Modelling Electrostatic Interactions and Solvation in Chromatin: from the single nucleosome towards the chromatin fibre

Chromatin is a complex of proteins and DNA found in the nuclei of eukaryotic cells. It reinforces the DNA and its topology tunes DNA transcription and gene expression. It is formed by nucleosomes, structures composed of an octameric protein core and approximately 147 base pairs of DNA. Chromatin is an extremely complex system, the behaviour of which is ruled by both mechanical and electrostatic factors that are depend on its structure, and biomolecular interactions occurring in the cell nucleus. In this thesis, I analyse chromatin compaction from an electrostatic perspective and focus on the role of electrostatics and solvation as determinants of the topology of chromatin. I examine the effect of the histone tails and propose a methodology to connect electrostatic calculations to the structural and functional features of protein-DNA systems. This methodology can also be combined with coarse-grained representations. I study the electrostatic forces acting on the phosphate atoms of the DNA backbone. I investigate the electrostatic origins of effects such as different stages in DNA unwrapping, nucleosome destabilisation upon histone tail truncation, and the role of specific arginines and lysines undergoing Post - Translational Modifications. I find that the positioning of the histone tails can oppose the attractive pull of the histone core, locally deform the DNA, and tune DNA unwrapping. I conduct an analysis of the porosity of nucleosomes and related to the importance of solvation phenomena. I complement and support my computational findings on nucleosome electrostatic interactions experimental Zeta Potential and Dynamic Light Scattering measurements on single nucleosomes under varying ionic concentrations, providing information on the surface charge and the size of nucleosomes. I present a comprehensive study of the electrostatic interactions between nucleosome pairs sampling different translations and rotations. My analysis aims to provide a cohesive description of nucleosome electrostatic interactions in the chromatin fibre, combining information on the energetics of different relative positions of nucleosomes, especially in very tight packing situations. In addition to numerical estimates of electrostatic interaction energy of nucleosomes at different relative distances and orientations, obtained within the Poisson-Boltzmann framework, I present their approximation by analytical asymptotic expressions, where nucleosomes are approximated as monopoles and dipoles centred in dielectric spheres immersed in an electrolytic solution. I am able to identify a non-linearity region around the nucleosomes, and to exploit the fact that that in points outside that region the electrostatic potential can be described by the linearised Poisson-Boltzmann Equation

Vulnerability and Resilience in West Africa: Understanding Human Mobility in the Context of Land Degradation

The loss of productive land is often one of the key drivers of human mobility. Land degradation might lead to increases in migration because of the need to diversify incomes, but it can also cause reduced mobility by eroding the financial or physical assets and capital required to finance migration. When on-site adaptation is either impossible or undesirable, migration allows people to modify their exposure to climate and environmental stressors. On one hand, temporary and circular labour migration, internal and international remittances, and family relocation are among the most common strategies used throughout history, and increasingly so in the past decades, to cope with harsh climatic variations, increasingly hostile natural environments, and natural disasters. On the other hand, land abandonment and out-migration can lead to further isolation and marginalization of both vulnerable rural populations (increasing their vulnerability if migration occurs in unplanned ways) and migrants who relocate toward areas of high environmental risk, such as resource-scarce or urban areas within insecure expanding cities. Based on existing evidence on the West Africa region, the research in this paper aims at gaining a better understanding of how land degradation interacts with drivers of migration by analysing the factors determining vulnerability at individual, household, and community levels, as well as those factors affecting capacities—whether inherent or acquired—and strategies that contribute to building resilience

Indolent lymphoma: the pathologist's viewpoint

Indolent lymphomas have recently been the object of numerous studies, which have focused on new aspects relevant both for the better comprehension of their histogenesis and the identification of new therapeutic strategies. As marginal-zone lymphoma (MZL) represents the category of indolent lymphomas that has obtained more benefit from such an approach, the authors focused on the most recent achievements and not yet solved controversies in this area. In spite of their postulated common derivation, the three categories of MZL of the WHO Classification appear dissimilar. In fact, they show significant molecular differences among them as well as a certain heterogeneity within each group. By no means, there is a cogent need of more refined tools to revise these neoplasms and to produce a more rational grouping. The recent identification of the IRTA gene family corresponding to IG-like receptors differentially expressed in B-cells might contribute to their better understandin

Indolent lymphoma: the pathologist's viewpoint

Abstract Indolent lymphomas have recently been the object of numerous studies, which have focused on new aspects relevant both for the better comprehension of their histogenesis and the identification of new therapeutic strategies. As marginal-zone lymphoma (MZL) represents the category of indolent lymphomas that has obtained more benefit from such an approach, the authors focused on the most recent achievements and not yet solved controversies in this area. In spite of their postulated common derivation, the three categories of MZL of the WHO Classification appear dissimilar. In fact, they show significant molecular differences among them as well as a certain heterogeneity within each group. By no means, there is a cogent need of more refined tools to revise these neoplasms and to produce a more rational grouping. The recent identification of the IRTA gene family corresponding to IG-like receptors differentially expressed in B-cells might contribute to their better understanding

A synthetic biology approach for consistent production of plant-made recombinant polyclonal antibodies against snake venom toxins

Antivenoms developed from the plasma of hyperimmunized animals are the only effective treatment available against snakebite envenomation but shortage of supply contributes to the high morbidity and mortality toll of this tropical disease. We describe a synthetic biology approach to affordable and cost-effective antivenom production based on plant-made recombinant polyclonal antibodies (termed pluribodies). The strategy takes advantage of virus superinfection exclusion to induce the formation of somatic expression mosaics in agroinfiltrated plants, which enables the expression of complex antibody repertoires in a highly reproducible manner. Pluribodies developed using toxin-binding genetic information captured from peripheral blood lymphocytes of hyperimmunized camels recapitulated the overall binding activity of the immune response. Furthermore, an improved plant-made antivenom (plantivenom) was formulated using an in vitro selected pluribody against Bothrops asper snake venom toxins and has been shown to neutralize a wide range of toxin activities and provide protection against lethal venom doses in mice.Fil: Julve Parreño, Jose Manuel. Universidad Politécnica de Valencia; EspañaFil: Huet, Estefanía. Universidad Politécnica de Valencia; EspañaFil: Fernández del Carmen, Asun. Universidad Politécnica de Valencia; EspañaFil: Segura, Alvaro. Universidad de Costa Rica; Costa RicaFil: Venturi, Micol. Universidad Politécnica de Valencia; EspañaFil: Gandía, Antoni. Universidad Politécnica de Valencia; EspañaFil: Pan, Wei-Song. Universidad Politécnica de Valencia; EspañaFil: Albaladejo, Irene. Universidad Politécnica de Valencia; EspañaFil: Forment, Javier. Universidad Politécnica de Valencia; EspañaFil: Pla, Davinia. Instituto de Biomedicina de Valencia; EspañaFil: Wigdorovitz, Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; ArgentinaFil: Calvete, Juan J.. Instituto de Biomedicina de Valencia; EspañaFil: Gutiérrez, Carlos. Universidad de Las Palmas de Gran Canaria; EspañaFil: Gutiérrez, José María. Universidad de Costa Rica; Costa RicaFil: Granell, Antonio. Universidad Politécnica de Valencia; EspañaFil: Orzáez, Diego. Universidad Politécnica de Valencia; Españ

Variations in “rescuability” of immunoglobulin molecules from different forms of human lymphoma: implications for anti-idiotype vaccine development

Idiotypic (Id) vaccination has shown promising results in patients with follicular lymphoma (FL). However, it still remains unclear whether the same approach might be suitable for the treatment of other B-cell malignancies. For this reason, we recently performed an interim analysis of patients proposed to receive this treatment at our center. The feasibility of employing idiotype vaccines was evaluated for five different B-cell malignancies in their first relapse, both in terms of induction and fusion, as well as overall treatment. Our data suggest that, unlike follicular lymphoma (87%), this approach is not feasible to treat other B-cell malignancies (0–20%) such as mantle cell, small lymphocytic, diffuse large cell and Burkitt’s lymphoma (P < 0.01). The main difficulties encountered were technical problems related to the survival of idiotype-producing hybridomas (83%) and the early loss of idiotype production by growing hybridomas (17%). However, it remains possible that an idiotype vaccine might still be produced through molecular means for most, if not all cases of relapsing B-cell malignancies

Active immunotherapy in the treatment of haematological neoplasias

Abstract The continuous search for therapeutic approaches that improve the conventional treatments of neoplasms, together with an improved understanding of the immune system, has led in recent years to the development of Immunotherapy. Basically, a distinction can be made between two forms of immunotherapy: passive immunotherapy, which consists in the transfer of antibodies or cells previously generated in vitro that are directed against the tumour, and active immunotherapy, which attempts to activate in vivo the immune system and induce it to elaborate a specific response against the tumor antibodies. Hematological neoplasms, specifically some B lymphomas, express in their membrane an immunoglobulin that is considered a specific antigen of the tumour, which is why these diseases have become the ideal target for immunotherapy treatments. There are many alternatives, ranging from protein vaccines, which have already shown clinical benefits, to those of the second generation, which make use of the new techniques of molecular biology to increase the efficacy of the vaccines and obtain their production in a quicker and less costly way, but with which there are not yet definitive clinical results