Ground truth based comparison of saliency maps algorithms

Deep neural networks (DNNs) have achieved outstanding results in domains such as image processing, computer vision, natural language processing and bioinformatics. In recent years, many methods have been proposed that can provide a visual explanation of decision made by such classifiers. Saliency maps are probably the most popular. However, it is still unclear how to properly interpret saliency maps for a given image and which techniques perform most accurately. This paper presents a methodology to practically evaluate the real effectiveness of saliency map generation methods. We used three state-of-the-art network architectures along with specially prepared benchmark datasets, and we proposed a novel metric to provide a quantitative comparison of the methods. The comparison identified the most reliable techniques and the solutions which usually failed in our tests.

Impact of elastic substrate on the dynamic heterogeneity of WC256 Walker carcinosarcoma cells

Cellular heterogeneity is a phenomenon in which cell populations are composed of subpopulations that vary in their behavior. Heterogeneity is particularly pronounced in cancer cells and can affect the efficacy of oncological therapies. Previous studies have considered heterogeneity dynamics to be indicative of evolutionary changes within subpopulations; however, these studies do not consider the short-time morphological plasticity of cells. Physical properties of the microenvironment elasticity have also been poorly investigated within the context of cellular heterogeneity, despite its role in determining cellular behavior. This article demonstrates that cellular heterogeneity can be highly dynamic and dependent on the micromechanical properties of the substrate. During observation, migrating Walker carcinosarcoma WC256 cells were observed to belong to different subpopulations, in which their morphologies and migration strategies differed. Furthermore, the application of an elastic substrate (E = 40 kPa) modified three aspects of cellular heterogeneity: the occurrence of subpopulations, the occurrence of transitions between subpopulations, and cellular migration and morphology. These findings provide a new perspective in the analysis of cellular heterogeneity, whereby it may not be a static feature of cancer cell populations, instead varying over time. This helps further the understanding of cancer cell behavior, including their phenotype and migration strategy, which may help to improve cancer therapies by extending their suitability to investigate tumor heterogeneity.

Bronchial Fibroblasts from Asthmatic Patients Display Impaired Responsiveness to Direct Current Electric Fields (dcEFs)

Accumulating evidence suggests that an important role is played by electric signals in modifying cell behaviour during developmental, regenerative and pathological processes. However, their role in asthma has not yet been addressed. Bronchial fibroblasts have recently been identified having important roles in asthma development. Therefore, we adapted an experimental approach based on the lineages of human bronchial fibroblasts (HBF) derived from non-asthmatic (NA) donors and asthmatic (AS) patients to elucidate whether their reactivity to direct current electric fields (dcEF) could participate in the asthmatic process. The efficient responsiveness of NA HBF to an electric field in the range of 2-4 V/cm was illustrated based on the perpendicular orientation of long axes of the cells to the field lines and their directional movement towards the anode. These responses were related to the activity of TGF-β signalling, as the electrotaxis and re-orientation of NA HBF polarity was impaired by the inhibitors of canonical and non-canonical TGF-β-dependent pathways. A similar tendency towards perpendicular cell-dcEF orientation was observed for AS HBF. However, their motility remained insensitive to the electric field applied at 2-4 V/cm. Collectively, these observations demonstrate the sensitivity of NA HBF to dcEF, as well as the inter-relations between this parameter and the canonical and non-canonical TGF-β pathways, and the differences between the electrotactic responses of NA and AS HBF point to the possible role of their dcEFs in desensitisation in the asthmatic process. This process may impair the physiologic behaviour of AS HBF functions, including cell motility, ECM deposition, and contractility, thus promoting bronchial wall remodelling, which is a characteristic of bronchial asthma.

Functionalization of graphenic surfaces by oxygen plasma toward enhanced wettability and cell adhesion: experiments corroborated by molecular modelling

Graphenic materials attract huge attention because of their outstanding properties, and have a wide range of applications as, i.e., components of biomaterials. Due to their hydrophobic nature, however, the surfaces need to be functionalized to improve wettability and biocompatibility. In this study, we investigate the functionalization of graphenic surfaces by oxygen plasma treatment, introducing surface functional groups in a controlled way. The AFM images and LDI-MS results clearly show that the graphenic surface exposed to plasma is decorated with -OH groups, whereas the surface topography remains intact. The measured water contact angle decreases significantly after oxygen plasma treatment from 99° to ca. 5°, making the surface hydrophilic. It is also reflected in the surface free energy values which increase from 48.18 mJ m^-2 to 74.53 mJ m^-2 when the number of surface oxygen groups reaches 4 -OH/84 Ų. The DFT (VASP) molecular models of unmodified and oxygen-functionalized graphenic surfaces were constructed and used for molecular interpretation of water-graphenic surface interactions. The computational models were validated by comparison of the theoretically determined water contact angle (based on the Young-Dupré equation) to the experimentally determined values. Additionally, the VASPsol (implicit water environment) results were calibrated against the explicit water models that can be used in further research. Finally, the biological role of functional groups on the graphenic surface was examined in terms of cell adhesion with the use of mouse fibroblast cell line (NIH/3T3). The obtained results illustrate the correlation between surface oxygen groups, wettability, and biocompatibility providing the guidelines for the molecular level-driven design of carbon materials for various applications.

Asthma-derived fibroblast to myofibroblast transition is enhanced in comparison to fibroblasts derived from non-asthmatic patients in 3D in vitro culture due to Smad2/3 signalling

The basic hallmarks of bronchial asthma, one of the most common chronic diseases occurring in the world, are chronic inflammation, remodelling of the bronchial wall and its hyperresponsiveness to environmental stimuli. It was found out that the fibroblast to myofibroblast transition (FMT), a key phenomenon in subepithelial fibrosis of the bronchial wall, was crucial for the development of asthma. Our previous studies showed that HBFs derived from asthmatic patients cultured in vitro display some inherent features which facilitate their TGF-b-induced FMT. Although usefulness of standard '2D' cultures is invaluable, they have many limitations. As HBFs interact with extracellular matrix proteins in the connective tissue, which can affect the FMT potential, we have decided to expand our '2D' model to in vitro cell cultures in 3D using collagen gels. Our results showed that 1.5 mg/ml concentration of collagen is suitable for HBFs growth, motility, and phenotypic shifts. Moreover, we demonstrated that in the TGF-β1-activated HBF populations derived from asthmatics, the expression of fibrosis-related genes (ACTA2, TAGLN, SERPINE1, COL1A1, FN1 and CCN2) was significantly increased in comparison to the non-asthmatic ones. We also confirmed that it is related to the TGF-β/Smad2/3 profibrotic pathway intensification. In summary, the results of our study undoubtedly demonstrate that HBFs from asthmatics have unique intrinsic features which predispose them, regardless the culture conditions, to the increased FMT under the influence of TGF-β1.

Fenofibrate Reduces the Asthma-Related Fibroblast-To-Myofibroblast Transition by TGF-Β/Smad2/3 Signaling Attenuation and Connexin 43-Dependent Phenotype Destabilization

The activation of human bronchial fibroblasts by transforming growth factor-β₁ (TGF-β₁) leads to the formation of highly contractile myofibroblasts in the process of the fibroblast–myofibroblast transition (FMT). This process is crucial for subepithelial fibrosis and bronchial wall remodeling in asthma. However, this process evades current therapeutic asthma treatment strategies. Since our previous studies showed the attenuation of the TGF-β₁-induced FMT in response to lipid-lowering agents (e.g., statins), we were interested to see whether a corresponding effect could be obtained upon administration of hypolipidemic agents. In this study, we investigated the effect of fenofibrate on FMT efficiency in populations of bronchial fibroblasts derived from asthmatic patients. Fenofibrate exerted a dose-dependent inhibitory effect on the FMT, even though it did not efficiently affect the expression of α-smooth muscle actin (α-SMA; marker of myofibroblasts); however, it considerably reduced its incorporation into stress fibers through connexin 43 regulation. This effect was accompanied by disturbances in the actin cytoskeleton architecture, impairments in the maturation of focal adhesions, and the fenofibrate-induced deactivation of TGF-β₁/Smad2/3 signaling. These data suggest that fenofibrate interferes with myofibroblastic differentiation during asthma-related subepithelial fibrosis. The data indicate the potential application of fenofibrate in the therapy and prevention of bronchial remodeling during the asthmatic process.

[FRET-based biosensors in cell migration research]

Cell migration is a complicated process, which is crucial for functioning of multicellular organisms. Multiple signalling pathways are deeply involved in the precise control of consecutive cell migration stages based on remodelling of the actin cytoskeleton. Small Rho GTPases (RhoA, Rac1 and Cdc42) as well as multiple protein and lipid kinases, calcium ions and mechanosensors are crucial components in this process. Exploration of those complicated correlations is possible with constant advancement of fluorescence microscopy. A significant progress in this field has been achieved since discovery of fluorescent proteins and subsequently FRET-based biosensors. Such protein constructs react with a change of FRET efficiency in response to the particular protein activity change. Properly designed and regularly improved biosensors offer the possibility of real-time imaging of signalling pathways dynamics in migrating cells. The perception of Rho GTPases involvement and some other signalling pathways connected with cell migration have been clarified with multiple experiments already carried out with such FRET-based biosensors.

Modelling the efficacy of hyperthermia treatment

Multimodal oncological strategies which combine chemotherapy or radiotherapy with hyperthermia, have a potential of improving the efficacy of the non-surgical methods of cancer treatment. Hyperthermia engages the heat-shock response (HSR) mechanism, the main component of which are heat-shock proteins. Cancer cells have already partially activated HSR, thereby hyperthermia may be more toxic to them relative to normal cells. On the other hand, HSR triggers thermotolerance, i.e. hyperthermia-treated cells show an impairment in their susceptibility to a subsequent heat-induced stress. This poses questions about efficacy and optimal strategy for anti-cancer therapy combined with hyperthermia treatment. To address these questions, we adapt our previous HSR model and propose its stochastic extension. We formalize the notion of a HSP-induced thermotolerance. Next, we estimate the intensity and the duration of the thermotolerance. Finally, we quantify the effect of a multimodal therapy based on hyperthermia and a cytotoxic effect of bortezomib, a clinically approved proteasome inhibitor. Consequently, we propose an optimal strategy for combining hyperthermia and proteasome inhibition modalities. In summary, by a mathematical analysis of HSR, we are able to support the common belief that the combination of cancer treatment strategies increases therapy efficacy.

Triterpene saponosides from Lysimachia ciliata differentially attenuate invasive potential of prostate cancer cells

Neither androgen ablation nor chemotherapeutic agents are effective in reducing the risk of prostate cancer progression. On the other hand, multifaceted effects of phytochemicals, such as triterpene saponins, on cancer cells have been suggested. A promising safety and tolerability profile indicate their possible application in the treatment of advanced prostate cancers. We analyzed the specificity, selectivity and versatility of desglucoanagalloside B effects on human prostate cancer cells derived from prostate cancer metastases to brain (DU-145 cells) and bone (PC-3 cells). Prominent growth arrest and apoptotic response of both cell types was observed in the presence of sub-micromolar desglucoanagalloside B concentrations. This was accompanied by cytochrome c release and caspase 3/7 activation. A relatively low cytostatic and pro-apoptotic response of cancer cells to a desglucoanagalloside B analog, anagallosaponin IV, illustrated the specificity of the effects of desglucoanagalloside B, whereas the low sensitivity of normal prostate PNT2 cells to desglucoanagalloside B showed the selectivity of its action. Inhibition of cancer cell motility was observed in the presence of both saponins, however only desglucoanagalloside B attenuated cancer cell invasive potential, predominantly through an effect on cell elastic properties. These data demonstrate the versatility of its effects on prostate cancer cells. In contrast to PNT2 cells, cancer cells tested in this study were relatively resistant to mitoxantrone. The multifaceted action of desglucoanagalloside B on basic cellular traits, crucial for prostate cancer progression, opens perspectives for elaboration of combined palliative therapies and new prostate cancer prophylaxis regimens.

Tav4SB: integrating tools for analysis of kinetic models of biological systems

Background

Progress in the modeling of biological systems strongly relies on the availability of specialized computer-aided tools. To that end, the Taverna Workbench eases integration of software tools for life science research and provides a common workflow-based framework for computational experiments in Biology.

Results

The Taverna services for Systems Biology (Tav4SB) project provides a set of new Web service operations, which extend the functionality of the Taverna Workbench in a domain of systems biology. Tav4SB operations allow you to perform numerical simulations or model checking of, respectively, deterministic or stochastic semantics of biological models. On top of this functionality, Tav4SB enables the construction of high-level experiments. As an illustration of possibilities offered by our project we apply the multi-parameter sensitivity analysis. To visualize the results of model analysis a flexible plotting operation is provided as well. Tav4SB operations are executed in a simple grid environment, integrating heterogeneous software such as Mathematica, PRISM and SBML ODE Solver. The user guide, contact information, full documentation of available Web service operations, workflows and other additional resources can be found at the Tav4SB project’s Web page: http://bioputer.mimuw.edu.pl/tav4sb/.

Conclusions

The Tav4SB Web service provides a set of integrated tools in the domain for which Web-based applications are still not as widely available as for other areas of computational biology. Moreover, we extend the dedicated hardware base for computationally expensive task of simulating cellular models. Finally, we promote the standardization of models and experiments as well as accessibility and usability of remote services.

Analyzing stationary States of gene regulatory network using petri nets

We introduce and formally define the notion of a stationary state for Petri nets. We also propose a fully automatic method for finding such states. The procedure makes use of the Presburger arithmetic to describe all the stationary states. Finally we apply this novel approach to find stationary states of a gene regulatory network describing the flower morphogenesis of A. thaliana. This shows that the proposed method can be successfully applied in the study of biological systems.

Analyzing stationary states of gene regulatory network using petri nets

We introduce and formally define the notion of a stationary state for Petri nets. We also propose a fully automatic method for finding such states. The procedure makes use of the Presburger arithmetic to describe all the stationary states. Finally we apply this novel approach to find stationary states of a gene regulatory network describing the flower morphogenesis of A. thaliana. This shows that the proposed method can be successfully applied in the study of biological systems.

Contextual alignment of biological sequences (Extended abstract)

We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which we assume that the cost of a substitution depends on the surrounding symbols. In this model the cost of transforming one sequence into another depends on the order of editing operations. We present efficient algorithms for calculating this cost, as well as reconstructing (the representation of) all the orders of operations which yield this optimal cost. A precise characterization of the families of linear orders which can emerge this way is given.