bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proton Transfer on the Molecular Surface of Proteins and Model Systems
Authors: Friedman Ran 
Published: August 2009

AbstractProton transfer (PT) reactions take place on the molecular surface of proteins, membranes, ionic polymers, and other molecules. The rates of the reactions can be followed experimentally, while the atomistic details can be elucidated by molecular modeling. This manuscript gives a brief overview of the use of computer simulations and molecular modeling, in conjuction with experiments, to study PT reactions on the surface of solvated molecules. An integrative approach is discussed, where molecular dynamics simulations are performed with a protein, and quantum‐mechanics‐based calculations are performed on a small molecule. The simulation results allow the identification of the necessary conditions that yield PT reactions on the molecular surface. The reactions are efficient when they involve a donor and acceptor located a few Å apart and under the influence of a negative electrostatic field. In proton‐pumping proteins, it is possible to identify such conditions a priori and locate proton‐attracting antenna domains without the need to mutate each potential donor and acceptor. Based on density functional theory calculations, the arrangement of water molecules that interconnect the donor and acceptor moieties is suggested as the rate‐limiting step for proton transfer on the molecular surface.
OHO Hydrogen Bond Geometries and NMR Chemical Shifts: From Equilibrium Structures to Geometric H/D Isotope Effects, with Applications for Water, Protonated Water, and Compressed Ice
Authors: Limbach Hans‐Heinrich , Tolstoy Peter M. , Pérez‐Hernández Natalia , Guo Jing , Shenderovich Ilya G. , Denisov Gleb S. 
Published: August 2009

AbstractHydrogen bond geometries and 1H NMR chemical shifts of OHO hydrogen‐bonded systems have been analyzed using an improved valence bond order model. This model predicts that the heavy atom hydrogen bond coordinate q2 = r1 + r2 is a function of the proton coordinate q1 = (r1 ‐ r2), where r1 and r2 represent the OH and the HO distances.In the first part, it is shown that this correlation reproduces published equilibrium geometries of the Zundel cation H5O2+ as well as those of water clusters in the gas phase and embedded in the fullerene C180. Using the example of the water hexamer, it is shown that changing the level of calculation shifts the calculated geometries along the correlation curve, but not away from the curve. In order to take quantum zero‐point vibrational effects (QZPVE) into account, an empirical correction is proposed. It is shown that this correction properly describes the calculated classical and quantum hydrogen bond geometries of compressed ice as well as calculated geometric H/D isotope effects. The improved valence bond order model is used to analyze a large number of OHO hydrogen bond geometries contained in the Cambridge Structural Database.In the second part, a relation between the geometries and the 1H NMR chemical shieldings of OHO hydrogen bonded systems is established using the valence bond order model. GIAO calculations of the isolated symmetric Zundel cation where H is located in the hydrogen bond center show only a small dependence of the chemical shifts on the O…O distance. This result is rationalized in terms of neighbor group effects and deshielding in the naked proton. The consequence is that the 1H NMR chemical shifts are not much affected by QZPVE. Calculations on water clusters indicate that the influence of the chemical environment of the OHO hydrogen bonds on their 1H NMR chemical shifts is smaller for the strong hydrogen bond regime but large for the weak hydrogen bond regime. A simple chemical shift vs. q1 relation is then used to calculate the average chemical shifts of water clusters in the regime of fast hydrogen bond exchange between hydrogen bonded and free OH groups. It is shown that average chemical shifts of about 6 ppm are possible as the clusters considered exhibit a broad distribution of stronger and weaker hydrogen bonds. The implications for water in organic solvents and for liquid water are discussed, based on published data on the 1H chemical shift distribution in the latter.
Excited‐State Proton Transfer in Chiral Environments: Photoracemization of BINOLs
Authors: Solntsev Kyril M. , Bartolo Elizabeth‐Ann , Pan George , Muller Gilles , Bommireddy Shruthi , Huppert Dan , Tolbert Laren M. 
Published: August 2009

AbstractWe have studied excited‐state proton transfer (ESPT) from chiral proton donors to chiral and achiral acceptors. The key role of the exergonicity of the reaction and the transition‐state position along the reaction coordinate for the existence of an enantiomeric effect was established. This effect was observed for “super” photoacids (ΔG ≪ 0) and vanished for endergonic reactions (ΔG > 0) where a “late” transition state similar to planar achiral binaphtholate anion occurs. As a result, photoracemization was observed, as confirmed by circular dichroism spectroscopy. The photoracemization effects were studied for several chiral photoacids (BINOLs and their ethers) and proton acceptors (amines, aminoalcohols, and water) using UV‐vis, steady‐state fluorescence, and time‐resolved fluorescence spectroscopies. The nature of the solvent and the proton acceptor, as well as the chemical structure of the BINOL, played a pivotal role in the photochemical reactivity of the system. Two proposed pathways competed for photoracemization: excited‐state inter‐ and intra‐molecular proton transfer, the former being more effective. Irradiation of the dimethoxy BINOL derivative, which lacks an acidic proton and cannot undergo ESPT, produced no appreciable reaction or racemization.
Cation‐Enhanced Deprotonation of Water by a Strong Photobase
Authors: Munitz Noga , Avital Yotam , Pines Dina , Nibbering Erik T. J. , Pines Ehud 
Published: August 2009

AbstractWe have used picosecond fluorescence spectroscopy to study the proton‐dissociation dynamics of bulk water and H2O molecules solvating Mg2+ ions in aqueous solutions. We have analyzed the photo‐initiated proton‐transfer reaction to a photobase 6‐aminoquinoline by the Collins‐Kimball approach and have modeled the ensuing bimolecular reaction dynamics by the Smoluchowski equation with radiation boundary conditions. We have found the on‐contact proton transfer rate to follow the Marcus free‐energy relation for proton transfer and estimate by this rate‐equilibrium correlation the considerable enhancement in the acidity of the water molecules solvating the Mg2+ ion. Our findings may be used in the study of metallo‐enzymes such as carbonic anhydrases (CAs), which catalyze the reversible addition reaction of OH− to CO2 by increasing the reactivity of the zinc‐bound water molecules by means of stabilizing the product of water dissociation, the OH− anion.
Comparison of Craniofacial and Dentoalveolar Morphologies of Three Japanese Monozygotic Twin Pairs with Cleft Lip and/or Palate Discordancy
Authors: Moriyama Keiji , Motohashi Nobuyoshi , Kitamura Atsushi , Kuroda Takayuki 
Published: August 2009

Objective In this study, we analyzed the craniofacial and dentoalveolar morphologies of three pairs of monozygotic twins discordant for cleft lip and/or palate (CL/P) in order to evaluate the effects of environmental factors on growth and development. Design Craniofacial and dentoalveolar morphologies revealed by analyses of cephalograms and dental casts were compared for each pair of twins discordant for CUP. Subjects In case 1, the subjects were 10-year-old male twins, one of whom had a repaired unilateral cleft lip and alveolus and one of whom had an unrepaired unilateral cleft lip. In case 2, the subjects were 13-year-old female twins, one of whom had a repaired bilateral cleft lip and palate and one of whom had an unrepaired unilateral cleft lip. In case 3, the subjects were 9-year-old female twins, one of whom had a repaired unilateral cleft lip and palate and one of whom had no cleft. Results Cephalometric analysis disclosed distinguished intrapair differences in the maxillary and mandibular morphologies in cases 2 and 3. However, the tooth axes of the incisors in operated subjects were consistently influenced in all three cases. Dental cast analysis indicated that the shapes and sizes of the alveolar and dental arches in the operated subjects were affected in case 2 and, more severely, in case 3, while they looked fairly similar in case 1. Conclusions Cephalometric and dental cast analyses demonstrated characteristic intrapair differences between the twins discordant for CL/P according to each cleft type. These morphological differences indicate that surgical closure of clefts may have considerable effects on craniofacial and dentoalveolar growth and development in CL/P patients.
Strongylid Community Structure of the Przewalski's Horses (Equus ferus Przewalskii) from the Biosphere Reserve "Askania-Nova", Ukraine
Authors: Kuzmina T. , Zvegintsova N. , Zharkikh T. 
Published: August 2009

Strongylid Community Structure of the Przewalski's Horses (Equus ferus Przewalskii) from the Biosphere Reserve "Askania-Nova", UkraineSpecies composition and the structure of strongylid community of the Przewalski's horse (Equus ferus przewalskiiPoljakov, 1881) semi-free population at the "Askania-Nova" Biosphere Reserve were studied by thein vivomethod of diagnostic deworming. After deworming of 24 adult Przewalski's horses by the anthelmintic "Univerm" (0.2% aversectin C, Russia), 25,815 strongylid specimens were collected and identified. Thirty-one strongylid species of 12 genera were found including 6 species of the subfamily Strongylinae and 25 — of Cyathostominae. Nine to 18 strongylid species (average 14.5 ± 2.5) were found per horse. Cyathostomes (Cyathostominae) dominated in the Przewalski's horse strongylid community: 9 species (Cyathostomum catinatum, C. pateratum, Cylicocyclus nassatus, C. insigne, C. leptostomum, C. ashworthi, Cylicostephanus longibursatus, C. goldi and C. minutus) were found in more than 80% of horses examined and composed 94.1% of the total number of strongylid collected. Strongyles (Strongylinae) were found in 100% of theE. ferus przewalskiiexamined; prevalence of separate species was from 4.2% to 58.3%. The general structure of the strongylid community was multimodal with dominant (9 species), subdominant (4), background (4) and rare (14) species. The list of strongylid species found in the Przewalski'si horses in Ukraine was enlarged to 37 species.
A New Species of the Genus Cymatosus (Diptera, Ulidiidae) from Central America, with a Key to Species
Authors: Kameneva E. 
Published: August 2009

A New Species of the Genus Cymatosus (Diptera, Ulidiidae) from Central America, with a Key to Species
Cymatosus icarus Kameneva, sp. n. from Costa Rica is described. It differs from the four previously described species by the wing pattern with an additional arcuate hyaline stripe parallel to the wing margin, and a rounded brown spot in the middle of the wing disc, resembling that in Callistomyia icarus Osten Sacken (Tephritidae). A key to the species of the genus Cymatosus Enderlein and notes on other species are provided.
MEKK1 Binds HECT E3 Ligase Itch by Its Amino-Terminal RING Motif to Regulate Th2 Cytokine Gene Expression
Authors: Enzler Thomas , Chang Xing , Facchinetti Valeria , Melino Gerry , Karin Michael , Su Bing , Gallagher Ewen 
Published: August 2009

Abstract
MEKK1-dependent signaling regulates HECT E3 ligase Itch, resulting in elevated catalytic activity. After TCR costimulation, MEKK1 predominantly induces JNK1 activation, whereas the related kinase MEKK2 regulates ERK5 activation. MEKK1 becomes phosphorylated on multiple sites and polyubiquitinated following TCR costimulation. E3 ligase Itch is recruited to activated MEKK1, but not MEKK2, and this novel scaffolding interaction is dependent on MEKK1 Thr1381 phosphorylation within the kinase domain and an intact MEKK1 RING finger motif. MEKK1 phosphorylation on Thr1381 is observed during Th2 differentiation, but not under Th1 differentiation. Both Itch and the MEKK1 kinase domain are important for Il4 and Il6 cytokine gene expression under Th2 conditions.
Regulation of Murine Splenic B Cell CR3 Expression by Complement Component 3
Authors: Jacobson Amanda C. , Roundy Kirstin M. , Weis Janis J. , Weis John H. 
Published: August 2009

Abstract
Complement component C3 has established roles in both innate and adaptive immune responses. C3 cleavage products function in B cell activation through the complement receptors CD21/35. Phenotypes of Ab production between CD21/35−/− and C3−/− mice are not always congruent, implicating additional roles for C3 in B cell responses. To further characterize complement and complement receptors, we have identified a role for C3 in the regulation of CR3 on splenic B cells. Splenic B2 cells are not defined as expressing CR3, yet the analysis of splenic B cells from C3−/− animals demonstrate cell surface expression of CR3. B cells from both wild-type (WT) and C3−/− animals express CR3/CD11b/Itgam (integrin α M) gene transcripts although the level of such transcripts is 2- to 3-fold higher in B cells from the C3−/− animal vs WT cells. C3−/− and WT animals have similar B cell subpopulations with identical CR3 expression on B220− cells from the spleen, marrow, and lymph nodes. The C3-deficient environment is responsible for altered CR3 expression as WT splenic B cells transferred into C3−/− animals expressed cell surface CR3 within 48 h while transfer of C3−/− splenic B cells into WT animals depressed surface expression of CR3. Furthermore, transfer of C3-producing splenic macrophages into C3−/− mice depressed CR3 expression by resident B cells. These data suggest a role for C3 in influencing the level of expression of CR3 by modulating the transcript levels encoding the CD11b α integrin protein.
Cutting Edge: TGF-β1 and IL-15 Induce FOXP3+ γδ Regulatory T Cells in the Presence of Antigen Stimulation
Authors: Casetti Rita , Agrati Chiara , Wallace Marianne , Sacchi Alessandra , Martini Federico , Martino Angelo , Rinaldi Alessandra , Malkovsky Miroslav 
Published: August 2009

Abstract
Several subsets of αβ regulatory T cells (Tregs) have been described and studied intensively, but the potential regulatory role of γδ T cells remains largely unclear. Lymphocytes expressing γδ TCR are involved in both innate and adaptive immune responses, and their major adult human peripheral blood subset (Vγ9Vδ2) displays a broad reactivity against microbial agents and tumors. In this study we report that γδ T lymphocytes with regulatory functions (Vδ2 Tregs) are induced in vitro in the presence of specific Ag stimulation and cytokines (TGF-β1 and IL-15). These cells express FOXP3 and, similarly as αβ Tregs, suppress the proliferation of anti-CD3/anti-CD28 stimulated-PBMC. Phenotypic and functional analyses of Vδ2 Tregs will very likely improve our understanding about the role of γδ T cells in the pathogenesis of autoimmune, infectious, and neoplastic diseases.
An Accessory Role for B Cells in the IL-12-Induced Activation of Resting Mouse NK Cells
Authors: Haddad Evette A. , Senger Laura K. , Takei Fumio 
Published: August 2009

Abstract
IL-12 is a potent proinflammatory cytokine. The effects of IL-12 are thought to be mediated by IFN-γ production by NK, NKT, and T cells. In this study, we show that although IL-12 stimulates NK and NK1.1+ T cells in bulk mouse splenocytes, it does not significantly stimulate purified NK cells, indicating that other cells are required. IL-12 stimulates T cell-deficient spleen cells and those depleted of macrophages. Unexpectedly, the depletion of dendritic cells also has little effect on the stimulation of spleen cells with IL-12. In contrast, B cell depletion almost completely inhibits IL-12-induced IFN-γ production and B cell-deficient spleen cells are poorly stimulated with IL-12. Furthermore, purified NK cells are stimulated with IL-12 in the presence of purified B cells. Thus, B cells are necessary and also sufficient for the stimulation of purified NK cells with IL-12. Whereas spleen cells from IL-18-deficient mice are not stimulated with IL-12, NK cells purified from IL-18-deficient mice are stimulated with IL-12 in the presence of wild-type (WT) B cells, and WT NK cells are not stimulated with IL-12 in the presence of IL-18-deficient B cells. Cell contact between B and NK cells is also required for IL-12-induced IFN-γ production. Finally, B cell-deficient mice injected with IL-12 produce significantly less IFN-γ and IL-18 in the sera than WT mice do. Thus, stimulation of NK cells with IL-12 requires B cell cooperation in vitro as well as in vivo.
Deficiency of Endothelial Heparan Sulfates Attenuates Allergic Airway Inflammation
Authors: Zuberi Riaz I. , Ge Xiao Na , Jiang Shuxia , Bahaie Nooshin S. , Kang Bit Na , Hosseinkhani Reza M. , Frenzel Elizabeth M. , Fuster Mark M. , Esko Jeffrey D. , Rao Savita P. , Sriramarao P. 
Published: August 2009

Abstract
The effect of targeted inactivation of the gene encoding N-deacetylase/N-sulfotransferase-1 (Ndst1), a key enzyme involved in the biosynthesis of heparan sulfate (HS) chains, on the inflammatory response associated with allergic inflammation in a murine model of OVA-induced acute airway inflammation was investigated. OVA-exposed Ndst1f/fTekCre+ (mutant) mice deficient in endothelial and leukocyte Ndst1 demonstrated significantly decreased allergen-induced airway hyperresponsiveness and inflammation characterized by a significant reduction in airway recruitment of inflammatory cells (eosinophils, macrophages, neutrophils, and lymphocytes), diminished IL-5, IL-2, TGF-β1, and eotaxin levels, as well as decreased expression of TGF-β1 and the angiogenic protein FIZZ1 (found in inflammatory zone 1) in lung tissue compared with OVA-exposed Ndst1f/fTekCre− wild-type littermates. Furthermore, murine eosinophils demonstrated significantly decreased rolling on lung endothelial cells (ECs) from mutant mice compared with wild-type ECs under conditions of flow in vitro. Treatment of wild-type ECs, but not eosinophils, with anti-HS Abs significantly inhibited eosinophil rolling, mimicking that observed with Ndst1-deficient ECs. In vivo, trafficking of circulating leukocytes in lung microvessels of allergen-challenged Ndst1-deficient mice was significantly lower than that observed in corresponding WT littermates. Endothelial-expressed HS plays an important role in allergic airway inflammation through the regulation of recruitment of inflammatory cells to the airways by mediating interaction of leukocytes with the vascular endothelium. Furthermore, HS may also participate by sequestering and modulating the activity of allergic asthma-relevant mediators such as IL-5, IL-2, and TGF-β1.
Blocking of CD27-CD70 Pathway by Anti-CD70 Antibody Ameliorates Joint Disease in Murine Collagen-Induced Arthritis
Authors: Oflazoglu Ezogelin , Boursalian Tamar E. , Zeng Weiping , Edwards Ana C. , Duniho Steve , McEarchern Julie A. , Law Che-Leung , Gerber Hans-Peter , Grewal Iqbal S. 
Published: August 2009

Abstract
Rheumatoid arthritis (RA) is characterized by inflammation and cellular proliferation in the synovial lining of joints that result in cartilage and bone destruction. Although the etiology of RA is unclear, activated lymphocytes and proinflammatory molecules, in particular TNF superfamily members, have been implicated in the disease pathology. A TNF superfamily member, CD70, is found on activated lymphocytes and shown to be important in memory and effector responses of lymphocytes. CD70 is expressed at high levels on chronically activated T cells in patients with autoimmune disorders, including RA. The involvement of CD70 in the progression of RA, however, remains unknown. In this study, we report effects of targeting CD70 on disease pathogenesis by using an anti-mouse CD70 Ab in a murine model of collagen-induced arthritis (CIA). In addition to blocking CD70 binding to its receptor CD27, the anti-CD70 Ab used also engages Fc-dependent effector functions including Ab-dependent cellular cytotoxicity, phagocytosis, and complement fixation. Treatment of mice with anti-CD70 Ab both before the onset or after the established disease in CIA model resulted in marked improvements in disease severity and significant reduction in the production of autoantibodies. Histopathological analyses of the joints of mice revealed a substantial reduction of inflammation, and bone and cartilage destruction in response to the anti-CD70 Ab treatment. These results uncover a novel role for CD27-CD70 interactions in the regulation of in vivo inflammatory response leading to arthritis, and provide a molecular basis to support the rationale for anti-CD70 therapy for autoimmune and inflammatory diseases.
CFD modeling of the Wurster bed coater
Authors: Karlsson Stina , Rasmuson Anders , van Wachem Berend , Björn Ingela Niklasson 
Published: August 2009

AbstractIn the Wurster bed coater, the wetting, drying, and circulation of particles are combined to produce a high quality coating. The drying and wetting conditions in a laboratory scale Wurster bed coater are modeled and compared with experimental data. A model combining multiphase fluid dynamics with heat and mass transfer is developed to model the particle and gas motion and the transport of thermal energy and moisture. A wetting region is defined, where a specified moisture content is set in the particle phase, above the jet inlet, to describe the injection of coating liquid. The simulation shows the characteristic circulation of particles in the equipment, as well as the behavior of the moisture in the system and agrees well with measurements. The simulation indicates how different process conditions influence the drying regions. The results show that most of the drying, under typical operating conditions, takes place in the Wurster tube. © 2009 American Institute of Chemical Engineers AIChE J, 2009
Analysis of stirred tanks with two‐zone models
Authors: Alopaeus Ville , Moilanen Pasi , Laakkonen Marko 
Published: August 2009

AbstractStirred tank turbulence and fluid flow characteristics are analyzed based on a two‐zone model. Instead of using the zonal model for stirred tank performance prediction as often proposed in the literature, the zoning is used here as a tool for mixing analysis. A systematic zoning approach is proposed, where the tank is divided into two nested regions. By gradually increasing the inner zone volume, continuous curves can be obtained for turbulent energy dissipation distribution and pumping numbers between the zones as functions of the zone sizes. It is shown here that these curves can be used as a powerful tool for visualizing stirred tank performance. They can be used, e.g., in impeller performance comparisons and analysis of mixing characteristics with changing rheology, or to examine various numerical aspects related to stirred tank CFD modeling. © 2009 American Institute of Chemical Engineers AIChE J, 2009