bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling of possible subunit arrangements in the eukaryotic chaperonin TRiC
Authors: Miller Erik J. , Meyer Anne S. , Frydman Judith 
Published: May 2006

AbstractThe eukaryotic cytosolic chaperonin TRiC (TCP‐1 Ring Complex), also known as CCT (Cytosolic Chaperonin containing TCP‐1), is a hetero‐oligomeric complex consisting of two back‐to‐back rings of eight different subunits each. The general architecture of the complex has been determined, but the arrangement of the subunits within the complex remains an open question. By assuming that the subunits have a defined arrangement within each ring, we constructed a simple model of TRiC that analyzes the possible arrangements of individual subunits in the complex. By applying the model to existing data, we find that there are only four subunit arrangements consistent with previous observations. Our analysis provides a framework for the interpretation and design of experiments to elucidate the quaternary structure of TRiC/CCT. This in turn will aid in the understanding of substrate binding and allosteric properties of this chaperonin.
Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity
Authors: Kristensen David M. , Chen Brian Y. , Fofanov Viacheslav Y. , Ward R. Matthew , Lisewski Andreas Martin , Kimmel Marek , Kavraki Lydia E. , Lichtarge Olivier 
Published: May 2006

AbstractThe annotation of protein function has not kept pace with the exponential growth of raw sequence and structure data. An emerging solution to this problem is to identify 3D motifs or templates in protein structures that are necessary and sufficient determinants of function. Here, we demonstrate the recurrent use of evolutionary trace information to construct such 3D templates for enzymes, search for them in other structures, and distinguish true from spurious matches. Serine protease templates built from evolutionarily important residues distinguish between proteases and other proteins nearly as well as the classic Ser‐His‐Asp catalytic triad. In 53 enzymes spanning 33 distinct functions, an automated pipeline identifies functionally related proteins with an average positive predictive power of 62%, including correct matches to proteins with the same function but with low sequence identity (the average identity for some templates is only 17%). Although these template building, searching, and match classification strategies are not yet optimized, their sequential implementation demonstrates a functional annotation pipeline which does not require experimental information, but only local molecular mimicry among a small number of evolutionarily important residues.
Population structure of Solanum carolinense along the Takano River in Kyoto, Japan as determined by amplified fragment length polymorphism analysis
Authors: IMAIZUMI T , KUROKAWA S , ITO M , AULD B , WANG G X 
Published: May 2006

SummaryAreas infested with Solanum carolinense, an introduced perennial weed, have increased quickly in Japan. The genetic structure of a S. carolinense population along the Takano River in Kyoto, Japan was investigated using amplified fragment length polymorphism (AFLP) analysis to reveal how introductions and local spread have contributed to the development of this population. Along a terrace beside the river and an adjacent roadside, we defined a cluster of above‐ground shoots in the population as a subpopulation and 60 subpopulations were identified. Seventeen of these were selected and 165 shoots were analyzed by AFLP analysis using three primer pairs. The AFLP profiles revealed 69 genotypes and the presence of several clones, i.e. genotypes that were present in more than one individual. In total, 19 clones, comprising 2–34 identical genotypes, could be identified in the population. Each of these clones, except one, was allocated within each of the subpopulations. Clustering of the subpopulations was supported by high bootstrap values in all cases. Therefore, introductions from distant regions have mainly contributed to the development of this population, and local spread by seed or vegetative reproduction has rarely been important. The most likely introduction route of S. carolinense to this population was via planting associated with construction works.
Physiological basis for antagonism induced by mixtures of quizalofop‐ethyl and bromoxynil in maize (Zea mays)
Authors: KIM J S , WON T J , LEE B H , YU J H , LEE C W 
Published: May 2006

SummaryIn this study, the physiological basis for antagonism induced by mixtures of quizalofop‐ethyl and bromoxynil was investigated in maize seedlings. In sequential applications, antagonism was observed when bromoxynil was applied before quizalofop‐ethyl or in a mixture with quizalofop‐ethyl, but was minimal when bromoxynil was applied afterwards. The degree of antagonism differed with application rates of bromoxynil and with the timing of the treatment. When test herbicides were applied locally to the second leaf, the inhibition of photosystem II (PS‐II) in the herbicide‐treated leaf was higher with the mixture than with bromoxynil or quizalofop‐ethyl alone. Subsequent growth of the untreated third leaf inhibited by quizalofop‐ethyl alone then recovered, depending on the dose of bromoxynil. There was no evidence that bromoxynil affected absorption of quizalofop‐ethyl. In local applications at different positions on the second leaf, antagonism was only observed when quizalofop‐ethyl was applied to the distal part of the leaf and bromoxynil applied to the proximal part. The antagonism of bromoxynil + quizalofop‐ethyl did not occur at the level of acetyl CoA carboxylase and Hill reaction, as revealed by in vitro assays. These results suggest that bromoxynil inhibits the phloem transport of quizalofop‐ethyl and thus antagonises its whole‐plant activity in maize.
The effect of varying levels of sodium bicarbonate on polychlorinated biphenyl dechlorination in Hudson River sediment cultures
Authors: Yan Tao , LaPara Timothy M. , Novak Paige J. 
Published: May 2006

SummaryThe addition of different concentrations of sodium bicarbonate had a profound effect on 2,3,4,5‐chlorobiphenyl (2,3,4,5‐CB) dechlorination in Hudson River sediment cultures. The most extensive dechlorination was observed in cultures to which 100 mg l−1 bicarbonate was added. Cultures amended with 1000 mg l−1 bicarbonate had the least extensive dechlorination, with 2,4‐CB and 2,5‐CB as predominant end‐products. A significant loss of total chlorinated biphenyl mass was observed in cultures to which ≤ 500 mg l−1 bicarbonate was added, suggesting that degradation beyond chlorinated biphenyls occurred. The dynamics of acetate formation were different among the treatments, with high acetate concentrations detected throughout the 303‐day experiment in cultures to which 1000 mg l−1 bicarbonate had been added. Sodium bicarbonate addition also had a significant impact on bacterial community structure as detected by polymerase chain reaction‐denaturant gradient gel electrophoresis (PCR‐DGGE) of 16S rRNA gene fragments. Three putative polychlorinated biphenyl (PCB) dechlorinators were identified; one Dehalococcoides‐like population was detected in all enrichment cultures, whereas two Dehalobacter‐like populations were only detected in the enrichment cultures with the most extensive dechlorination. These results suggest that the availability of bicarbonate, and potentially sodium, may affect PCB dechlorination in Hudson River sediment and thus need to be taken into consideration when assessing the fate of PCBs or implementing bioremediation.
An Analysis Paradigm for Investigating Multi‐locus Effects in Complex Disease: Examination of Three GABAA Receptor Subunit Genes on 15q11‐q13 as Risk Factors for Autistic Disorder.
Authors: Ashley‐Koch A. E. , Mei H. , Jaworski J. , Ma D. Q. , Ritchie M. D. , Menold M. M. , Delong G. R. , Abramson R. K. , Wright H. H. , Hussman J. P. , Cuccaro M. L. , Gilbert J. R. , Martin E. R. , Pericak‐Vance M. A. 
Published: May 2006

SummaryGene‐gene interactions are likely involved in many complex genetic disorders and new statistical approaches for detecting such interactions are needed. We propose a multi‐analytic paradigm, relying on convergence of evidence across multiple analysis tools. Our paradigm tests for main and interactive effects, through allele, genotype and haplotype association. We applied our paradigm to genotype data from three GABAA receptor subunit genes (GABRB3, GABRA5, and GABRG3) on chromosome 15 in 470 Caucasian autism families. Previously implicated in autism, we hypothesized these genes interact to contribute to risk. We detected no evidence of main effects by allelic (PDT, FBAT) or genotypic (genotype‐PDT) association at individual markers. However, three two‐marker haplotypes in GABRG3 were significant (HBAT). We detected no significant multi‐locus associations using genotype‐PDT analysis or the EMDR data reduction program. However, consistent with the haplotype findings, the best single locus EMDR model selected a GABRG3 marker. Further, the best pairwise genotype‐PDT result involved GABRB3 and GABRG3, and all multi‐locus EMDR models also selected GABRB3 and GABRG3 markers. GABA receptor subunit genes do not significantly interact to contribute to autism risk in our overall data set. However, the consistency of results across analyses suggests that we have defined a useful framework for evaluating gene‐gene interactions.
Assisting Women to Learn Myocardial Infarction Symptoms
Authors: McDonald Deborah Dillon , Goncalves Patricia Herrera , Almario Vivian E. , Krajewski Aleksandra L. , Cervera Patricia L. , Kaeser Donna M. , Lillvik Cherylynn A. , Sajkowicz Tammy L. , Moose Priscilla E. 
Published: May 2006

ABSTRACT
Objective: The purpose of this study was to test how teaching format (factual versus storytelling) and restructuring the social norm of caring for others to caring for self affects how women learn to identify and respond to myocardial infarction (MI) symptoms.Design: The study was a randomized pretest posttest full factorial experiment.Sample: One hundred and thirteen women participated.Measures: Before and after reading the intervention pamphlet, the women wrote all the MI symptoms that they knew and rated their intention to call 911 if symptoms occurred.Intervention: The women read one of the four MI pamphlets corresponding to the four conditions.Results: No significant effects for learning MI symptoms resulted from teaching format or social norms. Women learned three additional MI symptoms. All responded with high intention to call 911 if MI symptoms occurred.Conclusions: Women can learn additional MI symptoms from reading a brief pamphlet about MI symptoms. Use of a storytelling format and the social norm of caring for self might not impact how many MI symptoms women learn. Studies using audiovisuals and larger samples are needed to clarify whether storytelling format and the social norm of caring for self‐impact learning MI symptoms.
Cytokine accumulation in photochemically treated and gamma‐irradiated platelet concentrates during storage
Authors: Apelseth Torunn O. , Hervig Tor A. , Wentzel‐Larsen Tore , Bruserud Øystein 
Published: May 2006

BACKGROUND:  Photochemical treatment (PCT) for pathogen reduction of platelet concentrates (PCs) affects all cells containing DNA and/or RNA. Soluble mediators, which may cause transfusion reactions, are determined by the balance between secretion and/or cell destruction and binding and/or degradation.STUDY DESIGN AND METHODS:  Ten double‐dose single‐donor leukoreduced PCs were split in two identical units. Two study arms were created: Study Arm A consisting of five PCT PCs with corresponding untreated control PCs and Study Arm B consisting of five PCT PCs with corresponding gamma‐irradiated control PCs. PCs that had added PAS‐III (Intersol) were treated with amotosalen and ultraviolet A light. Corresponding controls PCs, to which PAS‐II (T‐sol) were added, received no treatment or were gamma‐irradiated before storage. Platelet (PLT)‐derived (CCL5/RANTES, CXCL4/PF4, CCL3/MIP‐1α, transforming growth factor [TGF]‐β, CXCL8/interleukin [IL]‐8, IL‐1β) as well as white blood cell (WBC)‐associated (IL‐6, IL‐10, IL‐11, IL‐12, tumor necrosis factor, interferon‐γ) cytokines were investigated by enzyme‐linked immunosorbent assay and cytometric bead array during storage for up to 12 days.RESULTS:  Independent of previous treatment we observed that all concentrates showed low levels of WBC‐associated cytokines. PLT‐derived cytokines were detected at higher levels and showed significant increase during storage. Statistical analysis showed lower PLT content per unit in PCT PCs, higher levels of activation variables in PCT PCs, and higher levels and accumulation rate of CCL5, CXCL4, TGF‐β, and CXCL8 in PCT PCs.CONCLUSION:  PLTs are the main source of released cytokines during storage of untreated, gamma‐irradiated, and PCT PCs. PCT may affect the level of PLT‐derived cytokines in PCs. No additional reduction of WBC‐associated cytokines were observed after PCT in prestorage leukoreduced PCs.
Selective inhibition of Porphyromonas gingivalis growth by a factor Xa inhibitor, DX‐9065a
Authors: Matsushita Kenji , Imamura Takahisa , Tancharoen Salunya , Tatsuyama Syouko , Tomikawa Munehiro , Travis James , Potempa Jan , Torii Mitsuo , Maruyama Ikuro 
Published: May 2006

Background:  Porphyromonas gingivalis is a causative bacterium of adult periodontitis. However, there is no drug specific for P. gingivalis and for its virulence factor.Objectives:  The objective of this study was to examine the effects of a new selective inhibitor of activated factor X, DX‐9065a, on growth of Porphyromonas gingivalis and other periodontopathic bacteria.Methods:  We incubated P. gingivalis and other periodontopathic bacteria in the presence or absence of DX‐9065a and examined the effect of DX‐9065a on bacterial growth and trypsin‐like activity in its cultures. We also examined the effects of DX9065a on amidolytic activity of purified trypsin‐like proteinases (gingipains RgpA and RgpB), from P. gingivalis and on trypsin‐like activity in gingival crevicular fluids from patients with adult periodontitis.Results:  DX‐9065a selectively inhibited the growth of P. gingivalis and Prevotella intermedia, and its effect on P. gingivalis was bactericidal. Trypsin‐like proteinase activity was detected in P. gingivalis, and the activity was strongly inhibited by DX‐9065a. DX‐9065a even inhibited amidolytic activity of RgpA and RgpB from P. gingivalis. Furthermore, trypsin‐like proteinase activity in gingival crevicular fluids was strongly inhibited by DX‐9065a.Conclusions:  DX‐9065a inhibits P. gingivalis growth in part through to its ability to inhibit the trypsin‐like proteinase activity in P. gingivalis and may be useful for a new drug for treatment of adult periodontitis.
1141101609 Beta endorphin regulates NK and NKT cell functions via distinct pathways
Authors: Ota I , Hayakawa S , Karasaki‐Suzuki M , Aizawa S , Chisima F , Yamamoto T 
Published: May 2006

Problem:  Opioid induced regulation of the mucosal immune system has been reported. We examined effects of β‐endorphin on large granular lymphocyte cell lines to investigate regulatory roles of placenta derived β‐endorphin on local immune system.Materials and Methods:  Large granular lymphocyte cell lines KHYG‐1 (NK) and MOTN‐1 (NKT) were maintained in RPMI1640 supplemented with 10% FCS. IFN‐γ1 production was evaluated by ELISPOT assay under stimulation with IL‐2 (100 IU/mL) and/or IL‐12 (10 IU/mL). Various concentrations of β‐endorphin were added into culture media with and without opioid antagonist naloxone.Results:  MOTN‐1 expressed opioid receptor κ and constitutively produced IFN‐γ1. Production was up‐regulated by IL‐2 and/or IL‐12. β‐endorphin suppressed constitutive and IL‐2 induced IFN‐γ1 production while it showed no effects on IL‐12 induced IFN‐γ1 production. Suppression was completely abrogated by simultaneous naloxone treatment. KHYG‐1 expressed none of 3 opioid receptors and showed non‐constitutive IFN‐γ1 secretion. β‐endorphin up‐regulated production in low concentrations while down‐regulated production at high concentrations. This regulation was not affected by naloxone.Conclusion:  β‐endorphin suppress IL‐2/STAT5 induced signaling of large granular NKT lymphocyte cell line MOTN‐1 while it affects large granular NK lymphocyte cell line KHYG‐1 via opioid receptor independent pathways.
1141154113 Expression of natural cytotoxicity receptors in peripheral blood NK cell subsets of women with recurrent spontaneous abortions (RSA) or implantation failures
Authors: Fukui A , Ntrivalas EI , Gilman‐Sachs A , Kwak‐Kim J , Beaman KD 
Published: May 2006

Problem:  Natural Cytotoxicity Receptors (NCRs) are unique markers of NK cells and regulate NK cell cytotoxicity and cytokine production. a2V‐ATPase is expressed in the cell membrane and can regulate the pH of the extracellular environment, which might facilitate NK cell killing or cytokine secretion. In this preliminary study we evaluated the expression of NCRs and a2V‐ATPase in peripheral blood NK cells of women with RSA or implantation (IVF‐ET) failures.Method of Study:  Peripheral blood was obtained from women with RSA (n = 10), or IVF‐ET failures (n = 9). CD56dim and CD56bright NK cells were analyzed for the expression of NCRs (NKp46, NKp44 and NKp30) and a2V‐ATPase using flow cytometry.Results:  For women with RSA, there were significant differences in the expression of NKp46 between CD56dim (36.9 ± 30.2) and CD56bright (76.0 ± 27.5) (P < 0.01), of NKp30 between CD56dim (30.9 ± 25.7) and CD56bright (55.8 ± 29.5) (P < 0.01), and of a2V‐ATPase between CD56dim (1.0 ± 0.9) and CD56bright (23.2 ± 15.1) (P < 0.01) NK cells. For women with IVF‐ET failures, there were significant differences in the expression of NKp46 between CD56dim (39.5 ± 21.5) and CD56bright (78.8 ± 26.0) (P < 0.01), of NKp30 between CD56dim (27.2 ± 17.9) and CD56bright (45.2 ± 29.8) (P < 0.05), and of a2V‐ATPase between CD56dim (1.6 ± 1.4) and CD56bright (21.2 ± 16.5) (P < 0.01) NK cells.Conclusions:  The differential expression of NCRs and a2V‐ATPase in NK cell subsets of women with RSA and IVF‐ET failures may have an effect in cytotoxicity and cytokine production. Additional studies are currently in effect to evaluate these activities. We suggest that the analysis of NCRs and a2V‐ATPase expression in peripheral blood NK cell subsets may contribute to a better understanding in the biology of NK cells in women with RSA or IVF‐ET failures.
1141610241 Altered expression of HuR, an mRNA stabilizing protein, mediates aberrant Placenta Growth Factor (PlGF) expression in preeclampsia
Authors: Schaecher CP , Groesch KA 
Published: May 2006

Background:  Control of mRNA stability is an essential regulatory process in eukaryotic gene expression. HuR, a 3’UTR mRNA binding protein, can protect AU‐rich mRNA from degradation in response to stresses. PlGF, an angiogenic growth factor, contains two consensus AU‐rich sites suggesting that under normal conditions HuR may protect PlGF mRNA from degradation. Trophoblast expression of PlGF is significantly decreased in preeclampsia and by hypoxia in vitro. We hypothesize that decreased levels of cytoplasmic HuR may contribute to decreased PlGF expression in hypoxic and preeclamptic trophoblast.Methods:  Western blots were used to determine relative effects of in vitro hypoxia on HuR protein expression and subcellular localization in trophoblast. Immunohistochemistry was used to compare HuR expression patterns in trophoblast of preeclamptic and normal placentae.Results:  Cytoplasmic expression of HuR was decreased 1.4 fold in the cytoplasm and 1.2 fold in the nucleus of JEG3 cells. A shift in HuR was more apparent in primary trophoblast with a greater than 2‐fold decrease in the cytoplasm and a 1.4 fold decrease in the nucleus following 24 hr of hypoxia. Immunohistochemical analyses detected HuR expression in near term trophoblast in situ. However, this technical approach did not detect a significant change in HuR expression between normal and preeclamptic trophoblast.Conclusions:  HuR expression is decreased in hypoxic trophoblast, at least in vitro, which may provide a causal link to decreased PlGF mRNA expression. Down regulation of trophoblast PlGF expression is thought to contribute to the pathophysiology associated with preeclampsia including the relative lack of perfusion of the placenta and systemic renal effects.
1141634395 Analysis of protein profiles of amniotic fluid in a pregnant woman with a fetus of Down syndrome by SELDI‐TOF mass spectrometry
Authors: Nakanishi K , Sawai H , Komori S , Koyama K 
Published: May 2006

Aim:  The identification of protein profiles of amniotic fluid in a pregnant woman with a normal fetus or fetus with down syndrome is a major issue in prenatal diagnosis.Methods:  In this study, we analyzed protein profiles of amniotic fluids of pregnant women with a normal fetus (50 cases) and with a fetus of Down syndrome (7 cases) using SELDI‐TOF mass spectrometry. We used a weak cation exchange chip (CM10) under the condition of pH 4.5 for analyzing protein profiles.Results:  We found 111 increased protein peaks in 3–10 kDa range, 111 peaks in 5–15 kDa and 53 peaks in 10–30 kDa, respectively. After comparing the protein profiles of normal to that of Down syndrome, we finally identified the increases in expression of a 5.4 kDa protein and a 13.4 kDa protein in pregnant women with a fetus of Down syndrome, whereas, 6.9 kDa, 12.5 kDa and 13.7 kDa proteins in pregnant women with a normal fetus.Conclusion:  We first identified the protein profiles of amniotic fluid in normal pregnant women and specific protein profiles in pregnant women with a fetus of Down syndrome. These protein profiles in amniotic fluid might be important and useful information for prenatal diagnosis.
RANS-Based Very Large
Eddy Simulation of Thermal and Magnetic Convection at Extreme
Conditions
Authors: Hanjalić K. , Kenjereš S. 
Published: May 2006

Abstract
For thermal and magnetic convection at very high Rayleigh and Hartman numbers, which are inaccessible to the conventional large eddy simulation, we propose a time-dependent Reynolds-average-Navier-Stokes (T-RANS) approach in which the large-scale deterministic motion is fully resolved by time and space solution, whereas the unresolved stochastic motion is modeled by a “subscale” model for which an one-point RANS closure is used. The resolved and modeled contributions to the turbulence moments are of the same order of magnitude and in the near-wall regions the modeled heat transport becomes dominant, emphasizing the role of the subscale model. This T-RANS approach, with an algebraic stress/flux subscale model, verified earlier in comparison with direct numerical simulation and experiments in classic Rayleigh-Bénard convection, is now expanded to simulate Rayleigh-Bénard (RB) convection at very high Ra numbers—at present up to O(1016)—and to magnetic convection in strong uniform magnetic fields. The simulations reproduce the convective cell structure and its reorganization caused by an increase in Ra number and effects of the magnetic field. The T-RANS simulations of classic RB indicate expected thinning of both the thermal and hydraulic wall boundary layer with an increase in the Ra number and an increase in the exponent of the Nu∝Ran correlation in accord with recent experimental findings and Kraichnan asymptotic theory.