An open source protein gel documentation system for proteome analyses

Data organization and data mining represents one of the main challenges for modern high throughput technologies in pharmaceutical chemistry and medical chemistry. The presented open source documentation and analysis system provides an integrated solution (tutorial, setup protocol, sources, executables) aimed at substituting the traditionally used lab-book. The data management solution provided incorporates detailed information about the processing of the gels and the experimental conditions used and includes basic data analysis facilities which can be easily extended. The sample database and User-Interface are available free of charge under the GNU license from http://webber.physik.uni-freiburg.de/~fallerd/tutorial.htm.     

Small-angle static light scattering of concentrated silica suspensions during in situ destabilization

The aggregation of concentrated aqueous silica suspensions is characterized by means of static light scattering. We use an in situ destabilization mechanism based on the enzyme-catalyzed hydrolysis of urea. This method enables us to continuously and homogeneously change the interparticle potential from repulsive to attractive without disturbing the aggregation process. Moreover, our electrostatically stabilized suspensions can be destabilized by two different methods. In the first method, the pH is shifted toward the isoelectric point of the particles ( Delta pH method), thereby leading to a decrease of their surface charge. In the second method, the ionic strength is continuously increased at constant pH ( Delta I method), leading to a compression of the electrical double layer around the charged particles. A laboratory-built flat-cell light-scattering instrument is used, which allows fast data acquisition and an adjustment of the sample cell thickness. To circumvent multiple scattering effects, we use a very small sample thickness ( approximately 13 microm). In addition, the refractive index difference between the aqueous phase and the particles is reduced by adding sucrose to the liquid phase of our suspensions. We are able to characterize the structural changes at the very early stages of the destabilization process, where no significant effects are yet detected in macroscopic rheological measurements. While during the Delta pH destabilization, the scattering curve shows significant changes only after some characteristic delay time, it changes continuously during the Delta I destabilization. The latter is attributed to the formation of a weak pre-gel structure in the suspensions, as a shallow secondary minimum appears in the interparticle potential. Data are evaluated by using a HMSA square-well structure factor model. Results are in good agreement with those predicted from DLVO theory.     

BIOSYNTHESIS OF PTERIDINES IN Neurospora crassa,Phycomyces blakesleeanus AND Euglena gracilis: DETECTION AND CHARACTERIZATION OF BIOSYNTHETIC ENZYMES*,†

Abstract— Occurrence, biosynthesis and some functions of tetrahydrobiopterin (H₄biopterin) in animals are well known. The biochemistry of H₄biopterin in other organisms than animals was hitherto not widely investigated. Recently H₄biopterin was found in the phytoflagellate Euglena gracilis, in the zygomycete Phycomyces blakesleeanus and in the ascomycete Neurospora crassa. In Euglena, Neurospora and Phycomyces the enzymatic activities of GTP cyclohydrolase I, 6-pyruvoyl tetrahydropterin synthase and sepiapterin reductase are detectable and the biosynthesis follows the same steps as were shown for animals. The biosynthetic enzymes, however, show a much lower sensitivity to those inhibitors that act on vertebrate enzymes. 2,4-Diamino-6-hydroxypyrimidine as inhibitor of GTP cyclohydrolase I and N-acetylserotonin or N-methoxyacetylserotonin as inhibitors of sepiapterin reductase can decrease pteridine biosynthesis significantly, in vitro and in vivo. The apparent K_mvalues are in general higher when compared with the respective animal enzymes. In Neurospora, the conversion of GTP to dihydroneopterin triphosphate was closely associated with subsequent production of 6-hydroxymethyl-7, 8-dihydropterin due to the high activity of dihydroneopterin aldolase, different from all other tested organisms. Investigations involving inhibition of pteridine synthesis might be a useful tool for evaluating the hypothesis that pteridines in fungi and plants are co-chromophores of various blue light-dependent, flavin-containing phototrcptors.     

Ultrathin functional films of titanium(IV) oxide

Chemistry and physics of thin semiconducting layers of various types are subjects of intense research. Especially when nanotechnology methods such as self-assembly are involved, amazing structural and/or functional properties may appear. Also modern physical methods using variously organized plasma arrangements are able to produce uniform structures with distinctive functionality. In this review, based virtually on our own work, discussions on the preparation, structure, morphology, and function of titanium(IV) oxide nanoscopic thin films are presented. It was shown that structurally and functionally similar titanium(IV) oxide films can be prepared via completely different preparation techniques. Function tests were arranged as “primary”, covering the assessment of the light induced charge separation efficiency, and “secondary”, based on photocatalytic surface oxidations.     

Measured and calculated oxidation potentials of 1-X-12-Y-CB11Me10- anions

Cyclic voltammetry of 31 icosahedral carborane anions 1-X-12-Y-CB(11)Me(10)(-) at a Pt electrode in liquid SO(2) revealed a completely reversible one-electron oxidation even at low scan rates, except for the anions with Y = I, which are oxidized irreversibly up to a scan rate of 5.0 V/s, and the anion with X = COOH and Y = H, whose oxidation is irreversible at scan rates below 1.0 V/s. Relative reversible oxidation potentials agree well with RI-B3LYP/TZVPP,COSMO and significantly less well with RI-BP86/TZVPP,COSMO or RI-HF/TZVPP,COSMO calculated adiabatic electron detachment energies. Correlations with HOMO energies of the anions are nearly as good, even though the oxidized forms are subject to considerable Jahn-Teller distortion. Except for the anion with X = F and Y = Me, the oxidation potentials vary linearly with substituent σ(p) Hammett constants. The slopes (reaction constants) are ~0.31 and ~0.55 V for positions 1 and 12, respectively.     

Physicochemical characterization of acrylamide/bisacrylamide hydrogels and their application for the conservation of easel paintings

Acrylamide chemical gels have been synthesized to obtain systems with mechanic and hydrophilic properties suitable for the cleaning of works of art. The gel characteristics were tailored by changing the polymer percentage present in the final hydrogel formulation from 2 to 10% w/w. Two different hydrogels have been selected in this interval for an in depth characterization (i.e., S 4% w/w and H 6% w/w). Water retention properties of the gels along with the free water index have been determined by the combination of standard dehydration tests and differential scanning calorimetry (DSC) measurements. The gels' structure has been determined by scanning electron microscopy (SEM) and small angle X-ray scattering (SAXS). The water retention capacity of hydrogel, H, was also determined. Cleaning tests on easel painting replicas, performed with both hydrogels loaded with an aqueous detergent system, showed good results in the removal of a widely used synthetic adhesive and hence offered these gels as a real alternative to the widely applied physical gel methodology with the advantage of being a residue-free technique. A preliminary SAXS investigation confirms the persistence of the detergent system nanostructure inside the hydrogel.