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Ponce, Toledo Rafael Isaac. "Origins and early evolution of photosynthetic eukaryotes." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS047/document.
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Les plastes primaires proviennent d'une cyanobactérie qui a établi une relationendosymbiotique avec un hôte eucaryote. Cet événement a donné naissance au super-groupeArchaeplastida qui inclut les Viridiplantae (algues vertes et plantes terrestres), les Rhodophyta (alguesrouges) et les Glaucophyta. Suite à l'endosymbiose primaire, les algues rouges et vertes ont étendu lacapacité de photosynthèse à d'autres lignées eucaryotes via des endosymbioses secondaires. Bien quedes progrès considérables aient été réalisés dans la compréhension de l'évolution des eucaryotesphotosynthétiques, d'importantes questions sont restées ouvertes, telles que l’identité de la lignéecyanobactérienne la plus proche des plastes primaires ainsi que le nombre et l'identité des partenairesdans les endosymbioses secondaires.Ma thèse a consisté à étudier l'origine et l'évolution précoce des eucaryotes photosynthétiques enutilisant des approches phylogénétiques et phylogénomiques. Je montre par mon travail que les plastesprimaires ont évolué à partir d'un symbiote phylogénétiquement proche de Gloeomargarita lithophora,une cyanobactérie représentant un clade s’étant diversifié précocement et qui a été détectéeuniquement dans les milieux terrestres. Ce résultat fournit des pistes nouvelles sur le contexteécologique dans lequel l'endosymbiose primaire a probablement eu lieu. En ce qui concerne l'évolutiondes lignées eucaryotes avec des plastes secondaires, je montre que les génomes nucléaires deschlorarachniophytes et des euglénophytes, deux lignées photosynthétiques avec des plastes dérivésd'algues vertes, encodent un grand nombre de gènes acquis par transferts depuis des algues rouges.Enfin, je mets en évidence que SELMA, la machinerie de translocation des protéines à travers laseconde membrane externe des plastes rouges secondaires à quatre membranes, a une histoireétonnamment compliquée aux implications évolutives importantes : les cryptophytes ont recruté unensemble de composants de SELMA différent de ceux des haptophytes, straménopiles et alvéolés.Ainsi, ma thèse a permis d’identifier pour la première fois la lignée cyanobactérienne la plus proche desplastes primaires et apporte de nouvelles pistes pour éclaircir les événements complexes qui ontjalonné l’évolution des eucaryotes photosynthétiques secondairesPrimary plastids derive from a cyanobacterium that entered into an endosymbioticrelationship with a eukaryotic host. This event gave rise to the supergroup Archaeplastida whichcomprises Viridiplantae (green algae and land plants), Rhodophyta (red algae) and Glaucophyta. Afterprimary endosymbiosis, red and green algae spread the ability to photosynthesize to other eukaryoticlineages via secondary endosymbioses. Although considerable progress has been made in theunderstanding of the evolution of photosynthetic eukaryotes, important questions remained debatedsuch as the present-day closest cyanobacterial lineage to primary plastids as well as the number andidentity of partners in secondary endosymbioses.The main objectives of my PhD were to study the origin and evolution of plastid-bearing eukaryotesusing phylogenetic and phylogenomic approaches to shed some light on how primary and secondaryendosymbioses occurred. In this work, I show that primary plastids evolved from a close relative ofGloeomargarita lithophora, a recently sequenced early-branching cyanobacterium that has been onlydetected in terrestrial environments. This result provide interesting hints on the ecological setting whereprimary endosymbiosis likely took place. Regarding the evolution of eukaryotic lineages with secondaryplastids, I show that the nuclear genomes of chlorarachniophytes and euglenids, two photosyntheticlineages with green alga-derived plastids, encode for a large number of genes acquired by transfersfrom red algae. Finally, I highlight that SELMA, the translocation machinery putatively used to importproteins across the second outermost membrane of secondary red plastids with four membranes, has asurprisingly complex history with strong evolutionary implications: cryptophytes have recruited a set ofSELMA components different from those present in haptophytes, stramenopiles and alveolates.In conclusion, during my PhD I identified for the first time the closest living cyanobacterium to primaryplastids and provided new insights on the complex evolution that have undergone secondary plastid-bearing eukaryotes
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Moustafa, Ahmed Bhattacharya Debashish. "Evolutionary and functional genomics of photosynthetic eukaryotes." Iowa City : University of Iowa, 2009. http://ir.uiowa.edu/etd/311.
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Hraber, Peter T. "Discovering molecular mechanisms of mututalism with computational approaches to endosymbiosis /." Color figures, full content, and supplementary materials are available online, 2001.
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Thesis (Ph. D.)--University of New Mexico, 2001."July, 2001." Includes bibliographical references (leaves 112-121). Color figures, full content, and supplementary materials are available online via www.santafe.edu/p̃th/dss.
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Wisecaver, Jennifer Hughes. "Horizontal Gene Transfer and Plastid Endosymbiosis in Dinoflagellate Gene Innovation." Diss., The University of Arizona, 2012. http://hdl.handle.net/10150/265594.
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Recent studies suggest that horizontal gene transfer (HGT) plays an important role in niche adaptation in some eukaryotes and may be a major evolutionary force in unicellular lineages. One subcategory of HGT is endosymbiotic gene transfer (EGT), which is characterized by a large influx of genes from endosymbiont to host nuclear genome and is a critical step in the establishment of permanent organelles, such as plastids. The dinoflagellates are a diverse group of mostly marine eukaryotes that have a propensity for both HGT and plastid endosymbiosis. Many dinoflagellates are predators and can acquire both genes and plastids from prey, blurring the distinction between HGT and EGT. Here, I measure genome mosaicism in dinoflagellates to investigate how HGT has impacted gene innovation and plastid endosymbiosis in this group. Because analysis of HGT depends on accurate phylogenetic trees, I first assessed the sensitivity of automated phylogenomic methods to variation in taxon sampling due to homolog selection parameters. Using methods based on this analysis, I showed that a large amount of HGT has occurred in dinoflagellates, particularly from bacterial donors. Further, I demonstrated that the dinoflagellate Alexandrium tamarense has the largest number of genes gained relative to related eukaryotes using ancestral gene content reconstruction. Additionally, dinoflagellates have lost several ubiquitous eukaryotic metabolic genes, but missing genes have been functionally replaced by xenologs from many evolutionarysources. Other transferred genes are involved in diverse functions. These results suggest that dinoflagellate genomes are heavily impacted by HGT. Also, I investigated the timing and consequences of HGT in plastid endosymbiosis. Using the dinflagellate Dinophysis acuminata, a mixotrophic species that sequesters and maintains prey plastids, I identified plastid-targeted proteins that function in photosystem stabilization and metabolite transport. Dinophysis acuminate may be able to extend the useful life of the stolen plastid by protecting the photosystem and replacing damaged transporters. Phylogenetic analyses showed that genes are derived from multiple sources indicating a complex evolutionary history involving HGT. Dinophysis acuminate can acquire both genes and plastids from prey, which suggests that HGT could play an important role in plastid acquisition during the earliest stages of this transition.
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Truitt, Amy Michelle. "Wolbachia-Host Interactions and the Implications to Insect Conservation and Management." PDXScholar, 2017. https://pdxscholar.library.pdx.edu/open_access_etds/3643.
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Parasitic reproductive endosymbionts are emerging as formidable threats to insect biodiversity. Wolbachia are prevalent maternally inherited intra-cellular bacteria found in >50% of arthropod species. These symbiotic bacteria interact with their hosts in diverse ways, most often they alter host reproduction causing four conditions that all selectively favor infected females: feminization, male killing, parthenogenesis, and cytoplasmic incompatibility (CI). Furthermore, depending on strain-type and host genetic background, Wolbachia are known to affect insect behavior, expand or shift host thermal tolerance ranges, and confer anti-viral protection to their hosts. Because Wolbachia both reside in and are transmitted with host cell cytoplasm, mitochondria and other cytoplasmically inherited genetic elements become linked with the bacteria. Thus, by enhancing their own transmission, Wolbachia-induced phenotypes can lead to mitochondrial selective sweeps, which may have profound impacts on vulnerable and small insect populations. Elucidating the extent to which endosymbionts influence biological and ecological functions is pivotal to making management decisions regarding imperiled insect species.
My dissertation investigates biological and ecological impacts of host-endosymbiont interactions by examining Wolbachia infections in three different host systems. First, I used the federally threatened butterfly species Speyeria zerene hippolyta to determine whether the general reproductive success of local populations was affected by the introduction of CI-inducing Wolbachia-infected butterflies through implemented species recovery programs. Next, by characterizing the Wolbachia infections of parasitoids associated with the Eurema butterfly clade, I analyzed whether host-parasitoid interactions provide a path for interspecies horizontal transmission. Finally, I conducted a laboratory experiment using an isogenic Drosophila melanogaster line to determine whether Wolbachia influence host temperature preference. Together, my research examines how the individual level effects of host-endosymbiont interactions can expand into populations, have broader impacts on insect communities, and potentially impede the conservation and management of insects in nature.
In chapter one, I screened S. z. hippolyta samples from three extant populations for Wolbachia infection. To examine the impacts of Wolbachia on small populations, I analyzed and compared infected and uninfected S. z. hippolyta reproductive data and showed that, in a population composed of infected and uninfected S. z. hippolyta, uninfected butterflies had reduced reproductive success (GLMM z = -8.067, P < 0.0001). I then developed a single-population demographic theoretical model using these same reproductive data to simulate and analyze different potential dynamics of small populations resulting from population supplementation with uninfected, CI-Wolbachia infected, or combined uninfected and infected butterflies. Analysis of model simulations revealed that supplementation with CI-inducing butterflies significantly suppressed host-population size (ANOVA F5,593 = 3349, PWolbachia-infected individuals (Tukey's post-hoc test P < 0.0001). In addition, supplementation by multiple releases using a combination of 50 infected and 300 uninfected butterflies has a less severe suppression effect, reducing the population by 75.8%, but the reduction occurs 42.6% faster than with the single release of 50 Wolbachia-infected butterflies (Tukey's post-doc test P < 0.0001).
Parasitoid-host interactions have emerged as probable ecological relationships to facilitate horizontal transmission of Wolbachia. In chapter two, I addressed horizontal transmission using Eurema butterflies and their associated parasitoids. From four locations in Northern Queensland, Australia, I collected a total of 404 Eurema hecabe butterfly larvae. Twenty-three parasitoids emerged from the larvae of which 21 were Diptera and two were Hymenoptera. I amplified COI loci fragments from each parasitoid for BLAST query searches and found that 20 individual Diptera parasitoids matched to the genus Exorista and one to the genus Senometopia. One of the Hymenoptera parasitoids matched to the genus Microoplitis and the other to the genus Cotesia. To characterize Wolbachia infections, I used Wolbachia Multi Locus Sequencing Technique (MLST) and discovered that all 20 Exorista parasitoids were infected with an identical Wolbachia strain (ST-41), which is the same strain infecting their Eurema hecabe butterfly hosts. Although, further experiments are necessary to definitively determine that ST-41 Wolbachia are incorporated into germline cells of the parasitoids, this is the first study to provide ecological evidence for inter-ordinal Wolbachia transmission between Lepidoptera and Diptera. Furthermore, this discovery exposes the risk of population augmentation programs that move insects, potentially facilitating the spread of Wolbachia between species within a community through the accidental introduction of new Wolbachia-infected parasitoids.
Finally, both Wolbachia and their insect hosts are temperature sensitive organisms. Wolbachia's replication behavior in their hosts is positively-temperature dependent, while environmental variation can have profound effects on insect's immune function, fitness, and fecundity. In chapter three, I conducted a laboratory experiment using a thermal gradient choice assay and an isogenic Drosophila melanogaster line with four different Wolbachia infection statuses -- uninfected, wMel, wMelCS, and wMelPop - to assess whether a relationship existed between Wolbachia infection and host temperature preference. Results from my laboratory experiment revealed that Wolbachia-infected flies preferred cooler temperatures compared to uninfected flies. Moreover, D. melanogaster temperature preferences varied depending on the Wolbachia strain variant with which they were infected; flies infected with the wMel strain had temperature preferences 2°C cooler compared to uninfected flies; flies infected with either wMelCS or wMelPop strains had preferred temperatures 8°C cooler compared to uninfected flies. Wolbachia-associated temperature preference variation within a species can lead to conspecifics occupying different microclimates, genetically adapting to different sets of specific environmental conditions, and may eventually result in ecological and reproductive isolation. While, reproduction isolation is recognized as one of the first stages in speciation, in small populations of endangered and threatened species, the inability to reproduce between conspecifics can drive species to extirpation or extinction.
Collectively, the three chapters of my dissertation set precedent for future integration of host-endosymbiont research prior to implementing population supplementation or translocation programs for the conservation of imperiled insects.
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Teberobsky, Debora Yurman. "Aphis fabae (Scopoli) subspecies their host plant utilization, endosymbiosis and taxonomy (Homoptera: Aphididae)." Thesis, University of York, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245896.
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Garrido, Clotilde. "De l’origine des peptides d’adressage aux organites (mitochondries et chloroplastes)." Electronic Thesis or Diss., Sorbonne université, 2021. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2021SORUS280.pdf.
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Les mitochondries et les chloroplastes sont des organites de cellules eucaryotes issus d’événements endosymbiotiques impliquant une bactérie et une cellule hôte il y a plus d’un milliard d’années. Aujourd’hui la très grande majorité des protéines présentes dans ces organites sont codées dans le noyau. Le ciblage des protéines cytosoliques vers les mitochondries et les chloroplastes pourrait dériver d’un mécanisme de résistance bactérienne aux attaques de peptides antimicrobiens, ces acteurs majeurs de l’immunité innée, présents dans tous les domaines du vivant. Cette hypothèse se base sur les similarités frappantes entre ces deux mécanismes. Au cours de mon doctorat, j’ai mis à l’épreuve cette hypothèse. Dans une première partie, j’ai pu montrer qu’un sous-ensemble de peptides antimicrobiens se structurant en hélice ↵-amphipathique et les peptides d’adressage possédaient des propriétés physico-chimiques communes, qui sont distinctes de celles partagées entre les peptides signaux de sécrétion bactériens et eucaryotes dont l’origine évolutive commune est bien établie. De plus, ils peuvent se complémenter fonctionnellement in vivo, confortant l’hypothèse de leur origine commune (Garrido et al. 2020). La transition moléculaire nécessaire pour passer d’un peptide antimicrobien à un peptide d’adressage comporte trois étapes cruciales : i) le remplacement des lysines par des arginines qui permet de diminuer l’activité microbienne et de favoriser l’activité d’adressage, ii) l’acquisition d’un site de clivage au sein des peptides d’adressage, iii) l’acquisition d’un domaine N-terminal peu structuré afin d’orienter l’adressage vers le chloroplaste et non vers la mitochondrie au sein des eucaryotes photosynthétiques (Caspari, Garrido et al., article soumis). Dans une deuxième partie, j’ai établi le catalogue exhaustif des familles d’homologues des peptidases impliquées dans la dégradation des peptides d’adressage dans l’arbre du vivant. J’ai pu démontrer que chacune de ces peptidases a été acquise via un évènement de transfert horizontal depuis une bactérie. En accord avec notre hypothèse, on retrouve de nombreux homologues de bactéries résistantes aux peptides antimicrobiens proches des peptidases des organites (Garrido et al., article soumis)Mitochondria and chloroplasts are eukaryotic organelles that originated from endosymbiotic events betweena bacteria and a host cell more than a billion years ago. Today, the vast majority of proteins present in theseorganelles are encoded in the nucleus. Targeting of cytosolic proteins to mitochondria and chloroplasts couldderive from a mechanism of bacterial resistance to the attacks of antimicrobial peptides, major actors of theinnate immunity system, present in all domains of life. This hypothesis is based on the striking similaritiesbetween these two mechanisms. During my PhD, I challenged this hypothesis. In a first part, I showed thata subset of antimicrobial peptides structuring in ↵-amphipathic helix and organelle targeting peptides havecommon physico-chemical properties, distinct from those shared by bacterial and eukaryotic secretory signalpeptides whose common evolutionary origin is well established. Furthermore, they can functionally complementeach other, supporting the hypothesis of their common origin (Garrido et al. 2020). The molecular transitionrequired for the emergence of a targeting peptide from an antimicrobial peptide involves 3 crucial steps : (i)the replacement of lysines with arginines, which decreases microbial activity and promotes addressing activity,(ii) the acquisition of a cleavage site and (iii) the acquisition of a loosely structured N-terminal domain forchloroplast specific targeting within photosynthetic eukaryotes (Caspari, Garrido et al. , submitted). In asecond part, I established the exhaustive catalog of peptidase homologous families involved in the degradationof taregting peptides across the tree of life. I showed that each of these peptidases was acquired via a horizontaltransfer event from a bacterium; and consistent with the hypothesis, many homologs from antimicrobialpeptide-resistant bacterial are closely related to the organelle peptidases (Garrido et al., submitted)
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Roopin, Modi M. Chadwick Nanette Elizabeth. "Symbiotic benefits to sea anemones from the metabolic byproducts of anemonefish." Auburn, Ala., 2007. http://hdl.handle.net/10415/1331.
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Gerhart, Jonathan Graham. "Evolution and Metabolic Potential of Francisella-like Endosymbionts of Ticks." PDXScholar, 2017. https://pdxscholar.library.pdx.edu/open_access_etds/3832.
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Endosymbiosis in arthropods involves intracellular bacteria that supply an array of benefits to the host. Endosymbionts likely enhance the health of ticks by provisioning amino acids such as cysteine and tyrosine, and cofactors such as biotin and folic acid that are not available in blood--the sole nutrient source of ticks. Endosymbionts of ticks are of special interest due to their close evolutionary relationship with tick-vectored pathogens that impact livestock and human health. For example, ticks typically contain Coxiella-like endosymbionts (CLEs) that are the closest relatives of the human pathogen Coxiella burnetii. In order to understand the evolutionary relationship between the mammalian pathogen Francisella tularensis, which is vectored by ticks, and the Francisella-like endosymbionts (FLEs) present in several ticks, we assembled the genomes of the FLEs in the hard tick Amblyomma maculatum and the soft tick Ornithodoros moubata using high-throughput sequencing. While this project was in progress, another group described the genome of an FLE in the soft tick Argus (Persicargas) arboreus. Utilizing the three genomes, we show that all FLEs evolved from a mammalian pathogen, a relationship that is converse to that of C. burnetii, which likely evolved from a tick-associated non-pathogenic ancestor. Additionally, our analyses indicate that FLEs are horizontally transferred between ticks, and due to their superior metabolic capabilities could replace ancestral endosymbionts with reduced genomes.
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Atyame, Nten Célestine Michelle. "Dynamique évolutive des bactéries endocellulaires Wolbachia et des incompatibilités cytoplasmiques chez le moustique Culex pipiens." Thesis, Montpellier 2, 2011. http://www.theses.fr/2011MON20031/document.
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Les Wolbachia sont des α-Protéobactéries endocellulaires transmises maternellement et qui manipulent la reproduction des Arthropodes pour augmenter leur transmission. Chez le moustique Culex pipiens, Wolbachia induit l'incompatibilité cytoplasmique (IC) qui se traduit par une forte mortalité embryonnaire lors de croisements entre individus infectés par des souches incompatibles de Wolbachia. Ce moustique se caractérise par une forte diversité génétique de ses Wolbachia (nommées wPip) et par des patrons d'IC complexes. Nous avons examiné les mécanismes qui façonnent la dynamique de cette association symbiotique aux niveaux génomique, phénotypique et populationnel. Nous avons montré que les souches wPip ont une origine génétique commune récente et qu'elles s'organisent en groupes génétiques présentant une structuration géographique. Nous avons mis en évidence des évènements de recombinaison entre souches wPip qui pourraient jouer un rôle majeur dans la diversité génétique des Wolbachia et dans l'évolution rapide des patrons d'IC. En croisant des lignées de moustiques d'origines géographiques diverses et infectées par des souches de différents groupes génétiques, nous avons montré que les IC (i) évoluent très rapidement chez Cx. pipiens; (ii) sont contrôlées par plusieurs déterminants génétiques, et (iii) qu'il y a une relation entre les patrons d'IC et les groupes génétiques des Wolbachia. Dans les populations naturelles, il apparaît que les IC sont contre sélectionnées au sein d'une population mais qu'une zone de contact entre populations infectées par des souches incompatibles peut se maintenir de façon stableWolbachia are maternally inherited endocellular α-Proteobacteria that manipulate the reproduction of Arthropods to promote their own transmission. In the mosquito Culex pipiens, Wolbachia induce cytoplasmic incompatibility (CI) which results in high embryonic mortality in crosses between mosquitoes infected with incompatible Wolbachia strains. This mosquito is characterized by high genetic diversity of its Wolbachia (referred as wPip strains) and by complex CI patterns. We examined mechanisms that shape the dynamics of this symbiotic association at genomic, phenotypic and field population levels to understand how it evolves. We showed that wPip strains have a unique and recent evolutionary origin and that their diversity clusters into distinct genetic groups with a geographic structure. We revealed the existence of extensive recombinations among wPip strains, which could influence their adaptive dynamics by creating new wPip strains and thus allow the rapid emergence of new CI patterns. The analysis of crossing relationships between mosquito lines from different geographic origins and infected with wPip strains belonging to different genetic groups showed that CIs (i) evolve rapidly in Cx. pipiens; (ii) are controlled by several genetic factors, and (iii) there is a significant relationship between CI patterns and genetic divergence of wPip strains. In field populations, it appears that CIs are selected against within a population but a contact zone between populations infected by incompatible Wolbachia strains can be stably maintained
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Moustafa, Ahmed. "Evolutionary and functional genomics of photosynthetic eukaryotes." Diss., University of Iowa, 2009. https://ir.uiowa.edu/etd/311.
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My dissertation focuses on genome and functional evolution of photosynthetic eukaryotes and the design and implementation of computational methods and tools to enable genome-wide studies to investigate these taxa. The work described here is grouped into two major topics, 1) endosymbiosis and genome evolution, and 2) harmful algal blooms. I discuss my work related to endosymbiosis and genome evolution in chapters 2-4. Chapters 5-6 cover the work related to harmful algal blooms. In chapter 1, I introduce the state-of-art of what is known about the history of plastids and evolution of photosynthesis in eukaryotes, an overview of marine harmful algae, and the specific aims of my dissertation.
In chapter 2, I describe the design and implementation of the phylogenetic sorting tool, PhyloSort and the assembly of a high-throughput phylogenomic pipeline. Together, PhyloSort and the pipeline has become a key tool for multiple subsequent studies. chapter 2 also presents a case study using these tools in which we provide an estimate of the number of cyanobacterial genes that have been transferred to the nuclear genome of Plantae through primary endosymbiotic gene transfer; I use the model unicellular green alga Chlamydomonas reinhardtii for this purpose.
In chapter 3, I discuss another case of prokaryotic contribution to the nucleus of photosynthetic eukaryotes. Here, the intriguing relationship of Chlamydiae-like bacteria and plants and algae is examined in a large-scale analysis, in which we scanned all available genomes of the primary photosynthetic organisms for genes of potential Chlamydiae origin. Surprisingly, we identified more than fifty Chlamydiae-derived genes in plants and algae. Here, we propose a model for the role that a Chlamydiae-like symbiont might have played in the establishment of the primary plastid in the common ancestor of Plantae.
In chapter 4, I describe a study in which we explored the complete protein models of two diatom organisms as representative for photosynthetic chromalveolates and looked for genes that might have been acquired through endosymbiotic (secondary) or horizontal transfers from red or green algae. In contradiction of the “chromalveolate hypothesis” which states that photosynthesis in chromalveolates originated via the engulfment of a red alga symbiont, our study shows an unexpected green algal contribution that is fourfold greater than that of the canonical red algal symbiont. Our data suggest that the chromalveolate history includes a previously unrecognized green algal endosymbiont that was captured and lost prior to the more recent establishment of the red alga plastid, which is widespread in extant photosynthetic chromalveolates.
In chapter 5, I discuss the identification of the phylogenetic origin of the genes involved in the biosynthetic pathway of saxitoxin in cyanobacteria. Here, we used a pyrosequencing approach to sequence de novo genomes of two strains of Anabaena circinalis, one of which is saxitoxin-producing and the other is non-toxic. Using comparative and phylogenetic analyses, I show that, within the saxitoxin gene cluster, genes that encode the key and unique enzymes in the pathway are of foreign origin that originated via horizontal transfer from non-cyanobacterial sources. These genes introduced the ability to produce saxitoxin in the ancestor of the toxic cyanobacterial clade.
In chapter 6, I describe a gene expression study in which we used massively parallel signature sequencing (MPSS) to investigate RNA abundance patterns in the toxic dinoflagellate Alexandrium tamarense. This work provides the first clear evidence for the utilization by dinoflagellates of transcriptional to regulation. Moreover, using MPSS, we provide an estimate of the number of the distinct genes in Alexandrium tamarense; i.e., remarkably 40,000 loci. Taken together, our data indicate that dinoflagellates possess a great metabolic flexibility that allows them to efficiently toggle between photoautotrophy and heterotrophy based on the environmental conditions.
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Maire, Justin. "Immune and developmental regulations in host-symbiont interactions in the cereal weevil Sitophilus spp." Thesis, Lyon, 2018. http://www.theses.fr/2018LYSEI094.
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La symbiose est un phénomène ubiquitaire dans la nature et joue un rôle évolutif majeur. Alors que la communauté scientifique reconnaît désormais l’importance des associations symbiotiques dans de nombreux processus biologiques et pathologiques chez les animaux, la compréhension des mécanismes de contrôle, de tolérance et de modulation des populations symbiotiques est un enjeu majeur. Pour aborder ces questions, j’ai étudié l’association entre le charançon Sitophilus et la bactérie intracellulaire Sodalis pierantonius. Sitophilus héberge son endosymbiote dans des cellules spécialisées, les bactériocytes, regroupées en un organe, le bactériome. En retour, S. pierantonius fournit à son hôte des nutriments présents en faibles quantités dans son alimentation, les céréales. S. pierantonius étant immunogène pour son hôte, dans un premier chapitre, j’ai étudié les régulations immunitaires spécifiques au bactériome assurant le maintien de l’homéostasie immunitaire. J’ai dans un premier temps montré que la compartimentalisation des endosymbiotes, limitant les contacts immunitaires avec l’hôte, repose sur l’expression IMD-dépendante d’un peptide antimicrobien, une régulation similaire aux réponses immunitaires aux pathogènes. Ensuite, j’ai montré comment l’immunogénicité des endosymbiotes, via son peptidoglycane, est limitée par des Protéines de Reconnaissance du PeptidoGlycane (PGRP). Le peptidoglycane symbiotique ne semble pas être reconnu dans le bactériome, et sa reconnaissance systémique est contenue par l’action locale de PGRP-LB. Cette protéine clive le peptidoglycane symbiotique, empêchant ainsi l’activation chronique du système immunitaire systémique. Dans un deuxième chapitre, j’ai étudié comment, au cours de la métamorphose, le bactériome se réorganise complètement. Le bactériome larvaire se dissocie, les bactériocytes migrent le long de l’intestin et forment de multiples nouveaux bactériomes. Une approche de dual-RNAseq nous a permis de révéler l’implication à la fois de l’hôte et du symbiote dans ce remodelage morphologique. Les résultats obtenus durant cette thèse montrent l’impact incommensurable des bactéries sur des processus immunitaires et développementaux, et sur l’évolution des animaux en généralSymbiosis is ubiquitous in nature and plays a crucial role in evolution. As the scientific community is becoming increasingly aware of the importance of such associations in both biological and pathological processes in animals, understanding how symbiotic populations are controlled, tolerated, and modulated, is becoming a major stake. To address these questions, I studied the mutualistic association between the weevil Sitophilus and the intracellular bacterium Sodalis pierantonius. Sitophilus houses S. pierantonius in specialized host cells, the bacteriocytes, which group together in an organ, the bacteriome. In return, S. pierantonius provides its host with nutrients scarecely present in its cereal-based diet. S. pierantonius being immunogenic for its host, I studied in a first chapter how specific bacteriome immune regulations ensure the maintenance of host immune homeostasis. In a first part, I showed that endosymbiont compartmentalization, which limits host-endosymbiont immune contacts, relies on the IMD-dependent expression of one antimicrobial peptide, a regulation similar to that of immune responses in pathogenic conditions. Then, I showed how endosymbiont immunogenicity, via its peptidoglycan, is tamed by PeptidoGlycan Recognition Proteins (PGRPs). While symbiotic peptidoglycan would not be recognized within the bacteriome, its systemic recognition is circumscribed by PGRP-LB local action. PGRP-LB cleaves symbiotic peptidoglycan, thereby preventing a chronical and detrimental activation of the host systemic immunity. In a second chapter, I studied how, during metamorphosis, the bacteriome is completely remodeled. The larval bacteriome dissociates, bacteriocytes migrate along the midgut, and settle in multiple new bacteriomes. A dual-RNAseq approach allowed us to pinpoint both host and symbiont implication in this drastic morphological reorganization. The results obtained during this PhD show the immeasurable impact bacteria bear on host immune and developmental processes, and more generally on animal evolution
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Fitzpatrick, Eileen Elizabeth. "First Bacterial Endosymbionts Found in the Phylum Ascomycota." PDXScholar, 2013. https://pdxscholar.library.pdx.edu/open_access_etds/675.
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Organisms belonging to the Kingdom Fungi are known to occupy a wide variety of ecological niches and are found globally in virtually all environments. Two members of the smallest of the fungal phylum, the Zygomycota, have also been found to harbor intercellular bacteria initially described as being from or closely related to organisms from the Genus Burkholderia. In this study two microaerophilic members of the species Verticilium from the phyla Ascomycota were characterized. Both appear to carry two bacterial endosymbionts. This is the first evidence of bacterial endosymbionts found within a member of the Ascomycota. Through the use of fluorescent stains, isolation of the intercellular bacteria, DNA analysis and fluorescent in situ hybridization (FISH) it appears that the newly isolated Verticilium sp. fungi contain not one but two bacterial endosymbionts from the family Proteobacteria. One putative symbiont is from the genus Bradyrhizobium, a member of the α-Proteobacteria, and one from the genus Burkholderia, a member of the β-Proteobacteria. This is the first evidence of a fungus containing not one, but two distinct endosymbionts from two separate bacterial families. Additionally the fungi were found to grow from spore across a large pH gradient (pH 1.2 to pH 13.5) and in conditions lacking given nutrient. They were tolerant of concentrations of Fe(II) up to 50mM and grew better with low oxygen levels (1.6%) than without.
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Miller, Lance Delano. "Characterization of the Chemotaxis System of the Endosymbiotic Bacterium Rhizobium leguminosarum." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/19707.
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Chemotaxis is the process by which motile bacteria navigate chemical gradients in order to position themselves in optimum environments for growth and metabolism. Sensory input from both the external environment and the internal cellular environment are sensed by chemotaxis transducers and transduced to a two-component system whose output interacts with the flagellum thereby regulating motility.
Chemotaxis has been implicated in establishing the endosymbiotic relationship between the motile alpha-proteobacterium Rhizobium leguminosarum biovar viciae and its host Pisum sativa, the pea plant. An approach combing bioinformatical sequence analysis, molecular genetics, and behavioral analysis was used to characterize the chemotaxis system of R. leguminosarum and determine its contribution to this bacterium s lifestyle.
A genome search revealed the presence of two chemotaxis gene clusters, che1 and che2. Homologs of each che cluster are major chemotaxis operons controlling flagellar motility in other bacterial species. For this reason we sought to determine the contribution of each che cluster to chemotaxis in R. leguminosarum. We found that while both che clusters contribute to the regulation of motility, che1 is the major che cluster controlling chemotaxis. Using competitive nodulation assays we determined that che1, but not che2, is essential for competitive nodulation.
The major che cluster, che1, encodes a chemotaxis transducer, IcpA-Rl, with a globin coupled sensor domain. Chemotaxis transducers with a globin coupled sensor domain comprise a large class of proteins found in bacteria and archaea. These proteins have been shown to bind heme and sense oxygen and are therefore termed HemATs for heme-binding aerotaxis transducers. However, sequence analysis of IcpA-Rl reveals that it lacks the requisite amino acid residues for heme-binding and is therefore unlikely to sense oxygen. We present evidence that IcpA-Rl is likely an energy transducer and represents a novel function of the globin coupled sensor domain in sensing energy related parameters.
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Genty, Lise-Marie. "Approche in situ de la régulation des interactions arthropode-symbiote." Thesis, Poitiers, 2013. http://www.theses.fr/2013POIT2324/document.
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La présence de Wolbachia dans les ovogonies assure la transmission verticale de la bactérie à la descendance de l'hôte. Cependant, nous montrons que chez l'hôte Armadillidium vulgare, l'efficacité de l'infection des descendants tient à un enrichissement en Wolbachia au cours de la maturation des ovaires et des ovocytes dû à une sélection en faveur des ovocytes infectés et/ou à l'entrée secondaire de Wolbachia dans les ovocytes en cours de maturation via l'infection des tissus somatiques. Dans ces tissus, nous avons précisé la localisation de Wolbachia au niveau cellulaire et révélé des morphotypes typiques de chaque tissu. Nous avons également observé Wolbachia chez des hôtes très inattendus; des nématodes non filaires infectant les cloportes, posant la question d'une transmission horizontale, et les A. vulgare mâles, sans qu'ils soient féminisés. Etonnamment, nous avons observé l'infection des gonades mâles dans des lignées d'hôtes chez lesquelles les femelles sont infectées de manière cryptique mais sans que leurs ovocytes ne soient infectés. Le maintien de l'infection entre les générations d'hôtes pourrait alors être dû à une transmission paternelle, inédite pour Wolbachia, ou à une capacité de transmission horizontale très efficace de la bactérie. Par immersion de tissus directement dans des broyats d'organes infectés nous avons en effet démontré que Wolbachia infecte très rapidement des cellules de novo. Les mécanismes d'entrée de Wolbachia dans les cellules sont inconnus mais en monitorant des voies métaboliques clefs de l'hôte nos résultats montrent que l'infection entraine une réponse globale des tissus et implique notamment un détournement de la voie autophagique chez l'hôteWolbachia presence in oogonia ensures bacteria to be vertically transmitted to host offspring. However, in Armadillidium vulgare, we show that the proportion of infected oocytes increases in the course of both ovary and oocyte maturation to reach the transmission rate at the end of ovary maturation. This enrichment can be explained by a preferential selection of oocytes infected with Wolbachia and/or by a secondary acquisition of the bacteria by oocytes. We suspect an acquisition through infected somatic tissues. We localize Wolbachia at the cell level in these tissues and showed particular morphotypes for each tissue. We also observe Wolbachia in unexpected hosts; non filarial nematodes infecting woodlice (suggesting horizontal transmission), and in A. vulgare males (without a feminizing effect of the bacteria). We also observe lineages in which females are cryptically infected. Surprisingly, we observe infected male gonads in these lineages for which female oocytes are uninfected. The infection maintenance across host generations could be due to a paternal transmission of the bacteria (a transmission never described for Wolbachia), or due to an astonishing ability of horizontal transmission. Nevertheless, immersion of uninfected tissues in a solution of crushed infected tissues proves that Wolbachia can quickly infect new tissues. Cellular mechanisms that allow Wolbachia internalization into the cell are still unknown. Thus, we monitor key host metabolic pathways in ovaries and we denote that infection enhances a global response of the entire tissue. Additionally, Wolbachia infection especially implicates a high-jacking of the autophagic pathway
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Masson, Florent. "Régulations immunitaires et cellulaires impliquées dans le maintien et le contrôle des bactéries endosymbiotiques du charançon des céréales du genre Sitophilus spp." Thesis, Lyon, INSA, 2015. http://www.theses.fr/2015ISAL0116/document.
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Plusieurs insectes se développant dans des milieux nutritionnellement déficients vivent en symbiose durable avec des bactéries intracellulaires (endosymbiotes) qui complémentent leur alimentation et améliorent leur pouvoir adaptatif. Alors que ces associations ont été largement étudiées sur les plans physiologiques et évolutifs, peu de travaux se sont consacrés à l’étude des mécanismes impliqués dans la tolérance et le contrôle des endosymbiotes par l’hôte. L’objectif de cette thèse est d’étudier, chez les charançons des céréales du genre Sitophilus, les particularités moléculaires et immunitaires du bactériome, un organe que l’insecte développe pour héberger les symbiotes et les isoler de sa réponse immunitaire systémique. Le bactériome du charançon exprime une réponse immunitaire modulée : des études transcriptomiques ont montré que les effecteurs de l’immunité sont peu exprimés dans cet organe, à l’exception d’un gène codant un peptide antimicrobien, la coléoptéricine A. Cette dernière interagit avec les endosymbiotes et participe à leur confinement intracellulaire. Dans une première partie, j’ai montré avec une approche d’interférence à l’ARN que l’expression du gène colA serait contrôlée par un système original qui impliquerait les gènes relish et tollip. Cette régulation « interne » au bactériome semble assurer le maintien des endosymbiotes et l’homéostasie de l’organe. Afin de comprendre comment le bactériome répond à une infection par les bactéries exogènes, j’ai suivi par RT-qPCR l’expression de gènes effecteurs de l’immunité dans le bactériome après injection systémique de bactéries à Gram positif ou négatif. Ceci a mis en évidence une réponse « externe », induite en cas d’infection, et qui aurait un rôle de protection des endosymbiotes contre les bactéries exogènes. Enfin, je me suis consacré à l’étude des changements de régulation accompagnant le passage du stade larvaire au stade adulte, marqué par une symbiose très dynamique. Le nombre d’endosymbiotes augmente fortement pendant les premiers jours de vie imaginale, puis diminue jusqu’à leur élimination complète par recyclage autophagique. Une analyse RNAseq a permis d’identifier les voies de signalisation dont l’activité accompagne cette dynamique. Une approche de RT-qPCR a également montré que l’immunité du bactériome est maintenue à un faible niveau d’activation pendant tout le processus de recyclage. Ce travail montre qu’au cours de leur évolution, les insectes ont sélectionné plusieurs stratégies pour assurer le maintien et l’ajustement de leur charge endosymbiotique en fonction de leurs besoins physiologiques : une signalisation immunitaire assurerait le confinement intracellulaire des endosymbiotes, et un ensemble de processus cellulaires incluant l’apoptose et l’autophagie semble être en associé aux voies métaboliques pour assurer le contrôle de la dynamique bactérienne et garantir le compromis bénéfice/coût de la symbioseMany insect species living on nutritionally unbalanced media depend on intracellular mutualistic bacteria, called obligatory endosymbionts, for their development and reproduction. Endosymbionts are housed in specialized host cells called bacteriocytes, that group together to form the bacteriome organ. Although such associations have been widely investigated on a physiological and evolutionary point of view, little is known about the mechanisms involved in the tolerance and the control of endosymbionts by the host. This work aims at deciphering the molecular and immune specificities of the bacteriome using the model system Sitophilus oryzae, the cereal weevil, and its obligate endosymbiont Sodalis pierantonius. The weevil bacteriome expresses a modulated immune response: transcriptomic studies showed that immune effector genes were lowly expressed despite the massive bacterial presence, with the exception of colA, a gene encoding for Coleoptericin A, an antimicrobial peptide. Coleoptericin A interacts with endosymbionts and participates in their intracellular seclusion. In a first chapter, I used RNA interference to demonstrate that colA gene expression may be controlled by an original system involving the genes relish and tollip. This “internal” regulation for endosymbiont control seems to maintain bacteriome homeostasis. In a second chapter, in order to understand how the bacteriome responds to an infection by exogenous bacteria, I followed up by RT-qPCR the expression of immune effector genes in the bacteriome after injection of Gram positive and Gram negative bacteria. This highlighted an “external” immune response, inducible upon infections, which may enable endosymbiont protection against exogenous intruders. In a third and last chapter, I focused on the regulation changes that accompany the switch from the larval stage to the imaginal stage, the latter being characterized by a very dynamic symbiosis. Endosymbiont load drastically increases during the first days of imaginal life, then rapidly decreases until complete elimination of the bacteria by autophagic recycling. RNAseq analysis allowed the identification of signaling pathways linked to this dynamic. A complementary RT-qPCR approach also showed that bacteriome immunity was laid low during the whole recycling process. This work shows that several strategies have been selected during host-symbiont coevolution to ensure the maintenance of the endosymbionts and the adjustment of their population depending on the insects physiological needs: immunity allows the intracellular seclusion in the bacteriocytes, and cell processes including autophagy and apoptosis are associated to metabolic pathways to control the endosymbiotic dynamics and secure the cost and benefit trade-off of symbiosis
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Badawi, Myriam. "Base génétique moléculaire de la féminisation induite par la bactérie endosymbiotique Wolbachia." Thesis, Poitiers, 2014. http://www.theses.fr/2014POIT2306/document.
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La symbiose est l'un des principaux moteurs de l'évolution. Le génotype du symbiote est capable d'altérer le phénotype de l'hôte, et vice-versa : c'est le « phénotype étendu ». Dans ce contexte, les endosymbioses à Wolbachia sont remarquables. Cette bactérie intracellulaire est un parasite de la reproduction capable d'induire la féminisation des mâles génétiques ou l'incompatibilité cytoplasmique chez ses hôtes crustacés isopodes terrestres. Actuellement, aucun mécanisme moléculaire régissant ces effets n'est connu. Dans le but d'identifier des gènes impliqués dans la féminisation, nous avons utilisé une approche intégrative qui combine à la fois des analyses génomiques, d'expression de gènes et phénotypiques. Nous avons tout d'abord analysé l'évolution moléculaire de la voie de la recombinaison homologue dans les génomes de Wolbachia, source importante de plasticité génomique pouvant être liée à la diversité des phénotypes. Ensuite, afin d'effectuer des études comparatives qui augmenteraient considérablement la compréhension des mécanismes de la féminisation, nous avons établi un système où la souche féminisante wVulC féminise deux hôtes isopodes (hôte naturel : Armadillidum vulgare : hôte hétérologue : Cylisticus convexus) présentant un timing différent de la différenciation sexuelle. En effet, l'effet féminisant étant supposé avoir lieu avant ou pendant la différenciation sexuelle, il est important de distinguer l'effet de Wolbachia dû à la différenciation sexuelle de celui dû au développement. Enfin, une approche par gènes candidats (du séquençage de génome bactérien à l'analyse comparative d'expression de gènes bactériens durant le développement de l'hôte) a permis de déterminer une liste réduite de 29 gènes (parmi les 1885 gènes de wVulC) dont la probabilité qu'ils soient impliqués dans la féminisation est élevée. Le rôle potentiel de ces gènes candidats comme effecteurs supposés de la féminisation induite par wVulC est ensuite discuté. Ce travail contribue grandement à l'identification de facteurs potentiels d'endosymbiotes qui ont un impact évolutif sur la détermination du sexe de leurs hôtesSymbiotic interactions are a major driver of evolution. The symbiont genotype is able to alter the host phenotype, and the other way round: it is called "the extended phenotype". In this respect, Wolbachia endosymbiosis is remarkable. This intracellular bacterium is a well-known reproductive parasite able to induce feminization of genetic males or cytoplasmic incompatibility in its terrestrial isopod crustacean hosts. Currently, no molecular genetic basis of these reproductive manipulations has been described. In order to identify genes involved in feminization, we used an integrative approach that combines genomic, gene expression and phenotypic studies. We first analysed the molecular evolution of the homologous recombination pathway in Wolbachia genomes, an important source of genomic plasticity that can be linked with phenotypic diversity. Then, in order to perform comparative studies that will substantially improve the understanding of the molecular mechanisms of feminization, we established a system in which the feminizing strain wVulC feminizes two different isopod hosts (natural host: Armadillidium vulgare ; heterologous host Cylisticus convexus) that have a different sexual differentiation timing. Indeed, as feminization is thought to happen before or during sexual differentiation, it is important to distinguish the effect of Wolbachia due to sexual differentiation from that due to development. Finally, a gene candidate approach (from bacterial genome sequencing to comparative bacterial gene expression during host developement) allowed us to determine a reduced list of 29 genes (among the 1885 genes of wVulC) that have a high probability to be involved in feminization. The potential roles of these candidate genes as putative effectors of feminization induced by wVulC is then discussed. This work substantially contributes to the identification of putative endosymbiont factors that have an evolutionary impact on sex determination of their hosts
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Binetruy, Florian. "Les communautés microbiennes au sein des populations de tiques : origine, diversité et structure." Thesis, Montpellier, 2019. http://www.theses.fr/2019MONTG038.
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Le microbiome désigne les communautés écologiques de microorganismes hébergées par un hôte. De nos jours, les microbiomes sont perçus comme de véritables génomes accessoires déterminant le phénotype étendu de leurs hôtes. Les microbiomes, à l’image de leurs hôtes, sont extrêmement divers et structurés par tout un panel de facteurs biotiques, abiotiques et stochastiques. Ces facteurs varient en fonction de l’échelle résolutive concernée : la structure des microbiomes ne sera pas impactée par les mêmes facteurs au niveau de l’individu hôte ou de la métacommunauté d’hôtes. Dans ce contexte fondamental de l’écologie des communautés, ma thèse a notamment essayé de déterminer quels sont les facteurs structurants d’un microbiome à différentes échelles résolutives. Pour répondre à cette question, nous avons étudié les cortèges microbiens abrités par les tiques de Guyane. Ce modèle est particulièrement pertinent pour deux raisons : 1/il est admis que les tiques hébergent des communautés microbiennes complexes qui potentiellement assujetties à des facteurs structurants complexes. 2/ Il n’existe aucune donnée récente sur la diversité, la biologie ou le risque infectieux associés aux tiques de Guyane. Par conséquent, ces travaux de thèses ont premièrement permis, de décrire des espèces de tiques jamais observées en Guyane et de caractériser des souches inconnues de bactéries potentiellement pathogènes, dont une nouvelle borrélie proche de celles responsables de la maladie de Lyme et de fièvres récurrentes. Deuxièmement, nous avons démontré qu’il existait de nombreux biais dans les études de microbiome des tiques et que cela impactait l’interprétation des données de structuration microbienne. Cela se traduit notamment par l’observation artéfactuelle d’une forte diversité microbienne lié essentiellement au microbiome cuticulaire. En réalité, les microbiomes des tiques apparaissent majoritairement structurés par l’identité, la présence/absence et les interactions entre des bactéries intracellulaires mutualistes des tiques, que se soit à une échelle intra-spécifique ou inter-spécifique. Enfin, nous avons mis en évidence que l’association entre les tiques et leur microbiome était également soumis à des patrons coévolutifs typiques des symbiontes intracellulaires d’arthropodes, ainsi qu’à des facteurs phylogéographique et bioécologique dépendant de l’hôte. Toutefois, il apparaît que la structuration des microbiomes chez les tiques est encore loin d’être totalement comprise et que, de futures études seront encore nécessaires pour démêler les différentes controverses sur la réalité biologique des microbiomes hébergés par les tiquesMicrobiome refers to the ecological communities of microorganisms hosted by a host. Microbiomes are now perceived as true accessory genomes that determine the extended phenotype of their hosts. They are, like theirs hosts, extremely diverse and structured by a wide range of biotic, abiotic and stochastic drivers. These factors vary according to the resolution scale: the structure of microbiomes will not be impacted by the same factors at an individual scale or an interspecific scale. In this fundamental context of community ecology, my thesis tried to determine what the microbiome drivers at different resolution scales are. To answer this question, we studied the microbial community sheltered by ticks in French Guiana. This model is particularly relevant for two reasons: 1/ It is recognized that ticks harbour complex microbial communities that appear to be subject to a diversity of potential drivers. 2/ There are no recent data on the diversity, biology or infectious risks associated with ticks in French Guiana. As a result, in this thesis we described tick species which were never observed in French Guiana and characterized unknown strains of potentially pathogenic bacteria, including a new borrelia related to Lyme disease and to relapsing fever ones. Then, we demonstrated the ubiquity of biases in tick microbiome studies and their impact on the interpretation of microbiome data by confusing cuticular and internal microbes. Tick microbiomes actually appear mainly structured by the identity, the presence/absence and the interactions between mutualistic intracellular bacteria of ticks, whether on an intra- or interspecific scale. Finally, we have shown that the association between ticks and their microbiome is also subject to co-evolutionary patterns, typical of intracellular symbionts of arthropods, as well as phylogeographic and bio-ecological factors depending of the tick hosts. However, the microbiome structure in ticks, is still far from being fully understood and future studies are necessary to resolve the various controversies on the biological reality of microbiomes hosted by ticks
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Pittis, Alexandros 1982. "Origin and evolution of eukaryotic compartmentalization." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/397755.
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The origin of eukaryotic compartmentalization stands as a major conundrum in biology. Current evidence indicates that the last eukaryotic common ancestor (LECA) already possessed many eukaryotic hallmarks, including a complex subcellular organization. The lack of evolutionary intermediates challenges the elucidation of the relative order of emergence of eukaryotic traits. Central in the discussion is the exogenous origin of mitochondria, ubiquitous eukaryotic organelles derived from an α-proteobacterial endosymbiont. Different hypotheses disagree on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host are debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. In this thesis, I have used phylogenomic methods to address different questions on the origin and evolution of subcellular compartmentalization in Eukaryotes. We provide evidence for extensive retargeting of proteins between the different compartments, and suggest an evolutionary link between mitochondria and peroxisomes. We focus on the evolution of calcium homeostasis in mitochondria and reveal strong co-evolution patterns among the components of the recently identified mitochondrial calcium uniporter complex. Through alternative methodologies we analyze the phylogenetic signal carried by LECA-inferred gene families. Our analyses indicate that the ancestral eukaryotic proteome is a composite of genes originating from different prokaryotic sources. Finally, our work provides strong support for the late acquisition of mitochondria by a complex host. Altogether, our findings shed light on long-standing questions on the origin of Eukaryotes and provide new grounds for further advancements, as new data become available.El origen de la compartimentación celular en Eucariotas se presenta como uno de los enigmas más importantes de la biología. Las evidencias actuales indican que el último ancestro común eucariota (LECA) ya poseía muchas de sus características avanzadas, incluyendo una organización subcelular compleja. Además, la falta de intermediarios evolutivos desafía la elucidación del orden en el que las características eucariotas aparecieron. En el centro de la discusión está el origen exógeno de las mitocondrias, orgánulos eucariotas derivados de α-proteobacteria vía endosimbiosis. Las diferentes hipótesis discrepan sobre si las mitocondrias fueron adquiridas al principio o al final durante el proceso de eucariogénesis. Del mismo modo, se debate la naturaleza y complejidad del hospedador, con modelos que van desde un simple hospedador procariota hasta un proto-eucariota dotado de cierta complejidad. En esta tesis, se han utilizado métodos filogenómicos para contestar a diferentes preguntas sobre la evolución de la compartimentación eucariota. Proporcionamos evidencia de una amplia relocalización de proteínas entre los diferentes compartimentos y sugerimos un vínculo evolutivo entre las mitocondrias y los peroxisomas. Nos centramos en la evolución de la homeostasis del calcio en las mitocondrias y observamos patrones de coevolución entre los componentes del sistema transportador mitocondrial de calcio. A través de metodologías diferentes se analiza la señal filogenética de familias de genes del ancestro común de Eucariotas. Nuestros análisis demuestran que el proteoma ancestral eucariota es un mosaico de genes de diferentes fuentes procariotas. Por último, nuestro trabajo proporciona un fuerte soporte a las hipótesis que la adquisición de la mitochondria tuvo lugar hacia el final de la eucariogénesis por parte de un hospedador complejo. En conjunto, nuestros resultados aclaran cuestiones que llevaban mucho tiempo abiertas sobre el origen de los Eucariotas y proporcionan nuevas bases para avances adicionales.
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Voss, Philipp A. [Verfasser], and Annika [Akademischer Betreuer] Guse. "Cellular processes underlying symbiosis establishment in Aiptasia, a model for cnidarian-dinoflagellate endosymbiosis / Philipp Alexander Voss ; Betreuer: Annika Guse." Heidelberg : Universitätsbibliothek Heidelberg, 2020. http://d-nb.info/1219303194/34.
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Voss, Philipp Alexander [Verfasser], and Annika [Akademischer Betreuer] Guse. "Cellular processes underlying symbiosis establishment in Aiptasia, a model for cnidarian-dinoflagellate endosymbiosis / Philipp Alexander Voss ; Betreuer: Annika Guse." Heidelberg : Universitätsbibliothek Heidelberg, 2020. http://d-nb.info/1219303194/34.
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Klein, Antonia [Verfasser], and Jürgen [Akademischer Betreuer] Heinze. "Endosymbiosis, Co-option and Recombination: Mechanisms to generate Evolutionary Novelty in the Ant Cardiocondyla obscurior / Antonia Klein. Betreuer: Jürgen Heinze." Regensburg : Universitätsbibliothek Regensburg, 2015. http://d-nb.info/1080609776/34.
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Munoz, Víctor Hugo Anaya. "A theoretical model on the role of lateral gene transfer in the evolution of endosymbiotic genomes." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://dx.doi.org/10.18452/16446.
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Laterale Gentransfer wurde zuerst von Schwartz und Dayhoff (1978) entdeckt, die es aber als eine Exzentrizität werteten und als solche ignorierten. Später, als mehrere DNS- und Eiweißsequenzen sequenziert und raffiniertere Phylogenien rekonstruiert wurden, hat die Rolle an Relevanz gewonnen, die der laterale (oder horizontale) Gentransfer in der evolutionären Geschichte von lebendigen Organismen gespielt hat. Außerdem existiert auch zwischen Endosymbionten und Zellkernen statt. Ich habe ein theoretisches Modell entwickelt, das den lateralen Gentransfer zwischen Endosymbionten und dem Zellkern repräsentiert. Das Modell erforscht die Bedeutung des Fehlens von Rekombination in den Organellen (Muller’s Ratchet) sowie Abweichungen von Muller’s Ratchet in Form der non-symmetrical homologous recombination in Gentransfermechanismen. Ich habe zum einen Zellkern-Inkompatibilitäten, die aus der Übertragung eines Gens resultieren, und zum anderen Zyto- und Zellkern-Inkompatibilitäten zwischen den mutierten endosymbiotischen Genomen und dem modifizierten Zellenkern untersucht. Die Ergebnisse zeigen, dass unter bestimmten Bedingungen die Existenz oder Nicht-Existenz von Rekombination die gleiche Wirkung haben können. Es zeigte sich auch, dass Rekombination, wenn sie vorkommt und wenn sie nicht symmetrisch ist, starke Auswirkungen auf die Allelenfrequenz einer Population haben kann. Es wurde auch klar, dass es eine starke Beziehung zwischen dem Zellkern und endosymbiotischen Genomen gibt, und dass das evolutionäre Schicksal des einen größtenteils von den evolutionären Kräften abhängig ist, die das andere beeinflussen. Wenn man Zellkern- und Cyto-Zellkerninkompatibilitäten in das Modell einführt, dann zeigen die Ergebnisse, dass die Inkompatibilitäten, die der laterale Gentransfer produziert hat, möglicherweise eine ähnliche Rolle im Speziationsmechanismus spielen könnten wie die Inkompatibilitäten zwischen Mitochondrien und Zellkernen in verschiedenen Nasonia-Arten.Lateral gene transfer has played a key role in the evolution of living beings. This process was first acknowledged in 1978 by Schwartz and Dayhoff but considered a relatively infrequent eccentricity and ignored. Later on, as DNA and protein sequences accumulated and more refined phylogenies were reconstructed, the contribution of lateral (or horizontal) gene transfer to the evolutionary history of living organisms gained relevance. Besides, gene transfer is known to occur not only between independent organisms but also, and more frequently between endosymbionts including eukaryotic organelles. I developed a theoretical model to study the lateral gene transfer process between cell organelles (but extendible to other endosymbionts) and the cell nucleus. The model explores the role of the lack of recombination in the organelles (Muller''s ratchet) as well as deviations from Muller''s ratchet in the form of non-symmetrical homologous recombination in relation with the gene transfer process. Also, nuclear incompatibilities resulting from the inclusion of a transferred gene, and cyto-nuclear incompatibilities between the mutant endosymbiotic genomes and the modified nuclear genome are investigated. The results obtained show that under certain circumstances the existence recombination or its non-existence produce the same results, and that deviations from symmetry in the recombination process might have important effects on the frequency of different alleles. It is also clear that there is a strong relation between nuclear and endosymbiotic genomes, and that the evolutionary fate of one largely depends on the forces affecting the other. When nuclear and cyto-nuclear incompatibilities are introduced in the model, the results show that lateral gene transfer-induced incompatibilities could potentially play a role in the speciation process similar to the one produced by mitochondria in the Nasonia species.
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Dorrell, Richard G. "Coevolution of plastid genomes and transcript processing pathways in photosynthetic alveolates." Thesis, University of Cambridge, 2014. https://www.repository.cam.ac.uk/handle/1810/246266.
Full textAbstract:
Following their endosymbiotic uptake, plastids undergo profound changes to genome content and to their associated biochemistry. I have investigated how evolutionary transitions in plastid genomes may impact on biochemical pathways associated with plastid gene expression, focusing on the highly unusual plastids found in one group of eukaryotes, the alveolates. The principal photosynthetic alveolate lineage is the dinoflagellate algae. Most dinoflagellate species harbour unusual plastids derived from red algae. The genome of this plastid has been fragmented into small, plasmid-like elements termed “minicircles”. Transcripts of this genome receive a 3’ poly(U) tail and, in some species, undergo extensive sequence editing. Some dinoflagellates have replaced their original plastids with others, in a process termed “serial endosymbiosis”. The major non-photosynthetic alveolates are the apicomplexans, which include the malaria parasite Plasmodium. Apicomplexans are descended from free-living algae and possess a vestigial plastid, which originated through the same endosymbiosis as the ancestral red dinoflagellate plastid. This plastid has lost all genes involved in photosynthesis and does not possess a poly(U) tail addition pathway. I have investigated the consequences of the fragmentation of the red algal dinoflagellate plastid genome on plastid transcription. I have characterised non-coding transcripts in plastids of the dinoflagellate Amphidinium carterae, including the first evidence for antisense transcripts in an algal plastid. Antisense transcripts in dinoflagellate plastids do not receive poly(U) tails, suggesting that poly(U) tail addition may play a role in strand discrimination during transcript processing. I have additionally characterised transcript processing in dinoflagellate plastids that were acquired through serial endosymbiosis. I have shown that poly(U) tail addition and editing occur in the haptophyte-derived serial endosymbionts of the fucoxanthin-containing dinoflagellates Karenia mikimotoi and Karlodinium veneficum. This is the first evidence that plastids acquired through serial endosymbiosis may be supported by pathways retained from previous symbioses. Transcript editing constrains the phenotypic consequences of divergent mutations in fucoxanthin plastid genomes, whereas poly(U) tail addition plays a central role in recognising and processing translationally functional fucoxanthin plastid mRNAs. I have additionally shown that certain genes within fucoxanthin plastids are located on minicircles. This demonstrates convergent evolution in the organisation of the fucoxanthin and red algal dinoflagellate plastid genomes since their endosymbiotic acquisition. Finally, I have investigated transcript processing in the algae Chromera velia and Vitrella brassicaformis. These species are closely related to apicomplexans but are still photosynthetic and apply poly(U) tails to plastid transcripts, as with dinoflagellates. I have shown that poly(U) tails in these species are preferentially associated with translationally functional mRNAs of photosynthesis genes. This is the first plastid transcript processing pathway documented to target a specific functional gene category. Poly(U) tail addition may direct transcript cleavage and allow photosynthesis gene transcripts to accumulate to high levels. The loss of this pathway from ancestors of apicomplexans may have contributed to their transition from photosynthesis to parasitism.
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Gueguen, Gwénaelle. "Les communautés endosymbiotiques des insectes vecteurs de virus : diversité bactérienne, effets phénotypiques, conséquences écologiques et épidémiologiques." Thesis, Lyon 1, 2009. http://www.theses.fr/2009LYO10135.
Full textAbstract:
Les bactéries symbiotiques facultatives, transmises verticalement de mère à descendants, sont connues pour avoir des effets importants sur la reproduction de leurs hôtes (incompatibilité cytoplasmique et biais de sex-ratio), sur l’adaptation à des situations de stress (spécialisation, résistance aux pathogènes et aux fortes températures) ainsi que sur l’évolution de l’ADN mitochondrial par l’induction de balayages sélectifs. Bemisia tabaci est un complexe d’espèces divisé en nombreux biotypes, principalement différenciés sur la base de marqueurs moléculaires (essentiellement mitochondrial). Cet insecte héberge 7 symbiotes, 1 symbiote nutritionnel obligatoire et 6 symbiotes facultatifs. Nos résultats ont montré une extrême diversité ainsi qu’une prévalence exceptionnelle des bactéries symbiotiques chez B. tabaci. Leur dynamique rapide a entraîné de nombreux balayages sélectifs sur l’ADN mitochondrial influençant nettement son évolution. La très forte fréquence des infections multiples chez cet insecte peut certainement être expliquée par la co-localisation de l’ensemble des bactéries au sein des mêmes cellules, avec le symbiote nutritionnelle. Enfin, la coexistence de différents cytotypes en sympatrie offre l’opportunité d’étudier les interactions qui se mettent en place entre différentes communautés symbiotiques et comment ces systèmes vont évoluerFacultative endosymbiotic bacteria that are vertically transmitted from mother to offsprings, have important effects on their host reproduction (cytoplasmic incompatibilities and sex-ratio biais), on host adaptation to situation of stress (specialization, resistance against pathogens or high temperature) and also on the evolution of mtDNA, by inducing selective sweeps. Bemisia tabaci is a species complex divided into numerous, mainly differentiated based on molecular markers (essentially mtDNA markers). This insect is infected by 7 bacterial symbionts, one nutritionnal symbiont that is obligatory and 6 facultative symbionts. Our results show an extreme diversity of symbionts in this insect and a very high prevalence in B. tabaci populations. Moreover their rapid dynamic has strongly influenced mtDNA evolution by inducing recurrent selective sweeps. The colocalization of the whole symbiotic community in the same cells, with the nutritional symbiont, might certainly explain the very high frequency of multiple infections in B. tabaci. Finally, coexistence of very different cytotypes in sympatry allows to study the interactions that take place between different symbiotic communities and how these systems will evolve
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Merville, Adrien. "Caractérisation de la symbiose bactérienne intracellulaire chez les charançons du genre Curculio et exploration de son rôle dans la coexistence d'espèces d'insectes en compétition." Thesis, Lyon 1, 2013. http://www.theses.fr/2013LYO10130.
Full textAbstract:
Parmi les théories explicatives de la biodiversité, la théorie des niches propose que des espèces en compétition puissent coexister durablement à la condition qu'elles expriment des différences de caractères phénotypiques conduisant à un partitionnement de leurs niches écologiques. Par ailleurs, l'acquisition de bactéries endosymbiotiques peut être assimilée à une extension du phénotype de l'hôte, susceptible de modifier sa niche écologique. Cependant, l'implication de ces micro-organismes endosymbiotiques dans la structure des communautés d'espèces d'insectes en compétition n'a encore jamais été envisagée. Mon hypothèse est que les communautés de bactéries endosymbiotiques hébergées par différentes espèces-hôtes en compétition pourraient impacter la dynamique des communautés d'hôtes en facilitant la différentiation de leurs traits et ainsi stabiliser leur coexistence. Réciproquement, les interactions de nature compétitive entre espèces-hôtes pourraient influencer la dynamique évolutive des cortèges endosymbiotiques de chacune de ces espèces en favorisant notamment les occasions de transfert horizontal de bactéries endosymbiotiques. Durant ma thèse, j'ai étudié les relations endosymbiotiques au sein des communautés composées de quatre espèces d'insectes phytophages spécialistes du chêne (Curculio spp., Coléoptères Curculionidés), qui sont en compétition pour les glands qui représentent le siège du développement larvaire. Afin d'envisager l'implication des endosymbiotes dans le partitionnement des niches écologiques de ces espèces, j'ai développé ma thèse autour de deux objectifs principaux visant à (i) décrire et comparer les cortèges de bactéries endosymbiotiques hébergés par les quatre espèces, par une caractérisation moléculaire des souches bactériennes et une mesure de leur prévalence dans les populations d'hôtes et (ii) identifier les cas de transferts horizontaux interspécifiques d'endosymbiotes à l'aide d'une approche multi-gènes couplée à l'estimation du taux de multi-infestation plurispécifique à l'échelle du gland. J'ai pu montrer que ces espèces d'insectes hébergent des cortèges endosymbiotiques distincts, trois des quatre espèces hébergeant leur propre endosymbiote secondaire majoritaire. Une telle différentiation pourrait contribuer au partitionnement de niches écologiques de ces quatre espèces, notamment au vu des différences, mises en évidence au cours de ma thèse, dans la période d'exploitation des glands au cours de la saison de reproduction. Par ailleurs, le fait que chaque espèce-hôte possède, en prévalence résiduelle, la plupart des symbiotes majoritaires chez d'autres espèces laisse suspecter des transferts horizontaux au sein de cette communauté. Cette hypothèse semble confirmée par la comparaison approfondie des souches de Wolbachia présentes dans ces communautés d'hôtes et par la proportion non négligeable de glands infestés simultanément par plusieurs espèces d'insectes. Les résultats obtenus au cours de ma thèse corroborent l'hypothèse d'un impact possible des communautés endosymbiotiques sur la dynamique des communautés d'hôtes en compétition et soulignent l'importance de prendre en compte l'échelle des communautés d'hôtes pour comprendre la dynamique des communautés bactériennes au sein des populations de l'espèce-hôteAmong biodiversity theories, the niche theory states that competing species can durably coexist whenever they exhibit differences in their traits leading to partitioning of their ecological niches. Moreover, housing symbiotic bacteria is now recognized as expanding the host phenotype and is thus likely to interfere with its ecological niche. Intriguingly, the question of whether endosymbionts are likely to shape communities of competing insect species has not yet been addressed in natural systems. My hypothesis is that endosymbiosis can be determinant in driving the dynamics of communities composed of competing host species by amplifying differences in theirs traits and thus, stabilizing their coexistence. Reciprocally, ecological interactions among these host species could have a decisive role in the evolutionary dynamic of endosymbiotic cortege of each species by providing opportunities of horizontal transfer of bacterial endosymbionts. During my PhD, I studied endosymbiotic relationships among communities consisting of four species of specialist oak weevil insects (Curculio spp., Coleoptera, Curculionidae) that are competing for egg-laying into acorns where the larva grow. The two main objectives of my thesis were (i) to describe and compare the endosymbiotic corteges housed by the four species, by means of molecular screening of the bacterial diversity in female ovaries and measuring their prevalence in males and females of host populations, and (ii) to check the existence horizontal transfers of endosymbionts between host species with a multigenic approach combined to estimating the probability for one acorn to be infested by larva belonging to distinct Curculio species. I found that the four weevil species overall harboured distinct endosymbiotic communities, and notably that three of the four species had their own major secondary symbiont. Additionally, I found that the four species had a clearly distinct period of larval development during the reproductive season. Such diversification of endosymbionts across species competing with each other might contribute to their temporal partitioning in the acorn use. Otherwise, the fact that each host species also hosts, with residual prevalence, most of endosymbionts found in the other species, argues for the existence of horizontal transfer among this community. This hypothesis seems to be confirmed by a fine-tuned comparison of the Wolbachia strains detected in these host communities and by the non negligible proportion of acorns which are simultaneously infested by two or more weevil species. These results support the hypothesis of an impact of endosymbiotic communities on the dynamics of competing host communities and point out the need to consider the host community scale in order to understand the dynamics of bacterial communities within host species populations
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Schwartz, Julie A. "A Functional Chlorophyll Biosynthesis Pathway Identified in the Kleptoplastic Sea Slug, Elysia chlorotica." Scholar Commons, 2015. https://scholarcommons.usf.edu/etd/5576.
Full textAbstract:
The sacoglossan sea slug, Elysia chlorotica, feeds upon and sequesters plastids from the heterokont alga, Vaucheria litorea, and maintains the metabolically active organelles for up to nine months under starvation conditions while utilizing the photosynthate to survive and reproduce. The photosynthetic pigment, chlorophyll a (Chla), is found in all oxygenic photosynthetic organisms and is responsible for capturing photons of light and converting them into chemical energy. Chlorophyll and its associated proteins involved in the light capturing process are subject to photo oxidative damage and must be continually replaced for ongoing photosynthesis to continue; however, genes encoding these proteins are present in the algal nucleus, presenting a conundrum for sustained plastid photosynthetic activity outside the algal cell. One possibility is that Chla is synthesized by the E. chlorotica-kleptoplast association, due to transfer of algal nuclear genes to the sea slug genome. For this study, molecular and biochemical techniques were employed to determine if Chla is synthesized by the animal. Using algal transcriptome sequences for primer design and amplification of target DNA using polymerase chain reaction (PCR), we have identified and sequenced three algal nuclear-encoded gene fragments that correspond to enzymes in the chlorophyll synthesis pathway and one enzyme in the porphyrin synthesis pathway in adult slug and veliger larvae. Sequences from these genes were nearly identical to those present in the alga. Furthermore, these genes are functional; incubation of slugs with radiolabeled 5-aminolevulinic acid (14C-5-ALA), a precursor of chlorophyll biosynthesis, resulted in production of 14C-labeled chlorophyll, as assayed and identified via HPLC resolution of extracts from slugs. In addition, Chla synthesis in the animal occurs for at least six months under starvation conditions. The discovery of chlorophyll synthesis in E. chlorotica is the first animal known to synthesize Chla; moreover, this finding helps elucidate how ongoing photosynthesis can occur in the sea slug after many months in the absence of its algal food.
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Delafont, Vincent. "Diversité et implication des amibes libres dans la survie et la persistance des mycobactéries non tuberculeuses au sein d'un réseau d'eau potable." Thesis, Poitiers, 2015. http://www.theses.fr/2015POIT2278/document.
Full textAbstract:
Les amibes libres sont des microorganismes unicellulaires eucaryotes dont l'écologie au sein des réseaux d'eau potable est mal connue. Les amibes libres représentent un enjeu de santé publique, du fait de leur capacité à favoriser la présence de bactéries potentiellement pathogènes, parmi lesquelles des mycobactéries.Une campagne de prélèvement menée sur le réseau d'eau potable de Paris a permis d'évaluer la diversité des amibes libres et de leur microbiome bactérien, par pyroséquençage ciblant les gènes ribosomaux (16S et 18S). Ces analyses ont suggéré la prédominance des genres Acanthamoeba, Vermamoeba, Echinamoeba et Protacanthamoeba. Le microbiome des amibes a révélé une grande diversité bactérienne, dominée par Pseudomonas, Stenotrophomonas, Bradyrhizobium, Sphingomonas et Pseudoxanthomonas. L'intégration des paramètres physicochimiques a permis de suggérer l'importance de l'origine de l'eau, la température, le pH et la concentration en chlore dans la dynamique des populations amibiennes. Une endosymbiose originale entre V. vermiformis et des bactéries du phylum TM6 a également été mise en évidence.Les amibes ont été fréquemment co-isolées avec des mycobactéries dans le réseau, principalement les espèces M. llatzerense et M. chelonae. Des expériences d'infection chez A. castellanii ont permis d'observer la capacité de ces mycobactéries à survivre et croitre en présence d'amibes. Par génomique comparative et analyses transcriptomiques, plusieurs facteurs de virulence, conservés entre M. llatzerense, M. chelonae et M. tuberculosis, ont été identifiés et sont surexprimés au cours de l'infection. Ces données suggérent leur implication dans la résistance à la prédation amibienne.L'ensemble de ces travaux a permis d'améliorer la connaissance des populations amibiennes et de leur microbiome au sein du réseau d'eau potable, apportant des éléments supplémentaires concernant leur implication dans la survie et la persistance des mycobactériesFree-living amoebae are unicellular eukaryotes whose ecology in drinking water networks remains poorly understood. They may represent a public health concern, because of their ability to favour the presence of potentially pathogenic bacteria, among which are mycobacteria.A sampling scheme based on Paris drinking water network allowed identifying the diversity of both freeliving amoebae and their bacterial microbiome, using ribosomal RNA targeted pyrosequencing. These analyses indicated the major presence of Acanthamoeba, Vermamoeba, Echinamoeba and Protacanthamoeba genera. The microbiome was highly diverse and dominated by Pseudomonas, Stenotrophomonas, Bradyrhizobium, Sphingomonas and Pseudoxanthomonas. The coupling of physicochemical parameters to this analysis allowed underlining the importance of water origin, temperature, pH and chlorine concentration in shaping amoebal populations. Also an original endosymbiosis between V. vermiformis and a bacterium of the TM6 phylum was described. Free-living amoebae were frequently co-isolated with mycobacteria in the water network, mainly M. llatzerense and M. chelonae species. Infection experiments on A. castellanii illustrated the capacity of these species to resist and grow in presence of amoebae. Through genomics and transcriptomics approaches, several virulence factors, conserved between M. llatzerense, M. chelonae and M. tuberculosis were identified, and found to be upregulated during infection experiments. These results suggest their involvement in mycobacterial resistance to amoebal predation.Altogether, this work helped to better understand the ecology of free-living amoebae and their microbiome in drinking water networks, as well as the role of free-living amoebae in the survival and persistence of mycobacteria in such environments
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Ebenezer, ThankGod Echezona. "The genome of Euglena gracilis : annotation, function and expression." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/275885.
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Euglena gracilis is a species of unicellular photosynthetic flagellate that inhibits aquatic ecosystems. E. gracilis belongs to the supergroup Excavata, and are an important component of the global biosphere, have biotechnological potential and is useful biological model due to their evolutionary history and complex biology. Whilst the evolutionary position of E. gracilis is now clear, their relationship with other protists such as Naegleria, Giardia, and Kinetoplastids, remains to be investigated in detail. Investigating and understanding the biology of this complex organism is a promising way to approach many evolutionary puzzles, including secondary endosymbiotic events and the evolution of parasitism, due to their relationship with Kinetoplastids. Here, I report a draft genome for E. gracilis, together with a high quality transcriptome and proteomic analysis. The estimated genome size is ~ 2 Gbp, with a GC content of ~ 50 % and a protein coding potential predicted at 36,526 Open Reading Frames (ORFs). Less than 25% of the genome is single copy sequence, indicating extensive repeat structure. There are evidences for large number of paralogs amongst specific gene families, indicating expansions and possible polyploidy as well as extensive sharing of genes with other non photosynthetic and photosynthetic eukaryotes: red and green algael genes, together with trypanosomes and other members of the excavates. Functional resolution into several of the biological systems indicates multiple similarities with the trypanosomatids in terms of orthology, paralogy, relatedness and complexity. Several biological systems such as nuclear architecture (e.g. chromosome segregation, nuclear pore complex, nuclear lamins), protein trafficking, translation, surface, consist of conserved and divergent components. For instance, several gene families likely associated with the cell surface and signal transduction possess very large numbers of lineage-specific paralogs, suggesting great flexibility in environmental monitoring and, together with divergent mechanisms for metabolic control, novel solutions to adaptation to extreme environments. I also demonstrate that the majority of control of protein expression levels is post-transcriptional and absence of transcriptional regulation, despite the presence of conventional introns. These data are a major advance in the understanding of the nuclear genome of Euglenids and provide a platform for investigation of the contributions of E. gracilis and relatives to the biosphere.
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Ribeiro, Lopes Mélanie. "Un nouveau type de mort cellulaire impliqué dans l’élimination des bactériocytes chez les pucerons : Mécanismes moléculaires et régulations physiologiques." Thesis, Lyon, 2020. http://www.theses.fr/2020LYSEI114.
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Les associations symbiotiques sont un moteur majeur de la diversification écologique et évolutive des organismes métazoaires. Chez les insectes qui sont physiologiquement dépendant de bactéries symbiotiques intracellulaires, ces dernières sont hébergées dans un nouveau type cellulaire, les bactériocytes. Ces cellules constituent une énigme fascinante en biologie cellulaire et développementale, les mécanismes moléculaires gouvernant leur dynamique en réponse à la physiologie de l’hôte restant largement méconnue. Dans cette étude, nous avons utilisé la symbiose entre le puceron du pois (Acyrthosiphon pisum) et la bactérie Buchnera aphidicola comme système modèle pour l’étude de la mort cellulaire bactériocytaire. Nous avons montré que, à partir des phases de vie adultes, les bactériocytes sont éliminés par un processus très lent de mort cellulaire non apoptotique, qui commence par l'hypervacuolisation du réticulum endoplasmique et implique une cascade de réponses au stress cellulaire, dont l’activation des systèmes autophagique et lysosomale. Nous avons mis en relation cette mort cellulaire avec une importante expansion des gènes codant les protéines Inhibitrices de l’APoptose (IAP) chez le puceron du pois, avec 28 gènes, contre les quatre identifiés chez Drosophila melanogaster. Des analyses génomiques comparatives ont révélé que cette expansion est commune et spécifique aux groupes des pucerons, et est associée à l’émergence d’innovations structurales au sein des IAP. Nous avons confirmé le rôle anti-apoptotique de plusieurs de ces IAP dans des expériences d'expression hétérologues dans l'œil en développement de D. melanogaster. Nous avons également montré que l’expression des gènes correspondants est induite de manière spécifique durant la mort cellulaire bactériocytaire. Cela suggère qu’au moins une partie des IAP, dans le contexte de la symbiose, aurait acquis de nouvelles fonctions, avec un rôle spécifique chez les bactériocytes, où leur induction bloquerait l’apoptose et assurerait la permanence de ces cellules et de leurs symbiotes jusqu’aux phases sénescentes de la vie de l’insecte. En accord avec cette hypothèse, nous avons montré que l’inactivation de ces gènes par RNAi, chez le puceron du pois, entraînait l’apparition d’un phénotype bactériocytaire faisant penser à de l’apoptose. Enfin, une étude transcriptomique à haut débit, suivant les bactériocytes des stades nymphaux jusqu’à la sénescence des pucerons, nous a permis d’identifier de possibles inducteurs et/ou régulateurs de la mort cellulaire bactériocytaire parmi lesquels les gènes de la voie UPR, connue pour être activée en cas de stress du réticulum endoplasmique et capable d’induire l’expression des IAPSymbiotic associations are a major driver of the ecological and evolutionary diversification of metazoan organisms. In insects that are physiologically dependent on intracellular symbiotic bacteria, the latter are housed in a new cell type, bacteriocytes. These cells constitute a fascinating enigma in cell and developmental biology, the molecular mechanisms governing their dynamics in response to host physiology remaining largely unknown. In this study, we used the symbiosis between the pea aphid (Acyrthosiphon pisum) and the bacterium Buchnera aphidicola as a model system for the study of bacteriocyte cell death. We have shown that, in adult aphids, bacteriocytes are eliminated by a very slow process of non-apoptotic cell death, which begins with a hypervacuolization of the endoplasmic reticulum and involves a cascade of cellular stress responses, including activation of the autophagic and lysosomal systems. We have linked this cell death with a significant expansion of the genes encoding the Inhibitor of APoptosis (IAP) proteins in the pea aphid, with 28 genes, against the four identified in Drosophila melanogaster. Comparative genomic analyzes have revealed that this expansion is common and specific of aphids, and is associated with the emergence of structural innovations within IAPs. We have confirmed the anti-apoptotic role of several of these IAPs in heterologous expression experiments in the developing eye of D. melanogaster. We have also shown that the expression of the corresponding genes is specifically induced during bacteriocyte cell death. This suggests that at least some of the IAPs, in the context of symbiosis, would have acquired new functions, with a specific role in bacteriocytes, where their induction could block apoptosis and ensure the permanence of these cells and their symbionts until the senescent phases of the insect's life. In agreement with this hypothesis, we have shown that the inactivation of these genes by RNAi, in the pea aphid, leads to the appearance of a phenotype reminiscent of apoptosis in bacteriocytes. Finally, a high-throughput transcriptomic study, following bacteriocytes from the nymphal stages to the senescence of aphids, allowed us to identify possible inducers and / or regulators of bacteriocyte cell death, including genes of the UPR pathway, known to be activated in the event of endoplasmic reticulum stress and capable of inducing the expression of IAPs
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Fasth, Ellen. "The metagenomes of root nodules in actinorhizal plants : A bioinformatic study of endophytic bacterial communities." Thesis, Umeå universitet, Institutionen för ekologi, miljö och geovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-183997.
Full textAbstract:
Actinorhizal plants are in symbiosis with the nitrogen-fixating soil bacterium Frankia, which forms nodules in the plant root. However, several studies also report other endophytic bacteria appearing in the nodules, but their function and interaction with the host plant or Frankia is not yet understood. This thesis used a bioinformatic approach to investigate the metagenomes of eighteen actinorhizal nodule samples to find out which bacteria are present, how the microbiomes differed from each other, and if the genomes of non-Frankia inhabitants could give indications of any functions. The results showed that the bacterial composition, richness, and diversity differed among the samples, especially between the samples sequenced from the field versus those primarily cultivated in a greenhouse. All samples had a substantial number of sequencing reads belonging to potential endophytes, such as strains of Enterobacteria, Pseudomonas, Streptomyces, Micromonospora, Mycobacteria and Pseudonocardia. There seemed to be a common microbial community shared among the plants on a family level, since no significant difference was found in the core microbiomes between the field and greenhouse groups. Some sequences found in the metagenomes were annotated as potential functions of the fellow travellers, such as antibiotic synthesis, proteins involved in regulating abiotic stresses, but also probable plant damaging compounds rather associated with pathogens than symbionts.
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Viale, E. "Symbiotic bacteria inhabiting tephritid flies: a worldwide specific interaction." Doctoral thesis, Università degli studi di Padova, 2014. http://hdl.handle.net/11577/3424062.
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Several insect lineages have evolved mutualistic associations with their symbiotic bacteria. This is the case of some members of Tephritinae, the most specialized subfamily of fruit flies (Diptera: Tephritidae), harboring co-evolved and vertically transmitted bacterial symbionts in their midgut, known as ‘Candidatus Stammerula spp.’. In the tephritid fly Bactrocera oleae, the major olive pest, symbionts are located in the oesophageal bulb, a diverticulum of the fly head, and designated as ‘Candidatus Erwinia dacicola’.
This research, based on two main studies, is focused on different aspects of the relationships between species of the family Tephritidae and their nonculturable symbiotic bacteria.
The first study investigated the presence of specific symbiotic bacteria in 15 of the 25 described endemic tephritids of the Hawaiian Archipelago, which represent a spectacular example of adaptive radiation, and their molecular relationships with symbionts of non-Hawaiian tephritids. Moreover the concordant evolution between host and symbiont phylogenies was tested. A specific symbiont was detected through PCR assays in all endemic individuals analyzed and it was designated as ‘Candidatus Stammerula trupaneae’ as it was included in Ca. Stammerula spp. monophyletic clade. The phylogeny of the insect host was reconstructed based on two regions of the mitochondrial DNA (16S rDNA and COI-tRNALeu-COII), while the bacterial 16S rRNA was used for the symbiont analysis. Host and symbiont phylogenies were then compared and evaluated for patterns of cophylogeny and strict cospeciation. Topological congruence between Hawaiian Tephritinae and their symbiotic bacteria phylogenies suggests a limited, but significant degree of host-symbiont cospeciation. The character evolution of three host traits, as island location, host lineage, and host tissue attacked, was finally reconstructed based on the symbiont phylogenies under the hypothesis of cospeciation.
The second study surveys the genetic variability of the olive fly symbiont, Ca. Erwinia dacicola, together with the patterns of genetic differentiation of B. oleae, over a large area of its geographical distribution, including most regions of the Mediterranean area, plus South Africa, California and Pakistan. Three bacterial haplotypes, showing a significative geographic distribution, were identified and the co-existence of different Ca. E. dacicola haplotypes in a single fly was never found. Our results reveal the presence of three symbiont haplotypes with a significant phylogeographic distribution related to the territory. In the Mediterranean populations only two bacterial lineages (htA and htB), previously recovered in Italian olive fly populations, have been found, showing a significative East-West genetic differentiation. The South African and Californian olive fly populations were represented only by one of these two lineages, respectively htA and htB. Moreover, a new haplotype (htC) was detected exclusively in the Pakistani population. On the other hand, a high degree of mitochondrial genetic variability with a substantial phylogeographic differentiation has been observed in the B. oleae populations analyzed, revealing the presence of 39 insect haplotypes. Symbiont and host haplotypes were then compared and a significant correlation was found suggesting the predominant presence of vertical transmission. Moreover, the bacterial haplotypes distribution seems to be more related to the territory than the numerous insect host haplotypes, representing an useful tool to reconstruct the debated olive fly’s historical origin.Diverse specie di insetto si sono evolute in associazione con i loro batteri simbionti. Questo è il caso di alcuni membri dei Tephritinae, la più specializzata sottofamiglia delle mosche della frutta (Diptera: Tephritidae), che ospitano nell’intestino batteri simbionti coevoluti e trasmessi in maniera verticale, conosciuti come “Candidatus Stammerula spp.”. Nella mosca dell’olivo, Bactrocera oleae, i batteri simbionti sono localizzati nel bulbo esofageo, un diverticolo presente nel capo della mosca, e identificati con il nome di “Candidatus Erwinia dacicola”. Questo lavoro, basato su due principali studi, si focalizza su diversi aspetti delle relazioni filogenetiche che intercorrono tra le mosche della frutta e i loro batteri simbionti. Il primo lavoro studia la presenza di specifici batteri simbionti in 15 delle 25 specie descritte di tefritidi endemici dell’Arcipelago delle Hawaii, uno spettacolare esempio di radiazione adattativa, e le relazioni molecolari che intercorrono con i simbionti delle Tephritinae non Hawaiiani. Inoltre è stata analizzata la concordanza evolutiva tra la filogenesi dell’insetto rispetto a quella del simbionte. Uno specifico simbionte è stato individuato mediante saggi di PCR in tutti gli individui analizzati e nominato “Candidatus Stammerula trupaneae”, in quanto incluso nel gruppo monofiletico formato da Ca. Stammerula spp. La filogenesi dell’insetto ospite è stata ricostruita analizzando due regioni del DNA mitocondriale (16S rDNA e COI-tRNALeu-COII), mentre il gene batterico 16S rRNA è stato utilizzato nell’analisi del simbionte. Le filogenesi dell’ospite e del simbionte sono state quindi comparate e valutate per lo studio del modello di congruenza filogenetica e cospeciazione. La congruenza tra la filogenesi delle Tephritinae Hawaiiane e i loro batteri simbionti suggerisce un ridotto, ma significativo livello di cospeciazione. L’evoluzione dei caratteri ancestrali, basata su tre aspetti dell’insetto quali l’isola di origine, la pianta ospite e il tessuto vegetale attaccato dalla mosca, è stata infine ricostruita sulla base della filogenesi del simbionte ipotizzando la presenza di cospeciazione. Il secondo studio analizza la variabilità genetica del simbionte della mosca dell’olivo, Ca. Erwinia dacicola, insieme al grado di differenziazione genetica di B. oleae, su un ampio raggio della sua distribuzione geografica, comprendendo molte regioni del Mediterraneo e alcuni campionamenti puntiformi in Sud Africa, California e Pakistan. Tre aplotipi batterici, con una significativa distribuzione geografica, sono stati identificati ed è stata esclusa la coesistenza di diversi aplotipi di Ca. E. dacicola nella stessa mosca. Nelle popolazioni della mosca dell’olivo raccolte nel Mediterraneo, solo due aplotipi batterici (htA e htB), identificati in precedenza nelle popolazioni Italiane, sono stati trovati, mostrando una significativa distribuzione Est-Ovest. Le popolazioni del Sud Africa e della California sono rappresentate in maniera esclusiva da uno dei due aplotipi, rispettivamente htA e htB. Un nuovo aplotipo (htC) inoltre è stato individuato esclusivamente nelle popolazioni Pakistane. D’altro lato, un alto grado di variabilita’ genetica caratterizzato da una certa differenziazione geografica è stato osservato nelle popolazioni di B. oleae analizzate; i nostri risultati mostrano la presenza di 39 aplotipi dell’insetto. Gli aplotipi del simbionte e quelli dell’insetto sono stati quindi confrontati e un’associazione significativa, con una stretta correlazione al territorio, è stata trovata, evidenziando la presenza di una prevalente trasmissione verticale del simbionte durante il ciclo vitale dell’insetto. Inoltre, il fatto che la distribuzione degli aplotipi batterici sia più strettamente correlata al territorio rispetto a quella ritrovata nei numerosi aplotipi dell’insetto ospite, può rappresentare un importante mezzo per ricostruire la dibattuta origine della mosca dell’olivo.
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Henicka, Gracieli da Silva. "O ensino introdutório da teoria da endossimbiose sequencial a luz da teoria da complexidade na educação de jovens e adultos, no município de Alta Floresta, MT." Universidade Federal de Mato Grosso, 2015. http://ri.ufmt.br/handle/1/263.
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Pesquisas apontam que é viável a inserção de conceitos relacionados à Teoria da Complexidade (TC) no ensino médio. O objetivo geral desse estudo foi averiguar a viabilidade e as dificuldades no processo de ensino-aprendizagem dos conceitos e princípios da Teoria da Endossimbiose Sequencial (TES) a luz da TC a partir de um produto educacional fundamentado em princípios da Teoria da Aprendizagem Significativa. O trabalho está fundamentado também na epistemologia de Kuhn, Maturana e Varela. Essa pesquisa investigou os conhecimentos prévios dos estudantes do segundo ano do ensino médio da Educação de Jovens e Adultos (EJA) acerca de conceitos de Ecologia, Evolução, Biologia Geral e Genética. Conceitos estes que apresentaram potencialidade para ancorar os novos conceitos relacionados à TES de Lynn Margulis, que foram abordados em seguida. Ao final da pesquisa produziu-se a título de produto educacional, um guia para o professor com orientações e sugestões de aprofundamento do tema, contendo ainda três apresentações em pptx, três textos-apoio para o professor, três textos-apoio para o aluno e sete testes. O material será disponibilizado no site do programa (http://fisica.ufmt.br/pgecn/) e da pesquisadora (www.alegriaeciencia.com.br). A metodologia foi quali-quanti com intervenção. A pesquisa aconteceu em Alta Floresta, MT e foi organizada em cinco encontros entre 19 de março de 2014 e 16 de abril de 2014. Participaram do estudo 94 alunos da EJA, sendo 37 do 2° ano noturno, 32 do 2° ano matutino e 27 do 2° ano vespertino. O 2° ano matutino apresentou em média, excluindo a entrevista, 66,51% de frequência nas atividades da pesquisa, o 2° ano vespertino 64,55% e o 2° ano noturno apenas 44,40%. A análise de todas as turmas juntas mostrou 57,44% de frequência média, o que sugere que os alunos faltaram muito aos encontros, especialmente os alunos do 2° ano noturno. Somente 77 alunos responderam ao pré-teste A onde se investigou o perfil dos alunos. Desses 63,64% são mulheres e 36,36% são homens. Ao analisar as turmas do dia esse cenário se repete, mas não é o caso da turma da noite, onde a maioria são homens na faixa etária de 18 a 22 anos, enquanto a faixa etária dos alunos do dia é mais diversificada, com a presença de alunos de até 62 anos. No tocante às aspirações pessoais a maioria dos alunos em todas as turmas demonstrou intenção em concluir o ensino médio e dar continuidade em sua formação, fazendo cursos técnicos e/ou faculdade. De maneira geral, os resultados das oficinas apontam algumas dificuldades de leitura e interpretação dos alunos o que dificultou o aprendizado, mas também apontam avanços na evolução da aprendizagem dos mesmos, há bons indícios de captação de significados conceituais que podem ser considerados precursores de aprendizagem significativa para alguns conceitos. Esse estudo demonstrou que é viável de inserção da Teoria da Endossimbiose Sequencial a luz da Teoria da Complexidade no ensino médio da EJA.
Researches show that the inclusion of concepts related to Complexity Theory (CT) is feasible in high school. The overall objective of this study was to investigate the feasibility and difficulties in the teaching-learning process of the concepts and principles of the Theory of Sequential Endosymbiosis (TSE) at the light of CT deriving from an educational product reasoned in the principles of the Theory of Meaningful Learning. The work is based also on Kuhn’s, Maturana’s and Varela’s epistemology. This research investigated the previous knowledge of students of the second year of high school of the Youth and Adult Education (EJA) about the concepts ecology of evolution, General Biology and Genetics. Such Concepts showed potential to anchor the new concepts related to TES by Lynn Margulis, which were covered below. At the end of the survey a teacher's guide with directions and issue of deepening suggestions has been created by way of educational product, still containing three presentations in PPTX, three texts-support for the teacher, three texts-support for the student and seven tests. The material will be available on the program website (http://fisica.ufmt.br/pgecn/) and researcher (www.alegriaeciencia.com.br). The methodology was qualitative and quantitative with participant observation. The research took place in Alta Floresta, MT and was organized in five meetings between March 19th 2014 and April 16th 2014. The participants were 94 students of EJA, 37 of the 2nd year from night shift, 32 of the 2nd year from morning shift and 27 the 2nd year from the afternoon shift. The morning shift group showed on average, excluding the interview, 66.51% attendance in the activities of research, the evening shift group 64.55% and the night shift group only 44.40%. The analysis of all the groups together showed 57.44% average rate, suggesting that students skipped many of the meetings, especially the students of the night shift. Only 77 students answered the pretest A which investigated the profile of the students. Of these, 63.64% are women and 36.36% are men. In analyzing the courses of the daytime, this scenario is repeated, but it is not the case of the night shift group, where most are men aged 18-22 years old, while the age group of students of the daytime is more diverse, with the presence students up to 62 years old. Regarding personal aspirations most students in each class demonstrated intention to complete high school and continue on their training, making technical courses and/or college. In general, the results from the workshops pointed to some difficulties in reading and interpreting of students hampering the learning, but also point advances in the evolution of learning, there was a good evidence of uptake of conceptual meanings that can be considered significant precursors to some e-learning concepts. This study demonstrated that it is feasible to insert Theory of Sequential Endosymbiosis at the light of Complexity Theory in high school of EJA.
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Klasson, Lisa. "Genome Evolution in Maternally Inherited Insect Endosymbionts." Doctoral thesis, Uppsala University, Department of Evolution, Genomics and Systematics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5885.
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Symbiosis is a widely common phenomenon in nature and has undoubtedly contributed to the evolution of all organisms on earth. Symbiotic associations can be of varying character, such as parasitic or mutualistic, but all imply a close relationship. To study the evolution of genomes of insect endosymbionts, we have sequenced the genomes of the mutualist Buchnera aphidicola from the aphid Schizaphis graminum (Sg) and the reproductive manipulator Wolbachia pipientis strain wRi from Drosophila simulans that show strikingly different evolutionary patterns.
The comparison between the genome of B.aphidicola (Sg) and the genome of B.aphidicola from the aphid Acyrthosiphon pisum (Ap), that are believed to have diverged 50 million years ago, revealed a perfect gene order conservation and loss of only 14 genes in either of the lineages. In contrast, the rate of nucleotide turnover is very fast probably due to relaxed selection and loss of DNA repair genes. The genomic stasis observed in Buchnera was attributed to the loss of repeats and of the gene recA.
In striking contrast to the genomes of B.aphidicola, a vast amount of repeats were found in the genome sequence of W.pipientis strain wMel. The comparison between the genomes of W.pipientis strain wRi and W.pipientis strain wMel shows that a lot of rearrangements have occurred since their divergence. The massive amount of repeats might stem from relaxed selection pressure but possibly also from selection to create variability via recombination.
Comparisons between pairs of genomes from closely related bacteria showed that the stability of gene order and content is connected to an intracellular lifestyle and indicated that homologous recombination between repeats is an important mechanisms for causing intrachromosomal rearrangements. Our studies show that the lifestyle of a bacterium to a great extent shapes the evolution of their genetic material and future capabilities to adapt to new environments.
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Gangaeva, Anna Evgenyevna. "Genome degeneration in obligate parasites and endosymbionts." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/4086.
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Microorganisms are a goidmine for evolutionary genetics as their genomes can
evolve at an extraordinary rate which results in some of the most extravagant adaptations
in terms of genome structure and function as well as survival in the most unusual
environments. One trend observed in several evolutionary scenarios is genome
degeneration. It is most prominent in endosymbionts and obligate intracellular parasites
and is a consequence of many constraints encountered in the intracellular environment.
The process involves loss of many protein-coding genes, resulting in greater dependence
on the host, and loss of non-coding DNA such as intergenic regions, which has a direct
impact on regulation of genome function. I have chosen two evolutionarily distinct
systems to analyze the stages and functional consequences of genome degeneration,
namely the impact of genome compression on transcription in an obligate parasite
Antonospora locustae (genus Microsporidia), and gene content in the mitochondrion of a
diatom endosymbiont found in the dinoflagellate Durinskia baltica. I have successfully
mapped transcriptional start and termination sites from 14 loci in Antonospora locustae,
and cloned fragments of two genes that are part of the electron transport chain from the
mitochondrion of the diatom endosymbiont in Durinskia baltica. My analysis reveals
that transcription in A. locustae is always initiated immediately upstream of the open
reading frame at a single point for every locus, whereas transcriptional termination can
occur at several points for a single gene and, in some instances overlaps with a
downstream reading frame. The identification ofNADH5 and ATPase9 from the
mitochondrion of the endosymbiont in D. baltica is further evidence for the preservation
of function in this enigmatic organelle.
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Dale, Colin. "The secondary (S-) endosymbionts of Glossina spp." Thesis, University of Liverpool, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.243102.
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Heyworth, Eleanor. "Insect facultative endosymbionts : phenotypic effects and competitive interactions." Thesis, University of York, 2015. http://etheses.whiterose.ac.uk/11854/.
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Facultative endosymbionts are ubiquitous in insect populations, and can affect a wide range of ecological and life-history traits. Symbiont infections, therefore, have the potential to affect insect responses to natural enemies and climate warming. Aphids are a model for endosymbiont research, and the work in this thesis uses pea aphids to explore symbiont effects and interactions. We manipulate symbiont infections in clonal genotypes of aphids to investigate the phenotypic effects of microbial infection and expose the insects to a range of stress and fecundity tests. We find that a single species of symbiont (known as X-type) can provide multiple ecological benefits to a host, but that there is a fitness cost to infection. We also discover that symbiont-mediated protection to heat is caused by two species of facultative symbiont protecting the obligate symbiont. Although many symbiont communities involve multiple species, much previous research has focused on individual infections. We create superinfections of symbionts to explore interactions between the microbes, and how these may affect host effects. We find that infections of two closely related symbionts can lead to loss of superinfections and that the microbes have different responses to competition. Our work suggests a dynamic, diverse and complex pool of symbiont effects and interactions, and that the symbiont-mediated effects can depend strongly on host and symbiont genotype. As a result, benefits caused by facultative symbionts may vary depending on host population, and determine how vulnerable insect communities are to disturbance and natural enemies. Loss of symbiont infection can also correspond to trait loss in aphid populations. Our work highlights that aphids are an ideal system for studying insect symbiosis and a simple model for more complex free-living or symbiotic microbial communities.
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Saeed, Abiya. "CHARACTERIZING THE MATERNALLY INHERITED ENDOSYMBIONTS OF SOLITARY BEES." UKnowledge, 2014. http://uknowledge.uky.edu/entomology_etds/10.
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Solitary bees are important pollinators of crops, with species in the family Megachilidae (mason bees) being used for orchard pollination. Commercial movement of these bees also moves their microbiota, including bacterial endosymbionts capable of reproductive manipulation. To test for presence of these bacteria, I screened commercially available species of US orchard pollinators and locally captured solitary bees from Kentucky. I also set up mason bee boxes in five apple orchards to examine recruitment of local pollinators. I conducted 454-pyrosequencing to determine bacterial diversity within four species followed by diagnostic PCR of 30 collected species (184 individuals) to determine infection frequency of selected endosymbionts. Consistent with literature, Wolbachia was abundant in these bees. I also found two other endosymbiotic bacteria, Sodalis (previously undetected in Hymenoptera), and Arsenophonus. Diagnostic screening demonstrated that Sodalis was present at moderate frequency in Osmia aglaia, whereas Arsenophonus was present at low frequency in Lasioglossum pilosum. Neither was found in other bees, but three bee species were infected with Sodalis-like endosymbionts. Although recruitment of bees to bee boxes was ineffective, I was able to independently collect native orchard pollinating Andrenidae species. My results demonstrate that other endosymbionts capable of reproductive manipulation, besides Wolbachia, are present in bees.
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Ellegaard, Kirsten Maren. "Genome Evolution and Niche Differentiation of Bacterial Endosymbionts." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-217724.
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Most animals contain chronic microbial infections that inflict no harm on their hosts. Recently, the gut microflora of humans and other animals have been characterized. However, little is known about the forces that shape the diversity of these bacterial communities. In this work, comparative genomics was used to investigate the evolutionary dynamics of host-adapted bacterial communities, using Wolbachia infecting arthropods and Lactobacteria infecting bees as the main model systems. Wolbachia are maternally inherited bacteria that cause reproductive disorders in arthropods, such as feminization, male killing and parthenogenesis. These bacteria are difficult to study because they cannot be cultivated outside their hosts. We have developed a novel protocol employing multiple displacement amplification to isolate and sequence their genomes. Taxonomically, Wolbachia is classified into different supergroups. We have sequenced the genomes of Wolbachia strain wHa and wNo that belong to supergroup A and B, respectively, and are present as a double-infection in the fruit-fly Drosophila simulans. Together with previously published genomes, a supergroup comparison of strains belonging to supergroups A and B indicated rampant homologous recombination between strains that belong to the same supergroup but were isolated from different hosts. In contrast, we observed little recombination between strains of different supergroups that infect the same host. Likewise, phylogenetically distinct members of Lactic acid bacteria co-exist in the gut of the honeybee, Apis mellifera, without transfer of genes between phylotypes. Nor did we find any evidence of co-diversification between symbionts and hosts, as inferred from a study of 13 genomes of Lactobacillus kunkeei isolated from diverse bee species and different geographic origins. Although Lactobacillus kunkeii is the most frequently isolated strain from the honey stomach, we hypothesize that the primary niche is the beebread where the bacteria are likely to contribute to the fermentation process. In the human gut, the microbial community has been shown to interact with the immune system, and likewise the microbial communities associated with insects are thought to affect the health of their host. Therefore, a better understanding of the role and evolution of endosymbiotic communities is important for developing strategies to control the health of their hosts.
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Arab, Daej A. Kh A. M. "Insects and their endosymbionts: phylogenetics and evolutionary rates." Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/25760.
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Obligate mutualistic intracellular endosymbionts have been acquired multiple times over the last few hundred million years by common ancestors of several major insect taxonomic groups. These ancient associations between hosts and endosymbionts mean that the phylogenies of the symbiotic partners are congruent. This allows the use of endosymbiont molecular phylogenies to resolve host relationships. Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Investigations of rate correlations between hosts and symbionts are lacking.
Here, I generate molecular phylogenies based on complete mitochondrial genomes from cockroach, termite and mantis species and generate the most comprehensive cockroach phylogeny based on 104 Blattabacterium. I also estimate divergence times of cockroaches, based on cockroach mtDNA and Blattabacterium genes.
Then, I demonstrate a correlation in molecular rates between the genomes of Blattabacterium cuenoti and the mitochondrial genomes of their cockroach hosts using the B. cuenoti dataset to compare phylogenetic relationships and evolutionary rates for 55 host/symbiont pairs. I find the first evidence of a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and the branch lengths of phylogenetically independent species pairs. Finally, I conduct the same analyses using genes from Buchnera aphidicola and Sulcia muelleri, and the mitochondrial genomes of their sap-feeding insect hosts. My results underscore the profound effects that ancient symbiosis can have on the biology of each symbiotic partner. The results here indicate that evolutionary rate correlations between hosts and long-term symbionts may be a widespread phenomenon.
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Fattouh, Nour. "Caractérisation du mode de vie intracellulaire des endosymbiotes Wolbachia." Thesis, Montpellier, 2018. http://www.theses.fr/2018MONTT079.
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Les bactéries intracellulaires Wolbachia ont développé une vaste gamme d’interactions symbiotiques, du parasitisme reproductif au mutualisme chez les arthropodes terrestres et les nématodes filaires, devenant ainsi les endosymbiotes les plus répandus sur terre. Bien qu’elles se développent lentement dans les cultures cellulaires d’insectes pour lesquelles les marqueurs sont limités et qu’elles ne sont génétiquement pas manipulables, il existe un intéret croissant de déchiffrer leur mode de vie intracellulaire pour 2 raisons. Premièrement, Wolbachia intervient dans le développement et la transmission des arbovirus et deuxièmement, les filarioses lymphatiques sont traitables grâce à la susceptibilité des Wolbachia qui infectent les nématodes filaires aux antibiotiques. Au début de ce projet, j’ai infecté 2 lignées cellulaires de Drosophila melanogaster qui sont transcriptomiquement divergentes par une même souche de Wolbachia pouvant naturellement infecter Drosophila melanogaster. J’ai utilisé ces 2 lignées cellulaires qui sont différentiellement permissive à l’infection pour explorer l’interaction de Wolbachia avec le réticulum endoplasmique. Les observations par microscopie à fluorescence en temps réel et par microscopie électronique prouvent que cet organite est une source de membranes pour Wolbachia et possiblement, une source de nutriments. Pourtant, les analyses d’expression génique et les approches d’immunofluorescence démontrent que Wolbachia n’induit ni un stress au niveau du réticulum endoplasmique ni une protéolyse via la voie de signalisation ERAD suggérant dès lors, que Wolbachia subvertissent d’autres mécanismes pour assurer leur besoin en acides aminés. Au cours de ce projet, j’ai commencé à mettre en place une technique pour transformer Wolbachia par biolistique. La validation de cette technique de transformation a ouvert la voie vers l’optimisation de la procédure de sélection des transformants pour enfin pouvoir génétiquement manipuler WolbachiaThe intracellular bacteria Wolbachia have developed a wide range of symbiotic interactions, from being opportunistic reproductive parasites to mutualists with terrestrial arthropods and filarial nematode species, making them the most common endosymbionts on earth. The discovery that they interfere with arboviruses development and transmission by mosquito vectors and that filarial diseases can be cured by targeting Wolbachia, have created a strong interest in deciphering the mechanisms underlying their intracellular lifestyle. However, being obligate intracellular endosymbionts, Wolbachia remain genetically intractable. They grow slowly in insect cell cultures, for which markers are limited. Despite these obstacles, and to limit cell line-specific phenotypes, I chose to infect 2 Drosophila melanogaster cell lines presenting different sets of expressed genes, with a unique Wolbachia strain, naturally hosted by Drosophila melanogaster. Using these 2 cell lines that are differently permissive to the infection, I explored the interaction of Wolbachia with the endoplasmic reticulum (ER). Through fluorescence time-lapse confocal and electron microscopy observations, I provide strong evidence that this organelle is the source of membrane for Wolbachia, and possibly a source of nutrients. However, gene expression analyses and immunofluorescence approaches demonstrate that Wolbachia do not induce ER stress nor an increased ERAD- induced proteolysis, suggesting; unlike previously reported, that Wolbachia salvage amino acids by other subversion mechanisms. Additionally, I pioneered biolistic bombardement of Wolbachia-infected cells and the validation of this transformation technique has paved the way towards optimization of transformant selection steps and ultimately to the genetic engineering of Wolbachia
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Christophersen, Claus. "Grain and artificial stimulation of the rumen change the abundance and diversity of methanogens and their association with ciliates." University of Western Australia. School of Animal Biology, 2008. http://theses.library.uwa.edu.au/adt-WU2008.0114.
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[Truncated abstract] In Australia, there is pressure to reduce the amount of methane produced by ruminant livestock because they are the single largest source of methane emitted from anthropogenic sources, accounting for 70.7% of agricultural methane emissions. In addition, methane production represents a loss of gross energy intake to the animal. The organisms that are responsible for methane production in the animal gut are a distinct group of Archaea called methanogens. Methanogens occupy three different niches within the rumen. Some live freely in the rumen digesta (planktonic), others are attached to the outer surface of the rumen ciliates (ectosymbiotic), and some reside within the ciliates (endosymbiotic). The types and number of methanogens, as well as rumen ciliates and their symbiotic interactions, influence the amount of methane produced from the rumen. These factors in turn are affected by many factors, including diet and ruminal retention time. In this thesis, I tested the general hypothesis that increasing the amount of grain in the diet and reducing the retention time would affect the abundance and diversity of methanogens in their different niches, including their association with ruminal ciliates. Twenty-four fistulated sheep were used in a complete factorial design with the sheep randomly divided into four groups. ... The change in DGGE banding patterns and Shannon indices when sheep were fed grain indicated that the types of methanogens changed when sheep were fed low and high grain diets, but their diversity did not. In contrast, the diversity of rumen ciliates decreased when sheep were fed a high grain diet. A total of 18 bands from the DGGE analysis of the ciliates were sequenced. All except one, which was 98% similar to Cycloposthium sp. not found previously in the rumen, matched the sequences for previously identified rumen ciliates. Some of the rumen ciliates identified were not present in sheep fed the high grain diet. On a high grain diet, methanogens associate endosymbiotically with rumen ciliates to get better access to hydrogen. It appears that the association between methanogens and rumen ciliates is dictated by the availability of hydrogen in the rumen and not the generic composition of the ciliate population. Furthermore, endosymbiotic methanogens appear to produce less methane than methanogens in other niches. The pot scrubbers did not change ruminal retention time but they did reduce the acetate/propionate measurements observed in sheep on the high grain treatment. The reason why pot scrubbers had this effect remains unknown, but it is interesting to consider that some physical interaction has occurred between the pot scrubbers, the grain and the sheep that has improved the fermentation parameters in sheep fed a high grain diet. The results from this study have advanced our understanding of the interaction between methanogens and ruminal ciliates, and methanogenesis in the rumen in response to dietary changes and mechanical challenges. Extending this work to look more specifically at the species of methanogens that are most closely linked to high methane production and how they interact with the ruminal ciliates will be critical for manipulating enteric greenhouse gas emissions.
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Belda, Cuesta Eugeni. "Genome evolution and systems biology in bacterial endosymbionts of insects." Doctoral thesis, Universitat de València, 2010. http://hdl.handle.net/10803/57466.
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Gene loss is the most important event in the process of genome reduction that appears associated with bacterial endosymbionts of insects. These small genomes were derived features evolved from ancestral prokaryotes with larger genome sizes, consequence of a massive process of genome reduction due to drastic changes in the ecological conditions and evolutionary pressures acting on these prokaryotic lineages during their ecological transition to host-dependent lifestyle. In the present thesis, the process of genome reduction is studied from different perspectives.
In the first chapter, genome rearrangements have been studied in a set of 31 complete γ-proteobacterial genomes that includes five genomes of bacterial endosymbionts of insects. This is carried out by comparing the order of a subset of 244 single-copy orthologous genes presents in all the genomes and calculating the number of inversions and breakpoints between each genome pair. This reveals that inversions were the main rearrangement event in γ-proteobacteria evolution, with a progressive increase in the number of rearrangements with increased evolutionary distance. However, significant heterogeneity in different γ-proteobacterial lineages was also detected, with a significant acceleration in the rates of genome rearrangements in bacterial endosymbionts of insects at initial stages of the association.
In the second chapter, the structure and functional capabilities of Sodalis glossinidius has been studied. S. glossinidius is the secondary endosymbiont of tsetse flies, and it´s at very initial stages of genome reduction process. It´s genome is experiencing a massive process of gene inactivation, with 972 pseudogenes (inactivated genes) that were described but not annotated in the original annotation of the genome. In this chapter, a complete functional re-annotation of this genome was carried out, that includes the characterization of 1501 pseudogenes though analysis of S. glossinidius intergenic regions. A massive presence of CDSs related with mobile genetic elements and surface proteins were detected, being also the functional classes most affected by pseudogenization. The reconstruction of the metabolic map of S. glossinidius revealed a functional profile very similar to that of free-living enterics, with inactivation of L-arginine biosynthesis pathway, whereas the comparison with Wigglesworthia glossinidia (tsetse primary endosymbiont) reveals possible cases of metabolic complementation between both tsetse endosymbionts at thiamine, coenzyme A and tetrahydrofolate biosynthesis level.
Finally, in the third chapter of the thesis, the complete reductive evolution process associated with S. glossinidius was studied from a systems biology perspective through the reconstruction of their genome-scale metabolic networks at different stages of this process and the prediction of their internal reaction fluxes under different external conditions through Flux Balance Analysis. This revealed the decisive role of the pseudogenization of genes involved in L-arginine and glycogen biosynthesis and specially the pseudogenization of the key anaplerotic enzyme phosphoenolpyruvate carboxylase in the ecological transition to a host-dependent lifestyle experienced by S. glossinidius. A progressive decrease in network robustness to gene deletion events and to changes in particular reaction fluxes were detected. Finally, reductive evolution simulations over the functional network of S. glossinidius under different external conditions revealed a higher plasticity in minimal networks evolved in a nutrient-rich environment, and allow defining different sets of essential and disposable genes based on their presence or absence in minimal metabolic networks. These essential genes had more optimized patterns of codon usage and more restricted patterns of sequence evolution than disposable genes that could be lost without affecting the functionality of the network. However, lineage-specific estimates of dN and dS in S. glossinidius and Escherichia coli revealed that common features of ancient bacterial endosymbionts like acceleration in the rates of sequence evolution and the loss of adaptative codon usage were starting to affect S. glossinidius evolution.En esta tesis doctoral, el proceso de reducción genómica característico de bacterias endosimbiontes de insectos ha sido estudiado utilizando diferentes aproximaciones computacionales basadas en la genómica comparada y la biología de sistemas. Por un lado, las dinámicas de reordenaciones genómicas han sido estudiadas en un subconjunto de 31 genomas completos de γ-proteobacterias que incluyen 5 genomas completos de endosimbiontes bacterianos de insectos, revelando una aceleración significativa de las tasas de reordenaciones en estos genomas en etapas iniciales del proceso de reducción. Posteriormente, el genoma de Sodalis glossinidius, el endosimbionte secundario de la mosca tsétsé, fue re-anotado con el objetivo de evaluar el impacto de los procesos de inactivación génica y proliferación de elementos genéticos móviles en etapas tempranas del proceso de reducción, asi como su impacto sobre las capacidades funcionales de la bacteria en el contexto ecológico de su coexistencia con el endosimbionte primario ancestral Wigglesworthia glossinidia. Finalmente, el proceso completo de reducción genómica en S. glossinidius ha sido estudiado a través de la reconstrucción de su red metabólica a diferentes etapas de este proceso y su análisis funcional mediante Análisis de Balance de Flujos, evaluando la robustez de las redes frente a sucesos de deleción asi como las dinámicas evolutivas de genes esenciales y no esenciales en base a su presencia en redes mínimas evolucionadas a partir de la red funcional. Este análisis permitió identificar sucesos de inactivación génica con efectos drásticos sobre las capacidades funcionales del sistema como los genes implicados en la biosíntesis de arginina y glicógeno, y especialmente la inactivación de la enzima fosfoenolpiruvato carboxilasa, asi como una disminución progresiva de la robustez de las redes frente a diferentes sucesos mutacionales asociada al proceso de pérdida génica. Finalmente, simulaciones de evolución reductiva sobre la red funcional bajo diferentes condiciones de entorno ha permitido definir conjuntos de genes esenciales y delecionables en base a su presencia o ausencia en las redes mínimas producto de las simulaciones, revelando una mayor conservación a nivel de secuencia y un uso de codones más optimizado en genes esenciales frente a genes cuya pérdida no afecta a la funcionalidad del sistema.
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Curry, Meghan M. "Endosymbiotic prevalence and reproductive manipulation of the spider Mermessus fradeorum." UKnowledge, 2013. http://uknowledge.uky.edu/entomology_etds/6.
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Spiders are host to a plethora of heritable endosymbiotic bacteria. Broad-taxa screening studies indicate that endosymbionts are particularly common among spiders, however, little is known about how these bacteria affect their spider hosts. In insects these bacteria ensure vertical transmission by either conveying a benefit to the host or manipulating host reproduction to eliminate males that serve as evolutionary dead-ends for maternally-inherited bacteria. Common modes of reproductive manipulation include parthenogenesis, male killing, feminization, and cytoplasmic incompatibility. Screening an assemblage of Mermessus genus spiders, I detected a high frequency and diversity of endosymbiont infection. Within a single species, M. fradeorum, I detected three endosymbionts in multiple combinations. Rearing two natural infection types of M. fradeorum demonstrated two distinct endosymbiotic reproductive manipulations. Mothers infected with Rickettsia and Wolbachia produced extremely female-biased offspring, and antibiotic elimination of the symbionts successfully restored the sex ratio to the expected 1:1 in subsequent generations. A two-way factorial mating assay detected strong cytoplasmic incompatibility induced by a different strain of Wolbachia: cured females mated with infected males produced 70% fewer offspring than all other pairings. These results show that M. fradeorum is subject to multiple layers of reproductive manipulation that likely drive host evolution and ecology.
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Fontanez, Kristina. "Evolution of Deep-Sea Mussels (Bathymodiolinae) and Their Chemosynthetic Endosymbionts." Thesis, Harvard University, 2011. http://dissertations.umi.com/gsas.harvard:10083.
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Symbiosis is one of the most widespread evolutionary strategies on Earth. In the deep-sea, symbioses between chemosynthetic bacteria and invertebrates are abundant at hydrothermal vents and cold seeps. These mutualisms, in which symbiont carbon fixation provides for host nutrition, are analogous to the ancient endosymbioses that resulted in the chloroplast and the eukaryotic mitochondrion. However, the evolutionary processes that led to the widespread dispersal of deep-sea organisms and the mechanisms by which symbioses are initiated and maintained are poorly characterized. This thesis examined the evolution of deep-sea mussels (Bathymodiolinae) and their chemosynthetic symbionts. Bathymodioline mussel taxonomy is in need of a comprehensive systematic revision because the majority of named genera do not constitute monophyletic groups. First, this thesis demonstrated that mussels found on the Northeast Pacific Ridges are members of Adipicola, a paraphyletic genus within Bathymodiolinae, refining the evolutionary history of this poorly characterized group. Second, an updated multi-locus phylogeny of bathymodiolines was presented and used to evaluate the statistical evidence for previously proposed hypotheses describing the directional evolution of bathymodioline traits. The results indicated that patterns of directional evolution in this group are not well supported and instead suggests that trait evolution has proceeded in a non-directional manner. Third, this thesis presented the first evidence of detection and abundance of bathymodioline symbionts in the deep-sea environment, providing direct evidence that these symbionts are environmentally acquired. Fourth, this thesis presented the first multi-locus phylogenies of bathymodioline symbionts and tested the hypothesis of environmental acquisition of symbionts in this group. The results demonstrated that symbiont and host lineages are decoupled, which is consistent with the environmental acquisition hypothesis. Finally, environmental acquisition implies that symbionts have opportunities to exchange genetic information with other bacterial strains and evidence for recombination in bathymodioline symbionts is also presented. This thesis advances our understanding of the evolutionary history of bathymodioline symbioses by clarifying host and symbiont evolutionary history and symbiont transmission strategy. In aggregate, these results suggest that bathymodiolines are more flexible with regard to the habitats they inhabit and the symbionts they harbor than previously understood.
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Hirakawa, Carlos Eduardo. "Modelando evolução por endossimbiose." Universidade do Estado do Rio de Janeiro, 2010. http://www.bdtd.uerj.br/tde_busca/arquivo.php?codArquivo=2478.
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Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorNesta dissertação é apresentada uma modelagem analítica para o processo evolucionário formulado pela Teoria da Evolução por Endossimbiose representado através de uma sucessão de estágios envolvendo diferentes interações ecológicas e metábolicas entre populações de bactérias considerando tanto a dinâmica populacional como os processos produtivos dessas populações. Para tal abordagem é feito uso do sistema de equações diferenciais conhecido como sistema de Volterra-Hamilton bem como de determinados conceitos geométricos envolvendo a Teoria KCC e a Geometria Projetiva. Os principais cálculos foram realizados pelo pacote de programação algébrica FINSLER, aplicado sobre o MAPLE.
This work presents an analytical approach for modeling the evolutionary process formulated by the Serial Endosymbiosis Theory represented by a succession of stages involving different metabolic and ecological interactions among populations of bacteria considering both the population dynamics and production processes of these populations. In such approach we make use of systems of differential equations known as Volterra-Hamilton systems as well as some geometric concepts involving the KCC Theory and the Projective Geometry. The main calculations were performed by the computer algebra software FINSLER based on MAPLE.
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Müller, Johann. "Étude des impacts des composés organiques au sein des écosystèmes planctoniques : facilitation, interférence et signaux moléculaires." Paris 6, 2010. http://www.theses.fr/2010PA066492.
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Les mécanismes tels que le recyclage des nutriments ou la diversification du vivant jouent un rôle prépondérant dans le fonctionnement et la structuration de la biosphère. Ces mécanismes sont régulés selon différents processus participant au fonctionnement des écosystèmes. Les relations intra et inter spécifiques contrôlant la mosaïque des communautés et son impact sur l’environnement, sont à la base de ce fonctionnement et leur étude est par conséquent essentielle pour la compréhension et la gestion de la biosphère. Lors de mon travail de thèse, je me suis intéressé plus particulièrement à l’une de ces relations interspécifiques : l’impact de composés organiques, relargués dans les écosystèmes lacustres par des organismes, sur les relations entre espèces. A travers plusieurs expériences, mon but a été d’explorer ces effets sous plusieurs angles. Dans une première étude, je me suis concentré sur les effets de composés allélopathiques sur la compétition interspécifique pour une ressource en utilisant un modèle qui servit de base à la compréhension de la compétition : le complexe symbiotique Paramecium bursaria – Chlorella vulgaris (Gause, 1935). L’impact des composés organiques tels que les cyanotoxines et autres composés contenus dans la cyanobactérie Planktothrix agardhii sur les traits de vie d’un organisme zooplanctonique herbivore majeur, Daphnia magna, a été étudié dans un second axe. Enfin, le comportement de ce cladocère face à ces molécules produites par différentes espèces de phytoplancton a constitué le sujet d’un troisième et dernier axe. Au travers de ce travail, nous avons montré dans un premier temps qu’endosymbiose et interactions allélopathiques peuvent interagir et changer l’issue de la compétition pour l’exploitation d’une ressource et entraîner la coexistence des espèces. Par la suite, nous avons mis en évidence l’effet de composés organiques issus de cyanobactéries, à la fois sur les traits de vie et sur le comportement migratoire d’un consommateur majeur de phytoplancton, cet effet pouvant agir sur le contrôle de la prolifération des cyanobactéries dans les lacs. Ces résultats mettent en relief la place que recouvrent les composés organiques au sein des relations interspécifiques et leurs effets sur la composition des communautés et, par extension, sur les processus écosystémiquesMechanisms such as nutrients recycling or life diversification play a major role in the structuring and functioning of the biosphere. These mechanisms are regulated by different processes involved in the functioning of ecosystems. Controlling the mosaic of communities and its impact on the environment, intra and inter specific relations are the basis of this functioning and their study is therefore essential for the understanding and management of the biosphere. During my PhD, I was particularly interested in one of these interspecific interactions: the impact of organic compounds released into the environment by organims on relationships between species. Through several experiments, I aimed to explore these effects in several ways. In a first study, I focused on the effect of allelopathic compounds on interspecific competition for a resource using a model that was the basis for understanding the competition: the symbiotic complex Paramecium bursaria - Chlorella vulgaris (Gause, 1935). The impact of organic compounds such as cyanotoxins and other compounds produced by the cyanobacteria Planktothrix agardhii on the life-history parameters of a major herbivorous zooplankton, Daphnia magna, was studied in a second axis. Finally, the migration behaviour of this cladoceran submitted to organic compounds produced by phytoplankton has been the subject of a third axis. Through this work, I showed that endosymbiosis and allelochemical-mediated interactions may interact and change the outcome of exploitation competition and govern species coexistence. Then, I showed that organic compounds produced by a cyanobacteria affect life history traits and migration behaviour of a major consumer of phytoplankton; this effect may impact the control of cyanobacteria bloom in lakes. These results highlight the role of organic compounds in the relationships between species and their effects on community composition and, by extension, on ecosystem processes
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Hadfield, S. J. "Interactions between the endosymbiotic bacteria Wolbachia and its Drosophila melanogaster host." Thesis, University of Oxford, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.393443.
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Hoffman, Michele Therese. "Bacterial Endosymbionts of Endophytic Fungi: Diversity, Phylogenetic Structure, and Biotic Interactions." Diss., The University of Arizona, 2010. http://hdl.handle.net/10150/196079.
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This dissertation comprises a series of studies designed to explore the associations between plants and the endophytic fungi they harbor in their above-ground tissues. By viewing endophyte diversity in ecologically and economically important hosts through the lenses of phylogenetic biology, microbiology, and biotechnology, this body of work links plant ecology with newly discovered symbiotic units comprised of endophytic fungi and the bacteria that inhabit them.This work begins with a large-scale survey of endophytic fungi from native and non-native Cupressaceae in Arizona and North Carolina. After isolating over 400 strains of endophytes, I inferred the evolutionary relationships among these fungi using both Bayesian and parsimony analyses. In addition to showing that native and introduced plants contained different endophytes, I found that the endophytes themselves harbor additional microbial symbionts, recovering members of the beta- and gamma-proteobacterial orders Burkholderiales, Xanthomonadales, and Enterobacteriales and numerous novel, previously uncultured bacteria. This work finds that phylogenetically diverse bacterial endosymbionts occur within living hyphae of multiple major lineages of ascomycetous endophytes.A focus on 29 fungal/bacterial associations revealed that bacterial and fungal phylogenies are incongruent with each other and did not reflect the phylogenetic relationships of host plants. Instead, both endophyte and bacterial assemblages were strongly structured by geography, consistent with local horizontal transmission. Endophytes could be cured of their bacterial endosymbionts using antibiotics, providing a tractable experimental system for comparisons of growth and metabolite production under varying conditions. Studies of seven focal fungal/bacterial pairs showed that bacteria could significantly alter growth of fungi at different nutrient and temperature levels in vitro, and that different members of the same bacterial lineages interact with different fungi in different ways.Focusing on one isolate, I then describe for the first time the production of indole-3-acetic acid (IAA) by a non-pathogenic, foliar endophytic fungus (Pestalotiopsis neglecta), suggesting a potential benefit to the host plant harboring this fungus. I show that this fungus is inhabited by an endohyphal bacterium (Luteibacter sp.) and demonstrate that mycelium containing this bacterium produces significantly more IAA in vitro than the fungus alone. I predict that the general biochemical pathway used by the fungal-endohyphal complex is L-tryptophan-dependent and measure effects of IAA production in vivo, focusing on root and shoot growth in tomato seedlings.
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Taraphdar, Tanushree. "Molecular genetic characterization of wolbachia endosymbionts in dipteran pest of silkworm." Thesis, Vidyasagar University, 2005. http://hdl.handle.net/123456789/1392.
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