Investigating the relationship between pollination strategies and the size-advantage model in zoophilous plants using the reproductive biology of Arum cylindraceum and other European Arum species as case studies

The size-advantage model (SAM) explains the temporal variation of energetic investment on reproductive structures (i.e. male and female gametes and reproductive organs) in long-lived hermaphroditic plants and animals. It proposes that an increase in the resources available to an organism induces a higher relative investment on the most energetically costly sexual structures. In plants, pollination interactions are known to play an important role in the evolution of floral features. Because the SAM directly concerns flower characters, pollinators are expected to have a strong influence on the application of the model. This hypothesis, however, has never been tested. Here, we investigate whether the identity and diversity of pollinators can be used as a proxy to predict the application of the SAM in exclusive zoophilous plants. We present a new approach to unravel the dynamics of the model and test it on several widespread Arum (Araceae) species. By identifying the species composition, abundance and spatial variation of arthropods trapped in inflorescences, we show that some species (i.e. A. cylindraceum and A. italicum) display a generalist reproductive strategy, relying on the exploitation of a low number of dipterans, in contrast to the pattern seen in the specialist A. maculatum (pollinated specifically by two fly species only). Based on the model presented here, the application of the SAM is predicted for the first two and not expected in the latter species, those predictions being further confirmed by allometric measures. We here demonstrate that while an increase in the female zone occurs in larger inflorescences of generalist species, this does not happen in species demonstrating specific pollinators. This is the first time that this theory is both proposed and empirically tested in zoophilous plants. Its overall biological importance is discussed through its application in other non-Arum systems.

Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae.

BACKGROUND: Major factors influencing the phenotypic diversity of a lineage can be recognized by characterizing the extent and mode of trait evolution between related species. Here, we compared the evolutionary dynamics of traits associated with floral morphology and climatic preferences in a clade composed of the genera Codonanthopsis, Codonanthe and Nematanthus (Gesneriaceae). To test the mode and specific components that lead to phenotypic diversity in this group, we performed a Bayesian phylogenetic analysis of combined nuclear and plastid DNA sequences and modeled the evolution of quantitative traits related to flower shape and size and to climatic preferences. We propose an alternative approach to display graphically the complex dynamics of trait evolution along a phylogenetic tree using a wide range of evolutionary scenarios. RESULTS: Our results demonstrated heterogeneous trait evolution. Floral shapes displaced into separate regimes selected by the different pollinator types (hummingbirds versus insects), while floral size underwent a clade-specific evolution. Rates of evolution were higher for the clade that is hummingbird pollinated and experienced flower resupination, compared with species pollinated by bees, suggesting a relevant role of plant-pollinator interactions in lowland rainforest. The evolution of temperature preferences is best explained by a model with distinct selective regimes between the Brazilian Atlantic Forest and the other biomes, whereas differentiation along the precipitation axis was characterized by higher rates, compared with temperature, and no regime or clade-specific patterns. CONCLUSIONS: Our study shows different selective regimes and clade-specific patterns in the evolution of morphological and climatic components during the diversification of Neotropical species. Our new graphical visualization tool allows the representation of trait trajectories under parameter-rich models, thus contributing to a better understanding of complex evolutionary dynamics.

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P��<��5������10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

Serum uric acid and gout: from the past to molecular biology.

Abstract Objectives: This review will briefly present the epidemiology and risk factors of gout, with a focus on recent advances. Methods: Key papers for inclusion were identified by a PubMed search, and articles were selected according to their relevance for the topic, according to authors' judgment. Results and conclusions: Gout therapy has remained very much unchanged for the last 50 years, but recently we have seen the approval of another gout treatment: the xanthine oxidase inhibitor febuxostat, and several new drugs are now in the late stages of clinical testing. Together with our enhanced level of understanding of the pathophysiology of the inflammatory process involved, we are entering a new era for the treatment of gout.

'Hearts and bones': the ups and downs of 'plasticity' in stem cell biology.

More than a decade ago, 'plasticity' suddenly became a 'fashionable' topic with overemphasized implications for regenerative medicine. The concept of 'plasticity' is supported by old transplantation work, at least for embryonic cells, and metaplasia is a classic example of plasticity observed in patients. Nevertheless, the publication of a series of papers showing rare conversion of a given cell type into another unrelated cell raised the possibility of using any unaffected tissue to create at will new cells to replace a different failing tissue or organ. This resulted in disingenuous interpretations and a reason not to fund anymore research on embryonic stem cells (ESc). Moreover, many papers on plasticity were difficult to reproduce and thus questioned; raising issues about plasticity as a technical artefact or a consequence of rare spontaneous cells fusion. More recently, reprogramming adult differentiated cells to a pluripotent state (iPS) became possible, and later, one type of differentiated cell could be directly reprogrammed into another (e.g. fibroblasts into neurons) without reverting to pluripotency. Although the latter results from different and more robust experimental protocols, these phenomena also exemplify 'plasticity'. In this review, we want to place 'plasticity' in a historical perspective still taking into account ethical and political implications.

Systems biology of plants : from intraspecific genome variation to computational morphodynamics

Recently, the introduction of second generation sequencing and further advance-ments in confocal microscopy have enabled system-level studies for the functional characterization of genes. The degree of complexity intrinsic to these approaches needs the development of bioinformatics methodologies and computational models for extracting meaningful biological knowledge from the enormous amount of experi��mental data which is continuously generated. This PhD thesis presents several novel bioinformatics methods and computational models to address specific biological questions in Plant Biology by using the plant Arabidopsis thaliana as a model system. First, a spatio-temporal qualitative analysis of quantitative transcript and protein profiles is applied to show the role of the BREVIS RADIX (BRX) protein in the auxin- cytokinin crosstalk for root meristem growth. Core of this PhD work is the functional characterization of the interplay between the BRX protein and the plant hormone auxin in the root meristem by using a computational model based on experimental evidence. Hyphotesis generated by the modelled to the discovery of a differential endocytosis pattern in the root meristem that splits the auxin transcriptional response via the plasma membrane to nucleus partitioning of BRX. This positional information system creates an auxin transcriptional pattern that deviates from the canonical auxin response and is necessary to sustain the expression of a subset of BRX-dependent auxin-responsive genes to drive root meristem growth. In the second part of this PhD thesis, we characterized the genome-wide impact of large scale deletions on four divergent Arabidopsis natural strains, through the integration of Ultra-High Throughput Sequencing data with data from genomic hybridizations on tiling arrays. Analysis of the identified deletions revealed a considerable portion of protein coding genes affected and supported a history of genomic rearrangements shaped by evolution. In the last part of the thesis, we showed that VIP3 gene in Arabidopsis has an evo-lutionary conserved role in the 3' to 5' mRNA degradation machinery, by applying a novel approach for the analysis of mRNA-Seq data from random-primed mRNA. Altogether, this PhD research contains major advancements in the study of natural genomic variation in plants and in the application of computational morphodynamics models for the functional characterization of biological pathways essential for the plant. - R��cemment, l'introduction du s��quen��age de seconde g��n��ration et les avanc��es dans la microscopie confocale ont permis des ��tudes �� l'��chelle des diff��rents syst��mes cellulaires pour la caract��risation fonctionnelle de g��nes. Le degr��s de complexit�� intrins��que �� ces approches ont requis le d��veloppement de m��thodologies bioinformatiques et de mod��les math��matiques afin d'extraire de la masse de donn��es exp��rimentale g��n��r��e, des information biologiques significatives. Ce doctorat pr��sente �� la fois des m��thodes bioinformatiques originales et des mod��les math��matiques pour r��pondre �� certaines questions sp��cifiques de Biologie V��g��tale en utilisant la plante Arabidopsis thaliana comme mod��le. Premi��rement, une analyse qualitative spatio-temporelle de profiles quantitatifs de transcripts et de prot��ines est utilis��e pour montrer le r��le de la prot��ine BREVIS RADIX (BRX) dans le dialogue entre l'auxine et les cytokinines, des phytohormones, dans la croissance du m��rist��me racinaire. Le noyau de ce travail de th��se est la caract��risation fonctionnelle de l'interaction entre la prot��ine BRX et la phytohormone auxine dans le m��rist��me de la racine en utilisant des mod��les informatiques bas��s sur des preuves exp��rimentales. Les hypoth��ses produites par le mod��le ont men�� �� la d��couverte d'un sch��ma diff��rentiel d'endocytose dans le m��rist��me racinaire qui divise la r��ponse transcriptionnelle �� l'auxine par le partitionnement de BRX de la membrane plasmique au noyau de la cellule. Cette information positionnelle cr��e une r��ponse transcriptionnelle �� l'auxine qui d��vie de la r��ponse canonique �� l'auxine et est n��cessaire pour soutenir l'expression d'un sous ensemble de g��nes r��pondant �� l'auxine et d��pendant de BRX pour conduire la croissance du m��rist��me. Dans la seconde partie de cette th��se de doctorat, nous avons caract��ris�� l'impact sur l'ensemble du g��nome des d��l��tions �� grande ��chelle sur quatre souches divergentes naturelles d'Arabidopsis, �� travers l'int��gration du s��quen��age �� ultra-haut-d��bit avec l'hybridation g��nomique sur puces ADN. L'analyse des d��l��tions identifi��es a r��v��l�� qu'une proportion consid��rable de g��nes codant ��tait affect��e, supportant l'id��e d'un historique de r��arrangement g��nomique model�� durant l'��volution. Dans la derni��re partie de cette th��se, nous avons montr�� que le g��ne V��P3 dans Arabidopsis a conserv�� un r��le ��volutif dans la machinerie de d��gradation des ARNm dans le sens 3' �� 5', en appliquant une nouvelle approche pour l'analyse des donn��es de s��quen��age d'ARNm issue de transcripts amplifi��s al��atoirement. Dans son ensemble, cette recherche de doctorat contient des avanc��es majeures dans l'��tude des variations g��nomiques naturelles des plantes et dans l'application de mod��les morphodynamiques informatiques pour la caract��risation de r��seaux biologiques essentiels �� la plante. - Le d��veloppement des plantes est ��crit dans leurs codes g��n��tiques. Pour comprendre comment les plantes sont capables de s'adapter aux changements environnementaux, il est essentiel d'��tudier comment leurs g��nes gouvernent leur formation. Plus nous essayons de comprendre le fonctionnement d'une plante, plus nous r��alisons la complexit�� des m��canismes biologiques, �� tel point que l'utilisation d'outils et de mod��les math��matiques devient indispensable. Dans ce travail, avec l'utilisation de la plante mod��le Arabidopsis thalicinci nous avons r��solu des probl��mes biologiques sp��cifiques �� travers le d��veloppement et l'application de m��thodes informatiques concr��tes. Dans un premier temps, nous avons investigu�� comment le g��ne BREVIS RADIX (BRX) r��gule le d��veloppement de la racine en contr��lant la r��ponse �� deux hormones : l'auxine et la cytokinine. Nous avons employ�� une analyse statistique sur des mesures quantitatives de transcripts et de produits de g��nes afin de d��montrer que BRX joue un r��le antagonisant dans le dialogue entre ces deux hormones. Lorsque ce-dialogue mol��culaire est perturb��, la racine primaire voit sa longueur dramatiquement r��duite. Pour comprendre comment BRX r��pond �� l'auxine, nous avons d��velopp�� un mod��le informatique bas�� sur des r��sultats exp��rimentaux. Les simulations successives ont men�� �� la d��couverte d'un signal positionnel qui contr��le la r��ponse de la racine �� l'auxine par la r��gulation du mouvement intracellulaire de BRX. Dans la seconde partie de cette th��se, nous avons analys�� le g��nome entier de quatre souches naturelles d'Arabidopsis et nous avons trouv�� qu'une grande partie de leurs g��nes ��taient manquant par rapport �� la souche de r��f��rence. Ce r��sultat indique que l'historique des modifications g��nomiques conduites par l'��volution d��termine une disponibilit�� diff��rentielle des g��nes fonctionnels dans ces plantes. Dans la derni��re partie de ce travail, nous avons analys�� les donn��es du transcriptome de la plante o�� le g��ne VIP3 ��tait non fonctionnel. Ceci nous a permis de d��couvrir le r��le double de VIP3 dans la r��gulation de l'initiation de la transcription et dans la d��gradation des transcripts. Ce r��le double n'avait jusqu'alors ��t�� d��montr��e que chez l'homme. Ce travail de doctorat supporte le d��veloppement et l'application de m��thodologies informatiques comme outils inestimables pour r��soudre la complexit�� des probl��mes biologiques dans la recherche v��g��tale. L'int��gration de la biologie v��g��tale et l'informatique est devenue de plus en plus importante pour l'avanc��e de nos connaissances sur le fonctionnement et le d��veloppement des plantes.

Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes

Mammalian sex chromosomes stem from ancestral autosomes and have substantially differentiated. It was shown that X-linked genes have generated duplicate intronless gene copies (retrogenes) on autosomes due to this differentiation. However, the precise driving forces for this out-of-X gene "movement" and its evolutionary onset are not known. Based on expression analyses of male germ-cell populations, we here substantiate and extend the hypothesis that autosomal retrogenes functionally compensate for the silencing of their X-linked housekeeping parental genes during, but also after, male meiotic sex chromosome inactivation (MSCI). Thus, sexually antagonistic forces have not played a major role for the selective fixation of X-derived gene copies in mammals. Our dating analyses reveal that although retrogenes were produced ever since the common mammalian ancestor, selectively driven retrogene export from the X only started later, on the placental mammal (eutherian) and marsupial (metatherian) lineages, respectively. Together, these observations suggest that chromosome-wide MSCI emerged close to the eutherian-marsupial split approximately 180 million years ago. Given that MSCI probably reflects the spread of the recombination barrier between the X and Y, crucial for their differentiation, our data imply that these chromosomes became more widely differentiated only late in the therian ancestor, well after the divergence of the monotreme lineage. Thus, our study also provides strong independent support for the recent notion that our sex chromosomes emerged, not in the common ancestor of all mammals, but rather in the therian ancestor, and therefore are much younger than previously thought

Evolutionary biology: genetics and bisexuality.

A population-genetic model indicates that if there is a gene responsible for homosexual behaviour it can readily spread in populations. The model also predicts widespread bisexuality in humans.

Omics meets hypothesis-driven research. Partnership for innovative discoveries in vascular biology and angiogenesis.

The emergence of omics technologies allowing the global analysis of a given biological or molecular system, rather than the study of its individual components, has revolutionized biomedical research, including cardiovascular medicine research in the past decade. These developments raised the prospect that classical, hypothesis-driven, single gene-based approaches may soon become obsolete. The experience accumulated so far, however, indicates that omic technologies only represent tools similar to those classically used by scientists in the past and nowadays, to make hypothesis and build models, with the main difference that they generate large amounts of unbiased information. Thus, omics and classical hypothesis-driven research are rather complementary approaches with the potential to effectively synergize to boost research in many fields, including cardiovascular medicine. In this article we discuss some general aspects of omics approaches, and review contributions in three areas of vascular biology, thrombosis and haemostasis, atherosclerosis and angiogenesis, in which omics approaches have already been applied (vasculomics).

In-vitro cell exposure studies for the assessment of nanoparticle toxicity in the lung: a dialog between aerosol science and biology

The introduction of engineered nanostructured materials into a rapidly increasing number of industrial and consumer products will result in enhanced exposure to engineered nanoparticles. Workplace exposure has been identified as the most likely source of uncontrolled inhalation of engineered aerosolized nanoparticles, but release of engineered nanoparticles may occur at any stage of the lifecycle of (consumer) products. The dynamic development of nanomaterials with possibly unknown toxicological effects poses a challenge for the assessment of nanoparticle induced toxicity and safety.In this consensus document from a workshop on in-vitro cell systems for nanoparticle toxicity testing11Workshop on 'In-Vitro Exposure Studies for Toxicity Testing of Engineered Nanoparticles' sponsored by the Association for Aerosol Research (GAeF), 5-6 September 2009, Karlsruhe, Germany. an overview is given of the main issues concerning exposure to airborne nanoparticles, lung physiology, biological mechanisms of (adverse) action, in-vitro cell exposure systems, realistic tissue doses, risk assessment and social aspects of nanotechnology. The workshop participants recognized the large potential of in-vitro cell exposure systems for reliable, high-throughput screening of nanoparticle toxicity. For the investigation of lung toxicity, a strong preference was expressed for air-liquid interface (ALI) cell exposure systems (rather than submerged cell exposure systems) as they more closely resemble in-vivo conditions in the lungs and they allow for unaltered and dosimetrically accurate delivery of aerosolized nanoparticles to the cells. An important aspect, which is frequently overlooked, is the comparison of typically used in-vitro dose levels with realistic in-vivo nanoparticle doses in the lung. If we consider average ambient urban exposure and occupational exposure at 5mg/m3 (maximum level allowed by Occupational Safety and Health Administration (OSHA)) as the boundaries of human exposure, the corresponding upper-limit range of nanoparticle flux delivered to the lung tissue is 3��10-5-5��10-3μg/h/cm2 of lung tissue and 2-300particles/h/(epithelial) cell. This range can be easily matched and even exceeded by almost all currently available cell exposure systems.The consensus statement includes a set of recommendations for conducting in-vitro cell exposure studies with pulmonary cell systems and identifies urgent needs for future development. As these issues are crucial for the introduction of safe nanomaterials into the marketplace and the living environment, they deserve more attention and more interaction between biologists and aerosol scientists. The members of the workshop believe that further advances in in-vitro cell exposure studies would be greatly facilitated by a more active role of the aerosol scientists. The technical know-how for developing and running ALI in-vitro exposure systems is available in the aerosol community and at the same time biologists/toxicologists are required for proper assessment of the biological impact of nanoparticles.

Biology and pathogenicity of "Chlamydia"- related organisms

Abstract : This thesis investigates the pathogenicity and biology of Parachlamydia acanthamoebae and other obligate intracellular bacteria related to chlamydiae. All these Chlamydia-like organisms replicate in amoebae. Some evolved to resist to macrophages and represent possible new agents of respiratory tract infection. Using serological and molecular approaches, we showed that Parachlamydia acanthameobae likely plays a role as an etiological agent of pneumonia [1,2]. We also showed that Parachlamydia was able to enter and survive within pneumocytes and lung fibroblasts [3]. Moreover, we developed an animal model of lung infection in mice, which fulfilled the third and fourth Koch postulate [4]. Given the likely role of Parachlamydia in pneumonia, we studied its antibiotic susceptibility. We showed that Chlamydia-related organisms were resistant to quinolones, mainly due to mutations in the QRDR of gyrA [5]. To have tools to investigate the role of other Chlamydia-related bacteria in pneumonia, we developed immunofluorescence assays and assessed the rate of serological cross-reactivity between all these Chlamydia-related bacteria [6]. We also developed new diagnostic specific PCRs [2,7] and sequenced additional genes that are useful for both taxonomic and diagnostic purposes [8]. Then, we applied these serological and molecular approaches to patients with and without respiratory tract infections. This led to the identification of a possible role of Protochlamydia naegleriophila [7] and of Waddlia chondrophila in pneumonia [1]. A significant part of the thesis also investigated interactions of Parachlamydia with macrophages [9] and the host range of Chlamydia-related bacteria [10]. In conclusion, there are growing body of evidence supporting the role of Chlamydia-like organisms as agents of pneumonia. Further studies are needed to precise their pathogenic role in this setting. The diagnostic tools developed during this thesis will be useful to investigate the role of these strict intracellular bacteria in other diseases in both humans and animals [11,12]. R��sum�� : Le but de cette th��se est de d��terminer le r��le pathog��ne de Parachlamydia et des bact��ries apparent��es aux Chlamydia ainsi que d'��tudier leur biologie. Parachlamydia acanthamoebae est une bact��rie intracellulaire apparent��e aux Chlamydia, et qui est r��sistante non seulement aux amibes mais aussi aux macrophages. Par une approche s��rologique et mol��culaire, nous avons montr�� que les bact��ries apparent��es aux Chlamydia jouent probablement un r��le comme agent de pneumonie [1,2]. De plus, nous avons d��montr�� que P. acanthameobae est capable d'entrer et de survivre dans les pneumocytes et fibroblastes pulmonaires [3]. Nous avons ensuite d��velopp�� un mod��le animal remplissant les troisi��me et quatri��me postulats de Koch [4]. Nous avons aussi d��montr�� que les bact��ries apparent��es aux Chlamydia sont r��sistantes aux quinolones, en raison de mutations dans la r��gion QRDR de gyrA [5]. Afin de mieux d��terminer le r��le pathog��ne de ces bact��ries, nous avons mis au point des techniques d' immunofluorescence et d��termin�� la cross-r��action s��rologique entre les diff��rentes bact��ries apparent��es aux Chlamydia [6]. Diff��rentes PCR diagnostiques ont aussi ��t�� d��velopp��es [2,7] et des g��nes suppl��mentaires ont ��t�� s��quenc��s, qui seront utiles �� la taxonomie ainsi qu'au d��veloppement de nouvelles m��thodes diagnostiques [8]. Ces m��thodes ont ��t�� appliqu��es �� des ��chantillons provenant de patient avec ou sans pneumonie et ont permis l'identification du possible r��le pathog��ne de Protochlamydia naegleriophila [7] et de Waddlia chondrophila [1]. L'interaction de Parachlamydia avec les macrophages [9] et la permissivit�� de diff��rentes cellules aux bact��ries apparent��es aux Chlamydia [10] ont ��galement ��t�� ��tudi��s dans le cadre de cette th��se. En conclusion, plusieurs nouveaux ��l��ments viennent renforcer l'hypoth��se que les bact��ries apparent��es aux Chlamydia sont des agents de pneumonies. Cependant, d'autres ��tudes doivent ��tre men��es pour confirmer leur r��le dans cette maladie. Les m��thodes diagnostiques d��velopp��es ici seront tr��s utiles pour d��terminer le r��le pathog��ne de ces bact��ries chez les humains et animaux [11,12]