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Are There Really Twice as Many Bovid Species as We Thought?
Get PDFA major reappraisal of the taxonomy of ungulates (hoofed mammals) was presented in 2011 (Groves and Grubb 2011; G&G henceforth). The reappraisal presents a drastic revision of the taxonomic diversity of the group. It nearly doubles the number of bovid species—a group comprising cattle, bison, buffalo, goats, sheep, and antelopes—currently recognized (IUCN 2012), raising the number of species from 143 to 279. In our opinion, this represents taxonomic inflation; ecotypes or subspecies have been raised to the level of full species based not on new data, but solely on a change in the species concept used (Isaac et al. 2004). As we argue below, the excessive splitting of species is unconvincing in many cases. Furthermore, we warn that such taxonomic inflation in the bovids may impede management and conservation efforts (Isaac et al. 2004; Mace 2004; Frankham et al. 2012).
The revised bovid species list of G&G was incorporated into the recently published “Handbook of the Mammals of the World—Volume 2” (Wilson and Mittermeier 2011; HMW henceforth) published in collaboration with the IUCN and Conservation International, 2 of the leading international authorities involved in the conservation of global biodiversity. Whereas G&G is a scientific revision intended for experts in the field, HMW is a multiauthored book series presenting the most up-to-date taxonomy of mammals for a broader readership. Collectively, these two volumes are likely to be highly influential and serve as a guideline for a wide-ranging audience including taxonomists, conservationists, ecologists, biodiversity managers, and policy makers.
Any taxonomic revision that doubles the number of species within a family must anticipate critical evaluation, not least when it occurs in a prominent group such as the bovids. Here, we discuss the revision and its potential consequences, which we believe may be detrimental in many respects. The critiques we are raising are two-fold. First, we call into question the scientific grounds for the species splitting in G&G. Second, we criticize HMW for singularly adopting the bovid species list of G&G without subjecting it to critical evaluation. We discuss some of the practical downstream consequences of these actions.Danish Council for Independent Research, Natural Sciences and a Marie Curie International Outgoing Fellowship, 7th European Community Framework Programme
Evolution of mir-92a Underlies Natural Morphological Variation in Drosophila melanogaster
Get PDFThe deposited article is a post-print version and has peer review. This deposit is composed by the main article, and it hasn't any supplementary materials associated. The supplementary materials are present in the publisher's page in the following link: http://www.sciencedirect.com/science/MiamiMultiMediaURL/1-s2.0-S0960982213001899/1-s2.0-S0960982213001899-mmc1.pdf/272099/html/S0960982213001899/187ecb1b8f94027ceebb87907c58eb3f/mmc1.pdfIdentifying the genetic mechanisms underlying phenotypic change is essential to understanding how gene regulatory networks and ultimately the genotype-to-phenotype map evolve. It is recognized that microRNAs (miRNAs) have the potential to facilitate evolutionary change [1-3]; however, there are no known examples of natural morphological variation caused by evolutionary changes in miRNA expression. Therefore, the contribution of miRNAs to evolutionary change remains unknown [1, 4]. Drosophila melanogaster subgroup species display a portion of trichome-free cuticle on the femur of the second leg called the "naked valley." It was previously shown that Ultrabithorax (Ubx) is involved in naked valley variation between D. melanogaster and D. simulans [5, 6]. However, naked valley size also varies among populations of D. melanogaster, ranging from 1,000 up to 30,000 μm(2). We investigated the genetic basis of intraspecific differences in the naked valley in D. melanogaster and found that neither Ubx nor shavenbaby (svb) [7, 8] contributes to this morphological difference. Instead, we show that changes in mir-92a expression underlie the evolution of naked valley size in D. melanogaster through repression of shavenoid (sha) [9]. Therefore, our results reveal a novel mechanism for morphological evolution and suggest that modulation of the expression of miRNAs potentially plays a prominent role in generating organismal diversity.Austrian Science Fund (FWF) grant: (M1059-B09); Oxford Brookes University; National Institute of General Medical Sciences of the National Institutes of Health grant: (R01-GM083300).info:eu-repo/semantics/publishedVersio
Q&A: Who needs a centrosome?
Get PDFThe centrosome has several functions. The central one
is as the major microtubule organizing center (MTOC)
in proliferating animal cells: thus, it helps to organize the
microtubules that form the mitotic spindle in dividing
cells, and orchestrate a wide variety of cellular processes,
including cell motility, signaling, adhesion, coordination of
protein trafficking by the microtubule cytoskeleton and
the acquisition of polarity. The centrosome has crucial
links to the nucleus, the Golgi, cell to cell junctions and
acto-myosin cytoskeleton that are very important in
positioning it and thus shaping the microtubule cytoskeleton
in relation to the cell and the organism (reviewed in [1]).
The role of the centrosome in organizing cellular
microtubules can differ from cell to cell and be regulated
differently in different phases of the life of a cell.Laboratório Associado de Oeiras, EMBO Installation Grant: (co-funded by FCT and Instituto Gulbenkian de Ciência), FCT, Instituto Gulbenkian de Ciência
Steroid Hormone Signaling Is Essential to Regulate Innate Immune Cells and Fight Bacterial Infection in Drosophila
Get PDFCoupling immunity and development is essential to ensure survival despite changing internal conditions in the organism. Drosophila metamorphosis represents a striking example of drastic and systemic physiological changes that need to be integrated with the innate immune system. However, nothing is known about the mechanisms that coordinate development and immune cell activity in the transition from larva to adult. Here, we reveal that regulation of macrophage-like cells (hemocytes) by the steroid hormone ecdysone is essential for an effective innate immune response over metamorphosis. Although it is generally accepted that steroid hormones impact immunity in mammals, their action on monocytes (e.g. macrophages and neutrophils) is still not well understood. Here in a simpler model system, we used an approach that allows in vivo, cell autonomous analysis of hormonal regulation of innate immune cells, by combining genetic manipulation with flow cytometry, high-resolution time-lapse imaging and tissue-specific transcriptomic analysis. We show that in response to ecdysone, hemocytes rapidly upregulate actin dynamics, motility and phagocytosis of apoptotic corpses, and acquire the ability to chemotax to damaged epithelia. Most importantly, individuals lacking ecdysone-activated hemocytes are defective in bacterial phagocytosis and are fatally susceptible to infection by bacteria ingested at larval stages, despite the normal systemic and local production of antimicrobial peptides. This decrease in survival is comparable to the one observed in pupae lacking immune cells altogether, indicating that ecdysone-regulation is essential for hemocyte immune functions and survival after infection. Microarray analysis of hemocytes revealed a large set of genes regulated at metamorphosis by EcR signaling, among which many are known to function in cell motility, cell shape or phagocytosis. This study demonstrates an important role for steroid hormone regulation of immunity in vivo in Drosophila, and paves the way for genetic dissection of the mechanisms at work behind steroid regulation of innate immune cells.FCT fellowships: (SFRH/BPD/44613/2008, SFRH/BD/51175/2010), EMBO: (ALTF 178-2009), Gulbenkian Institute PhD Program
Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ
Get PDFThe RNA-dependent protein kinase PKR plays a central role in the antiviral defense of vertebrates by shutting down protein translation upon detection of viral dsRNA in the cytoplasm. In some teleost fish, PKZ, a homolog of PKR, performs the same function, but surprisingly, instead of dsRNA binding domains, it harbors two Z-DNA/Z-RNA-binding domains belonging to the Zalpha domain family. Zalpha domains have also been found in other proteins, which have key roles in the regulation of interferon responses such as ADAR1 and DNA-dependent activator of IFN-regulatory factors (DAI) and in viral proteins involved in immune response evasion such as the poxviral E3L and the Cyprinid Herpesvirus 3 ORF112. The underlying mechanism of nucleic acids binding and stabilization by Zalpha domains is still unclear. Here, we present two crystal structures of the zebrafish PKZ Zalpha domain (DrZalpha(PKZ)) in alternatively organized complexes with a (CG)6 DNA oligonucleotide at 2 and 1.8 Å resolution. These structures reveal novel aspects of the Zalpha interaction with DNA, and they give insights on the arrangement of multiple Zalpha domains on DNA helices longer than the minimal binding site.FCT fellowship: (SFRH/BPD/71629/2010), ESRF BAG program, Instituto Gulbenkian de Ciência
inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis
Get PDFThis deposit is composed by the main article plus the supplementary materials of the publication.Tuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is growing evidence that the genetic diversity of Mycobacterium tuberculosis may have important clinical consequences. Therefore, combining genetic, clinical and socio-demographic data is critical to understand the epidemiology of this infectious disease, and how virulence and other phenotypic traits evolve over time. This requires dedicated bioinformatics platforms, capable of integrating and enabling analyses of this heterogeneous data.Instituto Gulbenkian de Ciência, Programa Nacional de Luta contra a Tuberculose, Instituto Nacional de Saúde Ricardo Jorge, Administração Regional de Saúde de Lisboa e Vale do Tejo
Hypothalamic melanin concentrating hormone neurons communicate the nutrient value of sugar
Get PDFSugars that contain glucose, such as sucrose, are generally preferred to artificial sweeteners owing to their post-ingestive rewarding effect, which elevates striatal dopamine (DA) release. While the post-ingestive rewarding effect, which artificial sweeteners do not have, signals the nutrient value of sugar and influences food preference, the neural circuitry that mediates the rewarding effect of glucose is unknown. In this study, we show that optogenetic activation of melanin-concentrating hormone (MCH) neurons during intake of the artificial sweetener sucralose increases striatal dopamine levels and inverts the normal preference for sucrose vs sucralose. Conversely, animals with ablation of MCH neurons no longer prefer sucrose to sucralose and show reduced striatal DA release upon sucrose ingestion. We further show that MCH neurons project to reward areas and are required for the post-ingestive rewarding effect of sucrose in sweet-blind Trpm5(-/-) mice. These studies identify an essential component of the neural pathways linking nutrient sensing and food reward. DOI: http://dx.doi.org/10.7554/eLife.01462.001.JPB Foundation; The Klarman Family Foundation for Eating Disorders; The Rockefeller Foundation; CNPq (Brazil); FCT; National Institutes of Health grants: (DC009997, DK085579, DP1 DK006850)
An ABC Method for Estimating the Rate and Distribution of Effects of Beneficial Mutations
Get PDFDetermining the distribution of adaptive mutations available to natural selection is a difficult task. These are rare events and most of them are lost by chance. Some theoretical works propose that the distribution of newly arising beneficial mutations should be close to exponential. Empirical data are scarce and do not always support an exponential distribution. Analysis of the dynamics of adaptation in asexual populations of microorganisms has revealed that these can be summarized by two effective parameters, the effective mutation rate, Ue, and the effective selection coefficient of a beneficial mutation, Se. Here, we show that these effective parameters will not always reflect the rate and mean effect of beneficial mutations, especially when the distribution of arising mutations has high variance, and the mutation rate is high. We propose a method to estimate the distribution of arising beneficial mutations, which is motivated by a common experimental setup. The method, which we call One Biallelic Marker Approximate Bayesian Computation, makes use of experimental data consisting of periodic measures of neutral marker frequencies and mean population fitness. Using simulations, we find that this method allows the discrimination of the shape of the distribution of arising mutations and that it provides reasonable estimates of their rates and mean effects in ranges of the parameter space that may be of biological relevance.Fundação Calouste Gulbenkian, FCT, LAO/ITQB, Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco (FACEPE), program PRONEX/MCT-CNPq-FACEPE
A two-step mechanism for epigenetic specification of centromere identity and function
Get PDFThe basic determinant of chromosome inheritance, the centromere, is specified in many eukaryotes by an epigenetic mark. Using gene targeting in human cells and fission yeast, chromatin containing the centromere-specific histone H3 variant CENP-A is demonstrated to be the epigenetic mark that acts through a two-step mechanism to identify, maintain and propagate centromere function indefinitely. Initially, centromere position is replicated and maintained by chromatin assembled with the centromere-targeting domain (CATD) of CENP-A substituted into H3. Subsequently, nucleation of kinetochore assembly onto CATD-containing chromatin is shown to require either the amino- or carboxy-terminal tail of CENP-A for recruitment of inner kinetochore proteins, including stabilizing CENP-B binding to human centromeres or direct recruitment of CENP-C, respectively.National Institutes of Health grant: (GM 074150); Ludwig Institute for Cancer Research; European Molecular Biology Organization (EMBO) long-term fellowship
Disengaging the Smc3/kleisin interface releases cohesin from Drosophila chromosomes during interphase and mitosis
Get PDFCohesin's Smc1, Smc3, and kleisin subunits create a tripartite ring within which sister DNAs are entrapped. Evidence suggests that DNA enters through a gate created by transient dissociation of the Smc1/3 interface. Release at the onset of anaphase is triggered by proteolytic cleavage of kleisin. Less well understood is the mechanism of release at other stages of the cell cycle, in particular during prophase when most cohesin dissociates from chromosome arms in a process dependent on the regulatory subunit Wapl. We show here that Wapl-dependent release from salivary gland polytene chromosomes during interphase and from neuroblast chromosome arms during prophase is blocked by translational fusion of Smc3's C-terminus to kleisin's N-terminus. Our findings imply that proteolysis-independent release of cohesin from chromatin is mediated by Wapl-dependent escape of DNAs through a gate created by transient dissociation of the Smc3/kleisin interface. Thus, cohesin's DNA entry and exit gates are distinct.FP7 Marie Curie Intra‐European Fellowship; ERC grant