The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data

Interpretation of microarray data remains a challenge, and most methods fail to consider the complex, nonlinear regulation of gene expression. To address that limitation, we introduce Learner of Functional Enrichment (LeFE), a statistical/machine learning algorithm based on Random Forest, and demonstrate it on several diverse datasets: smoker/never smoker, breast cancer classification, and cancer drug sensitivity. We also compare it with previously published algorithms, including Gene Set Enrichment Analysis. LeFE regularly identifies statistically significant functional themes consistent with known biology.     

Initial single-center experience with a new intracoronary stent

We investigated the safety and efficacy of the recently introduced intracoronary beStent(TM). High flexibility, zero shortening after expansion and delineating gold markers at either end of the stent are favorable features of this device. Between July 1996 and February 1997, 117 patients received a total of 126 stents, measuring 15, 25 and 35 mm in length. The majority of lesions were located in the LAD (n = 48; 38%), followed by lesions in the RCA (n = 41; 33%) and the circumflex artery (n = 28; 22%). Nine additional stents were delivered into vein grafts (7%). Successful stent deployment was achieved in 94% (n = 118), even in cases with complex lesion morphology and angulated segments. The markers proved to be helpful in placing the stent close to side-branches and whenever serial stents were used. Complications during hospitalization were as follows: one cardiac death unrelated to stenting, one subacute stent thrombosis after 30 min of effective anticoagulation and one Q-wave myocardial infarction due to peripheral thrombus embolization after stent placement in a vein graft. One patient was sent for elective CABG after an unsatisfactory procedural result. Stent loss occurred in four patients, and all stents could be retrieved successfully; in another four patients stent placement at the target site was impossible. We conclude that the investigated stent demonstrates several favorable stent characteristics which have proved to be useful in treating complex lesions by providing favorable acute results with a low complication rate.     

A modular treatment of molecular traffic through the active site of cholinesterase

We present a model for the molecular traffic of ligands, substrates, and products through the active site of cholinesterases (ChEs). First, we describe a common treatment of the diffusion to a buried active site of cationic and neutral species. We then explain the specificity of ChEs for cationic ligands and substrates by introducing two additional components to this common treatment. The first module is a surface trap for cationic species at the entrance to the active-site gorge that operates through local, short-range electrostatic interactions and is independent of ionic strength. The second module is an ionic-strength-dependent steering mechanism generated by long-range electrostatic interactions arising from the overall distribution of charges in ChEs. Our calculations show that diffusion of charged ligands relative to neutral isosteric analogs is enhanced approximately 10-fold by the surface trap, while electrostatic steering contributes only a 1.5- to 2-fold rate enhancement at physiological salt concentration. We model clearance of cationic products from the active-site gorge as analogous to the escape of a particle from a one-dimensional well in the presence of a linear electrostatic potential. We evaluate the potential inside the gorge and provide evidence that while contributing to the steering of cationic species toward the active site, it does not appreciably retard their clearance. This optimal fine-tuning of global and local electrostatic interactions endows ChEs with maximum catalytic efficiency and specificity for a positively charged substrate, while at the same time not hindering clearance of the positively charged products.     

In vitro and in vivo characterization of neural stem cells

Neural stem cells are defined as clonogenic cells with self-renewal capacity and the ability to generate all neural lineages (multipotentiality). Cells with these characteristics have been isolated from the embryonic and adult central nervous system. Under specific conditions, these cells can differentiate into neurons, glia, and non-neural cell types, or proliferate in long-term cultures as cell clusters termed "neurospheres". These cultures represent a useful model for neurodevelopmental studies and a potential cell source for cell replacement therapy. Because no specific markers are available to unequivocally identify neural stem cells, their functional characteristics (self-renewal and multipotentiality) provide the main features for their identification. Here, we review the experimental and ultrastructural studies aimed at identifying the morphological characteristics and the antigenic markers of neural stem cells for their in vitro and in vivo identification.     

Identification of an unconventional nuclear localization signal in human ribosomal protein S2

Ribosomal proteins must be imported into the nucleus after being synthesized in the cytoplasm. Since the rpS2 amino acid sequence does not contain a typical nuclear localization signal, we used deletion mutant analysis and rpS2-beta-galactosidase chimeric proteins to identify the nuclear targeting domains in rpS2. Nuclear rpS2 is strictly localized in the nucleoplasm and is not targeted to the nucleoli. Subcellular localization analysis of deletion mutants of rpS2-beta-galactosidase chimeras identified a central domain comprising 72 amino acids which is necessary and sufficient to target the chimeric beta-galactosidase to the nucleus. The nuclear targeting domain shares no significant similarity to already characterized nuclear localization signals in ribosomal proteins or other nuclear proteins. Although a Nup153 fragment containing the importinbeta binding site fused to VP22 blocks nuclear import of rpS2-beta-galactosidase fusion proteins, nuclear uptake of rpS2 could be mediated by several import receptors since it binds to importinalpha/beta and transportin.     

Modeling the bacterial photosynthetic reaction center 3: interpretation of effects of site-directed mutagenesis on the special-pair midpoint potential

Interpretation of changes in midpoint potential of the "special pair" in bacterial photosynthetic reaction centers caused by site-directed mutagenesis is discussed in terms of a simple tight-binding model which relates them to concomitant variations in spin distribution between the two bacteriochlorophyll molecules of the special pair. Our analysis improves on previous similar ones by Allen and co-workers [Artz, K., Williams, J. C., Allen, J. P., Lendzian, F., Rautter, J., and Lubitz, W. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 13582; Ivancich, A., Artz, K., Williams, J. C., Allen, J. P., and Mattioli, T. A. (1998) Biochemistry 37, 11812] in that it is both more complete, including electron-phonon coupling, and more accurate. It is applied to analyze data for a series of M160 mutants of Rhodobacter sphaeroides, yielding a value of 0.18+/-0.03 eV for the electronic coupling energy between the highest occupied levels of the two bacteriochlorophylls in the wild-type and a value of the energy offset E(o) between the highest occupied molecular orbitals of the L and M bacteriochlorophylls of 0.14+/-0.03 eV. For a mutant in which the electron hole in the special pair cation is located entirely on the reactive (L) side, a potential of 641+/-30 mV with respect to the normal hydrogen electrode is predicted. This agrees well with the average value ca. 650 mV observed for the heterodimer mutant HL(M202) in which the bacteriochlorophyll on the unreactive M side has been replaced by a bacteriopheophytin, causing extensive charge localization. However, the deduced coupling is found to be very sensitive to small changes in the assumptions used in the model, and various important chemical effects remain to be included.     

Adhesion,Vitality and Osteogenic Differentiation Capacity of Adipose Derived Stem Cells Seeded on Nitinol Nanoparticle Coatings

Autologous cells can be used for a bioactivation of osteoimplants to enhance osseointegration. In this regard, adipose derived stem cells (ASCs) offer interesting perspectives in implantology because they are fast and easy to isolate. However, not all materials licensed for bone implants are equally suited for cell adhesion. Surface modifications are under investigation to promote cytocompatibility and cell growth. The presented study focused on influences of a Nitinol-nanoparticle coating on ASCs. Possible toxic effects as well as influences on the osteogenic differentiation potential of ASCs were evaluated by viability assays, scanning electron microscopy, immunofluorescence and alizarin red staining. It was previously shown that Nitinol-nanoparticles exert no cell toxic effects to ASCs either in soluble form or as surface coating. Here we could demonstrate that a Nitinol-nanoparticle surface coating enhances cell adherence and growth on Nitinol-surfaces. No negative influence on the osteogenic differentiation was observed. Nitinol-nanoparticle coatings offer new possibilities in implantology research regarding bioactivation by autologous ASCs, respectively enhancement of surface attraction to cells.     

Steady-state models of glucose-perturbed Dictyostelium discoideum

Young sorocarps of Dictyostelium discoideum were incubated in the presence of 50 mM [14C]glucose, and nine metabolites were isolated over a period of 60 min to determine their specific radioactivity. The program TFLUX was used to construct models consisting of 17 metabolite pools and 40 reactions (excluding external pools). Net glucose uptake was 10% or less in the two experiments chosen for extensive analysis, and a single steady-state model was adequate to describe the data in both cases. Despite differences in metabolite levels, flux, and labeling kinetics, the models of glucose-perturbed metabolism confirm earlier conclusions regarding metabolic compartments.     

Obstructions to Sampling Qualitative Properties

Background

Sampling methods have proven to be a very efficient and intuitive method to understand properties of complicated spaces that cannot easily be computed using deterministic methods. Therefore, sampling methods became a popular tool in the applied sciences.

Results

Here, we show that sampling methods are not an appropriate tool to analyze qualitative properties of complicated spaces unless RP = NP. We illustrate these results on the example of the thermodynamically feasible flux space of genome-scale metabolic networks and show that with artificial centering hit and run (ACHR) not all reactions that can have variable flux rates are sampled with variables flux rates. In particular a uniform sample of the flux space would not sample the flux variabilities completely.

Conclusion

We conclude that unless theoretical convergence results exist, qualitative results obtained from sampling methods should be considered with caution and if possible double checked using a deterministic method.