Thesis, 2012. http://hdl.handle.net/1807/65486.
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The quaternary status of G protein-coupled receptors (GPCRs) is important, unknown and
controversial. Estimates of size from numerous pharmacological, biochemical and biophysical
studies range from monomers to octamers. Accounts of stability vary from constitutive oligomers
to a spontaneous, ligand-regulated interconversion between monomers and dimers. In the present
investigation, the oligomeric size of GPCRs in live Chinese hamster ovary (CHO) cells has been
examined by two methods. Both are based on the efficiency of Förster resonance energy transfer
(FRET) between fluorophore-tagged receptors, as determined from emission spectra via spectral
deconvolution. In the first, the apparent FRET efficiency (Eapp) was measured for cells expressing
eGFP- and eYFP-tagged M2 muscarinic receptors at different ratios of acceptor to donor. Eapp then
was related to the pair-wise efficiency (Ep) according to a model that enumerates all pathways for
the transfer of energy between single donors and acceptors within an oligomer of given size (n).
Each value n returned a distinct and well-defined value of Ep. Fluorescence lifetime imaging
provided an independent estimate of Ep that was in close agreement with the model-based value
when n = 4, identifying the M2 receptor as a tetramer. In the second approach, the M1 and M2
muscarinic receptors and the β1 and β2 adrenergic receptors were tagged with GFP2 and eYFP, and
the value of Eapp was estimated for each pixel in the image of a cell. The distributions of Eapp from
34–40 cells expressing each receptor were compared with those predicted for populations of dimers,
trimers and tetramers, the latter configured as a square and a rhombus. In each case, the combined
data were well described in terms of a rhombus. Distributions obtained for the M2 and β2 receptors
were not affected by agonists or inverse agonists, nor was there evidence for appreciable numbers
of dimers or larger oligomers. Taken together, the results suggest that GPCRs of Family 1 exist
largely or wholly as constitutive tetramers.
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Laha, B. "Influence of Thermal Perturbation of the Oligomeric Size of -Crystallin on its Chaperone Function – A Biophysical Study." Thesis, 2010. http://ethesis.nitrkl.ac.in/1588/2/Influence_of_Thermal_Perturbation_of_the_Oligomeric_Size_of.pdf.
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-Crystallin is the major protein component of the vertebrate eye lens and is composed of two subunits A- and B-, 20 kDa each having 57% sequence homology between them. Both subunits associate to form large oligomer of 800 kDa average molecular weight. It is a key member of the small heat shock protein (sHSP) superfamily having a conserved core ‘-crystallin domain’. -crystallin exhibit molecular chaperone properties and these features play an important role in maintaining the lens transparency. The relationship between oligomerization and chaperone function of -crystallin is less documented in literature. In this thesis, we explored the relationship between oligomeric size and chaperone activity using human recombinant A- and B-crystallin. We used thermal pre-incubation as a tool to vary the oligomeric size of A- and B-crystallin and study its effect on chaperone activity. With increase in pre-incubation temperature, the oligomeric size of both A- and B-crystallin was reduced but the chaperone activity of both proteins was enhanced. This observation leads us to conclude that chaperone activity of -crystallin is inversely proportional to its oligomeric size. Our results also showed that the high molecular weight aggregated species was formed on simple storage of both A- and B-crystallin which has very low chaperone activity. The result implies that loss of chaperone activity of -crystallin can be prevented by preventing its further association into larger oligomer.
Book chapters on the topic "Oligomeric size"
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Hastie, Kathryn, Vamseedhar Rayaprolu, and Erica Ollmann Saphire. "Analysis of Oligomeric and Glycosylated Proteins by Size-Exclusion Chromatography Coupled with Multiangle Light Scattering." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1241-5_24.
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Kandiyal, Pancham S., Ji Yoon Kim, Daniel L. Fortunati, and K. H. Mok. "Size Determination of Protein Oligomers/Aggregates Using Diffusion NMR Spectroscopy." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9678-0_13.
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Hayden, Eric Y., Joseph L. Conovaloff, Ashley Mason, Gal Bitan, and David B. Teplow. "Preparation of Pure Populations of Amyloid β-Protein Oligomers of Defined Size." In Methods in Molecular Biology. Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7816-8_1.
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Saito, Nozomi. "Homo-Double-Helix Formation of Ethynylhelicene Oligomers Possessing Various Side Chains." In Springer Theses. Springer Japan, 2013. http://dx.doi.org/10.1007/978-4-431-54514-9_3.
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Prokai, Laszlo, Stanley M. Stevens, and William J. Simonsick. "Size-Exclusion Chromatography Coupled to Mass Spectrometry and Tandem Mass Spectrometry for Oligomer Analysis." In ACS Symposium Series. American Chemical Society, 2004. http://dx.doi.org/10.1021/bk-2005-0893.ch012.
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Palacio-Castañeda, Valentina, Roland Brock, and Wouter P. R. Verdurmen. "Generation of Protein-Phosphorodiamidate Morpholino Oligomer Conjugates for Efficient Cellular Delivery via Anthrax Protective Antigen." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2010-6_8.
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AbstractPhosphorodiamidate morpholino oligomers (PMOs) offer great promise as therapeutic agents for translation blocking or splice modulation due to their high stability and affinity for target sequences. However, in spite of their neutral charge as compared to natural oligonucleotides or phosphorothioate analogs, they still show little permeability for cellular membranes, highlighting the need for effective cytosolic delivery strategies. In addition, the implementation of strategies for efficient cellular targeting is highly desirable to minimize side effects and maximize the drug dose at its site of action. Anthrax toxin is a three-protein toxin of which the pore-forming protein anthrax protective antigen (PA) can be redirected to a receptor of choice and lethal factor (LF), one of the two substrate proteins, can be coupled to various cargoes for efficient cytosolic cargo delivery. In this protocol, we describe the steps to produce the proteins and protein conjugates required for cytosolic delivery of PMOs through the cation-selective pore generated by anthrax protective antigen. The method relies on the introduction of a unique cysteine at the C-terminal end of a truncated LF (aa 1–254), high-yield expression of the (truncated) toxin proteins in E. coli, functionalization of a PMO with a maleimide group and coupling of the maleimide-functionalized PMO to the unique cysteine on LF by maleimide-thiol conjugation chemistry. Through co-administration of PA with LF-PMO conjugates, an efficient cytosolic delivery of PMOs can be obtained.
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Kondo, Jiro. "Crystallographic Studies of the Ribosomal A-Site Molecular Switches by Using Model RNA Oligomers." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-2763-0_20.
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Schubert, A., M. A. Krikunova, H. Stiel, J. Ehlert, D. Leupold, and H. Lokstein. "Determination of the Aggregate Size in Chlorophyll a Oligomers by Non-Linear Absorption Spectroscopy on the ps and fs Timescale." In Photosynthesis: Mechanisms and Effects. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-011-3953-3_112.
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Sugiura, Ken-ichi. "An Adventure in Macromolecular Chemistry Based on the Achievements of Dendrimer Science: Molecular Design, Synthesis, and Some Basic Properties of Cyclic Porphyrin Oligomers to Create a Functional Nano-Sized Space." In Topics in Current Chemistry. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/b11006.
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Shevchenko, Valery V., Alexandr V. Stryutsky, Mariana A. Gumenna, Nina S. Klimenko, and Valeri V. Klepko. "Synthesis, structure and properties of oligomeric ionic liquids of highly branched structure and special features of their self-arrangement." In NEW FUNCTIONAL SUBSTANCES AND MATERIALS FOR CHEMICAL ENGINEERING. PH “Akademperiodyka”, 2021. http://dx.doi.org/10.15407/akademperiodyka.444.199.
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Synthesis, features of structural organization and behavior in aqueous solution of amphiphilic reactive aprotic cationic oligomeric ionic liquids obtained on the basis of a mixture of oligomeric amino- and hydroxyl-containing silsesquioxanes were considered. The dependence of the glass transition temperature, the value of ionic conductivity, self-organization in dilute aqueous solutions and the ζ-potential on the length of the alkyl substituent near the quaternary nitrogen atom in the composition of the synthesized compounds was shown. It was found that quaternization of the tertiary nitrogen atom of the starting oligomer causes a sharp decrease in the glass transition temperature. The value of the latter increases with an increase in the length of the hydrophobic alkyl fragments due to their association. In this case the ionic conductivity under anhydrous conditions decreases and at temperatures above 100°C drops by almost an order of magnitude. The maximum conductivity was reached for the oligomeric ionic liquid with the short alkyl chain and its value was 10-3 S/cm at 120oC. In dilute aqueous solutions the synthesized oligomeric ionic liquids with the short alkyl chain form aggregates with an average size of 100 nm while increasing the length of the alkyl chain prevents aggregation of silsesquioxane nuclei and leads to formation of unimolecular micelles with an average size of 3 nm
Conference papers on the topic "Oligomeric size"
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Obeyesekere, Nihal, and Thusitha Wickramarachchi. "Transition from Combinatorial Chemistry to Present Day Robotics in Product Development for Oil Field Chemicals." In MECC 2023. AMPP, 2023. https://doi.org/10.5006/mecc2023-20245.
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Abstract In this paper, the slow evolution of combinatorial chemistry from its dawn in 1980’s to today’s oil field product development is discussed. Combinatorial chemistry comprises chemical synthetic methods that make it possible to prepare a vast number of compounds in a single process. These compound libraries can be made as mixtures, sets of individual compounds or chemical structures generated by computer software. This phenomenon was first invented by Arpad Furka (Lorand University, Budapest) in 1982. He described the principle of it, the combinatorial synthesis and a deconvolution procedure. The methodology was first used in drug discovery using a wide range of linear or wide range of macrocyclic chemical molecules: peptides, non-peptide oligomers, peptidomimetics, small-molecules, and natural product-like organic molecules. However, handling vast amounts of data and extremely small chemical recovery were a very difficult endeavor. To avoid this problem and help to refine the size of the chemical libraries, various software programs were utilized. This was achieved by utilizing a tool known as Design of Experiment (DoE). In this paper, the high throughput product screening to identify corrosion inhibitors was performed by utilizing critical micelle concentration (CMC). CMC was used to differentiate performance of libraries of chemical blends. Combinatorial synthesis (or blends) and combinatorial screening were performed by utilizing robotics methodologies. The corrosion inhibitor formulations predicted by DoE were built out by using combinatorial chemical methods and the arrays of chemical formulations were screened by utilizing high throughput robotics, using CMC as the selection guide. To validate the concept, several known corrosion inhibitor formulas were selected to optimize their efficacy. Each formula contained several active ingredients and a solvent package. These raw materials were blended in random but in a control, manner using combinatorial methodologies. After formulation of a vast array of formulation by using Design Expert solvent package. These raw materials were blended in random but in a control, manner using combinatorial methodologies. After formulation of a vast array of formulation by using Design Expert (DE) software, the products were screened for by CMC using automated surface tension workstation. Several formulations with lower CMC than the reference products were selected. The selected corrosion inhibitor formulations were identified and blended in larger scales. The efficacy of these products was tested by classical laboratory testing methods such as rotating cylinder electrode (RCE) and rotating cage autoclave (RCA) to determine their performance as anti-corrosion agents. These tests were performed against the original reference corrosion inhibitor. The testing indicated that several corrosion inhibitor formulations outperform the original blend thus validating the proof of concept.
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Gaffney, P. J., L. J. Creighton, A. Curry, B. MacMahon, and R. Thorpe. "MONOCLONAL ANTIBODIES OF THE IgM AND IgG CLASS SPECIFIC FOR CROSSLINKED FIBRIN DEGRADATION PRODUCTS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643651.
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Monoclonal antibodies (mabs) to crosslinked fibrin degradation products (XL-FDP) having the general formula D/Y[X]nY/D (known as X-oligomer) and D-D (known as D dimer) have been raised in balb/C mice by both a novel mtrasplenic and a conventional subcutaneous route of immunisation and by combinations of both these procedures. Mabs to X-oligomers (NIBn 52 and NIBn 123) obtained by an intrasplenic procedure have been demonstrated to crossreact only with X-oligomer in a 2-site ELISA procedure and not with D dimer or whole fibrinogen and have been shown to be of value m the examination of clinical material obtained from patients with various types of thrombosis and have also been useful in monitoring the efficacy of thrombolytic therapy. The X-oligomer mabs are immunoglobulins of the M class. It was demonstrated that their unique specificity for conformational epitopes on the large X-oligomer fragments does not reside in the IgM structure since alterative immunisation procedures have been used to generate mabs of the IgG class which have the same specificity. Using immunoglobulin class switching in culture rather than during immunisation was suggested by certain cell lines which produced both IgM and IgG specific for X-oligomer. This latter point needs rigorous validation.Immunoglobulin G type mabs to highly purified D dimer were raised by conventional subcutaneous immunisation of balb/C mice. One of these, NIBn-11, was found to crossreact with PVC-immobilised X-oligomer and D dimer but not with fibrinogen. However NIBn-11 did not bind to D dimer in a 2-site ELISA procedure while crossreactmg quite avidly with X-oligomer. This suggests that the D dimer epitope to which NIBn-11 is directed is expressed in some conformations and not m others and that these conformations are always expressed in the complex X-oligomer group of fragments. These mabs, whilst of value in measuring certain unique fibrin fragments m plasma, are useful in the epitope mapping of fibrinogen/fibrin and their plasmm-mediated
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Procyk, R., M. Block, and B. Blomback. "POLYMERIZATION OF FIBRINOGEN AND FIBRONECTIN CATALYZED BY FACTOR XIII." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643310.
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Factor XIII catalyzed the formation of gels in solutions containing physiological concentrations of fibrinogen and fibro-nectin. Oligomeric intermediates were isolated from reaction mixtures at early times prior to gel formation by chromatography on gelatin-Sepharose and by FPLC using Superose 6 columns. The products of two simultaneous polymerization reactions were characterized: fibrinogen oligomers (fibrinogenin) from the poly merization of fibrinogen, and conjugates of fibrinogen-fibro-nectin (heteronectin) from heteropolymer formation involving the two proteins.At a constant concentration of fibrinogen (2.5 mg/mL) and factor XIII (0.4 U/mL), the appearance of different sizes of fibrinogen polymers depended on the concentration of fibronectin added to the reaction mixture. At fibronectin concentrations in the range of the normal plasma level of 0.3 mg/mL, fibrinogen formed oligomers of various sizes up to heptamer before incorporating a molecule of fibronectin. At a high fibronectin concentration (3.2 mg/mL) most of the fibrinogen reacted with the fibronectin at the monomer stage, although small amounts of fibrinogen dimers and trimers were also formed.Heteronectin formation coincided with the appearance of filamentous and particulate matter. This material became incorporated into a gel structure if sufficient fibrinogen was present in the reaction mixture (about 0.5 mg/mL). If these factor XIII catalyzed polymerization reactions occur in the microvasculature under conditions where the fibrinogen concentration might be significantly lowered, the production of fibrinogen-fibronectin polymeric material without gel formation would be favored.
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Berk, H. R. "THE EFFECT OF SHEAR ON OLIGOMER FORMATION; EFFECTIVE REMOVAL OF MONOMERS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644220.
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Fibrin polymerization has been found to be influenced by shear flow conditions (Puryear,1980). In order to determine which mechanisms are responsible for theeffect reported it is necessary to look at the various stages in fibrin polymerization. It is known that the enzymatic attack of thrombin on fibrinogen is not influenced by shear (Sellers,1981). The next step, which is investigated in this study, is the oligomer-early protofibril stage.Fibrinogen (human, Kabi) is reacted with thrombin (human, Sigma) under Couette flow conditions (volume-averaged shear 0-250sec-l) in a pH 6.8, 4mM CaC12, HEPES buffered solution (I. S.-.15). The reaction time is chosen so that 6% of fibrinopeptide A (FPA) is released. The reaction is stopped by a 1,6 hexandiol-hirudin solution. The effect of shear on oligomer population is measured using large angle 1ightscattering techniques.In order to predict theoretical shear effects on oligomer formation, it is important to be able to predict the population size. This is done using Jamney’s (1983) predictions, for early reaction time, assuming q=16. Given a size distribution it is possible to apply low Reynold’s number hydrodynamic and Smoluchowski1 s( coagulation theories to predict possible shear affects.Hydrodynamic theory predicts no effect of shear on oligomer formation; Peclet numbers are too small. Smoluchowski coagulation theory, on the other hand, predicts that for oligomer sized particles in the shear range studied, orthokinetic (shear induced) coagulation becomes more important than peri kinetic (Brornian) coagulation.Results obtained from Zimm analysis show a dramatic increase in molecular weight, compared to the stagnant case, in the shear region corresponding to where orthokinetic coagulation dominates. The higher the thrombin concentration, the more extreme and earlier (i.e. lower shear) these effects are felt. After a peak is reached in molecular weight there is a sudden drop. This is caused by monomer exhaustion which shifts the population to a more homogeneous type. The concept of orthokinetic coagulation is important physiologically since it is advantageous to incorporate monomers onto fibers as quickly as possible.
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Hantgan, R. R. "LOCALIZATION OF THE DOMAINS OF FIBRIN INVOLVED IN BINDING TO PLATELETS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643773.
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The molecular basis of platelet-fibrin interactions has been investigated by using synthetic peptides as potential inhibitors of binding fibrin protofibrils and fibrinogen to ADP-stimulated platelets, adhesion of fibrin fibers to the platelet surface, and platelet-mediated clot retraction. Synthetic peptides RGDS and HHLGGAKQAGDV, corresponding to regions of the fibrinogen α and γ chains previously identified as platelet recognition sites, inhibited the binding of radiolabelled soluble fibrin oligomers to ADP-stimulated platelets with IC50 values of 12 and 40 μM, respectively. The IC50 values obtained with fibrinogen as the ligand were 3-fold higher. Synthetic GPRP and GHRP, corresponding to the N-terminal sequences of the fibrin α and β chains, were minimally effective in blocking soluble fibrin oligomer binding to ADP-stimulated platelets. The extent of fibrin:platelet adhesion was determined with a microfluorimetric technique which measures the quantity of fluorescein-labelled fibrin attached to the surface of platelets. The signal obtained from the brightly fluorescent platelet:fibrin adducts was time- and concentration-dependent, and was fully inhibited by a monoclonal antibody directed against the glycoprotein II:IIIa complex (HP1-1D, kindly provided by Dr. W. Nichols). Inhibition of fibrin:platelet adhesion by RGDS, HHGGAKQAGDV, and GHRP all exhibited a similar, linear dependence on the peptide concentration, reaching 1/2 maximum at about 200 μM, suggesting nonspecific effects. GPRP inhibited fibrin assembly but did not appear to have specific effects on fibrin:platelet adhesion. The time course of clot retraction was followed by right angle light scattering intensity measurements. Only RGDS affected clot retraction, causing a 4-fold decrease in rate at 230 μM. These results indicate that fibrinogen and fibrin protofibrils, which are obligatory intermediates in the fibrin assembly pathway, share a set of common platelet recognition sites located at specific regions of the α and γ chains of the multinodular fibrin(ogen) molecules. The RGDS site is also involved in mediating interactions between the three dimensional fibrin network and ADP-stimulated platelets.
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Samoc, Anna, Barry Luther-Davies, Marek Samoc, et al. "Optical properties of a nonlinear p -phenylenevinylene oligomer side chain polymer in films and fiber preforms." In International Symposium on Optical Science and Technology, edited by Manfred Eich and Mark G. Kuzyk. SPIE, 2002. http://dx.doi.org/10.1117/12.452120.
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Ravndal, Kristin T., and Roald Kommedal. "Modelling particle degradation and intermediate dynamics in a dispersed activated sludge microcosm." In 63rd International Conference of Scandinavian Simulation Society, SIMS 2022, Trondheim, Norway, September 20-21, 2022. Linköping University Electronic Press, 2022. http://dx.doi.org/10.3384/ecp192002.
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Municipal wastewater consists of a large fraction of particulate organic matter. During biological wastewater treatment these particles undergo extracellular depolymerisation before products are taken up by bacteria (MW < 0.6 kDa). Particle degradation and intermediate formation dynamics is important in process analysis of wastewater treatment as the transport regime differ. This work aims to develop a model for particle degradation that includes intermediate dynamics as observed in experimental work. A model for particle degradation including intermediate dynamics, bacterial growth and endogenous respiration is proposed. Particle hydrolysis was modelled using the particle breakup model. Depolymerisation products were separated into five different size groups: colloids; high, medium and low molecular weight (HMW, MMW and LMW) polymers; and one fraction for oligomers and monomers (SB). Depolymerisation of colloids, HMW and MMW polymers was modelled using first order kinetics. LMW polymer degradation was modelled using Michaelis-Menten kinetics, while growth was based on traditional Monod kinetics and endogenous respiration followed ASM3. The proposed model was implemented in AQUASIM for a batch reactor system, and parameter estimation by LSE fitting to experimental data on particulate starch degradation over 117 days in a dispersed biomass microcosm was performed. Validation of the model against experimental data gave a very good fit to the PBM. The intermediate dynamics seen in the experimental data was also qualitatively demonstrated by the model, with accumulation of HMW, MMW and LMW polymers in the bulk liquid. However, the accumulation of monomers and oligomers in the bulk liquid could not be reproduced in the suspended growth model proposed. Hence, a structured biomass model (biofilm) is suggested for future work.
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Go¨tzen, Reiner. "Freedom of Micro Manufacturing Tool-Free Series Production in Industrial Applications of Micro- and Nanotechnology." In ASME 2008 9th Biennial Conference on Engineering Systems Design and Analysis. ASMEDC, 2008. http://dx.doi.org/10.1115/esda2008-59501.
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RMPD®, which stands for Rapid Micro Product Development, is a family of technologies designed to generate with a parallel batch process, microstructures, microsystems and/or MEMS or MOEMS in a parallel batch process. Photo polymerized monomer, oligomere and hybrismaterial (sol-gel) polymerized with uv-light and generate the system. The technology’s 3D-CSP (tree dimensional chip sice packaging), RMPD®-multimat (volume specific material propertys), RMPD®-stick2 (mechanical parts directly to a foil, wafer and so on) and RMPD®-nanoface (surface roughness in sub-nm range) have since 1996 been key elements in this worldwide-patented family of technologies, which has allowed System in Packing SiP to develop into a virtually tool-free production process. Additive and parallel processes give these technologies a costefficient and customer oriented strategic direction.
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Özler, Berk, Saadet Güler, Ahmet Yavaş, and Serdar Yıldırım. "Photocatalytic Performance of 3D Printed Polymer Composites: Effect of Matrix Material." In 7th International Students Science Congress. Izmir International guest Students Association, 2023. http://dx.doi.org/10.52460/issc.2023.046.
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Additive manufacturing has started to be used in many sectors today (e.g. aerospace, dentistry, biomaterials, drug industry) and is still a developing material production method. Three-dimensional (3D) printers are the main devices used in this method, which enables production without the need for molds. These 3D printers are divided into mechanical, electrical and photochemical types. Photosensitive resins are used for production in photochemical three-dimensional printers. These resins contain monomer, oligomer, photoinitiator and optionally filler material. The change of monomer, oligomer, and filler materials in the structure also affects various characteristics of the obtained polymer including mechanical, electrical, magnetic, and photochemical roperties. To the extent of our literature review, it has been determined that there are not enough studies on the effect of the change in the matrix material of the polymer matrix composite materials produced with 3D printers on the photocatalytic performance. With this motivation, in this study, the photocatalytic performance of composite samples obtained by the incorporation of nano-sized TiO2 particles(1.5 wt.%) into two different acrylate-based resin mixtures was compared. Bisphenol-A glycidyl dimethacrylate (bis-GMA) and urethane dimethacrylate (UDMA) based monomers were used as matrix material, and triethylene glycol dimethacrylate (TEGDMA) was used as the diluent. TiO2 nanoparticles and photoinitiator were added into the prepared mixtures and mixed in a magnetic stirrer until a homogeneous mixture was obtained. Then, polymer samples were obtained by printing the resins with a 3D printer in 20x35x3 mm dimensions. The photocatalytic activity of the obtained polymers under visible light irradiation was tested. Experimental results revealed that even a small amount of TiO2 is effective in imparting photocatalytic activity to the structure, and besides, the effect of bis-GMA-based matrix material on photocatalytic performance is more pronounced than that of UDMA-based matrix material.
10
Özler, Berk, Saadet Güler, Ahmet Yavaş, and Serdar Yıldırım. "Photocatalytic Performance of 3D Printed Polymer Composites: Effect of Matrix Material." In 7th International Students Science Congress. Izmir International guest Students Association, 2023. http://dx.doi.org/10.52460/issc.2023.046.
Full textAbstract:
Additive manufacturing has started to be used in many sectors today (e.g. aerospace, dentistry, biomaterials, drug industry) and is still a developing material production method. Three-dimensional (3D) printers are the main devices used in this method, which enables production without the need for molds. These 3D printers are divided into mechanical, electrical and photochemical types. Photosensitive resins are used for production in photochemical three-dimensional printers. These resins contain monomer, oligomer, photoinitiator and optionally filler material. The change of monomer, oligomer, and filler materials in the structure also affects various characteristics of the obtained polymer including mechanical, electrical, magnetic, and photochemical roperties. To the extent of our literature review, it has been determined that there are not enough studies on the effect of the change in the matrix material of the polymer matrix composite materials produced with 3D printers on the photocatalytic performance. With this motivation, in this study, the photocatalytic performance of composite samples obtained by the incorporation of nano-sized TiO2 particles(1.5 wt.%) into two different acrylate-based resin mixtures was compared. Bisphenol-A glycidyl dimethacrylate (bis-GMA) and urethane dimethacrylate (UDMA) based monomers were used as matrix material, and triethylene glycol dimethacrylate (TEGDMA) was used as the diluent. TiO2 nanoparticles and photoinitiator were added into the prepared mixtures and mixed in a magnetic stirrer until a homogeneous mixture was obtained. Then, polymer samples were obtained by printing the resins with a 3D printer in 20x35x3 mm dimensions. The photocatalytic activity of the obtained polymers under visible light irradiation was tested. Experimental results revealed that even a small amount of TiO2 is effective in imparting photocatalytic activity to the structure, and besides, the effect of bis-GMA-based matrix material on photocatalytic performance is more pronounced than that of UDMA-based matrix material.