Search results for "formation"
showing 10 items of 21020 documents
Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P5S3during silicic acid condensation and silica de…
2017
The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5 S3 , a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains 5 protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5 S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2 ) at globally undersaturated concentrations. The secondary structure of P5 S3 during these 2 processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in …
Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives
2018
Abstract Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as ψ-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis-deriv…
High genetic stability of potato yellow mosaic Panama virus infecting tomato in Panama
2018
The relevant regions in Panama involved in commercial tomato production, including the Chiriqui, Veraguas, Herrera, Los Santos and Panama Oeste provinces, were surveyed for the distribution and genetic diversity of potato yellow mosaic Panama virus (PYMPV) in the growing seasons of 2011 and 2012. A total of 28 tomato plots were surveyed and 314 individual tomato plants were sampled. DNA was extracted from each plant for a subsequent rolling circle amplification (RCA) analysis, to confirm the presence of begomovirus infections. The samples displaying a positive RCA reaction were subsequently analysed by PCR with a specific primer pair to identify PYMPV. This virus was detected in samples col…
Quantum clustering in non-spherical data distributions: Finding a suitable number of clusters
2017
Quantum Clustering (QC) provides an alternative approach to clustering algorithms, several of which are based on geometric relationships between data points. Instead, QC makes use of quantum mechanics concepts to find structures (clusters) in data sets by finding the minima of a quantum potential. The starting point of QC is a Parzen estimator with a fixed length scale, which significantly affects the final cluster allocation. This dependence on an adjustable parameter is common to other methods. We propose a framework to find suitable values of the length parameter σ by optimising twin measures of cluster separation and consistency for a given cluster number. This is an extension of the Se…
Synaptic Phospholipid Signaling Modulates Axon Outgrowth via Glutamate-dependent Ca2+-mediated Molecular Pathways.
2015
Abstract Altered synaptic bioactive lipid signaling has been recently shown to augment neuronal excitation in the hippocampus of adult animals by activation of presynaptic LPA2-receptors leading to increased presynaptic glutamate release. Here, we show that this results in higher postsynaptic Ca2+ levels and in premature onset of spontaneous neuronal activity in the developing entorhinal cortex. Interestingly, increased synchronized neuronal activity led to reduced axon growth velocity of entorhinal neurons which project via the perforant path to the hippocampus. This was due to Ca2+-dependent molecular signaling to the axon affecting stabilization of the actin cytoskeleton. The spontaneous…
Gut microbiota imbalance and colorectal cancer
2016
International audience; The gut microbiota acts as a real organ. The symbiotic interactions between resident micro-organisms and the digestive tract highly contribute to maintain the gut homeostasis. However, alterations to the microbiome caused by environmental changes (e.g., infection, diet and/or lifestyle) can disturb this symbiotic relationship and promote disease, such as inflammatory bowel diseases and cancer. Colorectal cancer is a complex association of tumoral cells, non-neoplastic cells and a large amount of micro-organisms, and the involvement of the microbiota in colorectal carcinogenesis is becoming increasingly clear. Indeed, many changes in the bacterial composition of the g…
Efficient Algorithms for Sequence Analysis with Entropic Profiles
2017
Entropy, being closely related to repetitiveness and compressibility, is a widely used information-related measure to assess the degree of predictability of a sequence. Entropic profiles are based on information theory principles, and can be used to study the under-/over-representation of subwords, by also providing information about the scale of conserved DNA regions. Here, we focus on the algorithmic aspects related to entropic profiles. In particular, we propose linear time algorithms for their computation that rely on suffix-based data structures, more specifically on the truncated suffix tree (TST) and on the enhanced suffix array (ESA). We performed an extensive experimental campaign …
Enabling openness of valuable information resources: Curbing data subtractability and exclusion
2019
In this paper we investigate how data openness can be made possible in communal settings. We adopt a utility perspective that foregrounds the use value of data, conceptualizing them as “goods.” On the basis of this conceptualization we explore 2 key goods' attributes: subtractability and exclusion. Our theoretical basis is built upon concepts from the theory of the commons, power theorizing, and notions related to data and information. Empirically, we investigate openness in the genetics domain through a longitudinal study of the evolving communal infrastructure for data related to 2 genes influencing women's susceptibility to breast and ovarian cancer (BRCA1 and BRCA2). We follow the conti…
Influence of pathway topology and functional class on the molecular evolution of human metabolic genes
2018
Metabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection. Thanks to the genome data, the footprints of adaptive (positive) selection are detectable, and the strength of purifying selection can be measured. This has made possible to know where, in the metabolic network, adaptive selection has acted and where purifying selection is more or less strong and efficient. We have carried out a comprehensive molecular evolutionary study of all the genes involved in the human metabolism. We investigated the type and strength of the selective pressures that acted on the enzyme-coding genes belonging to metabolic pathways …
Applying Conceptual Modeling to Better Understand the Human Genome
2016
The objective of the work is to present the benefits of the application of Conceptual Modeling (CM) in complex domains, such as genomics. This paper explains the evolution of a Conceptual Schema of the Human Genome (CSHG), which seeks to provide a clear and precise understanding of the human genome. We want to highlighting all the advantages of the application of CM in a complex domain such as Genomic Information Systems (GeIS). We show how over time this model has evolved, thus we have discovered better forms of representation. As we advanced in exploring the domain, we understood that we should be extending and incorporating the new concepts detected into our model. Here we present and di…