A 3D Computational Study on the Formation and Progression of Tumor Cells in Diffuse Gastric Cancer.

Hereditary diffuse gastric cancer is characterized by an increased risk of diffuse gastric cancer and lobular breast cancer, and is caused by pathogenic germline variants of E-cadherin and -E-catenin, which are key regulators of cell-cell adhesion. However, how the loss of cell-cell adhesion promotes cell dissemination remains to be fully understood. Therefore, a three-dimensional computer model was developed to describe the initial steps of diffuse gastric cancer development.

TrajPy: empowering feature engineering for trajectory analysis across domains.

Motivation: Trajectories, which are sequentially measured quantities that form a path, are an important presence in many different fields, from hadronic beams in physics to electrocardiograms in medicine. Trajectory analysis requires the quantification and classification of curves, either by using statistical descriptors or physics-based features. To date, no extensive and user-friendly package for trajectory analysis has been readily available, despite its importance and potential application across various domains.

The ECM and tissue architecture are major determinants of early invasion mediated by E-cadherin dysfunction.

Germline mutations of E-cadherin cause Hereditary Diffuse Gastric Cancer (HDGC), a highly invasive cancer syndrome characterised by the occurrence of diffuse-type gastric carcinoma and lobular breast cancer. In this disease, E-cadherin-defective cells are detected invading the adjacent stroma since very early stages. Although E-cadherin loss is well established as a triggering event, other determinants of the invasive process persist largely unknown.

A mathematical model of fibrinogen-mediated erythrocyte-erythrocyte adhesion.

Erythrocytes are deformable cells that undergo progressive biophysical and biochemical changes affecting the normal blood flow. Fibrinogen, one of the most abundant plasma proteins, is a primary determinant for changes in haemorheological properties, and a major independent risk factor for cardiovascular diseases. In this study, the adhesion between human erythrocytes is measured by atomic force microscopy (AFM) and its effect observed by micropipette aspiration technique, in the absence and presence of fibrinogen.

How abundant are superoxide and hydrogen peroxide in the vasculature lumen, how far can they reach?

Paracrine superoxide (O) and hydrogen peroxide (HO) signaling critically depends on these substances' concentrations, half-lives and transport ranges in extracellular media. Here we estimated these parameters for the lumen of human capillaries, arterioles and arteries using reaction-diffusion-advection models. These models considered O and HO production by endothelial cells and uptake by erythrocytes and endothelial cells, O dismutation, O and HO diffusion and advection by the blood flow.

A mathematical model for the dependence of keratin aggregate formation on the quantity of mutant keratin expressed in EGFP-K14 R125P keratinocytes.

We examined keratin aggregate formation and the possible mechanisms involved. With this aim, we observed the effect that different ratios between mutant and wild-type keratins expressed in cultured keratinocytes may have on aggregate formation in vitro, as well as how keratin aggregate formation affects the mechanical properties of cells at the cell cortex. To this end we prepared clones with expression rates as close as possible to 25%, 50% and 100% of the EGFP-K14 proteins (either WT or R125P and V270M mutants).

Intratumoral VEGF nanotrapper reduces gliobastoma vascularization and tumor cell mass.

Glioblastoma multiforme (GBM) is the most aggressive and invasive malignant brain cancer. GBM is characterized by a dramatic metabolic imbalance leading to increased secretion of the pro-angiogenic factor VEGF and subsequent abnormal tumor vascularization. In 2009, FDA approved the intravenous administration of bevacizumab, an anti-VEGF monoclonal antibody, as a therapeutic agent for patients with GBM.

Cortical stiffness of keratinocytes measured by lateral indentation with optical tweezers.

Keratin intermediate filaments are the principal structural element of epithelial cells. Their importance in providing bulk cellular stiffness is well recognized, but their role in the mechanics of cell cortex is less understood. In this study, we therefore compared the cortical stiffness of three keratinocyte lines: primary wild type cells (NHEK2), immortalized wild type cells (NEB1) and immortalized mutant cells (KEB7).

Adhesion modulates cell morphology and migration within dense fibrous networks.

One of the most fundamental abilities required for the sustainability of complex life forms is active cell migration, since it is essential in diverse processes from morphogenesis to leukocyte chemotaxis in immune response. The movement of a cell is the result of intricate mechanisms, that involve the coordination between mechanical forces, biochemical regulatory pathways and environmental cues. In particular, epithelial cancer cells have to employ mechanical strategies in order to migrate through the tissue's basement membrane and infiltrate the bloodstream during the invasion stage of metastasis.

Notch signaling and taxis mechanisms regulate early stage angiogenesis: A mathematical and computational model.

During angiogenesis, new blood vessels sprout and grow from existing ones. This process plays a crucial role in organ development and repair, in wound healing and in numerous pathological processes such as cancer progression or diabetes. Here, we present a mathematical model of early stage angiogenesis that permits exploration of the relative importance of mechanical, chemical and cellular cues.

Resonances in the response of fluidic networks inherent to the cooperation between elasticity and bifurcations.

A global response function (GRF) of an elastic network is introduced as a generalization of the response function (RF) of a rigid network, relating the average flow along the network with the pressure difference at its extremes. The GRF can be used to explore the frequency behaviour of a fluid confined in a tree-like symmetric elastic network in which vessels bifurcate into identical vessels. We study such dynamic response for elastic vessel networks containing viscous fluids.

Soft culture substrates favor stem-like cellular phenotype and facilitate reprogramming of human mesenchymal stem/stromal cells (hMSCs) through mechanotransduction.

Biophysical cues influence many aspects of cell behavior. Stiffness of the extracellular matrix is probed by cells and transduced into biochemical signals through mechanotransduction protein networks, strongly influencing stem cell behavior. Cellular stemness is intimately related with mechanical properties of the cell, like intracellular contractility and stiffness, which in turn are influenced by the microenvironment.

Angiogenic Factors produced by Hypoxic Cells are a leading driver of Anastomoses in Sprouting Angiogenesis-a computational study.

Angiogenesis - the growth of new blood vessels from a pre-existing vasculature - is key in both physiological processes and on several pathological scenarios such as cancer progression or diabetic retinopathy. For the new vascular networks to be functional, it is required that the growing sprouts merge either with an existing functional mature vessel or with another growing sprout. This process is called anastomosis.

Localized redox relays as a privileged mode of cytoplasmic hydrogen peroxide signaling.

Hydrogen peroxide (HO) is a key signaling agent. Its best characterized signaling actions in mammalian cells involve the early oxidation of thiols in cytoplasmic phosphatases, kinases and transcription factors. However, these redox targets are orders of magnitude less HO-reactive and abundant than cytoplasmic peroxiredoxins.

The Force at the Tip--Modelling Tension and Proliferation in Sprouting Angiogenesis.

Sprouting angiogenesis, where new blood vessels grow from pre-existing ones, is a complex process where biochemical and mechanical signals regulate endothelial cell proliferation and movement. Therefore, a mathematical description of sprouting angiogenesis has to take into consideration biological signals as well as relevant physical processes, in particular the mechanical interplay between adjacent endothelial cells and the extracellular microenvironment. In this work, we introduce the first phase-field continuous model of sprouting angiogenesis capable of predicting sprout morphology as a function of the elastic properties of the tissues and the traction forces exerted by the cells.

Obstructions in Vascular Networks: Relation Between Network Morphology and Blood Supply.

We relate vascular network structure to hemodynamics after vessel obstructions. We consider tree-like networks with a viscoelastic fluid with the rheological characteristics of blood. We analyze the network hemodynamic response, which is a function of the frequencies involved in the driving, and a measurement of the resistance to flow.

Hypoxia in vascular networks: a complex system approach to unravel the diabetic paradox.

In this work we model the extent of hypoxia in the diabetic retina as a function of the area affected by vessel disruption. We find two regimes that differ on the ratio between the area of disrupted vasculature and the area of tissue in hypoxia. In the first regime the hypoxia is localized in the vicinity of the vascular disruption, while in the second regime there is a generalized hypoxia in the affected tissue.

Flow and anastomosis in vascular networks.

We analyze the effect that the geometrical place of anastomosis in the circulatory tree has on blood flow. We introduce an idealized model that consists of a symmetric network for the arterial and venous vascular trees. We consider that the network contains a viscoelastic fluid with the rheological characteristics of blood, and analyze the network hydrodynamic response to a time-dependent periodic pressure gradient.

Why do protein folding rates correlate with metrics of native topology?

For almost 15 years, the experimental correlation between protein folding rates and the contact order parameter has been under scrutiny. Here, we use a simple simulation model combined with a native-centric interaction potential to investigate the physical roots of this empirical observation. We simulate a large set of circular permutants, thus eliminating dependencies of the folding rate on other protein properties (e.

Tumor angiogenesis and vascular patterning: a mathematical model.

Understanding tumor induced angiogenesis is a challenging problem with important consequences for diagnosis and treatment of cancer. Recently, strong evidences suggest the dual role of endothelial cells on the migrating tips and on the proliferating body of blood vessels, in consonance with further events behind lumen formation and vascular patterning. In this paper we present a multi-scale phase-field model that combines the benefits of continuum physics description and the capability of tracking individual cells.

The protein folding transition state: insights from kinetics and thermodynamics.

We perform extensive lattice Monte Carlo simulations of protein folding to construct and compare the equilibrium and the kinetic transition state ensembles of a model protein that folds to the native state with two-state kinetics. The kinetic definition of the transition state is based on the folding probability analysis method, and therefore on the selection of conformations with 0.4 View Article and Find Full Text PDF

Non-native interactions play an effective role in protein folding dynamics.

Systematic Monte Carlo simulations of simple lattice models show that the final stage of protein folding is an ordered process where native contacts get locked (i.e., the residues come into contact and remain in contact for the duration of the folding process) in a well-defined order.