Chromosomes in Interphase and Mitosis

The three-dimensional organization of the chromatin fiber is driven by entropy. Therefore, the folding of the chromatin fiber is essentially a problem of statistical physics. In the present thesis, two questions in the context of chromatin folding which are still not fully understood are investigated: on the one hand the organization of chromatin in mitosis and on the other hand the changes of chromatin organization in the damage response to ionizing radiation. In the first part we develop a model that explains the condensation of mitotic chromosomes by size-restricted dynamic looping of the chromatin fiber. Our results show also that chromatin loops can contribute to the experimentally determined bending rigidity of mitotic chromatids and generate the correct force-extension behaviour. In a next step, this folding model is then extended to describe sister chromatids by including dynamic binding and unbinding of sister fibers. We assess the interplay between cohesion and condensation and show that alignment and cohesion of sister chromatids requires detailed control of the abundance of tethering points between them. In the second part we examine the damage response of interphase chromosomes. With an expression-dependent folding model and utilizing experimental data on the transcriptional activity of cells that were exposed to ionizing radiation, we first show that the overall organization of chromatin does not change after irradiation. By modeling actual fiber breaks in local environments we demonstrate that broken ends are passively transported to the surface of their domains and that this facilitates recognition of the break by diffusing proteins. Finally, we use a graph theoretical approach to analyze the structural changes of histone positions in localization microscopy images of cells that were exposed to ionizing radiation. We validate our previous results that no changes of the overall organization of chromatin is recognizable and demonstrate that highly packaged heterochromatic areas of the genome decondense upon irradiation

Single DNA conformations and biological function

From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We investigate the biophysical properties of DNA-looping and the equilibrium configurations of DNA-knots, whose relevance to biological processes are increasingly appreciated. We discuss how random DNA-looping may be related to the efficiency of the target search process of proteins for their specific binding site on the DNA molecule. And we dwell on the spontaneous formation of intermittent DNA nanobubbles and their importance for biological processes, such as transcription initiation. The physical properties of DNA may indeed turn out to be particularly suitable for the use of DNA in nanosensing applications.Comment: 53 pages, 45 figures. Slightly revised version of a review article, that is going to appear in the J. Comput. Theoret. Nanoscience; some typos correcte

Laboratory directed research and development. FY 1995 progress report

This document presents an overview of Laboratory Directed Research and Development Programs at Los Alamos. The nine technical disciplines in which research is described include materials, engineering and base technologies, plasma, fluids, and particle beams, chemistry, mathematics and computational science, atmic and molecular physics, geoscience, space science, and astrophysics, nuclear and particle physics, and biosciences. Brief descriptions are provided in the above programs

Developing A Novel Theranostic Nano-Platform For Simultaneous Multimodal Imaging And Radionuclide Therapy

The aim of this project was to develop and evaluate a theranostic nano-platform to enable Radionuclide Therapy (RNT) and multimodal imaging to improve the therapy and diagnosis of lymph node metastases. The work presented in this thesis consists of four main studies. First, Feraheme (FH) and two other superparamagnetic iron-oxide nanoparticles (SPIONs) were radiolabelled with radioisotopes commonly used in the clinic (89Zr, 177Lu and 90Y) for imaging and therapy utilising a novel chelate-free technique, which produced a high radiochemical yield and purity (up to 98%). FH nanoparticles were successfully radiolabelled with 90Y and 177Lu which was the first experimental demonstration that the HIR technique can be extended to radiolabel FH with these isotopes. In the second study, a series of phantom experiments were performed and results demonstrated that 89Zr-FH is a novel nanotechnology for simultaneous PET/MR imaging providing the capability of integrating the spatial resolution and tissue contrast provided by MR imaging with the high sensitivity of PET. An additional phantom study demonstrated the ability to image 177Lu-FH using Single Photon Emission Computed Tomography. The third study was a proof of concept for 90Y RNT. Results revealed that in RNT, the kinetics of DNA double strand break (DSB) induction, repair and misrepair must be considered when deriving radiobiological parameters. The fourth study, a Monte Carlo simulation study, was performed to study the subcellular mechanisms of dose delivery of the radionuclide 223Ra when treating metastases. These simulations showed that indirect cell damage may play an important role in RNT with alpha emitters due to the stochastic nature of alpha particle energy deposition. In conclusion, these results open a pathway towards a novel nuclear nanoplatform for multimodal imaging and RNT of lymph node metastases

A influência da conformação do DNA nas probabilidades de dano induzido por radiações

Orientador: Mario Antonio Bernal RodriguezDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb WataghinResumo: O objetivo deste trabalho é estudar a influência da conformação do DNA na probabilidade de dano direto produzido por partículas ionizantes. Além disso, os fundamentos mecanicísticos do modelo Linear-Quadrático são investigadas através de um modelo biofísico desenvolvido neste trabalho, baseado na TADR (Teoria da Ação Dual da Radiação). Para este fim, três modelos geométricos do material genético foram construídos. Os modelos têm resolução atomística e levam em conta ? 10^9 pares de base (bps) nas configurações A,B e Z do DNA. A partir de um único bp, os diferentes níveis organizacionais no interior do núcleo da célula foram criados por meio de transformações lineares. Em seguida, o código Monte Carlo (MC) GEANT4-DNA foi usado para simular o transporte de prótons de 0.5, 1, 5, 7 e 10 MeV assim como de partículas alfa de 2, 5, 7 e 10M eV . O número de partículas em cada caso é de tal modo que as doses absorvidas estão entre 0.5 ? 16Gy. Os três modelos foram consistentes com as dimensões das estruturas reais. Em particular, os modelos foram compatíveis com a exigência de que o diâmetro da cromatina seja de 30 nm, bem como com os volumes bp reportados em outros trabalhos. Os rendimentos tanto das quebras totais quanto das quebras duplas (TSBY e DSBY) foram obtidos para cada qualidade de radiação. Além disso, a probabilidade de impacto (SHP) definida como a razão entre o volume do DNA e o volume núcleo, foi calculada teoricamente e a partir das simulações. O modelo biofísico em conjunto com as simulações MC forneceu o número de lesões letais (N_LL) em função da dose, para prótons de 0,5 e 10 MeV, e para partículas alfa de 2 e 10 MeV . Os N_LL puderam ser divididos em aqueles criados por uma única trajetória e aqueles originados pela interacção de duas trajetórias. Concluiu-se que o TSBY é praticamente determinada pela SHP e depende fracamente da qualidade de radiação incidente. No entanto, o DSBY mostrou forte dependência tanto da conformação do DNA quanto da qualidade de radiação. Isto é devido à relação entre a capacidade de agrupamento das deposições de energia para uma radiação dada e o empacotamento do DNA. Por outro lado, a análise dos mecanismos de produção de dano, baseada na TADR e testada com o modelo biofísico desenvolvido, mostraram que os efeitos de uma única trajetória (de primeira ordem) dependem linearmente com a dose. Além disso, os efeitos inter-trajetórias seguem um comportamento quadrático com a dose, com um termo linear que influencia o mecanismo de primeira ordem. Isto significa que o comportamento linear-quadrático do N_LL com a dose, tem fundamentos mecanicistas, pelo menos, na primeira fase do danoAbstract: The aim of this work is to study the influence of the DNA conformation on the probability of direct damage induction by ionizing particles. Also, the mechanistic grounds of the Linear-Quadratic radiobiological model are investigated through the eyes of a home-made biophysical model based on the DRAT (Dual Radiation Action Theory). To this end, three geometrical models of the genetic material were constructed. The models have atomistic resolution and account for ? 10^9 base pairs (bps) in the A-, B- and Z-DNA configurations. Starting from a single bp, the different organizational levels inside the cell nucleus were created by means of linear transformations. Next, the Monte Carlo (MC) code GEANT4-DNA was used to simulate the transport of protons of 0.5, 1, 5, 7 and 10 MeV , and alpha particles of 2, 5, 7 and 10 MeV. The number of particles in each case is such that the absorbed doses range between 0.5 Gy and 16 Gy. The three models proved to be consistent with the dimensions of the real structures. In particular, the models were compatible with the 30 nm chromatin fiber diameter requirement as well as with the bp volumes reported in other works. The Total and Double Strand Break Yields (TSBY and DSBY) were obtained for every radiation quality. Also, the Site-Hit Probability (SHP) defined as the total target to the nucleus volume ratio, was computed theoretically and from the simulations. The biophysical model in conjunction with the MC simulations furnished the number of lethal lesions (N_LL) as a function of dose, for protons of 0.5 and 10 MeV , and for alpha particles of 2 and 10 MeV . The N_LL could be split into those created by a single track and those originated by interaction of two tracks. It is concluded that the TSBY is practically determined by the SHP and depends weakly on the incident radiation quality. Nevertheless, the DSBY showed strong dependence on both the DNA conformation and the radiation quality. This is due to the interplay between the energy deposition clustering capacity of a given radiation and the DNA spatial packing. On the other hand, the analysis of the mechanisms of damage production based on the DRAT and tested with the biophysical model developed, showed that single-track (first order) effects depend linearly on the dose. Moreover, inter-track effects follows a quadratic behavior with the dose, having a linear term that influences the first order mechanism. This means that the Linear-Quadratic behavior of the N_LL with the dose, has mechanistic groundings at least at the first stage of the damageMestradoFísicaMestre em Física1370449/2014CAPE