Revisiting the use of graph centrality models in biological pathway analysis.

The use of graph theory models is widespread in biological pathway analyses as it is often desired to evaluate the position of genes and proteins in their interaction networks of the biological systems. In this article, we argue that the common standard graph centrality measures do not sufficiently capture the informative topological organizations of the pathways, and thus, limit the biological inference. While key pathway elements may appear both upstream and downstream in pathways, standard directed graph centralities attribute significant topological importance to the upstream elements and evaluate the downstream elements as having no importance.We present a directed graph framework, Source/Sink Centrality (SSC), to address the limitations of standard models. SSC separately measures the importance of a node in the upstream and the downstream of a pathway, as a sender and a receiver of biological signals, and combines the two terms for evaluating the centrality. To validate SSC, we evaluate the topological position of known human cancer genes and mouse lethal genes in their respective KEGG annotated pathways and show that SSC-derived centralities provide an effective framework for associating higher positional importance to the genes with higher importance from a priori knowledge. While the presented work challenges some of the modeling assumptions in the common pathway analyses, it provides a straight-forward methodology to extend the existing models. The SSC extensions can result in more informative topological description of pathways, and thus, more informative biological inference.

Hydrated electrons induce the formation of interstrand cross-links in DNA modified by cisplatin adducts.

Double-stranded oligonucleotides containing cisplatin adducts, with and without a mismatched region, were exposed to hydrated electrons generated by gamma-rays. Gel electrophoresis analysis demonstrates the formation of cisplatin-interstrand crosslinks from the cisplatin-intrastrand species. The rate constant per base for the reaction between hydrated electrons and the double-stranded oligonucleotides with and without cisplatin containing a mismatched region was determined by pulse radiolysis to be 7 × 109 and 2 × 109 M-1 s-1, respectively. These results provide a better understanding of the radiosensitizing effect of cisplatin adducts in hypoxic tumors and of the formation of interstrand crosslinks, which are difficult for cells to repair.

Pulse radiolysis study on the reactivity of NO3˙ radical toward uranous(iv), hydrazinium nitrate and hydroxyl ammonium nitrate at room temperature and at 45 °C.

Concentrated nitric acid solutions subjected to radiation produce radicals of extreme importance in the reprocessing of spent nuclear fuel. Knowledge of the different rate constants of the reactions involved in this chemistry is needed to improve the efficiency of the process and to define safe operating practices. Pulse radiolysis measurements are performed to find the rate constant of the reaction between NO3˙ radicals and U(iv) in highly concentrated nitrate solution. The optimal stabilization conditions toward thermal oxidation are defined for the considered solutions at room temperature and at 45 °C by adding anti-nitrous agents such as hydrazinium nitrate (HN) and hydroxyl ammonium nitrate (HAN). The decay of the NO3˙ radical is monitored and its reaction rates with HN, HAN and U(iv) are found to be 1.3 × 105, 1.5 × 107 and 1.6 × 106 M-1 s-1 at room temperature. The latter value is more than 10 times lower than the one currently used in numerical codes for simulation of the long-term radiolytic degradation associated with the reprocessing and storage of spent nuclear waste. At 45 °C, conditions similar to the reprocessing of spent fuel, the values of the rate constants of NO3˙ radical toward HN, HAN and U(iv) increase and are found to be 2.6 × 105, 2.9 × 107 and 9.3 × 106 M-1 s-1.

Causal Disturbance Analysis: A Novel Graph Centrality Based Method for Pathway Enrichment Analysis.

Pathway enrichment analysis models (PEM) are the premier methods for interpreting gene expression profiles from high-throughput experiments. PEM often use a priori background knowledge to infer the underlying biological functions and mechanisms. A shortcoming of standard PEM is their disregarding of interactions for simplicity, which potentially results in partial and inaccurate inference. In this study, we introduce a graph-based PEM, namely Causal Disturbance Analysis (CADIA), that leverages gene interactions to quantify the topological importance of genes' expression profiles in pathways organizations. In particular, CADIA uses a novel graph centrality model, namely Source/Sink, to measure the topological importance. Source/Sink Centrality quantifies a gene's importance as a receiver and a sender of biological information, which allows for prioritizing the genes that are more likely to disturb a pathways functionality. CADIA infers an enrichment score for a pathway by deriving statistical evidence from Source/Sink centrality of the differentially expressed genes and combines it with classical over-representation analysis. Through real-world experimental and synthetic data evaluations, we show that CADIA can uniquely infer critical pathway enrichments that are not observable through other PEM. Our results indicate that CADIA is sensitive towards topologically central gene-level changes that and provides an informative framework for interpreting high-throughput data.

Dysregulation of AKT3 along with a small panel of mRNAs stratifies high-grade serous ovarian cancer from both normal epithelia and benign tumor tissues.

Screening methods of High-Grade Serous Ovarian Cancer (HGSOC) lack specificity and sensitivity, partly due to benign tumors producing false-positive findings. We utilized a differential expression analysis pipeline on malignant tumor (MT) and normal epithelial (NE) samples, and also filtered the results to discriminate between MT and benign tumor (BT). We report that a panel of 26 dysregulated genes stratifies MT from both BT and NE. We further validated our findings by utilizing unsupervised clustering methods on two independent datasets. We show that the 26-genes panel completely distinguishes HGSOC from NE, and produces a more accurate classification between HGSOC and BT. Pathway analysis reveals that AKT3 is of particular significance, because of its high fold change and appearance in the majority of the dysregulated pathways. mRNA patterns of AKT3 suggest essential connections with tumor growth and metastasis, as well as a strong biomarker potential when used with 3 other genes (PTTG1, MND1, CENPF). Our results show that dysregulation of the 26-mRNA signature panel provides an evidence of malignancy and contribute to the design of a high specificity biomarker panel for detection of HGSOC, potentially in an early more curable stage.

Quantifying yield behaviour in metals by X-ray nanotomography.

Nanoindentation of engineering materials is commonly used to study, at small length scales, the continuum mechanical properties of elastic modulus and yield strength. However, it is difficult to measure strain hardening via nanoindentation. Strain hardening, which describes the increase in strength with plastic deformation, affects fracture toughness and ductility, and is an important engineering material property. The problem is that the load-displacement data of a single nanoindentation do not provide a unique solution for the material's plastic properties, which can be described by its stress-strain behaviour. Three-dimensional mapping of the displacement field beneath the indentation provides additional information that can overcome this difficulty. We have applied digital volume correlation of X-ray nano-tomographs of a nanoindentation to measure the sub-surface displacement field and so obtain the plastic properties of a nano-structured oxide dispersion strengthened steel. This steel has potential applications in advanced nuclear energy systems, and this novel method could characterise samples where proton irradiation of the surface simulates the effects of fast neutron damage, since facilities do not yet exist that can replicate this damage in bulk materials.

Experience of a multidisciplinary task force with exome sequencing for Mendelian disorders.

BACKGROUND: In order to optimally integrate the use of high-throughput sequencing (HTS) as a tool in clinical diagnostics of likely monogenic disorders, we have created a multidisciplinary "Genome Clinic Task Force" at the University Hospitals of Geneva, which is composed of clinical and molecular geneticists, bioinformaticians, technicians, bioethicists, and a coordinator. METHODS AND RESULTS: We have implemented whole exome sequencing (WES) with subsequent targeted bioinformatics analysis of gene lists for specific disorders. Clinical cases of heterogeneous Mendelian disorders that could potentially benefit from HTS are presented and discussed during the sessions of the task force. Debate concerning the interpretation of identified variants and the content of the final report constitutes a major part of the task force's work. Furthermore, issues related to bioethics, genetic counseling, quality control, and reimbursement are also addressed. CONCLUSIONS: This multidisciplinary task force has enabled us to create a platform for regular exchanges between all involved experts in order to deal with the multiple complex issues related to HTS in clinical practice and to continuously improve the diagnostic use of HTS. In addition, this task force was instrumental to formally approve the reimbursement of HTS for molecular diagnosis of Mendelian disorders in Switzerland.

Transient electrochemistry: beyond simply temporal resolution.

Some physicochemical intrigues for which transient electrochemistry was necessary to solve the problem are summarized in this feature article. First, we highlight the main constraints to be aware of to access to low time scales, and particularly focus on the effects of stray capacitances. Then, the electron transfer rate constant measured for redox molecules in a self-assembled monolayer configuration is compared to the conductance measured through the same systems, but at the single molecule level. This evidences strong conformational changes when molecules are trapped in the nanogap created between both electrodes. We also report about dendrimers, for which a short electrochemical perturbation induces creation of a diffusion layer within the molecule, allowing the electron hopping rate to be measured and analyzed in terms of molecular motions of the redox centers. Finally, we show that transient electrochemistry provides also useful information when coupled to other methodologies. For example, when an ultrasonic field drives very fast movements of a bubble situated above the electrode surface, the motion can be detected indirectly through a modification of the diffusion flux. Another field concerns pulse radiolysis, and we describe how the reactivity (at the electrode or within the solution) of radicals created by a radiolytic pulse can be quantified, widening the possibilities of electrochemistry to operate in biological media.

Radiosensitization of DNA by Cisplatin Adducts Results from an Increase in the Rate Constant for the Reaction with Hydrated Electrons and Formation of Pt(I).

Pulse radiolysis measurements of the decay of hydrated electrons in solutions containing different concentrations of the oligonucleotide GTG with and without a cisplatin adduct show that the presence of a cisplatin moiety accelerates the reaction between hydrated electrons and the oligonucleotide. The rate constant of the reaction is found to be 2.23 × 10(10) mol(-1) L s(-1), which indicates that it is diffusion controlled. In addition, we show for the first time the formation of a Pt(I) intermediate as a result of the reaction of hydrated electrons with GTG-cisplatin. A putative reaction mechanism is proposed, which may form the basis of the radiosensitization of cancer cells in concomitant chemoradiation therapy with cisplatin.

Downregulation of HOXC6 in Serous Ovarian Cancer.

Homeobox (HOX) genes encode transcription factors critical to morphogenesis and cell differentiation. Although dysregulation of several HOX genes in ovarian cancer has been reported, little is known about HOXC6 expression in epithelial ovarian cancer. In this report, analysis of laser capture microdissected samples determined HOXC6 expression patterns in normal versus malignant serous ovarian carcinoma tissues. HOXC6 protein was quantified by ELISA in parallel serum samples and further validated in a larger cohort of serum samples collected from women with and without serous ovarian carcinoma. These data demonstrate significant downregulation of HOXC6 in serous ovarian cancer.

Guanosine radical reactivity explored by pulse radiolysis coupled with transient electrochemistry.

We follow the reactivity of a guanosine radical created by a radiolytic electron pulse both by spectroscopic and electrochemical methods. This original approach allows us to demonstrate that there is a competition between oxidation and reduction of these intermediates, an important result to further analyse the degradation or repair pathways of DNA bases.

State of Fukushima nuclear fuel debris tracked by Cs137 in cooling water.

It is still difficult to assess the risk originating from the radioactivity inventory remaining in the damaged Fukushima nuclear reactors. Here we show that cooling water analyses provide a means to assess source terms for potential future releases. Until now already about 34% of the inventories of (137)Cs of three reactors has been released into water. We found that the release rate of (137)Cs has been constant for 2 years at about 1.8% of the inventory per year indicating ongoing dissolution of the fuel debris. Compared to laboratory studies on spent nuclear fuel behavior in water, (137)Cs release rates are on the higher end, caused by the strong radiation field and oxidant production by water radiolysis and by impacts of accessible grain boundaries. It is concluded that radionuclide analyses in cooling water allow tracking of the conditions of the damaged fuel and the associated risks.

Mechanism of trivalent gold reduction and reactivity of transient divalent and monovalent gold ions studied by gamma and pulse radiolysis.

The detailed kinetics of the multistep mechanism of the Au(III) ion reduction into gold clusters have been investigated by radiation chemistry methods in 2-propanol. In particular, a discussion on the steady state radiolysis dose-dependence of the yields concludes to a comproportionation reaction of nascent gold atoms Au(0) with excess Au(III) ions into Au(II) and Au(I). This reaction should be achieved through Au(III) consumption before the coalescence of atoms Au(0) into gold clusters may occur. Then gold clusters catalyze the reduction of Au(I) by 2-propanol. It was also found that a long-lived Au(II) dimer, (Au(II))(2), was transiently formed according to the quantitative analysis of time-resolved absorbance signals obtained by pulse radiolysis. Then the disproportionation of Au(II) is intramolecular in the dimer instead of intermolecular, as usually reported. The yields, reaction rate constants, time-resolved spectra, and molar extinction coefficients are reported for the successive one-electron reduction steps, involving especially the transient species, such as Au(II), (Au(II))(2), and Au(I). The processes are discussed in comparison with other solvents and other metal ions.

Radiolytic yield of U(IV) oxidation into U(VI): a new mechanism for U(V) reactivity in acidic solution.

The yields of the radiolytic oxidation of U(IV) and of the U(VI) formation, measured by spectrophotometry, are found to be the same (G(-U(IV))(N2O) = G(U(VI))(N2O) = 8.4 x 10(-7) mol J(-1)) and almost double the H(2) formation yield (G(H(2)) = 4.4 x 10(-7) mol J(-1)) in the (60)Co gamma radiolysis of N(2)O-aqueous solutions in the presence of 2 mol L(-1) Cl(-) at pH = 0 (HCl). According to the mechanism of U(IV) radiolytic oxidation, we show that under the conditions of our experiments the U(V) ions do not disproportionate, but undergo a stoichiometric oxidation into U(VI) by H(+) with forming H(2).

Aqueous solution of UCl6(2-) in O2 saturated acidic medium: an efficient system to scavenge all primary radicals in spurs produced by irradiation.

Absorbance measurements find the yield of the oxidation of U(IV) to be (8.75 +/- 0.05) x 10(-7) mol J(-1) in the (60)Co gamma radiolysis of aqueous solutions containing 4.4 x 10(-3) mol L(-1) U(IV) in the presence of O(2) saturated 2 mol L(-1) Cl(-) at pH = 0. This high value of oxidation yield suggests that all primary radicals formed by water decomposition are scavenged in these solutions. Simulations using a nonhomogeneous stochastic kinetic track model agree with the experimental results and are used to explain the mechanism for scavenging radicals and oxidation of U(IV).

Correlation analysis of HOX, ErbB and IGFBP family gene expression in ovarian cancer.

Utilizing microarray gene expression data in cancer research possesses the ability to identify deregulated cellular pathways involved in malignant development. This study investigated the relationships of three gene families, HOX, ErbB and IGFBP, with regard to the development of ovarian cancer. These families were of interest because of similar chromosomal locations and their deregulated expression in ovarian cancer. Higher level statistics were used to differentially analyze microarray data in 65 ovarian samples to assess correlation and relationships among the gene families of interest. Fifteen genes in the three families were found to be significantly deregulated. Thirty-eight significant correlations were found within and between the genes of interest. Our data indicates that the significantly modeled relationships between HOX, ErbB and IGFBP gene pairs could provide insight into the underlying biological mechanisms in ovarian cancer.

Solvation dynamics of electron produced by two-photon ionization of liquid polyols. III. Glycerol.

The solvation dynamics of excess electrons in glycerol have been measured by the pump-probe femtosecond laser technique at 333 K. The electrons are produced by two-photon absorption at 263 nm. The change in the induced absorbance is followed up to 450 ps in the spectral range from 440 to 720 nm. The transient signals of electron solvation have been analyzed by two kinetic models: a stepwise mechanism and a continuous relaxation model, using a Bayesian data analysis method. The results are compared with those previously published for ethylene glycol (J. Phys. Chem. A 2006, 110, 175) and for propanediols (J. Phys. Chem. A 2007, 111, 4902). From the comparison, it is pointed out that solvation dynamics in glycerol is very fast despite its high viscosity. This is interpreted as the existence of efficient traps for the electrons in glycerol with low potential energy. The small shift of the absorption band of the excess electron indicates that the potential of these traps is very close to that corresponding to the fully solvated electron.

Solvation dynamics of electron produced by two-photon ionization of liquid polyols. II. Propanediols.

Temporal evolution of transient absorption spectra of electrons produced by two-photon ionization of two isomers, propane-1,2-diol (12PD) and propane-1,3-diol (13PD), with 263 nm femtosecond laser pulses has been studied on picosecond time scale. The two-photon absorption coefficients of 12PD and 13PD at 263 nm were determined to be beta = (2.0 +/- 0.3) x 10(-11) and (2.4 +/- 0.3) x 10(-11) m W(-1), respectively. Time-resolved absorption spectra ranging from 440 to 720 nm have been measured, showing a blue shift for the first tens of picoseconds for both solvents. However, the observed solvation dynamics of electron appears faster in 13PD than in 12PD. The transient signals of electron solvation have then been reconstructed with different models (stepwise mechanism or continuous relaxation model) using a Bayesian data analysis method. Results are discussed, compared with those previously obtained in ethylene glycol (J. Phys. Chem. A 2006, 110, 1705) and corroborate the interpretation, according to which the solvation of electrons is mainly governed by continuous solvent molecular motions.

Solvation dynamics of the electron produced by two-photon ionization of liquid polyols. 1. Ethylene glycol.

Solvated electrons have been produced in ethylene glycol by two-photon ionization of the solvent with 263 nm femtosecond laser pulses. The two-photon absorption coefficient of ethylene glycol at 263 nm is determined to be beta = (2.1 +/- 0.2) x 10(-11) m W(-1). The dynamics of electron solvation in ethylene glycol has been studied by pump-probe transient absorption spectroscopy. So, time-resolved absorption spectra ranging from 430 to 710 nm have been measured. A blue shift of the spectra is observed for the first tens of picoseconds. Using the Bayesian data analysis method, the observed solvation dynamics are reconstructed with different models: stepwise mechanisms, continuous relaxation models, or combinations of stepwise and continuous relaxation. Comparison between models is in favor of continuous relaxation, which is mainly governed by solvent molecular motions.

Accurate 3D reconstruction of complex blood vessel geometries from intravascular ultrasound images: in vitro study.

We present a technique that accurately reconstructs complex three dimensional blood vessel geometry from 2D intravascular ultrasound (IVUS) images. Biplane x-ray fluoroscopy is used to image the ultrasound catheter tip at a few key points along its path as the catheter is pulled through the blood vessel. An interpolating spline describes the continuous catheter path. The IVUS images are located orthogonal to the path, resulting in a non-uniform structured scalar volume of echo densities. Isocontour surfaces are used to view the vessel geometry, while transparency and clipping enable interactive exploration of interior structures. The two geometries studied are a bovine artery vascular graft having U-shape and a constriction, and a canine carotid artery having multiple branches and a constriction. Accuracy of the reconstructions is established by comparing the reconstructions to (1) silicone moulds of the vessel interior, (2) biplane x-ray images, and (3) the original echo images. Excellent shape and geometry correspondence was observed in both geometries. Quantitative measurements made at key locations of the 3D reconstructions also were in good agreement with those made in silicone moulds. The proposed technique is easily adoptable in clinical practice, since it uses x-rays with minimal exposure and existing IVUS technology.