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Multispecies Analysis of Expression Pattern Diversification in the Recently Expanded Insect Ly6 Gene Family
Get PDFThe deposited article version is a "MBE Advance Access" published on March 4, 2015" provided by Oxford University Press, and it contains attached the supplementary materials within the pdf.The deposited article is a post-print version.Some supplementary materials are not present in the uploaded version of the article.Gene families often consist of members with diverse expression domains reflecting their functions in a wide variety of tissues. However, how the expression of individual members, and thus their tissue-specific functions, diversified during the course of gene family expansion is not well understood. In this study, we approached this question through the analysis of the duplication history and transcriptional evolution of a rapidly expanding subfamily of insect Ly6 genes. We analyzed different insect genomes and identified seven Ly6 genes that have originated from a single ancestor through sequential duplication within the higher Diptera. We then determined how the original embryonic expression pattern of the founding gene diversified by characterizing its tissue-specific expression in the beetle Tribolium castaneum, the butterfly Bicyclus anynana, and the mosquito Anopheles stephensi and those of its duplicates in three higher dipteran species, representing various stages of the duplication history (Megaselia abdita, Ceratitis capitata, and Drosophila melanogaster). Our results revealed that frequent neofunctionalization episodes contributed to the increased expression breadth of this subfamily and that these events occurred after duplication and speciation events at comparable frequencies. In addition, at each duplication node, we consistently found asymmetric expression divergence. One paralog inherited most of the tissue-specificities of the founder gene, whereas the other paralog evolved drastically reduced expression domains. Our approach attests to the power of combining a well-established duplication history with a comprehensive coverage of representative species in acquiring unequivocal information about the dynamics of gene expression evolution in gene families.IAEA Seibersdorf (Austria); USDA; Duke University; McGill University; DRGC (Kyoto); DSHB (Iowa); Toulouse RIO Imaging Platform; Fundação para a Ciência e a Tecnologia grants: (SFRH/BPD/75139/2010, ANR-13-ISV7-0001-01, ANR-13-ISV7-0001-02, FCT-ANR/BIA-ANM/0003/2013); Fundação Calouste Gulbenkian; Instituto Gulbenkian de Ciência; Agence Nationale de la Recherche (ANR).info:eu-repo/semantics/publishedVersio
PLK4 trans-Autoactivation Controls Centriole Biogenesis in Space
Get PDFThe deposited article is a post-print version and has been submitted to peer review.This publication hasn't any creative commons license associated.The deposited article version contains attached the supplementary materials within the pdf.Centrioles are essential for cilia and centrosome assembly. In centriole-containing cells, centrioles always form juxtaposed to pre-existing ones, motivating a century-old debate on centriole biogenesis control. Here, we show that trans-autoactivation of Polo-like kinase 4 (PLK4), the trigger of centriole biogenesis, is a critical event in the spatial control of that process. We demonstrate that centrioles promote PLK4 activation through its recruitment and local accumulation. Though centriole removal reduces the proportion of active PLK4, this is rescued by concentrating PLK4 to the peroxisome lumen. Moreover, while mild overexpression of PLK4 only triggers centriole amplification at the existing centriole, higher PLK4 levels trigger both centriolar and cytoplasmatic (de novo) biogenesis. Hence, centrioles promote their assembly locally and disfavor de novo synthesis. Similar mechanisms enforcing the local concentration and/or activity of other centriole components are likely to contribute to the spatial control of centriole biogenesis under physiological conditions.Fundação Portuguesa para a Ciência e Tecnologia grants: (SFRH/BPD/87479/2012, PTDC/BBB-BEP/1724/2012, HMSP-CT/SAU-ICT/0075/2009, PTDC/SAU-OBD/105616/2008, EXPL/BIM-ONC/0830/2013, PTDC/BBB-BEP/1724/2012); EMBO installation grant; ERC starting grant: (PFE-GI-UE-ERC-2010-StG-261344).info:eu-repo/semantics/publishedVersio
Multiple enteropathogenic viruses in a gastroenteritis outbreak in a military exercise of the Portuguese Army
No full textThis deposit is composed by a publication in which the IGC's authors have had the role of collaboration (it's a collaboration publication). This type of deposit in ARCA is in restrictedAccess (it can't be in open access to the public), and can only be accessed by two ways: either by requesting a legal copy from the author (the email contact present in this deposit) or by visiting the following link: https://www.sciencedirect.com/science/article/pii/S1386653215001535?via%3Dihub#sec0040This work can also be accessed by visiting the following link: http://repositorio.insa.pt/handle/10400.18/3513This deposit is composed by the main article, and it hasn't any supplementary materials associated.This publication hasn't any creative commons license associated.Background
Gastroenteritis is one of the most common infectious diseases in the military populations and can diminish operational effectiveness and impede force readiness.
Objectives
The present study investigates the cause and the source of an acute gastroenteritis outbreak that occurred during a military exercise of the Portuguese Army, in February 2013.
Study Design
A retrospective investigation was performed and stool samples, food items and water were screened for common foodborne bacteria and viruses, namely Norovirus GI, Norovirus GII, Astrovirus, Rotavirus, Adenovirus and Sapovirus.
Results
From the total of 160 soldiers that participated in the military exercise 20 developed gastroenteritis (attack rate of 12.5%). Symptoms were predominantly vomiting (n = 17, 85%) and diarrhoea (n = 9, 45%). The first cases occurred 24–48 h after drinking water from the creek, the plausible origin of the outbreak. The epidemic peak was registered 2 days after and the last cases 6 days after, upon returning to base. No pathogenic bacteria were found in stools however virological analysis revealed the presence of multiple enteropathogenic viruses, namely Norovirus GI (GI.3), Norovirus GII (GII.4 New Orleans 2009), Astrovirus and Sapovirus, as single or co-infections. Food and water samples were not tested for the presence of viruses due to exhaustion of samples on bacteriological analysis.
Conclusions
To the best of our knowledge this is the first report of a viral gastroenteritis outbreak among military personnel in the Portuguese Army.There are no funders and sponsors indicated explicitly in the document.info:eu-repo/semantics/publishedVersio
Host adaptation to viruses relies on few genes with different cross-resistance properties
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 of the publication are only present in the editor's page of this article. This publication hasn't any creative commons license associated.Host adaptation to one parasite may affect its response to others. However, the genetics of these direct and correlated responses remains poorly studied. The overlap between these responses is instrumental for the understanding of host evolution in multiparasite environments. We determined the genetic and phenotypic changes underlying adaptation of Drosophila melanogaster to Drosophila C virus (DCV). Within 20 generations, flies selected with DCV showed increased survival after DCV infection, but also after cricket paralysis virus (CrPV) and flock house virus (FHV) infection. Whole-genome sequencing identified two regions of significant differentiation among treatments, from which candidate genes were functionally tested with RNAi. Three genes were validated--pastrel, a known DCV-response gene, and two other loci, Ubc-E2H and CG8492. Knockdown of Ubc-E2H and pastrel also led to increased sensitivity to CrPV, whereas knockdown of CG8492 increased susceptibility to FHV infection. Therefore, Drosophila adaptation to DCV relies on few major genes, each with different cross-resistance properties, conferring host resistance to several parasites.Fundação para a Ciência e a Tecnologia grants: (SFRH/BPD/62964/2009, SFRH/BD/82299/2011, PTDC/SAU-IMU/120673/2010); Austrian Science Fund grants: (P22725, P19467); European Research Council grant: (ArchAdapt); Instituto Gulbenkian de Ciência/Fundação Calouste Gulbenkian; Vetmeduni.info:eu-repo/semantics/publishedVersio
Subunits of the Drosophila actin-capping protein heterodimer regulate each other at multiple levels
Get PDFThe actin-Capping Protein heterodimer, composed of the α and β subunits, is a master F-actin regulator. In addition to its role in many cellular processes, Capping Protein acts as a main tumor suppressor module in Drosophila and in humans, in part, by restricting the activity of Yorkie/YAP/TAZ oncogenes. We aimed in this report to understand how both subunits regulate each other in vivo. We show that the levels and capping activities of both subunits must be tightly regulated to control F-actin levels and consequently growth of the Drosophila wing. Overexpressing capping protein α and β decreases both F-actin levels and tissue growth, while expressing forms of Capping Protein that have dominant negative effects on F-actin promote tissue growth. Both subunits regulate each other's protein levels. In addition, overexpressing one of the subunit in tissues knocked-down for the other increases the mRNA and protein levels of the subunit knocked-down and compensates for its loss. We propose that the ability of the α and β subunits to control each other's levels assures that a pool of functional heterodimer is produced in sufficient quantities to restrict the development of tumor but not in excess to sustain normal tissue growth.FCT- SFRH/BD/47261/200
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps
Get PDFThe accumulation of adaptive mutations is essential for survival in novel
environments. However, in clonal populations with a high mutational supply, the
power of natural selection is expected to be limited. This is due to clonal
interference - the competition of clones carrying different beneficial
mutations - which leads to the loss of many small effect mutations and fixation
of large effect ones. If interference is abundant, then mechanisms for
horizontal transfer of genes, which allow the immediate combination of
beneficial alleles in a single background, are expected to evolve. However, the
relevance of interference in natural complex environments, such as the gut, is
poorly known. To address this issue, we studied the invasion of beneficial
mutations responsible for Escherichia coli's adaptation to the mouse gut and
demonstrate the pervasiveness of clonal interference. The observed dynamics of
change in frequency of beneficial mutations are consistent with soft sweeps,
where a similar adaptive mutation arises repeatedly on different haplotypes
without reaching fixation. The genetic basis of the adaptive mutations revealed
a striking parallelism in independently evolving populations. This was mainly
characterized by the insertion of transposable elements in both coding and
regulatory regions of a few genes. Interestingly in most populations, we
observed a complete phenotypic sweep without loss of genetic variation. The
intense clonal interference during adaptation to the gut environment, here
demonstrated, may be important for our understanding of the levels of strain
diversity of E. coli inhabiting the human gut microbiota and of its
recombination rate.Howard Hughes Medical Institute (HHMI-55007436), LAO/ITQB, FCT Grants: FRH/BD/80257/2011 and SFRH/BPD/14299/2003
Abscisic Acid (ABA) Regulation of Arabidopsis SR Protein Gene Expression
Get PDFSerine/arginine-rich (SR) proteins are major modulators of alternative splicing, a key generator of proteomic diversity and flexible means of regulating gene expression likely to be crucial in plant environmental responses. Indeed, mounting evidence implicates splicing factors in signal transduction of the abscisic acid (ABA) phytohormone, which plays pivotal roles in the response to various abiotic stresses. Using real-time RT-qPCR, we analyzed total steady-state transcript levels of the 18 SR and two SR-like genes from Arabidopsis thaliana in seedlings treated with ABA and in genetic backgrounds with altered expression of the ABA-biosynthesis ABA2 and the ABA-signaling ABI1 and ABI4 genes. We also searched for ABA-responsive cis elements in the upstream regions of the 20 genes. We found that members of the plant-specific SC35-Like (SCL) Arabidopsis SR protein subfamily are distinctively responsive to exogenous ABA, while the expression of seven SR and SR-related genes is affected by alterations in key components of the ABA pathway. Finally, despite pervasiveness of established ABA-responsive promoter elements in Arabidopsis SR and SR-like genes, their expression is likely governed by additional, yet unidentified cis-acting elements. Overall, this study pinpoints SR34, SR34b, SCL30a, SCL28, SCL33, RS40, SR45 and SR45a as promising candidates for involvement in ABA-mediated stress responses.FCT PostDoctoral Fellowships: SFRH/BPD/80073/2011, SFRH/BPD/81830/2011
Heme oxygenase-1 derived carbon monoxide permits maturation of myeloid cells
Get PDFCritical functions of the immune system are maintained by the ability of myeloid progenitors to differentiate and mature into macrophages. We hypothesized that the cytoprotective gas molecule carbon monoxide (CO), generated endogenously by heme oxygenases (HO), promotes differentiation of progenitors into functional macrophages. Deletion of HO-1, specifically in the myeloid lineage (Lyz-Cre:Hmox1(flfl)), attenuated the ability of myeloid progenitors to differentiate toward macrophages and decreased the expression of macrophage markers, CD14 and macrophage colony-stimulating factor receptor (MCSFR). We showed that HO-1 and CO induced CD14 expression and efficiently increased expansion and differentiation of myeloid cells into macrophages. Further, CO sensitized myeloid cells to treatment with MCSF at low doses by increasing MCSFR expression, mediated partially through a PI3K-Akt-dependent mechanism. Exposure of mice to CO in a model of marginal bone marrow transplantation significantly improved donor myeloid cell engraftment efficiency, expansion and differentiation, which corresponded to increased serum levels of GM-CSF, IL-1α and MCP-1. Collectively, we conclude that HO-1 and CO in part are critical for myeloid cell differentiation. CO may prove to be a novel therapeutic agent to improve functional recovery of bone marrow cells in patients undergoing irradiation, chemotherapy and/or bone marrow transplantation.NIH grants:( HL-071797, HL-07616, R21CA169904), AHA grant: (10SDG2640091), Julie Henry Fund, Transplant Center of the BIDMC, Eleanor Shore Foundation
Fitness Measurements of Evolved Esherichia coli
Get PDFBacteria can adapt very rapidly to novel selective pressures. In the transition from commensalism to pathogenicity bacteria have to face and adapt to the host immune system. Specifically, the antagonistic interaction imposed by one of the first line of defense of innate immunity cells, macrophages, on commensal bacteria, such as Escherichia coli (E. coli), can lead to its rapid adaptation. Such adaptation is characterized by the emergence of clones with mutations that allow them to better escape macrophage phagocytosis. Here, we describe how to quantify the amount of fitness increase of bacterial clones that evolved under the constant selective pressure of macrophages, from a murine cell line RAW 264.7. The most widely used assay for measuring fitness changes along an evolutionary laboratory experiment is a competitive fitness assay. This assay consists of determining how fast an evolved strain outcompetes the ancestral in a competition where each starts at equal frequency. The strains compete in the same environment of the evolution experiment and if the evolved strain has acquired strong beneficial mutations it will become significantly overrepresented in repeated competitive fitness assays.LAO/ITQB, FCT
Conservation Status and Abundance of the Crowned Sifaka (Propithecus coronatus)
Get PDFThe crowned sifaka (Propithecus coronatus) is Endangered. It has a large but highly fragmented distribution; its known range extends from the Betsiboka River in the north of Madagascar, to the Mahavavy River in the north-west, and down to the Tsiribihina River in the south-west. The species lives in forest habitats that are highly and increasingly fragmented and are continuously suffering perturbations and destruction. In order to carry out effective conservation measures targeting P. coronatus, its conservation status needs to be updated so that measures can be taken before anthropogenic or natural environmental changes lead to the extirpation of the species in most of its forests. We (i) identified forest fragments where the species is still present and (ii) using the line-transect “Distance” sampling method, estimated the population size and density in the principal remaining forest fragments in the northern part of its range, including both protected and unprotected areas. We visited most of the forests in the northern part of its range in order to update the current area of occupancy, and to rate the state of its forests using a qualitative “forest quality index.” Our survey results have shown that (i) a large number of forests have disappeared or decreased in size in the last 10 years, and (ii) population densities vary considerably among forest fragments (ranging from 49 to 309 individuals per km²), with some very high densities in forests located along the Mahavavy River and in the Antrema area. Their abundance in the area surveyed is likely to be between 4,226 and 36,672 individuals, and most probably above 10,000. It is difficult to extrapolate from these estimates to the total abundance across the species’ entire range, but we estimate that it is likely to be large, probably between 130,000 and 220,000 individuals. Unfortunately, many field observations suggest that its populations continue to decline at a high rate due to habitat loss and hunting, and we argue for the re-evaluation of the conservation status from Endangered A2cd to Endangered A4acd, and the need to survey the rest of the range of P.coronatus.FCT grant: (SFRH/BD/64875/2009), Institut Français de la Biodiversité, Programme Biodiversité de l’Océan Indien (ref.CD-AOOI-07-003), the GDRI Madagascar, the "Laboratoire d’Excellence" (LABEX) entitled TULIP: (ANR -10-LABX-41), Instituto Gulbenkian de Ciência, “Optimus Alive!” Biodiversity grant, University of Mahajanga, Département de Biologie Animale et Ecologie, Fanamby NGO