Exact solution for the Anisotropic Ornstein-Uhlenbeck process.

Active-Matter models commonly consider particles with overdamped dynamics subject to a force (speed) with constant modulus and random direction. Some models also include random noise in particle displacement (a Wiener process), resulting in diffusive motion at short time scales. On the other hand, Ornstein-Uhlenbeck processes apply Langevin dynamics to the particles' velocity and predict motion that is not diffusive at short time scales.

Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection.

To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1 infection of a human lung epithelial cell line. Transcriptograms, a Bioinformatics tool to analyze genome-wide gene expression data, allow us to define an appropriate context-dependent threshold for mechanistic relevance of gene differential expression.

Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection.

To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1 infection of a human lung epithelial cell line. Transcriptograms, a Bioinformatics tool to analyze genome-wide gene expression data, allow us to define an appropriate context-dependent threshold for mechanistic relevance of gene differential expression.

CompuCell3D Simulations Reproduce Mesenchymal Cell Migration on Flat Substrates.

Mesenchymal cell crawling is a critical process in normal development, in tissue function, and in many diseases. Quantitatively predictive numerical simulations of cell crawling thus have multiple scientific, medical, and technological applications. However, we still lack a low-computational-cost approach to simulate mesenchymal three-dimensional (3D) cell crawling.

Transcriptional analyses of two soybean cultivars under salt stress.

Soybean is an economically important plant, and its production is affected in soils with high salinity levels. It is important to understand the adaptive mechanisms through which plants overcome this kind of stress and to identify potential genes for improving abiotic stress tolerance. RNA-Seq data of two Glycine max cultivars, a drought-sensitive (C08) and a tolerant (Conquista), subjected to different periods of salt stress were analyzed.

Identification of root transcriptional responses to shoot illumination in Arabidopsis thaliana.

The transcriptional profile of roots is highly affected by shoot illumination. Transcriptogram analysis allows the identification of cellular processes that are not detected by DESeq. Light is a key environmental factor regulating plant growth and development.

Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein-protein interaction.

Motivation: Several freely available tools perform analysis using algorithms developed to identify significant variation of gene expression individually. The transcriptogramer R package uses protein-protein interaction to perform differential expression of functionally associated genes. The software assesses expression profile of entire genetic systems and reveals which biological systems are significantly altered in case-control designed transcriptome experiments.

Geometrical Distribution of Mediates Flower-Like Biofilm Development.

Microbial biofilms are highly structured and dynamic communities in which phenotypic diversification allows microorganisms to adapt to different environments under distinct conditions. The environmentally ubiquitous pathogen colonizes many niches of the human body and implanted medical devices in the form of biofilms, an important virulence factor. A new approach was used to characterize the underlying geometrical distribution of cells during the adhesion stage of biofilm formation.

Transcriptional Analysis Allows Genome Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient Restriction during Infection.

is a human and animal pathogen that infects healthy hosts and caused the Pacific Northwest outbreak of cryptococcosis. The inhalation of infectious propagules can lead to internalization of cryptococcal cells by alveolar macrophages, a niche in which cells can survive and proliferate. Although the nutrient composition of macrophages is relatively unknown, the high induction of amino acid transporter genes inside the phagosome indicates a preference for amino acid uptake instead of synthesis.

Mean-cluster approach indicates cell sorting time scales are determined by collective dynamics.

Cell migration is essential to cell segregation, playing a central role in tissue formation, wound healing, and tumor evolution. Considering random mixtures of two cell types, it is still not clear which cell characteristics define clustering time scales. The mass of diffusing clusters merging with one another is expected to grow as t^{d/d+2} when the diffusion constant scales with the inverse of the cluster mass.

Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD.

Background: Autosomal dominant polycystic kidney disease (ADPKD) causes progressive loss of renal function in adults as a consequence of the accumulation of cysts. ADPKD is the most common genetic cause of end-stage renal disease. Mutations in polycystin-1 occur in 87% of cases of ADPKD and mutations in polycystin-2 are found in 12% of ADPKD patients.

3D simulations of wet foam coarsening evidence a self similar growth regime.

In wet liquid foams, slow diffusion of gas through bubble walls changes bubble pressure, volume and wall curvature. Large bubbles grow at the expenses of smaller ones. The smaller the bubble, the faster it shrinks.

Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks.

Whole genome protein-protein association networks are not random and their topological properties stem from genome evolution mechanisms. In fact, more connected, but less clustered proteins are related to genes that, in general, present more paralogs as compared to other genes, indicating frequent previous gene duplication episodes. On the other hand, genes related to conserved biological functions present few or no paralogs and yield proteins that are highly connected and clustered.

Growth laws and self-similar growth regimes of coarsening two-dimensional foams: transition from dry to wet limits.

We study the topology and geometry of two-dimensional coarsening foam with an arbitrary liquid fraction. To interpolate between the dry limit described by von Neumann's law and the wet limit described by Marqusee's equation, the relevant bubble characteristics are the Plateau border radius and a new variable: the effective number of sides. We propose an equation for the individual bubble growth rate as the weighted sum of the growth through bubble-bubble interfaces and through bubble-Plateau border interfaces.

Evolutionary plasticity determination by orthologous groups distribution.

Background: Genetic plasticity may be understood as the ability of a functional gene network to tolerate alterations in its components or structure. Usually, the studies involving gene modifications in the course of the evolution are concerned to nucleotide sequence alterations in closely related species. However, the analysis of large scale data about the distribution of gene families in non-exclusively closely related species can provide insights on how plastic or how conserved a given gene family is.

Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case.

Analysis of genome-wide expression data poses a challenge to extract relevant information. The usual approaches compare cellular expression levels relative to a pre-established control and genes are clustered based on the correlation of their expression levels. This implies that cluster definitions are dependent on the cellular metabolic state, eventually varying from one experiment to another.

cAMP diffusion in Dictyostelium discoideum: a Green's function method.

A Green's function method is developed to approach the spatiotemporal equations describing the cAMP production in Dictyostelium discoideum, markedly reducing numerical calculations times: cAMP concentrations and gradients are calculated just at the amoeba locations. A single set of parameters is capable of reproducing the different observed behaviors, from cAMP synchronization, spiral waves and reaction-diffusion patterns to streaming and mound formation. After aggregation, the emergence of a circular motion of amoebas, breaking the radial cAMP field symmetry, is observed.

ViaComplex: software for landscape analysis of gene expression networks in genomic context.

Unlabelled: ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous publications (Nucleic Acids Res., 35, 1859-1867, 2007; Nucleic Acids Res.

Evolutionary origins of human apoptosis and genome-stability gene networks.

Apoptosis is essential for complex multicellular organisms and its failure is associated with genome instability and cancer. Interactions between apoptosis and genome-maintenance mechanisms have been extensively documented and include transactivation-independent and -dependent functions, in which the tumor-suppressor protein p53 works as a 'molecular node' in the DNA-damage response. Although apoptosis and genome stability have been identified as ancient pathways in eukaryote phylogeny, the biological evolution underlying the emergence of an integrated system remains largely unknown.

Self-propelled particle model for cell-sorting phenomena.

A self-propelled particle model is introduced to study cell sorting occurring in some living organisms. This allows us to evaluate the influence of intrinsic cell motility separately from differential adhesion with fluctuations, a mechanism previously shown to be sufficient to explain a variety of cell rearrangement processes. We find that the tendency of cells to actively follow their neighbors greatly reduces segregation time scales.

Impaired expression of NER gene network in sporadic solid tumors.

Nucleotide repair genes are not generally altered in sporadic solid tumors. However, point mutations are found scattered throughout the genome of cancer cells indicating that the repair pathways are dysfunctional. To address this point, in this work we focus on the expression pathways rather than in the DNA structure of repair genes related to either genome stability or essential metabolic functions.

Chromosome aberrations in solid tumors have a stochastic nature.

An important question nowadays is whether chromosome aberrations are random events or arise from an internal deterministic mechanism, which leads to the delicate task of quantifying the degree of randomness. For this purpose, we have defined several Shannon information functions to evaluate disorder inside a tumor and between tumors of the same kind. We have considered 79 different kinds of solid tumors with 30 or more karyotypes retrieved from the Mitelman Database of Chromosome Aberrations in Cancer.