Tumor Extracellular Matrix Stiffness Promptly Modulates the Phenotype and Gene Expression of Infiltrating T Lymphocytes

The immune system is a fine modulator of the tumor biology supporting or inhibiting its progression, growth, invasion and conveys the pharmacological treatment effect. Tumors, on their side, have developed escaping mechanisms from the immune system action ranging from the direct secretion of biochemical signals to an indirect reaction, in which the cellular actors of the tumor microenvironment (TME) collaborate to mechanically condition the extracellular matrix (ECM) making it inhospitable to immune cells. TME is composed of several cell lines besides cancer cells, including tumor-associated macrophages, cancer-associated fibroblasts, CD4⁺ and CD8⁺ lymphocytes, and innate immunity cells. These populations interface with each other to prepare a conservative response, capable of evading the defense mechanisms implemented by the host’s immune system. The presence or absence, in particular, of cytotoxic CD8⁺ cells in the vicinity of the main tumor mass, is able to predict, respectively, the success or failure of drug therapy. Among various mechanisms of immunescaping, in this study, we characterized the modulation of the phenotypic profile of CD4⁺ and CD8⁺ cells in resting and activated states, in response to the mechanical pressure exerted by a three-dimensional in vitro system, able to recapitulate the rheological and stiffness properties of the tumor ECM.     

Advanced InSAR techniques for deformation studies and for simulating the PS-assisted calibration procedure of Sentinel-1 data: case study from Thessaloniki (Greece), based on the Envisat/ASAR archive

Using state-of-the-art InSAR techniques, namely persistent scatterers (PSs) and small baseline subset (SBAS) approaches, this study contributes to open geotechnical questions in the area of Thessaloniki (Greece) from a remote-sensing perspective. It also demonstrates the potential of these techniques for calibration purposes, with reference to the new C-band synthetic aperture radar (SAR) sensor on board the Sentinel-1 mission satellites. By exploiting the historical archive of Envisat/ASAR data, as well as a pair of the first Sentinel-1A SAR images, recent (2004–2010) deformation rates up to 18 mm year^–1 are detected over the study area. These results are then compared to the findings of previous InSAR and geophysical observations, indicating for example, subsidence or tectonic activity. On the other hand, the usefulness of the PS technique is shown over the same region for external SAR calibration purposes. This process simulates the PS-assisted calibration procedure to be applied systematically to Sentinel-1 SAR products.     

Computation of optimal composite re-parameterizations

Rational re-parameterizations of a polynomial curve that preserve the curve degree and [0,1] parameter domain are characterized by a single degree of freedom. The “optimal” re-parameterization in this family (that comes closest under the L₂ norm to arc-length parameterization) can be identified by solving a quadratic equation, but may exhibit too much residual parametric speed variation for motion control and other applications. Closer approximations to arc-length parameterizations require more flexible re-parameterization functions, such as piecewise-polynomial/rational forms. We show that, for fixed nodes, the optimal piecewise-rational parameterization of the same degree is defined by a simple recursion relation, and we analyze its convergence to the arc-length parameterization. With respect to the new curve parameter, this representation is only of C⁰ continuity, although the smoothness and geometry of the curve are unchanged. A C¹ parameterization can be obtained by using continuity conditions, rather than optimization, to fix certain free parameters, but the objective function is then highly non-linear and does not admit a closed-form optimization. Empirical results from implementations of these methods are presented.     

Targeting EphA2‐Sam and Its Interactome: Design and Evaluation of Helical Peptides Enriched in Charged Residues

The EphA2 receptor controls diverse physiological and pathological conditions and its levels are often upregulated in cancer. Targeting receptor overexpression, through modulation of endocytosis and consequent degradation, appears to be an appealing strategy for attacking tumor malignancy. In this scenario, the Sam domain of EphA2 plays a pivotal role because it is the site where protein regulators of endocytosis and stability are recruited by means of heterotypic Sam–Sam interactions. Because EphA2‐Sam heterotypic complexes are largely based on electrostatic contacts, we have investigated the possibility of attacking these interactions with helical peptides enriched in charged residues. Several peptide sequences with high predicted helical propensities were designed, and detailed conformational analyses were conducted by diverse techniques including NMR, CD, and molecular dynamics (MD) simulations. Interaction studies were also performed by NMR, surface plasmon resonance (SPR), and microscale thermophoresis (MST) and led to the identification of two peptides capable of binding to the first Sam domain of Odin. These molecules represent early candidates for the generation of efficient Sam domain binders and antagonists of Sam–Sam interactions involving EphA2.     

User Interaction and Data Management for Large Scale Grid Applications

In this paper we present a model that combines the X3DMMS application with the G3CPie execution framework, that enables the user to perform large scale computations on distributed computing environments. Such an approach facilitates the management and the preparation of the data required to define the input files for DL_POLY, a popular Molecular Dynamics (MD) package used for the study of molecular systems. The researcher can define in a intuitive way the initial configuration of the molecular system, making use of the X3DMMS virtual reality environment, and prepares the related MD package oriented input files. After having defined the initial conditions of the system, the researcher can carry out the required computations by using the G3CPie workflow environment, which controls the execution of the calculation on a distributed computing infrastructure. To test the validity of the developed model, implemented in the EGI infrastructure, we present the results carried out for a propane bulk system, where the solvation process of propane inside the bulk has been investigated. The presented approach provides a reusable example for other laboratories or groups interested both in acting through virtual representation of the molecular systems and porting their applications to distributed computing infrastructures.     

Heparin conjugated silica nanoparticle synthesis

We report on a facile method towards a synthesis of novel hybrid heparin silica nanoparticles involving a modification of the Stober method. Tetrapropyl orthosilicate (TPOS) was used instead of the traditional TEOS or TMOS; by this way we could overcome the solubility problems of heparin in ethanol and exploit the good solubility of heparin in proper isopropanol–water mixtures. Aminopropyl triethoxysilane (APTS) was also used to have a good link of heparin to silica particles. SEM, DLS, FTIR and NMR proved that we did find conditions in which heparin conjugated silica particles were produced.Thermogravimetry allowed to evaluate the heparin/silica weight ratio to be 0.61. The efficiency of heparin binding to the particles was appreciated to be 35 wt.%.     

Chitosan elicits mono-glucosylated stilbene production and release in fed-batch bioreactor cultures of grape cells

The present paper reports the study of the optimal conditions for grape (Vitis vinifera cv. Barbera) cell suspensions in batch and fed-batch bioreactor cultures, in order to specifically improve the production of mono-glucosylated stilbenes, which are resveratrol derivatives. These compounds are physiologically as active as free resveratrol in cardio- and chemoprotection, but are more stable and bioavailable after ingestion through diet. In fed-batch conditions the production of mono-glucosides was considerably increased together with that of free resveratrol. For the first time, an elicitor (chitosan) was tested in a bioreactor system, demonstrating its efficacy in inducing the production of stilbenes. The bioreactor culture conditions also allowed the accumulation of other polyphenols, such as catechins. The vast majority of the produced compounds was released into the culture media, which represents a relevant advantage for the recovery of specific molecules or of polyphenol-enriched mixtures. These results represent a further step toward the employment of grape cells in fed-batch cultures, as a promising alternative to whole plant extraction for the industrial production of plant polyphenols, considering the necessity for developing sustainable processes.