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.     

Application of the hypernetted chain approximation to the electrical double layer for 2:1 and 1:2 electrolytes

The equations needed to estimate the potential drop across the diffuse layer according to the hypernetted chain approximation (HNCA) are derived in this paper for 2:1 and 1:2 electrolytes at the restricted primitive level. It is shown that HNCA results can be expressed in the same format as the corresponding Gouy-Chapman equations with inclusion of two modifying functions. One function depends on the fraction of the solution volume occupied by the ions, and the other depends on the reciprocal thickness of the ionic atmosphere surrounding each ion. In addition, an expression for the potential profile in the diffuse layer for 2:1 and 1:2 electrolyte solutions is derived according to Gouy-Chapman theory. The modifying functions in the HNCA are then estimated using the Henderson-Blum approach for solutions containing ions with diameters of 300 and 400 pm for concentrations in the range from 0.1 to 2 M. It is shown that the Henderson-Blum approach is inadequate for systems with multivalent ions except for charge densities very close to the point of zero charge.     

N-butyl-,N-iso-butyl-andN-sec-butyl-2-picolinamineN-oxide complexes derived from copper(II) salts of polyatomic anions

Summary N-butyl-,N-iso-butyl- andN-sec-butyl-2-picolinamineN- oxide complexes have been prepared from copper(II) perchlorate, tetrafluoroborate and nitrate. Violet solids were isolated from the first two salts while complexes isolated from the nitrate salt were blue green or blue. The ligands coordinatevia both theN-oxide oxygen and the amine nitrogen to give bis (ligand) complexes and only in the case of the nitrate solids is there interaction between the copper(II) centre and the polyatomic anion. Resolution of the g feature in the powder spectra of several of these complexes results from the bulkiness of the butyl groups and therefore dilution of the copper(II) centers. In comparison to the previously studied 2 picolinamineN-oxides with lower alkyl substituents, the complexes have stronger in-plane bonding by the ligands.NATO Fellow on leave from Istanbul Medical Faculty, Istanbul University.     

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.     

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]     

What makes an N12 cage stable?

Much recent attention has been given to molecules containing only nitrogen atoms. Such molecules N(x) can undergo the reaction N(x) --> (x/2)N(2), which is very exothermic. These molecules are potential candidates for high energy density materials (HEDM). However, many all-nitrogen molecules dissociate too easily to be stable, practical energy sources. It is important to know which nitrogen molecules will be stable and which will not. In the current study, a variety of N(12) cages with all single bonds are examined by theoretical calculations to determine which ones are the most thermodynamically stable. Calculations are carried out using Hartree-Fock (HF) theory, gradient-corrected density functional theory (DFT), and Moller-Plesset perturbation theory (MP2 and MP4). Relative energies among the various isomers are calculated and trends are examined in order to determine which structural features lead to the most energetically favorable molecules.     

Synthesis of monofluorinated 1-(naphthalen-1-yl)piperazines

A series of regioisomerically monofluorinated 1-(naphthalen-1-yl)piperazines is described.     

A differential microcalorimetric study of whey proteins and their behaviour in oil-in-water emulsions

Oil-in-water emulsions (20% soya oil, 1% protein) have been prepared containing lysozyme or isolates of -lactalbumin and β-lactoglobulin from whey protein. The structural characteristics of these proteins adsorbed at an oil/water interface were determined by following their thermal transitions using differential scanning microcalorimetry. Thermograms of the proteins in the adsorbed state differed markedly from the corresponding transitions seen for the proteins in solution. This suggests that the proteins underwent substantial changes in secondary and tertiary structure upon adsorption. In general, for all the proteins studied, a net decrease in the total energy absorbed during denaturation was found when the proteins were in an adsorbed state. Both lysozyme and -lactalbumin were in part “surface denatured”, and they showed a certain degree of reversibility between solution and the adsorbed state. β-Lactoglobulin showed the highest degree of denaturation upon adsorption and the conformational change was irreversible.     

Development of xylose-fermenting yeasts for ethanol production at high acetic acid concentrations

Mutants resistant to comparatively high levels of acetic acid were isolated from the xylose-fermenting yeastsCandida shehatae andPichia stipitis by adapting these cultures to increasing concentrations of acetic acid grown in shake-flask cultures. These mutants were tested for their ability to ferment xylose in presence of high acetic acid concentrations, in acid hydrolysates of wood, and in hardwood spent sulfite liquor, and compared with their wild-type counterparts and between themselves. TheP. stipitis mutant exhibited faster fermentation times, better tolerance to acid hydrolysates, and tolerance to lower pH.     

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.