Concepts, perspectives and implications of a hybrid system made of nucleic acids biopolymers and hydroxyapatite mineral

The origin of building blocks of life and how life thrived on Earth remains a topic of high interest for researchers of the Origin of Life. In this thesis, we deal with concepts, perspectives and implications of the system termed hydroxyolite, a combination of outstanding biopolymers (nucleic acids such as DNA and RNA) and an exceptional mineral (hydroxyapatite). First we study, based on Revilla et al. (2013) and Bertran et al. (2014), how hydroxyapatite forms crystals able to encapsulate DNA or RNA when nucleic acids are used as a nucleating template. Later, in Bertran et al., (2016), we reported the mechanism of how the encapsulated nucleic acid is released to the surroundings when environmental conditions change, for instance becoming more acidic. As a consequence, we postulated that DNA existing in cells can be encapsulated and protected by hydroxyapatite against environmental attacks (i.e. poisonous gases, gamma radiation or enzymatic degradation) until they change, making feasible the reintroduction of nucleic acids in the mainstream of life. We hypothesized about the implications of such a system in the early history of life when mass extinction events occurred on Earth (Turon et al., 2015). Moreover, we extended the hydroxyolite concept, borrowed from the materials chemistry, to other disciplines such as paleontology, biology, biotechnology and medicine by considering hydroxyolites as equivalents to non-viral vectors that can introduce and release DNA into a cell (transfection). Such nucleic acid triggers the expression of foreign proteins if released in the cytosol or might be recombined with cell genome when DNA is released in the target cell nucleus. In the second part of the thesis, we studied the hydroxyolite system from a complementary perspective. We speculate about the consequences of being hydroxyapatite the first actor and not the nucleic acid. We propose that hydroxyapatite might act as an inorganic mold if considered as a catalytic substrate that facilitates the synthesis of simple organic molecules as the building blocks of life. Thus, we identified a prebiotic scenario, a volcanic eruption under lightning, where a phenomenon known as dirty storm usually occurs under certain conditions. Hydroxyapatite is known in nature to be part of igneous rocks and volcanic ash in small but significant concentrations. We replicated in the laboratory such extreme conditions by developing a thermally and electrically stimulated polarization. A process performed at 1000 ºC and under a difference of potential of 300 kV·m-1, to obtain permanently polarized hydroxyapatite (Turon et al., 2016; PCT/EP2017/069437) that turned out to be an enhanced catalyst compared to hydroxyapatite able to fix nitrogen and carbon from a gas mixture of N2, CO2 and CH4 (Rivas et al., 2018). The catalyst, under UV light, converts them into amino acids (Glycine and D/L-Alanine) and small organic molecules by means of a new inorganic photosynthetic process. In this work, we develop an integrative prebiotic model that describes how simple molecules might be synthesized from mildly reducing atmospheres by combining previous models such as volcanos as giant reactors, minerals as catalysts and photochemical reactions in the atmosphere under prebiotic sun light. All of them under the framework of a prebiotic inorganic photosynthesis, a process that might be considered the corner stone of the rise of the building blocks of life.L’origen de les molècules que van donar lloc a la vida i com la vida va prosperar a la Terra segueix essent un tema del màxim interès pels investigadors de l’origen de la vida. En aquesta tesi, discutim conceptes, perspectives de futur i implicacions del sistema que hem anomenat hidroxiolita (hydroxyolite), una combinació de biopolímers amb característiques molt especials (àcids nucleics com l’ADN i l’ARN) i un mineral excepcional (hidroxiapatita). En primer lloc, en els treballs Revilla et al., (2013) i Bertran et al., (2014) estudiem com els cristalls d’hidroxiapatita tenen la capacitat d’encapsular ADN o ARN quan l’àcid nucleic es comporta com agent nucleant. Reportem com l’àcid nucleic prèviament encapsulat pot ser alliberat si les condicions ambientals canvien, per exemple tornant-se lleugerament més àcides (Bertran et al., 2016). Com a conseqüència, postulem que l’ADN existent a les cèl·lules pot ser encapsulat per la hidroxiapatita protegint-lo contra atacs de l’entorn (per exemple, la influència de gasos tòxics, la radiació gamma o la degradació enzimàtica) fins que les condicions externes canvien i els àcids nucleics poder ser reintroduïts en el torrent principal de la vida. Discutim les implicacions d’aquest sistema híbrid a la història primitiva de la vida a la Terra, quan van ocórrer les grans catàstrofes que van donar lloc a extincions massives d’éssers vius. Tanmateix, estenem el concepte d’hidroxiolita a altres disciplines com la paleontologia, la biologia cel·lular, la biotecnologia i la medicina, considerant les hidroxiolites com a vectors no virals que poden introduir i alliberar ADN dins una cèl·lula (transfecció). Aquest àcid nucleic, si s’allibera en el citosol pot desencadenar l’expressió de proteïnes codificades en l’ADN introduït, o si s’allibera en el nucli podria recombinar-se amb el propi ADN de la cèl·lula diana de manera transitòria o permanent. A la segona part de la tesi, estudiem el sistema hidroxiolita des d’una perspectiva complementària. Especulem sobre les conseqüències de ser la hidroxiapatita l’actor principal del sistema i no l’àcid nucleic. Proposem que la hidroxiapatita pot actuar com un motlle inorgànic si es comporta com a substrat catalític que facilita la síntesi de molècules orgàniques, com les molècules que van donar lloc a la vida. A partir d’aquest concepte hem identificat un escenari prebiòtic, una erupció volcànica acompanyada de descàrregues elèctriques, fenomen que succeeix amb certa freqüència en funció de les característiques de l’erupció. La hidroxiapatita a la natura és coneguda per formar part de la composició de roques ígnies i de la cendra volcànica en petites però significatives quantitats. Al laboratori hem replicat aquestes condicions extremes i hem desenvolupat un procés de polarització mitjançant estimulació elèctrica i tèrmica, aplicant 1000 ºC i una diferència de potencial de 300 kV·m-1, que dóna com a resultat hidroxiapatita polaritzada permanentment que converteix el mineral en un catalitzador extraordinari comparat amb la hidroxiapatita i que té la capacitat de fixar nitrogen i carboni a partir d’una mescla de gasos composada per N2, CO2 i CH4 en presència d’aigua. El catalitzador, sota il·luminació de llum UV facilita la conversió d’aquests gasos en aminoàcids (Glicina i D/L-Alanina) i en molècules orgàniques simples a través d’un procés fotosintètic inorgànic. En aquest treball, desenvolupem un model prebiòtic que descriu com molècules senzilles van poder ser sintetitzades a partir d’atmosferes suaument reductores combinant models prebiòtics previs (volcans que es comporten com grans reactors, reaccions fotoquímiques que succeeixen a l’atmosfera sota el sol prebiòtic i minerals que actuen com a catalitzadors) sota el marc de la fotosíntesi inorgànica prebiòtica, un procés que podria ser considerat la pedra angular de l’aparició de les molècules que van donar lloc a la vida.El origen de las moléculas que dieron lugar a la vida y como la vida prosperó en la Tierra sigue siendo un tema del máximo interés para los investigadores del Origen de la Vida. En esta tesis discutimos conceptos, perspectivas de futuro e implicaciones del sistema que hemos denominado hidroxiolita (hydroxyolite), una combinación de biopolímeros con características muy especiales (ácidos nucleicos tales como el ADN y el ARN) y un mineral excepcional (hidroxiapatita). En primer lugar, en nuestros trabajos Revilla et al. (2013) y Bertrán et al. (2014) estudiamos como los cristales de hidroxiapatita tienen la capacidad de encapsular ADN o ARN cuando el ácido nucleico se comporta como un agente nucleante. A continuación, reportamos como el ácido nucleico previamente encapsulado puede ser liberado cuando las condiciones ambientales cambian, por ejemplo, cuando se vuelven ligeramente más ácidas (Bertrán et al., 2016). A consecuencia, postulamos que el ADN existente en las células puede ser encapsulado por la hidroxiapatita protegiéndolo contra ataques del entorno (por ejemplo, la influencia de gases tóxicos, la radiación gamma o la degradación enzimática) hasta que cambian las condiciones externas y los ácidos nucleicos pueden ser reintroducidos de nuevo en el torrente principal de la vida. A continuación, discutimos las implicaciones de este sistema híbrido en la historia primitiva de la vida en la Tierra, cuando ocurrieron las grandes catástrofes que dieron lugar a extinciones masivas de seres vivos (Turon et al., 2015). Asimismo, extendemos el concepto hidroxiolita, acuñado en la ciencia de materiales, a otras disciplinas como la paleontología, la biología celular, la biotecnología y la medicina, considerando las hidroxiolitas como vectores no virales que pueden introducir y liberar ADN dentro de una célula (transfección). Este ácido nucleico, si es liberado en el citosol puede desencadenar la expresión de proteínas codificadas en el ADN introducido, o si se libera en el núcleo podría recombinarse con el propio ADN de la célula diana de forma transitoria o permanente. En la segunda parte de la tesis, estudiamos el sistema hidroxiolita desde una perspectiva complementaria. Especulamos sobre las consecuencias de ser la hidroxiolita el actor principal y no el ácido nucleico. Proponemos que la hidroxiolita puede actuar como un molde inorgánico si se comporta como un sustrato catalítico que facilita la síntesis de moléculas orgánicas, como las moléculas que dieron lugar a la vida. Hemos identificado un escenario prebiótico basado en una erupción volcánica con descargas eléctricas, fenómeno que ocurre con cierta frecuencia en función de las características de la erupción. La hidroxiapatita es conocida en la naturaleza por formar parte de la composición de rocas ígneas y ceniza volcánica en bajas pero significativas concentraciones. Hemos replicado en el laboratorio estas condiciones extremas y hemos desarrollado un proceso de polarización mediante estimulación térmica y eléctrica, aplicando 1000ºC y una diferencia de potencial de 300 kV·m-1, que da como resultado hidroxiapatita permanentemente polarizada (Turón et al, 2016; PCT/EP2017/069437). Este proceso convierte el mineral en un catalizador extraordinario comparado con la hidroxiapatita y tiene la capacidad de fijar nitrógeno y carbono a partir de una mezcla de gases compuesta por N2, CO2 y CH4 (Rivas et al., 2018) en presencia de agua. El catalizador, bajo iluminación de luz UV, facilita la conversión de estos gases en aminoácidos (Glicina y D/L-Alanina) y en ácidos orgánicos simples a través de un proceso de fotosíntesis inorgánica. En este trabajo desarrollamos un modelo prebiótico que describe como moléculas sencillas pudieron ser sintetizadas a partir de atmósferas suavemente reductores combinando modelos prebióticos ya existentes (volcanes que se comportan grandes reactores, reacciones fotoquímicas que ocurren en la atmosfera bajo el sol prebiótico y minerales que actúan como catalizadores) bajo el marco de una fotosíntesis prebiótica inorgánica, un proceso que podría ser considerado la piedra angular en la que se basó la aparición de las moléculas que dieron lugar a la vida.Postprint (published version

Hydroxyapatite-based biphasic catalysts with plasticity properties and its potential in carbon dioxide fixation

The design of catalysts with controlled selectivity at will, also known as catalytic plasticity, is a very attractive approach for the recycling of carbon dioxide (CO2). In this work, we study how catalytically active hydroxyapatite (HAp) and brushite (Bru) interact synergistically, allowing the production of formic acid or acetic acid depending on the HAp/Bru ratio in the catalyst. Raman, wide angle X-ray scattering, X-ray photoelectron spectroscopy, scanning electron microscopy and electrochemical impedance spectroscopy studies, combined with an exhaustive revision of the crystalline structure of the catalyst at the atomic level, allowed to discern how the Bru phase can be generated and stabilized at high temperatures. Results clearly indicate that the presence of OH– groups to maintain the crystalline structural integrity in conjunction with Ca2+ ions less bonded to the lattice fixate carbon into C1, C2 and C3 molecules from CO2 and allow the evolution from formic to acetic acid and acetone. In this way, the plasticity of the HAp-Bru system is demonstrated, representing a promising green alternative to the conventional metal-based electrocatalysts used for CO2 fixation. Thus, the fact that no electric voltage is necessary for the CO2 reduction has a very favorable impact in the final energetic net balance of the carbon fixation reaction. © 202

Computer simulations on oxidative stress-induced reactions in SARS-CoV-2 spike glycoprotein: a multi-scale approach

Oxidative stress, which occurs when an organism is exposed to an adverse stimulus that results in a misbalance of antioxidant and pro-oxidants species, is the common denominator of diseases considered as a risk factor for SARS-CoV-2 lethality. Indeed, reactive oxygen species caused by oxidative stress have been related to many virus pathogenicity. In this work, simulations have been performed on the receptor binding domain of SARS-CoV-2 spike glycoprotein to study what residues are more susceptible to be attacked by ·OH, which is one of the most reactive radicals associated to oxidative stress. The results indicate that isoleucine (ILE) probably plays a crucial role in modification processes driven by radicals. Accordingly, QM/MM-MD simulations have been conducted to study both the ·OH-mediated hydrogen abstraction of ILE residues and the induced modification of the resulting ILE radical through hydroxylation or nitrosylation reactions. All in all, in silico studies show the importance of the chemical environment triggered by oxidative stress on the modifications of the virus, which is expected to help for foreseeing the identification or development of antioxidants as therapeutic drugs. Graphic abstrac

Polarized hydroxyapatite: wew insights and future perspectives through systematic electrical characterization at the interface

Design of hydroxyapatite (HAp) with customized electrical properties is of special interest for developing technological and biomedical applications with new improved functionalities. Polarized HAp, which is obtained by applying an external electric voltage at high temperature, has been successfully shown to be an alternative to doped-HAp that is limited by the biocompatibility of the dopants used. However, many aspects about such new material remain scarcely studied, as for example the relationship between the polarization conditions and the resultant electrical enhancement, hinder a solid progress in its application. In this work, polarized HAp has been extensively characterized using electrochemical impedance spectroscopy by means of proposing a unified electrical equivalent circuit model with physical sense. This allows to explain the properties of such material by separating the bulk and the interface contributions. Moreover, the limits of the polarization mechanism have been explored, enabling a precise control on the electrical resistivity of polarized HAp above or below the intrinsic resistivity of nonpolarized HAp. Overall, necessary insights on the polarization treatment have been reported, opening an appealing avenue for generating new biomedical and technological applications based on dopant-free polarized HAp.Peer ReviewedPostprint (published version

Regulating the superficial vacancies and OH- orientations on polarized hydroxyapatite electrocatalysts

Smart designs of hydroxyapatite (HAp) materials with customized electrical properties are drawing increasing attention for their wide range of potential applications. Such enhanced electrical properties directly arise from the number and orientation of OH- groups in the HAp lattice. Although different polarization treatments have been proposed to enhance the final conductivity by generating vacancies at high temperatures and imposing specific OH- orientations through electric voltages, no direct measurement showing the evolution that OH- groups undergo has been described yet. In this article, the first direct empirical observation that allows the characterization of both the generation of vacancies and the polarization of OH- groups is reported. The mechanisms behind the electrical enhancement are elucidated allowing to distinguish between charge accumulation at the crystal grains, which is due to the formed vacancies, and charge accumulation in the boundaries of particles. In addition, a linear dependence between the number of vacancies and the superficial charge is observed. Therefore, it is demonstrated that the charge accumulation at the micrometric grain boundaries has a great impact on the catalytic properties of the thermally stimulated polarized HAp. These results will be used for further optimization of the catalyst properties.Peer ReviewedPostprint (author's final draft

On the feasibility of the computational modelling of the endoluminal vacuum-assisted closure of an oesophageal anastomotic leakage

Endoluminal vacuum-assisted closure (E-VAC) is a promising therapy to treat anastomotic leakages of the oesophagus and bowel which are associated with high morbidity and mortality rates. An open-pore polyurethane foam is introduced into the leakage cavity and connected to a device that applies a suction pressure to accelerate the closure of the defect. Computational analysis of this healing process can advance our understanding of the biomechanical mechanisms at play. To this aim, we use a dual-stage finite-element analysis in which (i) the structural problem addresses the cavity reduction caused by the suction and (ii) a new constitutive formulation models tissue healing via permanent deformations coupled to a stiffness increase. The numerical implementation in an in-house code is described and a qualitative example illustrates the basic characteristics of the model. The computational model successfully reproduces the generic closure of an anastomotic leakage cavity, supporting the hypothesis that suction pressure promotes healing by means of the aforementioned mechanisms. However, the current framework needs to be enriched with empirical data to help advance device designs and treatment guidelines. Nonetheless, this conceptual study confirms that computational analysis can reproduce E-VAC of anastomotic leakages and establishes the bases for better understanding the mechanobiology of anastomotic defect healing

A flexible, smart and self-evolving actuator based on polypropylene mesh for hernia repair and a thermo-sensitive gel

Here, a smart mesh actuator, able to self-evolve under temperature and humidity control,has been developed. Thermo-responsive poly(N-isopropylacrylamide) (PNIPAAm)-based materialsare widely appliedin biomedical field owingto theirexcellent biocompatibility and abrupt conformational change at a critical temperature very close to that of human body(~32 °C) [1-2]. The actuator is based on PNIPAAmgrafted on a commercial polypropylene (PP)mesh used for hernia repair[3].Flexible devices composed of PP-g-PNIPAAm arranged inmonolayer (one layer of PNIPAAm) and bilayer (two layers of PNIPAAm) conformationswere synthesized. The microstructureof the gel chains (chain length measurements) and the macromotion(unfolding angle observations) behavior of the composite mesh in water and air at different temperatures were studied. The motion is affected by the amount and the position of the gel (upper fibers or among them) and by the crosslinking degree. For the first time,a self-evolving motion sensor based on commercial hernia repair mesh has beenproduced by using a biocompatible hydrogel. The strategy can be easily extrapolated to complex mesh architecturesPostprint (published version

The business foundations of social economic progress

We revisit the recently revived concept of social economic progress. We take a microeconomic perspective and address economic progress where it originates, with value creation at individual businesses. We begin with a brief history of thought on the concept. We continue by analyzing how a business creates private value through productivity growth, which is a necessary but not sufficient condition for a business to create social value. We then adopt an analytical approach to value creation from the perspective of a business, by analyzing how the creation of private value has implications for the distribution of income and creates social costs and benefits. We argue that a business creates social value, thereby contributing to social economic progress, only if it creates private value, it distributes the value it creates in a balanced way, and it generates social benefits having greater value than the value of the social costs it generates

Incorporation of functionalized calcium phosphate nanoparticles in living cells

Intracellular calcium (Ca2+) is a key signaling element that is involved in a great variety of fundamental biological processes. Thus, Ca2+ deregulation would be involved in the cancer cell progression and damage of mitochondrial membrane and DNA, which lead to apoptosis and necrosis. In this study, we have prepared amorphous calcium phosphate nanoparticles (ACP NPs) for studied their incorporation by endocytosis or electroporation to epithelial, endothelial and fibroblast cells (MCF-7, HUVEC and COS-1 cells, respectively). Our results showed that internalized ACP NPs have cytotoxic effects as a consequence of the increase of the intracellular calcium content. The endocytosis pathways showed a greater cytotoxic effect since calcium ions could easily be released from the nanoparticles and be accumulated in the lysosomes and mitochondria. In addition, the cytotoxic effect could be reversed when calcium ion was chelated with ethylene glycol-bis(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA). Modification of ACP NPs by coating with different compounds based on phosphates was also evaluated. The results indicated a reduction of the cytotoxic effect, in the order polyphosphate¿¿COS-1¿>¿MCF-7. The greater cytotoxic effect caused by the increase of intracellular calcium that is observed in normal cells and the greater resistance of cancer cells suggests new perspectives for cancer research.Peer ReviewedPostprint (published version