Semi-Supervised Multi-View Learning for Gene Network Reconstruction

The task of gene regulatory network reconstruction from high-throughput data is receiving increasing attention in recent years. As a consequence, many inference methods for solving this task have been proposed in the literature. It has been recently observed, however, that no single inference method performs optimally across all datasets. It has also been shown that the integration of predictions from multiple inference methods is more robust and shows high performance across diverse datasets. Inspired by this research, in this paper, we propose a machine learning solution which learns to combine predictions from multiple inference methods. While this approach adds additional complexity to the inference process, we expect it would also carry substantial benefits. These would come from the automatic adaptation to patterns on the outputs of individual inference methods, so that it is possible to identify regulatory interactions more reliably when these patterns occur. This article demonstrates the benefits (in terms of accuracy of the reconstructed networks) of the proposed method, which exploits an iterative, semi-supervised ensemble-based algorithm. The algorithm learns to combine the interactions predicted by many different inference methods in the multi-view learning setting. The empirical evaluation of the proposed algorithm on a prokaryotic model organism (E. coli) and on a eukaryotic model organism (S. cerevisiae) clearly shows improved performance over the state of the art methods. The results indicate that gene regulatory network reconstruction for the real datasets is more difficult for S. cerevisiae than for E. coli. The software, all the datasets used in the experiments and all the results are available for download at the following link: http://figshare.com/articles/Semi_supervised_Multi_View_Learning_for_Gene_Network_Reconstruction/1604827.     

HCC Development Is Associated to Peripheral Insulin Resistance in a Mouse Model of NASH

NAFLD is the most common liver disease worldwide but it is the potential evolution to NASH and eventually to hepatocellular carcinoma (HCC), even in the absence of cirrhosis, that makes NAFLD of such clinical importance. Aim: we aimed to create a mouse model reproducing the pathological spectrum of NAFLD and to investigate the role of possible co-factors in promoting HCC. Methods: mice were treated with a choline-deficient L-amino-acid-defined-diet (CDAA) or its control (CSAA diet) and subjected to a low-dose i.p. injection of CCl₄ or vehicle. Insulin resistance was measured by the euglycemic-hyperinsulinemic clamp method. Steatosis, fibrosis and HCC were evaluated by histological and molecular analysis. Results: CDAA-treated mice showed peripheral insulin resistance at 1 month. At 1–3 months, extensive steatosis and fibrosis were observed in CDAA and CDAA+CCl₄ groups. At 6 months, equal increase in steatosis and fibrosis was observed between the two groups, together with the appearance of tumor. At 9 months of treatment, the 100% of CDAA+CCl₄ treated mice revealed tumor versus 40% of CDAA mice. Insulin-like Growth Factor-2 (IGF-2) and Osteopontin (SPP-1) were increased in CDAA mice versus CSAA. Furthermore, Immunostaining for p-AKT, p-c-Myc and Glypican-3 revealed increased positivity in the tumors. Conclusions: the CDAA model promotes the development of HCC from NAFLD-NASH in the presence of insulin resistance but in the absence of cirrhosis. Since this condition is increasingly recognized in humans, our study provides a model that may help understanding mechanisms of carcinogenesis in NAFLD.     

Pyrazole-based cathepsin S inhibitors with improved cellular potency

High potency pyrazole-based noncovalent inhibitors of human cathepsin S (CatS) were developed by modification of the benzo-fused 5-membered ring heterocycles found in earlier series of CatS inhibitors. Although substitutions on this heterocyclic framework had a moderate impact on enzymatic potency, dramatic effects on cellular activity were observed. Optimization afforded indole- and benzothiophene-derived analogues that were high affinity CatS inhibitors (IC(50)=20-40 nM) with good cellular potency (IC(50)=30-340 nM).     

Noninvasive Evaluation of Heavy Metal Uptake and Storage in Micoralgae Using a Fluorescence Resonance Energy Transfer-Based Heavy Metal Biosensor

We have developed a fluorescence resonance energy transfer (FRET)-based heavy metal biosensor for the quantification of bioavailable free heavy metals in the cytoplasm of the microalga Chlamydomonas reinhardtii. The biosensor is composed of an end-to-end fusion of cyan fluorescent protein (CFP), chicken metallothionein II (MT-II), and yellow fluorescent protein (YFP). In vitro measurements of YFP/CFP fluorescence emission ratios indicated that the addition of metals to the purified biosensor enhanced FRET between CFP and YFP, consistent with heavy metal-induced folding of MT-II. A maximum YFP/CFP FRET ratio of 2.8 was observed in the presence of saturating concentrations of heavy metals. The sensitivity of the biosensor was greatest for Hg²⁺ followed by Cd²⁺ ≈ Pb²⁺ > Zn²⁺ > Cu²⁺. The heavy metal biosensor was unresponsive to metals that do not bind to MT-II (Na⁺ and Mg²⁺). When expressed in C. reinhardtii, we observed a differential metal-dependent response to saturating external concentrations (1.6 mm) of heavy metals (Pb²⁺ > Cd²⁺) that was unlike that observed for the isolated biosensor (in vitro). Significantly, analysis of metal uptake kinetics indicated that equilibration of the cytoplasm with externally applied heavy metals occurred within seconds. Our results also indicated that algae have substantial buffering capacity for free heavy metals in their cytosol, even at high external metal concentrations.Many proteins utilize metals to stabilize their structures or as cofactors to catalyze redox and other chemical reactions. Metals such as zinc, copper, iron, magnesium, cobalt, and manganese are required by most living organisms for their normal cellular functions. Essential metals are often present at low concentrations in the environment, however, and must be imported into cells, often at the expense of energy (Hanikenne et al., 2005; Merchant et al., 2006). In contrast to essential metals, toxic metals such as cadmium, lead, and mercury can disrupt cellular functions by competing with essential metals for their metal-binding sites and/or by altering the redox state of cells. Exposure of organisms to high concentrations of toxic metals can impair their cellular functions, growth, and reproduction. To prevent metal-induced cellular anomalies, organisms have evolved a variety of strategies to reduce the toxicity of heavy metals. One such strategy involves the selective binding of toxic metals in the cytoplasm by metal-binding proteins and other small molecules. As discussed below, both enzymatically and ribosomally synthesized Cys-rich peptides, including phytochelatins and metallothioneins (MTs), are utilized by a variety of organisms to sequester toxic heavy metals, including cadmium, mercury, lead, silver, and gold. The peptides may also serve as storage reserves for essential metals such as copper and zinc (Cobbett and Goldsbrough, 2002).Phytochelatins are enzymatically synthesized polypeptides containing repeating units of (γ-Glu-Cys)_n-Gly, where n = 2 to 11 (Rauser, 1990), whereas MTs are genetically encoded, ribosomally synthesized polypeptides (Cobbett and Goldsbrough, 2002). MTs have molecular mass values ranging from 6 to 7 kD and contain approximately 20 conserved Cys residues (Cobbett and Goldsbrough, 2002; Romero-Isart and Vasák, 2002). Metals are characteristically bound to MT via the thiolate sulfur ligands of Cys residues (Kägi, 1991). It is estimated that the metal-saturated MT contains about 10% thiolate sulfur and bound metals by mass (Romero-Isart and Vasák, 2002). Structural analyses of metal-free and metal-complexed MTs demonstrated that MTs undergo a structural transition from a metal-free random-coil structure to a metal-bound compact dumbbell-shaped structure having metal saturated α- and β-domains (Pearce et al., 2000; Romero-Isart and Vasak, 2002; Hong and Maret, 2003). The N-terminal β-domain binds three metal ion equivalents, and the C-terminal α-domain binds four metal ion equivalents (Romero-Isart and Vasák, 2002; Vasák, 2005). Furthermore, several decades of work on MTs have provided a great deal of information regarding their metal-binding affinity, specificity, and domain selectivity for select metals (Cobbett and Goldsbrough, 2002; Romero-Isart and Vasák, 2002; Vasák, 2005).Fluorescence resonance energy transfer (FRET) involves the nonradioactive transfer of energy between the excited state of a luminescent or fluorescent donor molecule and a nearby acceptor molecule that has overlapping excited state transitions. Proteins that are modified to have efficient energy donor and acceptor domains and that undergo structural changes upon binding a specific ligand are good candidates for FRET-based sensors. For ligand-specific FRET-based biosensors, the distance and/or the orientation between the energy donor and acceptor molecules is changed upon ligand binding in a concentration-dependent manner (Selvin, 1995; Weiss, 2000; Hong and Maret, 2003; Looger et al., 2005). Relevant to this discussion, a FRET-based biosensor with GFP variants fused to MT was previously shown to be an effective means to monitor metal release during nitric oxide-induced signaling in endothelial cells (Pearce et al., 2000).Unicellular algae such as Chlamydomonas species are often found in areas that might be contaminated by toxic heavy metals (Merchant et al., 2006). Chlamydomonas species have also been shown to sequester toxic metals (e.g. cadmium and mercury) and have potential use for bioremediation of these metals (Cai et al., 1999; Adhiya et al., 2002; Siripornadulsil et al., 2002; He et al., 2011; Priyadarshani et al., 2011). To determine the kinetics and selectivity of exogenous heavy metal uptake as well as free heavy metal concentration in the cytoplasm of Chlamydomonas species, we developed an MT, FRET-based metal-binding sensor and expressed this in the cytoplasm of the unicellular green alga Chlamydomonas reinhardtii. We demonstrate that heavy metal uptake is rapid in C. reinhardtii and that cytoplasmic free heavy metal concentrations are substantially lower than exogenous free heavy metal concentrations, implying that heavy metals are rapidly sequestered by various biological molecules in the cell.     

Thyreophagus corticalis as a vector of hypovirulence in Cryphonectria parasitica in chestnut stands

The natural spread of hypovirulence in Cryphonectria parasitica (Murr.) Barr. occurs in chestnut (Castanea sativa Mill) stands and orchards in Italy and other European countries, leading to spontaneous recovery of the diseased trees. Little is known about how hypovirulence spreads in chestnut stands but various corticolous mite species frequently detected on chestnut cankers could be one of the many factors playing a role in the spread. Artificial virulent cankers created in inoculation field tests and treated with Thyreophagus corticalis (Acari, Sarcoptiformes, Acaridae) raised on hypovirulent cultures showed similar growth to those treated with mycelia of the hypovirulent strain over 18 months of inoculation. Cultures re-isolated from virulent cankers treated with mites were found to contain hypovirus like those derived from pairings of virulent and hypovirulent strains. Viral dsRNA could be carried externally and/or ingested by mites from the hypovirulent mycelia and then transmitted to the mycelia of virulent strains, causing their conversion. In a laboratory study, all fecal pellets collected from mites reared on hypovirulent and virulent strains grown on semi-selective media gave rise to colonies of C. parasitica with similar morphological characters and virulence to the original cultures. Field inoculation of stump sprouts with the resulting colonies revealed that mite digestive tract passage did not alter the virulence of the studied strains. These results are of interest for the biological control of chestnut blight.     

Identification of novel deregulated RNA metabolism-related genes in non-small cell lung cancer

Lung cancer is a leading cause of cancer death worldwide. Several alterations in RNA metabolism have been found in lung cancer cells; this suggests that RNA metabolism-related molecules are involved in the development of this pathology. In this study, we searched for RNA metabolism-related genes that exhibit different expression levels between normal and tumor lung tissues. We identified eight genes differentially expressed in lung adenocarcinoma microarray datasets. Of these, seven were up-regulated whereas one was down-regulated. Interestingly, most of these genes had not previously been associated with lung cancer. These genes play diverse roles in mRNA metabolism: three are associated with the spliceosome (ASCL3L1, SNRPB and SNRPE), whereas others participate in RNA-related processes such as translation (MARS and MRPL3), mRNA stability (PCBPC1), mRNA transport (RAE), or mRNA editing (ADAR2, also known as ADARB1). Moreover, we found a high incidence of loss of heterozygosity at chromosome 21q22.3, where the ADAR2 locus is located, in NSCLC cell lines and primary tissues, suggesting that the downregulation of ADAR2 in lung cancer is associated with specific genetic losses. Finally, in a series of adenocarcinoma patients, the expression of five of the deregulated genes (ADAR2, MARS, RAE, SNRPB and SNRPE) correlated with prognosis. Taken together, these results support the hypothesis that changes in RNA metabolism are involved in the pathogenesis of lung cancer, and identify new potential targets for the treatment of this disease.     

Severe infantile encephalomyopathy caused by a mutation in COX6B1, a nucleus-encoded subunit of cytochrome c oxidase

Cytochrome c oxidase (COX) deficiency, one of the most common respiratory-chain defects in humans, has been associated with mutations in either mitochondrial DNA genes or nucleus-encoded proteins that are not part in but promote the biogenesis of COX. Mutations of nucleus-encoded structural subunits were sought for but never found in COX-defective patients, leading to the conjecture that they may be incompatible with extra-uterine survival. We report a disease-associated mutation in one such subunit, COX6B1. Nuclear-encoded COX genes should be reconsidered and included in the diagnostic mutational screening of human disorders related to COX deficiency.     

Cutinase production by <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> in liquid medium using central composite design

The objective of the present study was to measure the production of cutinase by Fusarium oxysporum in the presence of several carbon and nitrogen sources (glycides, fatty acids and oils, and several organic and inorganic nitrogen sources), trying to find a cost-effective substitute for cutin in the culture medium as an inducer of cutinase production. The results were evaluated by the Tukey test, and flaxseed oil was found to give the best results as a cutinase inducer. The authors optimized the composition of the growth medium employing response surface methodology. The experimental results were fitted to a second-order polynomial model at a 95% level of significance (p < 0.05). The greatest cutinolytic activity was obtained in a liquid mineral medium supplemented with flaxseed oil, showing an increase in enzymatic activity from 11 to 22.68 U/mL after 48 h of fermentation. A CCD study of the fermentation conditions was carried out, and the best production of cutinase was registered with the use of 30 °C and 100 rpm. These results support the use of flaxseed oil as a substitute for cutin, which is difficult and expensive to obtain, for the production of cutinase in a larger scale.