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.     

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]     

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.     

A chemically consistent graph architecture for massive reaction networks applied to solid-electrolyte interphase formation

Modeling reactivity with chemical reaction networks could yield fundamental mechanistic understanding that would expedite the development of processes and technologies for energy storage, medicine, catalysis, and more. Thus far, reaction networks have been limited in size by chemically inconsistent graph representations of multi-reactant reactions (e.g. A + B → C) that cannot enforce stoichiometric constraints, precluding the use of optimized shortest-path algorithms. Here, we report a chemically consistent graph architecture that overcomes these limitations using a novel multi-reactant representation and iterative cost-solving procedure. Our approach enables the identification of all low-cost pathways to desired products in massive reaction networks containing reactions of any stoichiometry, allowing for the investigation of vastly more complex systems than previously possible. Leveraging our architecture, we construct the first ever electrochemical reaction network from first-principles thermodynamic calculations to describe the formation of the Li-ion solid electrolyte interphase (SEI), which is critical for passivation of the negative electrode. Using this network comprised of nearly 6000 species and 4.5 million reactions, we interrogate the formation of a key SEI component, lithium ethylene dicarbonate. We automatically identify previously proposed mechanisms as well as multiple novel pathways containing counter-intuitive reactions that have not, to our knowledge, been reported in the literature. We envision that our framework and data-driven methodology will facilitate efforts to engineer the composition-related properties of the SEI – or of any complex chemical process – through selective control of reactivity.

A chemically consistent graph architecture enables autonomous identification of novel solid-electrolyte interphase formation pathways from a massive reaction network.     

Longitudinal nuclear relaxation measurements in hcp H2

Measurements of T₁ in the hep phase of H₂, over the temperature range 2°–12°K and the ortho concentration range between 0.5 and 0.97 are presented. At temperatures below 10°K, the thermally activated self-diffusion is negligible and the mechanism for nuclear relaxation is that attributed by Moryia and Motizuki and by Harris to intramolecular dipolar interaction, modulated by intennolecular electric quadrupole-quadrupole (EQQ) interaction. The gaussian approximation for the correlation function was used by these authors to predict T₁. From the comparison between experiment and theory, we determine the EQQ parameter Γ/k_B to be 0.67°K. Above 10°K the effect of diffusion influences T₁, and the experimental results for an 88 per cent ortho H₂ sample up to the melting point suggest that the relaxation mechanisms resulting from EQQ interaction and diffusion are not independent of one another.     

Projective Modules over the Non-Commutative Sphere

The positive cone of the K₀-group of the non-commutative sphereB is explicitly determined by means of the four basic unboundedtrace functionals discovered by Bratteli, Elliott, Evans andKishimoto. The C*-algebra B is the crossed product A x Z₂ ofthe irrational rotation algebra A by the flip automorphism defined on the canonical unitary generators U, V by (U) = U*,(V) = V*, where VU = e²ⁱ UV and is an irrational real number.This result combined with Rieffel's cancellation techniquesis used to show that cancellation holds for all finitely generatedprojective modules over B. Subsequently, these modules are determinedup to isomorphism as finite direct sums of basic modules. Italso follows that two projections p and q in a matrix algebraover B are unitarily equivalent if, and only if, their vectortraces are equal: [p] = [q]. These results will have the following ramifications. They areused (elsewhere) to show that the flip automorphism on A isan inductive limit automorphism with respect to the basic buildingblock construction of Elliott and Evans for the irrational rotationalgebra. This will, in turn, yield a two-tower proof of thefact that B is approximately finite dimensional, first provedby Bratteli and Kishimoto.     

Planar graphs,Hamilton cycles and extreme independence number

If a graph has too many edges, it must be Hamiltonian. We show how to construct graphs near the threshold: they have as many edges as possible without sacrificing planarity but are not Hamiltonian. We base our construction on the concepts of independent sets and 1-toughness.The work of the author was partially supported by CNPq-Brasil.