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Selected AbstractsHomeostasis of neuroactive amino acids in cultured cerebellar and neocortical neurons is influenced by environmental cuesJOURNAL OF NEUROSCIENCE RESEARCH, Issue 1-2 2005Helle Waagepetersen Abstract Neuronal function is highly influenced by the extracellular environment. To study the effect of the milieu on neurons from cerebellum and neocortex, cells from these brain areas were cultured under different conditions. Two sets of cultures, one neocortical and one cerebellar neurons, were maintained in media containing [U- 13C]glucose for 8 days at initial concentrations of 12 and 28 mM glucose, respectively. Other sets of cultures (8 days in vitro) maintained in a medium containing initially 12 mM glucose were incubated subsequently for 4 hr either by addition of [U- 13C]glucose to the culture medium (final concentration 3 mM) or by changing to fresh medium containing [U- 13C]glucose (3 mM) but without glutamine and fetal calf serum. 13C Nuclear magnetic resonance (NMR) spectra revealed extensive ,-aminobutyric acid (GABA) synthesis in both cultured neocortical and cerebellar neurons after maintenance in medium containing [U- 13C]glucose for 8 days, whereas no aspartate labeling was observed in these spectra. Mass spectrometry analysis, however, revealed high labeling intensity of aspartate, which was equal in the two types of neurons. Addition of [U- 13C]glucose (4 hr) on Day 8 in culture led to a similar extent of labeling of GABA in neocortical and in cerebellar cultures, but the cellular content of GABA was considerably higher in the neocortical neurons. The cellular content of alanine was similar regardless of culture type. Comparing the amount of labeling, however, cerebellar neurons exhibited a higher capacity for alanine synthesis. This is compatible with the fact that cerebellar neurons could ameliorate a low alanine content after culturing in low glucose (12 mM) by a 4-hr incubation in medium containing 3 mM glucose. A low glucose concentration during the culture period and a subsequent medium change were associated with decreases in glutathione and taurine contents. Moreover, glutamate and GABA contents were reduced in cerebellar cultures under either of these conditions. In neocortical neurons, the GABA content was decreased by simultaneous exposure to low glucose and change of medium. These conditions also led to an increase in the aspartate content in both types of cultures, although most pronounced in the neocortical neurons. Further experiments are needed to elucidate these phenomena that underline the impact of extracellular environment on amino acid homeostasis. © 2004 Wiley-Liss, Inc. [source] Shotgun proteomic analysis of human-induced sputumPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 15 2006Ben Nicholas Dr. Abstract Induced sputum is a readily accessible biological fluid whose composition may alter as a consequence of disease. To date, however, the proteins that routinely populate this biofluid are largely unknown, in part due to the technical difficulties in processing such mucin-rich samples. To provide a catalogue of sputum proteins, we have surveyed the proteome of human-induced sputum (sputome). A combination of 2-D gel analysis and GeLC-MS/MS allowed a total of 191 human proteins to be confidently assigned. In addition to the expected components, several hitherto unreported proteins were found to be present, including three members of the annexin family, kallikreins 1 and 11, and peroxiredoxins 1, 2 and 5. Other sets of proteins identified included four proteins previously annotated as hypothetical or conserved hypothetical. Taken together, these data represent the first extensive survey of the proteome of induced sputum and provide a platform for future identification of biomarkers of lung disease. [source] Shotgun proteomic analysis of Chlamydia trachomatisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2005Paul Skipp Abstract Chlamydiae are widespread bacterial pathogens responsible for a broad range of diseases, including sexually transmitted infections, pneumonia and trachoma. To validate the existence of hitherto hypothetical proteins predicted from recent chlamydial genome sequencing projects and to examine the patterns of expression of key components at the protein level, we have surveyed the expressed proteome of Chlamydia trachomatis strain,L2. A combination of two-dimensional gel analysis, multi-dimensional protein identification (MudPIT) and nanocapillary liquid chromatography-tandem mass spectrometry allowed a total of 328,chlamydial proteins to be unambiguously assigned. Proteins identified as being expressed in the metabolically inert form, elementary body, of Chlamydia include the entire set of predicted glycolytic enzymes, indicating that metabolite flux rather than de novo synthesis of this pathway is triggered upon infection of host cells. An enzyme central to cell wall biosynthesis was also detected in the intracellular form, reticulate body, of Chlamydia, suggesting that the peptidoglycan is produced during growth within host cells. Other sets of proteins identified include 17 outer membrane-associated proteins of potential significance in vaccine studies and 67,proteins previously annotated as hypothetical or conserved hypothetical. Taken together, ,35% of the predicted proteome for C.,trachomatis has been experimentally verified, representing the most extensive survey of any chlamydial proteome to date. [source] Site scores and conditional biplots in canonical correspondence analysisENVIRONMETRICS, Issue 1 2004Jan Graffelman Abstract Canonical correspondence analysis is an important multivariate technique in community ecology. It produces an interesting biplot that summarizes the data matrices involved in the analysis. The method produces two sets of site scores that can be used in a biplot. One set concerns site scores that are weighted averages of the species scores (WA scores), and the other set represents site scores that are linear combinations of the environmental variables (LC scores). We show that the use of both sets of scores in a CCA biplot can be justified. The use of the WA scores leads to the best possible representation of the species data conditional on the representation of the weighted averages. Likewise, the LC scores lead to the best possible representation of the environmental variables, also conditional on the representation of the weighted averages and on the use of a Mahalanobis metric. The eigenvalues obtained in CCA indicate how well the species data are represented when LC scores are used. The quality of representation of the species data when WA scores are used can be computed from the CCA eigenvalues and the variances of the WA scores. Scalar products between WA scores and environmental variable vectors do not form a biplot of the environmental data. Theoretical results are illustrated with Australian data from freshwater ecology. Copyright © 2003 John Wiley & Sons, Ltd. [source] Examination of cytotoxicity and mutagenicity of AH26 and AH Plus sealersINTERNATIONAL ENDODONTIC JOURNAL, Issue 5 2003I. Mileti Abstract Aim ,To study in vitro the cytotoxic and mutagenic effects of AH26 and AH Plus. Methodology ,Cytotoxic effects on Chinese hamster V79 cells were determined by counting viable cells following incubation with eluations of AH26 and AH Plus. In one set of experiments, the materials were mixed, set for 1 h and then eluted with dimethyl sulphoxide (DMSO) for 1 h, 24 h and 7 days. In the other set, AH26 and AH Plus were mixed and set for 1 h, 24 h and 7 days in physiological saline then crushed and eluted in DMSO for 24 h. The cytotoxic effects of these eluates were evaluated. Three concentrations were chosen to examine the mutagenic effects of AH26 and AH Plus: 5.57, 16.7 and 55.7 ,g mL,1. The structural chromosomal aberration analysis and micronucleus test were performed on human lymphocytes according to standard procedures. Results ,Dose,response curves of cell survival were obtained. Both materials were shown to be cytotoxic in doses larger than 55.7 ,g mL,1, except for AH26, after 7 days setting time. AH Plus was also shown to be toxic in concentrations of 16.7 ,g mL,1, except after 7 days setting time. Neither AH26 nor AH Plus induced a significant increase of chromosomal aberrations or micronuclei induction at any setting time or concentration. Conclusion ,There was no mutagenicity found for AH26 and AH Plus on human lymphocytes in highly controlled conditions in vitro. [source] Fine mapping and detection of the causative mutation underlying Quantitative Trait LociJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2010E. Uleberg Summary The effect on power and precision of including the causative SNP amongst the investigated markers in Quantitative Trait Loci (QTL) mapping experiments was investigated. Three fine mapping methods were tested to see which was most efficient in finding the causative mutation: combined linkage and linkage disequilibrium mapping (LLD); association mapping (MARK); a combination of LLD and association mapping (LLDMARK). Two simulated data sets were analysed: in one set, the causative SNP was included amongst the markers, while in the other set the causative SNP was masked between markers. Including the causative SNP amongst the markers increased both precision and power in the analyses. For the LLD method the number of correctly positioned QTL increased from 17 for the analysis without the causative SNP to 77 for the analysis including the causative SNP. The likelihood of the data analysis increased from 3.4 to 13.3 likelihood units for the MARK method when the causative SNP was included. When the causative SNP was masked between the analysed markers, the LLD method was most efficient in detecting the correct QTL position, while the MARK method was most efficient when the causative SNP was included as a marker in the analysis. The LLDMARK method, combining association mapping and LLD, assumes a QTL as the null hypothesis (using LLD method) and tests whether the ,putative causative SNP' explains significantly more variance than a QTL in the region. Thus, if the putative causative SNP does not only give an Identical-By-Descent (IBD) signal, but also an Alike-In-State (AIS) signal, LLDMARK gives a positive likelihood ratio. LLDMARK detected less than half as many causative SNPs as the other methods, and also had a relatively high false discovery rate when the QTL effect was large. LLDMARK may however be more robust against spurious associations, because the regional IBD is largely corrected for by fitting a QTL effect in the null hypothesis model. [source] Phase behavior and photo-responsive studies of photoactive liquid crystalline hyperbranched polyethers containing benzylidene moietyJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 11 2009V. Srinivasa Rao Abstract Two sets of hyperbranched polyether epoxies were synthesized to study the effect of substituent, rigidity, and nature of photoactive unit on the thermal and photoresponsive properties. Each set was comprised of one molecule with an acyclic moiety in the repeating unit, and two molecules with a cyclic moiety of varying rigidity (cycle size) in the repeating unit. Two substituents on aromatic rings in the repeating unit were present in one set, and other set was without a substituent. The mesogenic and photoresponsive properties were studied and correlated to the varied structural parameters. The effects of varied molecular structural parameters on phase behavior and photoresponsive properties were very prominent. Out of six monomeric diols, only four have exhibited liquid crystalline phase while the polymers corresponding to all monomeric diols revealed mesophase. The findings in photoresponsive properties were further supported by molecular modeling studies. The changes in refractive index, photoviscosity, and fluorescence intensity with irradiation time substantiated the spectral pattern observed in UV-Vis spectroscopy. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2774,2786, 2009 [source] High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlinesJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2008Masahiko Hiraki Sample-exchange robots that can exchange cryo-pins bearing protein crystals out of experimental hutches according to user instructions have been developed. The robots were designed based on the SAM (Stanford Synchrotron Research Laboratory automated mounting) system. In order to reduce the time required for the sample exchange, the single tongs of the SAM system were modified and a double-tongs system that can hold two cryo-pins at the same time was developed. Robots with double tongs can move to the goniometer head holding the next cryo-pin with one set of tongs, dismount the experimented cryo-pin with the other set, and then mount the next pin onto the goniometer head without leaving the diffractometer area. Two different types of tongs have been installed: single tongs at beamlines BL-5A and AR-NW12A, and a double-tongs system at beamline BL-17A of the Photon Factory. The same graphical user interface software for operation of the sample-exchange robots is used at all beamlines, however, so that users do not need to consider differences between the systems. In a trial, the robot with double tongs could exchange samples within 10,s. [source] Salivary mucin as related to oral Streptococcus mutans in elderly peopleMOLECULAR ORAL MICROBIOLOGY, Issue 1 2000L. W. Baughan MG1 (MUC5b and MUC4 ) and MG2 (MUC7), predominant mucins in human whole saliva, provide lubrication and antimicrobial protection for oral tissues. This study examines potential relationships between Streptococcus mutans titers in the oral cavity and the following: mucin concentrations; unstimulated and stimulated whole saliva flow rates; decayed, missing, and filled tooth surfaces; and age of 24 elderly patients. S. mutans titers were determined using Denticult SM. Mucin concentrations were determined using Stains-all, sodium dodecyl sulfate,polyacrylamide gel electrophoresis. Logistic regression was used to identify potential relationships between the above variables. S. mutans classification served as the dependent variable. The remaining variables were possible predictor variables. The best model for predicting S. mutans category contained log MG2 as a predictor variable for all of its parameter estimates. No other set of parameter estimates were statistically significant. These results suggest that elevated S. mutans titers are significantly associated with diminished concentrations of MG2 in unstimulated whole saliva, as quantified in mucin-dye binding units. [source] A comparative study of defect states in evaporated and selenized CIGS(S) solar cellsPROGRESS IN PHOTOVOLTAICS: RESEARCH & APPLICATIONS, Issue 7 2005P. K. Johnson Abstract Current-voltage, admittance spectroscopy, and drive-level capacitance profiling measurements were taken on Cu(In1,xGax)(Se1,ySy)2 solar cell devices. The devices were made using two different types of absorbers. One set of absorbers was deposited via physical vapor deposition, while the other set of absorbers was made by selenization of metal precursors. Additionally, each type of absorber was completed with one of two different types of buffer treatments: a CdS layer or a cadmium partial electrolyte surface modification. The devices with the evaporated absorbers had larger values of VOC, higher carrier densities, lower densities of trapping defects, and likely shallower gap states. Results were qualitatively similar for the CdS and partial electrolyte buffers. Copyright © 2005 John Wiley & Sons, Ltd. [source] Ping-pong cross-validation in real space: a method for increasing the phasing power of a partial model without risk of model biasACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2003John F. Hunt Experimental phases could only be obtained to 4.4,Å resolution for crystals of the SecA translocation ATPase. Density modification of these phases exploiting the 65% solvent content of the crystal produced a map from which an approximate backbone model could be built for 80% of the structure. Combining the phases inferred from this partial model with the MIR phases and repeating the density modification produced an improved map from which a more complete backbone model could be built. However, this procedure converged before yielding a map, that allowed unambiguous sequence assignment for the majority of the protein molecule. In order to avoid the likely model bias associated with a speculative attempt at sequence assignment, a real-space cross-validation procedure was employed to facilitate completion of the crystal structure based on partial model phasing. The protein was partitioned into two disjoint sets of residues. Models in which the side chains were built for residues in one of the two sets were used for phase combination and density modification in order to produce improved electron density for interpretation of residues in the other set that had not been included in the model. Residues in the two sets were therefore omitted from the model in alternation except at sites where the side chain could be identified definitively based on phasing with the other set. This ping-pong cross-validation procedure allowed partial model phasing to be used to complete the crystal structure of SecA without being impeded by model bias. These results show that the structure of a large protein molecule can be solved with exclusively low-resolution experimental phase information based on intensive use of partial model phasing and density modification. Real-space cross-validation can be applied to reduce the risk of model bias associated with partial model phasing, streamlining this approach and expanding its range of applicability. [source] Great ratios and Common Cycles: Do They Exist for the UK?BULLETIN OF ECONOMIC RESEARCH, Issue 1 2001Terence C. Mills This paper investigates the dynamic interactions between postwar, quarterly UK consumption, investment and income within a VAR framework. Use is made of two developments which allow sets of restrictions to be tested and imposed, and which potentially make the VAR framework much more economically interpretable. One set is placed by neoclassical growth theory and involves the presence of common stochastic trends linking the secular movement of the series (i.e. the great ratios), while the other set is placed by notions of common, or more generally, codependent cycles which have their origin in ideas of comovements between growth rates. Evidence is found to support the existence of the great ratios for the UK, and evidence is also found of a codependent cycle of order one in the growth rates of consumption, investment and income, so that although the cycles are not exactly synchronized, the response of the three growth rates to a shock will be similar from two quarters after the shock has occurred. Moreover, it is lagged consumption shocks that are primarily driving the cycle. [source] The Current Usage of Selectivity Coefficients for the Characterization of Ion-Selective Electrodes.ELECTROANALYSIS, Issue 12 2003A Critical Survey of the 2000/2001 Literature Abstract The articles describing new ion-selective electrodes published during the years 2000/2001 in eight leading analytical chemistry journals have been surveyed. Compliance with the IUPAC recommendations of the procedures used for characterizing the selectivity of the new electrodes has been checked. It was found that the information accompanying the selectivity data obtained according to the procedures recommended by IUPAC or their variations was frequently insufficient for interpreting of the electrode behavior and comparing with other sets of data, thus reducing the significance of the values provided. Some criteria for improving the communication between researchers in the field are suggested. [source] ECG Leads I and II to Evaluate Diuresis of Patients with Congestive Heart Failure Admitted to the Hospital via the Emergency DepartmentPACING AND CLINICAL ELECTROPHYSIOLOGY, Issue 1 2009SUTHAPORN LUMLERTGUL M.D. Background: Attenuation of electrocardiogram (ECG) QRS complexes is observed in patients with a variety of illnesses and peripheral edema (PERED), and augmentation with alleviation of PERED. Serial ECGs in stable individuals display variation in the amplitude of QRS complexes in leads V1,V6, stemming from careless placement of recording electrodes on the chestwall. Electrocardiographs record only leads I and II, and mathematically derive the other four limb leads in real time. This study evaluated the sum of the amplitudes of ECG leads I and II, along with other sets of ECG leads in the monitoring of diuresis in patients with congestive heart failure (CHF). Methods: Twenty patients with CHF had ECGs and weights recorded on admission and at discharge. The amplitude of the QRS complexes in all ECG leads were measured and sums of I and II, all limb leads, V1,V6, and all 12 leads were calculated. Results: There was a good correlation between the weight loss and the increase in the sums of the amplitudes of the QRS complexes from leads I and II (r = 0.55, P = 0.012), and the six limb leads (r = 0.68, P = 0.001), but a poor correlation with the V1,V6 leads (r = 0.04, P = 0.85) and all 12 leads (r = 0.1, P = 0.40). Conclusions: Sums of the amplitudes of the ECG QRS complexes from leads I and II constitute a reliable, easily obtainable, ubiquitously available, bedside clinical index, which can be employed in the diagnosis, monitoring of management, and follow-up of patients with CHF. [source] Some fundamental aspects of building protein structures from fragment librariesPROTEIN SCIENCE, Issue 6 2004J. Bradley Holmes Abstract We have investigated some of the basic principles that influence generation of protein structures using a fragment-based, random insertion method. We tested buildup methods and fragment library quality for accuracy in constructing a set of known structures. The parameters most influential in the construction procedure are bond and torsion angles with minor inaccuracies in bond angles alone causing >6 Å C,RMSD for a 150-residue protein. Idealization to a standard set of values corrects this problem, but changes the torsion angles and does not work for every structure. Alternatively, we found using Cartesian coordinates instead of torsion angles did not reduce performance and can potentially increase speed and accuracy. Under conditions simulating ab initio structure prediction, fragment library quality can be suboptimal and still produce near-native structures. Using various clustering criteria, we created a number of libraries and used them to predict a set of native structures based on nonnative fragments. Local C,RMSD fit of fragments, library size, and takeoff/landing angle criteria weakly influence the accuracy of the models. Based on a fragment's minimal perturbation upon insertion into a known structure, a seminative fragment library was created that produced more accurate structures with fragments that were less similar to native fragments than the other sets. These results suggest that fragments need only contain native-like subsections, which when correctly overlapped, can recreate a native-like model. For fragment-based, random insertion methods used in protein structure prediction and design, our findings help to define the parameters this method needs to generate near-native structures. [source] | |||||||||||||||||||||||||