Structurally robust biological networks

Background: The molecular circuitry of living organisms performs remarkably robust regulatory tasks, despite the often intrinsic variability of its components. A large body of research has in fact highlighted that robustness is often a structural property of biological systems. However, there are few systematic methods to mathematically model and describe structural robustness. With a few exceptions, numerical studies are often the preferred approach to this type of investigation. Results: In this paper, we propose a framework to analyze robust stability of equilibria in biological networks. We employ Lyapunov and invariant sets theory, focusing on the structure of ordinary differential equation models. Without resorting to extensive numerical simulations, often necessary to explore the behavior of a model in its parameter space, we provide rigorous proofs of robust stability of known bio-molecular networks. Our results are in line with existing literature. Conclusions: The impact of our results is twofold: on the one hand, we highlight that classical and simple control theory methods are extremely useful to characterize the behavior of biological networks analytically. On the other hand, we are able to demonstrate that some biological networks are robust thanks to their structure and some qualitative properties of the interactions, regardless of the specific values of their parameters

Design, modeling and synthesis of an in vitro transcription rate regulatory circuit

This paper describes the design, modeling and realization of a synthetic in vitro circuit that aims at regulating the rate of mRNA transcription. Two DNA templates are designed to interact through their transcripts, creating negative feedback loops that will equate their transcription rates at steady state. A mathematical model is developed for this circuit, consisting of a set of ODEs derived from the mass action laws and Michaelis-Menten kinetics involving all the present chemical species. The DNA strands were accordingly designed, following thermodynamics principles and minimizing unwanted interactions. Preliminary experimental results show that the circuit is performing the expected task, by matching at steady state the transcription rates of the two DNA templates

Microencapsulation of roasted coffee oil from chitosan nanoparticles-stabilized Pickering emulsions

Tesis por compendio[ES] El proceso de emulsificación de aceites ricos en compuestos bioactivos permite su mejor aplicación y conservación durante el tiempo de almacenamiento. Entre los diversos mecanismos de emulsificación, se destaca el método de Pickering ya que utiliza nanopartículas sólidas naturales en sustitución de los tensioactivos artificiales. Debido a sus propiedades antioxidantes, no toxicidad y disponibilidad, en este trabajo se estudiaron distintas modificaciones del quitosano para su potencial aplicación como partícula de Pickering. Las modificaciones estudiadas fueron la autoagregación, también denominada desprotonación, y el entrecruzamiento con tripolifosfato de sodio. Se evaluó el comportamiento de estas partículas emulsionando aceite de café tostado, un subproducto de la industria de café con un alto contenido de compuestos bioactivos y compuestos volátiles de interés. Posteriormente, se analizaron las propiedades físico-químicas y la estabilidad de las microcápsulas producidas tras el secado de las emulsiones mediante técnicas de secado por atomización y liofilización. Todas las emulsiones se caracterizaron por tener un comportamiento reológico pseudoplástico, sufriendo desintegración a lo largo del proceso de digestión. Las emulsiones formuladas con nanopartículas de quitosano desprotonadas y menor concentración de aceite mostraron una mejor estabilización y, en consecuencia, una mayor bioaccesibilidad de los compuestos fenólicos totales. Las diferentes nanopartículas de quitosano se caracterizaron estudiando su carga superficial, distribución del tamaño de partícula, microestructura y afinidad agua/aceite. A medida que se aumentó la concentración de estas partículas, se afectó positivamente la viscosidad de las emulsiones debido a la formación de una red tridimensional en la fase continua. Las nanopartículas obtenidas al entrecruzar quitosano con tripolifosfato de sodio fueron más pequeñas, dando como resultado emulsiones con gotas más pequeñas. Las emulsiones de Pickering que contenían un 10% de aceite de café tostado se secaron por atomización y se liofilizaron utilizando las diferentes nanopartículas de quitosano estudiadas y maltodextrina como agentes portadores. Las microcápsulas obtenidas tuvieron la humedad, actividad del agua y solubilidad adecuada para su manipulación y almacenamiento. La presencia de nanopartículas de quitosano permitió una mayor retención de aceite en las microcápsulas y mayor eficiencia de encapsulación. Los compuestos bioactivos y las propiedades antioxidantes se conservaron mejor durante la liofilización. Por otro lado, las microcápsulas obtenidas por atomización presentaron mayor protección de estos compuestos durante la digestión. Las microcápsulas formuladas con nanopartículas desprotonadas fueron sometidas a almacenamiento durante 30 días a 25 ºC. Durante el almacenamiento, se evaluó la protección contra la oxidación de lípidos y la liberación de volátiles. Las isotermas de sorción de agua de estas muestras se determinaron también previamente en las condiciones de almacenamiento. Ambas muestras presentaron isotermas del tipo II, lo que permitió un buen ajuste del modelo de GAB a los datos experimentales. La determinación del índice de peróxido y del contenido de dienos conjugados dio lugar a valores adecuados durante el almacenamiento, aunque las muestras liofilizadas presentaron una ligera tendencia a la oxidación debido a la mayor cantidad de aceite superficial. Aunque hubo ligeras diferencias entre las muestras secas, todas mostraron menos pérdida de aromas totales (~28%) en comparación con el aceite no encapsulado (~51%) al final del almacenamiento. Así, se concluyó que las nanopartículas de quitosano estudiadas fueron eficientes para encapsular el aceite de café tostado y preservar sus características frente a la acción de agentes externos.[CA] El procés d'emulsificació d'olis rics en compostos bioactius permet la seua millor aplicació i conservació durant el temps d'emmagatzematge. Entre els diversos mecanismes d'emulsificació, destaca el mètode de Pickering, ja que utilitza nanopartícules sòlides naturals en substitució als tensioactius artificials. A causa de la seua propietat antioxidant, de la no toxicitat i de la disponibilitat, aquest treball va buscar analitzar el quitosà i les seues modificacions com potencials partícules de Pickering. Les modificacions estudiades van ser la autoagregació, també anomenada desprotonació, i l'entrecreuament amb tripolifosfat de sodi. Es va avaluar el comportament d'aquestes partícules emulsionant oli de cafè torrat, un subproducte de la indústria del cafè amb un alt contingut de compostos bioactius i volàtils d'interès. Posteriorment, es van analitzar les propietats fisicoquímiques i l'estabilitat de les microcàpsules produïdes després de l'assecat de les emulsions mitjançant tècniques d'assecatge per atomització i liofilització. Totes les emulsions tenien un comportament reològic pseudoplàstic, sofrint desintegració al llarg del procés de digestió. Les emulsions formulades amb nanopartícules de quitosà desprotonades i menor concentració d'oli van mostrar una millor estabilització i, en conseqüència, una major bioaccesibilitat als compostos fenòlics totals. Les diferents nanopartícules de quitosà es van caracteritzar estudiant la seua càrrega superficial, distribució del tamany de partícula, microestructura i afinitat aigua/oli. A mesura que es va augmentar la concentració d'aquestes partícules, es va afectar positivament la viscositat de les emulsions a causa de la formació d'una xarxa tridimensional en la fase contínua. Les nanopartícules obtingudes a l'entrecreuar quitosà amb tripolifosfat de sodi van ser més menudes, donant com a resultat emulsions amb gotes més menudes també. Les emulsions de Pickering que contenien un 10% d'oli de cafè torrat es van assecar per atomització i es liofilitzaren utilitzant les diferents nanopartícules de quitosà estudiades i maltodextrina com a agents portadors. Les microcàpsules obtingudes van obtenir una humitat, activitat de l'aigua i solubilitat adequada per a la seua manipulació i emmagatzematge. La presència de nanopartícules de quitosà va permetre major retenció d'oli en les microcàpsules i major eficiència d'encapsulació. Els compostos bioactius i les propietats antioxidants es van conservar millor durant la liofilització. D'altra banda, les microcàpsules obtingudes per atomització presentaren major protecció d'aquests compostos durant la digestió. Les microcàpsules formulades amb nanopartícules desprotonades també van ser sotmeses a la prova d'emmagatzematge durant 30 dies a 25°C. Durant l'emmagatzematge, es va avaluar la seua protecció contra l'oxidació de lípids i l'alliberament de volàtils. Per això, les isotermes de sorció d'aigua d'aquestes mostres es van determinar prèviament en les condicions d'emmagatzematge. Les dues mostres van presentar isotermes de tipus II, el que va permetre un bon ajust del model de GAB a les dades experimentals. L'índex de peròxids i el contingut de diens conjugats van resultar en valors adequats durant l'emmagatzematge, encara que les mostres liofilitzades van presentar una lleugera tendència a l'oxidació a causa de la major quantitat d'oli superficial. Encara que va haver lleugeres diferències entre les mostres seques, totes van mostrar menys pèrdua d'aromes totals (~28%) en comparació amb l'oli no encapsulat (~51%) a la fi de l'emmagatzematge. Així, es va concloure que les nanopartícules de quitosà estudiades van ser eficients per encapsular l'oli de cafè torrat i preservar les seues característiques enfront de l'acció d'agents externs.[EN] The emulsification process of bioactive-rich oils makes possible their better application and preservation over the storage time. Among the many emulsification mechanisms, the Pickering method has been highlighted as it uses natural solid nanoparticles in replacement of artificial surfactants. Due to the antioxidant properties, non-toxicity and availability, this work aimed at studying chitosan modifications to produce potential Pickering particles. The studied modifications comprised self-aggregation, also called deprotonation, and crosslinking with sodium tripolyphosphate. The performance of these particles was evaluated in the emulsification of roasted coffee oil, a by-product of the coffee industry with a high content of bioactive and volatile compounds of interest. Subsequently, the physicochemical properties and stability of the microcapsules produced after drying the emulsions using spray-drying and lyophilization techniques were analyzed. All emulsions were characterized as shear-thinning, being them destabilized over the digestion process. Emulsions formulated with deprotonated chitosan nanoparticles and lower oil concentrations showed better stabilization and, consequently, greater bioaccessibility of total phenolic compounds. The different chitosan nanoparticles were characterized regarding surface charge, particle size distribution, microstructure and oil/water affinity. Deprotonated chitosan nanoparticles had a larger particle size, which resulted in emulsions with larger oil droplets. As the concentration of these particles increased, the viscosity of the emulsions was positively affected by the formation of a three-dimensional network in the continuous phase. The nanoparticles obtained by crosslinking with sodium tripolyphosphate were smaller, resulting in emulsions with smaller droplets. The viscosity of these emulsions was lower and little affected by the concentration of particles. Pickering emulsions containing 10% roasted coffee oil were spray-dried and freeze-dried, using the different studied chitosan nanoparticles and maltodextrin as carrier agents. The resulting microcapsules showed adequate moisture content, water activity and solubility for subsequent handling and storage. The presence of chitosan nanoparticles resulted in greater oil retention in the microcapsules and higher encapsulation efficiency. Microcapsules obtained by spray-drying had a more regular spherical shape, while the microparticles obtained by freeze-drying were larger with irregular morphology. Bioactive compounds and antioxidant properties were more preserved during freeze-drying. On the other hand, spray drying allowed greater protection of these compounds during the in vitro digestion. The spray- and freeze-dried microcapsules formulated with deprotonated nanoparticles were subjected to the storage test for 30 days at 25 ºC. During storage, their protection against lipid oxidation and volatile release were evaluated. The water sorption isotherms of these samples were previously determined under the storage conditions. Both samples presented type II isotherms, which resulted in a good fitting accuracy of the GAB model to the experimental data. The peroxide index and the conjugated dienes content resulted in adequate values during storage, although the freeze-dried samples showed a slightly higher tendency to oxidation due to the higher amount of surface oil. Although slight differences were observed between the dried samples, both of them showed less loss of total volatile compounds (~28%) when compared to the non-encapsulated oil (~51%) at the end of storage. Thus, it was concluded that the studied chitosan nanoparticles were efficient to encapsulate roasted coffee oil and to preserve its characteristics against the action of external agents.The authors would like to thank the project RTI-2018-099738-B-C22 from the ‘Ministerio de Ciencia, Innovación y Universidades’, the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (CAPES) - (Finance Code 001; Grant number 88887.468140/2019-00) and the São Paulo Research Foundation (FAPESP – Grant number 2016/22727-8) for the financial support.Franco Ribeiro, E. (2021). Microencapsulation of roasted coffee oil from chitosan nanoparticles-stabilized Pickering emulsions [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/163234TESISCompendi

Geometry of unsteady fluid transport during fluid–structure interactions

We describe the application of tools from dynamical systems to define and quantify the unsteady fluid transport that occurs during fluid–structure interactions and in unsteady recirculating flows. The properties of Lagrangian coherent structures (LCS) are used to enable analysis of flows with arbitrary time-dependence, thereby extending previous analytical results for steady and time-periodic flows. The LCS kinematics are used to formulate a unique, physically motivated definition for fluid exchange surfaces and transport lobes in the flow. The methods are applied to numerical simulations of two-dimensional flow past a circular cylinder at a Reynolds number of 200; and to measurements of a freely swimming organism, the Aurelia aurita jellyfish. The former flow provides a canonical system in which to compare the present geometrical analysis with classical, Eulerian (e.g. vortex shedding) perspectives of fluid–structure interactions. The latter flow is used to deduce the physical coupling that exists between mass and momentum transport during self-propulsion. In both cases, the present methods reveal a well-defined, unsteady recirculation zone that is not apparent in the corresponding velocity or vorticity fields. Transport rates between the ambient flow and the recirculation zone are computed for both flows. Comparison of fluid transport geometry for the cylinder crossflow and the self-propelled swimmer within the context of existing theory for two-dimensional lobe dynamics enables qualitative localization of flow three-dimensionality based on the planar measurements. Benefits and limitations of the implemented methods are discussed, and some potential applications for flow control, unsteady propulsion, and biological fluid dynamics are proposed

Interactions between financial and environmental networks in OECD countries

We analyse a multiplex of networks between OECD countries during the decade 2002-2010, which consists of five financial layers, given by foreign direct investment, equity securities, short-term, long-term and total debt securities, and five environmental layers, given by emissions of N O x, P M 10 SO 2, CO 2 equivalent and the water footprint associated with international trade. We present a new measure of cross-layer correlations between flows in different layers based on reciprocity. For the assessment of results, we implement a null model for this measure based on the exponential random graph theory. We find that short-term financial flows are more correlated with environmental flows than long-term investments. Moreover, the correlations between reverse financial and environmental flows (i.e. flows of different layers going in opposite directions) are generally stronger than correlations between synergic flows (flows going in the same direction). This suggests a trade-off between financial and environmental layers, where, more financialised countries display higher correlations between outgoing financial flows and incoming environmental flows from lower financialised countries, which could have important policy implications. Five countries are identified as hubs in this finance-environment multiplex: The United States, France, Germany, Belgium-Luxembourg and the United Kingdom.Comment: Supplementary Information provide

Design and performance of in vitro transcription rate regulatory circuits

This paper proposes a synthetic in vitro circuit that aims at regulating the rate of RNA transcription through positive feedback interactions. This design is dual to a previously synthesized transcriptional rate regulator based on self-repression. Two DNA templates are designed to interact through their transcripts, creating cross activating feedback loops that will equate their transcription rates at steady state. A mathematical model is developed for this circuit, consisting of a set of ODEs derived from the mass action laws and Michaelis-Menten kinetics involving all the present chemical species. This circuit is then compared to its regulatory counterpart based on negative feedback. A global sensitivity analysis reveals the fundamental features of the two designs by evaluating their equilibrium response to changes in the most crucial parameters of the system

Juvenile diabetes and visual impairment: Wolfram syndrome

This article is freely available via Open Access. Click on the Publisher URL to access it via the publisher's site.The Wellcome Trust, UK funded genetic testing.Published version, Accepted version (12 month embargo), Submitted versio

Application of CZE Method in Routine Analysis for Determination of B-Complex Vitamins in Pharmaceutical and Veterinary Preparations

A competitive CZE method for quality control analysis of multivitamin preparations and veterinary products containing B-group vitamins was developed. Vitamins of interest are thiamine hydrochloride (B1), thiamine monophosphate chloride (B1a), riboflavine (B2), riboflavine-5′monophosphate (B2a), nicotinamide (B3), d-pantothenic acid calcium salt (B5), pyridoxine hydrochloride (B6), folic acid (B9), and 4-aminobenzoic acid (B10). These analytes were separated optimizing the experimental conditions in 20 mM tetraborate buffer pH = 9.2 as a BGE (background electrolyte), on a Beckman P/ACE System MDQ instrument, using uncoated fused silica capillary. The effective capillary length was of 49.5 cm, I.D. = 50 μm, the applied voltage 20 kV and the temperature 25°C. Detection was performed by a diode array detector at 214 nm for all vitamins except B5 (190 nm) and B2a (260 nm). Separation time was about 9 min. After experimental conditions optimization, the proposed method was validated. Precision of migration time and corrected peak area, linearity range, LOD and LOQ, accuracy (recovery), robustness, and ruggedness were evaluated for each analyte demonstrating the good reliability of the method. Analyses of the pharmaceutical real samples were performed and confirmed the versatility of this method

Management of Clinically Insignificant Residual Fragments following Shock Wave Lithotripsy

Clinically insignificant residual fragments (CIRFs) are small fragments (less than 5 mm) that are present in upper urinary tract at the time of regular post-SWL followup. The term is controversial because they may remain silent and asymptomatic or become a risk factor for stone growth and recurrence, leading to symptomatic events, and need further urologic treatment. Although a stone-free state is the desired outcome of surgical treatment of urolithiasis, the authors believe that the presence of noninfected, nonobstructive, asymptomatic residual fragments can be managed metabolically in order to prevent stone growth and recurrence. Further urologic intervention is warranted if clinical indications for stone removal are present