GeneMCL in microarray analysis

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5,730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms.     

Plasma polymerization. V. A systematic investigation of the inductively coupled RF plasma polymerization of the isomeric tetrafluorobenzenes

A systematic investigation has been made of the composition, gross structural features, and rates of deposition of plasma polymer films produced from the excitation of inductively coupled RF plasmas in the isomeric tetrafluorobenzenes. ESCA data reveal that the dominant reaction involves rearrangement such that under a wide variety of experimental conditions the composition of the crosslinked products remains essentially the same as that of the starting material. Small differences in rates of deposition are observed for the different isomers, and theoretical SCF MO studies at the MNDO level provides a basis for discussion of the experimental data.     

A theoretical investigation of molecular core binding and relaxation energies in a series of oxygen-containing organic molecules of interest in the study of surface oxidation of polymers

Nonempirical LCAO MO SCF computations (in the ΔSCF formalism) have been carried out of binding energies and relaxation energies for an extensive series of oxygen-containing organic systems encompassing most of the common functionalities. The molecules for which experimental data are available for comparison demonstrate the adequacy of the treatment for describing the relative binding energies for both the C_ls and O_ls core levels. A sound basis is therefore provided for the discussion of relative core binding energies (C_ls and O_ls) for functionalities for which experimental data are not available, that is, hydroperoxides, peroxides, peroxyacids, and peroxyesters, a knowledge of which is essential for investigations of the surface oxidation of polymers by means of ESCA. C_ls shifts are discussed in terms of primary and secondary substituent effects of oxygen, which greatly simplify the analysis of complex unresolved spectra, whereas for the O_ls levels a similar but less straightforward situation exists. The relaxation energies associated with both C_ls and O_ls core ionization follow a dependence on the binding energy for a given structural type.     

Chimeric (alpha/beta + alpha)-peptide ligands for the BH3-recognition cleft of Bcl-XL: critical role of the molecular scaffold in protein surface recognition

Molecules that bind to specific surface sites on proteins are of great interest from both fundamental and practical perspectives. We are exploring a ligand development strategy that is based on oligomers with discrete folding propensities ("foldamers"); we target a specific cleft on the cancer-associated protein Bcl-xL because this system is well characterized structurally. In vivo, this cleft binds to alpha-helical segments (BH3 domains) of other proteins. We evaluated several types of helical foldamer, built entirely from beta-amino acid residues or from mixtures of alpha- and beta-amino acid residues, and ultimately identified foldamers in the latter class that bind very tightly to Bcl-xL. Our results suggest that combining different types of foldamer backbones will be an effective and general strategy for creating high-affinity and specific ligands for protein surface sites.     

Pulsed titration sensors: Part 1: A breath-by-breath CO2 sensor

A novel electrochemical sensor for the determination of CO₂ in expired breath is described. The sensor works by generating from the reduction of O₂ in dimethyl sulphoxide (DMSO) in a generating pulse. There is a rapid titration reaction between the and any CO₂ present. In the recovery pulse the amount of unreacted is determined. The larger the concentration of CO₂ the less is found in the recovery pulse. The solubilities and diffusion coefficients of O₂ and CO₂ in DMSO have been determined using rotating disc voltammetry and rotation speed step experiments. The stoichiometry, the product, and the rate constant of the titration reaction have been determined using ring—disc voltammetry and laser Raman spectroscopy. The operation and the effect of adventitious water on the sensor are described. Results are presented which show that the sensor can indeed measure the breath-by-breath rhythm of expired CO₂ from a human subject.     

A rapid 1H NMR assay for enantiomeric excess of alpha-substituted aldehydes

In situ derivatization of a variety of alpha-substituted aldehydes via reaction with chiral amines allows convenient and efficient determination of enantiomeric excess. (1)H NMR analysis of the imine diastereomer ratio can be conducted immediately after the aldehyde and amine have been mixed. The results correlate well with ee values determined by more traditional (and slower) methods. This approach may be broadly applicable to alpha-substituted aldehydes. [reaction: see text]     

Structure of the first parallel DNA quadruplex-drug complex

The first crystal structure of a drug (daunomycin) bound to a parallel-stranded intermolecular telomeric G4 quadruplex (d(TGGGGT)4) has been determined to high resolution. A planar assemblage of three daunomycin molecules stacks onto the 5' end of the G4 column, with the daunosamine substituents occupying three of the four quadruplex grooves. The surface area of the terminal G-quartet in this parallel DNA quadruplex, presently occupied by three daunomycins, is sufficiently large that it could easily accommodate other potential telomerase inhibitors such as substituted porphyrins or telomestatin.     

DNA photoreactivating enzyme from human tissues

Photoreactivating enzyme activity has been quantitated in human fetal skin, kidney, lung, liver, brain and intestine, and in neonatal human foreskin. In all the tissues examined there were at least two activities: one nominally greater than 10,000 Da, and one nominally less than 10,000 Da. Both can photolyze pyrimidine dimers in DNA using only light of wavelengths greater than 320 nm, thus excluding tryptophan-mediated dimer splitting as an important mechanism for these activities. The activities are inactivated by digestion with trypsin or pronase, and decreased partially or totally by heating to 65 degrees C. The activities from all six tissues, as well as that from neonatal foreskin, act catalytically in dimer photolysis. The properties of macromolecular size, heat lability, protease sensitivity and catalytic pyrimidine dimer photolysis by a non-tryptophan-mediated mechanism correspond to those of a true photoreactivating enzyme.