Extracellular matrix of the charophycean green algae

A comprehensive knowledge of cell wallstructure and function throughout the plant kingdom is essential to understanding cell wall evolution. The fundamental understanding of the charophycean green algal cell wall is broadening. The similarities and differences that exist between land plant and algal cell walls provide opportunities to understand plant evolution. A variety of polymers previously associated with higher plants were discovered in the charophycean green algae (CGA), including homogalacturonans, cross-linking glycans, arabinogalactan protein, β-glucans, and cellulose. The cellulose content of CGA cell walls ranged from 6% to 43%, with the higher valuescomparable to that found in the primary cell wall of land plants (20-30%). (1,3)β-glucans were found in the unicellular Chlorokybus atmophyticus, Penium margaritaceum, and Cosmarium turpini, the unbranched filamentous Klebsormidium flaccidum, and the multicellular Chara corallina. The discovery of homogalacturonan in Penium margaritaceum representsthe first confirmation of land plant-type pectinsin desmids and the second rigorous characterization of a pectin polymer from the charophycean algae. Homogalacturonan was also indicated from the basal species Chlorokybus atmophyticus and Klebsormidium flaccidum. There is evidence of branched pectins in Cosmarium turpini and linkage analysis suggests the presence of type I rhamnogalacturonan (RGI). Cross-linking β-glucans are associated with cellulose microfibrils during land plant cell growth, and were found in the cell wall of CGA. The evidence of mixed-linkage glucan (MLG) in the 11 charophytesis both suprising and significant given that MLG was once thought to be specific to some grasses. The organization and structure of Cosmarium turpini and Chara corallina MLG was found to be similar to that of Equisetumspp., whereas the basal species of the CGA, Chlorokybus atmophyticus and Klebsormidium flaccidum, have unique organization of alternating of 3- and 4-linkages. The significance of this result on the evolution of the MLG synthetic pathway has yet to be determined. The extracellular matrix (ECM) of Chlorokybus atmophyticus, Klebsormidium flaccidum, and Spirogyra spp. exhibits significant biochemical diversity, ranging from distinct “land plant” polymers to polysaccharides unique to these algae. The neutral sugar composition of Chlorokybus atmophyticus hot water extract and Spirogyra extracellular polymeric substance (EPS), combined with antibody labeling results, revealed the distinct possibility of an arabinogalactan protein in these organisms. Polysaccharide analysis of Zygnematales (desmid) EPS, indicated a probable range of different EPS backbones and substitution patterns upon the core portions of the molecules. Desmid EPS is predominately composed of a complex matrix of branched, uronic acid containing polysaccharides with ester sulfate substitutions and, as such, has an almost infinite capacity for various hydrogen bonding, hydrophobic interaction and ionic cross-bridging motifs, which characterize their unique function in biofilms. My observations support the hypothesis that members of the CGA represent the phylogenetic line that gave rise to vascular plants and that the primary cell wall of vascular plants many have evolved directly from structures typical of the cell wall of filamentous green algae found in the charophycean green algae.

Exploring the MHC-peptide matrix of central tolerance in the human thymus

Ever since it was discovered that central tolerance to self is imposed on developing T cells in the thymus through their interaction with self-peptide major histocompatibility complexes on thymic antigen-presenting cells, immunologists have speculated about the nature of these peptides, particularly in humans. Here, to shed light on the so-far unknown human thymic peptide repertoire, we analyse peptides eluted from isolated thymic dendritic cells, dendritic cell-depleted antigen-presenting cells and whole thymus. Bioinformatic analysis of the 842 identified natural major histocompatibility complex I and II ligands reveals significant cross-talk between major histocompatibility complex-class I and II pathways and differences in source protein representation between individuals as well as different antigen-presenting cells. Furthermore, several autoimmune- and tumour-related peptides, from enolase and vimentin for example, are presented in the healthy thymus. 302 peptides are directly derived from negatively selecting dendritic cells, thus providing the first global view of the peptide matrix in the human thymus that imposes self-tolerance in vivo.

(Table 2) Varimax factor matrix of planktonic foraminifera at DSDP Hole 72-517

Quaternary sediments were recovered at all four Sites at Leg 72. Planktonic foraminifers were abundant and well preserved, especially in the holes shielded from Antarctic Bottom Water (AABW) influence. The fauna belonged to the subtropical province marked by Globigerinoides ruber and to a lesser extent by Globorotalia inflata. Thirty planktonic foraminiferal species were distinguished, and a detailed study of the Site 517 stratigraphy was made. The Quaternary sequence of the Rio Grande Rise was subdivided slightly differently from the Bolli and Premoli Suva (1973) pattern. Five subzones were identified but some difficulties arose when a precise correlation became necessary in the subzones of the tropical provinces. Correlations could nevertheless be made, particularly with respect to the earliest Quaternary. Quaternary faunal data have been dated by isotopic stratigraphy (Vergnaud Grazzini et al.,1983) and partially contradict results previously published for this part of the Atlantic (Williams and Ledbetter, 1979). By studying the occurrence of planktonic foraminifers, we obtained more information about hydrologic variations during the Quaternary sequence of Hole 517; two broad periods were recognized. Finally, we identified the interaction between the Brazil Current and the subtropical convergence

Low frequency vibrational modes in proteins: Changes induced by point-mutations in the protein-cofactor matrix of bacterial reaction centers

As a step toward understanding their functional role, the low frequency vibrational motions (<300 cm−1) that are coupled to optical excitation of the primary donor bacteriochlorophyll cofactors in the reaction center from Rhodobacter sphaeroides were investigated. The pattern of hydrogen-bonding interaction between these bacteriochlorophylls and the surrounding protein was altered in several ways by mutation of single amino acids. The spectrum of low frequency vibrational modes identified by femtosecond coherence spectroscopy varied strongly between the different reaction center complexes, including between different mutants where the pattern of hydrogen bonds was the same. It is argued that these variations are primarily due to changes in the nature of the individual modes, rather than to changes in the charge distribution in the electronic states involved in the optical excitation. Pronounced effects of point mutations on the low frequency vibrational modes active in a protein-cofactor system have not been reported previously. The changes in frequency observed indicate a strong involvement of the protein in these nuclear motions and demonstrate that the protein matrix can increase or decrease the fluctuations of the cofactor along specific directions.

Study of interaction between Si(O,C) nanowires and the biological system

Nanomedicine is a new branch of medicine, based on the potentiality and intrinsic properties of nanomaterials. Indeed, the nanomaterials ( i.e. the materials with nano and under micron size) can be suitable to different applications in biomedicine. The nanostructures can be used by taking advantage of their properties (for example superparamagnetic nanoparticles) or functionalized to deliver the drug in a specific target, thanks the ability to cross biological barriers. The size and the shape of 1D-nanostructures (nanotubes and nanowires) have an important role on the cell fate: their morphology plays a key role on the interaction between nanostructure and the biological system. For this reason the 1D nanostructure are interesting for their ability to mime the biological system. An implantable material or device must therefore integrate with the surrounding extracellular matrix (ECM), a complex network of proteins with structural and signaling properties. Innovative techniques allow the generation of complex surface patterns that can resemble the structure of the ECM, such as 1D nanostructures. NWs based on cubic silicon carbide (3C-SiC), either bare (3C-SiC NWs) or surrounded by an amorphous shell (3C-SiC/SiO2 core/shell NWs), and silicon oxycarbide nanowires (SiOxCy NWs) can meet the chemical, mechanical and electrical requirements for tissue engineering and have a strong potential to pave the way for the development of a novel generation of implantable nano-devices. Silicon oxycarbide shows promising physical and chemical properties as elastic modulus, bending strength and hardness, chemical durability superior to conventional silicate glasses in aggressive environments and high temperature stability up to 1300 °C. Moreover, it can easily be engineered through functionalization and decoration with macro-molecules and nanoparticles. Silicon carbide has been extensively studied for applications in harsh conditions, as chemical environment, high electric field and high and low temperature, owing to its high hardness, high thermal conductivity, chemical inertness and high electron mobility. Also, its cubic polytype (3C) is highly biocompatible and hemocompatible, and some prototypes of biomedical applications and biomedical devices have been already realized starting from 3C-SiC thin films. Cubic SiC-based NWs can be used as a biomimetic biomaterial, providing a robust and novel biocompatible biological interface . We cultured in vitro A549 human lung adenocarcinoma epithelial cells and L929 murine fibroblast cells over core/shell SiC/SiO2, SiOxCy and bare 3C-SiC nanowire platforms, and analysed the cytotoxicity, by indirect and direct contact tests, the cell adhesion, and the cell proliferation. These studies showed that all the nanowires are biocompatible according to ISO 10993 standards. We evaluated the blood compatibility through the interaction of the nanowires with platelet rich plasma. The adhesion and activation of platelets on the nanowire bundles, assessed via SEM imaging and soluble P-selectin quantification, indicated that a higher platelet activation is induced by the core/shell structures compared to the bare ones. Further, platelet activation is higher with 3C-SiC/SiO2 NWs and SiOxCyNWs, which therefore appear suitable in view of possible tissue regeneration. On the contrary, bare 3C-SiC NWs show a lower platelet activation and are therefore promising in view of implantable bioelectronics devices, as cardiovascular implantable devices. The NWs properties are suitable to allow the design of a novel subretinal Micro Device (MD). This devices is based on Si NWs and PEDOT:PSS, though the well know principle of the hybrid ordered bulk heterojunction (OBHJ). The aim is to develop a device based on a well-established photovoltaic technology and to adapt this know-how to the prosthetic field. The hybrid OBHJ allows to form a radial p–n junction on a nanowire/organic structure. In addition, the nanowires increase the light absorption by means of light scattering effects: a nanowires based p-n junction increases the light absorption up to the 80%, as previously demonstrated, overcoming the Shockley-Queisser limit of 30 % of a bulk p-n junction. Another interesting employment of these NWs is to design of a SiC based epicardial-interacting patch based on teflon that include SiC nanowires. . Such contact patch can bridge the electric conduction across the cardiac infarct as nanowires can ‘sense’ the direction of the wavefront propagation on the survival cardiac tissue and transmit it to the downstream surivived regions without discontinuity. The SiC NWs are tested in terms of toxicology, biocompatibility and conductance among cardiomyocytes and myofibroblasts.

Covalent attachment of Candida rugosa lipase on chemically modified hybrid matrix of polysiloxane-polyvinyl alcohol with different activating compounds

Candida rugosa lipase was immobilized by covalent binding on hybrid matrix of polysiloxane-polyvinyl alcohol chemically modified with different activating agents as glutaraldehyde, sodium metaperiodate and carbonyldiimidazole. The experimental results suggested that functional activating agents render different interactions between enzyme and support, producing consequently alterations in the optimal reaction conditions. Properties of the immobilized systems were assessed and their performance on hydrolytic and synthetic reactions were evaluated and compared with the free enzyme. In hydrolytic reactions using p-nitrophenyl palmitate as substrate all immobilized systems showed higher thermal stability and optima pH and temperature values in relation to the free lipase. Among the activating compounds, carbonyldiimidazole resulted in a total recovery of activity on the support and the highest thermal stability. For the butyl butyrate synthesis, the best performance (molar conversion of 95% and volumetric productivity of 2.33 g L-1 h(-1)) was attained with the lipase immobilized on POS-PVA activated with sodium metaperiodate. The properties of the support and immobilized derivatives were also evaluated by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopies and chemical composition (FTIR). (c) 2007 Elsevier B.V. All rights reserved.

Learning Profile Identification Based on the Analysis of the User Context of Interaction

One of the e-learning environment goal is to attend the individual needs of students during the learning process. The adaptation of contents, activities and tools into different visualization or in a variety of content types is an important feature of this environment, bringing to the user the sensation that there are suitable workplaces to his profile in the same system. Nevertheless, it is important the investigation of student behaviour aspects, considering the context where the interaction happens, to achieve an efficient personalization process. The paper goal is to present an approach to identify the student learning profile analyzing the context of interaction. Besides this, the learning profile could be analyzed in different dimensions allows the system to deal with the different focus of the learning.

Capacity of the extracellular matrix of the bone marrow to induce proliferation of myeloid cells in vitro in model of protein malnutrition in mice

The aim of this study was to verify the capacity of the extracellular matrix (ECM) obtained from bone marrow of malnourished mice to sustain survival and to induce the proliferation of myeloid cells. We also verified the capacity of the tests to interact with in vitro hematopoietic cytokines. Male ""Swiss"" mice were submitted to protein malnutrition with a diet contents of 4% casein until they lost 20% of the original weight, while the group-control was kept with a diet content of 14% of casein. The bone marrow was extracted with 1.0 mg of aprotinin/mL in PBS. The proliferation tests were carried out with myeloid cell line FDCP-1, by the colorimetric method of reduction of the MTT. The obtained ECM from nourished and undernourished mice induced cellular proliferation in vitro. Tests performed with Il-3 and GM-CSF cytokines in a concentration of 10 and 500 rho g/mL displayed synergic and regulatory effects respectively. The ECM obtained from the malnourished group submitted to the binding to GM-CSF demonstrated higher cellular proliferation than the ECM obtained from the control group (p<0.05). The results suggest that the alterations in the composition of ECM of bone marrow caused by malnutrition might lead to modification of the GM-CSF activity modulation.

Generation and Analysis of Interaction Energy Maps of p-Substituted Benzoic Acid [(5-Nitro-thiophen-2-yl)-methylene]-Hydrazides Active against MRSA

In this preliminary study eighteen p-substituted benzoic acid [(5-nitro-thiophen-2-yl)-methylene]-hydrazides with antimicrobial activity were evaluated against multidrug-resistant Staphylococcus aureus, correlating the three-dimensional characteristics of the ligands with their respective bioactivities. The computer programs Sybyl and CORINA were used, respectively, for the design and three-dimensional conversion of the ligands. Molecular interaction fields were calculated using GRID program. Calculations using Volsurf resulted in a statistically consistent model with 48 structural descriptors showing that hydrophobicity is a fundamental property in the analyzed biological response.

Expression of proteins in the extracellular matrix of pulp tissue in human primary teeth during physiologic root resorption

Objectives: To analyze the expression of tenascin, fibronectin, collagens I and III, osteonectin, and bone morphogenetic protein 4 (BMP4) in the extracellular matrix of pulp tissue in primary teeth during physiologic root resorption. Method and Materials: Eighteen teeth were decalcified and equally distributed into 3 groups (group I, teeth with two-thirds root length; group II, teeth with one-third root length; and group III, teeth lacking the root). Results: Immunohistochemical analysis showed that all the proteins were expressed. Tenascin, collagen I, and osteonectin showed strong and broad reactivity in group I, with weaker and rare reactivity in groups II and III. The expression of fibronectin, collagen III, and BMP4 did not vary with root resorption phase. Conclusion: The expression of tenascin, collagen I, and osteonectin was reduced in the extracellular matrix and odontoblasts during root resorption. This fact may be related to the decreasing pulp response to damage and treatment during the progression of root resorption. (Quintessence Int 2009; 40: 553-558)

On a generalized Laguerre operational matrix of fractional integration

A new operationalmatrix of fractional integration of arbitrary order for generalized Laguerre polynomials is derived.The fractional integration is described in the Riemann-Liouville sense.This operational matrix is applied together with generalized Laguerre tau method for solving general linearmultitermfractional differential equations (FDEs).Themethod has the advantage of obtaining the solution in terms of the generalized Laguerre parameter. In addition, only a small dimension of generalized Laguerre operational matrix is needed to obtain a satisfactory result. Illustrative examples reveal that the proposedmethod is very effective and convenient for linear multiterm FDEs on a semi-infinite interval.

Dynamic adaptation of interaction models for stateful web services

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Benefits & drawbacks of different means of interaction for placing objects above a video footage

Public Display Systems (PDS) increasingly have a greater presence in our cities. These systems provide information and advertising specifically tailored to audiences in spaces such as airports, train stations, and shopping centers. A large number of public displays are also being deployed for entertainment reasons. Sometimes designing and prototyping PDS come to be a laborious, complex and a costly task. This dissertation focuses on the design and evaluation of PDS at early development phases with the aim of facilitating low-effort, rapid design and the evaluation of interactive PDS. This study focuses on the IPED Toolkit. This tool proposes the design, prototype, and evaluation of public display systems, replicating real-world scenes in the lab. This research aims at identifying benefits and drawbacks on the use of different means to place overlays/virtual displays above a panoramic video footage, recorded at real-world locations. The means of interaction studied in this work are on the one hand the keyboard and mouse, and on the other hand the tablet with two different techniques of use. To carry out this study, an android application has been developed whose function is to allow users to interact with the IPED Toolkit using the tablet. Additionally, the toolkit has been modified and adapted to tablets by using different web technologies. Finally the users study makes a comparison about the different means of interaction.

Mecanismo de interacción, calcio dependiente, entre Calcineurina y PERK, involucrado en el Estrés de Retículo Endoplásmico. Ca2+ -dependent mechanism of interaction between Calcineurin and PERK involved in Endoplasmic Reticulum Stress.

El Estrés de Retículo Endoplásmico (RE) es inducido por la acumulación de proteínas sin plegar en el lumen de la organela. Esto se puede observar en diversas situaciones fisio-patológicas como durante una infección viral o en proceso isquémico. Además, contribuye a la base molecular de numerosas enfermedades ya sea índole metabólico (Fibrosis quística o Diabetes Miellitus) o neurodegenerativas como mal de Alzheimer o Parkinson (Mutat Res, 2005, 569). Para restablecer la homeostasis en la organela se activa una señal de transducción (UPR), cuya respuesta inmediata es la atenuación de la síntesis de proteína debido a la fosforilación de subunidad alpha del factor eucariótico de iniciación de translación (eIF2α) vía PERK. Esta es una proteína de membrana de RE que detecta estrés. Bajo condiciones normales, PERK está inactiva debido a la asociación de su dominio luminar con la chaperona BIP (Nat Cell Biol, 2000, 2: 326). Frente a una situación de estrés, la chaperona se disocia causando desinhibición. Recientemente, (Plos One 5: e11925) se observó, bajo condiciones de estrés, un aumento de Ca2+ citosólico y un rápido incremento de la expresión de calcineurina (CN), una fosfatasa citosólica dependiente de calcio, heterodimérica formada por una subunidad catalítica (CN-A) y una regulatoria (CN-B). Además, CN interacciona, sin intermediarios, con el dominio citosólico de PERK favoreciendo su trans-autofosforilación. Resultados preliminares indican que, astrocitos CNAβ-/- exhibieron, en condiciones basales, un mayor número de células muertas y de niveles de eIF2α fosforilado que los astrocitos CNAα-/-. Hipótesis: CNAβ/B interacciona con PERK cuando el Ca2+ citosólico esta incrementado luego de haberse inducido Estrés de RE, lo cual promueve dimerización y auto-fosforilación de la quinasa, acentuándose así la fosforilación de eIF2α e inhibición de la síntesis de proteínas. Esta activación citosólica de PERK colaboraría con la ya descrita, desinhibición luminal llevada cabo por BIP. Cuando el Ca2+ citosólico retorna a los niveles basales, PERK fosforila a CN, reduciendo su afinidad de unión y disociándose el complejo CN/PERK. Objetivo general: Definir las condiciones por las cuales CN interacciona con PERK y regula la fosforilación de eIF2α e inhibición de la síntesis de proteína. Objetivos específicos: I-Estudiar la diferencia de afinidades y dependencia de Ca2+, de las dos isoformas de CN (α y β) en su asociación con PERK. Además verificar la posible participación de la subunidad B de CN en esta interacción. II-Determinar si la auto-fosforilación de PERK es diferencialmente regulada por las dos isoformas de CN. III-Discernir la relación del estado de fosforilación de CN con su unión a PERK. IV-Determinar efectos fisiológicos de la interacción de CN-PERK durante la respuesta de Estrés de RE. Para llevar a cabo este proyecto se realizarán experimentos de biología molecular, interacción proteína-proteína, ensayos de fosforilación in vitro y un perfil de polisoma con astrocitos CNAβ-/- , CNA-/- y astrocitos controles. Se espera encontrar una mayor afinidad de unión a PERK de la isoforma β de CN y en condiciones donde la concentración de Ca2+ sea del orden micromolar e imite niveles del ión durante un estrés. Con respecto al estado de fosforilación de CN, debido a los resultados preliminares, donde solo se la encontró fosforilada en condiciones basales, se piensa que CN podría interactuar con mayor afinidad con PERK cuando CN se encuentre desfosforilada. Por último, se espera encontrar un aumento de eIF2α fosforilado y una acentuación de la atenuación de la síntesis de proteína como consecuencia de la mayor activación de PERK por su asociación con la isoforma β de CN en astrocitos donde el Estrés de RE se indujo por privación de oxigeno y glucosa. Estos experimentos permitirán avanzar en el estudio de una nueva función citoprotectora de CN recientemente descrita por nuestro grupo de trabajo y sus implicancias en un modelo de isquemia. The accumulation of unfolded proteins into the Endoplasmic Reticulum (ER) activates a signal transduction cascade called Unfolding Protein Response (UPR), which attempts to restore homeostasis in the organelle. (PKR)-like-ER kinase (PERK) is an early stress response transmembrane protein that is generally inactive due to its association with the chaperone BIP. During ER stress, BIP is tritrated by the unfolded protein, leading PERK activation and phosphorylation of eukaryotic initiation factor-2 alpha (eIF2alpha), which attenuates protein síntesis. If ER damage is too great and homeostasis is not restored within a certain period of time, an apoptotic response is elicited. We recently demonstrated a cytosolic Ca2+ increase in Xenopus oocytes after induce ER stress. Moreover, calcineurin A/B, a an heterotrimeric Ca2+ dependent phosphatases (CN-A/B), associates with PERK increasing its auto-phosphorylation and significantly enhancing cell viability. Preliminary results suggest that, CN-Aβ-/- knockout astrocytes exhibit a significant higher eIF2α phosphorylated level compared to CN-Aα-/- astrocytes. Our working hypothesis establishes that: CN binds to PERK when cytosolic Ca2+ is initially increased by ER stress, promoting dimerization and autophosphorylation, which leads to phosphorylation of elF2α and subsequently attenuation of protein translation. When cytosolic Ca2+ returns to resting levels, PERK phosphorylates CN, reducing its binding affinity so that the CN/PERK complex dissociates. The goal of this project is to determine the conditions by which CN binding to PERK attenuates protein translation during the ER stress response and subsequently, to determine how the interaction of CN with PERK is terminated when stress is removed. To perform this project is planed to do molecular biology experiments, pull down assays, in vitro phosphorylations and assess overall mRNA translation efficiency doing a polisome profile.