In an experiment to understand colon carcinogenesis, all animals were exposed to a carcinogen while half the animals were also exposed to radiation. Spatially, we measured the existence of aberrant crypt foci (ACF), namely morphologically changed colonic crypts that are known to be precursors of colon cancer development. The biological question of interest is whether the locations of these ACFs are spatially correlated: if so, this indicates that damage to the colon due to carcinogens and radiation is localized. Statistically, the data take the form of binary outcomes (corresponding to the existence of an ACF) on a regular grid. We develop score??type methods based upon the Matern and conditionally autoregression (CAR) correlation models to test for the spatial correlation in such data, while allowing for nonstationarity. Because of a technical peculiarity of the score??type test, we also develop robust versions of the method. The methods are compared to a generalization of Moran??s test for continuous outcomes, and are shown via simulation to have the potential for increased power. When applied to our data, the methods indicate the existence of spatial correlation, and hence indicate localization of damage. Assuming that there are correlations in the locations of the ACF, the questions are how great are these correlations, and whether the correlation structures di?er when an animal is exposed to radiation. To understand the extent of the correlation, we cast the problem as a spatial binary regression, where binary responses arise from an underlying Gaussian latent process. We model these marginal probabilities of ACF semiparametrically, using ?xed-knot penalized regression splines and single-index models. We ?t the models using pairwise pseudolikelihood methods. Assuming that the underlying latent process is strongly mixing, known to be the case for many Gaussian processes, we prove asymptotic normality of the methods. The penalized regression splines have penalty parameters that must converge to zero asymptotically: we derive rates for these parameters that do and do not lead to an asymptotic bias, and we derive the optimal rate of convergence for them. Finally, we apply the methods to the data from our experiment.

Ziel der vorliegenden Arbeit war es, 1. die Einflüsse von Alter bzw. Parität auf Prävalenz und Entwicklung endometrialer Alterationen beim Rind zu untersuchen, 2. einen repräsentativen Überblick über die mittels Endometriumbiopsie erfassbaren Erkrankungen bei klinisch gesunden Kühen zu schaffen 3. die Entwicklung der histopathologischen Befunde nach einer weiteren Trächtigkeit zu dokumentieren. Grundlage dieser Arbeit sind sechs Endometriumbioptate von klinisch (inklusive rektaler Untersuchung) gesunden Färsen (Gruppe A), 165 Bioptate von klinisch gesunden Kühen (Gruppe B) sowie Bioptat-Paare (Gruppe C) von 46 Tieren, die im Abstand einer Trächtigkeit entnommen wurden. Die Proben der Gruppe A dienten als Kontrollgruppe, wobei die Gefäße als Grundlage für die Normalstruktur vor der ersten Trächtigkeit herangezogen wurden. Innerhalb der Endometriumbioptate der Färsen (Gruppe A) waren keine pathologischen Veränderungen (Endometritis, Endometrose, Angiosklerose) und keine Lymphfollikel nachweisbar. Bezüglich der Endometritis-Prävalenz, die bei 23,6 % lag, ließ sich in Gruppe B keine Abhängigkeit von der Parität oder dem Entnahmezeitpunkt nachweisen. Eine Endometrose trat überwiegend bei Erstkalbinnen (24,4 %) und Tieren mit fünf Abkalbungen (41,6 %) auf. Eine Korrelation mit dem Alter lag nicht vor. Auffällig war die signifikant höhere Endometrose-Prävalenz innerhalb der ersten acht Wochen p.p. (20,1 %), im Vergleich zu später entnommenen Proben (3,2 %). Für das Auftreten von Lymphfollikel, die im Mittel bei 53,3 % der Kühe auftraten, konnten keine Korrelationen mit der Parität oder dem Zeitpunkt der Bioptatentnahme ermittelt werden. Auch scheint weder das Vorliegen einer Endometritis die Entwicklung von Lymphfollikeln zu begünstigen, noch schützen Lymphfollikel im Endometrium vor einer Entzündung des Uterus. Mit steigender Parität war eine Zunahme der Angiosklerose-Prävalenz zu verzeichnen, allerdings konnte keine statistisch signifikante Korrelation zum Grad der Gefäßveränderungen (anhand der H.E.-Färbung) nachgewiesen werden. Innerhalb der Karunkel lagen signifikant höhergradige Veränderungen vor als in interkarunkulären Gefäßen. Da das Alter der Tiere eng mit der Anzahl der Abkalbungen korreliert, war eine gesonderte Betrachtung der altersassoziierten Einflüsse anhand des untersuchten Materials nicht möglich. Mittels der durchgeführten Untersuchungen ließ sich kein negativer Einfluss der vorwiegend geringgradigen histopathologischen Veränderungen im Endometrium (Endometritis, Endometrose, Angiosklerose, Lymphfollikel) auf die Fertilität (Erstbesamungserfolg, Rastzeit, Güstzeit, Gesamtträchtigkeitsrate) nachweisen. Innerhalb der Gruppe C konnte nach einer weiteren Trächtigkeit ein signifikanter Anstieg der Endometrose-Prävalenz von 7,0 % auf 25,6 % nachgewiesen werden, während der Anteil der Tiere mit einer Endometritis bzw. Angioskerose nahezu unverändert blieb. Bei einigen Tieren wurde allerdings in der ersten Probe, jedoch nicht im Folgebioptat, eine Endometrose diagnostiziert. Bei einer Kuh lag dabei sogar zuerst eine mittelgradige periglanduläre Fibrose vor, die im zweiten Bioptat nicht mehr nachweisbar war. Im Hinblick auf die Entwicklung vaskulärer Alterationen konnte nach einer weiteren Trächtigkeit eine signifikante Zunahme der Faserzubildungen (Pikrosiriusrot-Färbung) in der Tunica media interkarunkulärer arterieller Gefäße und karunkulärer Arterien sowie in der Tunica adventitia von interkarunkulären Arteriolen nachgewiesen werden. Weiterhin wurden im Zweitbioptat anhand der Pikrosiriusrot-Färbung signifikant höhergradigere Veränderungen (Gesamtschädigung) der karunkulären Arterien und Arteriolen diagnostiziert. Für alle übrigen Gefäßtypen lag zwar eine Zunahme der Gesamtschädigung im zweiten Bioptat vor, diese war jedoch nicht statistisch signifikant. Zu beiden Untersuchungszeitpunkten konnten innerhalb des untersuchten Materials vor allem Elastosen und Elastofibrosen nachgewiesen werden. Dabei lagen bezüglich der Art der zugebildeten Fasern keine signifikanten Unterschiede zwischen beiden Proben vor. Insgesamt konnten anhand des untersuchten Materials von klinisch gesunden Kühen zahlreiche pathologische Befunde im Endometrium diagnostiziert werden. Allerdings ist die Interpretation der Befunde bislang schwierig, da keine Einflüsse auf die Fertilität nachweisbar waren. Jedoch lagen besonders im Hinblick auf die Endometritis und Endometrose meist nur geringgradige Veränderungen vor, so dass sich diese vermutlich nicht negativ auf die Fruchtbarkeit auswirken. Weiterhin ist anhand der vorliegenden Ergebnisse fraglich, ob eine Endometrose beim Rind als irreversible Erkrankung angesehen werden muss. Hierzu sind weitere Studien erforderlich.

This thesis deals with infectious diseases transmitted by arthropods in the Czech Republic in period of 2002 - 2011. Meeting the objectives and answer the research questions, I managed using secondary analysis of reported cases infectious diseases transmitted by arthropods in the information system for reporting and recording of infectious diseases - EPIDAT and literature review and subsequent analysis of scientific articles. Important additional informations were provided by State Veterinary Institute in Prague and the National Reference Laboratory for arboviruses in Ostrava. Thesis does not deal with number of single values, but it is focused on epidemiological severity of analyzed cases, severity of clinical course and risk of introducing infection in the Czech Republic. Theoretical part of the thesis describes selected arboviruses infections. Tick-borne encephalitis is one of the most important diseases transmitted by arthropods in our surroundings. Number of reported cases of tick-borne encephalitis was quite constant in monitored period 2002 - 2011, according to my research and statistical verification. Highest morbidity was in 2006. The same year the highest incidence of disease Tick-borne encephalitic was reported in region of Vysočina. This number is far closer to number of reported cases in region of South Bohemia which was the most affected region thought the entire period. Prevention exists against tick-borne encephalitis. It is vaccination which is recommended for people staying in natural foci of infection in the Czech Republic and abroad. In the Czech republic becomes more important West Nile fever. Increased incidence of this disease is recorded in the USA, but also in many European countries (eg Greece, Hungary, Italy) in recent years. One of the goals of this thesis is to characterize the surveillance of West Nile fever in the Czech republic. Monitoring antibody titer against West Nile virus in the serum of horses is one of the basic elements of surveillance of this disease in our country. 5 samples of the blood serum was increased titers of antibodies to West Nile virus. Various geographic distribution of horses and high specific antibody titers indicate increasing activity of West Nile virus. Clinical disease of horses not being recorded in the Czech republic. In the field of human medicine have been reported three imported cases of West Nile fever. Other arboviruses infections, that appeared in our country, is dengue disease and viral disease Chikungunya. In the monitored period there were a total of 98 reported cases of imported disease. Most cases were imported from India. Three cases of Chikungunya disease were reported in 2006 in connection with a stay on the island of Mauritius, where was the epidemic at this time. People can travel freely and there is the risk of importing diseases from the tropics and subtropics. Some infections transmitted by arthropods are in areas where it was previously absent recently. Prevention is essential. Specific and non-specific prevention. Another important element of prevention is strict adherence to methods for surveillance of disease.Viral infections transmitted by arthropods are among the most important emergent infectious diseases. In addition to malaria, malnutrition and helminth infection are the largest public health problem, not only in third world countries.

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No. of bitstreams: 2 Dissertação - Lucas Fiorini Cruz - 2018.pdf: 23542908 bytes, checksum: 75e04989d0719a9b5d0d22225c38ce7a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2018-05-18 / Electroencephalography (EEG) measurements are widely used in clinical assessments for research due to its noninvasive nature and for providing several informations on the neural activity associated to both neural functions and disorders, including epilepsy syndromes. In cases related with partial epilepsy, surgical interventions are recommended and the accurate location of the seizure becomes a sine qua non prerequisite for those procedures. Brain source position estimation can help in the selection and classification of brain spots. In this sense, for control purposes, this work begins with the development of a mathematical model that is more electromagnetically representative than the usual model, presenting different aggregate characteristics such as refraction and, especially, frequency dependent attenuation of the wave. We also propose a new method that estimates the source positions from spectral peaks produced by the eigenvalues of the sum of the spatial covariance matrix of the EEG signals and a spatial covariance matrix related to a simulated source that is numerically swept throughout every point on different horizontal layers of the brain. The key approach was to select the eigenvalues that were less affected by the noise and use them to produce the search spectrum. In order to assess the accuracy and robustness of the proposed method, we compared its RMSE (Root Mean Square Error) performance at different SNRs (Signal-to-Noise Ratio) to those of MUSIC (Multiple Signal Classification), a method based on orthogonal subspaces, and NSF (Noise Subspace Fitting), a method based on subspace fitting. The results were produced for both the usual and proposed signal model in order to evaluate their accuracy. Subsequently, the signal models were compared after spatial filtering, aiming the determination of the waveform of a particular source. The proposed approach presents the lowest threshold SNR and the highest accuracy under noisy conditions for all analyzed cases and for both models. The new approach for the signal model made the estimation more accurate in all the studied cases, besides providing greater accuracy on spatial filtering, when compared to the usual model. / Sinais de eletroencefalografia (EEG) são amplamente utilizados em análises clínicas e para fins de pesquisas devido ao seu caráter não invasivo e por possuírem informações sobre as atividades neurais ligadas às funções e anomalias cerebrais, incluindo a epilepsia. Nos casos relacionados à epilepsia parcial, intervenções cirúrgicas são recomendadas e a precisa localização da região epileptogênica é uma condição sine qua non para tal procedimento. Nesse sentido, para fins de controle, este trabalho se inicia com a proposta de um novo modelo matemático das atividades elétricas do cérebro que, quando comparado ao modelo Dipolo elétrico - encontrado na literatura - aproxima-se mais do real, apresentando diferentes características agregadas como refração e, especialmente, atenuação dependente da frequência da onda. Em outro plano, também é proposto um novo método que estima as posições das fontes elétricas cerebrais a partir de picos espectrais produzidos por autovalores da soma da matriz de covariância espacial do sinal EEG com uma matriz de covariância espacial relacionada a uma fonte simulada que, numericamente, é posicionada em pontos de diferentes camadas horizontais do cérebro. A chave para essa abordagem é selecionar os autovalores menos afetados pelo ruído e utilizá-los para construir o espectro de busca. Para analisar a robustez e acurácia do método, avalia-se o seu desempenho em relação à raiz do erro médio quadrático (REMQ) para diferentes valores de relação sinal-ruído (SNR), comparando-o ao algoritmo MUSIC (Multiple Signal Classification), baseado em subespaços ortogonais, e ao NSF (Noise Subspace Fitting), método baseado em “distância” entre subespaços (subspace fitting). Todos os resultados são gerados para o modelo de sinal usual e o proposto, com fim de avaliar a acurácia conferida a cada um destes. Posteriormente, os modelos de sinal são comparados quanto à filtragem espacial, buscando a determinação da forma de onda de uma fonte em particular. A abordagem proposta apresenta uma menor SNR de limiar de desempenho e uma maior acurácia sob condições ruidosas em todos os casos analisados e nos dois modelos. O novo modelo do sinal tornou a estimação DOA mais precisa em todos os casos estudados, além de ter conferido maior precisão à filtragem espacial, quando comparado ao modelo usual.

O presente trabalho pretende contribuir com o aprofundamento da discussão em torno das dinâmicas espaciais urbanas materializadas nas permanências e transformações na paisagem urbana. A partir de tais dinâmicas se constituem os patrimônios históricos e culturais como proposta institucional para a consolidação e a permanência de determinados valores e identidades significativas. O objetivo geral é fornecer subsídios para compreensão de tais dinâmicas a partir da dimensão cultural da cidade, tomando o Centro de São Paulo como objeto. O objetivo específico é identificar e compreender as condições em que se constituem os significados do patrimônio ambiental urbano a partir das práticas sociais. Neste sentido, proponho a noção de focos qualitativos como lugares portadores de um potencial de significação que, independentemente de incluírem elementos arrolados oficialmente como bens patrimoniais, desempenham o papel de referência, orientação e identidade espacial na perspectiva do espaço vivido e do cotidiano do habitante. Esta hipótese implica em que os focos qualitativos constituam instrumento para a formulação das condições de qualificação do espaço urbano através da compreensão dos modos pelos quais os valores propostos pelo patrimônio ambiental urbano são vivenciados e apropriados nas práticas sociais e no cotidiano / The present work intends to contribute with the deepening of the discussion around the urban space dynamics, materialized in the permanence and changes in urban landscape. Such dynamics constitute the historic sites and cultural heritage as the institutional proposal to consolidate and conserve significant social values and identities. Thus, the general objective is to supply subsidies to understanding such dynamics from the perspective of the city\'s cultural dimension, taking São Paulo downtown as object. The specific objective is to identify and understand the conditions of constitution of the urban environmental heritage meanings from the perspective of social practices. In this way, I consider the notion of qualitative foci as places of potential meaning that, independently of being officially admitted as cultural heritage, play the role of reference, orientation and space identity in the perspective of the lived space and the daily life of the inhabitants. This hypothesis implies that qualitative foci constitute an instrument to formulate the conditions of urban space qualification through the understanding of the ways in which the values proposed by the environmental urban heritage are lived and appropriated in social practices and daily life.

Abstract In the Western world, colorectal cancer (CRC) is one of the most common cancers and causes of cancer deaths. It is estimated that up to a third of CRCs represent a recently defined subtype, serrated adenocarcinoma (SAC), which develops via the serrated pathway and differs from conventional cancer by molecular, histological, and clinicopathological characteristics. The oncogenic mutation of BRAF V600E is characteristic to the serrated pathway lesions, and VE1 is a novel antibody that has been reported to recognize this mutated BRAF protein. In these studies, two independent cohorts of CRCs and a cohort of 922 colorectal polyps (545 patients) consecutively removed in Oulu University Hospital were utilized to study potential immunohistochemical markers (annexin A10 and VE1) as markers for the serrated pathway lesions, to investigate the presence of ectopic crypt foci (ECF) in different colorectal polyps and CRCs, and to study the network of determinants and the clinical impact of tumor necrosis with special regard to SAC. VE1 immunohistochemistry was found a sensitive and accurate method in the detection of BRAF V600E mutation with potential applications in the recognition of the BRAF V600E-mutated SACs. Annexin A10 immunohistochemistry was indicated to be a marker with high specificity for the serrated pathway lesions. ECF were found to be frequently encountered in addition to traditional serrated adenomas also in the tubular, tubulovillous and villous adenomas. Tumor necrosis in CRC was associated with high tumor stage and inversely associated with the serrated histology. High tumor necrosis percentage correlated with poor survival in CRC independently of other clinicopathological factors. In conclusion, these studies add to the knowledge of the molecular and histological features of SAC and its precursors. The results suggest that VE1 and ANXA10 immunohistochemistry may help in the recognition of the serrated pathway lesions. ECF can be found in other colorectal polyps in addition to traditional serrated adenomas. Tumor necrosis represents a relevant histomorphological prognostic indicator in CRC. / Tiivistelmä Paksu-peräsuolisyöpä on yksi yleisimmistä syövistä länsimaissa. Arviolta kolmasosaa kaikista paksu-peräsuolisyövistä edustava sahalaitainen adenokarsinooma eroaa tavallisesta adenokarsinoomasta molekulaaristen muutostensa sekä histologisten ja kliinispatologisten piirteidensä perusteella. BRAF-onkogeenin V600E-mutaatiota tavataan vain paksu-peräsuolisyövän sahalaitaisen kehittymisreitin muutoksissa ja VE1-immunohistokemian on todettu tunnistavan tämän mutatoituneen BRAF-proteiinin. Tutkimuksessa käytettiin kahta itsenäistä paksu-peräsuolisyöpäaineistoa sekä polyyppiaineistoa, joka käsitti 922 Oulun yliopistollisessa sairaalassa peräkkäisissä kolonoskopioissa poistettua paksu-peräsuolen polyyppia (545 potilasta). Tutkimuksen tarkoituksena oli selvittää kahden immunohistokemiallisen merkkiaineen (VE1 ja annexin A10) spesifisyyttä sahalaitaiselle adenokarsinoomalle ja sen esiastemuutoksille, ektooppisten kryptafokusten esiintymistä paksu-peräsuolen polyypeissa sekä kasvaimen nekroosiin yhteydessä olevia tekijöitä ja nekroosin ennustevaikutusta. VE1-immunohistokemia oli sekä sensitiivinen että spesifinen BRAF V600E-mutaation toteamisessa, minkä vuoksi sitä voidaan käyttää BRAF V600E-mutatoituneiden sahalaitaisten adenokarsinoomien tunnistamisessa. Annexin A10-immunohistokemia osoittautui spesifiseksi sahalaitaisen kehittymisreitin muutosten toteamissa. Ektooppisia kryptafokuksia havaittiin traditionaalisen sahalaita-adenooman lisäksi myös tubulaarisissa, tubulovillooseissa ja villooseissa adenoomissa. Kasvaimen nekroosi oli vähäisempää sahalaitaisessa adenokarsinoomassa sekä matalan levinneisyysasteen kasvaimissa. Runsas nekroosin määrä oli kasvaimen levinneisyydestä riippumatta yhteydessä huonompaan ennusteeseen. Tutkimus lisää tietoa sahalaitaisesta adenokarsinoomasta ja sen esiastemuutoksista. Tulokset osoittavat, että VE1 ja annexin A10 -immuno¬histokemia auttaa sahalaitaisen kehittymisreitin muutosten tunnistamisessa; ektooppisia kryptafokuksia voidaan nähdä traditionaalisten sahalaita-adenoomien lisäksi myös muissa paksu-peräsuolen polyypeissa; lisäksi todettiin, että kasvaimen nekroosin määrällä on vaikutusta paksu-peräsuolisyövän ennusteen arvioinnissa.

Les cassures double-brin de l’ADN (CDB) sont des événements clés dans la réponse aux rayonnements ionisants qui, avec le profil génétique et épigénétique individuel, peuvent conditionner le devenir des tissus sains d’un individu exposé. À la suite des cassures de la molécule d’ADN et de la déstabilisation de la chromatine, une série de modifications post-traductionnelles des histones se produit, notamment la phosphorylation de la serine 139 de l'histone H2A.X (gamma-H2A.X), conduisant à la formation de foyers radio-induits. La réparation des CDB, et donc la disparition de ces foyers, a lieu dans les heures suivant l’exposition. Toutefois, une certaine proportion de ces foyers gamma-H2A.X persiste 24 heures après l’irradiation. La nature et le rôle de ces foyers persistants sont encore peu clairs. L’objectif de ce travail est d'explorer les caractéristiques de ces foyers persistants et leurs conséquences sur le devenir des cellules. Pour étudier la dynamique des foyers radio-induits, nous avons exposé des HUVEC synchronisées en phase G0/G1 à des doses de 1 et 5 Gy de rayons X. Les foyers radio-induits ont été étudiés à partir de 10 minutes et jusqu'à 7 jours après l'exposition par l’analyse de gamma-H2A.X et de l’association temporelle de la protéine 53BP1 et des CN-PML (corps nucléaires PML). L’impact des foyers persistants sur la prolifération cellulaire a également été exploré. Nous avons analysé en microscopie à fluorescence une moyenne de 4 000 cellules pour chaque condition à l'aide d'une analyse d’image permettant la détection automatique des noyaux et des foyers. L'analyse d'un grand nombre d‘évènements nous a permis de discriminer des sous-populations de cellules ou de foyers sur la base de différentes caractéristiques, telles que leur aire ou la phase du cycle cellulaire, et de mesurer leur représentativité dans l'ensemble de la population de cellules exposées. Ainsi, nous avons déterminé que les foyers gamma-H2A.X persistant ont une aire supérieure à 0,72 ± 0,11 µm² et qu’ils sont toujours colocalisés avec 53BP1. Plus de 70% des cellules exposées à 5 Gy ont au moins un foyer persistant 24 heures après l'exposition. De plus, ces foyers persistants sont observables au moins jusqu'à 7 jours après l’irradiation. Une association spatiale significative entre les CN-PML et les foyers gamma-H2A.X a été observée à partir de 10 minutes après l'exposition et 24 heures après l’exposition, environ 90% des foyers persistants sont associés à un CN-PML. De plus, la présence de foyers persistants ne bloque pas définitivement la prolifération des cellules. Cependant, la fréquence des foyers persistants est plus faible dans les cellules filles que dans les cellules irradiées, probablement en raison d'une certaine proportion de distribution asymétrique des foyers persistants entre les cellules filles. Nous avons également mesuré une corrélation positive entre la présence d'un foyer persistant et la probabilité de mauvaise ségrégation de l'ADN par l'observation de phénomènes de catastrophes mitotiques. Il semble donc que la structure formée après le passage d'un foyer persistant à travers les phases S et G2 soit susceptible d’empêcher la séparation correcte des chromatides sœurs du chromosome affecté. Nous suggérons donc que la nature des foyers persistants n’est pas la même avant et après la première division cellulaire due à une résolution anormale de l'anaphase. Ces assemblages chromosomiques atypiques résultants d’anaphases anormales pourraient être létaux pour la cellule ou entraîner un déséquilibre du dosage génique et une instabilité génomique accrue pouvant conduire à une mosaïque de phénotypes cellulaires. / The DNA double-stranded breaks (DSB) are key events in the cell response to ionizing radiation that may affect, with the individual genetic and epigenetic profile, the fate of healthy tissues of people exposed. Following initial breaks and chromatin destabilization, a set of post-translational modifications of histones occurs, including the phosphorylation of serine 139 of histone H2AX (gamma-H2A.X), which leads to the formation of ionizing radiation-induced foci (IRIF). DSB repair results in the disappearance of most IRIF within hours after exposure. However, a proportion of IRIF remains 24 hours upon irradiation. The nature and role of these persistent IRIF are still unclear. The goal of this work is to explore the characteristics of these persistent IRIF and their consequences on the cell behavior. To investigate the dynamic of IRIF in our model, we exposed G0/G1-phase synchronized HUVECs to 1 or 5 Gy of X-rays. IRIF were studied from 10 minutes up to 7 days after exposure by monitoring gamma-H2A.X foci, their temporal association with 53BP1 protein and PML NBs (Promyelocytic leukemia nuclear bodies), and their impact on cell proliferation. We analyzed a mean of 4 000 cells for each condition using an automated detection of nuclei and foci. The analysis of a large number of cells and foci allowed us to screen subpopulations of cells or foci through different characteristics, such as size, shape or cell cycle phase among others, and to weight their representativeness in the whole population of exposed cells. We identified that persistent gamma-H2A.X foci after irradiation had a size superior to 0.72 ± 0.11 µm² and always collocated with 53BP1. More than 70% of cells exposed to 5 Gy had at least one persistent IRIF 24 hours after exposure and we observed these persistent IRIF up to 7 days post irradiation. A significant spatial association between PML NBs and IRIF was observed from 10 minutes after exposure; at 24h post irradiation, around 90% of persistent IRIF were associated with PML NBs. Moreover we demonstrated that persistent IRIF did not block cell proliferation definitively. The frequency of IRIF was lower in daughter cells, probably due to a certain amount of asymmetric distribution of IRIF between them. We report a positive association between the presence of an IRIF and the likelihood of DNA missegregation by observation of mitotic catastrophes. Hence, the structure formed after the passage of a persistent IRIF across the S and G2 phases may impede the correct segregation of sister chromatids of the chromosome affected. Consequently, the nature of IRIF in the nucleus of daughter cells might differ before and after the first cell division due to an abnormal resolution of anaphase. The resulting atypical chromosomal assembly may be lethal or result in a gene dosage imbalance and possible enhanced genomic instability, and could lead to a patchwork of cell phenotypes.

Lors d’un examen ou radiologique, des rayonnements X de basse énergie sont utilisés (<100 keV). Pour certains traitements radiologiques, l’énergie utilisée est de plusieurs MeV. La publication 103 de la CIPR considère actuellement que les photons, indépendamment de leur énergie, ont le même facteur de pondération. Cependant, il existe des différences topologiques à l'échelle nanométrique du dépôt d'énergie des rayonnements X en fonction de leur spectre énergétique. En effet, à mesure que l’énergie des photons décroit, la nature de leurs interactions avec la matière vivante se modifie. Pour étudier ces différences, nous avons caractérisé nos conditions d'irradiation en termes d'énergies initiales des photons, mais surtout en termes de spectres d'énergie des électrons secondaires au niveau du volume cellulaire, en utilisant des simulations de Monte Carlo. Nous nous sommes intéressés à la signalisation des dommages de l'ADN en analysant un grand nombre de foyers γH2A.X après exposition de cellules endothéliales humaines synchronisées en phase G0/G1 à des doses allant de 0,25 à 5 Gy à 40 kV, 220 kV et 4 MV. Le nombre et la distribution spatiale des foyers γH2A.X ont été explorés. Aussi, nous avons étudié la fréquence de division et de mort cellulaire. Nous avons également étudié le taux d’anomalies de ségrégation après la division cellulaire. Nous avons mis en évidence un nombre plus élevé de cassures double-brin de l'ADN signalisées par γH2A.X pour 40 kVp et/ou 220 kVp, comparé à 4 MVp pour les plus fortes doses testées de 2 et 5 Gy. Entre 40 et 220 kVp, aucune différence biologique n’a été observée. Ce manque de différence pourrait s’expliquer par la grande similarité des spectres énergétiques des électrons secondaires, au niveau du volume cellulaire.Le spectre d'énergie des électrons secondaires semble être plus étroitement lié au niveau de dommage à l'ADN mesuré par γH2A.X que le spectre initial des paramètres d'énergie ou de tension des photons. Nos résultats indiquent qu'à mesure que le spectre d'énergie des électrons secondaires augmente, les dommages à l'ADN signalés par γH2A.X diminuent et cet effet est observable au-delà de 220 kVp. / In a radiological examination, low-energy X-radiation is used (<100 keV). For other radiological procedures, the energy used is several MeV. ICRP in publication 103 has currently considered that photons irrespective of their energy have the same radiation weighting factor. Nevertheless, there are topological differences at the nanoscale of X-ray energy deposition as a function of its energy spectrum, meaning that the different interactions with living matter could vary in biological efficacy. To study these differences, we characterized our irradiation conditions in terms of initial photon energies, but especially in terms of energy spectra of secondary electrons at the cell nucleus level, using Monte Carlo simulations. We evaluated signaling of DNA damage by monitoring a large number of γH2A.X foci after exposure of G0/G1-phase synchronized human primary endothelial cells at a dose from 0.25 to 5 Gy at 40 kV, 220 kV and 4 MV X-rays. Number and spatial distribution of γH2A.X foci were explored. In parallel, we investigated cell behavior through cell death and ability of a mother cell to produce two daughter cells. We also studied the missegregation rate after cell division. We report a higher number of DNA double-strand breaks signaled by γH2A.X for 40 kVp and/or 220 kVp compared to 4 MVp for the highest tested doses of 2 and 5 Gy. We observed no difference between the biological endpoint studies with 40 kVp and 220 kVp X-ray spectra. This lack of difference could be explained by the relative similarity of the calculated energy spectra of secondary electrons at the cell monolayer. The energy spectrum of secondary electrons seems to be more closely related to the level of DNA damage measured by γH2A.X than the initial spectrum of photon energy or voltage settings. Our results indicate that as the energy spectrum of secondary electrons increases, the DNA damage signaled by γH2A.X decreases and this effect is observable beyond 220 kVp.

Mutant mRNA and protein both contribute to the clinical manifestation of many repeat-associated neurodegenerative and neuromuscular disorders. The presence of nuclear RNA clusters is a feature shared amongst these diseases, such as C9ORF72/ALS and myotonic dystrophy 1/2 (DM1/2); however, this pathological hallmark has not been conclusively demonstrated in Huntington’s disease (HD) in vivo. Investigations into HD – caused by a CAG repeat expansion in exon 1 of the huntingtin (HTT) gene – have largely focused on toxic protein gain-of-function as a disease-causing feature, with fewer studies investigating the role of mutant HTT mRNA in pathology or pathogenesis. Here we report that in two HD mouse models, YAC128 and BACHD-97Q-ΔN17, mutant HTT mRNA is preferentially retained in the nucleus in vivo. Furthermore, we observed the early, widespread formation of large mutant HTT mRNA clusters (approximately 0.6 to 5 µm3 in size) present in over 50-75% of striatal and cortical neurons. Affected cells were limited to one cluster at most. Endogenous wild-type mouse Htt or human HTT mRNA containing 31 or fewer repeats did not form clusters. Additionally, the aberrantly spliced N-terminal exon 1-intron 1 RNA fragment, HTT1a, also formed clusters that fully co-localized with the mutant HTT mRNA clusters. These results suggest that multiple repeat-containing transcripts can coalesce to form a single cluster in a given cell. Treating YAC128 mice with antisense oligonucleotides efficiently silenced individual HTT mRNA foci but had limited impact on clusters. Our findings identify mutant HTT mRNA clustering as an early, robust molecular signature of HD, further supporting HD as a repeat expansion disease with suspected mRNA involvement.

DNA-Methylierung spielt eine wichtige Rolle bei der Kontrolle der Chromatinorganisation und Genregulation in höheren Eukaryoten und muss zusammen mit der genetischen Information in jedem Zellzyklus dupliziert werden. Bei Mammalia wird DNA durch die DNA-Methyltransferase 1 (DNMT1) methyliert, die dabei mit nuklearen Replikationsstellen (RF) assoziiert und so die Erhaltung des Methylierungsmusters mit der Duplikation der DNA verbindet. In dieser Arbeit wurden die Funktion der regulatorischen Sequenzen in der N-terminalen Domäne von DNMT1 bei der Kontrolle ihrer subnuklearen Lokalisierung während des Zellzyklus und die evolutionäre Konservierung dieser Sequenzen, sowie die Mechanismen die eine Assoziation von Proteinen mit RF vermitteln, untersucht. Es konnte gezeigt werden, dass DNMT1 eine dynamische Verteilung im Kern aufweist, die durch regulatorische Sequenzen zellzyklusabhängig gesteuert wird. Um die subnukleare Verteilung von DNMT1 während des Zellzyklus zu untersuchen, wurden RFP-Ligase Fusionsproteine hergestellt, die als Marker für die Identifikation von Zellzyklusstadien in lebenden Zellen dienen. Verschiedene, mit GFP fusionierte DNMT1 Mutanten wurden zusammen mit RFP-Ligase exprimiert und über einen ganzen Zellzyklus hinweg mit 4-dimensionaler Lebendzellmikroskopie verfolgt. Die PBD (PCNA-Bindungsdomäne) bewirkt die Lokalisierung von DNMT1 an RF während der S-Phase, und die TS (targeting sequence) vermittelt die Retention von DNMT1 an spät replizierendem Heterochromatin von der späten S- bis zur frühen G1-Phase. Im Gegensatz dazu scheint die PBHD (Polybromohomologiedomäne) für die Freisetzung von DNMT1 von perizentrischen Regionen während der G1-Phase notwendig zu sein. Eine Überexpression der TS zu Störung dieser Assoziation, senkt die Überlebensrate der Zellen und fördert die Bildung von Mikronuklei sowie die Verschmelzung von zentromerem Heterochromatin. Diese Ergebnisse zeigen eine neue Funktion für die TS bei der Assoziation von DNMT1 mit perizentrischem Heterochromatin von der später S- über die G2-Phase bis hin zur Mitose, die eine wichtige Voraussetzung für die Erhaltung der DNA-Methylierung und Heterochromatinstruktur und -funktion ist. Datenbankanalysen zeigten, dass es sich bei der TS um eine einzigartige Domäne innerhalb der DNMT1 Proteinfamilie handelt. Innerhalb der DNMT1 Familie besitzen nur die DNMT1 Proteine der Metazoen die PBD. Das lässt vermuten, dass die Verknüpfung von Beibehaltung der DNA Methylierung mit der DNA Replikation nur in Metazoen auftritt, während in Pflanzen und Pilzen alternative Mechanismen zur Aufrechterhaltung des Methylierungsmusters, wahrscheinlich vermittelt durch die TS, zur Anwendung kommen. Die evolutionäre Konservierung von Mechanismen, zur Assoziation von Proteine mit RF in Säugerzellen, wurde durch die Analyse der Säugerproteine PCNA, DNA Ligase I und DNMT1 in Drosophila-zellen direkt getestet. Von allen untersuchten Proteinen assoziiert nur PCNA mit RF, während die anderen nur eine diffuse Verteilung innerhalb des Kerns zeigten, obwohl sie eine funktionale PBD enthalten. Überraschenderweise assoziierte auch die Drosophila DNA Ligase I in Säugerzellen nicht aber in Drosophila-zellen mit RF. Diese Ergebnisse weisen auf Unterschiede in der Dynamik und dem Aufbau der Replikationsmaschinerie in diesen entfernt verwandten Organismen hin, was mit der Vergrösserung und höheren Komplexität des Säugergenoms korreliert. / DNA methylation constitutes an essential epigenetic mark controlling chromatin organization and gene regulation in higher eucaryotes, which has to be duplicated together with the genetic information at every cell division cycle. In mammals duplication of DNA methylation is mediated by DNA methyltransferase-1 (DNMT1). It associates with sites of nuclear DNA replication, called replication foci (RF), and thereby couples maintenance of DNA methylation to DNA duplication. In this work, we have analyzed the role of regulatory sequences in the N-terminal domain of DNMT1 in controlling its subnuclear localization throughout the cell cycle, and the evolutionary conservation of these sequences and of the mechanisms that mediate association of proteins with RF. We provide evidence that DNMT1 shows dynamic subnuclear distribution that is controlled by the regulatory sequences depending on the cell cycle stage. To determine the subnuclear distribution of DNMT1 throughout the cell cycle, an RFP-Ligase fusion protein was developed as a marker that allows identification of the cell cycle stage in live cells. Various DNMT1 mutants fused to GFP were coexpressed with RFP-Ligase and imaged by 4-dimensional live cell microscopy during an entire cell cycle. The PBD (PCNA binding domain) drives the localization of DNMT1 at RF throughout S phase and the TS (targeting sequence) mediates retention of DNMT1 only at the late replicating pericentric heterochromatin from late-S phase until early-G1. In contrast, the PBHD (polybromo homology domain) seems to be required for unloading DNMT1 from the pericentric regions in G1. Overexpression of the TS to interfere with this association lowers cell viability and induces the formation of micronuclei and coalescence of centromeric heterochromatin. These results bring forth a novel function of the TS in mediating association of DNMT1 with pericentric heterochromatin from late-S phase through G2 until mitosis, which is important for maintenance of DNA methylation, and heterochromatin structure and function. Database searches indicate that the TS is a domain unique to the DNMT1 family of proteins. Amongst the DNMT1 family, only the metazoan DNMT1 proteins have the PBD. This suggests that coupling of maintenance of DNA methylation with DNA replication occurs only in metazoans, while plants and fungi have alternative mechanisms that maintain DNA methylation patterns, probably mediated by the TS. The evolutionary conservation of the mechanisms by which proteins associate with RF in mammalian cells was directly tested by analyzing the ability of mammalian replication proteins PCNA and DNA Ligase I as well as DNMT1 to associate with RF in Drosophila cells. Of all the proteins tested, only PCNA associated with RF while the others showed diffused nuclear distribution although they contain a functional PBD. Surprisingly, Drosophila DNA Ligase I associates with RF in mammalian but not in Drosophila cells. These results suggest differences in the dynamics and organization of the replication machinery in these distantly related organisms, which correlates with the increased size and complexity of mammalian genomes.