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The evolution of metazoan α-carbonic anhydrases and their roles in calcium carbonate biomineralization
Get PDFThe carbonic anhydrase (CA; EC 4.2.1.1) superfamily is a class of ubiquitous metallo-enzymes that catalyse the reversible hydration of carbon dioxide. The ?-CA family, present in all metazoan clades, is a key enzyme involved in a wide range of physiological functions including pH regulation, respiration, photosynthesis, and biocalcification. This paper reviews the evolution of the ?-CA family, with an emphasis on metazoan ?-CA members involved in biocalcification. Phylogenetic analyses reveal a complex evolutionary history of ?-CAs, and suggest ?-CA was independently co-opted into a variety of skeleton forming roles (e.g. as a provider of HCO3? ions, a structural protein, a nucleation activator, etc.) in multiple metazoan lineages. This evolutionary history is most likely the result of multiple gene duplications coupled with the insertion of repetitive or non-repetitive low-complexity domains (RLCDs/LCDs). These domains, of largely unknown function, appear to be lineage-specific, and provide further support for the hypothesis of independent recruitment of ?-CAs to diverse metazoan biocalcification processes. An analysis of ?-CA sequences associated with biocalcification processes indicates that the domains involved in the activity and conformation of the active site are extremely conserved among metazoans.PhD Fellowship from the Ministère de l' Education Nationale et de la Recherche (contract number 27264–2007), ANR project (ACCRO-Earth, ref. BLAN06-2_159971, coordinator Gilles Ramstein, LSCE, Gif/Yvette, France) for years 2007–2011, SU (INTERRVIE project year 2010), COST network TD0903 "Biomineralix", ECTS (internship grant, 2012)
Independent recruitment of Igh alleles in V(D)J recombination
Get PDFHow the vast majority of B cells express only one of the two alleles at their immunoglobulin loci remains a biological puzzle. Here, in mice reconstituted with a single haematopoietic stem cell, we demonstrate that each of the two immunoglobulin heavy chain (Igh) alleles has a similar probability to be the first to undergo V(H) to DJ(H) rearrangement. We also observe this similar probability in clones from multipotent and common lymphoid precursors. The extreme biases in the expression of the alleles that we find in more differentiated subsets are mostly due to constraints imposed by early rearrangements. Our data demonstrate that each of the two Igh alleles in a B cell behaves independently of the other, up to the moment when a successful rearrangement in one allele triggers a feedback mechanism that prevents further recombination.FCT fellowship: (SFRH/BD/33217/2007)
New density estimates of a threatened sifaka species (Propithecus coquereli) in Ankarafantsika National Park
Get PDFPropithecus coquereli is one of the last sifaka species for which no reliable and extensive density estimates are yet available. Despite its endangered conservation status [IUCN, 2012] and recognition as a flagship species of the northwestern dry forests of Madagascar, its population in its last main refugium, the Ankarafantsika National Park (ANP), is still poorly known. Using line transect distance sampling surveys we estimated population density and abundance in the ANP. Furthermore, we investigated the effects of road, forest edge, river proximity and group size on sighting frequencies, and density estimates. We provide here the first population density estimates throughout the ANP. We found that density varied greatly among surveyed sites (from 5 to ∼100 ind/km2) which could result from significant (negative) effects of road, and forest edge, and/or a (positive) effect of river proximity. Our results also suggest that the population size may be ∼47,000 individuals in the ANP, hinting that the population likely underwent a strong decline in some parts of the Park in recent decades, possibly caused by habitat loss from fires and charcoal production and by poaching. We suggest community-based conservation actions for the largest remaining population of Coquerel's sifaka which will (i) maintain forest connectivity; (ii) implement alternatives to deforestation through charcoal production, logging, and grass fires; (iii) reduce poaching; and (iv) enable long-term monitoring of the population in collaboration with local authorities and researchers.Optimus!Alive- IGC fellowship, FCT fellowship: (SFRH/BD/64875/2009), University of Mahajanga, Groupement de Recherche International (GDRI), "Laboratoire d'Excellence" (LABEX) entitled TULIP (ANR-10-LABX-41), the Rufford Small Grant Foundation grant: (10941-1)
Extensive survey of the Endangered Coquerel’s sifaka Propithecus coquereli
Get PDFCoquerel’s sifaka Propithecus coquereli has a large but highly fragmented distribution. Despite its Endangered (EN) IUCN conservation status, uncertainties persist regarding its actual distribution and its presence in forests that are thought to be part of its distribution range. We provide here the first extensive population surveys of Coquerel’s sifaka across a large number of forest fragments neighboring 27 sites of its known and expected distribution range in northwestern Madagascar, including 12 previously visited sites. During our diurnal surveys carried out in the dry seasons from 2009 to 2011 we observed the species in 26 of the 27 visited sites. Combining our results with previously published data, we propose a refined update of the species’ distribution range and identify areas to be surveyed. We also recorded the support tree species on which sifakas were observed, and note that, surprisingly, P. coquereli was frequently seen around villages and in areas dominated by introduced tree species. Although the species was present at almost all the visited sites of its highly fragmented distribution range, it remains unclear how viable the populations of a significant proportion of these sites actually are. Due to political instability and high rates of deforestation, large-scale conservation actions are urgently needed. We thus (1) discuss the outline of a possible metapopulation conservation action plan for P. coquereli and (2) identify priority sites and actions.Fundação para a Ciência e a Tecnologia: SFRH/BD/64875/2009, Institut Français de la Biodiversité, Fondation pour la Recherche sur la Biodiversité, GDRI Madagascar, Laboratoire d’Excellence (LABEX) entitled TULIP (ANR-10-LABX-41), Instituto Gulbenkian de Ciência
A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing
Get PDFCork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management.FCT within a National Consortium (COEC – Cork Oak ESTs Consortium) that supported 12 sub-projects (SOBREIRO/033, 035, 014, 034, 015, 017, 038, 019, 029, 039, 030, 036/2009), FCT ten doctoral (BD) and post-doctoral (BPD) fellowships: (SFRH/BD/44410/2008, SFRH/BD/69785/2010, SFRH/BPD/20833/2004, SFRH/BPD/47563/2008, SFRH/BPD/63213/2009, SFRH/BPD/47679/2008, SFRH/BD/44474/2008, SFRH/BPD/64905/2009, SFRH/BD/47450/2008, SFRH/BPD/25661/2005), Programa Ciência 2007, financed by POPH (QREN), Programa Ciência 2008 POHP (QREN), iBET (PEst-OE/EQB/LA0004/2011), Instituto Gulbenkian de Ciência
Elucidating how the saprophytic fungus Aspergillus nidulans uses the plant polyester suberin as carbon source
Get PDFLipid polymers in plant cell walls, such as cutin and suberin, build recalcitrant hydrophobic protective barriers. Their degradation is of foremost importance for both plant pathogenic and saprophytic fungi. Regardless of numerous reports on fungal degradation of emulsified fatty acids or cutin, and on fungi-plant interactions, the pathways involved in the degradation and utilisation of suberin remain largely overlooked. As a structural component of the plant cell wall, suberin isolation, in general, uses harsh depolymerisation methods that destroy its macromolecular structure. We recently overcame this limitation isolating suberin macromolecules in a near-native state.work partially supported by a grant from Iceland, Liechtenstein and Norway through the EEA financial mechanism (Project PT015), FCT: grant (PEst-OE/EQB/LA0004/2013) and fellowships (SFRH/BD/38378/2007, SFRH/BD/66396/2009, SFRH/BD/66030/2009, SFRH/BD/48286/2008), Fundação Calouste Gulbenkian fellowship (21-95587-B)
V-ATPase Proton Pumping Activity Is Required for Adult Zebrafish Appendage Regeneration
Get PDFThe activity of ion channels and transporters generates ion-specific fluxes that encode electrical and/or chemical signals with biological significance. Even though it is long known that some of those signals are crucial for regeneration, only in recent years the corresponding molecular sources started to be identified using mainly invertebrate or larval vertebrate models. We used adult zebrafish caudal fin as a model to investigate which and how ion transporters affect regeneration in an adult vertebrate model. Through the combined use of biophysical and molecular approaches, we show that V-ATPase activity contributes to a regeneration-specific H+ ef`flux. The onset and intensity of both V-ATPase expression and H+ efflux correlate with the different regeneration rate along the proximal-distal axis. Moreover, we show that V-ATPase inhibition impairs regeneration in adult vertebrate. Notably, the activity of this H+ pump is necessary for aldh1a2 and mkp3 expression, blastema cell proliferation and fin innervation. To the best of our knowledge, this is the first report on the role of V-ATPase during adult vertebrate regeneration.FCT fellowships: ( SFRH/BD/45131/2008, SFRH/BPD/29957/2006), FCT grant (POCTI-ISFL-4-66), Ministerio de Ciencia e Innovación, Spain (Subprograma Ramon y Cajal, reference RYC-2008-02753 and grant BFU2009-12279)
Behavioural Stress Responses Predict Environmental Perception in European Sea Bass (Dicentrarchus labrax)
Get PDFIndividual variation in the response to environmental challenges depends partly on innate reaction norms, partly on experience-based cognitive/emotional evaluations that individuals make of the situation. The goal of this study was to investigate whether pre-existing differences in behaviour predict the outcome of such assessment of environmental cues, using a conditioned place preference/avoidance (CPP/CPA) paradigm. A comparative vertebrate model (European sea bass, Dicentrarchus labrax) was used, and ninety juvenile individuals were initially screened for behavioural reactivity using a net restraining test. Thereafter each individual was tested in a choice tank using net chasing as aversive stimulus or exposure to familiar conspecifics as appetitive stimulus in the preferred or non preferred side respectively (called hereafter stimulation side). Locomotor behaviour (i.e. time spent, distance travelled and swimming speed in each tank side) of each individual was recorded and analysed with video software. The results showed that fish which were previously exposed to appetitive stimulus increased significantly the time spent on the stimulation side, while aversive stimulus led to a strong decrease in time spent on the stimulation side. Moreover, this study showed clearly that proactive fish were characterised by a stronger preference for the social stimulus and when placed in a putative aversive environment showed a lower physiological stress responses than reactive fish. In conclusion, this study showed for the first time in sea bass, that the CPP/CPA paradigm can be used to assess the valence (positive vs. negative) that fish attribute to different stimuli and that individual behavioural traits is predictive of how stimuli are perceived and thus of the magnitude of preference or avoidance behaviour.FCT grants: FRH/BPD/72952/2010, SFRH/BD/80029/2011
Macrophages sense and kill bacteria through carbon monoxide-dependent inflammasome activation
Get PDFMicrobial clearance by eukaryotes relies on complex and coordinated processes that remain poorly understood. The gasotransmitter carbon monoxide (CO) is generated by the stress-responsive enzyme heme oxygenase-1 (HO-1, encoded by Hmox1), which is highly induced in macrophages in response to bacterial infection. HO-1 deficiency results in inadequate pathogen clearance, exaggerated tissue damage, and increased mortality. Here, we determined that macrophage-generated CO promotes ATP production and release by bacteria, which then activates the Nacht, LRR, and PYD domains-containing protein 3 (NALP3) inflammasome, intensifying bacterial killing. Bacterial killing defects in HO-1-deficient murine macrophages were restored by administration of CO. Moreover, increased CO levels enhanced the bacterial clearance capacity of human macrophages and WT murine macrophages. CO-dependent bacterial clearance required the NALP3 inflammasome, as CO did not increase bacterial killing in macrophages isolated from NALP3-deficient or caspase-1-deficient mice. IL-1β cleavage and secretion were impaired in HO-1-deficient macrophages, and CO-dependent processing of IL-1β required the presence of bacteria-derived ATP. We found that bacteria remained viable to generate and release ATP in response to CO. The ATP then bound to macrophage nucleotide P2 receptors, resulting in activation of the NALP3/IL-1β inflammasome to amplify bacterial phagocytosis by macrophages. Taken together, our results indicate that macrophage-derived CO permits efficient and coordinated regulation of the host innate response to invading microbes.NIH grants: (HL-071797, HL-076167, HL-106227), American Heart Association grants: (10SDG2640091 and NIH R21CA169904-01), Julie Henry Fund, Transplant Center of the BIDMC, FCT grants: (SFRH/BPD/25436/2005, PTDC/BIO/70815/2006, PTDC/BIA-BCM/101311/2008, PTDC/SAU-FCF/100762/2008), the European Community, 6th Framework grant LSH-2005-1.2.5-1 and ERC-2011-AdG, Howard Hughes Medical Institute
The quantitative architecture of centromeric chromatin
Get PDFThe centromere, responsible for chromosome segregation during mitosis, is epigenetically defined by CENP-A containing chromatin. The amount of centromeric CENP-A has direct implications for both the architecture and epigenetic inheritance of centromeres. Using complementary strategies, we determined that typical human centromeres contain ∼400 molecules of CENP-A, which is controlled by a mass-action mechanism. This number, despite representing only ∼4% of all centromeric nucleosomes, forms a ∼50-fold enrichment to the overall genome. In addition, although pre-assembled CENP-A is randomly segregated during cell division, this amount of CENP-A is sufficient to prevent stochastic loss of centromere function and identity. Finally, we produced a statistical map of CENP-A occupancy at a human neocentromere and identified nucleosome positions that feature CENP-A in a majority of cells. In summary, we present a quantitative view of the centromere that provides a mechanistic framework for both robust epigenetic inheritance of centromeres and the paucity of neocentromere formation.DOI: http://dx.doi.org/10.7554/eLife.02137.001.European Molecular Biology Organization: (EMBO Installation grant), European Commission: (FP7 Marie Curie Reintegration grant), National Institutes of Health grants: (GM082989, GM077238), Burroughs Wellcome Fund, Rita Allen Foundation, Beckman Laser Institute and Foundation, FCT fellowship: (SFRH/BD/74284/2010)