Search results for " Matrix"

PINCoC: a Co-Clustering based Method to Analyze Protein-Protein Interaction Networks

2007

Anovel technique to search for functionalmodules in a protein-protein interaction network is presented. The network is represented by the adjacency matrix associated with the undirected graph modelling it. The algorithm introduces the concept of quality of a sub-matrix of the adjacency matrix, and applies a greedy search technique for finding local optimal solutions made of dense submatrices containing the maximum number of ones. An initial random solution, constituted by a single protein, is evolved to search for a locally optimal solution by adding/removing connected proteins that best contribute to improve the quality function. Experimental evaluations carried out on Saccaromyces Cerevis…

Splittings of Toric Ideals

2019

Let $I \subseteq R = \mathbb{K}[x_1,\ldots,x_n]$ be a toric ideal, i.e., a binomial prime ideal. We investigate when the ideal $I$ can be "split" into the sum of two smaller toric ideals. For a general toric ideal $I$, we give a sufficient condition for this splitting in terms of the integer matrix that defines $I$. When $I = I_G$ is the toric ideal of a finite simple graph $G$, we give additional splittings of $I_G$ related to subgraphs of $G$. When there exists a splitting $I = I_1+I_2$ of the toric ideal, we show that in some cases we can describe the (multi-)graded Betti numbers of $I$ in terms of the (multi-)graded Betti numbers of $I_1$ and $I_2$.

Protein-protein interaction network querying by a "focus and zoom" approach

2008

We propose an approach to network querying in protein-protein interaction networks based on bipartite graph weighted matching. An algorithm is presented that first “focuses” the potentially relevant portion of the target graph by performing a global alignment of this one with the query graph, and then “zooms” on the actual matching nodes by considering their topological arrangement, hereby obtaining a (possibly) approximated occurrence of the query graph within the target graph. Approximation is related to node insertions, node deletions and edge deletions possibly intervening in the query graph. The technique manages networks of arbitrary topology. Moreover, edge labels are used to represe…

Plant Pigments: Properties, Analysis, Degradation

2005

Publisher Summary This chapter discusses the molecular structures, the general physicochemical properties of plant pigments, and the mechanisms involved in pigment degradation. The invasive and noninvasive methods used for pigment analysis, including the mechanisms involved in pigment degradation, are reviewed. The chapter presents different analytical methods that can be used to identify pigments. All the methods are invasive techniques that are time consuming and often expensive. To reduce sampling and analytical costs, and to speed up the analyses, noninvasive analytical procedures have been developed with the aim to characterize the pigment content of samples, and in the case of food pr…

The small heat-shock protein α B-crystallin is essential for the nuclear localization of Smad4: impact on pulmonary fibrosis

2014

Idiopathic pulmonary fibrosis (IPF) is a devastating disease characterized by the proliferation of myofibroblasts and the accumulation of extracellular matrix (ECM) in the lungs. TGF-β1 is the major profibrotic cytokine involved in IPF and is responsible for myofibroblast proliferation and differentiation and ECM synthesis. αB-crystallin is constitutively expressed in the lungs and is inducible by stress, acts as a chaperone and is known to play a role in cell cytoskeleton architecture homeostasis. The role of αB-crystallin in fibrogenesis remains unknown. The principal signalling pathway involved in this process is the Smad-dependent pathway. We demonstrate here that αB-crystallin is stron…

Human Macrophage Invasion: Gelatin‐Hyaluronan Click‐Crosslinked Cryogels Elucidate Human Macrophage Invasion Behavior (Adv. Funct. Mater. 28/2021)

2021

Synthesis of calcium carbonate biological materials: how many proteins are needed?

2013

In Nature, calcium carbonate biomineralizations are the most abundant mineralized structures of biological origin. Because many exhibit remarkable characteristics, several attempts have been made to use them as substitution materials for bone reconstruction or as models for generating biomimetic composites that exhibit tailored properties. CaCO3biomineralizations contain small amounts of amalgamate of proteins and polysaccharides that are secreted during the calcification process. They contribute to control the morphology of the crystallites and to spatially organize them in well-defined microstructures. These macromolecules, collectively defined as the skeletal matrix, have been the focus …

Variability of shell repair in the Manila clam Ruditapes philippinarum affected by the Brown Ring Disease: A microstructural and biochemical study

2011

11 pages; International audience; For more than two decades, the Manila clam Ruditapes philippinarum has been regularly affected by Brown Ring Disease (BRD), an epizootic event caused by the bacterium Vibrio tapetis and characterized by the development of a brown deposit on the inner face of valves. Although BRD infection is often lethal, some clams recover by mineralizing a new repair shell layer, which covers the brown deposit and fully isolates it from living tissues. In order to understand this specific shell repair process, the microstructures of repaired zones were compared to those of shells unaffected by BRD. In addition, the organic matrix associated with unaffected shells and to r…

Phosphorylation of serine residues is fundamental for the calcium-binding ability of Orchestin, a soluble matrix protein from crustacean calcium stor…

2003

International audience; Orchestia cavimana is a terrestrial crustacean, which cyclically stores calcium in diverticula of the midgut, in the form of calcified amorphous concretions. These concretions are associated with a proteinaceous matrix, the main constituent of the soluble matrix is Orchestin, an acidic calcium-binding protein [Testenière et al., Biochem. J. 361 (2002) 327-335]. In the present paper, we clearly demonstrate that Orchestin is phosphorylated on serine and tyrosine residues, but that calcium binding only occurs via the phosphoserine residues. To our knowledge, this is the first example of an invertebrate mineralization for which a post-translational modification is clearl…

The shell organic matrix of the crossed lamellar queen conch shell (Strombus gigas)

2014

10 pages; International audience; In molluscs, the shell organic matrix comprises a large set of biomineral-occluded proteins, glycoproteins and polysaccharides that are secreted by the calcifying mantle epithelium, and are supposed to display several functions related to the synthesis of the shell. In the present paper, we have characterized biochemically the shell matrix associated to the crossed-lamellar structure of the giant queen conch Strombus gigas. The acid-soluble (ASM) and acid-insoluble (AIM) matrices represent an extremely minor fraction of the shell. Both are constituted of polydisperse and of few discrete proteins among which three fractions, obtained by preparative SDS-PAGE …