bluuebunny/crossref_metadata_2025_split huggingface dataset:
Furin-Processed Antigens Targeted to the Secretory Route Elicit Functional TAP1−/−CD8+ T Lymphocytes In Vivo
Authors: Medina Francisco , Ramos Manuel , Iborra Salvador , de León Patricia , Rodríguez-Castro Marta , Del Val Margarita 
Published: September 2009

Abstract
Most pathogen-derived peptides recognized by CD8+ CTL are produced by proteasomes and delivered to the endoplasmic reticulum by the TAP transporters associated with Ag processing. Alternative proteases also produce antigenic peptides, but their actual relevance is unclear. There is a need to quantify the contribution of these supplementary pathways in vitro and in vivo. A well-defined TAP-independent secretory route of Ag processing involves the trans-Golgi network protease furin. Quantitation of this route by using OVA constructs encoded by vaccinia viruses indicates that it provides approximately one-third of all surface complexes of peptide and MHC class I molecules. Generation of the epitope carboxyl terminus is a dramatic rate-limiting step, since bypassing it increased efficiency by at least 1000-fold. Notably, the secretory construct activated a similar percentage of Ag-specific CD8+ T cells in wild type as in TAP1-deficient mice, which allow only secretory routes but which have a 10- to 20-fold smaller CD8 compartment. Moreover, these TAP1−/− OVA-specific CD8+ T lymphocytes accomplished elimination of epitope-bearing cells in vivo. The results obtained with this experimental system underscore the potential of secretory pathways of MHC class I Ag presentation to elicit functional CD8+ T lymphocytes in vivo and support the hypothesis that noncytosolic processing mechanisms may compensate in vivo for the lack of proteasome participation in Ag processing in persons genetically deficient in TAP and thus contribute to pathogen control.
Genomic and Functional Uniqueness of the TNF Receptor-Associated Factor Gene Family in Amphioxus, the Basal Chordate
Authors: Yuan Shaochun , Liu Tong , Huang Shengfeng , Wu Tao , Huang Ling , Liu Huiling , Tao Xin , Yang Manyi , Wu Kui , Yu Yanhong , Dong Meiling , Xu Anlong 
Published: September 2009

Abstract
The TNF-associated factor (TRAF) family, the crucial adaptor group in innate immune signaling, increased to 24 in amphioxus, the oldest lineage of the Chordata. To address how these expanded molecules evolved to adapt to the changing TRAF mediated signaling pathways, here we conducted genomic and functional comparisons of four distinct amphioxus TRAF groups with their human counterparts. We showed that lineage-specific duplication and rearrangement were responsible for the expansion of amphioxus TRAF1/2 and 3 lineages, whereas TRAF4 and 6 maintained a relatively stable genome and protein structure. Amphioxus TRAF1/2 and 3 molecules displayed various expression patterns in response to microbial infection, and some of them can attenuate the NF-κB activation mediated by human TRAF2 and 6. Amphioxus TRAF4 presented two unique functions: activation of the NF-κB pathway and involvement in somite formation. Although amphioxus TRAF6 was conserved in activating NF-κB pathway for antibacterial defense, the mechanism was not the same as that observed in humans. In summary, our findings reveal the evolutionary uniqueness of the TRAF family in this basal chordate, and suggest that genomic duplication and functional divergence of the TRAF family are important for the current form of the TRAF-mediated signaling pathways in humans.
A Novel Role for Plasmin-Mediated Degradation of Opsonizing Antibody in the Evasion of Host Immunity by Virulent, but Not Attenuated, Francisella tularensis
Authors: Crane Deborah D. , Warner Shayna L. , Bosio Catharine M. 
Published: September 2009

Abstract
Opsonization by Abs represents a critical component of the host immune response against many pathogens. The mechanisms by which virulent microbes evade this protective response are not completely understood. In disease mediated by Francisella tularensis, Ab can effectively protect against infections with attenuated strains, for example, LVS, but not virulent strains such as SchuS4. Thus, it is likely that SchuS4 has mechanisms, which are not present in LVS, that allow evasion of opsonization by Ab, dampening the protective effects of these host molecules. Here we demonstrate that evasion of Ab-mediated opsonization and phagocytosis by the highly virulent SchuS4 is associated with its ability to bind the host serine protease plasmin. SchuS4, but not the closely related LVS, bound active plasmin. Plasmin bound SchuS4 degraded exogenous and opsonizing Abs, whereas LVS failed to do so. Furthermore, plasmin-mediated inhibition of Ab opsonization by SchuS4 also inhibited Ab-mediated uptake of this bacterium by macrophages. Ab-mediated uptake of uncoated and opsonized SchuS4 elicited a strong proinflammatory response in infected macrophages. However, plasmin-coated, opsonized SchuS4 poorly elicited production of these protective proinflammatory cytokines. This unique host-pathogen interplay is a novel immune evasion strategy utilized by virulent F. tularensis, and it provides one explanation for the ability of Ab to protect against attenuated, but not virulent, strains of F. tularensis. This mechanism may also represent a more common hereto unrecognized strategy by which virulent bacteria evade detection and clearance by Ig.
Dimorphic Motifs in D0 and D1+D2 Domains of Killer Cell Ig-Like Receptor 3DL1 Combine to Form Receptors with High, Moderate, and No Avidity for the Complex of a Peptide Derived from HIV and HLA-A*2402
Authors: Sharma Deepti , Bastard Karine , Guethlein Lisbeth A. , Norman Paul J. , Yawata Nobuyo , Yawata Makoto , Pando Marcelo , Thananchai Hathairat , Dong Tao , Rowland-Jones Sarah , Brodsky Frances M. , Parham Peter 
Published: September 2009

Abstract
Comparison of mutant killer cell Ig-like receptor (KIR) 3DL1*015 substituted at natural positions of variation showed that tryptophan/leucine dimorphism at position 283 uniquely changes receptor conformation and can strongly influence binding of the A24nef tetramer. Dimorphic motifs at positions 2, 47, and 54 in D0 and 182 and 283 in D1+D2 distinguish the two 3DL1 lineages, typified by 3DL1*005 and 3DL1*015. The interlineage recombinant, KIR3DL1*001, combines D0 of 3DL1*005 with D1+D2 of 3DL1*015 and binds A24nef more strongly than either parent. In contrast, the reciprocal recombinant with D0 from 3DL1*015 and D1+D2 from 3DL1*005 cannot bind A24nef. Thus, D0 polymorphism directly affects the avidity of the KIR3DL1 ligand binding site. From these observations, multiple sequence alignment, and homology modeling, we constructed structural models for KIR3DL1 and its complex with A24nef. In these models, D0, D1, and D2 come together to form a binding surface for A24nef, which is contacted by all three Ig-like domains. A central pocket binds arginine 83, the only Bw4 motif residue essential for KIR3DL1 interaction, similar to the binding of lysine 80 in HLA-C by KIR2DL1. Central to this interaction is a salt bridge between arginine 83 of Bw4 and glutamate 282 of 3DL1, which juxtaposes the functionally influential dimorphism at position 283. Further 3DL1 mutants were tested and shown to have A24nef-binding properties consistent with the models. A24nef was not bound by KIR3DS1, the activating counterpart of KIR3DL1. Moreover, introducing any one of three residues specific to KIR3DS1, serine 163, arginine 166, or leucine 199, into 3DL1*015, abrogated A24nef binding.
Siderophore‐Binding Periplasmatic ProteinFhuDand Related Periplasmic Binding Proteins Involved in Bacterial Iron Uptake
Authors: Krewulak Karla D. , Köster Wolfgang , Vogel Hans J. 
Published: September 2009

AbstractTo fulfill their nutritional requirement for iron, many microorganisms synthesize low‐molecular‐weight iron‐chelating compounds calledsiderophores. These iron sources are transported into the gram‐negative bacterial cellviaspecific uptake pathways that include an outer membrane receptor, a periplasmic binding protein (PBP), and an inner membrane ATP‐binding cassette (ABC) transporter. Gram‐positive bacteria lack an outer membrane, and thus the uptake of the ferric siderophore involves a membrane‐anchored PBP and an ABC transporter. Siderophores are classified as hydroxamate, catecholate, or hydroxycarboxylate type siderophores. This review details what is currently known about the PBP, FhuD (Fhu — ferric hydroxamate uptake), involved in the uptake of hydroxamate‐type siderophores. In addition, several structurally related periplasmic binding proteins that mediate bacterial metal ion transport are also discussed.
Iron‐Binding Protein
Fut
A
1
Authors: Koropatkin Nicole , Pakrasi Himadri B , Smith Thomas J 
Published: September 2009

Abstract

FutA1 belongs to the bacterial extracellular solute‐binding protein family 1 and is part of an ATP‐binding cassette‐type (ABC‐type) transport system involved in the uptake of iron. In
Synechocystis
6803, the
futA1
(
slr1295)
and
futA2
(
slr0513
) genes encode periplasmic binding proteins that have been proposed to be part of a high‐affinity iron‐transport system, although these genes, along with those encoding the transmembrane pore and intracellular ATPase proteins, are widely distributed throughout the genome. While the solute‐binding domains in the cluster 9 ABC transport systems have a relatively rigid α‐helix running down the back of the protein, which restricts domain movement, FutA1 has two β‐strands connecting the two domains of the protein. It is likely that these β‐strands permit the large domain movement observed during iron binding and release. In FutA1, iron is chelated by four tyrosine and one histidine residues. These tyrosine residues do not move during the opening and closing of the binding‐site cleft. This is likely due to a strong secondary shell of interacting residues which also improve iron‐tyrosine interactions by increasing the electronegativity of the tyrosine hydroxyls. Unlike a number of other periplasmic iron‐binding proteins, there are no apparent anion interactions with the bound ferric iron.
[
Ni
Fe
] Hydrogenase Maturing Proteins
Hyp
C
,
Hyp
D
,
Hyp
E
Authors: Watanabe Satoshi , Miki Kunio 
Published: September 2009

Abstract

[NiFe] hydrogenases carry an NiFe(CO)(CN)
2
center at the active site, which catalyzes the reversible oxidation of molecular hydrogen. Hyp proteins (HypABCDEF) are required for the maturation of [NiFe] hydrogenase. HypA and HypB are involved in the insertion of the nickel atom. HypE and HypF catalyze the biosynthesis of the cyanide ligand in the form of HypE‐thiocyanate. HypC and HypD are assumed to deliver the iron atom with diatomic ligands to the active site of hydrogenase. The structures of HypC consist of an OB‐fold like β‐barrel domain and C‐terminal one or two α helices. The C‐terminal helices are shown to be quite flexible. The structure of HypE consists of two α/β domains and is similar to other PurM superfamily proteins. The C‐terminal tail of HypE adopts an outward extended conformation in the absence of adenosine 5′ triphosphate (ATP) or an inward closed conformation in the presence of ATP. The structure of HypD is composed of two α/β domains and an Fe–S cluster binding domain. Conserved regions of HypD show its probable iron binding and active sites for cyanation. The [4Fe–4 S] cluster environment of HypD is shown to be quite similar to that of ferredoxin : thioredoxin reductase (FTR). The cyanation reaction can be catalyzed through thiol redox signaling in the HypCDE complex.
Amyloids and Protein Aggregation—Analytical Methods
Authors: Li Huiyuan , Rahimi Farid , Sinha Sharmistha , Maiti Panchanan , Bitan Gal , Murakami Kazuma 
Published: September 2009

AbstractMore than 30 diseases are associated with amyloid‐forming proteins, which undergo conformational alterations and “misfolding” under particular conditions. These proteins deposit as insoluble proteinaceous aggregates generating disease‐specific histopathologic lesions. The proteins contributing to each disease have dissimilar sequences and native structures, yet they share the commonality of forming insoluble amyloid aggregates characterized by fibrillar morphology and cross‐β structure. Presently, it is thought that the predominant agents causing cell toxicity and tissue damage are soluble, prefibrillar assemblies of these proteins. Because of the metastable nature of these prefibrillar assemblies and the noncrystalline nature of fibrillar protein aggregates, structural study of amyloid proteins is difficult. As a result, structural characterization of these proteins is typically done using combinations of low‐resolution analytical methods. Here, we present a compendium of analytical methods used to study the secondary, tertiary, and quaternary structures, and morphology of prefibrillar and fibrillar assemblies of amyloid‐forming proteins.
Depth Profiling
Authors: Martin Guillaume , Garcia Philippe , Sauvage Thierry 
Published: September 2009

Abstract
Elemental depth profiles up to few micrometers below the surface of samples can be determined using nuclear methods. Two types of depth profiling techniques are mainly distinguished on the basis of the shape of the cross section of the reaction between incident particles and target atoms. First, for nonresonant reactions with a cross section that extends over a wide range of energies, the energy of detected ions may vary as a function of the depth at which they are emitted. The analysis of the target at a given incident energy therefore enables its elemental depth profiling by converting the energy of detected ions into their emission depth. Second, resonant reactions that show a sharp and strong resonance at a given energy usually provide the best depth resolutions. As incident ions penetrate the analyzed material, their energy decreases and most of detected particles originate from depths at which the incident ions have reached the resonance energy. In this case, several analyses are needed to probe the target at all relevant depths. The procedure to perform depth profiling analyses requires firstly the determination of the experimental conditions that optimize the depth resolution and secondly extracting from the experimental spectra depth profiles with accurate error bars.
Coprecipitation in Trace Element Analysis
Authors: Inagaki Kazumi , Zhu Yanbei , Miura Tsutomu , Chiba Koichi 
Published: September 2009

AbstractCoprecipitation is one of the classical, but quite useful, techniques for separation/preconcentration for trace element analysis. Many elements can be easily collected with a carrier precipitate, and the handling is simpler and easier compared to that of other techniques such as solvent extraction and solid‐phase extraction. In addition, selective separation can also be designed by controlling of chemical and physical conditions in the procedure. In this section, mechanisms of coprecipitation, selection of a carrier precipitates, selectivity in coprecipitation, and typical examples of coprecipitation in trace element analysis are described.
Differential‐associative processing: A new strategy for learning highly‐similar concepts
Authors: Hannon Brenda , Lozano Gregorio , Frias Sarah , Picallo‐Hernandez Sandra , Fuhrman Robert 
Published: September 2009

AbstractFor many students concepts like fluid and crystallized intelligence are difficult to learn because they have highly‐similar definitions that are easy to confuse. The challenge of learning these highly‐similar, yet often confused concepts is further complicated by the fact that students are tested on exams about differences between the concepts. In this theoretically‐motivated research we test a new strategy for learning highly‐similar pairs of concepts, called differential‐associative processing. The results revealed that performance on multiple‐choice questions was higher when students learned highly‐similar concepts using differential‐associative processing rather than a strategy of their own choice, text‐based elaboration, or identifying similarities and differences. The results also revealed that students spontaneously transferred differential‐associative processing to a neutral control condition. Taken as a whole, the present study supports differential‐associative processing as a useful strategy for learning similar concepts. Copyright © 2009 John Wiley & Sons, Ltd.
Interactive elements for dynamically linked multiple representations in computer simulations
Authors: Rey Günter Daniel 
Published: September 2009

AbstractSeventy‐three students learned central concepts about signal detection theory with an introductory text followed by a computer simulation. Each learner was randomly assigned to one of the three treatment groups: text boxes, scrollbars or drag and drop opportunities to modify parameters in the simulation. These three interactive elements were used for linking the different multiple representations in the simulation dynamically. Retention and transfer test, evaluation of the instructional material as well as time spent with the simulation were used as dependent measures. Learners who had to use scrollbars or had to modify parameters per drag and drop performed better on transfer, but not on retention, than did learners who had to use text boxes. Learners who had to modify parameters per drag and drop also evaluated the instructional material better than did learners who had to use text boxes. These results are consistent with the split‐attention principle. Copyright © 2009 John Wiley & Sons, Ltd.
Structural Evolution and Copper‐Ion Release Behavior of Cu‐pHEMA Hybrids Synthesized In Situ
Authors: Liu Yen‐Yu , Tung Tsan‐Hua , Liu Kun‐Ho , Chen San‐Yuan , Liu Dean‐Mo 
Published: September 2009

AbstractA novel Cu‐pHEMA hybrid was successfully prepared by in situ photopolymerization of 2‐hydroxyethyl methacrylate (HEMA) monomer in the presence of Cu(II) copper ions, following an in situ chemical reduction. Experimental observations indicate that intermolecular interactions such as the coupling force and hydrogen bonding between the Cu and the hydroxyl groups further stabilize the hybrid structure to a considerable extent. Localization of the metallic copper particles within the pHEMA network structure as a result of those intermolecular interactions gives rise to the formation of discretely distributed nanocrystallites with particle sizes ranging from 5 to 25 nm in diameter. A crystallographic change of the Cu nanophase from an amorphous‐like to a crystalline structure is observed as the H2O:HEMA molar ratio increases, upon synthesis, accompanied with an increase in the particle size. A relatively slow and sustained release of the Cu (in the form of cupric ions) from the hybrids was measured for a time period of about 10 days, which also illustrates a Cu(II)‐induced proliferation of the endothelial cells over a relatively small range of release rate of the Cu from the hybrids. Such a new type of Cu‐loaded hybrid hydrogel is expected to be compatible and may be considered as a candidate biomaterial for biomedical/therapeutic uses.
Determination of Materials Selection Performance Indices Through the Combination of Numerical Modeling and Optimization Methods
Authors: Castillo German , Wargnier Hervé , Danis Michel , Brechet Yves 
Published: September 2009

AbstractAfter translation, the first stages traditionally involved in the materials selection are filtration and classification, which require formulation of criteria (constraints or objectives) deduced from information written in the set of material requirements. These criteria, which are representative of the behavior of the material and the studied structure, must be formulated analytically in order to be used during selection stage. However, for complex behavior, analytical processing of models is no longer possible and it can be replaced by a combination of numerical resolution methods and an optimization method which make it possible to obtain approximate formal expressions of the criteria. In this paper, a complete selection method is proposed. The method is applied to the constraints as well as the objectives, in order to carry out the filtration and classification stages at the same time. The study of the thermomechanical behavior of a machine tool frame has been used to demonstrate the validity of the proposed method.
Insights into the Role of New Palladium Pincer Complexes as Robust and Recyclable Precatalysts for Suzuki–Miyaura Couplings in Neat Water
Authors: Inés Blanca , SanMartin Raul , Moure María Jesús , Domínguez Esther 
Published: September 2009

AbstractSuzuki–Miyaura biaryl and diarylmethane syntheses via the coupling of arylboronic acids with aryl and arylmethyl bromides are performed in water by means of two new CNC‐type palladium pincer complexes. Good to excellent results (including high TON values and extended recycling procedures) are obtained in most cases for a range of electronically dissimilar halides and boronic acids. On the basis of a series of kinetics studies, transmission electron microscopy (TEM), mercury drop tests, and quantitative poisoning experiments, the real role of the latter palladacycles, closely linked to the formation and active participation of palladium nanoparticles, is discussed.
Proteinbiochips in der Biomedizin und Biotechnologie
Authors: Weinrich Dirk , Jonkheijm Pascal , Niemeyer Christof M. , Waldmann Herbert 
Published: September 2009

AbstractDank Fortschritten bei Immobilisierungsstrategien für Proteine sind Proteinbiochips in den letzten Jahren immer besser verfügbar geworden. Durch die Integration dieser Assay‐ und Analyseplattformen in die biomedizinische und biotechnologische Forschung konnte das Repertoire an Methoden für die Proteomik, die Biomarkerforschung und die Wirkstoffentwicklung deutlich vergrößert werden. In diesem Kurzaufsatz werden ausgewählte Entwicklungen bei der Anwendung von Proteinbiochips auf diesen Forschungsgebieten beleuchtet.
Applications of Protein Biochips in Biomedical and Biotechnological Research
Authors: Weinrich Dirk , Jonkheijm Pascal , Niemeyer Christof M. , Waldmann Herbert 
Published: September 2009

AbstractProgress in the development of protein‐immobilization strategies and methods has made protein biochips increasingly accessible. The integration of these assay and analysis platforms into biomedical and biotechnological research has substantially expanded the repertoire of methods available for proteomics and biomarker research and for drug development. This Minireview highlights selected developments in the application of protein biochips in these fields.
Mechanical, thermal, and structural characterization of poly(ethylene terephthalate) and poly(butylene terephthalate) blend systems by the addition of postconsumer poly(ethylene terephthalate)
Authors: Baxi R. N. , Pathak S. U. , Peshwe D. R. 
Published: September 2009

AbstractThe focus of this study was mainly on the use of scrap poly(ethylene terephthalate) (PET) in poly(butylene terephthalate)‐rich blend systems. A good combination of tensile and impact properties was observed in the newly formed blend system with scrap PET. The morphology depicted controlled and well‐dispersed phases. The thorough mixing of the constituents was observed in the thermal study. For this innovative blend system, an attempt to correlate the mechanical, thermal, structural, morphological properties and the chemistry of the blend system seemed to be technoeconomical. This study contributed to the recycling of waste material. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010