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1
Hwang, Chanwoong, Hyosik Kim, Hooki Lee, and Taejin Lee. "Effective DGA-Domain Detection and Classification with TextCNN and Additional Features." Electronics 9, no. 7 (June 30, 2020): 1070. http://dx.doi.org/10.3390/electronics9071070.
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Malicious codes, such as advanced persistent threat (APT) attacks, do not operate immediately after infecting the system, but after receiving commands from the attacker’s command and control (C&C) server. The system infected by the malicious code tries to communicate with the C&C server through the IP address or domain address of the C&C server. If the IP address or domain address is hard-coded inside the malicious code, it can analyze the malicious code to obtain the address and block access to the C&C server through security policy. In order to circumvent this address blocking technique, domain generation algorithms are included in the malware to dynamically generate domain addresses. The domain generation algorithm (DGA) generates domains randomly, so it is very difficult to identify and block malicious domains. Therefore, this paper effectively detects and classifies unknown DGA domains. We extract features that are effective for TextCNN-based label prediction, and add additional domain knowledge-based features to improve our model for detecting and classifying DGA-generated malicious domains. The proposed model achieved 99.19% accuracy for DGA classification and 88.77% accuracy for DGA class classification. We expect that the proposed model can be applied to effectively detect and block DGA-generated domains.
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Doan, Ninh, and Peter G. W. Gettins. "Human α2-macroglobulin is composed of multiple domains, as predicted by homology with complement component C3." Biochemical Journal 407, no. 1 (September 12, 2007): 23–30. http://dx.doi.org/10.1042/bj20070764.
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Human α2M (α2-macroglobulin) and the complement components C3 and C4 are thiol ester-containing proteins that evolved from the same ancestral gene. The recent structure determination of human C3 has allowed a detailed prediction of the location of domains within human α2M to be made. We describe here the expression and characterization of three α2M domains predicted to be involved in the stabilization of the thiol ester in native α2M and in its activation upon bait region proteolysis. The three newly expressed domains are MG2 (macroglobulin domain 2), TED (thiol ester-containing domain) and CUB (complement protein subcomponents C1r/C1s, urchin embryonic growth factor and bone morphogenetic protein 1) domain. Together with the previously characterized RBD (receptor-binding domain), they represent approx. 42% of the α2M polypeptide. Their expression as folded domains strongly supports the predicted domain organization of α2M. An X-ray crystal structure of MG2 shows it to have a fibronectin type-3 fold analogous to MG1–MG8 of C3. TED is, as predicted, an α-helical domain. CUB is a spliced domain composed of two stretches of polypeptide that flank TED in the primary structure. In intact C3 TED interacts with RBD, where it is in direct contact with the thiol ester, and with MG2 and CUB on opposite, flanking sides. In contrast, these α2M domains, as isolated species, show negligible interaction with one another, suggesting that the native conformation of α2M, and the consequent thiol ester-stabilizing domain–domain interactions, result from additional restraints imposed by the physical linkage of these domains or by additional domains in the protein.
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Fillion, Marie-Hélène, and John Hadjigeorgiou. "Quantifying influence of drilling additional boreholes on quality of geological model." Canadian Geotechnical Journal 56, no. 3 (March 2019): 347–63. http://dx.doi.org/10.1139/cgj-2017-0653.
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Geotechnical stability analysis in open-pit mines requires access to a representative geotechnical model. The confidence level in the collected geotechnical data influences slope design. This paper investigates the influence of the number of boreholes, drilled to collect geological information, on the quality of one component of the geotechnical model, the geological model. The number of boreholes influences the number of rock core samples collected for the identification of rock type, and the definition of geotechnical domains and their boundaries within the rock mass. A challenge in the definition of the geotechnical domains is the determination of the drill hole density that minimizes the variation in the interpreted geological model from the actual rock mass. To quantify the influence of the drill hole density, boreholes are simulated in the most recently updated geological model for three mine sites. The simulated drill hole density is increased progressively until the variation of the interpreted section, compared with the original section, is minimized. A classification strategy was developed to determine the complexity level for each geotechnical domain. Furthermore, a series of empirical quantitative guidelines are presented prescribing the minimum drill hole density per domain complexity, while limiting variations from the actual rock mass.
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Slep, Kevin C. "The role of TOG domains in microtubule plus end dynamics." Biochemical Society Transactions 37, no. 5 (September 21, 2009): 1002–6. http://dx.doi.org/10.1042/bst0371002.
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The XMAP215 (Xenopus microtubule-associated protein 215) and CLASP [CLIP-170 (cytoskeletal linker protein 170) associated protein] microtubule plus end tracking families play central roles in the regulation of interphase microtubule dynamics and the proper formation of mitotic spindle architecture and flux. XMAP215 members comprise N-terminally-arrayed hexa-HEAT (huntingtin, elongation factor 3, the PR65/A subunit of protein phosphatase 2A and the lipid kinase Tor) repeats known as TOG (tumour overexpressed gene) domains. Higher eukaryotic XMAP215 members are monomeric and have five TOG domains. Yeast counterparts are dimeric and have two TOG domains. Structure determination of the TOG domain reveals that the six HEAT repeats are aligned to form an oblong scaffold. The TOG domain face composed of intra-HEAT loops forms a contiguous, conserved tubulin-binding surface. Nested within the conserved intra-HEAT loop 1 is an invariant, signature, surface-exposed tryptophan residue that is a prime determinant in the TOG domain–tubulin interaction. The arrayed organization of TOG domains is critical for the processive mechanism of XMAP215, indicative that multiple tubulin/microtubule-binding sites are required for plus end tracking activity. The CLASP family has been annotated as containing a single N-terminal TOG domain. Using XMAP215 TOG domain structure determinants as a metric to analyse CLASP sequence, it is anticipated that CLASP contains two additional cryptic TOGL (TOG-like) domains. The presence of additional TOGL domains implicates CLASP as an ancient XMAP215 relative that uses a similar, multi-TOG-based mechanism to processively track microtubule ends.
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Li, Yongzhong, and Scott M. Leisner. "Multiple Domains Within the Cauliflower mosaic virus Gene VI Product Interact with the Full-Length Protein." Molecular Plant-Microbe Interactions® 15, no. 10 (October 2002): 1050–57. http://dx.doi.org/10.1094/mpmi.2002.15.10.1050.
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The Cauliflower mosaic virus (CaMV) gene VI product (P6) is a multifunctional protein essential for viral propagation. It is likely that at least some of these functions require P6 self-association. The work described here was performed to confirm that P6 self-associates and to identify domains involved in this interaction. Yeast two-hybrid analyses indicated that full-length P6 self-associates and that this interaction is specific. Additional analyses indicated that at least four independent domains bind to full-length P6. When a central domain (termed domain D3) was removed, these interactions were abolished. However, this deleted P6 was able to bind to the full-length wild-type protein and to isolated domain D3. Viruses lacking domain D3 were incapable of producing a systemic infection. Isolated domain D3 was capable of binding to at least two of the other domains but was unable to self-associate. This suggests that domain D3 facilitates P6 self-association by binding to the other domains but not itself. The presence of multiple domains involved in P6 self-association may help explain the ability of this protein to form the intracellular inclusions characteristic of caulimoviruses.
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Guo, Han, Ramakanth Pasunuru, and Mohit Bansal. "Multi-Source Domain Adaptation for Text Classification via DistanceNet-Bandits." Proceedings of the AAAI Conference on Artificial Intelligence 34, no. 05 (April 3, 2020): 7830–38. http://dx.doi.org/10.1609/aaai.v34i05.6288.
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Domain adaptation performance of a learning algorithm on a target domain is a function of its source domain error and a divergence measure between the data distribution of these two domains. We present a study of various distance-based measures in the context of NLP tasks, that characterize the dissimilarity between domains based on sample estimates. We first conduct analysis experiments to show which of these distance measures can best differentiate samples from same versus different domains, and are correlated with empirical results. Next, we develop a DistanceNet model which uses these distance measures, or a mixture of these distance measures, as an additional loss function to be minimized jointly with the task's loss function, so as to achieve better unsupervised domain adaptation. Finally, we extend this model to a novel DistanceNet-Bandit model, which employs a multi-armed bandit controller to dynamically switch between multiple source domains and allow the model to learn an optimal trajectory and mixture of domains for transfer to the low-resource target domain. We conduct experiments on popular sentiment analysis datasets with several diverse domains and show that our DistanceNet model, as well as its dynamic bandit variant, can outperform competitive baselines in the context of unsupervised domain adaptation.
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Kazakevich, Vladimir Mikhailovich, Galina Vasilevna Pichugina, and Galina Iurevna Semenova. "Succession and integration of the renovated general compulsory and additional education." Moscow University Pedagogical Education Bulletin, no. 1 (March 30, 2018): 69–89. http://dx.doi.org/10.51314/2073-2635-2018-1-69-89.
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The analysis of the semantic categories used in systems of general compulsory and additional education, first of all categories “continuity” and “integration” is provided in article. Features of an intersubject, retrospective, semantic continuity are revealed. It is shown that the continuity of the compulsory and additional education is expressed by the established semantic, structural, intersubject and hierarchical links between their contents, forms, methods and means. Specifics of the formal, non-formal and informal education in the modern social and educational situation are disclosed, adequate determination and interpretations of an entity of these concepts are offered. The conclusion is drawn that organizational and methodical models of an continuity and integration of specific subject content of compulsory general and additional education shall be developed taking into account specifics of subject domain. The integrative entity of subject domain “Technology” which allows to consider it as the “link” indirectly providing integration of the compulsory general education in all subject domains with additional education is shown. Postulates for the integration of the compulsory general and additional education are formulated.
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Sandouka, Soha B., Yakoub Bazi, Haikel Alhichri, and Naif Alajlan. "Unified Generative Adversarial Networks for Multidomain Fingerprint Presentation Attack Detection." Entropy 23, no. 8 (August 21, 2021): 1089. http://dx.doi.org/10.3390/e23081089.
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With the rapid growth of fingerprint-based biometric systems, it is essential to ensure the security and reliability of the deployed algorithms. Indeed, the security vulnerability of these systems has been widely recognized. Thus, it is critical to enhance the generalization ability of fingerprint presentation attack detection (PAD) cross-sensor and cross-material settings. In this work, we propose a novel solution for addressing the case of a single source domain (sensor) with large labeled real/fake fingerprint images and multiple target domains (sensors) with only few real images obtained from different sensors. Our aim is to build a model that leverages the limited sample issues in all target domains by transferring knowledge from the source domain. To this end, we train a unified generative adversarial network (UGAN) for multidomain conversion to learn several mappings between all domains. This allows us to generate additional synthetic images for the target domains from the source domain to reduce the distribution shift between fingerprint representations. Then, we train a scale compound network (EfficientNetV2) coupled with multiple head classifiers (one classifier for each domain) using the source domain and the translated images. The outputs of these classifiers are then aggregated using an additional fusion layer with learnable weights. In the experiments, we validate the proposed methodology on the public LivDet2015 dataset. The experimental results show that the proposed method improves the average classification accuracy over twelve classification scenarios from 67.80 to 80.44% after adaptation.
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Vallati, Mauro, Lukáš Chrpa, and Diane Kitchin. "ASAP: An Automatic Algorithm Selection Approach for Planning." International Journal on Artificial Intelligence Tools 23, no. 06 (December 2014): 1460032. http://dx.doi.org/10.1142/s021821301460032x.
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Despite the advances made in the last decade in automated planning, no planner outperforms all the others in every known benchmark domain. This observation motivates the idea of selecting different planning algorithms for different domains. Moreover, the planners' performances are affected by the structure of the search space, which depends on the encoding of the considered domain. In many domains, the performance of a planner can be improved by exploiting additional knowledge, for instance, in the form of macro-operators or entanglements. In this paper we propose ASAP, an automatic Algorithm Selection Approach for Planning that: (i) for a given domain initially learns additional knowledge, in the form of macro-operators and entanglements, which is used for creating different encodings of the given planning domain and problems, and (ii) explores the 2 dimensional space of available algorithms, defined as encodings–planners couples, and then (iii) selects the most promising algorithm for optimising either the runtimes or the quality of the solution plans.
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Chiu, Po-Lin, George M. Bou-Assaf, Ekta Seth Chhabra, Melissa G. Chambers, Robert T. Peters, John D. Kulman, and Thomas Walz. "Mapping the interaction between factor VIII and von Willebrand factor by electron microscopy and mass spectrometry." Blood 126, no. 8 (August 20, 2015): 935–38. http://dx.doi.org/10.1182/blood-2015-04-641688.
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Key PointsElectron microscopy and hydrogen-deuterium exchange establish the C1 domain as the major binding site for the VWF D′D3 domain on FVIII. Additional sites implicated in the FVIII-VWF interaction are located within the a3 acidic peptide and the A3 and C2 domains of FVIII.
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Ramiro, Sofia, Matthew J. Page, Samuel L. Whittle, Hsiaomin Huang, Arianne P. Verhagen, Dorcas E. Beaton, Pamela Richards, et al. "The OMERACT Core Domain Set for Clinical Trials of Shoulder Disorders." Journal of Rheumatology 46, no. 8 (February 1, 2019): 969–75. http://dx.doi.org/10.3899/jrheum.181070.
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Objective.To reach consensus on the core domains to be included in a core domain set for clinical trials of shoulder disorders using the Outcome Measures in Rheumatology (OMERACT) Filter 2.1 Core Domain Set process.Methods.At OMERACT 2018, the OMERACT Shoulder Working Group conducted a workshop that presented the OMERACT 2016 preliminary core domain set and its rationale based upon a systematic review of domains measured in shoulder trials and international Delphi sessions involving patients, clinicians, and researchers, as well as a new systematic review of qualitative studies on the experiences of people with shoulder disorders. After discussions in breakout groups, the OMERACT core domain set for clinical trials of shoulder disorders was presented for endorsement by OMERACT 2018 participants.Results.The qualitative review (n = 8) identified all domains included in the preliminary core set. An additional domain, cognitive dysfunction, was also identified, but confidence that this represents a core domain was very low. The core domain set that was endorsed by the OMERACT participants, with 71% agreement, includes 4 “mandatory” trial domains: pain, function, patient global — shoulder, and adverse events including death; and 4 “important but optional” domains: participation (recreation/work), sleep, emotional well-being, and condition-specific pathophysiological manifestations. Cognitive dysfunction was voted out of the core domain set.Conclusion.OMERACT 2018 delegates endorsed a core domain set for clinical trials of shoulder disorders. The next step includes identification of a core outcome measurement set that passes the OMERACT 2.1 Filter for measuring each domain.
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Galperin, Michael Y. "Structural Classification of Bacterial Response Regulators: Diversity of Output Domains and Domain Combinations." Journal of Bacteriology 188, no. 12 (June 15, 2006): 4169–82. http://dx.doi.org/10.1128/jb.01887-05.
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ABSTRACT CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. In this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. Previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. Transcriptional regulators of the OmpR, NarL, and NtrC families were found to comprise almost 60% of all response regulators; transcriptional regulators with other DNA-binding domains (LytTR, AraC, Spo0A, Fis, YcbB, RpoE, and MerR) account for an additional 6%. The remaining one-third is represented by the stand-alone REC domain (∼14%) and its combinations with a variety of enzymatic (GGDEF, EAL, HD-GYP, CheB, CheC, PP2C, and HisK), RNA-binding (ANTAR and CsrA), protein- or ligand-binding (PAS, GAF, TPR, CAP_ED, and HPt) domains, or newly described domains of unknown function. The diversity of domain architectures and the abundance of alternative domain combinations suggest that fusions between the REC domain and various output domains is a widespread evolutionary mechanism that allows bacterial cells to regulate transcription, enzyme activity, and/or protein-protein interactions in response to environmental challenges. The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html .
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Denis, Antonia, Mario Alberto Martínez-Núñez, Silvia Tenorio-Salgado, and Ernesto Perez-Rueda. "Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638." Life 8, no. 4 (September 21, 2018): 40. http://dx.doi.org/10.3390/life8040040.
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In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.
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Wierstra, Inken, and Jürgen Alves. "Despite its strong transactivation domain, transcription factor FOXM1c is kept almost inactive by two different inhibitory domains." Biological Chemistry 387, no. 7 (July 1, 2006): 963–76. http://dx.doi.org/10.1515/bc.2006.120.
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Abstract FOXM1c (MPP2) is an activating transcription factor with several nuclear localization signals, a forkhead domain for DNA binding, and a very strong acidic transactivation domain. Despite its very strong transactivation domain, FOXM1c is kept almost inactive by two different independent inhibitory domains, the N-terminus and the central domain. The N-terminus as a specific negative-regulatory domain directly binds to and thus inhibits the transactivation domain completely. However, it lacks any transrepression potential. In contrast, the central domain functions as a strong RB-independent transrepression domain and as an RB-recruiting negative-regulatory domain. The N-terminus alone is sufficient to eliminate transactivation, while the central domain alone represses the transactivation domain only partially. This hierarchy of the two inhibitory domains offers the possibility to activate the almost inactive wild type in two steps in vitro: deletion of the N-terminus results in a strong transactivator, while additional deletion of the central domain in a very strong transactivator. We suggest that the very high potential of the transactivation domain has to be tightly controlled by these two inhibitory domains because FOXM1 stimulates proliferation by promoting G1/S transition, as well as G2/M transition, and because deregulation of such potent activators of proliferation can result in tumorigenesis.
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Allen, C. Leigh, and Andrew M. Gulick. "Structural and bioinformatic characterization of anAcinetobacter baumanniitype II carrier protein." Acta Crystallographica Section D Biological Crystallography 70, no. 6 (May 30, 2014): 1718–25. http://dx.doi.org/10.1107/s1399004714008311.
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Microorganisms produce a variety of natural productsviasecondary metabolic biosynthetic pathways. Two of these types of synthetic systems, the nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), use large modular enzymes containing multiple catalytic domains in a single protein. These multidomain enzymes use an integrated carrier protein domain to transport the growing, covalently bound natural product to the neighboring catalytic domains for each step in the synthesis. Interestingly, some PKS and NRPS clusters contain free-standing domains that interact intermolecularly with other proteins. Being expressed outside the architecture of a multi-domain protein, these so-called type II proteins present challenges to understand the precise role they play. Additional structures of individual and multi-domain components of the NRPS enzymes will therefore provide a better understanding of the features that govern the domain interactions in these interesting enzyme systems. The high-resolution crystal structure of a free-standing carrier protein fromAcinetobacter baumanniithat belongs to a larger NRPS-containing operon, encoded by the ABBFA_003406–ABBFA_003399 genes ofA. baumanniistrain AB307-0294, that has been implicated inA. baumanniimotility, quorum sensing and biofilm formation, is presented here. Comparison with the closest structural homologs of other carrier proteins identifies the requirements for a conserved glycine residue and additional important sequence and structural requirements within the regions that interact with partner proteins.
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P, Karunakaran. "Deep Learning Approach to DGA Classification for Effective Cyber Security." December 2020 2, no. 4 (January 6, 2021): 203–13. http://dx.doi.org/10.36548/jucct.2020.4.003.
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In recent years, invaders are increasing rapidly in an internet world. Generally, in order to detect the anonymous attackers algorithm needs more number of features. Many algorithms fail in the efficiency of detection malicious code. Immediately this codes will not infect the system; it will attack server after communicate later. Our research focuses on analyzing the traffic of botnets for the domain name determination to the IP address of the server. This botnet creates the domain name differently. Many domains are generated by attackers and create the huge Domain Name System (DNS) traffic. In this research paper, uses both public and real time environments datasets to detect the text features as well as knowledge based feature extraction. The classifying of Domain Generation Algorithm (DGA) generated malicious domains randomly making the efficiency down in many algorithms which were used preprocessing without proper feature extraction. Effectively, our proposed algorithm is used to detect DGA which generates malicious domains randomly. This effective detection of our proposed algorithm performs with text based label prediction and additional features for extraction to improve the efficiency of the model. Our proposed model achieved 94.9% accuracy for DGA classification with help of additional feature extraction and knowledge based extraction in the deep learning architecture.
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Soejima, Kenji, Masanori Matsumoto, Koichi Kokame, Hideo Yagi, Hiromichi Ishizashi, Hiroaki Maeda, Chikateru Nozaki, Toshiyuki Miyata, Yoshihiro Fujimura, and Tomohiro Nakagaki. "ADAMTS-13 cysteine-rich/spacer domains are functionally essential for von Willebrand factor cleavage." Blood 102, no. 9 (November 1, 2003): 3232–37. http://dx.doi.org/10.1182/blood-2003-03-0908.
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AbstractA severe lack of von Willebrand factor–cleaving protease (VWF-CP) activity can cause thrombotic thrombocytopenic purpura (TTP). This protease was recently identified as a member of the ADAMTS family, ADAMTS-13. It consists of a preproregion, a metalloprotease domain, a disintegrin-like domain, a thrombospondin type-1 motif (Tsp1), a cysteine-rich domain, a spacer domain, additional Tsp1 repeats, and CUB domains. To explore the structural and functional relationships of ADAMTS-13, we prepared here 13 sequential COOH-terminal truncated mutants and a single-point mutant (ArgGlyAsp [RGD] to ArgGlyGlu [RGE] in the cysteine-rich domain) and compared the activity of each mutant with that of the wild-type protein. The results revealed that the truncation of the cysteine-rich/spacer domains caused a remarkable reduction in VWF-CP activity. We also prepared immunoglobulin G (IgG) fractions containing inhibitory autoantibodies against ADAMTS-13 from plasma from 3 patients with acquired TTP, and we performed mapping of their epitopes using the aforementioned mutants. The major epitopes of these antibodies were found to reside within the cysteine-rich/spacer domains. These results suggest that the ADAMTS-13 cysteine-rich/spacer domains are essential for VWF-CP activity.
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Raiborg, Camilla, Bjørn Bremnes, Anja Mehlum, David J. Gillooly, Antonello D’Arrigo, Espen Stang, and Harald Stenmark. "FYVE and coiled-coil domains determine the specific localisation of Hrs to early endosomes." Journal of Cell Science 114, no. 12 (June 15, 2001): 2255–63. http://dx.doi.org/10.1242/jcs.114.12.2255.
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Hrs, an essential tyrosine kinase substrate, has been implicated in intracellular trafficking and signal transduction pathways. The protein contains several distinctive domains, including an N-terminal VHS domain, a phosphatidylinositol 3-phosphate (PtdIns(3)P)-binding FYVE domain and two coiled-coil domains. Here we have investigated the roles of these domains in the subcellular localisation of Hrs. Hrs was found to colocalise extensively with EEA1, an established marker of early endosomes. While the membrane association of EEA1 was abolished in the presence of a dominant negative mutant of the endosomal GTPase Rab5, the localisation of Hrs to early endosomes was Rab5 independent. The VHS-domain was nonessential for the subcellular targeting of Hrs. In contrast, the FYVE domain as well as the second coiled-coil domain, which has been shown to bind to SNAP-25, were required for targeting of Hrs to early endosomes. A small construct consisting of only these two domains was correctly localised to early endosomes, whereas a point mutation (R183A) in the PtdIns(3)P-binding pocket of the FYVE domain inhibited the membrane targeting of Hrs. Thus, like EEA1, the endosomal targeting of Hrs is mediated by a PtdIns(3)P-binding FYVE domain in cooperation with an additional domain. We speculate that binding to PtdIns(3)P and a SNAP-25-related molecule may target Hrs specifically to early endosomes.
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Goto, Eiko, Hirono Ishikawa, Kazuhiro Nakayama, and Takahiro Kiuchi. "Comprehensive Health Literacy and Health-Related Behaviors Within a General Japanese Population: Differences by Health Domains." Asia Pacific Journal of Public Health 30, no. 8 (November 2018): 717–26. http://dx.doi.org/10.1177/1010539518806806.
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The present study aimed to explore how different health-related domains of health literacy, as measured by the European Health Literacy Survey Questionnaire, were associated with health-related behaviors among a general population in Japan. We conducted a cross-sectional observational study of 1002 Japanese residents. Our questionnaire addressed socioeconomic status, health status, health-related behaviors, and health literacy. Among the 3 health-related domains of health literacy (health care, disease prevention, and health promotion), a multivariate model revealed that the disease prevention domain was associated with exercise behavior and alcohol consumption. The health promotion domain was associated with dietary behavior and exercise behavior. There were strong correlations among all health-related domains of health literacy; however, there were different associations between health literacy and health-related behaviors depending on those domains. Additional research is needed to determine how and to what extent each domain of health literacy is related to what health behaviors and outcomes.
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MacKay, Julie O., Kelly H. Soanes, Ajay Srivastava, Andrew Simmonds, William J. Brook, and John B. Bell. "An in Vivo Analysis of the vestigial Gene in Drosophila melanogaster Defines the Domains Required for Vg Function." Genetics 163, no. 4 (April 1, 2003): 1365–73. http://dx.doi.org/10.1093/genetics/163.4.1365.
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Abstract Considerable evidence indicates an obligate partnership of the Drosophila melanogaster Vestigial (VG) and Scalloped (SD) proteins within the context of wing development. These two proteins interact physically and a 56-amino-acid motif within VG is necessary and sufficient for this binding. While the importance of this SD-binding domain has been clearly demonstrated both in vitro and in vivo, the remaining portions of VG have not been examined for in vivo function. Herein, additional regions within VG were tested for possible in vivo functions. The results identify two additional domains that must be present for optimal VG function as measured by the loss of ability to rescue vg mutants, to induce ectopic sd expression, and to perform other normal VG functions when they are deleted. An in vivo study such as this one is fundamentally important because it identifies domains of VG that are necessary in the cellular context in which wing development actually occurs. The results also indicate that an additional large portion of VG, outside of these two domains and the SD-binding domain, is dispensable in the execution of these normal VG functions.
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Yang, Haitong, Tao Zhuang, and Chengqing Zong. "Domain Adaptation for Syntactic and Semantic Dependency Parsing Using Deep Belief Networks." Transactions of the Association for Computational Linguistics 3 (December 2015): 271–82. http://dx.doi.org/10.1162/tacl_a_00138.
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In current systems for syntactic and semantic dependency parsing, people usually define a very high-dimensional feature space to achieve good performance. But these systems often suffer severe performance drops on out-of-domain test data due to the diversity of features of different domains. This paper focuses on how to relieve this domain adaptation problem with the help of unlabeled target domain data. We propose a deep learning method to adapt both syntactic and semantic parsers. With additional unlabeled target domain data, our method can learn a latent feature representation (LFR) that is beneficial to both domains. Experiments on English data in the CoNLL 2009 shared task show that our method largely reduced the performance drop on out-of-domain test data. Moreover, we get a Macro F1 score that is 2.32 points higher than the best system in the CoNLL 2009 shared task in out-of-domain tests.
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Anderson, Eric W., Monica S. Frazer, and Sandra E. Schellinger. "Expanding the Palliative Care Domains to Meet the Needs of a Community-Based Supportive Care Model." American Journal of Hospice and Palliative Medicine® 35, no. 2 (April 20, 2017): 258–65. http://dx.doi.org/10.1177/1049909117705061.
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Background: Whole person care is appropriate for seriously ill persons. The current framework of palliative care domains in the National Consensus Project (NCP) Guidelines for Quality Palliative Care offers an opportunity to reassess the domains of care delivered at home, earlier in the course of illness. Objective: This qualitative study was used to test the applicability of a proposed, expanded set of domains. The results were used to inform a home-based, upstream model of supportive care for serious illness. Methods: Quotes relating to the experience of late-life serious illness were derived from transcripts of 12 semi-structured group interviews conducted with patients, family, and professionals. Quotes originally coded to the NCP domains of palliative care were then coded to the proposed domain set, which included new categories of family/caregiver, legal/financial, and legacy/bereavement domains. Results: A total of 489 quotes were assigned to the proposed expanded set of domains. One hundred one (19%) coded to the family/caregiver domain, 28 (5%) to the legacy/bereavement domain, and 27 (5%) to the legal/financial domain. Ninety-seven (87%) of the 111 quotes coded to family/caregiver had been initially coded to the NCP social aspects of care. Family/caregiver themes included challenges, rewards, insights, and family growth. Conclusion: The preponderance of family-related issues suggests that including the family domain may promote recognition and support of family caregivers and the services they provide. Although this study provides some support for including the legacy/bereavement and legal/financial domains, additional research is needed to determine whether there is a basis for including them in the domain structure.
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Gallop, Jennifer L., and Harvey T. McMahon. "BAR domains and membrane curvature: bringing your curves to the BAR." Biochemical Society Symposia 72 (January 1, 2005): 223–31. http://dx.doi.org/10.1042/bss0720223.
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BAR (bin, amphiphysin and Rvs161/167) domains are a unique class of dimerization domains, whose dimerization interface is edged by a membrane-binding surface. In its dimeric form, the membrane-binding interface is concave, and this gives the ability to bind better to curved membranes, i.e. to sense membrane curvature. When present at higher concentrations, the domain can stabilize membrane curvature, generating lipid tubules. This domain is found in many contexts in a wide variety of proteins, where the dimerization and membrane-binding function of this domain is likely to have a profound effect on protein activity. If these proteins function as predicted, then there will be membrane subdomains based on curvature, and thus there is an additional layer of compartmentalization on membranes. These and other possible functions of the BAR domain are discussed.
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Hadrawi, Waqiyuddin Hilmi, Anas Norazman, Fairolniza Mohd Shariff, Mohd Shukuri Mohamad Ali, and Raja Noor Zaliha Raja Abd Rahman. "Understanding the Effect of Multiple Domain Deletion in DNA Polymerase I from Geobacillus Sp. Strain SK72." Catalysts 10, no. 8 (August 15, 2020): 936. http://dx.doi.org/10.3390/catal10080936.
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The molecular structure of DNA polymerase I or family A polymerases is made up of three major domains that consist of a single polymerase domain with two extra exonuclease domains. When the N-terminal was deleted, the enzyme was still able to perform basic polymerase activity with additional traits that used isothermal amplification. However, the 3′-5′ exonuclease domain that carries a proofreading activity was disabled. Yet, the structure remained attached to the 5′-3′ polymerization domain without affecting its ability. The purpose of this non-functional domain still remains scarce. It either gives negative effects or provides structural support to the DNA polymerase. Here, we compared the effect of deleting each domain against the polymerase activity. The recombinant wild type and its variants were successfully purified and characterized. Interestingly, SK72-Exo (a large fragment excluding the 5′-3′ exonuclease domain) exhibited better catalytic activity than the native SK72 (with all three domains) at similar optimum temperature and pH profile, and it showed longer stability at 70 °C. Meanwhile, SK72-Exo2 (polymerization domain without both the 5′-3′ and 3′-5′ exonuclease domain) displayed the lowest activity with an optimum at 40 °C and favored a more neutral environment. It was also the least stable among the variants, with almost no activity at 50 °C for the first 10 min. In conclusion, cutting both exonuclease domains in DNA polymerase I has a detrimental effect on the polymerization activity and structural stability.
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Wei, Wei, Xiaofan Zhu, Renchi Yang, and Bin Zhang. "Characterization of Missense Mutations in Factor VIII That Lead to Abnormal N-Linked Glycosylation." Blood 128, no. 22 (December 2, 2016): 3764. http://dx.doi.org/10.1182/blood.v128.22.3764.3764.
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Abstract Most secreted proteins are glycosylated on the asparagine (N) residue with the consensus sequence N-X-S/T(X≠Proline).Coagulation factor VIII (FVIII) is heavily N-linked glycosylated with 5 consensus sites outside the B domain. However, the roles of these glycans are not well understood. Meanwhile, missense mutations which could create additional N-linked glycosylation sites have largely not been characterized in hemophilia A patients. In this study we first expressed individual domains of FVIII and determined that the A2, Cand C2 domains are efficiently secreted. The A1(N42,N239), A3 (N1810)and C1 (N2118)domains are glycosylated, whereas N582 in the A2 domain is not glycosylated. Only one hemophilia A missense mutation, S241C in the A1 domain, was found to abolish the consensus sequence for N-linked glycosylation at N239. We confirmed that the S241C mutant lost one glycan and became unstable inside cells. We also tested the other three glycosylation sites and found that elimination of the N-linked glycan at N2118 (N2118Q mutation) impaired the secretion of the C domain. This defect could not be rescued by adding another N-linked glycan (at N2062) in the C1 domain, indicating that the N2118 glycan is specifically required for the secretion of the C domain. We next searched the CHAMP F8 Mutation Database and the FVIII Variant Database and identified 19 missense mutations that potentially create an ectopic glycosylation site.These mutations are located in A1, A2, A3 and C1 domains, but none in the C2 domain. Only two mutations (I566T and M1772T) have previously been characterized.We found that all but one (I2071T) of these mutations gained an additional N-linked glycan. We further studied missense mutations in the A2 (A469T, A469S, I566T, M614T and G701S) and the C domain (W2062S, I2071T and D2131N) because these domains are secreted in cell culture. Whereas secretion of I566T, W2062S and D2131N mutants was comparable to their wild-type counterparts, secretion of other mutants decreased to 5%-30% of WT (P<0.05). Mutants that secreted into culture media nevertheless have low FVIII activity (<2%), indicating that these mutations cause cross reactive material positive hemophilia A. The consequences of additional N-linked glycan were further investigated using the A2 domain mutants, since this domain is normally unglycosylated. After treating with tunicamycin to block the N-linked glycosylation process in the endoplasmic reticulum (ER),the secretion of A2 domain with I566T andG701Smutants, which had relatively high secretion levels, decreased significantly. On the other hand, removing the additional glycan boosted the secretion of A469S and A469T, two low-secretion mutants.Tunicamycin treatment had no effect on another low secretion mutant,M614T.These results suggest that amino acid substitution in I566T andG701Smutationsis detrimental to the proper folding of the protein and the additional N-glycan plays a stabilization role. On the other hand, additional N-glycan plays a destabilization role in A469S and A469T mutations, contributing to disruption of folding in these mutants. For theM614Tmutation,the amino acid substitution alone is likely sufficient todestroy the protein folding. We also studied interactions of abnormally glycosylated mutants with ER chaperones.All the mutants with low secretion levels significantly induced expression of GRP78 to 1.5-2.0 folds(P<0.05), while mutants that maintain higher secretion levels did not affect GRP78 expression. The low secretion mutants also had increased binding to GRP78 and calreticulin, but not to calnexin.Therefore ER chaperones play a key role in the ER quality control of FVIII mutants. In conclusion, our results indicate that the effects of abnormal N-linked glycosylation on FVIII folding and secretionvary widely, from detrimental to beneficial. The impact of a particular glycan is likely determined by the location and the underlying amino acid change caused by the mutation. Disclosures No relevant conflicts of interest to declare.
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Reeves, Rosalind A., Moreland D. Gibbs, Daniel D. Morris, Katherine R. Griffiths, David J. Saul, and Peter L. Bergquist. "Sequencing and Expression of Additional Xylanase Genes from the Hyperthermophile Thermotoga maritimaFjSS3B.1." Applied and Environmental Microbiology 66, no. 4 (April 1, 2000): 1532–37. http://dx.doi.org/10.1128/aem.66.4.1532-1537.2000.
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ABSTRACT Two genes, xynB and xynC, coding for xylanases were isolated from Thermotoga maritima FjSS3B.1 by a genomic-walking–PCR technique. Sequencing of the genes showed that they encode multidomain family 10 xylanases. Only XynB exhibited activity against xylan substrates. The temperature optimum (87°C) and pH optimum (pH 6.5) of XynB are different from the previously reported xylanase, XynA (also a family 10 enzyme), from this organism. The catalytic domain expressed without other domains has a lower temperature optimum, is less thermostable, and has optimal activity at pH 6.5. Despite having a high level of sequence similarity toxynB, xynC appears to be nonfunctional since its encoded protein did not show significant activity on xylan substrates.
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Whitney, Carolyn. "Social supports among college students and measures of alcohol use, perceived stress, satisfaction with life, emotional intelligence, and coping." Journal of Student Wellbeing 4, no. 1 (November 15, 2010): 49. http://dx.doi.org/10.21913/jsw.v4i1.588.
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In this study I examined three domains of social supports among college students (close friends, casual friends and safe adults to turn to) in relation to indices of wellbeing and coping. Measures of positive wellbeing were most strongly associated with the safe adults domain of social support followed by the close friends domain of social support. Casual friends were associated only with measures of problem alcohol consumption but not with indices of wellbeing. Students with five or more safe adults to turn to as compared to four or fewer reported significantly lower perceived stress, greater satisfaction with life, higher emotional intelligence, better academic performance and lower problem drinking scores. The domain of safe adults was associated with the largest array of wellbeing indices of all three social support domains. Future research should examine additional measures of wellbeing that may be associated with distinct domains of support.
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Fiorentini, Filippo, Diego Esposito, and Katrin Rittinger. "Does it take two to tango? RING domain self-association and activity in TRIM E3 ubiquitin ligases." Biochemical Society Transactions 48, no. 6 (November 10, 2020): 2615–24. http://dx.doi.org/10.1042/bst20200383.
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TRIM proteins form a protein family that is characterized by a conserved tripartite motif domain comprising a RING domain, one or two B-box domains and a coiled-coil region. Members of this large protein family are important regulators of numerous cellular functions including innate immune responses, transcriptional regulation and apoptosis. Key to their cellular role is their E3 ligase activity which is conferred by the RING domain. Self-association is an important characteristic of TRIM protein activity and is mediated by homodimerization via the coiled-coil region, and in some cases higher order association via additional domains of the tripartite motif. In many of the TRIM family proteins studied thus far, RING dimerization is an important prerequisite for E3 ligase enzymatic activity though the propensity of RING domains to dimerize differs significantly between different TRIMs and can be influenced by other regions of the protein.
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Denega, Iryna. "Estimation of the products of the inner radii of domains with an additional symmetry condition." Proceedings of the Institute of Applied Mathematics and Mechanics NAS of Ukraine 33 (December 27, 2019): 83–90. http://dx.doi.org/10.37069/1683-4720-2019-33-6.
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In geometric function theory of complex variable extremal problems on non-overlapping domains are well-known classic direction. A lot of such problems are reduced to determination of the maximum of product of inner radii on the system of non-overlapping domains satisfying a certain conditions. Based on these elementary estimates a number of new estimates for functions realizing a conformal mapping of a disc onto domains with certain special properties are obtained. Estimates of this type are fundamental to solving some metric problems arising when considering the cor\-res\-pon\-dence of boundaries under a conformal mapping. Also, on the basis of the results concerning various extremal properties of conformal mappings, the problem of the representability of functions of a complex variable by a uniformly convergent series of polynomials is solved. In this paper, we consider the problem on maximum the products of the inner radii of $n$ disjoint domains with an additional symmetry condition that contain points of extended complex plane and the degree $\gamma$ of the inner radius of the domain that contains the zero point. An upper estimate for the maximum of this product is found for all values of $\gamma\in(0,\,n]$. The main result of the paper generalizes and strengthens the results of the predecessors [1-4] for the case of an arbitrary arrangement of points systems on $\overline{\mathbb{C}}$. In proving the main theorem, the arguments of proving of Lemma 1 [5] and the ideas of proving Theorem 1 [3] played a key role. We also established the conditions under which the structure of points and domains is not important. The corresponding results are obtained for the case when the points are placed on the unit circle and in the case of any fixed $n$-radial system of points.
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Gerwin, N., A. La Rosée, F. Sauer, H. P. Halbritter, M. Neumann, H. Jäckle, and U. Nauber. "Functional and conserved domains of the Drosophila transcription factor encoded by the segmentation gene knirps." Molecular and Cellular Biology 14, no. 12 (December 1994): 7899–908. http://dx.doi.org/10.1128/mcb.14.12.7899.
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The Drosophila gap gene knirps (kni) is required for abdominal segmentation. It encodes a steroid/thyroid orphan receptor-type transcription factor which is distributed in a broad band of nuclei in the posterior region of the blastoderm. To identify essential domains of the kni protein (KNI), we cloned and sequenced the DNA encompassing the coding region of nine kni mutant alleles of different strength and kni-homologous genes of related insect species. We also examined in vitro-modified versions of KNI in various assay systems both in vitro and in tissue culture. The results show that KNI contains several functional domains which are arranged in a modular fashion. The N-terminal 185-amino-acid region which includes the DNA-binding domain and a functional nuclear location signal fails to provide kni activity to the embryo. However, a truncated KNI protein that contains additional 47 amino acids exerts rather strong kni activity which is functionally defined by a weak kni mutant phenotype of the embryo. The additional 47-amino-acid stretch includes a transcriptional repressor domain which acts in the context of a heterologous DNA-binding domain of the yeast transcriptional activator GAL4. The different domains of KNI as defined by functional studies are conserved during insect evolution.
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Gerwin, N., A. La Rosée, F. Sauer, H. P. Halbritter, M. Neumann, H. Jäckle, and U. Nauber. "Functional and conserved domains of the Drosophila transcription factor encoded by the segmentation gene knirps." Molecular and Cellular Biology 14, no. 12 (December 1994): 7899–908. http://dx.doi.org/10.1128/mcb.14.12.7899-7908.1994.
Full textAbstract:
The Drosophila gap gene knirps (kni) is required for abdominal segmentation. It encodes a steroid/thyroid orphan receptor-type transcription factor which is distributed in a broad band of nuclei in the posterior region of the blastoderm. To identify essential domains of the kni protein (KNI), we cloned and sequenced the DNA encompassing the coding region of nine kni mutant alleles of different strength and kni-homologous genes of related insect species. We also examined in vitro-modified versions of KNI in various assay systems both in vitro and in tissue culture. The results show that KNI contains several functional domains which are arranged in a modular fashion. The N-terminal 185-amino-acid region which includes the DNA-binding domain and a functional nuclear location signal fails to provide kni activity to the embryo. However, a truncated KNI protein that contains additional 47 amino acids exerts rather strong kni activity which is functionally defined by a weak kni mutant phenotype of the embryo. The additional 47-amino-acid stretch includes a transcriptional repressor domain which acts in the context of a heterologous DNA-binding domain of the yeast transcriptional activator GAL4. The different domains of KNI as defined by functional studies are conserved during insect evolution.
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Youn, Ji-Young, Helena Friesen, Takuma Kishimoto, William M. Henne, Christoph F. Kurat, Wei Ye, Derek F. Ceccarelli, et al. "Dissecting BAR Domain Function in the Yeast Amphiphysins Rvs161 and Rvs167 during Endocytosis." Molecular Biology of the Cell 21, no. 17 (September 2010): 3054–69. http://dx.doi.org/10.1091/mbc.e10-03-0181.
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BAR domains are protein modules that bind to membranes and promote membrane curvature. One type of BAR domain, the N-BAR domain, contains an additional N-terminal amphipathic helix, which contributes to membrane-binding and bending activities. The only known N-BAR-domain proteins in the budding yeast Saccharomyces cerevisiae, Rvs161 and Rvs167, are required for endocytosis. We have explored the mechanism of N-BAR-domain function in the endocytosis process using a combined biochemical and genetic approach. We show that the purified Rvs161–Rvs167 complex binds to liposomes in a curvature-independent manner and promotes tubule formation in vitro. Consistent with the known role of BAR domain polymerization in membrane bending, we found that Rvs167 BAR domains interact with each other at cortical actin patches in vivo. To characterize N-BAR-domain function in endocytosis, we constructed yeast strains harboring changes in conserved residues in the Rvs161 and Rvs167 N-BAR domains. In vivo analysis of the rvs endocytosis mutants suggests that Rvs proteins are initially recruited to sites of endocytosis through their membrane-binding ability. We show that inappropriate regulation of complex sphingolipid and phosphoinositide levels in the membrane can impinge on Rvs function, highlighting the relationship between membrane components and N-BAR-domain proteins in vivo.
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Yi, Jae Youn, Innoc Han, and Eok-Soo Oh. "Transmembrane DomainDependent Functional Oligomerization of Syndecans." Scientific World JOURNAL 6 (2006): 457–59. http://dx.doi.org/10.1100/tsw.2006.92.
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Cell surface adhesion receptors of the syndecan family initiate intracellular events through clustering of receptors. This crucial clustering occurs through receptor dimerization or oligomerization, which is mediated by receptor transmembrane domains. However, the exact role of the transmembrane domain during receptor activation is not fully understood. Researchers have not yet determined whether the transmembrane domain functions solely in the physical aspects of receptor clustering, or whether the domain has additional functional roles. Here we review recent advances in understanding the functionality of transmembrane domain–dependent oligomerization of syndecan cell adhesion receptor.
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Fromm, George, Christina de Vries, Rachel Byron, Jennifer Fields, Steven Fiering, Mark Groudine, M. A. Bender, James Palis, and Michael Bulger. "Histone hyperacetylation within the β-globin locus is context-dependent and precedes high-level gene expression." Blood 114, no. 16 (October 15, 2009): 3479–88. http://dx.doi.org/10.1182/blood-2009-03-210690.
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Abstract Active gene promoters are associated with covalent histone modifications, such as hyperacetylation, which can modulate chromatin structure and stabilize binding of transcription factors that recognize these modifications. At the β-globin locus and several other loci, however, histone hyperacetylation extends beyond the promoter, over tens of kilobases; we term such patterns of histone modifications “hyperacetylated domains.” Little is known of either the mechanism by which these domains form or their function. Here, we show that domain formation within the murine β-globin locus occurs before either high-level gene expression or erythroid commitment. Analysis of β-globin alleles harboring deletions of promoters or the locus control region demonstrates that these sequences are not required for domain formation, suggesting the existence of additional regulatory sequences within the locus. Deletion of embryonic globin gene promoters, however, resulted in the formation of a hyperacetylated domain over these genes in definitive erythroid cells, where they are otherwise inactive. Finally, sequences within β-globin domains exhibit hyperacetylation in a context-dependent manner, and domains are maintained when transcriptional elongation is inhibited. These data narrow the range of possible mechanisms by which hyperacetylated domains form.
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Rounge, Trine B., Thomas Rohrlack, Ave Tooming-Klunderud, Tom Kristensen, and Kjetill S. Jakobsen. "Comparison of Cyanopeptolin Genes in Planktothrix, Microcystis, and Anabaena Strains: Evidence for Independent Evolution within Each Genus." Applied and Environmental Microbiology 73, no. 22 (October 5, 2007): 7322–30. http://dx.doi.org/10.1128/aem.01475-07.
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ABSTRACT The major cyclic peptide cyanopeptolin 1138, produced by Planktothrix strain NIVA CYA 116, was characterized and shown to be structurally very close to the earlier-characterized oscillapeptin E. A cyanopeptolin gene cluster likely to encode the corresponding peptide synthetase was sequenced from the same strain. The 30-kb oci gene cluster contains two novel domains previously not detected in nonribosomal peptide synthetase gene clusters (a putative glyceric acid-activating domain and a sulfotransferase domain), in addition to seven nonribosomal peptide synthetase modules. Unlike in two previously described cyanopeptolin gene clusters from Anabaena and Microcystis, a halogenase gene is not present. The three cyanopeptolin gene clusters show similar gene and domain arrangements, while the binding pocket signatures deduced from the adenylation domain sequences and the additional tailoring domains vary. This suggests loss and gain of tailoring domains within each genus, after the diversification of the three clades, as major events leading to the present diversity. The ABC transporter genes associated with the cyanopeptolin gene clusters form a monophyletic clade and accordingly are likely to have evolved as part of the functional unit. Phylogenetic analyses of adenylation and condensation domains, including domains from cyanopeptolins and microcystins, show a closer similarity between the Planktothrix and Microcystis cyanopeptolin domains than between these and the Anabaena domain. No clear evidence of recombination between cyanopeptolins and microcystins could be detected. There were no strong indications of horizontal gene transfer of cyanopeptolin gene sequences across the three genera, supporting independent evolution within each genus.
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Adayel, Reham, Yakoub Bazi, Haikel Alhichri, and Naif Alajlan. "Deep Open-Set Domain Adaptation for Cross-Scene Classification based on Adversarial Learning and Pareto Ranking." Remote Sensing 12, no. 11 (May 27, 2020): 1716. http://dx.doi.org/10.3390/rs12111716.
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Most of the existing domain adaptation (DA) methods proposed in the context of remote sensing imagery assume the presence of the same land-cover classes in the source and target domains. Yet, this assumption is not always realistic in practice as the target domain may contain additional classes unknown to the source leading to the so-called open set DA. Under this challenging setting, the problem turns to reducing the distribution discrepancy between the shared classes in both domains besides the detection of the unknown class samples in the target domain. To deal with the openset problem, we propose an approach based on adversarial learning and pareto-based ranking. In particular, the method leverages the distribution discrepancy between the source and target domains using min-max entropy optimization. During the alignment process, it identifies candidate samples of the unknown class from the target domain through a pareto-based ranking scheme that uses ambiguity criteria based on entropy and the distance to source class prototype. Promising results using two cross-domain datasets that consist of very high resolution and extremely high resolution images, show the effectiveness of the proposed method.
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Vyas, Payal, and David T. Brown. "N- and C-terminal Domains Determine Differential Nucleosomal Binding Geometry and Affinity of Linker Histone Isotypes H10 and H1c." Journal of Biological Chemistry 287, no. 15 (February 10, 2012): 11778–87. http://dx.doi.org/10.1074/jbc.m111.312819.
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Eukaryotic linker or H1 histones modulate DNA compaction and gene expression in vivo. In mammals, these proteins exist as multiple isotypes with distinct properties, suggesting a functional significance to the heterogeneity. Linker histones typically have a tripartite structure composed of a conserved central globular domain flanked by a highly variable short N-terminal domain and a longer highly basic C-terminal domain. We hypothesized that the variable terminal domains of individual subtypes contribute to their functional heterogeneity by influencing chromatin binding interactions. We developed a novel dual color fluorescence recovery after photobleaching assay system in which two H1 proteins fused to spectrally separable fluorescent proteins can be co-expressed and their independent binding kinetics simultaneously monitored in a single cell. This approach was combined with domain swap and point mutagenesis to determine the roles of the terminal domains in the differential binding characteristics of the linker histone isotypes, mouse H10 and H1c. Exchanging the N-terminal domains between H10 and H1c changed their overall binding affinity to that of the other variant. In contrast, switching the C-terminal domains altered the chromatin interaction surface of the globular domain. These results indicate that linker histone subtypes bind to chromatin in an intrinsically specific manner and that the highly variable terminal domains contribute to differences between subtypes. The methods developed in this study will have broad applications in studying dynamic properties of additional histone subtypes and other mobile proteins.
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KIANI, Chris, Vivian LEE, Liu CAO, Liwen CHEN, Yaojiong WU, Yaou ZHANG, Mark E. ADAMS, and Burton B. YANG. "Roles of aggrecan domains in biosynthesis, modification by glycosaminoglycans and product secretion." Biochemical Journal 354, no. 1 (February 8, 2001): 199–207. http://dx.doi.org/10.1042/bj3540199.
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Aggrecan is a member of the chondroitin sulphate (CS) proteoglycan family, which also includes versican/PG-M, neurocan and brevican. Members of this family exhibit structural similarity: a G1 domain at the N-terminus and a G3 domain at the C-terminus, with a central sequence for modification by CS chains. A unique feature of aggrecan is the insertion of three additional domains, an inter-globular domain (IGD), a G2 domain and a keratan sulphate (KS) domain (sequence modified by KS chains), between the G1 domain and the CS domain (sequence modified by CS chains). The G1 and G3 domains have been implicated in product secretion, but G2, although structurally similar to the tandem repeats of G1, performs an unknown function. To define the functions of each aggrecan domain in product processing, we cloned and expressed these domains in various combinations in COS-7 cells. The results indicated that the G3 domain enhanced product secretion, alone or in combination with the KS or CS domain, and promoted glycosaminoglycan (GAG) chain attachment. Constructs containing the G1 domain were not secreted. Addition of a CS domain sequence to G1 reduced this inhibition, but GAG chain attachment was still decreased. The potential GAG chain attachment site in the IGD was occupied by GAGs, and IGD product was secreted efficiently. The KS domain was modified by GAG chains and secreted. Finally, the G2 domain was expressed but not secreted, and inhibited secretion of the IGD when expressed as an IGD–G2 combination.
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Headey, Stephen J., Kerri S. Leeding, Raymond S. Norton, and Leon A. Bach. "Contributions of the N- and C-terminal domains of IGF binding protein-6 to IGF binding." Journal of Molecular Endocrinology 33, no. 2 (October 2004): 377–86. http://dx.doi.org/10.1677/jme.1.01547.
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Insulin-like growth factors IGF-I and IGF -II are important mediators of growth. A family of six high affinity IGF binding proteins (IGFBPs) modulate IGF action. IGFBPs have three domains, of which the N- and C-domains are involved in high affinity IGF binding. IGFBP-6 is unique in its 20–100-fold IGF-II binding specificity over IGF-I. The aim of this study was to determine the contributions of the N- and C-domains of IGFBP-6 to its IGF binding properties. We confirmed that differential dissociation kinetics are responsible for the IGF-II binding preference of IGFBP-6. The N-domain has rapid association kinetics, similar to full-length IGFBP-6, but both IGF-I and -II dissociate rapidly from this domain, thereby reducing its binding affinity for IGF-II ~50-fold. However, the N-domain binds IGF-I and -II with similar affinities and it has a similar IGF-I binding affinity to full-length IGFBP-6. This suggests that the C-domain confers the IGF-II binding preference of IGFBP-6; indeed, IGF-I bound inconsistently with very low affinity to the C-domain. Coincubation studies showed that isolated N- and C-domains of IGFBP-6 do not strongly cooperate to enhance IGF binding. The results of the binding studies are supported by the effects of the IGFBP-6 domains on IGF-induced colon cancer cell proliferation; the N-domain inhibited IGF-II induced proliferation with ~20-fold lower potency than IGFBP-6 and it was equipotent in inhibiting IGF-I- and IGF-II-induced proliferation. Coincubation of C-domain had no additional effect on N-domain-induced inhibition of proliferation. In conclusion, both the N- and C-domains of IGFBP-6 are involved in IGF binding, the C-domain is responsible for the IGF-II binding preference of IGFBP-6 and intact IGFBP-6 is necessary for high affinity IGF binding.
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Kang, Byung Ok, Hyeong Bae Jeon, and Jeon Gue Park. "Speech Recognition for Task Domains with Sparse Matched Training Data." Applied Sciences 10, no. 18 (September 4, 2020): 6155. http://dx.doi.org/10.3390/app10186155.
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We propose two approaches to handle speech recognition for task domains with sparse matched training data. One is an active learning method that selects training data for the target domain from another general domain that already has a significant amount of labeled speech data. This method uses attribute-disentangled latent variables. For the active learning process, we designed an integrated system consisting of a variational autoencoder with an encoder that infers latent variables with disentangled attributes from the input speech, and a classifier that selects training data with attributes matching the target domain. The other method combines data augmentation methods for generating matched target domain speech data and transfer learning methods based on teacher/student learning. To evaluate the proposed method, we experimented with various task domains with sparse matched training data. The experimental results show that the proposed method has qualitative characteristics that are suitable for the desired purpose, it outperforms random selection, and is comparable to using an equal amount of additional target domain data.
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Lehrenfeld, Christoph, and Maxim Olshanskii. "An Eulerian finite element method for PDEs in time-dependent domains." ESAIM: Mathematical Modelling and Numerical Analysis 53, no. 2 (March 2019): 585–614. http://dx.doi.org/10.1051/m2an/2018068.
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The paper introduces a new finite element numerical method for the solution of partial differential equations on evolving domains. The approach uses a completely Eulerian description of the domain motion. The physical domain is embedded in a triangulated computational domain and can overlap the time-independent background mesh in an arbitrary way. The numerical method is based on finite difference discretizations of time derivatives and a standard geometrically unfitted finite element method with an additional stabilization term in the spatial domain. The performance and analysis of the method rely on the fundamental extension result in Sobolev spaces for functions defined on bounded domains. This paper includes a complete stability and error analysis, which accounts for discretization errors resulting from finite difference and finite element approximations as well as for geometric errors coming from a possible approximate recovery of the physical domain. Several numerical examples illustrate the theory and demonstrate the practical efficiency of the method.
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Martin-Serrano, Juan, David Perez-Caballero, and Paul D. Bieniasz. "Context-Dependent Effects of L Domains and Ubiquitination on Viral Budding." Journal of Virology 78, no. 11 (June 1, 2004): 5554–63. http://dx.doi.org/10.1128/jvi.78.11.5554-5563.2004.
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ABSTRACT Many enveloped viruses encode late assembly domains, or L domains, that facilitate virion egress. PTAP-type L domains act by recruiting the ESCRT-I (endosomal sorting complex required for transport I) component Tsg101, and YPXL/LXXLF-type L domains recruit AIP-1/ALIX, both of which are class E vacuolar protein sorting (VPS) factors, normally required for the generation of vesicles within endosomes. The binding cofactors for PPXY-type L domains have not been unambiguously resolved but may include Nedd4-like ubiquitin ligases. Largely because they act as autonomous binding sites for host factors, L domains are generally transferable and active in a context-independent manner. Ebola virus matrix protein (EbVP40) contains two overlapping L-domain motifs within the sequence ILPTAPPEYMEA. Here, we show that both motifs are required for efficient EbVP40 budding. However, upon transplantation into two different retroviral contexts, the relative contributions of the PTAP and PPEY motifs differ markedly. In a murine leukemia virus carrying the EbVP40 sequence, both motifs contributed to overall L domain activity, and budding proceeded in a partly Tsg101-independent manner. Conversely, when transplanted into the context of human immunodeficiency virus type 1 (HIV-1), EbVP40 L-domain activity was entirely due to a PTAP-Tsg101 interaction. In fact, a number of PPXY-type L domains were inactive in the context of HIV-1. Surprisingly, PTAP and YPXL-type L domains that simulated HIV-1 budding reduced the amount of ubiquitin conjugated to Gag, while inactive PPXY-type L domains increased Gag ubiquitination. These observations suggest that active L domains recruit deubiquitinating enzymes as a consequence of class E VPS factor recruitment. Moreover, context-dependent L-domain function may reflect distinct requirements for host functions during the morphogenesis of different viral particles or the underlying presence of additional, as yet undiscovered L domains.
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Majerus, Elaine M., Patricia J. Anderson, and J. Evan Sadler. "Characterization of the Binding Interaction between ADAMTS13 and von Willebrand Factor (VWF)." Blood 104, no. 11 (November 16, 2004): 515. http://dx.doi.org/10.1182/blood.v104.11.515.515.
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Abstract VWF multimers are cleaved into smaller less thrombogenic fragments in plasma by ADAMTS13. Deficiency of ADAMTS13 activity leads to thombotic thrombocytopenic purpura (TTP), a disease characterized by thrombocytopenia, microangiopathic hemolytic anemia, fever, neurological decline, and renal insufficiency. ADAMTS13 is a member of the A Disintegrin and Metalloprotease with ThromboSpondin repeats family that has characteristic motifs including a signal sequence, a propeptide, a catalytic metalloprotease domain, a disintegrin domain, a thrombospondin-1 (TSP1) repeat, a cysteine-rich region, and a spacer domain. These domains are followed in ADAMTS13 by seven additional TSP1 repeats and two C-terminal CUB domains. Previous work has shown that ADAMTS13 truncated after the spacer domain retains proteolytic activity towards VWF, but little is known about the potential role of the additional C-terminal TSP1 and CUB domains in VWF binding or cleavage. We therefore developed an enzyme-linked immunosorbent assay (ELISA)-based system to study ADAMTS13-VWF binding. VWF was immobilized in microtiter wells and incubated with plasma or recombinant ADAMTS13 variants. Bound ADAMTS13 was detected directly by solubilization and Western blotting, or indirectly by ELISA. ADAMTS13 proteolytic activity towards VWF is enhanced by denaturation of VWF with urea or guanidine, but ADAMTS13 bound specifically to VWF without prior denaturation. EDTA increased the binding of ADAMTS13 to VWF and prevented proteolysis of the immobilized VWF. Binding was saturable and time-dependent with maximal binding in two hours. Binding was reversible with a half-time for dissociation of four hours. ADAMTS13 in normal human plasma but not in plasma from a patient with TTP bound immobilized VWF. The stoichiometry of VWF monomers to ADAMTS13 at saturation was approximately 2 (range 1–4) and the Kd of recombinant ADAMTS13 binding to VWF was 12 nM (range 5–26 nM). This Kd for binding is similar to the Km for VWF cleavage of 16 nM determined independently, and both are comparable to the estimated plasma ADAMTS13 concentration of 8 nM. The properties of C-terminally truncated ADAMTS13 constructs suggest a regulatory function for certain domains. Truncation after the 8th TSP1 domain decreased the Kd 2-fold. Further truncation after either the 6th or 7th TSP1 domain increased the Kd 2-fold relative to full-length ADAMTS13. Truncation after the spacer domain gave binding properties indistinguishable from full-length ADAMTS13. Truncation after the metalloprotease domain gave no detectable binding to VWF. Therefore, binding of ADAMTS13 to VWF requires sequences in the cysteine-rich or spacer domains, and is modulated by sequences in at least the 8th TSP1 repeat and the CUB domains.
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Sheets, Michael F., and Dorothy A. Hanck. "Molecular Action of Lidocaine on the Voltage Sensors of Sodium Channels." Journal of General Physiology 121, no. 2 (February 1, 2003): 163–75. http://dx.doi.org/10.1085/jgp.20028651.
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Block of sodium ionic current by lidocaine is associated with alteration of the gating charge-voltage (Q-V) relationship characterized by a 38% reduction in maximal gating charge (Qmax) and by the appearance of additional gating charge at negative test potentials. We investigated the molecular basis of the lidocaine-induced reduction in cardiac Na channel–gating charge by sequentially neutralizing basic residues in each of the voltage sensors (S4 segments) in the four domains of the human heart Na channel (hH1a). By determining the relative reduction in the Qmax of each mutant channel modified by lidocaine we identified those S4 segments that contributed to a reduction in gating charge. No interaction of lidocaine was found with the voltage sensors in domains I or II. The largest inhibition of charge movement was found for the S4 of domain III consistent with lidocaine completely inhibiting its movement. Protection experiments with intracellular MTSET (a charged sulfhydryl reagent) in a Na channel with the fourth outermost arginine in the S4 of domain III mutated to a cysteine demonstrated that lidocaine stabilized the S4 in domain III in a depolarized configuration. Lidocaine also partially inhibited movement of the S4 in domain IV, but lidocaine's most dramatic effect was to alter the voltage-dependent charge movement of the S4 in domain IV such that it accounted for the appearance of additional gating charge at potentials near −100 mV. These findings suggest that lidocaine's actions on Na channel gating charge result from allosteric coupling of the binding site(s) of lidocaine to the voltage sensors formed by the S4 segments in domains III and IV.
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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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Bykerk, Vivian P., Elisabeth Lie, Susan J. Bartlett, Rieke Alten, Annelies Boonen, Robin Christensen, Daniel E. Furst, et al. "Establishing a Core Domain Set to Measure Rheumatoid Arthritis Flares: Report of the OMERACT 11 RA Flare Workshop." Journal of Rheumatology 41, no. 4 (March 1, 2014): 799–809. http://dx.doi.org/10.3899/jrheum.131252.
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Objective.The OMERACT Rheumatoid Arthritis (RA) Flare Group (FG) is developing a data-driven, patient-inclusive, consensus-based RA flare definition for use in clinical trials, longterm observational studies, and clinical practice. At OMERACT 11, we sought endorsement of a proposed core domain set to measure RA flare.Methods.Patient and healthcare professional (HCP) qualitative studies, focus groups, and literature review, followed by patient and HCP Delphi exercises including combined Delphi consensus at Outcome Measures in Rheumatology 10 (OMERACT 10), identified potential domains to measure flare. At OMERACT 11, breakout groups discussed key domains and instruments to measure them, and proposed a research agenda. Patients were active research partners in all focus groups and domain identification activities. Processes for domain selection and patient partner involvement were case studies for OMERACT Filter 2.0 methodology.Results.A pre-meeting combined Delphi exercise for defining flare identified 9 domains as important (> 70% consensus from patients or HCP). Four new patient-reported domains beyond those included in the RA disease activity core set were proposed for inclusion (fatigue, participation, stiffness, and self-management). The RA FG developed preliminary flare questions (PFQ) to measure domains. In combined plenary voting sessions, OMERACT 11 attendees endorsed the proposed RA core set to measure flare with ≥ 78% consensus and the addition of 3 additional domains to the research agenda for OMERACT 12.Conclusion.At OMERACT 11, a core domain set to measure RA flare was ratified and endorsed by attendees. Domain validation aligning with Filter 2.0 is ongoing in new randomized controlled clinical trials and longitudinal observational studies using existing and new instruments including a set of PFQ.
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Muller, A. J., A. M. Pendergast, M. H. Havlik, L. Puil, T. Pawson, and O. N. Witte. "A limited set of SH2 domains binds BCR through a high-affinity phosphotyrosine-independent interaction." Molecular and Cellular Biology 12, no. 11 (November 1992): 5087–93. http://dx.doi.org/10.1128/mcb.12.11.5087.
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SH2 (src homology region 2) domains are implicated in protein-protein interactions involved in signal transduction pathways. Isolated SH2 domains bind proteins that are tyrosine phosphorylated. A novel, phosphotyrosine-independent binding interaction between BCR, the Philadelphia chromosome breakpoint cluster region gene product, and the SH2 domain of its translocation partner c-ABL has recently been reported. We have examined the ability of additional SH2 domains to bind phosphotyrosine-free BCR and compared this with their ability to bind tyrosine-phosphorylated c-ABL 1b. Of 11 individual SH2 domains examined, 8 exhibited relatively high affinity for c-ABL 1b, whereas only 4 exhibited relatively high affinity for BCR. Binding of tyrosine-phosphorylated c-ABL 1b by the relatively high-affinity ABL and ARG SH2 domains was quantitatively analyzed, and equilibrium dissociation constants for both interactions were estimated to be in the range of 5 x 10(-7) M. The ABL SH2 domain exhibited relatively high affinity for phosphotyrosine-free BCR as well; however, this interaction appears to be about two orders of magnitude weaker than binding of tyrosine-phosphorylated c-ABL 1b. The ARG SH2 domain exhibited relatively weak affinity for BCR and was determined to bind about 10-fold less strongly than the ABL SH2 domain. The ABL and ARG SH2 domains differ by only 10 of 91 amino acids, and the substitution of ABL-specific amino acids into either the amino- or carboxy-terminal half of the ARG SH2 domain was found to increase its affinity for BCR. We discuss these results in terms of a model which has been proposed for peptide binding by class I histocompatibility glycoproteins.
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Muller, A. J., A. M. Pendergast, M. H. Havlik, L. Puil, T. Pawson, and O. N. Witte. "A limited set of SH2 domains binds BCR through a high-affinity phosphotyrosine-independent interaction." Molecular and Cellular Biology 12, no. 11 (November 1992): 5087–93. http://dx.doi.org/10.1128/mcb.12.11.5087-5093.1992.
Full textAbstract:
SH2 (src homology region 2) domains are implicated in protein-protein interactions involved in signal transduction pathways. Isolated SH2 domains bind proteins that are tyrosine phosphorylated. A novel, phosphotyrosine-independent binding interaction between BCR, the Philadelphia chromosome breakpoint cluster region gene product, and the SH2 domain of its translocation partner c-ABL has recently been reported. We have examined the ability of additional SH2 domains to bind phosphotyrosine-free BCR and compared this with their ability to bind tyrosine-phosphorylated c-ABL 1b. Of 11 individual SH2 domains examined, 8 exhibited relatively high affinity for c-ABL 1b, whereas only 4 exhibited relatively high affinity for BCR. Binding of tyrosine-phosphorylated c-ABL 1b by the relatively high-affinity ABL and ARG SH2 domains was quantitatively analyzed, and equilibrium dissociation constants for both interactions were estimated to be in the range of 5 x 10(-7) M. The ABL SH2 domain exhibited relatively high affinity for phosphotyrosine-free BCR as well; however, this interaction appears to be about two orders of magnitude weaker than binding of tyrosine-phosphorylated c-ABL 1b. The ARG SH2 domain exhibited relatively weak affinity for BCR and was determined to bind about 10-fold less strongly than the ABL SH2 domain. The ABL and ARG SH2 domains differ by only 10 of 91 amino acids, and the substitution of ABL-specific amino acids into either the amino- or carboxy-terminal half of the ARG SH2 domain was found to increase its affinity for BCR. We discuss these results in terms of a model which has been proposed for peptide binding by class I histocompatibility glycoproteins.
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Brehm, A., K. Ohbo, and H. Schöler. "The carboxy-terminal transactivation domain of Oct-4 acquires cell specificity through the POU domain." Molecular and Cellular Biology 17, no. 1 (January 1997): 154–62. http://dx.doi.org/10.1128/mcb.17.1.154.
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The POU transcription factor Oct-4 is expressed in totipotent and pluripotent cells of the early mouse embryo and the germ cell lineage. Transactivation capacities of regions flanking the DNA binding domain of Oct-4 were analyzed in undifferentiated and differentiated cell lines. The amino- and carboxy-terminal regions (N domain and C domain) fused to the Gal4 DNA binding domain both functioned as transactivation domains in all cell lines tested. However, the C domain failed to activate transcription in some cell lines in the context of the native protein. The underlying regulatory mechanism appears to involve the POU domain of Oct-4 and can discriminate between different POU domains, since constructs in which the C domain was instead fused to the POU domain of Pit-1 were again equally active in all cell lines. These results indicate that the C domain is subject to cell-type-specific regulation mediated by the Oct-4 POU domain. Phosphopeptide analysis revealed that the cell-type-specific difference of C-domain activity correlates with a difference in Oct-4 phosphorylation status. Since Oct-4 is expressed in a variety of distinct cell types during murine embryogenesis, these results suggest an additional regulatory mechanism for determining Oct-4 function in rapidly changing cell types during development.
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Oliver, Antony W., Sarah A. Jones, Stephen Mark Roe, Steve Matthews, Graham H. Goodwin, and Laurence H. Pearl. "Crystal structure of the proximal BAH domain of the polybromo protein." Biochemical Journal 389, no. 3 (July 26, 2005): 657–64. http://dx.doi.org/10.1042/bj20050310.
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The BAH domain (bromo-associated homology domain) was first identified from a repeated motif found in the nuclear protein polybromo – a large (187 kDa) modular protein comprising six bromodomains, two BAH domains and an HMG box. To date, the BAH domain has no ascribed function, although it is found in a wide range of proteins that contain additional domains involved in either transcriptional regulation (e.g. SET, PHD and bromodomain) and/or DNA binding (HMG box and AT hook). The molecular function of polybromo itself also remains unclear, but it has been identified as a key component of an SWI/SNF (switching/sucrose non-fermenting)-related, ATP-dependent chromatin-remodelling complex PBAF (polybromo, BRG1-associated factors; also known as SWI/SNF-B or SWI/SNFβ). We present in this paper the crystal structure of the proximal BAH domain from chicken polybromo (BAH1), at a resolution of 1.6 Å (1 Å=0.1 nm). Structure-based sequence analysis reveals several features that may be involved in mediating protein–protein interactions.