Search results for "structural"
showing 10 items of 5047 documents
New gellan gum-graft-poly(D,L-lactide-co-glycolide) copolymers as promising bioinks: Synthesis and characterization
2020
This research focused on the aim of tackling the urgent demand of printable biomaterials, hence we synthetized and characterized three gellan gum-graft-poly(d,l-lactide-co-glycolide) copolymers (GGm-PLGA a, b and c) which differed in the graft substitution degree. We investigated the effect of the polyester chain grafted onto hydrophilic backbone of gellan gum in terms of physicochemical properties and the ability of the system to print 3D cell laden constructs. In particular, we evaluated thermo-rheological, ionotropic crosslinking, shear thinning, swelling and stability properties of these copolymers and their derived biomaterials and findings related to the degree of functionalization. M…
Impact of hydrologically driven hillslope erosion and landslide occurrence on soil organic carbon dynamics in tropical watersheds
2016
The dynamics of soil organic carbon (SOC) in tropical forests play an important role in the global carbon (C) cycle. Past attempts to quantify the net C exchange with the atmosphere in regional and global budgets do not systematically account for dynamic feedbacks among linked hydrological, geomorphological, and biogeochemical processes, which control the fate of SOC. Here we quantify effects of geomorphic perturbations on SOC oxidation and accumulation in two adjacent wet tropical forest watersheds underlain by contrasting lithology (volcaniclastic rock and quartz diorite) in the Luquillo Critical Zone Observatory. This study uses the spatially-explicit and physically-based model of SOC dy…
Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser.
2014
Light absorption can trigger biologically relevant protein conformational changes. The light-induced structural rearrangement at the level of a photoexcited chromophore is known to occur in the femtosecond timescale and is expected to propagate through the protein as a quake-like intramolecular motion. Here we report direct experimental evidence of such ‘proteinquake’ observed in myoglobin through femtosecond X-ray solution scattering measurements performed at the Linac Coherent Light Source X-ray free-electron laser. An ultrafast increase of myoglobin radius of gyration occurs within 1 picosecond and is followed by a delayed protein expansion. As the system approaches equilibrium it underg…
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti
2013
Abstract Background Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed. Results We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connect…
A motif-independent metric for DNA sequence specificity
2011
Abstract Background Genome-wide mapping of protein-DNA interactions has been widely used to investigate biological functions of the genome. An important question is to what extent such interactions are regulated at the DNA sequence level. However, current investigation is hampered by the lack of computational methods for systematic evaluating sequence specificity. Results We present a simple, unbiased quantitative measure for DNA sequence specificity called the Motif Independent Measure (MIM). By analyzing both simulated and real experimental data, we found that the MIM measure can be used to detect sequence specificity independent of presence of transcription factor (TF) binding motifs. We…
Evolution and biomineralization of pteropod shells
2021
12 pages; International audience; Shelled pteropods, known as sea butterflies, are a group of small gastropods that spend their entire lives swimming and drifting in the open ocean. They build thin shells of aragonite, a metastable polymorph of calcium carbonate. Pteropod shells have been shown to experience dissolution and reduced thickness with a decrease in pH and therefore represent valuable bioindicators to monitor the impacts of ocean acidification. Over the past decades, several studies have highlighted the striking diversity of shell microstructures in pteropods, with exceptional mechanical properties, but their evolution and future in acidified waters remains uncertain. Here, we re…
Genesis of amorphous calcium carbonate containing alveolar plates in the ciliate Coleps hirtus (Ciliophora, Prostomatea).
2013
7 pages; International audience; In the protist world, the ciliate Coleps hirtus (phylum Ciliophora, class Prostomatea) synthesizes a peculiar biomineralized test made of alveolar plates, structures located within alveolar vesicles at the cell cortex. Alveolar plates are arranged by overlapping like an armor and they are thought to protect and/or stiffen the cell. Although their morphology is species-specific and of complex architecture, so far almost nothing is known about their genesis, their structure and their elemental and mineral composition. We investigated the genesis of new alveolar plates after cell division and examined cells and isolated alveolar plates by electron microscopy, e…
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 matrix of the european thorny oyster, Spondylus gaederopus: microstructural and molecular characterization.
2020
17 pages; International audience; Molluscs, the largest marine phylum, display extraordinary shell diversity and sophisticated biomineral architectures. However, mineral-associated biomolecules involved in biomineralization are still poorly characterised.We report the first comprehensive structural and biomolecular study of Spondylus gaederopus, a pectinoid bivalve with a peculiar shell texture. Used since prehistoric times, this is the best-known shell of Europe’s cultural heritage. We find that Spondylus microstructure is very poor in mineral-bound organics, which are mostly intercrystalline and concentrated at the interface between structural layers.Using high-resolution liquid chromatog…
Shell proteome of rhynchonelliform brachiopods.
2015
7 pages; International audience; Brachiopods are a phylum of marine invertebrates that have an external bivalved shell to protect their living tissues. With few exceptions, this biomineralized structure is composed of calcite, mixed together with a minor organic fraction, comprising secreted proteins that become occluded in the shell structure, once formed. This organic matrix is thought to display several functions, in particular, to control mineral deposition and to regulate crystallite shapes. Thus, identifying the primary structure of matrix proteins is a prerequisite for generating bioinspired materials with tailored properties. In this study, we employed a proteomic approach to identi…