A dynamic-shape-prior guided snake model with application in visually tracking dense cell populations

This paper proposes a dynamic-shape-prior guided snake (DSP G-snake) model that is designed to improve the overall stability of the point-based snake model. The dynamic shape prior is first proposed for snakes, that efficiently unifies different types of high-level priors into a new force term. To be specific, a global-topology regularity is first introduced that settles the inherent self-intersection problem with snakes. The problem that a snake’s snaxels tend to unevenly distribute along the contour is also handled, leading to good parameterization. Unlike existing methods that employ learning templates or commonly enforce hard priors, the dynamic-template scheme strongly respects the deformation flexibility of the model, while retaining a decent global topology for the snake. It is verified by experiments that the proposed algorithm can effectively prevent snakes from selfcrossing, or automatically untie an already self-intersected contour. In addition, the proposed model is combined with existing forces and applied to the very challenging task of tracking dense biological cell populations. The DSP G-snake model has enabled an improvement of up to 30% in tracking accuracy with respect to regular model-based approaches. Through experiments on real cellular datasets, with highly dense populations and relatively large displacements, it is confirmed that the proposed approach has enabled superior performance, in comparison to modern active-contour competitors as well as the state-of-the-art cell tracking frameworks

L'élongation embryonnaire précoce du Caenorhabditis elegans : caractérisation de la voie PIX-1/PAK-1

La morphogenèse des tissus est essentielle pour le développement des métazoaires. Elle requiert une coordination d'évènements cellulaires variés, tels que l'adhésion, la migration et le remodelage du cytosquelette d'actine, qui dépendent de la régulation des GTPases Rho. La compréhension des évènements morphogénétiques est un problème multi-échelle qui se traduit par une intégration des niveaux moléculaire, cellulaire, tissulaire et organique. En outre, faire le lien entre les réseaux de régulation protéique et la morphogénèse reste un défit majeur. Le nématode Caenorhabditis elegans est un modèle de choix dans l'étude du développement embryonnaire et de la morphogenèse. Au laboratoire, nous étudions l'élongation embryonnaire du C. elegans, une étape tardive du développement qui permet à l'embryon ovoïde d'acquérir sa forme de ver. Spécifiquement, je me suis intéressé à l'étape précoce de l'élongation embryonnaire. Cette étape est dirigée par la contraction des filaments d'actine-myosine au pôle apical des cellules latérales de l'épiderme. Selon le modèle accepté au début de mes travaux, les cellules ventrales et dorsales sont dans un état relâché pendant toute l'élongation précoce. Deux voies de signalisation redondantes dirigent la contraction du cytosquelette, la voie mel-11/let-502 et la voie pak-1. Afin de mieux caractériser les voies contrôlant l'élongation précoce, nous avons développé des méthodes permettant l'analyse des embryons à l'échelle de l'organisme ainsi qu'à l'échelle cellulaire. Ces analyses nous ont révélé que PIX-1/β-PIX, une GEF pour les GTPases Rac et Cdc42, contrôle l'élongation précoce dans la voie PAK-1, en parallèle de la voie MEL-11/LET-502. Elles ont aussi montré que PIX-1 et PAK-1 régulent principalement la réduction de la largeur de la tête à ce stade, alors que LET-502 contrôle la réduction de la largeur de la tête et de la queue de l'embryon. Spécifiquement, PIX-1 et PAK-1 régulent le remodelage des jonctions apicales et la formation de lamellipodes polarisés dans les cellules dorsales antérieures. LET-502 contrôle le remodelage des jonctions apicales et la morphologie de protrusions de type amiboïde dans les cellules latérales. Cette étude révèle donc que l'adoption d'un programme pix-1/pak-1 ou let-502 par la cellule définit son comportement et sa morphologie au cours de l'élongation. Enfin, nous avons montré que la dominance cellulaire d'un programme est contrôlée par l'antagonisme entre pix-1/pak-1 et let-502. En conclusion, ce travail démontre que les voies pix-1/pak-1 et let-502 agissent de façon redondantes et synergiques à l'échelle de l'organisme, et antagonistes à l'échelle cellulaire. Ce travail apporte des modifications majeures au modèle précédemment établi permettant d'expliquer la base moléculaire de l'élongation embryonnaire précoce du C. elegans.\ud ______________________________________________________________________________ \ud MOTS-CLÉS DE L’AUTEUR : GTPases Rho, morphogenèse, épiderme, C. elegans, PIX, PA

Tracking Epithelial Cell Junctions in C. elegans Embryogenesis with Active Contours Guided by SIFT Flow

Quantitative analysis of cell shape in live samples is an important goal in developmental biology. Automated or semiautomated segmentation and tracking of cell nuclei has been successfully implemented in several biological systems. Segmentation and tracking of cell surfaces has been more challenging. Here, we present a new approach to tracking cell junctions in the developing epidermis of C. elegans embryos. Epithelial junctions as visualized with DLG-1::GFP form lines at the subapical circumference of differentiated epidermal cells and delineate changes in epidermal cell shape and position. We develop and compare two approaches for junction segmentation. For the first method (projection approach), 3-D cell boundaries are projected into 2D for segmentation using active contours with a nonintersecting force, and subsequently tracked using scale-invariant feature transform (SIFT) flow. The resulting 2-D tracked boundaries are then back-projected into 3-D space. The second method (volumetric approach) uses a 3-D extended version of active contours guided by SIFT flow in 3-D space. In both methods, cell junctions are manually located at the first time point and tracked in a fully automated way for the remainder of the video. Using these methods, we have generated the first quantitative description of ventral epidermal cell movements and shape changes during epidermal enclosure

Grand Celebration: 10th Anniversary of the Human Genome Project

In 1990, scientists began working together on one of the largest biological research projects ever proposed. The project proposed to sequence the three billion nucleotides in the human genome. The Human Genome Project took 13 years and was completed in April 2003, at a cost of approximately three billion dollars. It was a major scientific achievement that forever changed the understanding of our own nature. The sequencing of the human genome was in many ways a triumph for technology as much as it was for science. From the Human Genome Project, powerful technologies have been developed (e.g., microarrays and next generation sequencing) and new branches of science have emerged (e.g., functional genomics and pharmacogenomics), paving new ways for advancing genomic research and medical applications of genomics in the 21st century. The investigations have provided new tests and drug targets, as well as insights into the basis of human development and diagnosis/treatment of cancer and several mysterious humans diseases. This genomic revolution is prompting a new era in medicine, which brings both challenges and opportunities. Parallel to the promising advances over the last decade, the study of the human genome has also revealed how complicated human biology is, and how much remains to be understood. The legacy of the understanding of our genome has just begun. To celebrate the 10th anniversary of the essential completion of the Human Genome Project, in April 2013 Genes launched this Special Issue, which highlights the recent scientific breakthroughs in human genomics, with a collection of papers written by authors who are leading experts in the field

The HBP1 tumor suppressor is a negative epigenetic regulator of MYCN driven neuroblastoma through interaction with the PRC2 complex

C

Genetic variants associated with ectopic calcifications

Diffuse idiopathic skeletal hyperostosis (DISH) is a common skeletal disorder characterized by the presence of new bone formation in ligaments and entheses. DISH can co-exist with Chondrocalcinosis (CC) and it has been suggested that both diseases share the same pathogenic mechanism. To date, two genes, COL6A1 and FGF2, have been shown to have a weak positive association with DISH susceptibility. The main objective of this thesis was to investigate the genetic basis of the DISH/CC disease, making use of Next Generation Sequencing technology, association and expression studies, in a group of DISH/CC samples from the Azores biobank. Two regulatory variants in the RSPO4 gene were significantly more frequent in controls than in DISH/CC patients. These may protect against the DISH/CC phenotype, possibly by altering gene expression of the RSPO4 gene. Using whole exome sequencing we identified a significant association between the DISH/CC disease and a genetic variant in BMP4 (rs17563), a gene involved in endochondral bone formation. Another of the candidate genes associated with DISH/CC was ABCC6 that is of relevance in ectopic calcification disorders. Although inconclusive, the expression studies performed in human cartilage tissue indicated overexpression of ABCC6 in DISH and CC patients relative to the controls, raising the hypothesis that this gene may be involved in calcium pyrophosphate formation in DISH and CC. A comparative approach using teleosts revealed that the abcc6 gene is expressed in skin but was not associated with ectopic calcification of the scales. Furthermore, comparative genomics revealed the abcc6 has only been retained in the genome of bony vertebrates. In summary, I identify for the first time potential gene variants that protect (RSPO4) or predispose (BMP4) to DISH/CC. The relevance of the ABCC6 gene in this phenotype remains to be proven. It is unlikely that one major gene is responsible for DISH/CC and instead it appears to be a polygenic disease.A hiperostose idiopática difusa do esqueleto (DISH) é uma doença musculoesquelética comum caracterizada pela formação óssea de novo em ligamentos e enteses. A DISH pode coexistir com a condrocalcinose e por isso tem sido sugerido que ambas partilham o mesmo mecanismo patogénico. COL6A1 e FGF2 são os dois genes de suscetibilidade conhecidos com uma ligação genética fraca à DISH. O objetivo principal desta tese foi investigar a genética da DISH/CC, utilizando a sequenciação de nova geração e estudos de associação e expressão, num grupo de amostras de doentes com DISH/CC do AZORBIO. Duas variantes na região reguladora do gene RSPO4 são significativamente mais frequentes nos controlos do que nos doentes DISH/CC. Estas variantes podem afetar a expressão do gene, conferindo proteção à doença. Utilizando a sequenciação exómica identificamos uma associação significativa entre a DISH/CC e a variante genética rs17563 no gene BMP4, um gene diretamente envolvido na formação óssea endocondral. Outro gene candidato estudado foi o ABCC6, que parece ser relevante em doenças caracterizadas por calcificações ectópicas. Embora inconclusivos, os estudos de expressão em tecidos de cartilagem humana mostraram que o gene ABCC6 apresenta expressão superior nos doentes DISH e CC em relação a um doente controlo, levantando a hipótese de que este aumento de expressão poderá estar envolvido com a deposição de cristais de pirofosfato de cálcio nestes doentes. Uma abordagem comparativa utilizando teleósteos revelou que o gene abcc6 está expresso na pele dos peixes, mas não está associado com a calcificação ectópica das escamas. Além disso, nos resultados da genómica comparativa o gene abcc6 só foi encontrado no genoma de vertebrados ósseos, indicando que este gene poderá estar envolvido em inovações específicas dos vertebrados. Concluindo, foi identificado pela primeira vez potenciais variantes genéticas que protegem (RSPO4) ou predispõem (BMP4) à DISH/CC. A relevância do gene ABCC6 neste fenótipo necessita de ser provada. É pouco provável que um único gene esteja envolvido no aparecimento de DISH/CC, e por isso a doença parece ser poligénica.O trabalho foi co-financiado pelo Fundo Regional da Ciência e Tecnologia dos Açores através do projeto M3.1.2/F/023/201

Smoking and Second Hand Smoking in Adolescents with Chronic Kidney Disease: A Report from the Chronic Kidney Disease in Children (CKiD) Cohort Study

The goal of this study was to determine the prevalence of smoking and second hand smoking [SHS] in adolescents with CKD and their relationship to baseline parameters at enrollment in the CKiD, observational cohort study of 600 children (aged 1-16 yrs) with Schwartz estimated GFR of 30-90 ml/min/1.73m2. 239 adolescents had self-report survey data on smoking and SHS exposure: 21 [9%] subjects had “ever” smoked a cigarette. Among them, 4 were current and 17 were former smokers. Hypertension was more prevalent in those that had “ever” smoked a cigarette (42%) compared to non-smokers (9%), p\u3c0.01. Among 218 non-smokers, 130 (59%) were male, 142 (65%) were Caucasian; 60 (28%) reported SHS exposure compared to 158 (72%) with no exposure. Non-smoker adolescents with SHS exposure were compared to those without SHS exposure. There was no racial, age, or gender differences between both groups. Baseline creatinine, diastolic hypertension, C reactive protein, lipid profile, GFR and hemoglobin were not statistically different. Significantly higher protein to creatinine ratio (0.90 vs. 0.53, p\u3c0.01) was observed in those exposed to SHS compared to those not exposed. Exposed adolescents were heavier than non-exposed adolescents (85th percentile vs. 55th percentile for BMI, p\u3c 0.01). Uncontrolled casual systolic hypertension was twice as prevalent among those exposed to SHS (16%) compared to those not exposed to SHS (7%), though the difference was not statistically significant (p= 0.07). Adjusted multivariate regression analysis [OR (95% CI)] showed that increased protein to creatinine ratio [1.34 (1.03, 1.75)] and higher BMI [1.14 (1.02, 1.29)] were independently associated with exposure to SHS among non-smoker adolescents. These results reveal that among adolescents with CKD, cigarette use is low and SHS is highly prevalent. The association of smoking with hypertension and SHS with increased proteinuria suggests a possible role of these factors in CKD progression and cardiovascular outcomes