Proteolytic mechanisms of cell injury following glucose -oxygen deprivation in primary neuronal cultures

Researchers have historically emphasized the contribution of caspase-3 to apoptotic but not necrotic cell death, while calpain has been implicated primarily in necrosis and, to a lesser extent, in apoptosis. Activation of these proteases occurs in vivo following various CNS insults including ischemia. In addition, both necrotic and apoptotic cell death phenotypes are detected following ischemia. However, the contributions of calpain and caspase-3 to apoptotic and necrotic cell death phenotypes following CNS insults are relatively unexplored. To date, no study has examined the concurrent activation of calpain and caspase-3 in necrotic and apoptotic cell death phenotypes following any CNS insult. The present study employed oxygen-glucose deprivation (OGD) to determine the relative contributions of caspase-3 and calpain to apoptotic and necrotic cell death following OGD. Experiments characterized a model of OGD by evaluating cell viability and characterizing the cell death phenotypes following OGD in primary septo-hippocampal co-cultures. Furthermore, cell markers (NeuN and MAP2 or GFAP) assessed the effects of OGD on neuronal and astroglial viability, respectively. In addition, calpain and caspase-3 mediated proteolysis of α-spectrin was examined using Western blot techniques. Activation of these proteases in individual cells phenotypically characterized as apoptotic and necrotic was also evaluated by using antibodies specific for calpain or caspase-3 mediated breakdown products to α-spectrin. Administration of appropriate caspase-3 and calpain inhibitors also examined the effects of protease inhibition on cell death. OGD produced prominent expression of apoptotic cell death phenotypes primarily in neurons, with relatively little damage to astroglia. Although Western blot data suggested greater proteolysis of α-spectrin by calpain than caspase-3, co-activation of both proteases was usually detected in cells exhibiting apoptotic or necrotic cell death phenotypes. While inhibition of calpain and caspase-3 activity decreased LDH release following OGD, it was not clear whether this effect was also associated with a decrease in cell death and the appearance of apoptotic cell death phenotypes. These data demonstrate that both calpain and caspase-3 contribute to the expression of apoptotic cell death phenotypes following OGD, and that calpain could potentially have a larger role in the expression of apoptotic cell death than previously thought. ^

Electronic damage in quartz (c-SiO2) by MeV ion irradiations: Potentiality for optical waveguiding applications

The damage induced on quartz (c-SiO2) by heavy ions (F, O, Br) at MeV energies, where electronic stopping is dominant, has been investigated by RBS/C and optical methods. The two techniques indicate the formation of amorphous layers with an isotropic refractive index (n = 1.475) at fluences around 1014 cm−2 that are associated to electronic mechanisms. The kinetics of the process can be described as the superposition of linear (possibly initial Poisson curve) and sigmoidal (Avrami-type) contributions. The coexistence of the two kinetic regimes may be associated to the differential roles of the amorphous track cores and preamorphous halos. By using ions and energies whose maximum stopping power lies inside the crystal (O at 13 MeV, F at 15 MeV and F at 30 MeV) buried amorphous layer are formed and optical waveguides at the sample surface have been generated.

Intraply fracture of fiber-reinforced composites: microscopic mechanisms and modeling

The fracture behavior parallel to the fibers of an E-glass/epoxy unidirectional laminate was studied by means of three-point tests on notched beams. Selected tests were carried out within a scanning electron microscope to ascertain the damage and fracture micromechanisms upon loading. The mechanical behavior of the notched beam was simulated within the framework of the embedded cell model, in which the actual composite microstructure was resolved in front of the notch tip. In addition, matrix and interface properties were independently measured in situ using a nanoindentor. The numerical simulations very accurately predicted the macroscopic response of the composite as well as the damage development and crack growth in front of the notch tip, demonstrating the ability of the embedded cell approach to simulate the fracture behavior of heterogeneous materials. Finally, this methodology was exploited to ascertain the influence of matrix and interface properties on the intraply toughness.

Ionoluminescence on α-quartz: mechanisms and modeling

Ionoluminescence of α - quartz exhibits two dominant emission bands peaking at 1.9 eV. (NBOHCs) and 2.7 eV (STEs. The evolution of the red emission yield does not show a correlation with the concentrations of neither the NBOHC nor with that of other color centers. The blue emission yield closely follows the amorphization kinetics independently measured by RBS/C spectrometry. A simple theoretical model has been proposed; it assumes that the formation and recombination of STEs are the primary event and both, the light emissions and the lattice structural damage are a consequence this phenomenon. The model leads to several simple mathematical equations that can be used to simulate the IL yields and provide a reasonable fit to experimental kinetic data.

A continuum damage model characterization based on the soft tissue mesostructure

Material properties of soft tissues are highly conditioned by the hierarchical structure of this kind of composites. These collagen-based tissues present a complex framework of fibres, fibrils, tropocollagen molecules and amino-acids. As the structural mechanisms that control the degradation of soft tissues are related with the behaviour of its fundamental constituents, the relationship between the molecular and intermolecular properties and the tissue behaviour needs to be studied.

Atomistic modeling of Ge damage accumulation, amorphization and solid phase epitaxial regrowth

En los últimos años, el Ge ha ganado de nuevo atención con la finalidad de ser integrado en el seno de las existentes tecnologías de microelectrónica. Aunque no se le considera como un canddato capaz de reemplazar completamente al Si en el futuro próximo, probalemente servirá como un excelente complemento para aumentar las propiedades eléctricas en dispositivos futuros, especialmente debido a su alta movilidad de portadores. Esta integración requiere de un avance significativo del estado del arte en los procesos de fabricado. Técnicas de simulación, como los algoritmos de Monte Carlo cinético (KMC), proporcionan un ambiente atractivo para llevar a cabo investigación y desarrollo en este campo, especialmente en términos de costes en tiempo y financiación. En este estudio se han usado, por primera vez, técnicas de KMC con el fin entender el procesado “front-end” de Ge en su fabricación, específicamente la acumulación de dañado y amorfización producidas por implantación iónica y el crecimiento epitaxial en fase sólida (SPER) de las capas amorfizadas. Primero, simulaciones de aproximación de clisiones binarias (BCA) son usadas para calcular el dañado causado por cada ión. La evolución de este dañado en el tiempo se simula usando KMC sin red, o de objetos (OKMC) en el que sólamente se consideran los defectos. El SPER se simula a través de una aproximación KMC de red (LKMC), siendo capaz de seguir la evolución de los átomos de la red que forman la intercara amorfo/cristalina. Con el modelo de amorfización desarrollado a lo largo de este trabajo, implementado en un simulador multi-material, se pueden simular todos estos procesos. Ha sido posible entender la acumulación de dañado, desde la generación de defectos puntuales hasta la formación completa de capas amorfas. Esta acumulación ocurre en tres regímenes bien diferenciados, empezando con un ritmo lento de formación de regiones de dañado, seguido por una rápida relajación local de ciertas áreas en la fase amorfa donde ambas fases, amorfa y cristalina, coexisten, para terminar en la amorfización completa de capas extensas, donde satura el ritmo de acumulación. Dicha transición ocurre cuando la concentración de dañado supera cierto valor límite, el cual es independiente de las condiciones de implantación. Cuando se implantan los iones a temperaturas relativamente altas, el recocido dinámico cura el dañado previamente introducido y se establece una competición entre la generación de dañado y su disolución. Estos efectos se vuelven especialmente importantes para iones ligeros, como el B, el cual crea dañado más diluido, pequeño y distribuido de manera diferente que el causado por la implantación de iones más pesados, como el Ge. Esta descripción reproduce satisfactoriamente la cantidad de dañado y la extensión de las capas amorfas causadas por implantación iónica reportadas en la bibliografía. La velocidad de recristalización de la muestra previamente amorfizada depende fuertemente de la orientación del sustrato. El modelo LKMC presentado ha sido capaz de explicar estas diferencias entre orientaciones a través de un simple modelo, dominado por una única energía de activación y diferentes prefactores en las frecuencias de SPER dependiendo de las configuraciones de vecinos de los átomos que recristalizan. La formación de maclas aparece como una consecuencia de esta descripción, y es predominante en sustratos crecidos en la orientación (111)Ge. Este modelo es capaz de reproducir resultados experimentales para diferentes orientaciones, temperaturas y tiempos de evolución de la intercara amorfo/cristalina reportados por diferentes autores. Las parametrizaciones preliminares realizadas de los tensores de activación de tensiones son también capaces de proveer una buena correlación entre las simulaciones y los resultados experimentales de velocidad de SPER a diferentes temperaturas bajo una presión hidrostática aplicada. Los estudios presentados en esta tesis han ayudado a alcanzar un mejor entendimiento de los mecanismos de producción de dañado, su evolución, amorfización y SPER para Ge, además de servir como una útil herramienta para continuar el trabajo en este campo. In the recent years, Ge has regained attention to be integrated into existing microelectronic technologies. Even though it is not thought to be a feasible full replacement to Si in the near future, it will likely serve as an excellent complement to enhance electrical properties in future devices, specially due to its high carrier mobilities. This integration requires a significant upgrade of the state-of-the-art of regular manufacturing processes. Simulation techniques, such as kinetic Monte Carlo (KMC) algorithms, provide an appealing environment to research and innovation in the field, specially in terms of time and funding costs. In the present study, KMC techniques are used, for the first time, to understand Ge front-end processing, specifically damage accumulation and amorphization produced by ion implantation and Solid Phase Epitaxial Regrowth (SPER) of the amorphized layers. First, Binary Collision Approximation (BCA) simulations are used to calculate the damage caused by every ion. The evolution of this damage over time is simulated using non-lattice, or Object, KMC (OKMC) in which only defects are considered. SPER is simulated through a Lattice KMC (LKMC) approach, being able to follow the evolution of the lattice atoms forming the amorphous/crystalline interface. With the amorphization model developed in this work, implemented into a multi-material process simulator, all these processes can be simulated. It has been possible to understand damage accumulation, from point defect generation up to full amorphous layers formation. This accumulation occurs in three differentiated regimes, starting at a slow formation rate of the damage regions, followed by a fast local relaxation of areas into the amorphous phase where both crystalline and amorphous phases coexist, ending in full amorphization of extended layers, where the accumulation rate saturates. This transition occurs when the damage concentration overcomes a certain threshold value, which is independent of the implantation conditions. When implanting ions at relatively high temperatures, dynamic annealing takes place, healing the previously induced damage and establishing a competition between damage generation and its dissolution. These effects become specially important for light ions, as B, for which the created damage is more diluted, smaller and differently distributed than that caused by implanting heavier ions, as Ge. This description successfully reproduces damage quantity and extension of amorphous layers caused by means of ion implantation reported in the literature. Recrystallization velocity of the previously amorphized sample strongly depends on the substrate orientation. The presented LKMC model has been able to explain these differences between orientations through a simple model, dominated by one only activation energy and different prefactors for the SPER rates depending on the neighboring configuration of the recrystallizing atoms. Twin defects formation appears as a consequence of this description, and are predominant for (111)Ge oriented grown substrates. This model is able to reproduce experimental results for different orientations, temperatures and times of evolution of the amorphous/crystalline interface reported by different authors. Preliminary parameterizations for the activation strain tensors are able to also provide a good match between simulations and reported experimental results for SPER velocities at different temperatures under the appliance of hydrostatic pressure. The studies presented in this thesis have helped to achieve a greater understanding of damage generation, evolution, amorphization and SPER mechanisms in Ge, and also provide a useful tool to continue research in this field.

Oxidative damage during aging targets mitochondrial aconitase

The mechanisms that cause aging are not well understood. The oxidative stress hypothesis proposes that the changes associated with aging are a consequence of random oxidative damage to biomolecules. We hypothesized that oxidation of specific proteins is critical in controlling the rate of the aging process. Utilizing an immunochemical probe for oxidatively modified proteins, we show that mitochondrial aconitase, an enzyme in the citric acid cycle, is a specific target during aging of the housefly. The oxidative damage detected immunochemically was paralleled by a loss of catalytic activity of aconitase, an enzyme activity that is critical in energy metabolism. Experimental manipulations which decrease aconitase activity should therefore cause a decrease in life-span. This expected decrease was observed when flies were exposed to hyperoxia, which oxidizes aconitase, and when they were given fluoroacetate, an inhibitor of aconitase. The identification of a specific target of oxidative damage during aging allows for the assessment of the physiological age of a specific individual and provides a method for the evaluation of treatments designed to affect the aging process.

Identification of the prooxidant site of human ceruloplasmin: A model for oxidative damage by copper bound to protein surfaces

Free transition metal ions oxidize lipids and lipoproteins in vitro; however, recent evidence suggests that free metal ion-independent mechanisms are more likely in vivo. We have shown previously that human ceruloplasmin (Cp), a serum protein containing seven Cu atoms, induces low density lipoprotein oxidation in vitro and that the activity depends on the presence of a single, chelatable Cu atom. We here use biochemical and molecular approaches to determine the site responsible for Cp prooxidant activity. Experiments with the His-specific reagent diethylpyrocarbonate (DEPC) showed that one or more His residues was specifically required. Quantitative [14C]DEPC binding studies indicated the importance of a single His residue because only one was exposed upon removal of the prooxidant Cu. Plasmin digestion of [14C]DEPC-treated Cp (and N-terminal sequence analysis of the fragments) showed that the critical His was in a 17-kDa region containing four His residues in the second major sequence homology domain of Cp. A full length human Cp cDNA was modified by site-directed mutagenesis to give His-to-Ala substitutions at each of the four positions and was transfected into COS-7 cells, and low density lipoprotein oxidation was measured. The prooxidant site was localized to a region containing His426 because CpH426A almost completely lacked prooxidant activity whereas the other mutants expressed normal activity. These observations support the hypothesis that Cu bound at specific sites on protein surfaces can cause oxidative damage to macromolecules in their environment. Cp may serve as a model protein for understanding mechanisms of oxidant damage by copper-containing (or -binding) proteins such as Cu, Zn superoxide dismutase, and amyloid precursor protein.

UV-damage-mediated induction of homologous recombination in Arabidopsis is dependent on photosynthetically active radiation

Plants are continuously subjected to UV-B radiation (UV-B; 280–320 nm) as a component of sunlight causing damage to the genome. For elimination of DNA damage, a set of repair mechanisms, mainly photoreactivation, excision, and recombination repair, has evolved. Whereas photoreactivation and excision repair have been intensely studied during the last few years, recombination repair, its regulation, and its interrelationship with photoreactivation in response to UV-B-induced DNA damage is still poorly understood. In this study, we analyzed somatic homologous recombination in a transgenic Arabidopsis line carrying a β-glucuronidase gene as a recombination marker and in offsprings of crosses of this line with a photolyase deficient uvr2–1 mutant. UV-B radiation stimulated recombination frequencies in a dose-dependent manner correlating linearly with cyclobutane pyrimidine dimer (CPD) levels. Genetic deficiency for CPD-specific photoreactivation resulted in a drastic increase of recombination events, indicating that homologous recombination might be directly involved in eliminating CPD damage. UV-B irradiation stimulated recombination mainly in the presence of photosynthetic active radiation (400–700 nm) irrespective of photolyase activities. Our results suggest that UV-B-induced recombination processes may depend on energy supply derived from photosynthesis.

DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination

Proceedings of the National Academy of Sciences Colloquium on the roles of homologous recombination in DNA replication are summarized. Current findings in experimental systems ranging from bacteriophages to mammalian cell lines substantiate the idea that homologous recombination is a system supporting DNA replication when either the template DNA is damaged or the replication machinery malfunctions. There are several lines of supporting evidence: (i) DNA replication aggravates preexisting DNA damage, which then blocks subsequent replication; (ii) replication forks abandoned by malfunctioning replisomes become prone to breakage; (iii) mutants with malfunctioning replisomes or with elevated levels of DNA damage depend on homologous recombination; and (iv) homologous recombination primes DNA replication in vivo and can restore replication fork structures in vitro. The mechanisms of recombinational repair in bacteriophage T4, Escherichia coli, and Saccharomyces cerevisiae are compared. In vitro properties of the eukaryotic recombinases suggest a bigger role for single-strand annealing in the eukaryotic recombinational repair.

Traumatic brain damage prevented by the non-N-methyl-D-aspartate antagonist 2,3-dihydroxy-6-nitro-7-sulfamoylbenzo[f] quinoxaline.

The mechanisms of neuronal degeneration following traumatic head injury are not well understood and no adequate treatment is currently available for the prevention of traumatic brain damage in humans. Traumatic head injury leads to primary (at impact) and secondary (distant) damage to the brain. Mechanical percussion of the rat cortex mimics primary damage seen after traumatic head injury in humans; no animal model mimicking the secondary damage following traumatic head injury has yet been established. Rats subjected to percussion trauma of the cortex showed primary damage in the cortex and secondary damage in the hippocampus. Morphometric analysis demonstrated that both cortical and hippocampal damage was mitigated by pretreatment with either the N-methyl-D-aspartate (NMDA) antagonist 3-((+/-)- 2-carboxypiperazin-4-yl)-propyl-1-phosphonate (CPP) or the non-NMDA antagonist 2,3-dihydroxy-6-nitro-7-sulfamoyl-benzo[f]quinoxaline (NBQX). Neither treatment prevented primary damage in the cortex when therapy was started after trauma. Surprisingly, delayed treatment of rats with NBQX, but not with CPP, beginning between 1 and 7 hr after trauma prevented hippocampal damage. No protection was seen when therapy with NBQX was started 10 hr after trauma. These data indicate that both NMDA- and non-NMDA-dependent mechanisms contribute to the development of primary damage in the cortex, whereas non-NMDA mechanisms are involved in the evolution of secondary damage in the hippocampus in rats subjected to traumatic head injury. The wide therapeutic time-window documented for NBQX suggests that antagonism at non-NMDA receptors may offer a novel therapeutic approach for preventing deterioration of the brain after head injury.

Discovery of adrenomedullin in rat ischemic cortex and evidence for its role in exacerbating focal brain ischemic damage.

Focal brain ischemia is the most common event leading to stroke in humans. To understand the molecular mechanisms associated with brain ischemia, we applied the technique of mRNA differential display and isolated a gene that encodes a recently discovered peptide, adrenomedullin (AM), which is a member of the calcitonin gene-related peptide (CGRP) family. Using the rat focal stroke model of middle cerebral artery occlusion (MCAO), we determined that AM mRNA expression was significantly increased in the ischemic cortex up to 17.4-fold at 3 h post-MCAO (P < 0.05) and 21.7-fold at 6 h post-MCAO (P < 0.05) and remained elevated for up to 15 days (9.6-fold increase; P < 0.05). Immunohistochemical studies localized AM to ischemic neuronal processes, and radioligand (125I-labeled CGRP) displacement revealed high-affinity (IC50 = 80.3 nmol) binding of AM to CGRP receptors in brain cortex. The cerebrovascular function of AM was studied using synthetic AM microinjected onto rat pial vessels using a cranial window or applied to canine basilar arteries in vitro. AM, applied abluminally, produced dose-dependent relaxation of preconstricted pial vessels (P < 0.05). Intracerebroventricular (but not systemic) AM administration at a high dose (8 nmol), prior to and after MCAO, increased the degree of focal ischemic injury (P < 0.05). The ischemia-induced expression of both AM mRNA and peptide in ischemic cortical neurons, the demonstration of the direct vasodilating effects of the peptide on cerebral vessels, and the ability of AM to exacerbate ischemic brain damage suggests that AM plays a significant role in focal ischemic brain injury.

Characterization of the instability mechanisms affecting slopes on carbonatic Flysch: Alicante (SE Spain), case study

The studied Flysch sequence of Alicante occupies a widely populated area crossed by main communication routes. The slopes existing on this area usually suffer slope instabilities that cause substantial damage and a very high maintenance cost. In order to assess the type of instability mechanisms affecting these heterogeneous carbonatic slopes, in this paper a wide inventory of 194 Flysch rock slopes has been performed, reporting the existing lithologies, their competence and their relative arrangement and the geometrical relationship between bedding and the slope and the associated instability mechanism. All these data have been jointly used for performing an instability mechanisms characterization. For systematically characterizing the wide type of complex rock exposures existing in the study area, they are divided into basic units referred as lithological pattern columns to which the different observed instability mechanisms are associated. Inventoried instability mechanisms are diverse and sometimes are combined with each other. Rockfalls are a very common instability mechanism associated to the differential weathering and sapping of the marly lithologies which are present in a wide number of geometrical combinations. The other instability mechanisms closely depend on the combination of the geometrical and lithological parameters. Therefore, this work provides a new basic tool which can be easily used during preliminary project stages for knowing the instability mechanisms which can affect rock slopes excavated on carbonatic Flysch heterogeneous geological formations.

Subsidence damage assessment of a Gothic church using differential interferometry and field data

The Santas Justa and Rufina Gothic church (fourteenth century) has suffered several physical, mechanical, chemical, and biochemical types of pathologies along its history: rock alveolization, efflorescence, biological activity, and capillary ascent of groundwater. However, during the last two decades, a new phenomenon has seriously affected the church: ground subsidence caused by aquifer overexploitation. Subsidence is a process that affects the whole Vega Baja of the Segura River basin and consists of gradual sinking in the ground surface caused by soil consolidation due to a pore pressure decrease. This phenomenon has been studied by differential synthetic aperture radar interferometry techniques, which illustrate settlements up to 100 mm for the 1993–2009 period for the whole Orihuela city. Although no differential synthetic aperture radar interferometry information is available for the church due to the loss of interferometric coherence, the spatial analysis of nearby deformation combined with fieldwork has advanced the current understanding on the mechanisms that affect the Santas Justa and Rufina church. These results show the potential interest and the limitations of using this remote sensing technique as a complementary tool for the forensic analysis of building structures.

Mechanisms of negative regulation of inflammasome activation

Thesis (Ph.D.)--University of Washington, 2016-06