Characterization of the ‘reserve cellulose’ of the endosperm of Carum carvi as a β(1–4)-mannan

The reserve polysaccharide of the endosperm of Carum carvi consists of more than 90% mannose and was characterized as a β(1–4)-mannan. Total or partial acid hydrolysis, enzymatic breakdown or acetolysis of either palm or Carum carvi mannan yielded the same mono- and oligosaccharides, indicating a similar chemical structure of the two reserve polysaccharides. However, Carum carvi contains only traces of the alkali soluble mannan A dominant in the palm endosperm polysaccharide.     

Gas chromatographic enantioseparation of unfunctionalized chiral alkanes: a challenge in separation science (overview, state of the art, and perspectives)

The chromatographic enantioseparation of small unfunctionalized chiral alkanes C*HR(1)R(2)R(3) (R = alkyl) represents a challenge in separation science. Because of the lack of any functional groups, enantiorecognition in the presence of a chiral selector is solely based upon weak enantioselective Van der Waals forces. Racemic alkanes containing seven and eight carbon atoms, i.e. 3-methylhexane (C7), 2,3-dimethylpentane (C7), 3-methylheptane (C8), 3,4-dimethylhexane (C8), 2,4-dimethylhexane (C8), 2,3-dimethylhexane (C8), and 2,2,3-trimethylpentane (C8) have been gas chromatographically enantioseparated on different modified cyclodextrins. The substitution pattern and cavity size of the cyclodextrin selectors have a pronounced effect on the degree of enantiorecognition observed. Thermodynamic parameters of enantiorecognition between four chiral alkanes and octakis(6-O-methyl-2,3-di-O-pentyl)-gamma-cyclodextrin (Lipodex G) have been determined. The possible role of molecular inclusion is indicated by the complete loss of enantioselectivity when the cyclodextrins are replaced by the corresponding linear dextrins ("acyclodextrins"). The enantioseparations of all seven chiral C7-C8 alkanes, six of them simultaneously, has been achieved on mixed binary selector systems whereby two different modified cyclodextrins are present in one gas chromatographic column. The smallest chiral (nonisotopically labeled) allene, i.e., 2,3-pentadiene, has been resolved gas chromatographically on a cyclodextrin selector.     

A selective inhibitor reveals PI3Kγ dependence of T(H)17 cell differentiation

We devised a high-throughput chemoproteomics method that enabled multiplexed screening of 16,000 compounds against native protein and lipid kinases in cell extracts. Optimization of one chemical series resulted in CZC24832, which is to our knowledge the first selective inhibitor of phosphoinositide 3-kinase γ (PI3Kγ) with efficacy in in vitro and in vivo models of inflammation. Extensive target- and cell-based profiling of CZC24832 revealed regulation of interleukin-17-producing T helper cell (T(H)17) differentiation by PI3Kγ, thus reinforcing selective inhibition of PI3Kγ as a potential treatment for inflammatory and autoimmune diseases.     

Mass spectrometry approaches to monitor protein-drug interactions

Recent advances in mass spectrometry-based approaches have enabled the investigation of drug-protein interactions in various ways including the direct detection of drug-target complexes, the examination of drug-induced changes in the target protein structure, and the monitoring of enzymatic target activity. Mass spectrometry-based proteomics methods also permit the unbiased analysis of changes in protein abundance and post-translational modifications induced by drug action. Finally, chemoproteomic affinity enrichment studies enable the deconvolution of drug targets under close to physiological conditions. This review provides an overview of current methods for the characterization of drug-target interactions by mass spectrometry and describes a protocol for chemoproteomic target binding studies using immobilized bioactive molecules.     

Histological heterogeneity of human glioblastomas investigated with an unsupervised neural network (SOM)

The histological variability of Glioblastomas (GB) precludes the modern assimilation of theses tumors into a single histological tumor group. As an alternative to statistical histological evaluation, we investigated 1489 human GB in order to discover whether they could be correctly classified using Self-Organizing Maps (SOM). In all tumors 50 histological features, as well as the age and sex of the patients, were examined. Four clusters of GB with a significance of 52 (maximal significance 60) were found. Cluster C1 contained 37.47% of all GB and 41.09% of all polymorphic glioblastomas (PG). Cluster C2 included 35.06% of all GB and 44.96% of all giant cell glioblastomas (GCG). Cluster C3 contained 16.45% of all GB with a significant component of astroblasts, glioblasts and oligodendroglia. Cluster C4 included 11.01% of all GB, 87.80% of the gliosarcomas (GS) and 36.72% of all GCG. Placing a series of component windows with their maps side by side allows the immediate recognition of the dependencies on variables and the determination of variables necessary to build the specific clusters. The SOM allow a realistic histological classification, comparable to the actual classification by the WHO. In addition, we found new, small subclusters of human GB which may have a clinical significance. With SOM one can learn to discriminate, discard and delete data, select histological and clinical or genetic variables that are meaningful, and consequently influence the result of patient management.     

Ambruticin S production in air-lift and stirred-tank bioreactors

Summary Using the method of equi-inocular synchronized comparative fermentation (EISCF) the cultivation of Sorangium cellulosum So ce 10 and production of the polyketide antibiotic ambruticin S was compared in stirred-tank and air-lift reactors of different geometry. This method requires that inocula originate from the same pre-culture and cultivation parameters are synchronized to similar values. Similar ambruticin yields were obtained from both reactor systems provided that the concentration of dissolved oxygen (DO) was maintained above a certain value (ca. 40%). For cultivation of S. cellulosum it is the DO level rather than the oxygen transfer rate which presents the proper criterion for scale-up and comparative reactor studies. Offprint requests to: W.-D. Deckwer     

Recombinant domain IV of perlecan binds to nidogens, laminin-nidogen complex, fibronectin, fibulin-2 and heparin.

Domain IV of mouse perlecan, which consists of 14 immunoglobulin superfamily (IG) modules, was prepared from recombinant human cell culture medium in the form of two fragments, IV-1 (IG2-9, 100 kDa) and IV-2 (IG10-15, 66 kDa). Both fragments bound to a heparin column, being eluted at ionic strengths either below (IV-2) or above (IV-1) physiological level, and could thus be readily purified. Electron microscopy demonstrated an elongated shape (20-25 nm), and folding into a native structure was indicated by immunological assay and CD spectroscopy. Solid-phase and surface plasmon resonance assays demonstrated strong binding of fragment IV-1 to fibronectin, nidogen-1, nidogen-2 and the laminin-1-nidogen-1 complex, with Kd values in the range 4-17 nM. The latter binding apparently occurs through nidogen-1, as shown by the formation of ternary complexes. Only moderate binding was observed for fibulin-2 and collagen IV and none for fibulin-1 and BM-40. Fragment IV-2 showed a more restricted pattern of binding, with only weaker binding to fibronectin and fibulin-2. None of these activities could be demonstrated for recombinant fragments corresponding to the N-terminal perlecan domains I to III. This indicates a special role for domain IV in the integration of perlecan into basement membranes and other extracellular structures via protein-protein interactions.     

Cystic fibrosis transmembrane conductance regulator inhibits epithelial Na+ channels carrying Liddle's syndrome mutations.

Epithelial Na+ channels (ENaC) are inhibited by the cystic fibrosis transmembrane conductance regulator (CFTR) upon activation by protein kinase A. It is, however, still unclear how CFTR regulates the activity of ENaC. In the present study we examined whether CFTR interacts with ENaC by interfering with the Nedd4- and ubiquitin-mediated endocytosis of ENaC. Various C-terminal mutations were introduced into the three alpha-, beta-, and gamma-subunits of the rat epithelial Na+ channel, thereby eliminating PY motifs, which are important binding domains for the ubiquitin ligase Nedd4. When expressed in Xenopus oocytes, most of the ENaC stop (alpha-H647X, beta-P565X, gamma-S608X) or point (alpha-P671A, beta-Y618A, gamma-P(624-626)A) mutations induced enhanced Na+ currents when compared with wild type alpha,beta,gamma-rENaC. However, ENaC currents formed by either of the mutant alpha-, beta-, or gamma-subunits were inhibited during activation of CFTR by forskolin (10 micromol/l) and 3-isobutyl-1-methylxanthine (1 mmol/l). Antibodies to dynamin or ubiquitin enhanced alpha,beta,gamma-rENaC whole cell Na+ conductance but did not interfere with inhibition of ENaC by CFTR. Another mutant, beta-T592M,T593A-ENaC, also showed enhanced Na+ currents, which were down-regulated by CFTR. Moreover, activation of ENaC by extracellular proteases and xCAP1 does not disturb CFTR-dependent inhibition of ENaC. We conclude that regulation of ENaC by CFTR is distal to other regulatory limbs and does not involve Nedd4-dependent ubiquitination.     

The Temperature Gradient-Forming Device,an Accessory Unit for Normal Light Microscopes To Study the Biology of Hyperthermophilic Microorganisms

To date, the behavior of hyperthermophilic microorganisms in their biotope has been studied only to a limited degree; this is especially true for motility. One reason for this lack of knowledge is the requirement for high-temperature microscopy—combined, in most cases, with the need for observations under strictly anaerobic conditions—for such studies. We have developed a custom-made, low-budget device that, for the first time, allows analyses in temperature gradients up to 40°C over a distance of just 2 cm (a biotope-relevant distance) with heating rates up to ∼5°C/s. Our temperature gradient-forming device can convert any upright light microscope into one that works at temperatures as high as 110°C. Data obtained by use of this apparatus show how very well hyperthermophiles are adapted to their biotope: they can react within seconds to elevated temperatures by starting motility—even after 9 months of storage in the cold. Using the temperature gradient-forming device, we determined the temperature ranges for swimming, and the swimming speeds, of 15 selected species of the genus Thermococcus within a few months, related these findings to the presence of cell surface appendages, and obtained the first evidence for thermotaxis in Archaea.