An experimental study of the temperature-dependent DNA elasticity using optical tweezers

Màster Oficial en Física Avançada, Facultat de Física, Universitat de Barcelona, Curs: 2014, Tutor: Félix Ritort FarranTemperature plays a key role in all biological processes. Slight changes of temperature may lead to completely di erent behaviors of biological systems. In fact, living matter carry out its function in a small range of temperature. Therefore, it is interesting to study and understand what is the effect of temperature in biological systems. Single-stranded DNA (ssDNA) is one of the most relevant molecules in biological processes, providing us an excellent scenario to understand how the temperature a ect its properties. In this project we aim to understand and characterize the elastic response of ssDNA at di erent temperatures. We have used the Laser Optical Tweezers (LOT) technique in order to measure the Force-Distance Curves (FDC) of ssDNA under the e ect of a mechanical force at di erent temperatures. By tting the stretching response of ssDNA to two semi exible polymer models we have obtained the temperature dependence of the elastic parameters. We have found that persistence length and Kuhn length increase with temperature while the stretching modulus seems to be insensitive to temperature changes. Finally, we have found that the persistence length is proportional to the Debye screening length and that it varies with temperature according to a power law with exponent < 1

Free energy and information-content measurements in thermodynamic and molecular ensembles

[eng] Single-molecule experiments have emerged as a powerful tool that allow researchers to investigate the physical behavior of individual molecules with unprecedented resolution. The feasibility exerting forces at the piconewton scale (10^-12 N) and measuring nanometric displacements in the sub-millisecond scale, offer a widespread range of exciting possibilities. The major part of this thesis is devoted to address fundamental topics of statistical physics using single-molecule experiments. In particular, in the first part of the thesis, we aimed to study one of the eldest questions in statistical mechanics: the issue of ensemble inequivalence. By performing single- molecule experiments on a well-known molecule (the CD4 DNA hairpin), we have been able of exploring two conjugate ensembles: the fixed-extension and the force-fixed ensemble. Both ensembles are conjugate with respect to energy since the product force times extension equals has energy dimensions. We carried out experiments in the fixed-force ensemble using both optical tweezers and magnetic tweezers, and in the fixed-extension using optical tweezers. We have found that these two conjugate ensembles are not equivalent at the level of thermodynamics nor in kinetics. Moreover, we showed that the often-neglected boundary terms in the definition of the thermodynamic work are essential to the validity of the fluctuation theorem. The second part of this thesis is also merely theoretical. Recent single-molecule assays confirmed the connection between information theory and statistical physics. Single- molecule experiments have turned out to be the perfect playground to explore the thermodynamic implications of having —or lacking— information. It is worthwhile to mention the experimental realization of the Szilard engine and the experimental verification of Landauer’s limit. With the current existing results, the information-to- energy connection is well established. We have been able to experimentally demonstrate, for the first time, the reversed implication. We have been able to quantify the information-content of neutral molecular ensembles by means of thermodynamic measurements. That is, we experimentally demonstrated the energy- to-information conversion. Our works are built on what we call ensemble force spectroscopy, a systematic procedure capable of obtaining a robust characterization of molecular ensembles in the best tradition of statistical physics, by measuring few tens of molecules. In the final part of the thesis we aimed to measure the specific binding energy of a metallic ion to the tertiary structure of a three-way RNA junction belonging to the central domain of the 16S ribosomal RNA (rRNA). From the physics perspective, to the best of our knowledge, first time we have been able to discern the free energy contribution due to the specific binding of magnesium ions to an RNA substrate by means of single-molecule assays. On the other hand, such molecule is able to form, besides its native conformation, a force-induced misfolded state. Despite this fact was already pointed out in previous single-molecule studies, there was a lack of knowledge regarding the molecular kinetics and the folding pathway. Aiming to fill this gap, we performed a thorough study of the three-helix RNA junction using dynamic force spectroscopy. As a result, we have characterized the full folding pathway of the molecule, including both the native and the misfolded structure. Furthermore, we have experimentally confirmed the fact that the presence of magnesium promotes the stabilization of the native structure and we have measured this contribution. We have found that magnesium is able to rescue the native structure from the misfolded structure via electrostatic interactions due to magnesium binding. This fact is biologically relevant, since we have been able to characterize the conditions in which a misfolded molecule is able to recover its native conformation.[spa] En esta tesis hemos abordado cuestiones fundamentales de la física estadística. En particular, hemos estudiado el problema de la equivalencia entre colectivos estadísticos, la conversión de energía a información y el estudio de las energías específicas de unión de iones metálicos a sustratos de RNA. Esta tesis doctoral se ha llevado a cabo empleando dos de los instrumentos de molécula individual más conocidos, las pinzas ópticas y las pinzas magnéticas. Ambas son técnicas que permiten la aplicación controlada de fuerzas mecánicas a los extremos de una molécula individual. El poder aplicar fuerzas a sistemas moleculares permite llevar a cabo una profunda caracterización de las propiedades físicas de los llamados sistemas pequeños. Las dimensiones de estos sistemas abarcan desde unos pocos nanómetros —una millonésima parte del metro— hasta varios cientos de nanómetros. Además, los sistemas pequeños están lejos del llamado límite termodinámico y están dominados por las fluctuaciones térmicas del entorno. Por lo tanto, debido a estas peculiaridades, el estudio de sistemas pequeños mediante los instrumentos de molécula individual permite impulsar y extender los horizontes de la física de no equilibrio

Drivers and barriers of university social responsibility: integration into strategic plans

The implementation of University Social Responsibility (USR) in its strategic plans is a subject of great social interest. However, the lack of understanding produces deficient stakeholder’s engagement, obstructing USR applications and potential benefits. USR in a formal context and as part of strategy should be a path that leads to its fulfilment. A Delphi method was used and several experts have participated in it. Results show that USR is related to student’s issues, among main drivers are to work under a code of ethics and acquire civic competences as a part of their vocational training. Among barriers to be involved in social responsibility activities is the lack of engagement of university community. The insufficient communication into the university community is mentioned as one of the main obstacles to incorporate USR into strategic planning. Relevance of this work relies on the holistic points of views of the results.Postprint (author's final draft

Catalysts of university social responsability into strategic planning by thematic analysis and deductive coding

The relevance of higher education institutions (HEI) for social development is unquestionable because of their potential for contributing intellectual solutions for the social, economic, and environmental welfare of society. The current study aims to: 1) examine which are the main catalysts of university social responsibility (USR) from a strategic management perspective; 2) show the relations among those catalysts through semantic networks; and 3) analyse the role of university promotion of entrepreneurship. The method uses a content analysis in a sample of 23 universities and examines the subject and codes to clarify the catalysts. The semantic networks are shown to reveal these connections. It was found that a high percentage of universities orient their efforts towards enhancing the employability of students, mainly through entrepreneurial projects intended to achieve social responsibility.Postprint (author's final draft

Utilización racional del estiércol fluido de porcino (EFP) como fertilizante agrícola

4 Pags.- 3 Tabls.- 2 Figs.En este trabajo se presentan los estudios estadísticos y ecuaciones de correlación entre parámetros, obtenidos de los resultados de los análisis laboratoriales de más de 300 muestras de EFP, de forma que resulte más sencillo el conocimiento de la composición cualitativa y cuantitativa para su aplicación agrícola.Peer reviewe

Reflexionar sobre el género desde escenas de práctica escolar

Este artículo muestra algunas escenas escolares cotidianas. La mayor parte de ellas están centradas en juegos, por ser un contenido habitual en las clases de Educación Física y una actividad presente en los patios escolares, sobre todo en Primaria. Los adultos hemos configurado una imagen del mismo muy bondadosa y nos cuesta ver los conflictos y desequilibrios que quedan enmascarados por el movimiento y el entusiasmo general, pero es necesario descubrirlos. En este artículo hemos puesto más énfasis en detectar los problemas que en las vías para su transformación. Las sesiones de las que hemos tomado las escenas no tenían como objetivo prioritario la reducción de estereotipos, aunque sí tenían entre sus preocupaciones la creación de ambientes de aprendizaje más coeducativos. En todo caso, no pretenden ser modélicas y su valor es el de ayudarnos a hacer visible alguna de las múltiples concreciones en la que el género se agazapa y transmuta presentándose ante nuestros ojos sin ser, en muchos casos, identificado como tal

Reflexionar sobre el gènere des d’escenes de pràctica escolar

Aquest article mostra algunes escenes escolars quotidianes. La major part es troben centrades en jocs, perquè aquest és un contingut habitual a les classes d’Educació Física i una activitat present als patis escolars, sobretot a Primària. Els adults n’hem configurat una imatge molt bondadosa i ens costa de veure els conflictes i desequilibris que queden emmascarats pel moviment i l’entusiasme general, però cal descobrir-los. En aquest article hem posat més èmfasi a detectar els problemes que en les vies per a la seva transformació. Les sessions de les quals hem pres les escenes no tenien com a objectiu prioritari la reducció d’estereotips, encara que sí que tenien, entre les seves preocupacions, la creació d’ambients d’aprenentatge més coeducatius. En qualsevol cas, no pretenen de ser modèliques i el seu valor és el d’ajudar-nos a fer visible alguna de les múltiples concrecions en la qual el gènere s’agotzona i transmuta, tot presentant-se davant els nostres ulls sense ser, en molts casos, identificat com a tal

Hydrazones as Singular Reagents in Asymmetric Organocatalysis

This Minireview summarizes strategies and developments regarding the use of hydrazones as reagents in asymmetric organocatalysis, their distinct roles in nucleophile–electrophile, cycloaddition, and cyclization reactions. The key structural elements governing the reactivity of these reagents in a preferred pathway will be discussed, as well as their different interactions with organocatalysts, leading to diverse activation modes. Along these studies, the synthetic equivalence of N-monoalkyl, N,N-dialkyl, and N-acyl hydrazones with several synthons is also highlighted. Emphasis is also put on the mechanistic studies performed to understand the observed reactivities. Finally, the functional group transformations performed from the available products has also been analyzed, highlighting the synthetic value of these methodologies, which served to access numerous families of valuable multifunctional compounds and nitrogen-containing heterocycles.Ministerio de Economía y Competitividad CTQ2013-48164-C2-1-P, CTQ201348164-C2-2-PEuropean FEDER fundsJunta de Andalucía 2012/FQM 107

Static range of motion of the first metatarsal in the sagittal and frontal planes

The first metatarsal and medial cuneiform form an important functional unit in the foot, called “first ray”. The first ray normal range of motion (ROM) is difficult to quantify due to the number of joints that are involved. Several methods have previously been proposed. Controversy exists related to normal movement of the first ray frontal plane accompanying that in the sagittal plane. The objective of this study was to investigate the ROM of the first ray in the sagittal and frontal planes in normal feet. Anterior-posterior radiographs were done of the feet of 40 healthy participants with the first ray in a neutral position, maximally dorsiflexed and maximally plantarflexed. They were digitalized and the distance between the tibial malleolus and the intersesamoid crest in the three positions mentioned was measured. The rotation of the first ray in these three positions was measured. A polynomic function that fits a curve describing the movement observed in the first ray was obtained using the least squares method. ROM of the first ray in the sagittal plane was 6.47 (SD 2.59) mm of dorsiflexion and 6.12 (SD 2.55) mm of plantarflexion. ROM in the frontal plane was 2.69 (SD 4.03) degrees of inversion during the dorsiflexion and 2.97 (SD 2.72) degrees during the plantarflexion. A second-degree equation was obtained, which represents the movement of the first ray. Passive dorsiflexion and plantarflexion of the first ray were accompanied by movements in the frontal plane: 0.45 degrees of movement were produced in the frontal plane for each millimeter of displacement in the sagittal plane. These findings might be useful for the future design of instruments for clinically quantifying first ray mobility

Análisis del proceso de implementación del proyecto de intoxicación por plomo en el Callao

Estudios realizados por la Dirección General de Salud Ambiental del Ministerio de Salud (DIGESA) con el apoyo de la Agencia Internacional de Desarrollo de los Estados Unidos- USAID arrojaron que los niños del Callao que viven y estudian alrededor de los depósitos mineros están expuestos a grandes cantidades de plomo en la sangre que afectan su salud y desarrollo. Ante dicha realidad, el Gobierno Regional del Callao decide implementar el proyecto “Control de la Intoxicación por plomo a los alumnos de las Instituciones Educativas afectadas en el Callao” que pretende reducir los efectos del plomo en la sangre de los niños con capacitaciones en higiene ambiental y alimentación adecuada con productos quelantes. En la actualidad no se cuenta con información que reporte los avances del mismo ni que analice la eficiencia y eficacia de dicha política. En tal sentido, esta tesis pretende generar información al respecto y, en particular, de los aciertos y desaciertos en la implementación del mismo. Los principales resultados de la investigación realizada sugieren que si bien los beneficiarios valoran el proyecto y consideran que este habría impactado en la motivación, la vitalidad y han sensibilizado a los padres sobre la problemática existente y como abordarla, sin embargo, el proyecto no muestra mejoras en el rendimiento escolar y buenas practicas nutricionales y medio ambientales en el hogar. La evidencia generada por esta investigación resulta relevante para el Gobierno Regional del Callao en la medida que identifica los aciertos y desaciertos en la implementación del proyecto y pone en evidencia la necesidad de modificarla o fortalecerla para el logro de los objetivos esperados. Esto resulta especialmente urgente, en la medida que surgen nuevas denuncias de contaminación por plomo en otros distritos del Callao, que además de requerir profundizar en la regulación podrían requerir una intervención de este tipo para minimizar el impacto negativo del tránsito de minerales por el puerto del Callao.Studies conducted by the General Division of Environmental Health of the Ministry of Health (DIGESA) and the United States Agency for International Development (USAID) confirm that the children living and studying around mining deposits in Callao have been exposed lead pollution and observe large amounts of lead in their blood, a condition that affects both their health and their development opportunities. In this context, the Regional Government of Callao decided to implement the project "Control of lead poisoning to students of affected schools in Callao". The objective of the project is to reduce the effects of lead in children´s blood both with the environmental hygiene and adequate nutrition. There is no information that reports the progress of the project not the effectiveness of such policy. In this sense, this thesis aims to generate information on this regard and, in particular, the successes and failures in its implementation. Results suggest that although the beneficiaries value the project and consider that it has impacted student motivation and vitality and has sensitized parents on the existing problem and how to approach it, the project does not show improvements on health or education due to low implementation of good nutritional and environmental practices at home. The evidence generated by this research is relevant for the Regional Government of Callao since it identifies successes and failures in the implementation of the project and highlights the need to modify or strengthen it to achieve the expected objectives. This is particularly urgent, as new reports of lead contamination in other districts of Callao arise, which, in addition to requiring further regulation, may require such intervention to minimize the negative impact of the transit of minerals through the port of Callao.Tesi