bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solid‐state NMR studies and DFT calculations of flavonoids: baicalein, baicalin and wogonoside
Authors: Wolniak Michał , Oszmiański Jan , Wawer Iwona 
Published: December 2007

AbstractThree flavonoids of pharmaceutical importance—baicalein, baicalin, and wogonoside—were isolated from a Chinese medicinal plant Scutellaria baicalensis Georgi and studied by 13C NMR in solution and solid state. Two‐dimensional (2D) NMR spectroscopy in the liquid phase and dipolar dephasing (DD) experiments in magic‐angle spinning (MAS) spectra enabled the assignment of 13C resonances. The cross‐polarization (CP) time constants TCH and relaxation times TH1ρ were obtained from the variable‐contact time experiments. The principal elements of the 13C chemical shift tensor were determined in the spectra recorded under slow sample spinning (2 kHz) using phase‐adjusted spinning sideband (PASS)‐2D NMR technique, and were verified by density functional theory gauge‐independent atomic orbital (DFT GIAO) calculations of shielding constants. Analysis of the 13C δii and comparison with shielding parameters calculated for different conformers of compounds 1–3 enabled the selection of the most reliable geometry in the solid phase. In all three compounds, an intramolecular hydrogen bond C5OH···C4 is formed; the existence of baicalein and baicalin with ‘anticlockwise’ orientation of OH groups is more probable. Copyright © 2007 John Wiley & Sons, Ltd.
Diffusion‐based MR methods for bone structure and evolution
Authors: Sigmund E.E. , Cho H. , Chen P. , Byrnes S. , Song Y.‐Q. , Guo X.E. , Brown T. R. 
Published: December 2007

AbstractA new approach to MR trabecular bone characterization is presented. This method probes the diffusion of spins through internal magnetic field gradients due to the susceptibility contrast between the bone and water (or marrow) phases. The resulting spin magnetization decay encodes properties of the underlying structure. This method, termed decay due to diffusion in the internal field (DDIF), is well established as a probe of pore size and structure. In the present work its application is shown for in vitro experiments on excised bovine tibiae samples. A comparison with pulsed field gradient (PFG) measurement of restricted diffusion shows a strong correlation of DDIF with the surface‐to‐volume ratio (SVR) of bones. Calculation of the internal magnetic field within the bone structure also supports this interpretation. These NMR measurements compare well with the image analysis from microscopic computed tomography (μCT). The SVR is not accessible in the clinically standard densitometry measurements, and provides vital information on bone strength and therefore on its fracture risk. The DDIF and PFG methods derive this information from a straightforward pulse sequence that does not employ either high applied field gradients or microimaging, and thus may have clinical potential. Magn Reson Med 59:28–39, 2008. © 2007 Wiley‐Liss, Inc.
Cs + ADC in rat brain decreases markedly at death
Authors: Goodman James A. , Ackerman Joseph J.H. , Neil Jeffrey J. 
Published: December 2007

AbstractSpectroscopic resolution of intracellular and extracellular compartments can be used to probe the kinetic environment of those spaces and the compartment‐specific changes that occur following injury. This is important for understanding the biophysical mechanisms that underlie the remarkable diffusion‐weighted MRI contrast of injured central nervous system (CNS) tissue. Cesium‐133 is a physiologic analog of potassium that is actively taken up by cells and resides primarily in the intracellular space. The 133Cs+ signal can, thus, be exploited to probe the kinetic environment of the intracellular space. Two principal 133Cs+ resonances were observed at 11.74 T. These resonances arise separately from 133Cs+ in brain and temporalis muscle. The apparent diffusion coefficient (ADC) of Cs+ in brain decreased from 1.0 ± 0.2 μm2/ms in healthy tissue to 0.24 ± 0.04 μm2/ms following global ischemia (average ADC ± average uncertainty), while there was no significant change in the ADC of Cs+ in temporalis muscle after injury. This finding underscores the tissue‐specific nature of the decrease in ADC that accompanies brain injury. Further, as the Cs+ ADC should reflect water ADC in the intracellular space, these results strongly support the hypothesis that the decrease in water ADC associated with CNS injury arises largely from kinetic changes taking place in the intracellular space. Magn Reson Med 59:65–72, 2008. © 2007 Wiley‐Liss, Inc.
PlyC, a novel bacteriophage lysin for compartment‐ dependent proteomics of group A streptococci
Authors: Köller Thomas , Nelson Daniel , Nakata Masanobu , Kreutzer Michael , Fischetti Vincent A. , Glocker Michael O. , Podbielski Andreas , Kreikemeyer Bernd 
Published: December 2007

AbstractStreptococcus pyogenes (Spy) (group A streptococci) is an important and exclusively human bacterial pathogen, which uses secreted and surface‐associated proteins to circumvent the innate host defense mechanisms and to adhere and internalize into host cells. Thus, investigation of the bacterial extracellular compartments, including secreted and cell wall‐associated subproteomes, is crucial for understanding adherence, invasion, and internalization mechanisms as major steps of Spy pathogenesis. Here, we compared a bacteriophage encoded cell wall hydrolase, PlyC, a multimeric lysin of the C1 bacteriophage, with the established glycosidase, mutanolysin, from Streptomyces globisporus for their suitability to efficiently digest Spy cell walls and release cell wall‐anchored Spy proteins for subsequent proteome research. Our results show that PlyC is superior for cell wall protein extraction compared to mutanolysin due to its higher activity and specificity as an N‐acetylmuramoyl‐L‐alanine amidase. Furthermore, our experimental design allowed us to delineate the actual localization of the proteins despite contamination with intracellular proteins.
Early manganese‐toxicity response in Vigna unguiculata L. – a proteomic and transcriptomic study
Authors: Führs Hendrik , Hartwig Moritz , Molina Laura Elisa Buitrago , Heintz Dimitri , Van Dorsselaer Alain , Braun Hans‐Peter , Horst Walter J. 
Published: December 2007

AbstractThe apoplast is known to play a predominant role in the expression of manganese (Mn) toxicity in cowpea (Vigna unguiculata L.) leaves. To unravel early Mn‐toxicity responses after 1–3 days Mn treatment also in the leaf symplast, we studied the symplastic reactions induced by Mn in two cultivars differing in Mn tolerance on a total cellular level. Comparative proteome analyses of plants exposed to low or high Mn allowed to identify proteins specifically affected by Mn, particularly in the Mn‐sensitive cowpea cultivar. These proteins are involved in CO2 fixation, stabilization of the Mn cluster of the photosystem II, pathogenesis‐response reactions and protein degradation. Chloroplastic proteins important for CO2 fixation and photosynthesis were of lower abundance upon Mn stress suggesting scavenging of metabolic energy for a specific stress response. Transcriptome analyses supported these findings, but additionally revealed an upregulation of genes involved in signal transduction only in the Mn‐sensitive cultivar. In conclusion, a coordinated interplay of apoplastic and symplastic reactions seems to be important during the Mn‐stress response in cowpea.
Proteome analysis of matrix vesicles isolated from femurs of chicken embryo
Authors: Balcerzak Marcin , Malinowska Agata , Thouverey Cyril , Sekrecka Anna , Dadlez Michal , Buchet Rene , Pikula Slawomir 
Published: December 2007

AbstractMatrix vesicles (MVs) are extracellular organelles that initiate mineral formation, accumulating inorganic phosphate (Pi) and calcium leading to the formation of hydroxyapatite (HA) crystals, the main mineral component of bones. MVs are produced during bone formation, as well as during the endochondral calcification of cartilage. MVs are released into the extracellular matrix from osseous cells such as osteoblasts and hypertrophic chondrocytes. In this report, using 1‐D SDS‐PAGE, in‐gel tryptic digestion and an LC‐MS‐MS/MS protein identification protocol, we characterized the proteome of MVs isolated from chicken embryo (Gallus gallus) bones and cartilage. We identified 126 gene products, including proteins related to the extracellular matrix and ion transport, as well as enzymes, cytoskeletal, and regulatory proteins. Among the proteins recognized for the first time in MVs were aquaporin 1, annexin A1 (AnxA1), AnxA11, glycoprotein HT7, Gi protein α2, and scavenger receptor type B. The pathways for targeting the identified proteins into MVs and their particular functions in the biomineralization process are discussed. Obtaining a knowledge of the functions and roles of these proteins during embryonic mineralization is a prerequisite for the overall understanding of the initial mineral formation mechanisms.
Frontiers in glycomics: Bioinformatics and biomarkers in disease An NIH White Paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11–13, 2006)
Authors: Packer Nicolle H. , von der Lieth Claus‐Wilhelm , Aoki‐Kinoshita Kiyoko F. , Lebrilla Carlito B. , Paulson James C. , Raman Rahul , Rudd Pauline , Sasisekharan Ram , Taniguchi Naoyuki , York William S. 
Published: December 2007

AbstractKey issues relating to glycomics research were discussed after the workshop entitled “Frontiers in Glycomics: Bioinformatics and Biomarkers in Disease” by two focus groups nominated by the organizers. The groups focused on two themes: (i) glycomics as the new frontier for the discovery of biomarkers of disease and (ii) requirements for the development of informatics for glycomics and glycobiology. The mandate of the focus groups was to build consensus on these issues and develop a summary of findings and recommendations for presentation to the NIH and the greater scientific community. A list of scientific priorities was developed, presented, and discussed at the workshops. Additional suggestions were solicited from workshop participants and collected using the workshop mailing list. The results are summarized in this White Paper, authored by the co‐chairs of the focus groups.
Comparative effect of phthalazinone units in sulfonated poly(arylene ether ether ketone ketone) copolymers as proton exchange membrane materials
Authors: Kim Dae Sik , Guiver Michael D. 
Published: December 2007

AbstractA new series of aromatic poly(arylene ether ether ketone ketone) copolymers containing pendant sulfonic acid groups (SPAEEKK‐D) were synthesized from commercially available monomers 1,3‐bis(4‐fluorobenzoyl)‐benzene, sodium 6,7‐dihydroxy‐2‐naphthalenesulfonate, and 4‐(4‐hydroxyphenyl)‐2,3‐phthalazin‐1‐one (DHPZ). Structure–property relationships of the phthalazinone SPAEEKK‐D series poly(arylene ether ether ketone ketone) copolymer were compared with copolymers SPAEEKK‐B and SPAEEKK‐H containing different diols such as 4,4′‐biphenol and hydroquinone, respectively, prepared in our earlier work. Ion exchange capacity (IECw, weight‐based; IECv, volume‐based), thermal stabilities, swelling, proton and methanol transport properties of the membranes were investigated in relation to their structures and compared with those of perfluorinated ionomer (Nafion 117). The SPAEEKK‐D membrane incorporating the phthalazinone monomer DHPZ showed relatively lower water uptake and methanol permeability compared with earlier SPAEEKK‐B and SPAEEKK‐H membranes incorporating biphenol and hydroquinone monomers, respectively. Inclusion of phthalazinone in the SPAEEKK‐D copolymers led to lower water absorption, enabling increased proton exchange concentrations in the hydrated polymer matrix that resulted in more desirable membrane properties for future direct methanol fuel cell applications. The SPAEEKK‐D membranes also showed improved mechanical and thermal properties and oxidative stability compared with the earlier SPAEEKK‐B and ‐H membranes. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 989–1002, 2008
A pilot survey of socio-economic differences in child-feeding behaviours among parents of primary-school children
Authors: Clark Heather R , Goyder Elizabeth , Bissell Paul , Blank Lindsay , Walters Stephen J , Peters Jean 
Published: December 2007

AbstractObjectiveParents’ child-feeding behaviours have been implicated in children’s food choices and weight, but little is known about the social class distribution of parent’s child-feeding behaviours in the UK. The present study compares parents’ self-reported child-feeding behaviours in two socio-economically contrasting areas.DesignA cross-sectional survey using the Parental Feeding Style Questionnaire. Mean scores were calculated for five child-feeding behaviours: control over eating, emotional feeding, encouragement/prompting, instrumental feeding and restriction. Parents’ self-reported child-feeding behaviours were compared with their sociodemographic characteristics.SettingThree primary schools in two contrasting electoral wards of Sheffield, UK.SubjectsTwo hundred and ten parents of children aged 4 to 11 years, recruited from a convenience sample.ResultsParents in the least deprived ward reported using all five types of child-feeding behaviour more frequently than parents in the most deprived ward. After adjusting for parent sex, parent age, single parent status, employment status and level of education, emotional feeding was the only behaviour showing any evidence of a difference between wards. The most frequently used behaviours were control, encouragement and restriction – behaviours that might be used to directly influence children’s food intake and weight.ConclusionsChild-feeding behaviours differ between areas within a single city and within a largely white population, and this distribution is related to socio-economic and educational factors. Experimental and longitudinal studies are needed to further investigate the potential role of child-feeding behaviours in childhood overweight and obesity.
Identification of 19 Polymorphic Major Outer Membrane Protein Genes and Their Immunogenic Peptides inEhrlichia ewingiifor Use in a Serodiagnostic Assay
Authors: Zhang Chunbin , Xiong Qingming , Kikuchi Takane , Rikihisa Yasuko 
Published: December 2007

ABSTRACTEhrlichia ewingii, a tick-transmitted rickettsia previously known only as a canine pathogen, was recently recognized as a human pathogen.E. ewingiihas yet to be cultivated, and there is no serologic test available to diagnoseE. ewingiiinfection. Previously, a fragment (505 bp) of a singleE. ewingiigene homologous to 1 of 22 genes encodingEhrlichia chaffeensisimmunodominant major outer membrane proteins 1 (OMP-1s)/P28s was identified. The purposes of the present study were to (i) determine theE. ewingii omp-1gene family, (ii) determine each OMP-1-specific peptide, and (iii) analyze all OMP-1 synthesized peptides for antigenicity. Using nested touchdown PCR and a primer walking strategy, we found 19omp-1paralogs inE. ewingii. These genes are arranged in tandem downstream oftr1and upstream ofsecAin a 24-kb genomic region. Predicted molecular masses of the 19 matureE. ewingiiOMP-1s range from 25.1 to 31.3 kDa, with isoelectric points of 5.03 to 9.80. Based on comparative sequence analyses among OMP-1s fromE. ewingiiand three otherEhrlichiaspp., eachE. ewingiiOMP-1 oligopeptide that was predicted to be antigenic, bacterial surface exposed, unique in comparison to the otherE. ewingiiOMP-1s, and distinct from those of otherEhrlichiaspp. was synthesized for use in an enzyme-linked immunosorbent assay. Plasmas from experimentallyE. ewingii-infected dogs reacted significantly with most of the OMP-1-specific peptides, indicating that multiple OMP-1s were expressed and immunogenic in infected dogs. The results support the utility of the tailored OMP-1 peptides asE. ewingiiserologic test antigens.
Simultaneous Detection ofChlamydophila pneumoniaeandMycoplasma pneumoniaeby Use of Molecular Beacons in a Duplex Real-Time PCR
Authors: Gullsby Karolina , Storm Martin , Bondeson Kåre 
Published: December 2007

ABSTRACTA real-time PCR was designed for detection ofChlamydophila pneumoniaeandMycoplasma pneumoniaesuch that each pathogen could be detected in a single tube and differentiated using molecular beacons marked with different fluorochromes. This duplex PCR, targeting the P1 adhesion gene forM. pneumoniaeand theompAgene forC. pneumoniae, was compared with two conventional PCR assays targeting the 16S rRNA gene and theompAgene. A total of 120 clinical throat and nasopharyngeal swab samples were tested. DNA extraction was performed using an alkali denaturation/neutralization method, and real-time amplification, detection, and data analysis were performed using a Rotor-Gene 2000 real-time rotary analyzer (Corbett Life Science, Sydney, Australia). Using conventional PCR as a reference in an analysis of 120 samples, 13 of 14 samples positive forC. pneumoniaewere detected by the novel real-time PCR. In an analysis ofM. pneumoniae, 22 samples were positive in the conventional PCR and the novel assay detected 24 positive samples. When using the conventional PCR as a reference, sensitivity and specificity were 93% and 100%, respectively, forC. pneumoniaeand 100% and 98%, respectively, forM. pneumoniae. With an overall agreement of 98.8%, this suggests that performance of the new duplex real-time PCR is comparable to that of conventional PCR.
Interaction between the Human Immunodeficiency Virus Type 1 Gag Matrix Domain and Phosphatidylinositol-(4,5)-Bisphosphate Is Essential for Efficient Gag Membrane Binding
Authors: Chukkapalli Vineela , Hogue Ian B. , Boyko Vitaly , Hu Wei-Shau , Ono Akira 
Published: December 2007

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) particle assembly mediated by the viral structural protein Gag occurs predominantly on the plasma membrane (PM). Although it is known that the matrix (MA) domain of Gag plays a major role in PM localization, molecular mechanisms that determine the location of assembly remain to be elucidated. We observed previously that overexpression of polyphosphoinositide 5-phosphatase IV (5ptaseIV) that depletes PM phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P
2
] impairs virus particle production and redirects processed Gag to intracellular compartments. In this study, we examined the impact of PI(4,5)P
2
depletion on the subcellular localization of the entire Gag population using Gag-fluorescent protein chimeras. Upon 5ptaseIV overexpression, in addition to perinuclear localization, Gag also showed a hazy cytosolic signal, suggesting that PI(4,5)P
2
depletion impairs Gag membrane binding. Indeed, Gag was less membrane bound in PI(4,5)P
2
-depleted cells, as assessed by biochemical analysis. These observations are consistent with the hypothesis that Gag interacts with PI(4,5)P
2
. To examine a putative Gag interaction with PI(4,5)P
2
, we developed an in vitro binding assay using full-length myristoylated Gag and liposome-associated PI(4,5)P
2
. Using this assay, we observed that PI(4,5)P
2
significantly enhances liposome binding of wild-type Gag. In contrast, a Gag derivative lacking MA did not require PI(4,5)P
2
for efficient liposome binding. To analyze the involvement of MA in PI(4,5)P
2
binding further, we examined MA basic amino acid substitution mutants. These mutants, previously shown to localize in perinuclear compartments, bound PI(4,5)P
2
-containing liposomes weakly. Altogether, these results indicate that HIV-1 Gag binds PI(4,5)P
2
on the membrane and that the MA basic domain mediates this interaction.
The Programmed Death-1 and Interleukin-10 Pathways Play a Down-Modulatory Role in LP-BM5 Retrovirus-Induced Murine Immunodeficiency Syndrome
Authors: Green Kathy A. , Okazaki Taku , Honjo Tasuku , Cook W. James , Green William R. 
Published: December 2007

ABSTRACTPathology due to the immune system's response to viral infections often represents a delicate balance between inhibition of viral pathogenesis and regulation of protective immunity. In susceptible C57BL/6 (B6) mice, the murine retroviral isolate LP-BM5 induces splenomegaly, hypergammaglobulinemia, profound B- and T-cell immunodeficiency, and increased susceptibility to opportunistic pathogens and terminal B-cell lymphomas. Here, we report that B6.PD-1 (programmed death-1) and B6.IL-10 knockout mice are substantially more susceptible to LP-BM5-induced disease than wild-type B6 mice. LP-BM5-infected B6.PD-1−/−mice developed more severe splenomegaly, hypergammaglobulinemia, and immunodeficiency than infected B6 mice: PD-1−/−mice are more susceptible to lower doses of LP-BM5 and show more exaggerated disease early postinfection. LP-BM5-infected B6.IL-10−/−mice also develop exaggerated LP-BM5-induced disease, compared to B6 mice, without a significant change in the retroviral load. By reciprocal reconstitution experiments, comparing wild-type versus PD-1−/−sources of the requisite cells for LP-BM5 pathogenesis—CD4 T and B cells, PD-1+B cells appear to be crucial in the normal limitation of LP-BM5-induced disease in B6 mice. Also, infected B6 mice have increased CD11b+spleen cells that express interleukin-10 (IL-10). However, PD-1−/−mice, though showing an even greater expansion of CD11b+cells after LP-BM5 inoculation, did not show an equivalent increase in IL-10-producing cells. Thus, it appears that PD-1/PD-L interactions and IL-10 are primarily important in moderating the effects of LP-BM5-induced disease in B6 mice.
Identification of Cellular Proteins That Maintain Retroviral Epigenetic Silencing: Evidence for an Antiviral Response
Authors: Poleshko Andrey , Palagin Ivan , Zhang Rugang , Boimel Pamela , Castagna Carolyn , Adams Peter D. , Skalka Anna Marie , Katz Richard A. 
Published: December 2007

ABSTRACT
Integrated retroviral DNA is subject to epigenetic gene silencing, resulting in loss of expression of viral genes as well as reporter or therapeutic genes transduced by retroviral vectors. Possible mediators of such silencing include the histone deacetylase (HDAC) family of cellular proteins. We previously isolated HeLa cell populations that harbored silent avian sarcoma virus-based green fluorescent protein (GFP) vectors that could be reactivated by treatment with HDAC inhibitors. Here, we developed a small interfering RNA (siRNA)-based approach to identify specific host factors that participate in the maintenance of silencing. Knockdown of HDAC1, the transcriptional repressor Daxx (a binding partner of HDAC1), or heterochromatin protein 1 gamma resulted in robust and specific GFP reporter gene reactivation. Analyses of cell clones and diverse GFP vector constructs revealed that the roles of HDAC1 and Daxx in retroviral silencing are largely independent of the integration site or the promoter controlling the silent GFP reporter gene. Previous findings from our laboratory and those of others have suggested that Daxx and HDAC proteins may act broadly as part of an antiviral response to repress viral gene transcription. Expression of presumptive viral “countermeasure” proteins that are known to inhibit Daxx or HDACs (pp71, IE2, and Gam1) resulted in the reactivation of GFP reporter gene expression. This study has identified individual host factors that maintain retroviral silencing and supports the proposal that these factors participate in an antiviral response. Furthermore, our results indicate that siRNAs can be used as specific reagents to interrupt the maintenance of epigenetic silencing.