The activation of fibroblast growth factors (FGFs) by glycosaminoglycans: influence of the sulfation pattern on the biological activity of FGF-1

Six synthetic heparin-like oligosaccharides have been used to investigate the effect of the oligosaccharide sulfation pattern on the stimulation of acidic fibroblast growth factor (FGF-1) induced mitogenesis signaling and the biological significance of FGF-1 trans dimerization in the FGF-1 activation process. It has been found that some molecules with a sulfation pattern that does not contain the internal trisaccharide motif, which has been proposed for high affinity for FGF-1, stimulate FGF-1 more efficiently than those with the structure of the regular region of heparin. In contrast to regular region oligosaccharides, in which the sulfate groups are distributed on both sides of their helical three-dimensional structures, the molecules containing this particular sulfation pattern display the sulfate groups only on one side of the helix. These results and the fact that these oligosaccharides do not promote FGF-1 dimerization according to sedimentation-equilibrium analysis, confirm the importance of negative-charge distribution in the activation process and strongly suggest that FGF dimerization is not a general and absolute requirement for biological activity.     

NMR and modeling studies of protein-carbohydrate interactions: synthesis, three-dimensional structure, and recognition properties of a minimum hevein domain with binding affinity for chitooligosaccharides

HEV32, a 32-residue, truncated hevein lacking eleven C-terminal amino acids, was synthesized by solid-phase methodology and correctly folded with three cysteine bridge pairs. The affinities of HEV32 for small chitin fragments--in the forms of N,N',N"-triacetylchitotriose ((GlcNAc)3) (millimolar) and N,N',N",N"',N",N"'-hexaacetylchitohexaose ((GlcNAc)6) (micromolar)--as measured by NMR and fluorescence methods, are comparable with those of native hevein. The HEV32 ligand-binding process is enthalpy driven, while entropy opposes binding. The NMR structure of ligand-bound HEV32 in aqueous solution was determined to be highly similar to the NMR structure of ligand-bound hevein. Solvated molecular-dynamics simulations were performed in order to monitor the changes in side-chain conformation of the binding site of HEV32 and hevein upon interaction with ligands. The calculations suggest that the Trp21 side-chain orientation of HEV32 in the free form differs from that in the bound state; this agrees with fluorescence and thermodynamic data. HEV32 provides a simple molecular model for studying protein-carbohydrate interactions and for understanding the physiological relevance of small native hevein domains lacking C-terminal residues.     

Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST

Recent technological advances have made multidimensional peptide separation techniques coupled with tandem mass spectrometry the method of choice for high-throughput identification of proteins. Due to these advances, the development of software tools for large-scale, fully automated, unambiguous peptide identification is highly necessary. In this work, we have used as a model the nuclear proteome from Jurkat cells and present a processing algorithm that allows accurate predictions of random matching distributions, based on the two SEQUEST scores Xcorr and DeltaCn. Our method permits a very simple and precise calculation of the probabilities associated with individual peptide assignments, as well as of the false discovery rate among the peptides identified in any experiment. A further mathematical analysis demonstrates that the score distributions are highly dependent on database size and precursor mass window and suggests that the probability associated with SEQUEST scores depends on the number of candidate peptide sequences available for the search. Our results highlight the importance of adjusting the filtering criteria to discriminate between correct and incorrect peptide sequences according to the circumstances of each particular experiment.     

Changes in wine yeast storage carbohydrate levels during preadaptation,rehydration and low temperature fermentations

The metabolism of glycogen and trehalose was analysed in a wine yeast strain fermenting at 25 and 13 degrees C. Trehalose and glycogen degradation were completed during the lag phase of fermentation. Ammonia was taken up rapidly and once it had been reduced to negligible amounts, the synthesis of trehalose started. Glycogen followed a similar pattern. If trehalose synthesis was taken as a stress indicator, the fermentation at 13 degrees C could not be considered stressful because the maximum concentrations are similar at both temperatures. In industrial fermentations, and after a preadaptation in grape must for several hours at 18 degrees C, the lag phase was reduced significantly, and this may be why trehalose and glycogen were completely depleted at the beginning of the low temperature fermentation. Various preadaptation conditions were tested so that their influence on trehalose and glycogen degradation could be determined. The presence of fermentable carbon sources, such as glucose or fructose, triggered the mobilisation and use of trehalose. However, just increasing the osmotic pressure did not reduce the trehalose content. No such differences were observed in glycogen metabolism.     

Use of a sample translation technique to minimize adverse effects of laser irradiation in surface-enhanced Raman spectrometry

Surface-enhanced Raman spectroscopy (SERS) has proven to be a very powerful tool in the analysis of a wide range of compounds. However, continuous irradiation of the laser beam over the SERS substrate can promote the gross decomposition of the sample analytes and significantly broaden and diminish the intensities of observed spectral bands. In addition, the incident radiation can promote thermal or photolytic fragmentation of analytes, thereby altering the observable bands and possibly leading to a misinterpretation of analytical data. Finally, chemical or morphological changes in the SERS substrate are possible. This work presents the use of a sample translation technique (STT) as a means to minimize these adverse effects. By spinning the sample rapidly, the effective residence time of analytes and substrate within the irradiated zone is dramatically decreased without reduction of spectral acquisition time or the density of analyte in the zone. The technique is studied by acquiring SERS spectra of Naproxen USP, riboflavin, folic acid, Rhodamine 6G, and 4-aminothiophenol using silver islands on glass and silver-poly(dimethylsiloxane) composite substrates under various spinning and stationary conditions. In all cases, spectra show improvements upon spinning at laser powers as low as 4.2 (+/- 0.1) mW. Specific differences in the appearance of the spectra and the potential use of STT for improved SERS qualitative and quantitative determinations are presented.     

Peptide rearrangement during quadrupole ion trap fragmentation: added complexity to MS/MS spectra

The emergence of proteomics has placed great interest in the understanding of the mechanisms of MS/MS fragmentation of peptides under low-energy collision-induced dissociation. In this work, we describe the presence of anomalous fragments, which correspond to neutral loss elimination of internal amino acids from ions of the b series in quadrupole ion trap MS/MS spectra from naturally occurring peptides. Internal amino acid elimination occurred preferentially with aliphatic amino acids. The phenomenon was more apparent when doubly charged precursors were fragmented and was inhibited when peptides were N-acetylated at the N-terminus. Fragmentation of isomeric peptides where some internal amino acids were relocated in N-terminal position produced MSn spectra indistinguishable from those of the original peptides, indicating that some b ions underwent a structural rearrangement process. Formation of anomalous fragments required a minimum activation time. Our data are consistent with a nucleophile attack of the N-terminal nitrogen over the electrophilic carbonyl carbon at one peptide bond, forming a cyclic b ion intermediate that, by reopening at preferential sites, exposes internal amino acids to the C-terminal side.     

Sponsored Research and Its Impact on Universities, Faculty, and Journals

University promotion and tenure committees use sponsored research to judge a faculty member’s contribution to a discipline’s body of knowledge. Sponsored research is usually a crucial indicator in making promotion and tenure decisions.     

Effects of Iron on Chemical Sulfide Oxidation in Wastewater from Sewer Networks

Effects of iron on the kinetics and stoichiometry of aerobic chemical sulfide oxidation in wastewater from two different sites were studied at pH 8 and 20°C. Iron(III) chloride was added to the wastewater in concentrations of up to 20?g?Fe?m?3. The rate of aerobic chemical sulfide oxidation increased linearly with the iron(III) additions resulting in equal effects with wastewater from the two sites. Despite the significant effect of the iron(III) additions, the background concentrations of iron cannot explain the significant temporal and spatial variability of aerobic chemical sulfide oxidation kinetics reported in this study and in the literature. In this respect, other metals are probably also important. In addition to the impacts on the oxidation kinetics, the iron(III) additions resulted in a change of the oxidation stoichiometry. With increasing amounts of iron(III) added to the wastewater, less dissolved oxygen was required for the sulfide oxidation.     

Response Surface Estimates of the Cross-Sectionally Augmented IPS Tests for Panel Unit Roots

This paper estimates response surface coefficients for a large range of quantiles of the cross-sectionally augmented IPS (CIPS) test of Pesaran (2007), for different specifications of the deterministic components. An Excel programme is available to calculate the P value associated with a CIPS test statistic.     

Improving large-scale search engines with semantic annotations

Traditional search engines have become the most useful tools to search the World Wide Web. Even though they are good for certain search tasks, they may be less effective for others, such as satisfying ambiguous or synonym queries. In this paper, we propose an algorithm that, with the help of Wikipedia and collaborative semantic annotations, improves the quality of web search engines in the ranking of returned results. Our work is supported by (1) the logs generated after query searching, (2) semantic annotations of queries and (3) semantic annotations of web pages. The algorithm makes use of this information to elaborate an appropriate ranking. To validate our approach we have implemented a system that can apply the algorithm to a particular search engine. Evaluation results show that the number of relevant web resources obtained after executing a query with the algorithm is higher than the one obtained without it.