Journal articles: 'Domain Studies'

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Dix, Samuel R., Ruyue Sun, Matthew J. Harris, Sarah L. Batters, Svetlana E. Sedelnikova, Patrick J. Baker, Mark S. Thomas, and David W. Rice. "TssA from Aeromonas hydrophila: expression, purification and crystallographic studies." Acta Crystallographica Section F Structural Biology Communications 74, no. 9 (September 1, 2018): 578–82. http://dx.doi.org/10.1107/s2053230x18010439.

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TssA is a core subunit of the type VI secretion system, which is a major player in interspecies competition in Gram-negative bacteria. Previous studies on enteroaggregative Escherichia coli TssA suggested that it is comprised of three putative domains: a conserved N-terminal domain, a middle domain and a ring-forming C-terminal domain. X-ray studies of the latter two domains have identified their respective structures. Here, the results of the expression and purification of full-length and domain constructs of TssA from Aeromonas hydrophila are reported, resulting in diffraction-quality crystals for the middle domain (Nt2) and a construct including the middle and C-terminal domains (Nt2-CTD).

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Sherman, Michael B., Alexis N. Williams, Hong Q. Smith, B. Montgomery Pettitt, Christiane E. Wobus, and Thomas J. Smith. "Structural Studies on the Shapeshifting Murine Norovirus." Viruses 13, no. 11 (October 26, 2021): 2162. http://dx.doi.org/10.3390/v13112162.

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Noroviruses are responsible for almost a fifth of all cases of gastroenteritis worldwide. The calicivirus capsid is composed of 180 copies of VP1 with a molecular weight of ~58 kDa. This coat protein is divided into the N-terminus (N), the shell (S) and C-terminal protruding (P) domains. The S domain forms a shell around the viral RNA genome, while the P domains dimerize to form protrusions on the capsid surface. The P domain is subdivided into P1 and P2 subdomains, with the latter containing the binding sites for cellular receptors and neutralizing antibodies. Reviewed here are studies on murine norovirus (MNV) showing that the capsid responds to several physiologically relevant cues; bile, pH, Mg2+, and Ca2+. In the initial site of infection, the intestinal tract, high bile and metal concentrations and low pH cause two significant conformational changes: (1) the P domain contracts onto the shell domain and (2) several conformational changes within the P domain lead to enhanced receptor binding while blocking antibody neutralization. In contrast, the pH is neutral, and the concentrations of bile and metals are low in the serum. Under these conditions, the loops at the tip of the P domain are in the open conformation with the P domain floating on a linker or tether above the shell. This conformational state favors antibody binding but reduces interactions with the receptor. In this way, MNV uses metabolites and environmental cues in the intestine to optimize cellular attachment and escape antibody binding but presents a wholly different structure to the immune system in the serum. To our knowledge, this is the first example of a virus shapeshifting in this manner to escape the immune response.

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Barité, Mario, and Mirtha Rauch. "Terminological studies as domain analysis." Brazilian Journal of Information Science: research trends 16 (April 5, 2022): e02140. http://dx.doi.org/10.36311/1981-1640.2022.v16.e02140.

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This paper aims to thoroughly analyze terminological studies as a particular modality of domain analysis (DA). To this end, we establish the following methodological sequence: i) a broad description of the field of terminology, with emphasis on a general characterization of the theoretical currents and the two traditional types of research: systematic research and punctual research; ii) review of the background information on the theoretical and methodological intersection between terminology and knowledge organization (KO); iii) the problematization of terminological studies seen as DA, based on the study of background information and a series of trigger questions. The answers to these questions will allow us to progress in their understanding. The results show the need to further define the profile of terminological studies to use them in KO better. They also suggest considering terminological studies as a separate DA category, specifically in relation to language for special purposes (LSP) and discourse analysis. Finally, the preliminary conclusions will guide future research in the field. In particular, we stress that terminological research methods seem not to be sufficiently recognized as suitable for application in KO.

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Hutchings, J. B. "Time-Domain Studies with Astrosat." Proceedings of the International Astronomical Union 14, S339 (November 2017): 117–20. http://dx.doi.org/10.1017/s1743921318002351.

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AbstractAstrosat is a multi-instrument orbiting observatory that was launched in 2015 by the Indian Space Research Organization (ISRO). The same field of view is observed simultaneously at wavelengths ranging from gamma ray to the optical blue. This talk described the observatory’s performance, with emphasis on time-domain studies, and gave examples of results.

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Ponomarev, D. M., A. V. Goryachev, V. N. Zhavoronkov, and S. V. Goryunova. "Experimental time-domain antenna studies." Radiophysics and Quantum Electronics 30, no. 8 (August 1987): 763–67. http://dx.doi.org/10.1007/bf01083488.

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Lee, C. H. "Time-domain studies of M31." Astronomical Review 12, no. 1-4 (October 2016): 1–23. http://dx.doi.org/10.1080/21672857.2016.1270028.

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Patel, S. D., and C. I. Ragan. "Structural studies on mitochondrial NADH dehydrogenase using chemical cross-linking." Biochemical Journal 256, no. 2 (December 1, 1988): 521–28. http://dx.doi.org/10.1042/bj2560521.

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The structure of bovine heart mitochondrial NADH dehydrogenase was investigated by cross-linking constituent subunits with disuccinimidyl tartrate, (ethylene glycol)yl bis(succinimidyl succinate) and dimethyl suberimidate. Cross-linked products were identified by Western blotting with monospecific antisera to nine subunits of the enzyme. Cross-links between subunits within the flavoprotein, iron-protein and hydrophobic domains of the enzyme were identified. Cross-linking between the 75 kDa iron-protein-domain subunit and the 51 kDa flavoprotein-domain subunit was modulated by the substrate NADH. Cross-linking of subunits of the iron-protein and flavoprotein domains to constituents of the hydrophobic domain was also found. This was further substantiated by photolabelling subunits of the latter region, which were in contact with the membrane lipid, with 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine. One such subunit of Mr 19,000 could be cross-linked to components of the iron-protein domain.

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Du, Jiangfeng, Kanin Wichapong, Tilman M. Hackeng, and Gerry A. F. Nicolaes. "Molecular simulation studies of human coagulation factor VIII C domain-mediated membrane binding." Thrombosis and Haemostasis 113, no. 02 (March 2015): 373–84. http://dx.doi.org/10.1160/th14-02-0180.

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SummaryThe C-terminal C domains of activated coagulation factor VIII (FVIIIa) are essential to membrane binding of this crucial coagulation cofactor protein. To provide an overall membrane binding mechanism for FVIII, we performed simulations of membrane binding through coarsegrained molecular dynamics simulations of the C1 and C2 domain, and the combined C-domains (C1+C2). We found that the C1 and C2 domain have different membrane binding properties. The C1 domain uses hydrophobic spikes 3 and 4, of its total of four spikes, as major loops to bind the membrane, whereas all four of its hydrophobic loops of the C2 domain appear essential for membrane binding. Interestingly, in the C1+C2 system, we observed cooperative binding of the C1 and C2 domains such that all four C2 domain spikes bound first, after which all four loops of the C1 domain inserted into the membrane, while the net binding energy was higher than that of the sum of the isolated C domains. Several residues, mutations of which are known to cause haemophilia A, were identified as key residues for membrane binding. In addition to these known residues, we identified residues from the C1 and C2 domains, which are involved in the membrane binding process, that have not been reported before as a cause for haemophilia A, but which contribute to overall membrane binding and which are likely candidates for novel causative missense mutations in haemophilia A.

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Inoue, T., and K. Goto. "Studies of Single-Domain Particles of Sm2Co17 by Domain Observation." IEEE Translation Journal on Magnetics in Japan 1, no. 8 (November 1985): 992–93. http://dx.doi.org/10.1109/tjmj.1985.4549044.

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Feke, Ann, Morgan Vanderwall, Wei Liu, and Joshua M. Gendron. "Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function." PLOS ONE 16, no. 3 (March 17, 2021): e0235938. http://dx.doi.org/10.1371/journal.pone.0235938.

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The small LOV/F-box/Kelch family of E3 ubiquitin ligases plays an essential role in the regulation of plant circadian clocks and flowering time by sensing dusk. The family consists of three members, ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX PROTEIN 1 (FKF1), which share a unique protein domain architecture allowing them to act as photoreceptors that transduce light signals via altering stability of target proteins. Despite intensive study of this protein family we still lack important knowledge about the biochemical and functional roles of the protein domains that comprise these unique photoreceptors. Here, we perform comparative analyses of transgenic lines constitutively expressing the photoreceptor LOV domain or the Kelch repeat protein-protein interaction domains of ZTL, FKF1, and LKP2. Expression of each domain alone is sufficient to disrupt circadian rhythms and flowering time, but each domain differs in the magnitude of effect. Immunoprecipitation followed by mass spectrometry with the ZTL Kelch repeat domain identified a suite of potential interacting partners. Furthermore, the ZTL Kelch repeat domain can interact with the ZTL homologs, LKP2 and FKF1, and the LOV domain of ZTL itself. This suggests a hypothesis that the Kelch repeat domain of ZTL may mediate inter- and intra-molecular interactions of the three LOV/F-box/Kelch proteins and provides added insight into the composition of the protein complexes and an additional role for the Kelch repeat domain.

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Peek, James, and Dinesh Christendat. "Structural studies on dehydroshikimate dehydratase." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C475. http://dx.doi.org/10.1107/s2053273314095242.

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The soil bacterium, Pseudomonas putida, is capable of using the alicyclic compound quinate as a sole carbon source. During this process, quinate is converted to 3-dehydroshikimate, which subsequently undergoes a dehydration to form protocatechuate. The latter transformation is performed by the enzyme dehydroshikimate dehydratase (DSD). We have recombinantly produced DSD from P. putida and are currently performing x-ray crystallographic studies on the enzyme to gain structural insight into its catalytic mechanism and mode of substrate recognition. Initial crystals of DSD diffracted to 2.7 Ä resolution, but exhibited strong twinning. A redesigned construct has recently yielded crystals that diffract to similar resolution, but with a significantly reduced tendency toward twinning. Interestingly, sequence analysis of P. putida DSD reveals that the protein is in fact a fusion of two distinct domains: an N-terminal sugar phosphate isomerase-like domain associated with DSD activity, and a C-terminal hydroxyphenylpyruvate dioxygenase (HPPD)-like domain with unknown functional significance. Structural characterization of the protein may provide novel insight into the functional relevance of the unusual HPPD-like domain.

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Liljas, Anders, Arnthor Ævarsson, Salam Al-Karadaghi, Maria Garber, Julia Zheltonosova, and Evgeni Brazhnikov. "Crystallographic studies of elongation factor G." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 1995): 1209–16. http://dx.doi.org/10.1139/o95-130.

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The elongation factors G (EF-G) and Tu (EF-Tu) go through a number of conformation states in their functional cycles. Since they both are GTPases, have similar G domains and domains II, and have similar interactions with the nucleotides, then GTP hydrolysis must occur in similar ways. The crystal structures of two conformational states are known for EF-G and three are known for EF-Tu. The conformations of EF-G∙GDP and EF-Tu∙GTP are closely related. EF-Tu goes through a large conformational change upon GTP cleavage. This conformational change is to a large extent due to an altered interaction between the G domain and domains II and III. A number of kirromycin-resistant mutations are situated at the interface between domains I and III. The interface between the G domain and domain V in EF-G corresponds with this dynamic interface in EF-Tu. The contact area in EF-G is small and dominated by interactions between charged amino acids, which are part of a system that is observed to undergo conformational changes. Furthermore, a number of fusidic acid resistant mutants have been identified in this area. All of this evidence makes it likely that EF-G undergoes a large conformational change in its functional cycle. If the structures and conformational states of the elongation factors are related to a scheme in which the ribosome oscillates between two conformations, the pretranslocational and posttranslocational states, a model is arrived at in which EF-Tu drives the reaction in one direction and EF-G in the opposite. This may lead to the consequence that the GTP state of one factor is similar to the GDP state of the other. At the GTP hydrolysis state, the structures of the factors will be close to superimposable.Key words: elongation factor G, elongation factor Tu, crystal structures, conformational changes, ribosomal conformation.

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Amin, Nader T., A. Katrine Wallis, Stephen A. Wells, Michelle L. Rowe, Richard A. Williamson, Mark J. Howard, and Robert B. Freedman. "High-resolution NMR studies of structure and dynamics of human ERp27 indicate extensive interdomain flexibility." Biochemical Journal 450, no. 2 (February 15, 2013): 321–32. http://dx.doi.org/10.1042/bj20121635.

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ERp27 (endoplasmic reticulum protein 27.7 kDa) is a homologue of PDI (protein disulfide-isomerase) localized to the endoplasmic reticulum. ERp27 is predicted to consist of two thioredoxin-fold domains homologous with the non-catalytic b and b′ domains of PDI. The structure in solution of the N-terminal b-like domain of ERp27 was solved using high-resolution NMR data. The structure confirms that it has the thioredoxin fold and that ERp27 is a member of the PDI family. 15N-NMR relaxation data were obtained and ModelFree analysis highlighted limited exchange contributions and slow internal motions, and indicated that the domain has an average order parameter S2 of 0.79. Comparison of the single-domain structure determined in the present study with the equivalent domain within full-length ERp27, determined independently by X-ray diffraction, indicated very close agreement. The domain interface inferred from NMR data in solution was much more extensive than that observed in the X-ray structure, suggesting that the domains flex independently and that crystallization selects one specific interdomain orientation. This led us to apply a new rapid method to simulate the flexibility of the full-length protein, establishing that the domains show considerable freedom to flex (tilt and twist) about the interdomain linker, consistent with the NMR data.

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Cavet, M., CM Tse, S. Akhter, C. Yun, and M. Donowitz. "Structure-function studies of membrane domain-cytoplasmic domain and membrane domain-membrane doman chimeras of Na+/H+ exchanger isoforms NHE1 and NHE3." Gastroenterology 114 (April 1998): A357. http://dx.doi.org/10.1016/s0016-5085(98)81447-9.

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Kolade, O. O., P. Bellini, M. Wexler, A. W. B. Johnston, J. G. Grossmann, and A. M. Hemmings. "Structural studies of the Fur protein from Rhizobium leguminosarum." Biochemical Society Transactions 30, no. 4 (August 1, 2002): 771–74. http://dx.doi.org/10.1042/bst0300771.

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The X-ray crystal structure of the apo-form of the Fur protein from Rhizobium leguminosarum has been solved at 2.7 å resolution. Small-angle X-ray scattering was used to give information on the solution conformation of the protein. The Fur homodimer folds into two domains. The N-terminal domain is formed from the packing of two helix-turn-helix motifs while the C-terminal domain appears primarily to stabilize the dimeric state of the protein.

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Yamamoto, R., Y. Ueda, H. Yamamoto, A. Kikuchi, N. Shibata, and Y. Higuchi. "Crystallographic studies of Axin-DIX domain." Seibutsu Butsuri 43, supplement (2003): S37. http://dx.doi.org/10.2142/biophys.43.s37_4.

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Cheville, R. A., and D. Grischkowsky. "Time domain terahertz impulse ranging studies." Applied Physics Letters 67, no. 14 (October 2, 1995): 1960–62. http://dx.doi.org/10.1063/1.114579.

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Papathanassiou, A. N., J. Grammatikakis, and N. G. Bogris. "Frequency-domain dielectric studies in LiF:Ca2+." Physical Review B 49, no. 20 (May 15, 1994): 14160–64. http://dx.doi.org/10.1103/physrevb.49.14160.

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Nagaraja, H. S., K. K. Nagaraja, F. Rossignol, F. Dumas-Bouchiat, C. Champeaux, and A. Catherinot. "Magnetic Domain Studies of Cobalt Nanostructures." Journal of Superconductivity and Novel Magnetism 25, no. 6 (March 28, 2012): 1901–6. http://dx.doi.org/10.1007/s10948-012-1508-2.

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YUZAWA, MASAMICHI. "From Design Studies for Domain-Specific Conceptual Changes Back to Studies Dealing with Domain-General Skills :." Annual Report of Educational Psychology in Japan 53 (2014): 166–79. http://dx.doi.org/10.5926/arepj.53.166.

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Darch, Peter T., and Christine L. Borgman. "Ship space to database: emerging infrastructures for studies of the deep subseafloor biosphere." PeerJ Computer Science 2 (November 14, 2016): e97. http://dx.doi.org/10.7717/peerj-cs.97.

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BackgroundAn increasing array of scientific fields face a “data deluge.” However, in many fields data are scarce, with implications for their epistemic status and ability to command funding. Consequently, they often attempt to develop infrastructure for data production, management, curation, and circulation. A component of a knowledge infrastructure may serve one or more scientific domains. Further, a single domain may rely upon multiple infrastructures simultaneously. Studying how domains negotiate building and accessing scarce infrastructural resources that they share with other domains will shed light on how knowledge infrastructures shape science.MethodsWe conducted an eighteen-month, qualitative study of scientists studying the deep subseafloor biosphere, focusing on the Center for Dark Energy Biosphere Investigations (C-DEBI) and the Integrated Ocean Drilling Program (IODP) and its successor, the International Ocean Discovery Program (IODP2). Our methods comprised ethnographic observation, including eight months embedded in a laboratory, interviews (n = 49), and document analysis.ResultsDeep subseafloor biosphere research is an emergent domain. We identified two reasons for the domain’s concern with data scarcity: limited ability to pursue their research objectives, and the epistemic status of their research. Domain researchers adopted complementary strategies to acquire more data. One was to establish C-DEBI as an infrastructure solely for their domain. The second was to use C-DEBI as a means to gain greater access to, and reconfigure, IODP/IODP2 to their advantage. IODP/IODP2 functions as infrastructure for multiple scientific domains, which creates competition for resources. C-DEBI is building its own data management infrastructure, both to acquire more data from IODP and to make better use of data, once acquired.DiscussionTwo themes emerge. One is data scarcity, which can be understood only in relation to a domain’s objectives. To justify support for public funding, domains must demonstrate their utility to questions of societal concern or existential questions about humanity. The deep subseafloor biosphere domain aspires to address these questions in a more statistically intensive manner than is afforded by the data to which it currently has access. The second theme is the politics of knowledge infrastructures. A single scientific domain may build infrastructure for itself and negotiate access to multi-domain infrastructure simultaneously. C-DEBI infrastructure was designed both as a response to scarce IODP/IODP2 resources, and to configure the data allocation processes of IODP/IODP2 in their favor.

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Snyder, Greg, Jiansheng Jiang, Kang Chen, Theresa Fresquez, Patrick Smith, Nathaniel Snyder, Timothy Luchetti, et al. "Structural studies of Toll like receptor signaling adaptors. (136.45)." Journal of Immunology 184, no. 1_Supplement (April 1, 2010): 136.45. http://dx.doi.org/10.4049/jimmunol.184.supp.136.45.

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Abstract Signaling downstream of the Toll like receptors (TLRs) involves Toll-IL-1R homology (TIR) domains as well as recruitment of critical signaling adaptors MyD88 and TIRAP/Mal. Studies in human patients, dominant negative mutants and knockout mice have shown that mutations in Arg196, the BB loop, DD loop, “Poc” site Ile179 are critical for MyD88 TIR domain signaling and appropriate responses to pathogen stimuli. We previously reported the structure of MyD88 TIR domain that showed a unique conformation for its BB loop, as well as a crystallographic lattice that reveals interactions between the BB-DD and BB-EE loops. We now report additional crystal forms which retain BB-DD and BB-EE interactions as well as extend the resolution to 1.4 Å. A yeast two-hybrid analysis of the domain interface residues observed from the crystal structure lattice shows that key residues including the human Arg196Cys mutation are critically important for homotypic TIR domain binding. Additionally, we report NMR solution studies showing binding between MyD88 and bacterial TIR domain protein TcpC, which has been demonstrated to negatively regulate MyD88-dependent TLR adaptor signaling. Finally, we report the X-ray structure of a second critical TIR adaptor protein, TIRAP/Mal. We observe key residues and loops important for TIRAP/Mal adaptor function. Structural insights from these studies may aid our understanding of the molecular mechanisms by which TLRs and TIR domain adaptors interact and signal.

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Chandran, Anu V., J. Rajan Prabu, G. P. Manjunath, K. Neelakanteshwar Patil, K. Muniyappa, and M. Vijayan. "Crystallization and preliminary X-ray studies of the C-terminal domain ofMycobacterium tuberculosisLexA." Acta Crystallographica Section F Structural Biology and Crystallization Communications 66, no. 9 (August 28, 2010): 1093–95. http://dx.doi.org/10.1107/s174430911003068x.

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The C-terminal domain ofMycobacterium tuberculosisLexA has been crystallized in two different forms. The form 1 and form 2 crystals belonged to space groupsP3121 andP31, respectively. Form 1 contains one domain in the asymmetric unit, while form 2 contains six crystallographically independent domains. The structures have been solved by molecular replacement.

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Jacobsson, Mattias, and Anders Söderholm. "Project Studies Beyond the Straitjacket: An Escape Artist’s Manual." Project Management Journal 51, no. 4 (June 16, 2020): 411–19. http://dx.doi.org/10.1177/8756972820929916.

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This article provides insights into ways in which project studies can be extended to make further impact on and contributions to other research domains, including more general management and organization studies. Inspired by literature on the phenomenology of science, publication practices, logics of research communities, and theory building, we analyze some examples of project studies that reach beyond the project domain. Based on this analysis, we present an “escape artist’s manual” consisting of strategies and practices for how researchers could think about and design project studies to enable contributions beyond the home domain.

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Pigott, R., L. A. Needham, R. M. Edwards, C. Walker, and C. Power. "Structural and functional studies of the endothelial activation antigen endothelial leucocyte adhesion molecule-1 using a panel of monoclonal antibodies." Journal of Immunology 147, no. 1 (July 1, 1991): 130–35. http://dx.doi.org/10.4049/jimmunol.147.1.130.

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Abstract We have produced a panel of mAb to the endothelial activation Ag endothelial leucocyte adhesion molecule-1 (ELAM-1), using both a conventional immunization protocol and one involving immunosuppression. By constructing ELAM-1 mutants we have demonstrated that seven of these antibodies recognize epitopes within the lectin domain of ELAM-1 and that one binds within the complement regulatory protein domains. These studies also suggest that the EGF-like domain is important in maintaining the conformation of the neighbouring lectin domain. In functional studies, U937 cells bound to Cos cells expressing either ELAM-1 or ELAM-1 with the complement regulatory protein domains deleted. No adhesion was observed to Cos cells expressing ELAM-1 mutants lacking either the lectin or EGF-like domains. The fact that antibodies directed against the lectin domain can inhibit adhesion suggest that this domain is directly involved in cell binding.

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Li, J., G. I. Lee, S. R. Van Doren, and J. C. Walker. "The FHA domain mediates phosphoprotein interactions." Journal of Cell Science 113, no. 23 (December 1, 2000): 4143–49. http://dx.doi.org/10.1242/jcs.113.23.4143.

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The forkhead-associated (FHA) domain is a phosphopeptide-binding domain first identified in a group of forkhead transcription factors but is present in a wide variety of proteins from both prokaryotes and eukaryotes. In yeast and human, many proteins containing an FHA domain are found in the nucleus and involved in DNA repair, cell cycle arrest, or pre-mRNA processing. In plants, the FHA domain is part of a protein that is localized to the plasma membrane and participates in the regulation of receptor-like protein kinase signaling pathways. Recent studies show that a functional FHA domain consists of 120–140 amino acid residues, which is significantly larger than the sequence motif first described. Although FHA domains do not exhibit extensive sequence similarity, they share similar secondary and tertiary structures, featuring a sandwich of two anti-parallel (beta)-sheets. One intriguing finding is that FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine, distinguishing them from other well-studied phosphoprotein-binding domains. The diversity of proteins containing FHA domains and potential differences in binding specificities suggest the FHA domain is involved in coordinating diverse cellular processes.

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Gill, David J., Hsiangling Teo, Ji Sun, Olga Perisic, Dmitry B. Veprintsev, Yvonne Vallis, Scott D. Emr, and Roger L. Williams. "Structural studies of phosphoinositide 3-kinase-dependent traffic to multivesicular bodies." Biochemical Society Symposia 74 (January 12, 2007): 47–57. http://dx.doi.org/10.1042/bss2007c05.

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Three large protein complexes known as ESCRT I, ESCRT II and ESCRT III drive the progression of ubiquitinated membrane cargo from early endosomes to lysosomes. Several steps in this process critically depend on PtdIns3P, the product of the class III phosphoinositide 3-kinase. Our work has provided insights into the architecture, membrane recruitment and functional interactions of the ESCRT machinery. The fan-shaped ESCRT I core and the trilobal ESCRT II core are essential to forming stable, rigid scaffolds that support additional, flexibly-linked domains, which serve as gripping tools for recognizing elements of the MVB (multivesicular body) pathway: cargo protein, membranes and other MVB proteins. With these additional (non-core) domains, ESCRT I grasps monoubiquitinated membrane proteins and the Vps36 subunit of the downstream ESCRT II complex. The GLUE (GRAM-like, ubiquitin-binding on Eap45) domain extending beyond the core of the ESCRT II complex recognizes PtdIns3P-containing membranes, monoubiquitinated cargo and ESCRT I. The structure of this GLUE domain demonstrates that it has a split PH (pleckstrin homology) domain fold, with a non-typical phosphoinositide-binding pocket. Mutations in the lipid-binding pocket of the ESCRT II GLUE domain cause a strong defect in vacuolar protein sorting in yeast.

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Stockman, Caroline, and Fred Truyen. "Cultural Studies as Performative Research in a Digital Age." European Review 22, no. 2 (May 2014): 309–20. http://dx.doi.org/10.1017/s1062798714000131.

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This paper aims to explore the nature of digital culture research, and the fitting methodology. Although it is still felt to be a novelty, it is not so different from the more general domain of Cultural Studies. The aim of research for both domains is meaning, or the challenge to understand the dynamics of the encoding and decoding process. Both domains endorse a wide variety of subjects, although typically the concrete methodology of Cultural Studies still remains restricted to qualitative approaches. The question of quantitative data and their analysis is highlighted in digital culture, and we should consider both its opportunities and limitations for the research at hand. In our reflection, Cultural Studies research emerges as a performative enterprise, and this is one of its unique distinctions as a research domain.

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Crawford, C., N. R. Brown, and A. C. Willis. "Studies of the active site of m-calpain and the interaction with calpastatin." Biochemical Journal 296, no. 1 (November 15, 1993): 135–42. http://dx.doi.org/10.1042/bj2960135.

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Calpain autolyses in the presence of Ca2+. In the case of m-calpain (80 + 30 kDa) the first product is an 80 + 18 kDa species which has an intact large subunit and the C-terminal Ca(2+)-binding domain of the small subunit. It was possible to bind E64 into the active site of calpain in the presence of Ca2+ before cleavage of either calpain subunit. This suggests that the active site is functional before any autolysis has occurred and that calpain is not a proenzyme. Prolonged autolysis generates several fragments including a 42 kDa active-site domain fragment that showed no proteolytic activity and Ca(2+)-binding domain fragments. Some of the Ca(2+)-binding domain fragments were found to exist as heterodimers (23 + 18 kDa and 22 + 18 kDa), with the Ca(2+)-binding domain of the large subunit interacting with the Ca(2+)-binding domain of the small subunit. These species were true heterodimers, as they showed co-elution of the two Ca(2+)-binding domains on ion-exchange and gel-filtration chromatography, and immunoprecipitation of both polypeptides with an antiserum specific for the small-subunit Ca(2+)-binding domain. The generation of the dimer species after only 15 min autolysis suggests that the interaction between the Ca(2+)-binding domains is present in the native calpain structure. The interaction of calpain with calpastatin was investigated using an assay based on binding to calpastatin-Sepharose and a competitive binding assay. Calpain, active-site-blocked calpain and calpain fragments generated by autolysis were studied. Calpain bound to calpastatin in the presence of Ca2+; however, the isolated active-site-containing 80 kDa large subunit (proteolytically inactive), a 42 kDa active-site-containing fragment (proteolytically inactive) and Ca(2+)-binding domain fragments of calpain did not. Active-site-blocked calpain bound to calpastatin, but with an affinity reduced by approximately two orders of magnitude when compared with native calpain.

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Schorb, J. "MASTERS OF THEIR DOMAIN." GLQ: A Journal of Lesbian and Gay Studies 15, no. 3 (January 1, 2009): 516–18. http://dx.doi.org/10.1215/10642684-2008-036.

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Aluru, Chaitanya, and Mona Singh. "Improved inference of tandem domain duplications." Bioinformatics 37, Supplement_1 (July 1, 2021): i133—i141. http://dx.doi.org/10.1093/bioinformatics/btab329.

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Abstract Motivation Protein domain duplications are a major contributor to the functional diversification of protein families. These duplications can occur one at a time through single domain duplications, or as tandem duplications where several consecutive domains are duplicated together as part of a single evolutionary event. Existing methods for inferring domain-level evolutionary events are based on reconciling domain trees with gene trees. While some formulations consider multiple domain duplications, they do not explicitly model tandem duplications; this leads to inaccurate inference of which domains duplicated together over the course of evolution. Results Here, we introduce a reconciliation-based framework that considers the relative positions of domains within extant sequences. We use this information to uncover tandem domain duplications within the evolutionary history of these genes. We devise an integer linear programming approach that solves our problem exactly, and a heuristic approach that works well in practice. We perform extensive simulation studies to demonstrate that our approaches can accurately uncover single and tandem domain duplications, and additionally test our approach on a well-studied orthogroup where lineage-specific domain expansions exhibit varying and complex domain duplication patterns. Availability and implementation Code is available on github at https://github.com/Singh-Lab/TandemDuplications. Supplementary information Supplementary data are available at Bioinformatics online.

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Zhou, Jia, Bin He, Yaoyu He, Wei Huang, Hongxu Zhu, Mengmeng Zhang, and Yuhuan Wang. "Measurement properties of family resilience assessment questionnaires: a systematic review." Family Practice 37, no. 5 (April 9, 2020): 581–91. http://dx.doi.org/10.1093/fampra/cmaa027.

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Abstract Background There have been numerous measurement questionnaires to estimate the level of family resilience. However, we lack published evidence regarding the most appropriate family resilience questionnaire in different adversity domains. Objective This study critically assesses and contrasts the measurement properties of questionnaires measuring family resilience in two domains: health care domain and social domain. Methods Ten electronic databases were searched for studies concerning the establishment, adaptation or evaluation of the measurement properties of a family resilience assessment questionnaire. The methodological quality of included studies was assessed using the COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) checklist. On the basis of methodological quality and scoring criteria for the quality of questionnaires, the overall evidence of each questionnaire was rated. Results A total of 4084 initial studies were obtained, 23 of which met our inclusion criteria assessing 12 different questionnaires. The structural validity (23 studies) and internal consistency (22 studies) were the most frequently used measurement properties. Only two studies tested responsiveness, and the measurement error was not examined in any studies. The Family Resilience Assessment Scale (FRAS) and Italian version of the Walsh Family Resilience Questionnaire (Walsh-IT) showed positive evidence in health care domain. The FRAS performed well in social domain with specific adversity, and the Family Resilience Questionnaire (FRQ) received a good score in social domain without specific adversity. Conclusion For health care domain, we recommend the FRAS and Walsh-IT. For social domain with specific adversity, we recommend the FRAS questionnaire. For social domain without specific adversity, the FRQ is recommended.

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Wong, Kathy, Yinglu Zhang, Guennadi Kozlov, and Kalle Gehring. "Structural studies of Legionella effectors." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C583. http://dx.doi.org/10.1107/s2053273314094169.

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Legionella pneumophila is a gram-negative bacterium that causes Legionnaires' disease. It uses a Dot/Icm type IV secretion system to inject effector proteins into the host cell to manipulate host processes. Currently, about 300 Icm/Dot dependent effectors of L.pneumophila have been identified. Lpg1496 is an effector protein, which contains a conserved domain from the SidE family. To date, the middle domain and the conserved SidE domain have been crystallized and the structure solved at a resolution of 1.15Å and 2.3Å, respectively. A structural homology search using the middle domain suggested a similarity to phosphoribosylaminoimidazolesuccinocarboxamide (SAICAR) synthase, an ATPase involved in purine nucleotide synthesis. We performed 1H–15N HSQC NMR titrations to show that this domain binds ATP, ADP and AMP, with the highest binding affinity for ADP. A structural homology search using the SidE domain showed a similarity to cyclic nucleotide phosphodiesterases. To further elucidate the function of lpg1496, other fragments have been cloned, expressed, and subjected to crystallization trials. Currently, we have successfully crystallized the N-terminal domain, with crystals diffracting to <2.0Å. Obtaining the crystal structure of lpg1496 and revealing its function will not only lead to a better understanding of the virulence of L. pneumophila, but also contribute to the development of novel therapeutic treatments of Legionnaires' disease.

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Van de Wiele, Ben, Arne Vansteenkiste, Bartel Van Waeyenberge, Luc Dupré, and Daniel De Zutter. "A 2.5D micromagnetic modeling approach for magnetic domain and domain wall studies." International Journal of Numerical Modelling: Electronic Networks, Devices and Fields 27, no. 3 (November 28, 2013): 450–60. http://dx.doi.org/10.1002/jnm.1953.

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Wells, C., K. E. Warriner, and C. R. Bagshaw. "Fluorescence studies on the nucleotide- and Ca2+-binding domains of molluscan myosin." Biochemical Journal 231, no. 1 (October 1, 1985): 31–38. http://dx.doi.org/10.1042/bj2310031.

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The effects of nucleotides and Ca2+ on the intrinsic tryptophan fluorescence of molluscan myosin and its proteolytic fragments were studied. By using these proteins from the scallop, Pecten maximus, the existence of two distinct tryptophan-containing domains was established, which respond independently to ATP and Ca2+-specific binding. The latter is located in the ‘neck’ region of the myosin, which constitutes the regulatory domain. Subfragment 1, lacking the regulatory domain, responded only to ATP binding. On the other hand a tryptic fragment comprising the regulatory domain responded only to Ca2+ binding. Subfragment 1, containing the regulatory domain, responded to both ATP and Ca2+, but its ATPase activity was Ca2+-insensitive. By contrast, the ATPase activity of HMM was Ca2+-sensitive. Increasing the ionic strength had a detrimental effect on Ca2+-sensitivity, and fluorescence studies on solubilized myosin were therefore of limited value. Myosin and its fragments from other molluscan species which were investigated produced similar changes to those of Pectan maximus.

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Cheang, Qing Wei, Lingyi Xin, Rachel Yuen Fong Chea, and Zhao-Xun Liang. "Emerging paradigms for PilZ domain-mediated C-di-GMP signaling." Biochemical Society Transactions 47, no. 1 (February 1, 2019): 381–88. http://dx.doi.org/10.1042/bst20180543.

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Abstract PilZ domain-containing proteins constitute a large family of bacterial signaling proteins. As a widely distributed protein domain for the binding of the second messenger c-di-GMP, the canonical PilZ domain contains a set of motifs that define the binding site for c-di-GMP and an allosteric switch for propagating local conformational changes. Here, we summarize some new insights gathered from recent studies on the commonly occurring single-domain PilZ proteins, YcgR-like proteins and PilZ domain-containing cellulose synthases. The studies collectively illuminate how PilZ domains function as cis- or trans-regulatory domains that enable c-di-GMP to control the activity of its cellular targets. Overall, the review highlights the diverse protein structure, biological function and regulatory mechanism of PilZ domain-containing proteins, as well as the challenge of deciphering the function and mechanism of orphan PilZ proteins.

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Mathivanan, Subashini, Sreeja Chellappan, R. Thippeswamy, M. Nagesh, H. S. Savithri, and M. R. N. Murthy. "Structural studies on oxalate decarboxylase from Photorhabdus luminescens." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1821. http://dx.doi.org/10.1107/s2053273314081790.

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As a part of exploration of novel bacterial genes coding for insecticidal proteins, we have initiated structural and functional studies on oxalate decarboxylase from Photorhabdus luminescens, a symbiotic bacteria inhabiting guts of nematodes that parasitize insects. Oxalate decarboxylases (OXDC) are enzymes that catalyze the conversion of oxalate to formate and carbondioxide (CO2) in the presence of manganese and dioxygen. Structures of OXDC in complex with ethylene glycol (EDO), EDO/formate (FMT) and FMT/CO2 were determined at resolutions of 1.97Å, 2.36Å and 2.5Å, respectively. The asymmetric unit of these crystals contained a trimeric molecule. A protomer of the enzyme consists of two β-barrel domains belonging to the cupin family of proteins. All the three ligand bound structures of OXDC resemble the closed form of OXDC from B. subtilis reported earlier. Comparison of these structures with the open and closed forms of B. subtilis OXDC indicated that the conformation of Glu166 (corresponding to Glu162 of B. subtilis) in cupin domain I but not in domain II is in a conformation suitable to function as the catalytic base/acid and hence only domain I may be catalytically active. It is observed that the hydrogen bonding interaction between Arg95 and Thr169 of cupin domain I is essential for the positioning of Glu166 for catalysis. A corresponding threonine residue is absent in cupin domain II. An analysis of the similarities and differences between OXDC structures from P. luminescens and other reported bacterial OXDC structures and oxalate oxidase from Hordeum vulgare has been carried out with the view of understanding substrate and functional specificities of these enzymes. The structure provides the molecular framework required to investigate the mode of action of the enzyme, which may be a suitable candidate for developing P. luminescens as a bio-insecticide against plant pests.

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38

Franchot, Jenny. "Invisible Domain: Religion and American Literary Studies." American Literature 67, no. 4 (December 1995): 833. http://dx.doi.org/10.2307/2927901.

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Bone, S., B. Z. Ginzburg, H. Morgan, G. Wilson, and B. Zaba. "Time-domain reflectometry studies onHalobacterium halobiumandHalobacterium marismortui." Physics in Medicine and Biology 41, no. 1 (January 1, 1996): 45–54. http://dx.doi.org/10.1088/0031-9155/41/1/004.

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Kitadokoro, K., M. Ponassi, G. Galli, R. Petracca, F. Falugi, G. Grandi, and M. Bolognesi. "Structural studies of human CD81 extracellular domain." Acta Crystallographica Section A Foundations of Crystallography 61, a1 (August 23, 2005): c230—c231. http://dx.doi.org/10.1107/s0108767305090173.

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Comegys, G., W. Powell, and L. Stadler. "Public domain tools clarify power flow studies." IEEE Computer Applications in Power 12, no. 2 (April 1999): 43–45. http://dx.doi.org/10.1109/67.755645.

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Goicoechea, Luis J., and Vyacheslav N. Shalyapin. "Time-Domain Studies of Gravitationally Lensed Quasars." Proceedings of the International Astronomical Union 7, S285 (September 2011): 315–17. http://dx.doi.org/10.1017/s1743921312000919.

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AbstractWe present an overview and current results of an ongoing optical/NIR monitoring of seven gravitationally-lensed quasars (GLQs) with the 2-m Liverpool Robotic Telescope. The photometric data from the first seven years (2005–2011) of this programme are leading to high-quality light curves, which in turn are being used as key tools for different standard and novel studies. While brightness records of non-lensed distant quasars may contain unrecognized extrinsic variations, one can disentangle intrinsic from extrinsic signals in certain GLQs. Thus, some GLQs in our sample allow us to assess their extrinsic and intrinsic variations; we then discuss the origin of both kinds of fluctuations. We also demonstrate the usefulness of GLQ time-domain data for obtaining successful reverberation maps of the inner regions of accretion disks around distant supermassive black holes, and for estimating the redshifts of distant lensing galaxies.

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Baron, M., and J. U. Bowie. "Structural studies of the Shank SAM domain." Acta Crystallographica Section A Foundations of Crystallography 58, s1 (August 6, 2002): c283. http://dx.doi.org/10.1107/s0108767302096289.

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Lodder, J., D. Wind, Th Popma, and A. Hubert. "Domain studies of CoCr with perpendicular anisotropy." IEEE Transactions on Magnetics 23, no. 5 (September 1987): 2055–57. http://dx.doi.org/10.1109/tmag.1987.1065610.

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Richardson, M. D., C. A. Meisner, C. S. Hoveland, and K. J. Karnok. "Time Domain Reflectometry in Closed Container Studies." Agronomy Journal 84, no. 6 (November 1992): 1061–63. http://dx.doi.org/10.2134/agronj1992.00021962008400060029x.

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Squire, P. T., A. P. Thomas, M. R. J. Gibbs, and M. Kuzminski. "Domain studies of field-annealed amorphous ribbon." Journal of Magnetism and Magnetic Materials 104-107 (February 1992): 109–10. http://dx.doi.org/10.1016/0304-8853(92)90723-2.

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Constantine, K. L., S. A. Brew, K. C. Ingham, and M. Llinás. "1H-n.m.r. studies of the fibronectin 13kDa collagen-binding fragment. Evidence for autonomous conserved type I and type II domain folds." Biochemical Journal 283, no. 1 (April 1, 1992): 247–54. http://dx.doi.org/10.1042/bj2830247.

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A 1H-n.m.r. study of a 117-residue (13 kDa) gelatin-binding fragment of human fibronectin, which contains the sixth (from the N-terminus) type I domain and the first type II domain, was undertaken. The resolution of the 1H-n.m.r. spectrum indicates that the domains are independent and mobile relative to each other. Analysis of two-dimensional 1H-n.m.r. experiments recorded at 500 MHz afforded spin-system identifications for all aromatic and a number of aliphatic residues. Utilizing the fact that phenylalanine residues occur only in the type II portion of this fragment, many spin systems were localized to either the type I or the type II module via analysis of two-dimensional nuclear-Overhauser-effect (NOESY) experiments. This allowed unambiguous assignment of the two tryptophan residues, as they occur singly in each domain. Patterns of NOESY connectivities are found to be consistent with known type I and type II domain structures; this affords a number of tentative sequence-specific assignments. For both domains, evidence of conserved hydrophobic cores and secondary-structure elements is obtained. In addition, 1H-n.m.r.-monitored thermal-melting studies demonstrate conclusively that the domains are independently folded and that the type I domain has high thermal stability relative to the type II domain. This is consistent with the results of calorimetric studies, and also confirms the localization of spin systems determined from the NOESY data.

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Demczyk, B. G. "Domains and domain nucleation in magnetron-sputtered CoCr thin films." Proceedings, annual meeting, Electron Microscopy Society of America 51 (August 1, 1993): 1046–47. http://dx.doi.org/10.1017/s0424820100151064.

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CoCr thin films have been of interest for a number of years due to their strong perpendicular anisotropy, favoring magnetization normal to the film plane. The microstructure and magnetic properties of CoCr films prepared by both rf and magnetron sputtering have been examined in detail. By comparison, however, relatively few systematic studies of the magnetic domain structure and its relation to the observed film microstructure have been reported. In addition, questions still remain as to the operative magnetization reversal mechanism in different film thickness regimes. In this work, the magnetic domain structure in magnetron sputtered Co-22 at.%Cr thin films of known microstructure were examined by Lorentz transmission electron microscopy. Additionally, domain nucleation studies were undertaken via in-situ heating experiments.It was found that the 50 nm thick films, which are comprised of columnar grains, display a “dot” type domain configuration (Figure 1d), characteristic of a perpendicular magnetization. The domain size was found to be on the order of a few structural columns in diameter.

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Xie, Renchunzi, Hongxin Wei, Lei Feng, and Bo An. "GearNet: Stepwise Dual Learning for Weakly Supervised Domain Adaptation." Proceedings of the AAAI Conference on Artificial Intelligence 36, no. 8 (June 28, 2022): 8717–25. http://dx.doi.org/10.1609/aaai.v36i8.20851.

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This paper studies a weakly supervised domain adaptation (WSDA) problem, where we only have access to the source domain with noisy labels, from which we need to transfer useful information to the unlabeled target domain. Although there have been a few studies on this problem, most of them only exploit unidirectional relationships from the source domain to the target domain. In this paper, we propose a universal paradigm called GearNet to exploit bilateral relationships between the two domains. Specifically, we take the two domains as different inputs to train two models alternately, and a symmetrical Kullback-Leibler loss is used for selectively matching the predictions of the two models in the same domain. This interactive learning schema enables implicit label noise canceling and exploit correlations between the source and target domains. Therefore, our GearNet has the great potential to boost the performance of a wide range of existing WSDA methods. Comprehensive experimental results show that the performance of existing methods can be significantly improved by equipping with our GearNet.

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Pong, Hok-Ko. "The Correlation between Spiritual Well-Being and Burnout of Teachers." Religions 13, no. 8 (August 19, 2022): 760. http://dx.doi.org/10.3390/rel13080760.

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This study examines the correlation between spiritual well-being and burnout symptoms, including emotional exhaustion (EE), depersonalisation (DP), and personal accomplishment (PA), among Chinese secondary school teachers in Hong Kong. The data were collected from 427 Chinese secondary school teachers (189 males, 238 females) aged 25–37 from different schools with one to eight years of teaching experience. The participants completed the Spiritual Health and Life-orientation Measure (SHALOM) to evaluate the status of their spiritual well-being in the personal and communal, environmental, and transcendental domains. The Maslach Burnout Inventory—Human Services Survey (MBI-HSS) was also used to measure the extent of burnout in the workplace. All domains of spiritual well-being were negatively associated with EE and DP, while the personal and communal domain and the transcendental domain of spiritual well-being were positively associated with PA. Multiple regression analysis revealed that all the specific domains of spiritual well-being explained 68.6% and 54.0% of the variance in teachers’ EE and DP, respectively. Meanwhile, the same analysis found that the personal–communal and transcendental domains explained 74.9% of the variance in teachers’ PA. The personal–communal domain of spiritual well-being was the strongest predictor of burnout.

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Journal articles on the topic 'Domain Studies'

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